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Urhan A, Cosma BM, Earl AM, Manson AL, Abeel T. SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings. Bioinformatics 2024; 40:btae328. [PMID: 38775729 PMCID: PMC11147799 DOI: 10.1093/bioinformatics/btae328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/08/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
MOTIVATION Today, we know the function of only a small fraction of the protein sequences predicted from genomic data. This problem is even more salient for bacteria, which represent some of the most phylogenetically and metabolically diverse taxa on Earth. This low rate of bacterial gene annotation is compounded by the fact that most function prediction algorithms have focused on eukaryotes, and conventional annotation approaches rely on the presence of similar sequences in existing databases. However, often there are no such sequences for novel bacterial proteins. Thus, we need improved gene function prediction methods tailored for bacteria. Recently, transformer-based language models-adopted from the natural language processing field-have been used to obtain new representations of proteins, to replace amino acid sequences. These representations, referred to as protein embeddings, have shown promise for improving annotation of eukaryotes, but there have been only limited applications on bacterial genomes. RESULTS To predict gene functions in bacteria, we developed SAFPred, a novel synteny-aware gene function prediction tool based on protein embeddings from state-of-the-art protein language models. SAFpred also leverages the unique operon structure of bacteria through conserved synteny. SAFPred outperformed both conventional sequence-based annotation methods and state-of-the-art methods on multiple bacterial species, including for distant homolog detection, where the sequence similarity to the proteins in the training set was as low as 40%. Using SAFPred to identify gene functions across diverse enterococci, of which some species are major clinical threats, we identified 11 previously unrecognized putative novel toxins, with potential significance to human and animal health. AVAILABILITY AND IMPLEMENTATION https://github.com/AbeelLab/safpred.
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Affiliation(s)
- Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Delft XE 2628, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Bianca-Maria Cosma
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Delft XE 2628, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Delft XE 2628, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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Verma P, Sánchez Alvarado A, Duncan EM. Chromatin remodeling protein BPTF regulates transcriptional stability in planarian stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595819. [PMID: 38826365 PMCID: PMC11142235 DOI: 10.1101/2024.05.24.595819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Trimethylation of histone H3 lysine 4 (H3K4me3) correlates strongly with gene expression in many different organisms, yet the question of whether it plays a causal role in transcriptional activity remains unresolved. Although H3K4me3 does not directly affect chromatin accessibility, it can indirectly affect genome accessibility by recruiting the ATP-dependent chromatin remodeling complex NuRF (Nucleosome Remodeling Factor). The largest subunit of NuRF, BPTF/NURF301, binds H3K4me3 specifically and recruits the NuRF complex to loci marked by this modification. Studies have shown that the strength and duration of BPTF binding likely also depends on additional chromatin features at these loci, such as lysine acetylation and variant histone proteins. However, the exact details of this recruitment mechanism vary between studies and have largely been tested in vitro. Here, we use stem cells isolated directly from live planarian animals to investigate the role of BPTF in regulating chromatin accessibility in vivo. We find that BPTF operates at gene promoters and is most effective at facilitating transcription at genes marked by Set1-dependent H3K4me3 peaks, which are significantly broader than those added by the lysine methyltransferase MLL1/2. Moreover, BPTF is essential for planarian stem cell biology and its loss of function phenotype mimics that of Set1 knockdown. Together, these data suggest that BPTF and H3K4me3 are important mediators of both transcription and in vivo stem cell function.
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MacDonald N, Raven N, Diep W, Evans S, Pannipitiya S, Bramwell G, Vanbeek C, Thomas F, Russell T, Dujon AM, Telonis-Scott M, Ujvari B. The molecular evolution of cancer associated genes in mammals. Sci Rep 2024; 14:11650. [PMID: 38773187 PMCID: PMC11109183 DOI: 10.1038/s41598-024-62425-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Cancer is a disease that many multicellular organisms have faced for millions of years, and species have evolved various tumour suppression mechanisms to control oncogenesis. Although cancer occurs across the tree of life, cancer related mortality risks vary across mammalian orders, with Carnivorans particularly affected. Evolutionary theory predicts different selection pressures on genes associated with cancer progression and suppression, including oncogenes, tumour suppressor genes and immune genes. Therefore, we investigated the evolutionary history of cancer associated gene sequences across 384 mammalian taxa, to detect signatures of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and B2M). This approach allowed us to conduct a fine scale analysis of gene wide and site-specific signatures of selection across mammalian lineages under the lens of cancer susceptibility. Phylogenetic analyses revealed that for most species the evolution of cancer associated genes follows the species' evolution. The gene wide selection analyses revealed oncogenes being the most conserved, tumour suppressor and immune genes having similar amounts of episodic diversifying selection. Despite BRCA2's status as a key caretaker gene, episodic diversifying selection was detected across mammals. The site-specific selection analyses revealed that the two apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are under opposing forces of selection (positive and negative respectively), highlighting the importance of site-specific selection analyses to understand the evolution of highly complex gene families. Our results highlighted the need to critically assess different types of selection pressure on cancer associated genes when investigating evolutionary adaptations to cancer across the tree of life. This study provides an extensive assessment of cancer associated genes in mammals with highly representative, and substantially large sample size for a comparative genomic analysis in the field and identifies various avenues for future research into the mechanisms of cancer resistance and susceptibility in mammals.
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Affiliation(s)
- Nick MacDonald
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Nynke Raven
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Wendy Diep
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Samantha Evans
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Senuri Pannipitiya
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Georgina Bramwell
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Caitlin Vanbeek
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France
| | - Tracey Russell
- Faculty of Science, School of Life and Environmental Sciences, Sydney, NSW, Australia
| | - Antoine M Dujon
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Burwood, Burwood, VIC, 3125, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia.
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4
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Kwon JJ, Pan J, Gonzalez G, Hahn WC, Zitnik M. On knowing a gene: A distributional hypothesis of gene function. Cell Syst 2024:S2405-4712(24)00123-6. [PMID: 38810640 DOI: 10.1016/j.cels.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 02/25/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
As words can have multiple meanings that depend on sentence context, genes can have various functions that depend on the surrounding biological system. This pleiotropic nature of gene function is limited by ontologies, which annotate gene functions without considering biological contexts. We contend that the gene function problem in genetics may be informed by recent technological leaps in natural language processing, in which representations of word semantics can be automatically learned from diverse language contexts. In contrast to efforts to model semantics as "is-a" relationships in the 1990s, modern distributional semantics represents words as vectors in a learned semantic space and fuels current advances in transformer-based models such as large language models and generative pre-trained transformers. A similar shift in thinking of gene functions as distributions over cellular contexts may enable a similar breakthrough in data-driven learning from large biological datasets to inform gene function.
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Affiliation(s)
- Jason J Kwon
- Dana-Farber Cancer Institute and Harvard Medical School, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua Pan
- Dana-Farber Cancer Institute and Harvard Medical School, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guadalupe Gonzalez
- Department of Computing, Faculty of Engineering, Imperial College, London SW7 2AZ, UK
| | - William C Hahn
- Dana-Farber Cancer Institute and Harvard Medical School, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Marinka Zitnik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02115, USA; Harvard Data Science Initiative, Harvard University, Cambridge, MA 02138, USA; Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Allston, MA 02134, USA.
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Thöneböhn S, Fischer D, Kreiling V, Kemmler A, Oberheim I, Hager F, Schmid NE, Thormann KM. Identifying components of the Shewanella phage LambdaSo lysis system. J Bacteriol 2024:e0002224. [PMID: 38771038 DOI: 10.1128/jb.00022-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Phage-induced lysis of Gram-negative bacterial hosts usually requires a set of phage lysis proteins, a holin, an endopeptidase, and a spanin system, to disrupt each of the three cell envelope layers. Genome annotations and previous studies identified a gene region in the Shewanella oneidensis prophage LambdaSo, which comprises potential holin- and endolysin-encoding genes but lacks an obvious spanin system. By a combination of candidate approaches, mutant screening, characterization, and microscopy, we found that LambdaSo uses a pinholin/signal-anchor-release (SAR) endolysin system to induce proton leakage and degradation of the cell wall. Between the corresponding genes, we found that two extensively nested open-reading frames encode a two-component spanin module Rz/Rz1. Unexpectedly, we identified another factor strictly required for LambdaSo-induced cell lysis, the phage protein Lcc6. Lcc6 is a transmembrane protein of 65 amino acid residues with hitherto unknown function, which acts at the level of holin in the cytoplasmic membrane to allow endolysin release. Thus, LambdaSo-mediated cell lysis requires at least four protein factors (pinholin, SAR endolysin, spanin, and Lcc6). The findings further extend the known repertoire of phage proteins involved in host lysis and phage egress. IMPORTANCE Lysis of bacteria can have multiple consequences, such as the release of host DNA to foster robust biofilm. Phage-induced lysis of Gram-negative cells requires the disruption of three layers, the outer and inner membranes and the cell wall. In most cases, the lysis systems of phages infecting Gram-negative cells comprise holins to disrupt or depolarize the membrane, thereby releasing or activating endolysins, which then degrade the cell wall. This, in turn, allows the spanins to become active and fuse outer and inner membranes, completing cell envelope disruption and allowing phage egress. Here, we show that the presence of these three components may not be sufficient to allow cell lysis, implicating that also in known phages, further factors may be required.
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Affiliation(s)
- Svenja Thöneböhn
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Dorian Fischer
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Vanessa Kreiling
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Alina Kemmler
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Isabella Oberheim
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Fabian Hager
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Nicole E Schmid
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
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Zhang F, Liu N, Chen T, Xu H, Li R, Wang L, Zhou S, Cai Q, Hou X, Wang L, Qian X, Zhu Z, Zhou K. Genome-wide identification of GH28 family and insight into its contributions to pod shattering resistance in Brassica napus L. BMC Genomics 2024; 25:492. [PMID: 38760719 PMCID: PMC11102225 DOI: 10.1186/s12864-024-10406-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024] Open
Abstract
Rapeseed (Brassica napus L.), accounts for nearly 16% of vegetable oil, is the world's second produced oilseed. However, pod shattering has caused significant yield loses in rapeseed production, particularly during mechanical harvesting. The GH28 genes can promote pod shattering by changing the structure of the pod cell wall in Arabidopsis. However, the role of the GH28 gene family in rapeseed was largely unknown. Therefore, a genome-wide comprehensive analysis was conducted to classify the role of GH28 gene family on rapeseed pod shattering. A total of 37 BnaGH28 genes in the rapeseed genome were identified. These BnaGH28s can be divided into five groups (Group A-E), based on phylogenetic and synteny analysis. Protein property, gene structure, conserved motif, cis-acting element, and gene expression profile of BnaGH28 genes in the same group were similar. Specially, the expression level of genes in group A-D was gradually decreased, but increased in group E with the development of silique. Among eleven higher expressed genes in group E, two BnaGH28 genes (BnaA07T0199500ZS and BnaC06T0206500ZS) were significantly regulated by IAA or GA treatment. And the significant effects of BnaA07T0199500ZS variation on pod shattering resistance were also demonstrated in present study. These results could open a new window for insight into the role of BnaGH28 genes on pod shattering resistance in rapeseed.
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Affiliation(s)
- Fugui Zhang
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Nian Liu
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Tianhua Chen
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Hong Xu
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Rui Li
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Liyan Wang
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Shuo Zhou
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Qing'ao Cai
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Xinzhe Hou
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Ling Wang
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Xingzhi Qian
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Zonghe Zhu
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Kejin Zhou
- College of Agronomy, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China.
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Shao L, Shen Z, Li M, Guan C, Fan B, Chai Y, Zhao Y. ccdC Regulates Biofilm Dispersal in Bacillus velezensis FZB42. Int J Mol Sci 2024; 25:5201. [PMID: 38791239 PMCID: PMC11120784 DOI: 10.3390/ijms25105201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Bacillus velezensis FZB42 is a plant growth-promoting rhizobacterium (PGPR) and a model microorganism for biofilm studies. Biofilms are required for the colonization and promotion of plant growth in the rhizosphere. However, little is known about how the final stage of the biofilm life cycle is regulated, when cells regain their motility and escape the mature biofilm to spread and colonize new niches. In this study, the non-annotated gene ccdC was found to be involved in the process of biofilm dispersion. We found that the ccdC-deficient strain maintained a wrinkled state at the late stage of biofilm formation in the liquid-gas interface culture, and the bottom solution showed a clear state, indicating that no bacterial cells actively escaped, which was further evidenced by the formation of a cellular ring (biofilm pellicle) located on top of the preformed biofilm. It can be concluded that dispersal, a biofilm property that relies on motility proficiency, is also positively affected by the unannotated gene ccdC. Furthermore, we found that the level of cyclic diguanylate (c-di-GMP) in the ccdC-deficient strain was significantly greater than that in the wild-type strain, suggesting that B. velezensis exhibits a similar mechanism by regulating the level of c-di-GMP, the master regulator of biofilm formation, dispersal, and cell motility, which controls the fitness of biofilms in Pseudomonas aeruginosain. In this study, we investigated the mechanism regulating biofilm dispersion in PGPR.
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Affiliation(s)
- Lin Shao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grass, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Zizhu Shen
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Meiju Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grass, Nanjing Forestry University, Nanjing 210037, China
| | - Chenyun Guan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grass, Nanjing Forestry University, Nanjing 210037, China
| | - Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grass, Nanjing Forestry University, Nanjing 210037, China
- College of Life Science, Nanjing Forestry University, Nanjing 210037, China
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yinjuan Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grass, Nanjing Forestry University, Nanjing 210037, China
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Zhu Q, Zheng H, Hu X, Liu Y, Zheng X, Li L, Tang M. Genome-Wide Analysis of the SAUR Gene Family and Its Expression Profiles in Response to Salt Stress in Santalum album. PLANTS (BASEL, SWITZERLAND) 2024; 13:1286. [PMID: 38794357 PMCID: PMC11125248 DOI: 10.3390/plants13101286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024]
Abstract
The SAUR (small auxin-up RNA) family constitutes a category of genes that promptly respond to the hormone auxin and play a pivotal role in diverse biological processes encompassing plant growth and the response to abiotic stress. Santalum album L., a semi-parasitic evergreen tree, is renowned for its economically valuable essential oils, positioning it among the most prized tree species. In this study, a meticulous identification and comprehensive analysis of 43 SAUR genes was conducted within S. album. Based on phylogenetic relationships, the SaSAUR genes were systematically categorized into five groups. A collinearity analysis revealed intriguing insights, disclosing 14 segmental duplications and 9 tandem duplications within the SaSAUR genes, emphasizing the pivotal role of duplication in the expansion of this gene family. Noteworthy variations in the expression levels of SaSAUR genes were observed by delving into the SaSAUR transcriptome data from various tissues, including leaves, roots, and heartwood, as well as under salt-stress conditions. Notably, SaSAUR08 and SaSAUR13 were significantly upregulated in heartwood compared with roots and leaves, while SaSAUR18 was markedly more expressed in roots compared with heartwood and leaves. Furthermore, SaSAUR27 and SaSAUR28 were found to respond closely to salt stress, hinting at their potential involvement in the salt-stress response mechanism. This research offers a comprehensive investigation of SAUR genes in S. album and establishes a foundation for future exploration of the SAUR gene family, particularly its relation to growth and salt-stress responses.
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Affiliation(s)
- Qing Zhu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Haoyue Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Xu Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yi Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Xinyi Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Libei Li
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Collaborative Innovation Center of Ecological Civilization, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Zhang BX, Liu FF, Liu F, Qi WX, Si YQ, Ren HY, Rao XJ. SfMBP: A novel microbial binding protein and pattern recognition receptor in the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105142. [PMID: 38309673 DOI: 10.1016/j.dci.2024.105142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/05/2024]
Abstract
The fall armyworm, Spodoptera frugiperda, poses a significant threat as a highly destructive agricultural pest in many countries. Understanding the complex interplay between the insect immune system and entomopathogens is critical for optimizing biopesticide efficacy. In this study, we identified a novel microbial binding protein, SfMBP, in S. frugiperda. However, the specific role of SfMBP in the immune response of S. frugiperda remains elusive. Encoded by the LOC118269163 gene, SfMBP shows significant induction in S. frugiperda larvae infected with the entomopathogen Beauveria bassiana. Consisting of 115 amino acids with a signal peptide, an N-terminal flexible region and a C-terminal β-sheet, SfMBP lacks any known functional domains. It is expressed predominantly during early larval stages and in the larval epidermis. Notably, SfMBP is significantly induced in larvae infected with bacteria and fungi and in SF9 cells stimulated by peptidoglycan. While recombinant SfMBP (rSfMBP) does not inhibit bacterial growth, it demonstrates binding capabilities to bacteria, fungal spores, peptidoglycan, lipopolysaccharides, and polysaccharides. This binding is inhibited by monosaccharides and EDTA. Molecular docking reveals potential Zn2+-interacting residues and three cavities. Furthermore, rSfMBP induces bacterial agglutination in the presence of Zn2+. It also binds to insect hemocytes and SF9 cells, enhancing phagocytosis and agglutination responses. Injection of rSfMBP increased the survival of S. frugiperda larvae infected with B. bassiana, whereas blocking SfMBP with the antibody decreased survival. These results suggest that SfMBP acts as a pattern recognition receptor that enhances pathogen recognition and cellular immune responses. Consequently, this study provides valuable insights for the development of pest control measures.
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Affiliation(s)
- Bang-Xian Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China; School of Biological Science and Food Engineering, Chuzhou, 239000, China
| | - Fang-Fang Liu
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China
| | - Feng Liu
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China
| | - Wen-Xuan Qi
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China
| | - Yan-Qin Si
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China
| | - Hai-Yan Ren
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China
| | - Xiang-Jun Rao
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Agri-products Quality and Biosafety (Anhui Agricultural University), Ministry of Education, China.
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10
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Aksoy E, Yavuz C, Yagiz AK, Unel NM, Baloğlu MC. Genome-wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato. PLANT DIRECT 2024; 8:e569. [PMID: 38659972 PMCID: PMC11042883 DOI: 10.1002/pld3.569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 04/26/2024]
Abstract
GATA is one of the prominent transcription factor families conserved among many organisms in eukaryotes and has different biological roles in many pathways, particularly in light regulation in plants. Although GATA transcription factors (TFs) have been identified in different crop species, their roles in abiotic stress tolerance have not been studied in potato. In this study, we identified 32 GATA TFs in potato (Solanum tuberosum) by in silico analyses, and expression levels of selected six genes were investigated in drought-tolerant (Sante) and sensitive (Agria) cultivars under light, drought, and combined (light + drought) stress conditions. According to the phylogenetic results, StGATA TFs were divided into four main groups (I, II, III, and IV) and different sub-groups in I and II (eight and five, respectively). StGATA genes were uniformly localized to each chromosome with a conserved exon/intron structure. The presence of cis-elements within the StGATA family further supported the possible involvement in abiotic stress tolerance and light response, tissue-specific expression, and hormonal regulation. Additional PPI investigations showed that these networks, especially for Groups I, II, and IV, play a significant role in response to light and drought stress. Six StGATAs were chosen from these groups for expressional profiling, and their expression in both Sante and Agria was mainly downregulated under purple and red lights, drought, and combined stress (blue + drought and purple + drought). The interactomes of selected StGATAs, StGATA3, StGATA24, and StGATA29 were analyzed, and the accessions with GATA motifs were checked for expression. The results showed that the target proteins, cyclin-P3-1, SPX domain-containing protein 1, mitochondrial calcium uniporter protein 2, mitogen-activated protein kinase kinase kinase YODA, and splicing factor 3 B subunit 4-like, mainly play a role in phytochrome-mediated stomatal patterning, development, and activity. Understanding the interactions between drought stress and the light response mechanisms in potato plants is essential. It will eventually be possible to enhance potato resilience to climate change by manipulating the TFs that play a role in these pathways.
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Affiliation(s)
- Emre Aksoy
- Faculty of Arts and Sciences, Department of BiologyMiddle East Technical UniversityAnkaraTürkiye
| | - Caner Yavuz
- Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic EngineeringNiğde Ömer Halisdemir UniversityNiğdeTürkiye
| | - Ayten Kübra Yagiz
- Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic EngineeringNiğde Ömer Halisdemir UniversityNiğdeTürkiye
| | - Necdet Mehmet Unel
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and ArchitectureKastamonu UniversityKastamonuTürkiye
- Research and Application CenterKastamonu UniversityKastamonuTürkiye
| | - Mehmet Cengiz Baloğlu
- Plantomics Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering and ArchitectureKastamonu UniversityKastamonuTürkiye
- Sabancı University Nanotechnology Research and Application Center (SUNUM)Sabancı UniversityTuzlaTürkiye
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11
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Pan X, Deng Z, Wu R, Yang Y, Akher SA, Li W, Zhang Z, Guo Y. Identification of CEP peptides encoded by the tobacco (Nicotiana tabacum) genome and characterization of their roles in osmotic and salt stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 209:108525. [PMID: 38518396 DOI: 10.1016/j.plaphy.2024.108525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Members of the CEP (C-terminally Encoded Peptide) gene family have been shown to be involved in various developmental processes and stress responses in plants. In order to understand the roles of CEP peptides in stress response, a comprehensive bioinformatics approach was employed to identify NtCEP genes in tobacco (Nicotiana tabacum L.) and to analyze their potential roles in stress responses. Totally 21 NtCEP proteins were identified and categorized into two subgroups based on their CEP domains. Expression changes of the NtCEP genes in response to various abiotic stresses were analyzed via qRT-PCR and the results showed that a number of NtCEPs were significant up-regulated under drought, salinity, or temperature stress conditions. Furthermore, application of synthesized peptides derived from NtCEP5, NtCEP13, NtCEP14, and NtCEP17 enhanced plant tolerance to different salt stress treatments. NtCEP5, NtCEP9 and NtCEP14, and NtCEP17 peptides were able to promote osmotic tolerance of tobacco plants. The results from this study suggest that NtCEP peptides may serve as important signaling molecules in tobacco's response to abiotic stresses.
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Affiliation(s)
- Xiaolu Pan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Rongrong Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China; Qingdao Agricultural University, Qingdao, China
| | - Yalun Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China; Qingdao Agricultural University, Qingdao, China
| | - Sayed Abdul Akher
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China.
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China; (Q)ingdao Municipal Key Laboratory of Plant Molecular Pharming, Qingdao, China.
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12
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Huang X, Yang S, Zhang Y, Shi Y, Shen L, Zhang Q, Qiu A, Guan D, He S. Temperature-dependent action of pepper mildew resistance locus O 1 in inducing pathogen immunity and thermotolerance. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2064-2083. [PMID: 38011680 DOI: 10.1093/jxb/erad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/25/2023] [Indexed: 11/29/2023]
Abstract
Plant diseases tend to be more serious under conditions of high-temperature/high-humidity (HTHH) than under moderate conditions, and hence disease resistance under HTHH is an important determinant for plant survival. However, how plants cope with diseases under HTHH remains poorly understood. In this study, we used the pathosystem consisting of pepper (Capsicum annuum) and Ralstonia solanacearum (bacterial wilt) as a model to examine the functions of the protein mildew resistance locus O 1 (CaMLO1) and U-box domain-containing protein 21 (CaPUB21) under conditions of 80% humidity and either 28 °C or 37 °C. Expression profiling, loss- and gain-of-function assays involving virus-induced gene-silencing and overexpression in pepper plants, and protein-protein interaction assays were conducted, and the results showed that CaMLO1 acted negatively in pepper immunity against R. solanacearum at 28 °C but positively at 37 °C. In contrast, CaPUB21 acted positively in immunity at 28 °C but negatively at 37 °C. Importantly, CaPUB21 interacted with CaMLO1 under all of the tested conditions, but only the interaction in response to R. solanacearum at 37 °C or to exposure to 37 °C alone led to CaMLO1 degradation, thereby turning off defence responses against R. solanacearum at 37 °C and under high-temperature stress to conserve resources. Thus, we show that CaMLO1 and CaPUB21 interact with each other and function distinctly in pepper immunity against R. solanacearum in an environment-dependent manner.
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Affiliation(s)
- Xueying Huang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Sheng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yapeng Zhang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuanyuan Shi
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Qixiong Zhang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ailian Qiu
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Deyi Guan
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shuilin He
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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13
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Li Z, Na Wu X, Jacquot A, Chaput V, Adamo M, Neuhäuser B, Straub T, Lejay L, Schulze WX. Phosphoregulation in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1 and kinase HPCAL1 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2127-2142. [PMID: 38066636 DOI: 10.1093/jxb/erad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 03/28/2024]
Abstract
NRT2.1, the major high affinity nitrate transporter in roots, can be phosphorylated at five different sites within the N- and the C-terminus. Here, we characterized the functional relationship of two N-terminal phosphorylation sites, S21 and S28, in Arabidopsis. Based on a site-specific correlation network, we identified a receptor kinase (HPCAL1, AT5G49770), phosphorylating NRT2.1 at S21 and resulting in active nitrate uptake. HPCAL1 itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, HPCAL1 was found to interact with the N-terminus of NRT2.1, mainly when S28 was dephosphorylated. Phosphorylation of NRT2.1 at S21 resulted in a reduced interaction of NRT2.1 with its activator NAR2.1, but nitrate transport activity remained. By contrast, phosphorylated NRT2.1 at S28 enhanced the interaction with NAR2.1, but reduced the interaction with HPCAL1. Here we identified HPCAL1 as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21.
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Affiliation(s)
- Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Aurore Jacquot
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Valentin Chaput
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Mattia Adamo
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Benjamin Neuhäuser
- Department of Crop Physiology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Tatsiana Straub
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Laurence Lejay
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
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14
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Cao D, Liu C, Zhang W, Zheng C, Zhang S, Jia H, Yang Y. Characterization of the DUF868 gene family in Nicotiana and functional analysis of NtDUF868-E5 involved in pigment metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108493. [PMID: 38447423 DOI: 10.1016/j.plaphy.2024.108493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
Domains of unknown function (DUF) proteins represent a large group of uncharacterized protein families. The DUF868 gene family in Nicotiana has not yet been described. In the present study, we identified 12, 11, and 25 DUF868 family members in the genome of Nicotiana sylvestris, N. tomentosiformis, and N. tabacum, respectively. Based on phylogenetic analysis, these were categorized into five groups (A-E). Within each group, the gene structures, motifs, and tertiary structures showed high similarity. NtDUF868 family expansion during evolution was mainly driven by segmental duplication events. MicroRNA (miRNA) target site prediction identified 12 miRNA members that target 16 NtDUF868 family genes. The promoters of these genes contain cis-regulatory elements responsive to light, phytohormones, and abiotic stresses. Expression profiling revealed their tissue- and stage-specific expression patterns. RNA-sequencing and quantitative reverse transcription PCR revealed that the NtDUF868 family genes are potentially involved in the response to abiotic and biotic stresses, particularly drought and hormone stresses, and in the resistance to black shank and bacterial wilt. We generated transformed plants using NtDUF868-E5 overexpression and gene-editing vectors. NtDUF868-E5 overexpression resulted in enhanced tobacco plant growth and development, leading to increased leaf photosynthetic capacity and higher chlorophyll and carotenoid contents. This study provided a comprehensive genome-wide analysis of the DUF868 gene family, shedding light on their potential roles in plant growth and stress responses.
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Affiliation(s)
- Dejun Cao
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Che Liu
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Wenhan Zhang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Cong Zheng
- China Tobacco Fujian Company, Pucheng Branch, Nanping, 353000, China.
| | - Songtao Zhang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Hongfang Jia
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Yongxia Yang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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15
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Li X, Sun D, Wang Z, Zhao Q, Liu Y, Hou Z. Transcriptional regulatory mechanism of NR2F2 and ZNF423 in avian preadipocyte differentiation. Gene 2024; 897:148106. [PMID: 38128789 DOI: 10.1016/j.gene.2023.148106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]
Abstract
In the poultry industry, excessive abdominal fat deposition is not conducive to meat quality. Therefore, selection for optimal fat content levels in poultry has become a major breeding goal. We previously constructed NR2F2 overexpression (NR2F2OE) and knockout (NR2F2Δ/Δ/83-125aa) cell lines using Piggybac and CRISPR/Cas9 techniques, and confirmed that the transcription factor NR2F2 can significantly inhibit the differentiation of avian preadipocytes. In this study, we identified a downstream gene ZNF423 regulated by NR2F2, which is also involved in regulating avian fat deposition. First, we performed transcriptome analysis of the NR2F2-edited lines, which has been proven to be an inhibitor of avian fat deposition in our previous studies. Our findings revealed that NR2F2 affects a series of candidate regulators related to adipogenesis. Among these, we focused on ZNF423, which was significantly down-regulated in the NR2F2OE cell line and up-regulated in the NR2F2Δ/Δ/83-125aa cell line. Next, dual luciferase reporter assay results showed that the DNA-binding domain (DBDΔ72-143aa) of transcription factor NR2F2 may negatively affect the expression of downstream target gene ZNF423 by binding to its distal promoter region (-2356 to -2346). Moreover, we constructed a function analytical model and found that overexpression of ZNF423 significantly facilitated the differentiation of adipocytes in immortalized chicken preadipocytes (ICP1). Consistent with these findings, global transcriptome analysis of the ZNF423-overexpressed cell line (ZNF423OE) further demonstrated that the process of adipogenesis was significantly enriched. These results indicate that ZNF423 is a positive regulator of avian adipocyte differentiation. Overexpression of ZNF423 in the NR2F2OE cell line compensated for the inhibition of fat deposition phenotype, further suggesting that ZNF423 is a downstream target gene of NR2F2. These findings uncover a novel function of ZNF423 in avian adipocyte differentiation and analyzed the transcriptional regulation by its upstream transcription factor NR2F2. Additionally, we identified a list of functional candidate genes, providing important insights for further research on the mechanism of avian fat deposition.
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Affiliation(s)
- Xiaoqin Li
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Dandan Sun
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zheng Wang
- College of Life Sciences, Shanxi Agricultural University, Taiyuan 030801, China
| | - Qiangsen Zhao
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yongtong Liu
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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16
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Wang R, Liu CN, Segar ST, Jiang YT, Zhang KJ, Jiang K, Wang G, Cai J, Chen LF, Chen S, Cheng J, Compton SG, Deng JY, Ding YY, Du FK, Hu XD, Hu XH, Kang L, Li DH, Lu L, Li YY, Tang L, Tong X, Wang ZS, Xu WW, Yang Y, Zang RG, Zu ZX, Zhang YY, Chen XY. Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests. Nat Commun 2024; 15:1683. [PMID: 38395938 PMCID: PMC10891123 DOI: 10.1038/s41467-024-45836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.
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Affiliation(s)
- Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.
| | - Chao-Nan Liu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Simon T Segar
- Agriculture & Environment Department, Harper Adams University, Newport, United Kingdom
| | - Yu-Ting Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | | | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Lu-Fan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jing Cheng
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | | | - Jun-Yin Deng
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Ding
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Fang K Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao-Di Hu
- Novogene Bioinformatics Institute, Beijing, China
| | - Xing-Hua Hu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, China
| | - Ling Kang
- Novogene Bioinformatics Institute, Beijing, China
| | - Dong-Hai Li
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Ling Lu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Liang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou, China
| | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zheng-Shi Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Wei-Wei Xu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yang Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Run-Guo Zang
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Zhuo-Xin Zu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
| | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.
- Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
- Institute of Eco-Chongming, Shanghai, China.
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Sun L, Wang D, Liu X, Zhou Y, Huang W, Guan X, Zhang X, Xie Z. The volatile organic compound acetoin enhances the colonization of Azorhizobium caulinodans ORS571 on Sesbania rostrata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169006. [PMID: 38040356 DOI: 10.1016/j.scitotenv.2023.169006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
Chemoreceptors play a crucial role in assisting bacterial sensing and response to environmental stimuli. Genome analysis of Azorhizobium caulinodans ORS571 revealed the presence of 43 putative chemoreceptors, but their biological functions remain largely unknown. In this study, we identified the chemoreceptor AmaP (methyl-accepting protein of A. caulinodans), characterized by the presence of the CHASE3 domain and exhibited a notable response to acetoin. Thus, we investigated the effect of acetoin sensing on its symbiotic association with the host. Our findings uncovered a compelling role for acetoin as a key player in enhancing various facets of A. caulinodans ORS571's performance including biofilm formation, colonization, and nodulation abilities. Notably, acetoin bolstered A. caulinodans ORS571's efficacy in promoting the growth of S. rostrata, even under moderate salt stress conditions. This study not only broadens our understanding of the AmaP protein with its distinctive CHASE3 domain but also highlights the promising potential of acetoin in fortifying the symbiotic relationship between A. caulinodans and Sesbania rostrata.
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Affiliation(s)
- Li Sun
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Dandan Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yanan Zhou
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Weiwei Huang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Xin Guan
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Xuexian Zhang
- School of Natural Sciences, Massey University at Albany, Auckland 0745, New Zealand
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, China.
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Tran VK, Cao MH, Nguyen TTH, Le PT, Tran HA, Vu DC, Nguyen HT, Nguyen MTP, Bui TH, Nguyen TB, Ta TV, Tran TH. A novel IGHMBP2 variant and clinical diversity in Vietnamese SMARD1 and CMT2S patients. Front Pediatr 2024; 12:1165492. [PMID: 38415210 PMCID: PMC10896978 DOI: 10.3389/fped.2024.1165492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024] Open
Abstract
Background Pathogenic variants in the IGHMBP2 gene are associated with two distinct autosomal recessive neuromuscular disorders: spinal muscular atrophy with respiratory distress type 1 (SMARD1; OMIM #604320) and Charcot-Marie-Tooth type 2S (CMT2S; OMIM #616155). SMARD1 is a severe and fatal condition characterized by infantile-onset respiratory distress, diaphragmatic palsy, and distal muscular weakness, while CMT2S follows a milder clinical course, with slowly progressive distal muscle weakness and sensory loss, without manifestations of respiratory disorder. Methods Whole-exome sequencing of the IGHMBP2 gene was performed for eight Vietnamese patients with IGHMBP2-related neuromuscular disorders including five patients with SMARD1 and the others with CMT2S. Results We identified one novel IGHMBP2 variant c.1574T > C (p.Leu525Pro) in a SMARD1 patient. Besides that, two patients shared the same pathogenic variants (c.1235 + 3A > G/c.1334A > C) but presented completely different clinical courses: one with SMARD1 who deceased at 8 months of age, the other with CMT2S was alive at 3 years old without any respiratory distress. Conclusion This study is the first to report IGHMBP-2-related neuromuscular disorders in Vietnam. A novel IGHMBP2 variant c.1574T > C (p.Leu525Pro) expressing SMARD1 phenotype was detected. The presence of three patients with the same genotype but distinct clinical outcomes suggested the interaction of variants and other factors including relating modified genes in the mechanism of various phenotypes.
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Affiliation(s)
- Van Khanh Tran
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- Department of Molecular Pathology, Faculty of Medical Laboratory Technology, Hanoi Medical University, Hanoi, Vietnam
| | - My Ha Cao
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | | | - Phuong Thi Le
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Hai Anh Tran
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Dung Chi Vu
- Department of Endocrinology, Metabolism and Genetics, National Hospital of Pediatrics, Hanoi, Vietnam
| | - Ha Thu Nguyen
- Department of Endocrinology, Metabolism and Genetics, National Hospital of Pediatrics, Hanoi, Vietnam
| | | | - The-Hung Bui
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
- Center for Molecular Medicine, Clinical Genetics Unit, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Thanh Binh Nguyen
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Thanh Van Ta
- Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
- Clinical Laboratory, Hanoi Medical University Hospital, Hanoi Medical University, Hanoi, Vietnam
| | - Thinh Huy Tran
- Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
- Clinical Laboratory, Hanoi Medical University Hospital, Hanoi Medical University, Hanoi, Vietnam
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19
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Kaur A, Yadav VG, Pawar SV, Sembi JK. Insights to Phenylalanine Ammonia Lyase (PAL) and Secondary Metabolism in Orchids: An in silico Approach. Biochem Genet 2024; 62:413-435. [PMID: 37358673 DOI: 10.1007/s10528-023-10428-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 06/27/2023]
Abstract
The phenylalanine ammonia lyase (PAL) catalyses the first step of phenylpropanoid metabolic pathway which leads to the biosynthesis of a diverse group of secondary metabolites. Orchids serve as a rich source of metabolites and the availability of genome or transcriptome for selected orchid species provides an opportunity to analyse the PAL genes in orchids. In the present study, 21 PAL genes were characterized using bioinformatics tools in nine orchid species (Apostasia shenzhenica, Cypripedium formosanum, Dendrobium catenatum, Phalaenopsis aphrodite, Phalaenopsis bellina, Phalaenopsis equestris, Phalaenopsis lueddemanniana, Phalaenopsis modesta and Phalaenopsis schilleriana). Multiple sequence alignment confirmed the presence of PAL-specific conserved domains (N-terminal, MIO, core, shielding and C-terminal domain). All these proteins were predicted to be hydrophobic in nature and to have cytoplasmic localisation. Structural modelling depicted the presence of alpha helices, extended strands, beta turns and random coils in their structure. Ala-Ser-Gly triad known for substrate binding and catalysis of MIO-domain was found to be completely conserved in all the proteins. Phylogenetic study showed that the PALs of pteridophytes, gymnosperms and angiosperms clustered together in separate clades. Expression profiling showed tissue-specific expression for all the 21 PAL genes in the various reproductive and vegetative tissues which suggested their diverse role in growth and development. This study provides insights to the molecular characterization of PAL genes which may help in developing biotechnological strategies to enhance the synthesis of phenylpropanoids in orchids and other heterologous systems for pharmaceutical applications.
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Affiliation(s)
- Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Vikramaditya G Yadav
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
| | - Sandip V Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Jaspreet K Sembi
- Department of Botany, Panjab University, Chandigarh, 160014, India.
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20
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Hannon CE, Eisen MB. Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors. eLife 2024; 12:RP88221. [PMID: 38275292 PMCID: PMC10945700 DOI: 10.7554/elife.88221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
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Affiliation(s)
- Colleen E Hannon
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
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21
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Kim YR, Han JY, Choi YE. A Pinus strobus transcription factor PsbHLH1 activates the production of pinosylvin stilbenoids in transgenic Pinus koraiensis calli and tobacco leaves. FRONTIERS IN PLANT SCIENCE 2024; 15:1342626. [PMID: 38304739 PMCID: PMC10830828 DOI: 10.3389/fpls.2024.1342626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024]
Abstract
Transcription factors (TFs) play an important role in regulating the biosynthesis of secondary metabolites. In Pinus strobus, the level of methylated derivatives of pinosylvin is significantly increased upon pine wood nematode (PWN) infection, and these compounds are highly toxic to PWNs. In a previous study, we found that the expression of a basic helix-loop-helix TF gene, PsbHLH1, strongly increased in P. strobus plants after infection with PWNs. In this study, we elucidated the regulatory role of the PsbHLH1 gene in the production of methylated derivatives of pinosylvin such as pinosylvin monomethyl ether (PME) and dihydropinoylvin monomethyl ether (DPME). When PsbHLH1 was overexpressed in Pinus koraiensis calli, the production of PME and DPME was significantly increased. Overexpression of the stilbene synthase (PsSTS) and pinosylvin methyl transferase (PsPMT) genes, known as key enzymes for the biosynthesis of methylated pinosylvins, did not change PME or DPME production. Moreover, PME and DPME were not produced in tobacco leaves when the PsSTS and PsPMT genes were transiently coexpressed. However, the transient expression of three genes, PsSTS, PsPMT, and PsbHLH1, resulted in the production of PME and DPME in tobacco leaves. These results prove that PsbHLH1 is an important TF for the pinosylvin stilbene biosynthesis in pine plants and plays a regulatory role in the engineered production of PME and DPME in tobacco plants.
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Affiliation(s)
| | | | - Yong Eui Choi
- Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Republic of Korea
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22
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Park JR, Kim EG, Jang YH, Kim KM. Utilization of the Winkler scale of plants using big data temperature presented by the Korea Meteorological Administration. FRONTIERS IN PLANT SCIENCE 2024; 14:1349606. [PMID: 38283972 PMCID: PMC10811219 DOI: 10.3389/fpls.2023.1349606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
Introduction Rice is an important food source that can provide a stable supply of calories for most people around the world. However, owing to the recent rapid temperature rise, we are facing social issues related to the increase in the Winkler scale. In this study, a strategy for screening potential candidate genes related to the yield according to the Winkler scale is presented, and the possibility of using a candidate gene identified through sequence haplotype and homology analysis as a breeding source is suggested. Methods QTL for the Winkler scale was identified using a population of 120 double haploids derived from a cross between Cheongchoneg, Indica, and Nagdong, Japonica. Results and discussion A total of 79 candidate genes were detected in the identified QTL region, and OsHAq8 was finally screened. Through haplotype analysis, OsHAq8 was derived from the Indica group and orthologous to Graminae's activator of Hsp90 ATPase, suggesting that it is a candidate gene involved in yield according to temperature during the growing period. The expression level of OsHAq8 increased as the Winkler scale increased. The findings of this study can serve as a crucial indicator for predicting harvest time and grain quality while achieving a stable yield through marker selection and adaptation to climate change. Climate change occurs more frequently. In these situations, it is very important to predict harvest time and apply relevant candidate genes to breeding. The candidate genes presented in this study can be effectively applied to rice breeding in preparation for climate change.
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Affiliation(s)
- Jae-Ryoung Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Eun-Gyeong Kim
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Yoon-Hee Jang
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung-Min Kim
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu, Republic of Korea
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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23
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Ahmed J, Sajjad Y, Latif A, Lodhi MS, Huzafa M, Situ C, Ahmad R, Shah MM, Hassan A. Genome-wide identification and characterization of wall-associated kinases, molecular docking and polysaccharide elicitation of monoterpenoid indole alkaloids in micro-propagated Catharanthus roseus. JOURNAL OF PLANT RESEARCH 2024; 137:125-142. [PMID: 37962734 DOI: 10.1007/s10265-023-01504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/06/2023] [Indexed: 11/15/2023]
Abstract
Wall-associated kinases (WAKs) are a unique family of proteins that are predominantly localized on the plasma membrane and simultaneously bound to the cell wall. WAKs play a pivotal role in signal transduction to regulate growth, defense, and response to environmental stimuli in plants. These kinases have been identified and characterized in various plant species, however, similar information for Catharanthus roseus is scarce. C. roseus is an evergreen ornamental plant that produces a repertoire of biologically active compounds. The plant is best characterized for the production of antineoplastic monoterpenoid indole alkaloids (MIAs) namely vinblastine and vincristine. Owing to the diverse composition of phytochemicals, C. roseus is known as a "model non-model" plant for secondary metabolite research. Genome analyses showed 37 putative CrWAK genes present in C. roseus, largely localized on the plasma membrane. Phylogenetic analysis revealed six clusters of CrWAKs. Diverse cis-acting elements, including those involved in defense responses, were identified on the promotor regions of CrWAK genes. The highest binding affinity (- 12.6 kcal/mol) was noted for CrWAK-22 against tri-galacturonic acid. Tri-galacturonic acid stimulated 2.5-fold higher production of vinblastine, sixfold upregulation of the expression of ORCA3 transcription factor, and 6.14-fold upregulation of CrWAK-22 expression. Based on these results it was concluded that the expression of CrWAK genes induced by biotic elicitors may have an important role in the production of MIAs. The current findings may serve as a basis for functional characterization and mechanistic explanation of the role of CrWAK genes in the biosynthesis of MIAs upon elicitation.
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Affiliation(s)
- Jawad Ahmed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast, BT9 5DL, UK
| | - Yasar Sajjad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Aasia Latif
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Mohammad Saeed Lodhi
- Department of Management Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Muhammad Huzafa
- Department of Plant Sciences, Quaid-e-Azam University Islamabad, Islamabad, Pakistan
| | - Chen Situ
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast, BT9 5DL, UK
| | - Raza Ahmad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Muhammad Maroof Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
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24
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Ahmed J, Sajjad Y, Gatasheh MK, Ibrahim KE, Huzafa M, Khan SA, Situ C, Abbasi AM, Hassan A. Genome-wide identification of NAC transcription factors and regulation of monoterpenoid indole alkaloid biosynthesis in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2023; 14:1286584. [PMID: 38223288 PMCID: PMC10785006 DOI: 10.3389/fpls.2023.1286584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/01/2023] [Indexed: 01/16/2024]
Abstract
NAC transcription factors (TFs) are crucial to growth and defense responses in plants. Though NACs have been characterized for their role in several plants, comprehensive information regarding their role in Catharanthus roseus, a perennial ornamental plant, is lacking. Homology modelling was employed to identify and characterize NACs in C. roseus. In-vitro propagation of C. roseus plants was carried out using cell suspension and nodal culture and were elicited with two auxin-antagonists, 5-fluoro Indole Acetic Acid (5-F-IAA) and α-(phenyl ethyl-2-oxo)-Indole-Acetic-Acid (PEO-IAA) for the enhanced production of monoterpenoid indole alkaloids (MIAs) namely catharanthine, vindoline, and vinblastine. Analyses revealed the presence of 47 putative CrNAC genes in the C. roseus genome, primarily localized in the nucleus. Phylogenetic analysis categorized these CrNACs into eight clusters, demonstrating the highest synteny with corresponding genes in Camptotheca acuminata. Additionally, at least one defense or hormone-responsive cis-acting element was identified in the promoter region of all the putative CrNACs. Of the two elicitors, 5-F-IAA was effective at 200 µM to elicit a 3.07-fold increase in catharanthine, 2.76-fold in vindoline, and 2.4-fold in vinblastine production in nodal culture. While a relatively lower increase in MIAs was recorded in suspension culture. Validation of RNA-Seq by qRT-PCR showed upregulated expression of stress-related genes (CrNAC-07 and CrNAC-24), and downregulated expression of growth-related gene (CrNAC-25) in elicited nodal culture of C. roseus. Additionally, the expression of genes involved in the biosynthesis of MIAs was significantly upregulated upon elicitation. The current study provides the first report on the role of CrNACs in regulating the biosynthesis of MIAs.
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Affiliation(s)
- Jawad Ahmed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast, United Kingdom
| | - Yasar Sajjad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Khalid Elfaki Ibrahim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Huzafa
- Department of Plant Sciences, Quaid-e-Azam University, Islamabad, Pakistan, Pakistan
| | - Sabaz Ali Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Chen Situ
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast, United Kingdom
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University, Islamabad, Abbottabad, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
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25
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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26
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Mamun MAA, Maruyama JI. Fungal transglutaminase domain-containing proteins are involved in hyphal protection at the septal pore against wounding. Mol Biol Cell 2023; 34:ar127. [PMID: 37756125 PMCID: PMC10848947 DOI: 10.1091/mbc.e23-01-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
Transglutaminase (TG) is a ubiquitous enzyme that crosslinks substrates. In humans, TG participates in blood clotting and wound healing. However, the functions related to the cellular protection of microbial TG are unknown. In filamentous fungi, we previously identified SppB, which contains the transglutaminase core (TGc) domain and functions in hyphal protection at the septal pore upon wounding. Here, we further analyzed the cytokinesis-related protein Cyk3 and peptide N-glycanase Png1, as both contain the TGc domain. All three proteins exhibited functional importance in wound-related hyphal protection at the septal pore. Upon wounding, SppB and AoPng1 accumulated at the septal pore, whereas AoCyk3 and AoPng1 normally localized around the septal pore. The putative Cys-His-Asp catalytic triad of SppB is conserved with the human TGc domain-containing kyphoscoliosis peptidase. Catalytic triad disruptive mutants of SppB and AoCyk3 exhibited septal pore plugging defects. Similar to other TGs, SppB underwent wound-induced truncation of the N-terminal region. Notably, TG activity was detected in vivo at the septal pore of wounded hyphae using a fluorescent-labeled substrate; however, the activity was inhibited by the TG inhibitor cystamine. Our study suggests a conserved role for TGc domain-containing proteins in wound-related protection in fungi, similar to that in humans.
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Affiliation(s)
- Md. Abdulla Al Mamun
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Jun-ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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27
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Xiao PX, Li Y, Lu J, Zuo H, Pingcuo G, Ying H, Zhao F, Xu Q, Zeng X, Jiao WB. High-quality assembly and methylome of a Tibetan wild tree peony genome ( Paeonia ludlowii) reveal the evolution of giant genome architecture. HORTICULTURE RESEARCH 2023; 10:uhad241. [PMID: 38156287 PMCID: PMC10753165 DOI: 10.1093/hr/uhad241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/14/2023] [Indexed: 12/30/2023]
Abstract
Tree peony belongs to one of the Saxifragales families, Paeoniaceae. It is one of the most famous ornamental plants, and is also a promising woody oil plant. Although two Paeoniaceae genomes have been released, their assembly qualities are still to be improved. Additionally, more genomes from wild peonies are needed to accelerate genomic-assisted breeding. Here we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild Tibetan tree peony, Paeonia ludlowii, which features substantial sequence divergence, including around 75% specific sequences and gene-level differentials compared with other peony genomes. Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and, together with rosids, they are the sister taxon to asterids. The P. ludlowii genome is characterized by frequent chromosome reductions, centromere rearrangements, broadly distributed heterochromatin, and recent continuous bursts of transposable element (TE) movement in peony, although it lacks recent whole-genome duplication. These recent TE bursts appeared during the uplift and glacial period of the Qinghai-Tibet Plateau, perhaps contributing to adaptation to rapid climate changes. Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation, TE removal, and DNA methylation silencing. Such interactions also impact numerous recently duplicated genes, particularly those related to oil biosynthesis and flower traits. This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.
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Affiliation(s)
- Pei-Xuan Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuanrong Li
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Jin Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hao Zuo
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China
| | - Gesang Pingcuo
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Hong Ying
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Fan Zhao
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Wang S, Zhao Y, Chen Y, Gao M, Wang Y. The Association between BZIP Transcription Factors and Flower Development in Litsea cubeba. Int J Mol Sci 2023; 24:16646. [PMID: 38068969 PMCID: PMC10705912 DOI: 10.3390/ijms242316646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors among eukaryotic organisms. Members of the bZIP family play various roles in regulating the intricate process of flower development in plants. Litsea cubeba (Lour.) (family: Lauraceae) is an aromatic, dioecious plant used in China for a wide range of applications. However, no study to date has undertaken a comprehensive analysis of the bZIP gene family in L. cubeba. In this work, we identified 68 members of the bZIP gene family in L. cubeba and classified them into 12 subfamilies based on previous studies on Arabidopsis thaliana. Transcriptome data analysis revealed that multiple LcbZIP genes exhibit significantly high expression levels in the flowers of L. cubeba, while some also demonstrate distinct temporal specificity during L. cubeba flower development. In particular, some LcbZIP genes displayed specific and high expression levels during the stamen and pistil degradation process. Using differential gene expression analysis, weighted gene co-expression network analysis, and Gene Ontology enrichment analysis, we identified six candidate LcbZIP genes that potentially regulate stamen or pistil degradation during flower development. In summary, our findings provide a framework for future functional analysis of the LcbZIP gene family in L. cubeba and offer novel insights for investigating the mechanism underlying pistil and stamen degeneration in this plant.
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Affiliation(s)
- Siqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
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Liu Z, Ma K, Zhang X, Song X, Qin Y. Different Putative Methyltransferases Have Different Effects on the Expression Patterns of Cellulolytic Genes. J Fungi (Basel) 2023; 9:1118. [PMID: 37998923 PMCID: PMC10671955 DOI: 10.3390/jof9111118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Putative methyltranferase LaeA and LaeA-like proteins, conserved in many filamentous fungi, regulate fungal growth, development, virulence, the biosynthesis of secondary metabolites, and the production of cellulolytic enzymes. Penicillium oxaliucm is a typical fungus that produces cellulolytic enzymes. In this study, we reported the biological function of eight putative methyltransferases (PoMtr23C/D/E/F/G/H and PoMtr25A/B) containing a methyltransf_23 or methyltransf_25 domain, with a focus on their roles in the production of cellulolytic enzymes. In P. oxalicum, various methyltransferase genes displayed different transcriptional levels. The genes Pomtr23C and Pomtr25A exhibited high transcriptional levels, while Pomtr23D/E/F/G/H and Pomtr25B were transcribed constantly at low levels. The gene deletion mutants (Δmtr23C/D/E/F/G/H and Δmtr25A/B) were constructed. Various mutants have different patterns in cellulolytic enzyme production. Compared to the WT, the largest increase in filter paper activity (FPA, indicating total cellulase activity) was observed in the Δmtr23G mutant, the only mutant with a cellulolytic halo surrounding the colony. Three mutants (Δmtr23C/D and Δmtr25A) also showed increased cellulolytic enzyme production. The Δmtr23E and Δmtr25B mutants displayed decreased FPA activity, while the Δmtr23F and Δmtr23H mutants displayed similar patterns of cellulolytic enzyme production compared with the WT. The assay of transcriptional levels of cellobiohydrolase gene Pocbh1 and β-1,4-endoglucanase Poeg1 supported that higher cellulolytic gene transcription resulted in higher production of cellulolytic enzymes, and vice versa. The transcriptional levels of two transcription factors, activator XlnR and repressor CreA, were measured. The high transcription level of the PoxlnR gene in the Δmtr23D mutant should be one reason for the increased transcription of its cellulolytic enzyme gene. Both XlnR and CreA transcriptional levels increased in the Δmtr23G mutant, but the former showed a more significant increase than the latter, indicating that the activation effect predominated. The PoMtr25A is localized in the nucleus. The catalytic subunit SNF2 of the SWI/SNF chromatin-remodeling complex was found as one of the interacting proteins of PoMtr25A via tandem affinity purification coupled with mass spectrometry. PoMtr25A may affect not only the transcription of repressor CreA but also by recruiting SWI/SNF complexes that affect chromatin structure, thereby regulating the transcription of target genes.
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Affiliation(s)
- Zhongjiao Liu
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
| | - Kexuan Ma
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiujun Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Xin Song
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China; (Z.L.); (K.M.); (X.Z.); (X.S.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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30
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Yu M, Ma D, Eszterhas S, Rollenhagen C, Lee SA. The Early Endocytosis Gene PAL1 Contributes to Stress Tolerance and Hyphal Formation in Candida albicans. J Fungi (Basel) 2023; 9:1097. [PMID: 37998902 PMCID: PMC10672141 DOI: 10.3390/jof9111097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
The endocytic and secretory pathways of the fungal pathogen Candida albicans are fundamental to various key cellular processes such as cell growth, cell wall integrity, protein secretion, hyphal formation, and pathogenesis. Our previous studies focused on several candidate genes involved in early endocytosis, including ENT2 and END3, that play crucial roles in such processes. However, much remains to be discovered about other endocytosis-related genes and their contributions toward Candida albicans secretion and virulence. In this study, we examined the functions of the early endocytosis gene PAL1 using a reverse genetics approach based on CRISPR-Cas9-mediated gene deletion. Saccharomyces cerevisiae Pal1 is a protein in the early coat complex involved in clathrin-mediated endocytosis that is later internalized with the coat. The C. albicans pal1Δ/Δ null mutant demonstrated increased resistance to the antifungal agent caspofungin and the cell wall stressor Congo Red. In contrast, the null mutant was more sensitive to the antifungal drug fluconazole and low concentrations of SDS than the wild type (WT) and the re-integrant (KI). While pal1Δ/Δ can form hyphae and a biofilm, under some hyphal-inducing conditions, it was less able to demonstrate filamentous growth when compared to the WT and KI. The pal1Δ/Δ null mutant had no defect in clathrin-mediated endocytosis, and there were no changes in virulence-related processes compared to controls. Our results suggest that PAL1 has a role in susceptibility to antifungal agents, cell wall integrity, and membrane stability related to early endocytosis.
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Affiliation(s)
- Miranda Yu
- Thayer School of Engineering at Dartmouth, Dartmouth College, Hanover, NH 03755, USA;
- Medicine Service, White River Junction VA Medical Center, Hartford, VT 05009, USA; (D.M.); (S.E.)
| | - Dakota Ma
- Medicine Service, White River Junction VA Medical Center, Hartford, VT 05009, USA; (D.M.); (S.E.)
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Susan Eszterhas
- Medicine Service, White River Junction VA Medical Center, Hartford, VT 05009, USA; (D.M.); (S.E.)
- Department of Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA;
| | - Christiane Rollenhagen
- Department of Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA;
| | - Samuel A. Lee
- Department of Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA;
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31
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Höpfner D, Cichy A, Pogenberg V, Krisp C, Mezouar S, Bach NC, Grotheer J, Zarza SM, Martinez E, Bonazzi M, Feige MJ, Sieber SA, Schlüter H, Itzen A. The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3. Commun Biol 2023; 6:1124. [PMID: 37932372 PMCID: PMC10628234 DOI: 10.1038/s42003-023-05494-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
The intracellular bacterial pathogen Coxiella burnetii evades the host response by secreting effector proteins that aid in establishing a replication-friendly niche. Bacterial filamentation induced by cyclic AMP (Fic) enzymes can act as effectors by covalently modifying target proteins with the posttranslational AMPylation by transferring adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to a hydroxyl-containing side chain. Here we identify the gene product of C. burnetii CBU_0822, termed C. burnetii Fic 2 (CbFic2), to AMPylate host cell histone H3 at serine 10 and serine 28. We show that CbFic2 acts as a bifunctional enzyme, both capable of AMPylation as well as deAMPylation, and is regulated by the binding of DNA via a C-terminal helix-turn-helix domain. We propose that CbFic2 performs AMPylation in its monomeric state, switching to a deAMPylating dimer upon DNA binding. This study unveils reversible histone modification by a specific enzyme of a pathogenic bacterium.
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Affiliation(s)
- Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Adam Cichy
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Group of Proteinchemistry, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Vivian Pogenberg
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Soraya Mezouar
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Nina C Bach
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Jan Grotheer
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Sandra Madariaga Zarza
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Martinez
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matteo Bonazzi
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matthias J Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Stephan A Sieber
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
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He Z, Chao H, Zhou X, Ni Q, Hu Y, Yu R, Wang M, Li C, Chen J, Chen Y, Chen Y, Cui C, Zhang L, Chen M, Chen D. A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development. HORTICULTURE RESEARCH 2023; 10:uhad196. [PMID: 38023476 PMCID: PMC10673659 DOI: 10.1093/hr/uhad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.
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Affiliation(s)
- Zhenxiang He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoyu Chao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Minghuai Wang
- Forest Protection Department, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Jingzhen Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yunzhu Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yong Chen
- Xishan Forest Farm, Dazu District, Chongqing 402360, China
| | - Chunyi Cui
- Longshan Forest Farm, Lechang 512221, China
| | - Liangbo Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
- Hunan Horticultural Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Al Mamun MA, Reza MA, Islam MS. Identification of novel proteins regulating lipid droplet biogenesis in filamentous fungi. Mol Microbiol 2023; 120:702-722. [PMID: 37748926 DOI: 10.1111/mmi.15170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Lipid droplets (LDs) are storage organelles for neutral lipids which are critical for lipid homeostasis. Current knowledge of fungal LD biogenesis is largely limited to budding yeast, while LD regulation in multinucleated filamentous fungi which exhibit considerable metabolic activity remains unexplored. In this study, 19 LD-associated proteins were identified in the multinucleated species Aspergillus oryzae using a colocalization screening of a previously established enhanced green fluorescent protein (EGFP) fusion library. Functional screening identified 12 lipid droplet-regulating (LDR) proteins whose loss of function resulted in irregular LD biogenesis, particularly in terms of LD number and size. Bioinformatics analysis, targeted mutagenesis, and microscopy revealed four LDR proteins that localize to LD via the putative amphipathic helices (AHs). Further analysis revealed that LdrA with an Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis involving a novel AH. Phylogenetic analysis demonstrated that the patterns of gene evolution were predominantly based on gene duplication. Our study identified a set of novel proteins involved in the regulation of LD biogenesis, providing unique molecular and evolutionary insights into fungal lipid storage.
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Affiliation(s)
- Md Abdulla Al Mamun
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - M Abu Reza
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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Eisner D, Neher E, Taschenberger H, Smith G. Physiology of intracellular calcium buffering. Physiol Rev 2023; 103:2767-2845. [PMID: 37326298 DOI: 10.1152/physrev.00042.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/08/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
Calcium signaling underlies much of physiology. Almost all the Ca2+ in the cytoplasm is bound to buffers, with typically only ∼1% being freely ionized at resting levels in most cells. Physiological Ca2+ buffers include small molecules and proteins, and experimentally Ca2+ indicators will also buffer calcium. The chemistry of interactions between Ca2+ and buffers determines the extent and speed of Ca2+ binding. The physiological effects of Ca2+ buffers are determined by the kinetics with which they bind Ca2+ and their mobility within the cell. The degree of buffering depends on factors such as the affinity for Ca2+, the Ca2+ concentration, and whether Ca2+ ions bind cooperatively. Buffering affects both the amplitude and time course of cytoplasmic Ca2+ signals as well as changes of Ca2+ concentration in organelles. It can also facilitate Ca2+ diffusion inside the cell. Ca2+ buffering affects synaptic transmission, muscle contraction, Ca2+ transport across epithelia, and the killing of bacteria. Saturation of buffers leads to synaptic facilitation and tetanic contraction in skeletal muscle and may play a role in inotropy in the heart. This review focuses on the link between buffer chemistry and function and how Ca2+ buffering affects normal physiology and the consequences of changes in disease. As well as summarizing what is known, we point out the many areas where further work is required.
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Affiliation(s)
- David Eisner
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Erwin Neher
- Membrane Biophysics Laboratory, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Godfrey Smith
- School of Cardiovascular and Metabolic Health, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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35
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Li J, Dong B, Zhong Y, Li Z. Transinfected Wolbachia strains induce a complex of cytoplasmic incompatibility phenotypes: Roles of CI factor genes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:370-382. [PMID: 37194361 PMCID: PMC10472523 DOI: 10.1111/1758-2229.13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/05/2023] [Indexed: 05/18/2023]
Abstract
Wolbachia can modulate the reproductive development of their hosts in multiple modes, and cytoplasmic incompatibility (CI) is the most well-studied phenotype. The whitefly Bemisia tabaci is highly receptive to different Wolbachia strains: wCcep strain from the rice moth Corcyra cephalonica and wMel strain from the fruit fly Drosophila melanogaster could successfully establish and induce CI in transinfected whiteflies. Nevertheless, it is unknown what will happen when these two exogenous Wolbachia strains are co-transinfected into a new host. Here, we artificially transinferred wCcep and wMel into the whitefly and established double- and singly-transinfected B. tabaci isofemale lines. Reciprocal crossing experiments showed that wCcep and wMel induced a complex of CI phenotypes in the recipient host, including unidirectional and bidirectional CI. We next sequenced the whole genome of wCcep and performed a comparative analysis of the CI factor genes between wCcep and wMel, indicating that their cif genes were phylogenetically and structurally divergent, which can explain the crossing results. The amino acid sequence identity and structural features of Cif proteins may be useful parameters for predicting their function. Structural comparisons between CifA and CifB provide valuable clues for explaining the induction or rescue of CI observed in crossing experiments between transinfected hosts.
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Affiliation(s)
- Jing Li
- Department of Entomology and Key Laboratory of Pest Monitoring and Green Management, MOA, College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Bei Dong
- Jinan Academy of Agricultural SciencesJinanChina
| | - Yong Zhong
- Pingxiang Customs Comprehensive Technical Service CenterPingxiangChina
| | - Zheng‐Xi Li
- Department of Entomology and Key Laboratory of Pest Monitoring and Green Management, MOA, College of Plant ProtectionChina Agricultural UniversityBeijingChina
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Qian T, Wang X, Liu J, Shi M, Zhao J, Sun P, Zheng G, Fang C, Xie X. ATP-binding cassette protein ABCC8 promotes anthocyanin accumulation in strawberry fruits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108037. [PMID: 37722280 DOI: 10.1016/j.plaphy.2023.108037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Anthocyanins are important health-promoting flavonoid compounds that substantially contribute to fruit quality. Anthocyanin biosynthesis and most regulatory mechanisms are relatively well understood. However, the functions of anthocyanin transport genes in strawberry fruit remain unclear. In this study, a gene encoding an ATP-binding cassette (ABC) protein of type C, ABCC8, was isolated from strawberry fruits. qRT-PCR analysis demonstrated that the transcript levels of FvABCC8 were the highest and were strongly correlated with anthocyanin accumulation during strawberry fruit ripening. Transient overexpression and RNAi of FvABCC8 led to an increase and decrease in anthocyanin content in strawberry fruits, respectively. Moreover, the ABCC8 promoter was activated by MYB and bHLH transcription factors MYB10, bHLH33, and MYC1. Sucrose enhanced anthocyanin accumulation in FvABCC8-overexpressing Arabidopsis, particularly at higher concentrations. FvABCC8-overexpressing lines were less sensitive to ABA during seed germination and seedling development. These results suggest that strawberry vacuolar anthocyanin transport may be mediated by the ABCC transporter ABCC8, the expression of which may be regulated by transcription factors MYB10, bHLH33, and MYC1.
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Affiliation(s)
- Ting Qian
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaoshan Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jingjing Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Mengyun Shi
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Zhao
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Peipei Sun
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Guanghui Zheng
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Congbing Fang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
| | - Xingbin Xie
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
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Chen K, Wang Y, Nong X, Zhang Y, Tang T, Chen Y, Shen Q, Yan C, Lü B. Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.). BMC Genomics 2023; 24:544. [PMID: 37704940 PMCID: PMC10500787 DOI: 10.1186/s12864-023-09654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Domains of unknown function (DUF) proteins are a number of uncharacterized and highly conserved protein families in eukaryotes. In plants, some DUFs have been predicted to play important roles in development and response to abiotic stress. Among them, DUF568-containing protein family is plant-specific and has not been described previously. A basic analysis and expression profiling was performed, and the co-expression and interaction networks were constructed to explore the functions of DUF568 family in rice. RESULTS The phylogenetic tree showed that the 8, 9 and 11 DUF568 family members from rice, Arabidopsis and maize were divided into three groups. The evolutionary relationship between DUF568 members in rice and maize was close, while the genes in Arabidopsis were more distantly related. The cis-elements prediction showed that over 82% of the elements upstream of OsDUF568 genes were responsive to light and phytohormones. Gene expression profile prediction and RT-qPCR experiments revealed that OsDUF568 genes were highly expressed in leaves, stems and roots of rice seedling. The expression of some OsDUF568 genes varied in response to plant hormones (abscisic acid, 6-benzylaminopurine) and abiotic stress (drought and chilling). Further analysis of the co-expression and protein-protein interaction networks using gene ontology showed that OsDUF568 - related genes were enriched in cellular transports, metabolism and processes. CONCLUSIONS In summary, our findings suggest that the OsDUF568 family may be a vital gene family for the development of rice roots, leaves and stems. In addition, the OsDUF568 family may participate in abscisic acid and cytokinin signaling pathways, and may be related to abiotic stress resistance in these vegetative tissues of rice.
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Affiliation(s)
- Kai Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Yilin Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Xiaoyan Nong
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yichi Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Huaiyin Normal University, Huaian, 223300, China
| | - Yun Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qikun Shen
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Changjie Yan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Bing Lü
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Province Engineering Research Center of Knowledge Management and Intelligent Service, College of Information Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
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Tan Q, Li R, Liu L, Wang D, Dai XF, Song LM, Zhang DD, Kong ZQ, Klosterman SJ, Usami T, Subbarao KV, Liang WX, Chen JY. Functional Characterization of Verticillium dahliae Race 3-Specific Gene VdR3e in Virulence and Elicitation of Plant Immune Responses. Microbiol Spectr 2023; 11:e0108323. [PMID: 37378525 PMCID: PMC10434166 DOI: 10.1128/spectrum.01083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Verticillium dahliae is a soilborne fungal pathogen that causes disease on many economically important crops. Based on the resistance or susceptibility of differential cultivars in tomato, isolates of V. dahliae are divided into three races. Avirulence (avr) genes within the genomes of the three races have also been identified. However, the functional role of the avr gene in race 3 isolates of V. dahliae has not been characterized. In this study, bioinformatics analysis showed that VdR3e, a cysteine-rich secreted protein encoded by the gene characterizing race 3 in V. dahliae, was likely obtained by horizontal gene transfer from the fungal genus Bipolaris. We demonstrate that VdR3e causes cell death by triggering multiple defense responses. In addition, VdR3e localized at the periphery of the plant cell and triggered immunity depending on its subcellular localization and the cell membrane receptor BAK1. Furthermore, VdR3e is a virulence factor and shows differential pathogenicity in race 3-resistant and -susceptible hosts. These results suggest that VdR3e is a virulence factor that can also interact with BAK1 as a pathogen-associated molecular pattern (PAMP) to trigger immune responses. IMPORTANCE Based on the gene-for-gene model, research on the function of avirulence genes and resistance genes has had an unparalleled impact on breeding for resistance in most crops against individual pathogens. The soilborne fungal pathogen, Verticillium dahliae, is a major pathogen on many economically important crops. Currently, avr genes of the three races in V. dahliae have been identified, but the function of avr gene representing race 3 has not been described. We investigated the characteristics of VdR3e-mediated immunity and demonstrated that VdR3e acts as a PAMP to activate a variety of plant defense responses and induce plant cell death. We also demonstrated that the role of VdR3e in pathogenicity was host dependent. This is the first study to describe the immune and virulence functions of the avr gene from race 3 in V. dahliae, and we provide support for the identification of genes mediating resistance against race 3.
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Affiliation(s)
- Qian Tan
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, People’s Republic of China
| | - Lei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Dan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, People’s Republic of China
| | - Li-Min Song
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Steve J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, California, USA
| | - Toshiyuki Usami
- Graduate School of Horticulture, Chiba University, Matsudo City, Japan
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California—Davis, c/o U.S. Agricultural Research Station, Salinas, California, USA
| | - Wen-Xing Liang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, People’s Republic of China
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Patel CK, Rani C, Kumar R, Mukherjee TK. Macromolecular Crowding Promotes Re-entrant Liquid-Liquid Phase Separation of Human Serum Transferrin and Prevents Surface-Induced Fibrillation. Biomacromolecules 2023; 24:3917-3928. [PMID: 37503577 DOI: 10.1021/acs.biomac.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein aggregation and inactivation upon surface immobilization are major limiting factors for analytical applications in biotechnology-related fields. Protein immobilization on solid surfaces often requires multi-step surface passivation, which is time-consuming and inefficient. Herein, we have discovered that biomolecular condensates of biologically active human serum transferrin (Tf) can effectively prevent surface-induced fibrillation and preserve the native-like conformation of phase-separated Tf over a period of 30 days. It has been observed that macromolecular crowding promotes homotypic liquid-liquid phase separation (LLPS) of Tf through enthalpically driven multivalent hydrophobic interactions possibly via the involvement of its low-complexity domain (residues 3-20) containing hydrophobic amino acids. The present LLPS of Tf is a rare example of salt-mediated re-entrant phase separation in a broad range of salt concentrations (0-3 M) solely via the involvement of hydrophobic interactions. Notably, no liquid-to-solid-like phase transition has been observed over a period of 30 days, suggesting the intact conformational integrity of phase-separated Tf, as revealed from single droplet Raman, circular dichroism, and Fourier transform infrared spectroscopy measurements. More importantly, we discovered that the phase-separated condensates of Tf completely inhibit the surface-induced fibrillation of Tf, illustrating the protective role of these liquid-like condensates against denaturation and aggregation of biomolecules. The cell mimicking compact aqueous compartments of biomolecular condensates with a substantial amount of interfacial water preserve the structure and functionality of Tf. Our present study highlights an important functional aspect of biologically active protein condensates and may have wide-ranging implications in cell physiology and biotechnological applications.
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Affiliation(s)
- Chinmaya Kumar Patel
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Chanchal Rani
- Department of Physics, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Rajesh Kumar
- Department of Physics, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
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Cimdins-Ahne A, Naemi AO, Li F, Simm R, Römling U. Characterisation of Variants of Cyclic di-GMP Turnover Proteins Associated with Semi-Constitutive rdar Morphotype Expression in Commensal and Uropathogenic Escherichia coli Strains. Microorganisms 2023; 11:2048. [PMID: 37630608 PMCID: PMC10459773 DOI: 10.3390/microorganisms11082048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Expression of rdar (red, dry, and rough) colony morphology-based biofilm formation in Escherichia coli is highly variable. To investigate the molecular mechanisms of semi-constitutive rdar morphotype formation, we compared their cyclic di-GMP turnover protein content and variability to the highly regulated, temperature-dependent morphotype of the historical and modern ST10 isolates E. coli MG1655 and Fec10, respectively. Subsequently, we assessed the effects of cyclic di-GMP turnover protein variants of the EAL phosphodiesterases YcgG and YjcC and the horizontally transferred diguanylate cyclase DgcX on biofilm formation and motility. The two YcgG variants with truncations of the N-terminal CSS signaling domain were oppositely effective in targeting downregulation of rdar biofilm formation compared to the full-length reference protein. Expression of the C-terminal truncated variants YjcCFec67 and YjcCTob1 showed highly diminished apparent phosphodiesterase activity compared to the reference YjcCMG1655. For YjcCFec101, substitution of the C-terminus led to an apparently inactive enzyme. Overexpression of the diguanylate cyclase DgcX contributed to upregulation of cellulose biosynthesis but not to elevated expression of the major biofilm regulator csgD in the "classical" rdar-expressing commensal strain E. coli Fec10. Thus, the c-di-GMP regulating network is highly complex with protein variants displaying substantially different apparent enzymatic activities.
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Affiliation(s)
- Annika Cimdins-Ahne
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; (A.C.-A.); (F.L.)
| | - Ali-Oddin Naemi
- Institute of Oral Biology, University of Oslo, 0313 Oslo, Norway; (A.-O.N.); (R.S.)
| | - Fengyang Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; (A.C.-A.); (F.L.)
| | - Roger Simm
- Institute of Oral Biology, University of Oslo, 0313 Oslo, Norway; (A.-O.N.); (R.S.)
- Norwegian Veterinary Institute, 0106 Oslo, Norway
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; (A.C.-A.); (F.L.)
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41
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Langhammer F, Maroofian R, Badar R, Gregor A, Rochman M, Ratliff JB, Koopmans M, Herget T, Hempel M, Kortüm F, Heron D, Mignot C, Keren B, Brooks S, Botti C, Ben-Zeev B, Argilli E, Sherr EH, Gowda VK, Srinivasan VM, Bakhtiari S, Kruer MC, Salih MA, Kuechler A, Muller EA, Blocker K, Kuismin O, Park KL, Kochhar A, Brown K, Ramanathan S, Clark RD, Elgizouli M, Melikishvili G, Tabatadze N, Stark Z, Mirzaa GM, Ong J, Grasshoff U, Bevot A, von Wintzingerode L, Jamra RA, Hennig Y, Goldenberg P, Al Alam C, Charif M, Boulouiz R, Bellaoui M, Amrani R, Al Mutairi F, Tamim AM, Abdulwahab F, Alkuraya FS, Khouj EM, Alvi JR, Sultan T, Hashemi N, Karimiani EG, Ashrafzadeh F, Imannezhad S, Efthymiou S, Houlden H, Sticht H, Zweier C. Genotype-phenotype correlations in RHOBTB2-associated neurodevelopmental disorders. Genet Med 2023; 25:100885. [PMID: 37165955 DOI: 10.1016/j.gim.2023.100885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
PURPOSE Missense variants clustering in the BTB domain region of RHOBTB2 cause a developmental and epileptic encephalopathy with early-onset seizures and severe intellectual disability. METHODS By international collaboration, we assembled individuals with pathogenic RHOBTB2 variants and a variable spectrum of neurodevelopmental disorders. By western blotting, we investigated the consequences of missense variants in vitro. RESULTS In accordance with previous observations, de novo heterozygous missense variants in the BTB domain region led to a severe developmental and epileptic encephalopathy in 16 individuals. Now, we also identified de novo missense variants in the GTPase domain in 6 individuals with apparently more variable neurodevelopmental phenotypes with or without epilepsy. In contrast to variants in the BTB domain region, variants in the GTPase domain do not impair proteasomal degradation of RHOBTB2 in vitro, indicating different functional consequences. Furthermore, we observed biallelic splice-site and truncating variants in 9 families with variable neurodevelopmental phenotypes, indicating that complete loss of RHOBTB2 is pathogenic as well. CONCLUSION By identifying genotype-phenotype correlations regarding location and consequences of de novo missense variants in RHOBTB2 and by identifying biallelic truncating variants, we further delineate and expand the molecular and clinical spectrum of RHOBTB2-related phenotypes, including both autosomal dominant and recessive neurodevelopmental disorders.
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Affiliation(s)
- Franziska Langhammer
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Rueda Badar
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Anne Gregor
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michelle Rochman
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA
| | - Jeffrey B Ratliff
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA
| | - Marije Koopmans
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Delphine Heron
- Department of Genetics, La Pitié-Salpêtrière Hospital, APHP, Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, APHP, Sorbonne University, Paris, France
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, APHP, Sorbonne University, Paris, France
| | - Susan Brooks
- Division of Medical Genetics, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Christina Botti
- Division of Medical Genetics, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Bruria Ben-Zeev
- The Neurology Department at Sheba Medical Center, Ramat Gan, Israel
| | - Emanuela Argilli
- Brain Development Research Program, Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Elliot H Sherr
- Brain Development Research Program, Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Varunvenkat M Srinivasan
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ; Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ; Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
| | - Mustafa A Salih
- Division of Pediatric Neurology, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, Almughtaribeen University, Khartoum, Sudan
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Eric A Muller
- Clinical Genetics, Stanford Children's Health, San Francisco, CA
| | - Karli Blocker
- Clinical Genetics, Stanford Children's Health, San Francisco, CA
| | - Outi Kuismin
- Department of Clinical Genetics, PEDEGO Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Kristen L Park
- Anschutz Medical Campus Department of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO
| | - Aaina Kochhar
- Section of Genetics, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
| | - Kathleen Brown
- Section of Genetics, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
| | | | - Robin D Clark
- Division of Genetics, Loma Linda University Health, San Bernardino, CA
| | - Magdeldin Elgizouli
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Gia Melikishvili
- Department of pediatrics, MediClubGeorgia Medical Center, Tbilisi, Georgia
| | - Nazhi Tabatadze
- Department of pediatrics, MediClubGeorgia Medical Center, Tbilisi, Georgia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA; Department of Pediatrics, University of Washington, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Jinfon Ong
- Child Neurology Consultants of Austin, Austin, TX
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Andrea Bevot
- Department of Pediatric Neurology and Developmental Medicine, Children's Hospital, University Hospital of Tuebingen, Tuebingen, Germany
| | | | - Rami A Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Yvonne Hennig
- Department of Pediatrics, University of Leipzig Medical Center, Leipzig, Germany
| | - Paula Goldenberg
- Division of Medical Genetics, Massachusetts General Hospital, Boston, MA
| | - Chadi Al Alam
- Pediatric Neurology Department, American Center for Psychiatry and Neurology, Abu Dhabi, United Arab Emirates; Pediatric Neurology department, Haykel Hospital, El Koura, Lebanon
| | - Majida Charif
- Genetics Unit, Medical Sciences Research Laboratory, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco; BRO Biobank, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco; Genetics and Immuno-Cell Therapy Team, Mohammed First University, Oujda, Morocco
| | - Redouane Boulouiz
- Genetics Unit, Medical Sciences Research Laboratory, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco; BRO Biobank, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco
| | - Mohammed Bellaoui
- Genetics Unit, Medical Sciences Research Laboratory, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco; BRO Biobank, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco
| | - Rim Amrani
- Department of Neonatology, Mohammed VI University Hospital, Faculty of Medicine and Pharmacy, University Mohammed Premier, Oujda, Morocco
| | - Fuad Al Mutairi
- Genetic and Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdullah M Tamim
- Pediatric Neurology Section-Pediatric Department, King Faisal Specialist Hospital & Research Center (Gen. Org) - Jeddah Branch, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal M Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Javeria R Alvi
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | - Narges Hashemi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan G Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, United Kingdom
| | - Farah Ashrafzadeh
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Imannezhad
- Department of Pediatric Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christiane Zweier
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland.
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Nagle MF, Nahata SS, Zahl B, Niño de Rivera A, Tacker XV, Elorriaga E, Ma C, Goralogia GS, Klocko AL, Gordon M, Joshi S, Strauss SH. Knockout of floral and meiosis genes using CRISPR/Cas9 produces male-sterility in Eucalyptus without impacts on vegetative growth. PLANT DIRECT 2023; 7:e507. [PMID: 37456612 PMCID: PMC10345981 DOI: 10.1002/pld3.507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/28/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023]
Abstract
Eucalyptus spp. are widely cultivated for the production of pulp, energy, essential oils, and as ornamentals. However, their dispersal from plantings, especially when grown as an exotic, can cause ecological disruptions. To provide new tools for prevention of sexual dispersal by pollen as well as to induce male-sterility for hybrid breeding, we studied the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated knockout of three floral genes in both FT-expressing (early-flowering) and non-FT genotypes. We report male-sterile phenotypes resulting from knockout of the homologs of all three genes, including one involved in meiosis and two regulating early stages of pollen development. The targeted genes were Eucalyptus homologs of REC8 (EREC8), TAPETAL DEVELOPMENT AND FUNCTION 1 (ETDF1), and HECATE3 (EHEC3-like). The erec8 knockouts yielded abnormal pollen grains and a predominance of inviable pollen, whereas the etdf1 and ehec3-like knockouts produced virtually no pollen. In addition to male-sterility, both erec8 and ehec3-like knockouts may provide complete sterility because the failure of erec8 to undergo meiosis is expected to be independent of sex, and ehec3-like knockouts produce flowers with shortened styles and no visible stigmas. When comparing knockouts to controls in wild-type (non-early-flowering) backgrounds, we did not find visible morphological or statistical differences in vegetative traits, including average single-leaf mass, stem volume, density of oil glands, or chlorophyll in leaves. Loss-of-function mutations in any of these three genes show promise as a means of inducing male- or complete sterility without impacting vegetative development.
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Affiliation(s)
- Michael F. Nagle
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Surbhi S. Nahata
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Bahiya Zahl
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Alexa Niño de Rivera
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Xavier V. Tacker
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Estefania Elorriaga
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Cathleen Ma
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Greg S. Goralogia
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Amy L. Klocko
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Michael Gordon
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Sonali Joshi
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregonUSA
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Wangsanut T, Amsri A, Pongpom M. Antibody screening reveals antigenic proteins involved in Talaromyces marneffei and human interaction. Front Cell Infect Microbiol 2023; 13:1118979. [PMID: 37404721 PMCID: PMC10315666 DOI: 10.3389/fcimb.2023.1118979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/30/2023] [Indexed: 07/06/2023] Open
Abstract
Talaromycosis is a fungal infection that generally affects immunocompromised hosts and is one of the most frequent systemic mycoses in HIV patients, especially in endemic areas such as Southeast Asia. Talaromyces marneffei, the causative agent of talaromycosis, grows as a mold in the environment but adapts to the human body and host niches by transitioning from conidia to yeast-like cells. Knowledge of the human host and T. marneffei interaction has a direct impact on the diagnosis, yet studies are still lacking. The morbidity and mortality rates are high in taloromycosis patients if the diagnosis and treatments are delayed. Immunogenic proteins are excellent candidates for developing detection tools. Previously, we identified antigenic proteins that were recognized by antibodies from talaromycosis sera. Three of these identified proteins have been previously characterized in detail, while the others have not been explored. To expedite the progress of antigen discovery, the complete list of antigenic proteins and their features was fully reported in this study. Functional annotation and Gene Ontology examination revealed that these proteins showed a high association with membrane trafficking. Further bioinformatics analyses were performed to search for antigenic protein characteristics, including functional domains, critical residues, subcellular localization, secretory signals, and epitope peptide sequences. Expression profiling of these antigenic encoding genes was investigated using quantitative real-time PCR. The results demonstrated that most genes were expressed at low levels in the mold form, but were highly upregulated in the pathogenic yeast phase, consistent with the antigenic role of these genes during the human-host interaction. Most transcripts accumulated in the conidia, suggesting a role during phase transition. The collection of all antigen-encoding DNA sequences described here is freely accessible at GenBank, which could be useful for the research community to develop into biomarkers, diagnostic tests, research detection tools, and even vaccines.
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Gao H, Suo X, Zhao L, Ma X, Cheng R, Wang G, Zhang H. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. PLANT CELL REPORTS 2023; 42:1003-1024. [PMID: 37012438 DOI: 10.1007/s00299-023-03009-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE This paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response. The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.
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Affiliation(s)
- Hui Gao
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoman Suo
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ling Zhao
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xinlei Ma
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Haoshan Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
- Chinese Academy of Agricultural Sciences Institute of Crop Sciences, Beijing, 100081, China.
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Zhang X, Xun X, Meng D, Li M, Chang L, Shi J, Ding W, Sun Y, Wang H, Bao Z, Hu X. Transcriptome Analysis Reveals the Genes Involved in Oxidative Stress Responses of Scallop to PST-Producing Algae and a Candidate Biomarker for PST Monitoring. Antioxidants (Basel) 2023; 12:1150. [PMID: 37371880 DOI: 10.3390/antiox12061150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/13/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
Paralytic shellfish toxins (PST) could be accumulated in bivalves and cause safety problems. To protect public health, bivalves are examined for PST contamination before entering the market, usually by high-performance liquid chromatography (HPLC) or LC-tandem mass spectrometry (LC-MS/MS) in the lab, which needs PST standards not all available and is time-consuming for large sample sizes. To detect PST toxicity in bivalves rapidly and sensitively, a biomarker gene is highly demanded, but the related study is very limited. In this study, we fed a commercially important bivalve, Patinopecten yessoensis, with the PST-producing dinoflagellate Alexandrium catenella. After 1, 3, and 5 days of exposure, both PST concentrations and toxicity levels in the digestive gland continuously increased. Transcriptome analysis revealed that the differentially expressed genes were significantly enriched in oxidation-reduction process, which included the cytochrome P450 genes (CYPs), type I iodothyronine deiodinase (IOD1s), peroxidasin (PXDN), and acyl-Coenzyme A oxidase 1 (ACOX1) at day 1 and a superoxide dismutase (SOD) at day 5, highlighting the crucial roles of these genes in response to oxidative stress induced by PST. Among the 33 continuously upregulated genes, five showed a significant correlation between gene expression and PST concentration, with the highest correlation present in PyC1QL4-1, the gene encoding Complement C1Q-like protein 4, C1QL4. In addition, the correlation between PyC1QL4-1 expression and PST toxicity was also the highest. Further analysis in another aquaculture scallop (Chlamys farreri) indicated that the expression of CfC1QL4-1, the homolog of PyC1QL4-1, also exhibited significant correlations with both PST toxicity and concentration. Our results reveal the gene expression responses of scallop digestive glands to PST-producing algae and indicate that the C1QL4-1 gene might be a potential biomarker for PST monitoring in scallops, which may provide a convenient way for the early warning and sensitive detection of PST contamination in the bivalves.
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Affiliation(s)
- Xiangchao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Deting Meng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lirong Chang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiaoxia Shi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yue Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Huizhen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Ashwood LM, Elnahriry KA, Stewart ZK, Shafee T, Naseem MU, Szanto TG, van der Burg CA, Smith HL, Surm JM, Undheim EAB, Madio B, Hamilton BR, Guo S, Wai DCC, Coyne VL, Phillips MJ, Dudley KJ, Hurwood DA, Panyi G, King GF, Pavasovic A, Norton RS, Prentis PJ. Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family. BMC Biol 2023; 21:121. [PMID: 37226201 DOI: 10.1186/s12915-023-01617-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The ShK toxin from Stichodactyla helianthus has established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in Actiniarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family in Actinia tenebrosa and Telmatactis stephensoni, characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom of T. stephensoni. RESULTS We identified ten SA8-family genes in two clusters and six SA8-family genes in five clusters for T. stephensoni and A. tenebrosa, respectively. Nine SA8 T. stephensoni genes were found in a single cluster, and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While the functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity. CONCLUSIONS Our results provide the first demonstration that SA8 is a unique gene family in Actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom of T. stephensoni.
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Affiliation(s)
- Lauren M Ashwood
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
| | - Khaled A Elnahriry
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Zachary K Stewart
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Thomas Shafee
- Department of Animal Plant & Soil Sciences, La Trobe University, Melbourne, Australia
- Swinburne University of Technology, Melbourne, VIC, Australia
| | - Muhammad Umair Naseem
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Tibor G Szanto
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Chloé A van der Burg
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand
| | - Hayden L Smith
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Eivind A B Undheim
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindern, PO Box 1066, 0316, Oslo, Norway
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Bruno Madio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Brett R Hamilton
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Shaodong Guo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Victoria L Coyne
- Research Infrastructure, Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Matthew J Phillips
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Kevin J Dudley
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Research Infrastructure, Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - David A Hurwood
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre for Innovations in Peptide and Protein Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ana Pavasovic
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, 3052, Australia
| | - Peter J Prentis
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
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Kin K, Chen ZH, Forbes G, Lawal H, Schilde C, Singh R, Cole C, Barton GJ, Schaap P. The protein kinases of Dictyostelia and their incorporation into a signalome. Cell Signal 2023; 108:110714. [PMID: 37187217 DOI: 10.1016/j.cellsig.2023.110714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
Protein kinases are major regulators of cellular processes, but the roles of most kinases remain unresolved. Dictyostelid social amoebas have been useful in identifying functions for 30% of its kinases in cell migration, cytokinesis, vesicle trafficking, gene regulation and other processes but their upstream regulators and downstream effectors are mostly unknown. Comparative genomics can assist to distinguish between genes involved in deeply conserved core processes and those involved in species-specific innovations, while co-expression of genes as evident from comparative transcriptomics can provide cues to the protein complement of regulatory networks. Genomes and developmental and cell-type specific transcriptomes are available for species that span the 0.5 billion years of evolution of Dictyostelia from their unicellular ancestors. In this work we analysed conservation and change in the abundance, functional domain architecture and developmental regulation of protein kinases across the 4 major taxon groups of Dictyostelia. All data are summarized in annotated phylogenetic trees of the kinase subtypes and accompanied by functional information of all kinases that were experimentally studied. We detected 393 different protein kinase domains across the five studied genomes, of which 212 were fully conserved. Conservation was highest (71%) in the previously defined AGC, CAMK, CK1, CMCG, STE and TKL groups and lowest (26%) in the "other" group of typical protein kinases. This was mostly due to species-specific single gene amplification of "other" kinases. Apart from the AFK and α-kinases, the atypical protein kinases, such as the PIKK and histidine kinases were also almost fully conserved. The phylogeny-wide developmental and cell-type specific expression profiles of the protein kinase genes were combined with profiles from the same transcriptomic experiments for the families of G-protein coupled receptors, small GTPases and their GEFs and GAPs, the transcription factors and for all genes that upon lesion generate a developmental defect. This dataset was subjected to hierarchical clustering to identify clusters of co-expressed genes that potentially act together in a signalling network. The work provides a valuable resource that allows researchers to identify protein kinases and other regulatory proteins that are likely to act as intermediates in a network of interest.
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Affiliation(s)
- Koryu Kin
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | - Zhi-Hui Chen
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Gillian Forbes
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS, École Normale Supérieure de Lyon and Université Claude Bernard Lyon-1, Lyon 69007, France.
| | - Hajara Lawal
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Christina Schilde
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; D'Arcy Thompson Unit, School of Life Sciences, University of Dundee, DD1 4HN, United Kingdom.
| | - Reema Singh
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Vaccine and Infectious Disease Organization, University of Saskatchewan,120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada.
| | - Christian Cole
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital, Dundee DD1 9SY, United Kingdom
| | - Geoffrey J Barton
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Pauline Schaap
- Molecular Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
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Sheraz A, Zhu H, Dong Q, Wang T, Zong S, Wang H, Ge L, Wu T. The superoxide dismutase (SOD) genes family mediates the response of Nilaparvata lugens to jinggangmycin and sugar. Front Physiol 2023; 14:1197395. [PMID: 37260593 PMCID: PMC10228653 DOI: 10.3389/fphys.2023.1197395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction: Brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera: Delphacidae), is a major rice pest causing significant damage to rice throughout the world. Intensive pesticide usage often causes resistance in these seasonal pests, mainly through the modulation of antioxidant machinery. The superoxide dismutase (SOD) gene family is known for regulating BPH response to pesticides. Methods: In the present study, we identified eight NlSOD genes from the NCBI using the BLASTP program. The bioinformatics analysis includes a phylogenetic tree, conserved domain, motifs, gene ontology (GO) analysis, Kyoto encyclopedia of genes and genomes (KEGG) pathways, and protein-protein interaction, highlighting the distinctive functional elements of NlSOD genes. Results and discussion: Additionally, the NlSOD genes showed expression in all developmental stages of BPH. Under three sugars (glucose, sucrose, and trehalose) treatment, the respective upregulation of NlSOD8, NlSOD6, and NlSOD2 was noted. The NlSOD1 induced significantly under jinggamycin (JGM) deduced its potential as a key regulator of BPH response to the pesticide. Our study has provided detailed knowledge of the NlSOD gene family in-silico analysis and the defensive response to insecticide and high sugar of BPH. We hope the results of this research will help to shed light on the resistance of BPH towards insecticide toxicity and high sugar and help to control it more efficiently.
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Affiliation(s)
- Ahmad Sheraz
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Haowen Zhu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Qiaoqiao Dong
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Tingting Wang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Suman Zong
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Huaiqi Wang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Linquan Ge
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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Chakraborty S, Gangwar R, Zahra S, Poddar N, Singh A, Kumar S. Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes. Sci Rep 2023; 13:5914. [PMID: 37041245 PMCID: PMC10090146 DOI: 10.1038/s41598-023-33226-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/10/2023] [Indexed: 04/13/2023] Open
Abstract
Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.
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Affiliation(s)
- Srija Chakraborty
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rashmi Gangwar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shafaque Zahra
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nikita Poddar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Amarjeet Singh
- Stress Signalling Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Rather MA, Agarwal D, Bhat TA, Khan IA, Zafar I, Kumar S, Amin A, Sundaray JK, Qadri T. Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. Int J Biol Macromol 2023; 233:123549. [PMID: 36740117 DOI: 10.1016/j.ijbiomac.2023.123549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.
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Affiliation(s)
- Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India.
| | - Deepak Agarwal
- Institute of Fisheries Post Graduation Studies OMR Campus, Vaniyanchavadi, Chennai, India
| | | | - Irfan Ahamd Khan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Sujit Kumar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Adnan Amin
- Postgraduate Institute of Fisheries Education and Research Kamdhenu University, Gandhinagar-India University of Kurasthra, India; Department of Aquatic Environmental Management, Faculty of Fisheries Rangil- Ganderbel -SKUAST-K, India
| | - Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Tahiya Qadri
- Division of Food Science and Technology, SKUAST-K, Shalimar, India
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