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Kim DS, Li Y, Ahn HK, Woods-Tör A, Cevik V, Furzer OJ, Ma W, Tör M, Jones JDG. ATR2 C ala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition. THE NEW PHYTOLOGIST 2024; 243:330-344. [PMID: 38742296 DOI: 10.1111/nph.19790] [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: 03/11/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Arabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. To reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2 and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. ATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. Two additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. We compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all four genes are present in all ATR2Cala2-recognizing accessions.
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Affiliation(s)
- Dae Sung Kim
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yufei Li
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Woods-Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Volkan Cevik
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
| | - Oliver J Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mahmut Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
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2
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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional regulators with broad expression in the zebrafish spinal cord. Dev Dyn 2024. [PMID: 38850245 DOI: 10.1002/dvdy.717] [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: 01/23/2024] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. RESULTS We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. CONCLUSIONS Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
| | - Paul C Campbell
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, New York, USA
| | - Richard L Bates
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, Syracuse, New York, USA
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3
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Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [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: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
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Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
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Grau-Bové X, Subirana L, Meister L, Soubigou A, Neto A, Elek A, Naranjo S, Fornas O, Gomez-Skarmeta JL, Tena JJ, Irimia M, Bertrand S, Sebé-Pedrós A, Escriva H. An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm. Nat Commun 2024; 15:4550. [PMID: 38811547 PMCID: PMC11136973 DOI: 10.1038/s41467-024-48774-4] [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: 06/22/2023] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Anaël Soubigou
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Ana Neto
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Oscar Fornas
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France.
- Institut universitaire de France (IUF), Paris, France.
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France.
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5
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Fox JA, Hunt DAGA, Hendry AP, Chapman LJ, Barrett RDH. Counter-gradient variation in gene expression between fish populations facilitates colonization of low-dissolved oxygen environments. Mol Ecol 2024:e17419. [PMID: 38808559 DOI: 10.1111/mec.17419] [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: 11/13/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
The role of phenotypic plasticity during colonization remains unclear due to the shifting importance of plasticity across timescales. In the early stages of colonization, plasticity can facilitate persistence in a novel environment; but over evolutionary time, processes such as genetic assimilation may reduce variation in plastic traits such that species with a longer evolutionary history in an environment can show lower levels of plasticity than recent invaders. Therefore, comparing species in the early stages of colonization to long-established species provides a powerful approach for uncovering the role of phenotypic plasticity during different stages of colonization. We compared gene expression between low-dissolved oxygen (DO) and high-DO populations of two cyprinid fish: Enteromius apleurogramma, a species that has undergone a recent range expansion, and E. neumayeri, a long-established native species in the same region. We sampled tissue either immediately after capture from the field or after a 2-week acclimation under high-DO conditions, allowing us to test for both evolved and plastic differences in low-DO vs high-DO populations of each species. We found that most genes showing candidate-evolved differences in gene expression did not overlap with those showing plastic differences in gene expression. However, in the genes that did overlap, there was counter-gradient variation such that plastic and evolved gene expression responses were in opposite directions in both species. Additionally, E. apleurogramma had higher levels of plasticity and evolved divergence in gene expression between field populations. We suggest that the higher level of plasticity and counter-gradient variation may have allowed rapid genetic adaptation in E. apleurogramma and facilitated colonization. This study shows how counter-gradient variation may impact the colonization of divergent oxygen environments.
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Affiliation(s)
- Janay A Fox
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - David A G A Hunt
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hendry
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
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6
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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional Regulators with Broad Expression in the Zebrafish Spinal Cord. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580357. [PMID: 38405913 PMCID: PMC10888778 DOI: 10.1101/2024.02.14.580357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. Results We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. Conclusions Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
- Samantha J. England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Paul C. Campbell
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY 13045, USA
| | - Richard L. Bates
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - William F. Fancher
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Katharine E. Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
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7
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Shankar UN, Shiraz M, Kumar P, Akif M. A comprehensive in silico analysis of putative outer membrane and secretory hydrolases from the pathogenic Leptospira: Possible implications in pathogenesis. Biotechnol Appl Biochem 2024. [PMID: 38733098 DOI: 10.1002/bab.2596] [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: 11/22/2023] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Outer surface/membrane and virulent secretory proteins are primarily crucial for pathogenesis. Secreted and outer membrane hydrolases of many pathogens play an important role in attenuating the host immune system. Leptospira expresses many such proteins, and few have been characterized to display various roles, including host immune evasion. However, identification, classification, characterization, and elucidation of the possible role of Leptospira's outer membrane and secretory hydrolases have yet to be explored. In the present study, we used bioinformatics tools to predict exported proteins from the pathogenic Leptospira proteome. Moreover, we focused on secretory and outer membrane putative hydrolases from the exported proteins to generate a deeper understanding. Our analysis yielded four putative outer/secretory hydrolases, LIC_10995, LIC_11183, LIC_11463, and LIC_12988, containing α/β hydrolase fold and displayed similarity with lipase motif. Moreover, their conservation analysis of the predicted hydrolases across the spectrum of different Leptospira species showed high clustering with the pathogenic species. Outer membrane and secretory proteins with lipolytic activity may have a role in pathogenesis. This is the first bioinformatics analysis of secretory and outer membrane α/β hydrolases from leptospiral species. However, experimental studies are indeed required to unravel this possibility.
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Affiliation(s)
- Umate Nachiket Shankar
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mohd Shiraz
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Pankaj Kumar
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mohd Akif
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Chen J, Wu Y, Chen J, Lu H, Cheng G, Tu ZJ, Liao C, Han Q. Roles of a newly lethal cuticular structural protein, AaCPR100A, and its upstream interaction protein, G12-like, in Aedes aegypti. Int J Biol Macromol 2024; 268:131704. [PMID: 38670198 DOI: 10.1016/j.ijbiomac.2024.131704] [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: 02/03/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Mosquitoes form a vital group of vector insects, which can transmit various diseases and filarial worms. The cuticle is a critical structure that protects mosquitoes from adverse environmental conditions and penetration resistance. Thus, cuticle proteins can be used as potential targets for controlling the mosquito population. In the present study, we found that AaCPR100A is a structural protein in the soft cuticle, which has flexibility and elasticity allowing insects to move or fly freely, of Aedes aegypti. RNA interference (RNAi) of AaCPR100A caused high mortality in Aedes aegypti larvae and adults and significantly decreased the egg hatching rate. Transmission electron microscopy (TEM) analysis revealed that the larval microstructure had no recognizable endocuticle in AaCPR100A-deficient mosquitoes. A yeast two-hybrid assay was performed to screen proteins interacting with AaCPR100A. We verified that the G12-like protein had the strongest interaction with AaCPR100A using yeast two-hybrid and GST pull-down assays. Knockdown of G12-like transcription resulted in high mortality in Ae. aegypti larvae, but not in adults. Interestingly, RNAi of G12-like rescued the high mortality of adults caused by decreased AaCPR100A expression. Additionally, adults treated with G12-like dsRNA were found to be sensitive to low temperature, and their eggshell formation and hatching were decreased. Overall, our results demonstrated that G12-like may interacts with AaCPR100A, and both G12-like and AaCPR100A are involved in Ae. aegypti cuticle development and eggshell formation. AaCPR100A and G12-like can thus be considered newly potential targets for controlling the Ae. aegypti mosquito.
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Affiliation(s)
- Jing Chen
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan, China; Collaborative Innovation Center of One Health, Hainan University, Haikou, China
| | - Yuchen Wu
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan, China; Collaborative Innovation Center of One Health, Hainan University, Haikou, China
| | - Jiukai Chen
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan, China; Collaborative Innovation Center of One Health, Hainan University, Haikou, China
| | - Haoran Lu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Zhijian Jake Tu
- Department of Biochemistry and the Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Chenghong Liao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan, China; Collaborative Innovation Center of One Health, Hainan University, Haikou, China.
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan, China; Collaborative Innovation Center of One Health, Hainan University, Haikou, China.
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9
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Wu Q, Gu Z, Shang B, Wan D, Zhang Q, Zhang X, Xie P, Cheng S, Zhang W, Zhang K. Circulating tumor cell clustering modulates RNA splicing and polyadenylation to facilitate metastasis. Cancer Lett 2024; 588:216757. [PMID: 38417668 DOI: 10.1016/j.canlet.2024.216757] [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: 10/11/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Circulating tumor cell (CTC) clusters exhibit significantly higher metastatic potential compared to single CTCs. However, the underlying mechanism behind this phenomenon remains unclear, and the role of posttranscriptional RNA regulation in CTC clusters has not been explored. Here, we conducted a comparative analysis of alternative splicing (AS) and alternative polyadenylation (APA) profiles between single CTCs and CTC clusters. We identified 994 and 836 AS events in single CTCs and CTC clusters, respectively, with ∼20% of AS events showing differential regulation between the two cell types. A key event in this differential splicing was observed in SRSF6, which disrupted AS profiles and contributed to the increased malignancy of CTC clusters. Regarding APA, we found a global lengthening of 3' UTRs in CTC clusters compared to single CTCs. This alteration was primarily governed by 14 core APA factors, particularly PPP1CA. The modified APA profiles facilitated the cell cycle progression of CTC clusters and indicated their reduced susceptibility to oxidative stress. Further investigation revealed that the proportion of H2AFY mRNA with long 3' UTR instead of short 3' UTR was higher in CTC clusters than single CTCs. The AU-rich elements (AREs) within the long 3' UTR of H2AFY mRNA enhance mRNA stability and translation activity, resulting in promoting cell proliferation and invasion, which potentially facilitate the establishment and rapid formation of metastatic tumors mediated by CTC clusters. These findings provide new insights into the mechanisms driving CTC cluster metastasis.
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Affiliation(s)
- Quanyou Wu
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China; State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaoru Gu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bingqing Shang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Duo Wan
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peipei Xie
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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10
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Wang Z, Shang Q, Zhang W, Huang D, Pan X. Identification of ARF genes in Juglans Sigillata Dode and analysis of their expression patterns under drought stress. Mol Biol Rep 2024; 51:539. [PMID: 38642202 DOI: 10.1007/s11033-024-09441-5] [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: 12/04/2023] [Accepted: 03/12/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Auxin response factor (ARF), a transcription factors that controls the expression of genes responsive to auxin, plays a key role in the regulation of plant growth and development. Analyses aimed at identifying ARF family genes and characterizing their functions in Juglans sigillata Dode are lacking. METHODS AND RESULTS We used bioinformatic approaches to identify members of the J. sigillata ARF gene family and analyze their evolutionary relationships, collinearity, cis-acting elements, and tissue-specific expression patterns. The expression patterns of ARF gene family members under natural drought conditions were also analyzed. The J. sigillata ARF gene family contained 31 members, which were unevenly distributed across 16 chromosomes. We constructed a phylogenetic tree of JsARF genes and other plant ARF genes. Cis-acting elements in the promoters of JsARF were predicted. JsARF28 showed higher expressions in both the roots and leaves. A heat map of the transcriptome data of the cluster analysis under drought stress indicated that JsARF3/9/11/17/20/26 are responsive to drought. The expression of the 11 ARF genes varied under PEG treatment and JsARF18 and JsARF20 were significantly up-regulated. CONCLUSIONS The interactions between abiotic stresses and plant hormones are supported by our cumulative data, which also offers a theoretical groundwork for comprehending the ARF mechanism and drought resistance in J. sigillata.
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Affiliation(s)
- Zhifan Wang
- College of Agriculture, Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Qing Shang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Wen'e Zhang
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Dong Huang
- College of Agriculture, Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China.
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Xuejun Pan
- College of Agriculture, Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China.
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
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11
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Abdulla MF, Mostafa K, Aydin A, Kavas M, Aksoy E. GATA transcription factor in common bean: A comprehensive genome-wide functional characterization, identification, and abiotic stress response evaluation. PLANT MOLECULAR BIOLOGY 2024; 114:43. [PMID: 38630371 PMCID: PMC11024004 DOI: 10.1007/s11103-024-01443-y] [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: 11/05/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
The GATA transcription factors (TFs) have been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance to abiotic stress has not yet been studied in the common bean. This study analyzed the functional identity of the GATA gene family in the P. vulgaris genome under different abiotic and phytohormonal stress. The GATA gene family was systematically investigated in the P. vulgaris genome, and 31 PvGATA TFs were identified. The study found that 18 out of 31 PvGATA genes had undergone duplication events, emphasizing the role of gene duplication in GATA gene expansion. All the PvGATA genes were classified into four significant subfamilies, with 8, 3, 6, and 13 members in each subfamily (subfamilies I, II, III, and IV), respectively. All PvGATA protein sequences contained a single GATA domain, but subfamily II members had additional domains such as CCT and tify. A total of 799 promoter cis-regulatory elements (CREs) were predicted in the PvGATAs. Additionally, we used qRT-PCR to investigate the expression profiles of five PvGATA genes in the common bean roots under abiotic conditions. The results suggest that PvGATA01/10/25/28 may play crucial roles in regulating plant resistance against salt and drought stress and may be involved in phytohormone-mediated stress signaling pathways. PvGATA28 was selected for overexpression and cloned into N. benthamiana using Agrobacterium-mediated transformation. Transgenic lines were subjected to abiotic stress, and results showed a significant tolerance of transgenic lines to stress conditions compared to wild-type counterparts. The seed germination assay suggested an extended dormancy of transgenic lines compared to wild-type lines. This study provides a comprehensive analysis of the PvGATA gene family, which can serve as a foundation for future research on the function of GATA TFs in abiotic stress tolerance in common bean plants.
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Affiliation(s)
- Mohamed Farah Abdulla
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, 55200, Samsun, Türkiye
| | - Karam Mostafa
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, 55200, Samsun, Türkiye
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), 12619, Giza, Egypt
| | - Abdullah Aydin
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, 55200, Samsun, Türkiye
| | - Musa Kavas
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, 55200, Samsun, Türkiye.
| | - Emre Aksoy
- Faculty of Arts and Sciences, Department of Biology, Middle East Technical University, 06800, Ankara, Türkiye
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12
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Gomes-Dos-Santos A, Fonseca E, Riccardi N, Hinzmann M, Lopes-Lima M, Froufe E. The transcriptome assembly of the European freshwater mussel Unio elongatulus C. Pfeiffer, 1825. Sci Data 2024; 11:377. [PMID: 38609426 PMCID: PMC11014934 DOI: 10.1038/s41597-024-03226-y] [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: 10/26/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Freshwater mussels of the order Unionida are a global conservation concern. Species of this group are strictly freshwater, sessile, slow-growing animals and, extremely sensitive to environmental changes. Human-mediated changes in freshwater habitats are imposing enormous pressure on the survival of freshwater mussels. Although a few flagship species are protected in Europe, other highly imperilled species receive much less attention. Moreover, knowledge about biology, ecology, and evolution and proper conservation assessments of many European species are still sparse. This knowledge gap is further aggravated by the lack of genomic resources available, which are key tools for conservation. Here we present the transcriptome assembly of Unio elongatulus C. Pfeiffer, 1825, one of the least studied European freshwater mussels. Using the individual sequencing outputs from eight physiologically representative mussel tissues, we provide an annotated panel of tissue-specific Relative Gene Expression profiles. These resources are pivotal to studying the species' biological and ecological features, as well as helping to understand its vulnerability to current and future threats.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.
| | - Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal
| | | | - Mariana Hinzmann
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal
| | - Manuel Lopes-Lima
- BIOPOLIS Program in Genomics, Biodiversity and Ecosystems, CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, Cambridge, UK
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.
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13
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Riera-Ferrer E, Mazanec H, Mladineo I, Konik P, Piazzon MC, Kuchta R, Palenzuela O, Estensoro I, Sotillo J, Sitjà-Bobadilla A. An inside out journey: biogenesis, ultrastructure and proteomic characterisation of the ectoparasitic flatworm Sparicotyle chrysophrii extracellular vesicles. Parasit Vectors 2024; 17:175. [PMID: 38570784 PMCID: PMC10993521 DOI: 10.1186/s13071-024-06257-x] [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: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Helminth extracellular vesicles (EVs) are known to have a three-way communication function among parasitic helminths, their host and the host-associated microbiota. They are considered biological containers that may carry virulence factors, being therefore appealing as therapeutic and prophylactic target candidates. This study aims to describe and characterise EVs secreted by Sparicotyle chrysophrii (Polyopisthocotyla: Microcotylidae), a blood-feeding gill parasite of gilthead seabream (Sparus aurata), causing significant economic losses in Mediterranean aquaculture. METHODS To identify proteins involved in extracellular vesicle biogenesis, genomic datasets from S. chrysophrii were mined in silico using known protein sequences from Clonorchis spp., Echinococcus spp., Fasciola spp., Fasciolopsis spp., Opisthorchis spp., Paragonimus spp. and Schistosoma spp. The location and ultrastructure of EVs were visualised by transmission electron microscopy after fixing adult S. chrysophrii specimens by high-pressure freezing and freeze substitution. EVs were isolated and purified from adult S. chrysophrii (n = 200) using a newly developed ultracentrifugation-size-exclusion chromatography protocol for Polyopisthocotyla, and EVs were characterised via nanoparticle tracking analysis and tandem mass spectrometry. RESULTS Fifty-nine proteins involved in EV biogenesis were identified in S. chrysophrii, and EVs compatible with ectosomes were observed in the syncytial layer of the haptoral region lining the clamps. The isolated and purified nanoparticles had a mean size of 251.8 nm and yielded 1.71 × 108 particles · mL-1. The protein composition analysis identified proteins related to peptide hydrolases, GTPases, EF-hand domain proteins, aerobic energy metabolism, anticoagulant/lipid-binding, haem detoxification, iron transport, EV biogenesis-related, vesicle-trafficking and other cytoskeletal-related proteins. Several identified proteins, such as leucyl and alanyl aminopeptidases, calpain, ferritin, dynein light chain, 14-3-3, heat shock protein 70, annexin, tubulin, glutathione S-transferase, superoxide dismutase, enolase and fructose-bisphosphate aldolase, have already been proposed as target candidates for therapeutic or prophylactic purposes. CONCLUSIONS We have unambiguously demonstrated for the first time to our knowledge the secretion of EVs by an ectoparasitic flatworm, inferring their biogenesis machinery at a genomic and transcriptomic level, and by identifying their location and protein composition. The identification of multiple therapeutic targets among EVs' protein repertoire provides opportunities for target-based drug discovery and vaccine development for the first time in Polyopisthocotyla (sensu Monogenea), and in a fish-ectoparasite model.
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Affiliation(s)
- Enrique Riera-Ferrer
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal, Consejo Superior de Investigaciones Científicas (IATS, CSIC), Ribera de Cabanes, 12595, Castellón, Spain
| | - Hynek Mazanec
- Laboratory of Helminthology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, (BC CAS), České Budějovice, Czech Republic
| | - Ivona Mladineo
- Laboratory of Functional Helminthology, Institute of Parasitology, Biology Centre Czech Academy of Sciences (BC CAS), České Budějovice, Czech Republic
| | - Peter Konik
- Faculty of Science, University of South Bohemia, Branišovská 1160/31, 370 05, České Budějovice, Czech Republic
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal, Consejo Superior de Investigaciones Científicas (IATS, CSIC), Ribera de Cabanes, 12595, Castellón, Spain
| | - Roman Kuchta
- Laboratory of Helminthology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, (BC CAS), České Budějovice, Czech Republic
| | - Oswaldo Palenzuela
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal, Consejo Superior de Investigaciones Científicas (IATS, CSIC), Ribera de Cabanes, 12595, Castellón, Spain
| | - Itziar Estensoro
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal, Consejo Superior de Investigaciones Científicas (IATS, CSIC), Ribera de Cabanes, 12595, Castellón, Spain.
| | - Javier Sotillo
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal, Consejo Superior de Investigaciones Científicas (IATS, CSIC), Ribera de Cabanes, 12595, Castellón, Spain
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14
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Gomes-Dos-Santos A, Domingues M, Ruivo R, Fonseca E, Froufe E, Deyanova D, Franco JN, C Castro LF. An historical "wreck": A transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978. Mar Genomics 2024; 74:101097. [PMID: 38485291 DOI: 10.1016/j.margen.2024.101097] [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: 12/27/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024]
Abstract
Historically famous for their negative impact on human-built marine wood structures, mollusc shipworms play a central ecological role in marine ecosystems. Their association with bacterial symbionts, providing cellulolytic and nitrogen-fixing activities, underscores their exceptional wood-eating and wood-boring behaviours, improving energy transfer and the recycling of essential nutrients locked in the wood cellulose. Importantly, from a molecular standpoint, a minute of omic resources are available from this lineage of Bivalvia. Here, we produced and assembled a transcriptome from the globally distributed naval shipworm, Teredo navalis (family Teredinidae). The transcriptome was obtained by sequencing the total RNA from five equidistant segments of the whole body of a T. navalis specimen. The quality of the produced assembly was accessed with several statistics, revealing a highly contiguous (1194 N50) and complete (over 90% BUSCO scores for Eukaryote and Metazoan databases) transcriptome, with nearly 38,000 predicted ORF, more than half being functionally annotated. Our findings pave the way to investigate the unique evolutionary biology of these highly modified bivalves and lay the foundation for an adequate gene annotation of a full genome sequence of the species.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
| | - Marcos Domingues
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Raquel Ruivo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Diana Deyanova
- Department of Biological and Environmental Sciences, University of Gothenburg, Kristineberg, Fiskebäckskil, Sweden
| | - João N Franco
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network, ESTM, Polytechnic of Leiria, 2520-641 Peniche, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal.
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15
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Sarwar MF, Waseem QUA, Awan MF, Ali S, Ahmad A, Malook SU, Ali Q. In-silico characterization of LSDV132 protein divulged its BCL-2-like nature. Heliyon 2024; 10:e27657. [PMID: 38510042 PMCID: PMC10951589 DOI: 10.1016/j.heliyon.2024.e27657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Lumpy skin disease virus (LSDV) belongs to Poxviridae family. This virus possesses various proteins which impart potential functions to it including assembly of newly synthesized viruses in the replication cycle and forming their structure. LSDV132 protein is also one of such proteins. Its key characteristics were unknown because, no any relevant study was reported about it. This study aimed to investigate its characteristic features and essential functions using several bioinformatics techniques. These analyses included physiochemical characterization and exploring the crucial functional and structural perspectives. Upon analysis of the physiochemical properties, the instability index was computed to be 30.89% which proposed LSDV132 protein to be a stable protein. Afterwards, the phosphorylation sites were explored. Several sites were found in this regard which led to the hypothesis that it might be involved in the regulation of apoptosis and cell signaling, among other cellular processes. Furthermore, the KEGG analysis and the analysis of protein family classification confirmed that the LSDV132 protein possessed Poxvirus-BCL-2-like motifs, indicating that it might be responsible in modulating the apoptosis of host cells. This crucial finding suggested that the protein under study possessed BCL-2-like features. Proceeding this very important finding, the molecular docking analysis was performed. In this context, various viral BCL-2 inhibitors were retrieved from the ChEMBL database for docking purpose. The docking results revealed that pelcitoclax exhibited best docking scores i.e., -9.1841 kcal/mol, among all of the other docked complexes. This fact signified that this compound might serve as an inhibitor of LSDV132 protein.
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Affiliation(s)
- Muhammad Farhan Sarwar
- Department of Biotechnology, Knowledge Unit of Science, University of Management and Technology (UMT) Sialkot, Pakistan
| | - Qurat ul Ain Waseem
- Department of Biotechnology, Knowledge Unit of Science, University of Management and Technology (UMT) Sialkot, Pakistan
| | - Mudassar Fareed Awan
- Department of Biotechnology, Knowledge Unit of Science, University of Management and Technology (UMT) Sialkot, Pakistan
| | - Sajed Ali
- Department of Biotechnology, Knowledge Unit of Science, University of Management and Technology (UMT) Sialkot, Pakistan
| | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, 11451 Riyadh, Saudi Arabia
| | - Saif ul Malook
- Department of Entomology & Nematology, University of Florida, USA
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agriculture Sciences, University of the Punjab, Lahore, Pakistan
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16
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Bhandare S, Lawal OU, Colavecchio A, Cadieux B, Zahirovich-Jovich Y, Zhong Z, Tompkins E, Amitrano M, Kukavica-Ibrulj I, Boyle B, Wang S, Levesque RC, Delaquis P, Danyluk M, Goodridge L. Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species. Microorganisms 2024; 12:695. [PMID: 38674639 PMCID: PMC11052255 DOI: 10.3390/microorganisms12040695] [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: 03/08/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.
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Affiliation(s)
- Sudhakar Bhandare
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham LE12 5RD, UK
| | - Opeyemi U. Lawal
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Anna Colavecchio
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Brigitte Cadieux
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Yella Zahirovich-Jovich
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Zeyan Zhong
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Elizabeth Tompkins
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Margot Amitrano
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Irena Kukavica-Ibrulj
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Brian Boyle
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Siyun Wang
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Roger C. Levesque
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada
| | - Michelle Danyluk
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Lawrence Goodridge
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
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17
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Li S, Wei L, Gao Q, Xu M, Wang Y, Lin Z, Holford P, Chen ZH, Zhang L. Molecular and phylogenetic evidence of parallel expansion of anion channels in plants. PLANT PHYSIOLOGY 2024; 194:2533-2548. [PMID: 38142233 DOI: 10.1093/plphys/kiad687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Aluminum-activated malate transporters (ALMTs) and slow anion channels (SLACs) are important in various physiological processes in plants, including stomatal regulation, nutrient uptake, and in response to abiotic stress such as aluminum toxicity. To understand their evolutionary history and functional divergence, we conducted phylogenetic and expression analyses of ALMTs and SLACs in green plants. Our findings from phylogenetic studies indicate that ALMTs and SLACs may have originated from green algae and red algae, respectively. The ALMTs of early land plants and charophytes formed a monophyletic clade consisting of three subgroups. A single duplication event of ALMTs was identified in vascular plants and subsequent duplications into six clades occurred in angiosperms, including an identified clade, 1-1. The ALMTs experienced gene number losses in clades 1-1 and 2-1 and expansions in clades 1-2 and 2-2b. Interestingly, the expansion of clade 1-2 was also associated with higher expression levels compared to genes in clades that experienced apparent loss. SLACs first diversified in bryophytes, followed by duplication in vascular plants, giving rise to three distinct clades (I, II, and III), and clade II potentially associated with stomatal control in seed plants. SLACs show losses in clades II and III without substantial expansion in clade I. Additionally, ALMT clade 2-2 and SLAC clade III contain genes specifically expressed in reproductive organs and roots in angiosperms, lycophytes, and mosses, indicating neofunctionalization. In summary, our study demonstrates the evolutionary complexity of ALMTs and SLACs, highlighting their crucial role in the adaptation and diversification of vascular plants.
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Affiliation(s)
- Shanshan Li
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lanlan Wei
- College of Life Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Min Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St.Louis, MO 63104, USA
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Liangsheng Zhang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
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18
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Chen Q, Zhao FQ, Han B, Jiang C, Liu H. Methionyl-Methionine Dipeptide Enhances Mammogenesis and Lactogenesis by Suppressing the Expression of a Novel Long Noncoding RNA MGPNCR to Inhibit eIF4B Dephosphorylation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6414-6423. [PMID: 38501560 DOI: 10.1021/acs.jafc.4c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Previous research has demonstrated that in pregnant mice deficient in l-methionine (Met), the mixture of the dipeptide l-methionyl-l-methionine (Met-Met) with Met was more effective than Met alone in promoting mammogenesis and lactogenesis. This study aimed to investigate the role of a novel long noncoding RNA (lncRNA), named mammary gland proliferation-associated lncRNA (MGPNCR), in these processes. Transcriptomic analysis of mammary tissues from Met-deficient mice, supplemented either with a Met-Met/Met mixture or with Met alone, revealed significantly higher MGPNCR expression in the Met group compared to the mixture group, a finding recapitulated in a mammary epithelial cell model. Our findings suggested that MGPNCR hindered mammogenesis and milk protein synthesis by binding to eukaryotic initiation factor 4B (eIF4B). This interaction promoted the dephosphorylation of eIF4B at serine-422 by enhancing its association with protein phosphatase 2A (PP2A). Our study sheds light on the regulatory mechanisms of lncRNA-mediated dipeptide effects on mammary cell proliferation and milk protein synthesis. These insights underscore the potential benefits of utilizing dipeptides to improve milk protein in animals and potentially in humans.
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Affiliation(s)
- Qiong Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Feng-Qi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Bingqing Han
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Hongyun Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
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19
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Radwan IT, Khater HF, Mohammed SH, Khalil A, Farghali MA, Mahmoud MG, Selim A, Manaa EA, Bagato N, Baz MM. Synthesis of eco-friendly layered double hydroxide and nanoemulsion for jasmine and peppermint oils and their larvicidal activities against Culex pipiens Linnaeus. Sci Rep 2024; 14:6884. [PMID: 38519561 PMCID: PMC10959945 DOI: 10.1038/s41598-024-56802-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: 09/28/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Mosquito-borne diseases represent a growing health challenge over time. Numerous potential phytochemicals are target-specific, biodegradable, and eco-friendly. The larvicidal activity of essential oils, a jasmine blend consisting of Jasmine oil and Azores jasmine (AJ) (Jasminum sambac and Jasminum azoricum) and peppermint (PP) Mentha arvensis and their nanoformulations against 2nd and 4th instar larvae of Culex pipiens, was evaluated after subjecting to different concentrations (62.5, 125, 250, 500, 1000, and 2000 ppm). Two forms of phase-different nanodelivery systems of layered double hydroxide LDH and oil/water nanoemulsions were formulated. The synthesized nanoemulsions showed particle sizes of 199 and 333 nm for AJ-NE and PP-NE, with a polydispersity index of 0.249 and 0.198, respectively. Chemical and physiochemical analysis of TEM, SEM, XRD, zeta potential, drug loading capacity, and drug release measurements were done to confirm the synthesis and loading efficiencies of essential oils' active ingredients. At high concentrations of AJ and PP nanoemulsions (2000 ppm), O/W nanoemulsions showed higher larval mortality than both LDH conjugates and crude oils. The mortality rate reached 100% for 2nd and 4th instar larvae. The relative toxicities revealed that PP nanoemulsion (MA-NE) was the most effective larvicide, followed by AJ nanoemulsion (AJ-NE). There was a significant increase in defensive enzymes, phenoloxidase, and α and β-esterase enzymes in the treated groups. After treatment of L4 with AJ, AJ-NE, PP, and PP-NE, the levels of phenoloxidase were 545.67, 731.00, 700.00, and 799.67 u/mg, respectively, compared with control 669.67 u/mg. The activity levels of α-esterase were 9.71, 10.32, 8.91, and 10.55 mg α-naphthol/min/mg protein, respectively. It could be concluded that the AJ-NE and PP-NE nanoformulations have promising larvicidal activity and could act as safe and effective alternatives to chemical insecticides.
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Affiliation(s)
- Ibrahim Taha Radwan
- Supplementary General Sciences Department, Faculty of Oral and Dental Medicine, Future University in Egypt, Cairo, 11835, Egypt.
| | - Hanem F Khater
- Department of Parasitology, Faculty of Veterinary Medicine, Benha University, Toukh, 13736, Egypt
| | - Shaimaa H Mohammed
- Zoology and Entomology Department, Faculty of Science, Al-Azhar, University (Girls Branch), Cairo, Egypt
| | - Abdelwahab Khalil
- Entomology Division, Zoology Department, Faculty of Science, Beni-Suef University, Beni -Suef, 62521, Egypt
| | - Mohamed A Farghali
- Nanotechnology and Advanced Materials Central Lab (NAMCL), Regional Center for Food & Feed (RCFF), Agricultural Research Center (ARC), Giza, Egypt
| | - Mohammed G Mahmoud
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Abdelfattah Selim
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Benha University, Toukh, 13736, Egypt
| | - Eman A Manaa
- Animal and Poultry Production, Department of Animal Wealth Development, Faculty of Veterinary Medicine, Benha University, Toukh, 13736, Egypt
| | - Noha Bagato
- Egyptian Petroleum Research Institute (EPRI), PO Box 11727, Nasr City, Cairo, Egypt
| | - Mohamed M Baz
- Departments of Entomology, Faculty of Science, Benha University, Benha, 13518, Egypt.
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20
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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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21
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Mostafa K, Yerlikaya BA, Abdulla MF, Aydin A, Yerlikaya S, Kavas M. Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses. THE PLANT GENOME 2024; 17:e20432. [PMID: 38327143 DOI: 10.1002/tpg2.20432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.
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Affiliation(s)
- Karam Mostafa
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza, Egypt
| | - Bayram Ali Yerlikaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Mohamed Farah Abdulla
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Abdullah Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Seher Yerlikaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
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22
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Klinger CM, Jimenez-Ruiz E, Mourier T, Klingl A, Lemgruber L, Pain A, Dacks JB, Meissner M. Evolutionary analysis identifies a Golgi pathway and correlates lineage-specific factors with endomembrane organelle emergence in apicomplexans. Cell Rep 2024; 43:113740. [PMID: 38363682 DOI: 10.1016/j.celrep.2024.113740] [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: 08/11/2023] [Revised: 12/20/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
The organelle paralogy hypothesis (OPH) aims to explain the evolution of non-endosymbiotically derived organelles. It predicts that lineage-specific pathways or organelles should result when identity-encoding membrane-trafficking components duplicate and co-evolve. Here, we investigate the presence of such lineage-specific membrane-trafficking machinery paralogs in Apicomplexa, a globally important parasitic lineage. We are able to identify 18 paralogs of known membrane-trafficking machinery, in several cases co-incident with the presence of new endomembrane organelles in apicomplexans or their parent lineage, the Alveolata. Moreover, focused analysis of the apicomplexan Arf-like small GTPases (i.e., ArlX3) revealed a specific post-Golgi trafficking pathway. This pathway appears involved in delivery of proteins to micronemes and rhoptries, with knockdown demonstrating reduced invasion capacity. Overall, our data have identified an unforeseen post-Golgi trafficking pathway in apicomplexans and are consistent with the OPH mechanism acting to produce endomembrane pathways or organelles at various evolutionary stages across the alveolate lineage.
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Affiliation(s)
- Christen M Klinger
- Division of Infectious Diseases, Department of Medicine and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Elena Jimenez-Ruiz
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Tobias Mourier
- Pathogen Genomics Laboratory, Bioscience Programme, Biological, and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Andreas Klingl
- Pflanzliche Entwicklungsbiologie, Biozentrum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Leandro Lemgruber
- Cellular Analysis Facility, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, Bioscience Programme, Biological, and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; International Institute for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Japan
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Centre for Life's Origin and Evolution, Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Markus Meissner
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany.
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23
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Beletskiy A, Zolotar A, Fortygina P, Chesnokova E, Uroshlev L, Balaban P, Kolosov P. Downregulation of Ribosomal Protein Genes Is Revealed in a Model of Rat Hippocampal Neuronal Culture Activation with GABA(A)R/GlyRa2 Antagonist Picrotoxin. Cells 2024; 13:383. [PMID: 38474347 DOI: 10.3390/cells13050383] [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: 01/11/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Long-read transcriptome sequencing provides us with a convenient tool for the thorough study of biological processes such as neuronal plasticity. Here, we aimed to perform transcriptional profiling of rat hippocampal primary neuron cultures after stimulation with picrotoxin (PTX) to further understand molecular mechanisms of neuronal activation. To overcome the limitations of short-read RNA-Seq approaches, we performed an Oxford Nanopore Technologies MinION-based long-read sequencing and transcriptome assembly of rat primary hippocampal culture mRNA at three time points after the PTX activation. We used a specific approach to exclude uncapped mRNAs during sample preparation. Overall, we found 23,652 novel transcripts in comparison to reference annotations, out of which ~6000 were entirely novel and mostly transposon-derived loci. Analysis of differentially expressed genes (DEG) showed that 3046 genes were differentially expressed, of which 2037 were upregulated and 1009 were downregulated at 30 min after the PTX application, with only 446 and 13 genes differentially expressed at 1 h and 5 h time points, respectively. Most notably, multiple genes encoding ribosomal proteins, with a high basal expression level, were downregulated after 30 min incubation with PTX; we suggest that this indicates redistribution of transcriptional resources towards activity-induced genes. Novel loci and isoforms observed in this study may help us further understand the functional mRNA repertoire in neuronal plasticity processes. Together with other NGS techniques, differential gene expression analysis of sequencing data obtained using MinION platform might provide a simple method to optimize further study of neuronal plasticity.
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Affiliation(s)
- Alexander Beletskiy
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Anastasia Zolotar
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Polina Fortygina
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Ekaterina Chesnokova
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Leonid Uroshlev
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Pavel Balaban
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Peter Kolosov
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
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24
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Wu JW, Zhao ZY, Hu RC, Huang YF. Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs. PLANT MOLECULAR BIOLOGY 2024; 114:20. [PMID: 38363403 PMCID: PMC10873456 DOI: 10.1007/s11103-023-01410-z] [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: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024]
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.
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Affiliation(s)
- Jia-Wen Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150000, China
| | - Zi-Yi Zhao
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China
| | - Ren-Chuan Hu
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China
| | - Yun-Feng Huang
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China.
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25
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Gable SM, Bushroe N, Mendez J, Wilson A, Pinto B, Gamble T, Tollis M. Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579686. [PMID: 38405926 PMCID: PMC10888918 DOI: 10.1101/2024.02.09.579686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jasmine Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Brendan Pinto
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
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26
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Danoff JS, Carter CS, Gordevičius J, Milčiūtė M, Brooke RT, Connelly JJ, Perkeybile AM. Maternal oxytocin treatment at birth increases epigenetic age in male offspring. Dev Psychobiol 2024; 66:e22452. [PMID: 38533486 PMCID: PMC10963051 DOI: 10.1002/dev.22452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/26/2023] [Indexed: 03/28/2024]
Abstract
Exogenous oxytocin (OT) is widely used to induce or augment labor with little understanding of the impact on offspring development. In rodent models, including the prairie vole (Microtus ochrogaster), it has been shown that oxytocin administered to mothers can affect the nervous system of the offspring with long lasting behavioral effects especially on sociality. Here, we examined the hypothesis that perinatal oxytocin exposure could have epigenetic and transcriptomic consequences. Prairie voles were exposed to exogenous oxytocin, through injections given to the mother just prior to birth, and were studied at the time of weaning. The outcome of this study revealed increased epigenetic age in oxytocin-exposed animals compared to the saline-exposed group. Oxytocin exposure led to 900 differentially methylated CpG sites (annotated to 589 genes), and 2 CpG sites (2 genes) remained significantly different after correction for multiple comparisons. Differentially methylated CpG sites were enriched in genes known to be involved in regulation of gene expression and neurodevelopment. Using RNA-sequencing we also found 217 nominally differentially expressed genes (p<0.05) in nucleus accumbens, a brain region involved in reward circuitry and social behavior; after corrections for multiple comparisons 6 genes remained significantly differentially expressed. Finally, we found that maternal oxytocin administration led to widespread alternative splicing in the nucleus accumbens. These results indicate that oxytocin exposure during birth may have long lasting epigenetic consequences. A need for further investigation of how oxytocin administration impacts development and behavior throughout the lifespan is supported by these outcomes.
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Affiliation(s)
- Joshua S Danoff
- Department of Psychology, University of Virginia, Charlottesville, VA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ
| | - C Sue Carter
- Department of Psychology, University of Virginia, Charlottesville, VA
- Kinsey Institute, Indiana University, Bloomington IN
| | | | | | | | | | - Allison M Perkeybile
- Department of Psychology, University of Virginia, Charlottesville, VA
- Kinsey Institute, Indiana University, Bloomington IN
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27
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Hkimi C, Kamoun S, Khamessi O, Ghedira K. Mycobacterium tuberculosis-THP-1 like macrophages protein-protein interaction map revealed through dual RNA-seq analysis and a computational approach. J Med Microbiol 2024; 73. [PMID: 38314675 DOI: 10.1099/jmm.0.001803] [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] [Indexed: 02/06/2024] Open
Abstract
Introduction. Infection caused by Mycobacterium tuberculosis (M. tb) is still a leading cause of mortality worldwide with estimated 1.4 million deaths annually.Hypothesis/Gap statement. Despite macrophages' ability to kill bacterium, M. tb can grow inside these innate immune cells and the exploration of the infection has traditionally been characterized by a one-sided relationship, concentrating solely on the host or examining the pathogen in isolation.Aim. Because of only a handful of M. tb-host interactions have been experimentally characterized, our main goal is to predict protein-protein interactions during the early phases of the infection.Methodology. In this work, we performed an integrative computational approach that exploits differentially expressed genes obtained from Dual RNA-seq analysis combined with known domain-domain interactions.Results. A total of 2381 and 7214 genes were identified as differentially expressed in M. tb and in THP-1-like macrophages, respectively, revealing different transcriptional profiles in response to infection. Over 48 h of infection, the host-pathogen network revealed 25 016 PPIs. Analysis of the resulting predicted network based on cellular localization information of M. tb proteins, indicated the implication of interacting nodes including the bacterial PE/PPE/PE_PGRS family. In addition, M. tb proteins interacted with host proteins involved in NF-kB signalling pathway as well as interfering with the host apoptosis ability via the potential interaction of M. tb TB16.3 with human TAB1 and M. tb GroEL2 with host protein kinase C delta, respectively.Conclusion. The prediction of the full range of interactions between M. tb and host will contribute to better understanding of the pathogenesis of this bacterium and may provide advanced approaches to explore new therapeutic targets against tuberculosis.
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Affiliation(s)
- Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia
| | - Selim Kamoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia
| | - Oussema Khamessi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Ariana BP-66, Manouba 2010, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
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Zhang X, Wan H, Jin M, Huang L, Zhang X. Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses. J Adv Res 2024; 56:87-102. [PMID: 37054879 PMCID: PMC10834809 DOI: 10.1016/j.jare.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/30/2023] [Accepted: 04/08/2023] [Indexed: 04/15/2023] Open
Abstract
INTRODUCTION Viruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles. OBJECTIVES However, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses. METHODS The viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses. RESULTS In this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems. CONCLUSIONS Therefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.
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Affiliation(s)
- Xinyi Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Haitao Wan
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Min Jin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, People's Republic of China
| | - Liquan Huang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China.
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Zambon A, Zecchina R, Tiana G. Structure of the space of folding protein sequences defined by large language models. Phys Biol 2024; 21:026002. [PMID: 38237200 DOI: 10.1088/1478-3975/ad205c] [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: 11/15/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the protein sequence landscape as defined by an effective energy that is a proxy of sequence foldability. This landscape shares characteristics with optimization challenges encountered in machine learning and constraint satisfaction problems. Our analysis reveals that natural proteins predominantly reside in wide, flat minima within this energy landscape. To investigate further, we employ statistical mechanics algorithms specifically designed to explore regions with high local entropy in relatively flat landscapes. Our findings indicate that these specialized algorithms can identify valleys with higher entropy compared to those found using traditional methods such as Monte Carlo Markov Chains. In a proof-of-concept case, we find that these highly entropic minima exhibit significant similarities to natural sequences, especially in critical key sites and local entropy. Additionally, evaluations through Molecular Dynamics suggests that the stability of these sequences closely resembles that of natural proteins. Our tool combines advancements in machine learning and statistical physics, providing new insights into the exploration of sequence landscapes where wide, flat minima coexist alongside a majority of narrower minima.
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Affiliation(s)
- A Zambon
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - R Zecchina
- Bocconi University, via Roentgen 1, 20136 Milano, Italy
| | - G Tiana
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
- INFN, Sezione di Milano, Via Celoria 16, 20133 Milano, Italy
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30
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Yamamoto R, Kon T. Functional and structural significance of the inner-arm-dynein subspecies d in ciliary motility. Cytoskeleton (Hoboken) 2024. [PMID: 38214410 DOI: 10.1002/cm.21828] [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: 10/06/2023] [Revised: 12/11/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
Motile cilia play various important physiological roles in eukaryotic organisms including cell motility and fertility. Inside motile cilia, large motor-protein complexes called "ciliary dyneins" coordinate their activities and drive ciliary motility. The ciliary dyneins include the outer-arm dyneins, the double-headed inner-arm dynein (IDA f/I1), and several single-headed inner-arm dyneins (IDAs a, b, c, d, e, and g). Among these single-headed IDAs, one of the ciliary dyneins, IDA d, is of particular interest because of its unique properties and subunit composition. In addition, defects in this subspecies have recently been associated with several types of ciliopathies in humans, such as primary ciliary dyskinesia and multiple morphologic abnormalities of the flagellum. In this mini-review, we discuss the composition, structure, and motor properties of IDA d, which have been studied in the model organism Chlamydomonas reinhardtii, and further discuss the relationship between IDA d and human ciliopathies. In addition, we provide future perspectives and discuss remaining questions regarding this intriguing dynein subspecies.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
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Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575219. [PMID: 38260631 PMCID: PMC10802568 DOI: 10.1101/2024.01.11.575219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From >85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
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Affiliation(s)
- Emma F. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Biová J, Kaňovská I, Chan YO, Immadi MS, Joshi T, Bilyeu K, Škrabišová M. Natural and artificial selection of multiple alleles revealed through genomic analyses. Front Genet 2024; 14:1320652. [PMID: 38259621 PMCID: PMC10801239 DOI: 10.3389/fgene.2023.1320652] [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: 10/12/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.
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Affiliation(s)
- Jana Biová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Ivana Kaňovská
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Manish Sridhar Immadi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
- Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, United States
| | - Kristin Bilyeu
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
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Aspromonte MC, Nugnes MV, Quaglia F, Bouharoua A, Tosatto SCE, Piovesan D. DisProt in 2024: improving function annotation of intrinsically disordered proteins. Nucleic Acids Res 2024; 52:D434-D441. [PMID: 37904585 PMCID: PMC10767923 DOI: 10.1093/nar/gkad928] [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: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
DisProt (URL: https://disprot.org) is the gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions. The latest version of DisProt brings significant advancements, including a broader representation of functions and an enhanced curation process. These improvements aim to increase both the quality of annotations and their coverage at the sequence level. Higher coverage has been achieved by adopting additional evidence codes. Quality of annotations has been improved by systematically applying Minimum Information About Disorder Experiments (MIADE) principles and reporting all the details of the experimental setup that could potentially influence the structural state of a protein. The DisProt database now includes new thematic datasets and has expanded the adoption of Gene Ontology terms, resulting in an extensive functional repertoire which is automatically propagated to UniProtKB. Finally, we show that DisProt's curated annotations strongly correlate with disorder predictions inferred from AlphaFold2 pLDDT (predicted Local Distance Difference Test) confidence scores. This comparison highlights the utility of DisProt in explaining apparent uncertainty of certain well-defined predicted structures, which often correspond to folding-upon-binding fragments. Overall, DisProt serves as a comprehensive resource, combining experimental evidence of disorder information to enhance our understanding of intrinsically disordered proteins and their functional implications.
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Affiliation(s)
| | | | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy
| | - Adel Bouharoua
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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Fu X, Wang Z. DHCR24 in Tumor Diagnosis and Treatment: A Comprehensive Review. Technol Cancer Res Treat 2024; 23:15330338241259780. [PMID: 38847653 PMCID: PMC11162140 DOI: 10.1177/15330338241259780] [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: 06/10/2024] Open
Abstract
As an important nutrient in the human body, cholesterol can not only provide structural components for the body's cells, but also can be transformed into a variety of active substances to regulate cell signaling pathways. As an important cholesterol synthase, DHCR24 participates in important regulatory processes in the body. The application of DHCR24 in tumor clinical diagnosis and treatment also attracts much attention. This article reviews the structure and regulatory characteristics of DHCR24, and the research of DHCR24 on tumor progression. We summarize the possible mechanisms of DHCR24 promoting tumor progression through reactive oxygen species (ROS), p53, Ras and PI3K-AKT pathways. Through our review, we hope to provide more research ideas and reference value for the application of DHCR24 in tumor prevention and treatment.
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Affiliation(s)
- Xin Fu
- Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhaosong Wang
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Laboratory Animal Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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35
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Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [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: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
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Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
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Kinkar OU, Kumar A, Prashar A, Yadav B, Hadapad AB, Hire RS, Makde RD. The crystal structure of insecticidal protein Txp40 from Xenorhabdus nematophila reveals a two-domain unique binary toxin with homology to the toxin-antitoxin (TA) system. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 164:104045. [PMID: 38040266 DOI: 10.1016/j.ibmb.2023.104045] [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: 05/13/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
Txp40 is a ubiquitous, conserved, and novel toxin from Xenorhabdus and Photorhabdus bacteria, toxic to a wide range of insect pests. However, the three-dimensional structure and toxicity mechanism for Txp40 or any of its sequence homologs are not yet known. Here, we are reporting the crystal structure of the insecticidal protein Txp40 from Xenorhabdus nematophila at 2.08 Å resolution. The Txp40 was structurally distinct from currently known insecticidal proteins. Txp40 consists of two structurally different domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), primarily joined by a 33-residue long linker peptide. Txp40 displayed proteolytic propensity. Txp40 gets proteolyzed, removing the linker peptide, which is essential for proper crystal packing. NTD adopts a novel fold composed of nine amphipathic helices and has no shared sequence or structural homology to any known proteins. CTD has structural homology with RNases of type II toxin-antitoxin (TA) complex belonging to the RelE/ParE toxin domain superfamily. NTD and CTD were individually toxic to Galleria mellonella larvae. However, maximal toxicity was observed when both domains were present. Our results suggested that the Txp40 acts as a two-domain binary toxin, which is unique and different from any known binary toxins and insecticidal proteins. Txp40 is also unique because it belongs to the prokaryotic RelE/ParE toxin family with a toxic effect on eukaryotic organisms, in contrast to other members of the same family. Broad insect specificity and unique binary toxin complex formation make Txp40 a viable candidate to overcome the development of resistance in insect pests.
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Affiliation(s)
- Omkar U Kinkar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Beena Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashok B Hadapad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ramesh S Hire
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
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Li L, Qin C, Chen Y, Zhao W, Zhu Q, Dai D, Zhan S, Guo J, Zhong T, Wang L, Cao J, Zhang H. The novel RNA-RNA activation of H19 on MyoD transcripts promoting myogenic differentiation of goat muscle satellite cells. Int J Biol Macromol 2023; 253:127341. [PMID: 37852400 DOI: 10.1016/j.ijbiomac.2023.127341] [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: 01/31/2023] [Revised: 10/01/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
The elaborate interplay of coding and noncoding factors governs muscle growth and development. Here, we reported a mutual activation between long noncoding RNA (lncRNA) H19 and MyoD (myogenic determination gene number 1) in the muscle process. We successfully cloned the two isoforms of goat H19, which were significantly enriched and positively correlated with MyoD transcripts in skeletal muscles or differentiating muscle satellite cells (MuSCs). To systematically screen genes altered by H19, we performed RNA-seq using cDNA libraries of differentiating H19-deficiency MuSCs and consequently anchored MyoD as the critical genes in mediating H19 function. Intriguingly, some transcripts of MyoD and H19 overlapped in the cytoplasm, which was dramatically damaged when the core complementary nucleotides were mutated. Meanwhile, MyoD RNA successfully pulled down H19 in MS2-RIP experiments. Furthermore, HuR could bind both H19 and MyoD transcripts, while H19 or its truncated mutants successfully stabilized MyoD mRNA, with or without HuR deficiency. In turn, novel functional MyoD protein-binding sites were identified in the promoter and exons of the H19 gene. Our results suggest that MyoD activates H19 transcriptionally, and RNA-RNA hybridization is critical for H19-promoted MyoD expression, which extends our knowledge of the hierarchy of regulatory networks in muscle growth.
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Affiliation(s)
- Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Chenyu Qin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Yuan Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Wei Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Qi Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Dinghui Dai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China.
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Ambadas DA, Singh A, Jha RK, Chauhan D, B. S, Sharma VK. Genome-wide dissection of AT-hook motif nuclear-localized gene family and their expression profiling for drought and salt stress in rice ( Oryza sativa). FRONTIERS IN PLANT SCIENCE 2023; 14:1283555. [PMID: 38148863 PMCID: PMC10749976 DOI: 10.3389/fpls.2023.1283555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023]
Abstract
AT-hook motif nuclear localized (AHL) genes are functionally very less explored, but their nature is very diverse. In the present study, we identified 20 AHL genes in rice. Phylogenetic analyses and evolutionary classification of AHL genes showed that they are conserved in plants, but the number of genes is still expanding in different crops and regulating new biological functions. Gene structure analysis showed that OsAHLs are with and without intron types of genes, suggesting that AHL genes added intron during evolution for neofunctionalization. The cis analysis of OsAHL genes suggested its motif diversity. In order to understand the function, 19 transcriptomes were identified from various tissues and different developmental stages of rice, and they were divided into eight groups by different temporal and spatial expression. Through co-expression analysis, 11 OsAHLs and 13 novel genes with intricate networks that control many biological pathways in rice were identified. The interactions of OsAHL proteins showed that they co-regulate important processes including flowering, reproductive organ development, and photosynthesis activity. The functionality of all 20 genes of OsAHL for drought and salt stress in leaf tissues of two contrasting genotypes (IR64 and NL44) of rice was studied using qRT-PCR. The result clearly showed significant upregulation of OsAHL genes under drought and salt conditions over the control. The differential expression between IR64 and NL44 showed a significant upregulation of OsAHL genes in NL44 as compared to the IR64 genotype under drought and salt stress. Overall, the result indicates that AHL genes might be involved in mediating drought and salt-signaling transduction pathways. The drought- and salt-tolerant nature of NL44 was also confirmed by expression profiling.
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Affiliation(s)
- Dhanorkar A. Ambadas
- Department of AB&MB, CBSH, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Ratnesh Kumar Jha
- Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Divya Chauhan
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Aliyabad, Rajasthan, India
| | - Santhosh B.
- Department of AB&MB, CBSH, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Vinay Kumar Sharma
- Department of AB&MB, CBSH, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
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Jo E, Choi S, Lee SJ, Kim J, Choi EK, Cho M, Kim J, Chung S, Lee J, Kim JH, Park H. Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna. Sci Data 2023; 10:891. [PMID: 38086886 PMCID: PMC10716251 DOI: 10.1038/s41597-023-02811-x] [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: 10/16/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
The Antarctic whitefin plunderfish Pogonophryne albipinna belongs to the family Artedidraconidae, a key component of Antarctic benthic ecosystems within the order Perciformes and the suborder Notothenioidei. While genome research on P. albipinna using short-read sequencing is available, high-quality genome assembly and annotation employing long-read sequencing have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for P. albipinna, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The resulting genome assembly spans approximately 1.07 Gb, with a longest scaffold measuring 59.39 Mb and an N50 length of 41.76 Mb. Of the 1,111 Hi-C scaffolds, 23 exceeded 10 Mb and were thus classified as chromosome-level. BUSCO completeness was assessed at 95.6%. The assembled genome comprises 50.68% repeat sequences, and a total of 31,128 protein-coding genes were predicted. This study will enhance our understanding of the genomic characteristics of cryonotothenioids and facilitate comparative analyses of their adaptation and evolution in extreme environments.
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Affiliation(s)
- Euna Jo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
- Division of Life Sciences, Korea Polar Research Institute (KOPRI), Incheon, 21990, Korea
| | - Soyun Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Seung Jae Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Jinmu Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Eun Kyung Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Minjoo Cho
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Jangyeon Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Sangdeok Chung
- National Institute of Fisheries Science (NIFS), Busan, 46083, Korea
| | - Jaebong Lee
- National Institute of Fisheries Science (NIFS), Busan, 46083, Korea
| | - Jeong-Hoon Kim
- Division of Life Sciences, Korea Polar Research Institute (KOPRI), Incheon, 21990, Korea
| | - Hyun Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea.
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Sekiguchi Y, Teramoto K, Tourlousse DM, Ohashi A, Hamajima M, Miura D, Yamada Y, Iwamoto S, Tanaka K. A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry. Genome Biol 2023; 24:257. [PMID: 38049850 PMCID: PMC10696839 DOI: 10.1186/s13059-023-03096-4] [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: 03/30/2023] [Accepted: 10/24/2023] [Indexed: 12/06/2023] Open
Abstract
MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra. We further demonstrate its utility by identifying uncultured strains from mouse feces with metagenomics, allowing the identification of new strains by customizing the database with metagenome-assembled genomes.
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Affiliation(s)
- Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan.
| | | | - Dieter M Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Yoshihiro Yamada
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
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Qu K, Liu A, Yin M, Mu W, Wu S, Hu H, Chen J, Su X, Dou Q, Ren G. A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera. Commun Biol 2023; 6:1223. [PMID: 38042963 PMCID: PMC10693610 DOI: 10.1038/s42003-023-05620-5] [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: 02/22/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale genome assembly for the genus Orinus (Orinus kokonorica as representative) and preform comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and the two subgenomes of O. kokonorica display neither fractionation bias nor global homoeolog expression dominance. We find substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes may have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations and extensive SVs between orthologs of flower and rhizome related genes may contribute to the morphological differences between the two genera. Our results provide new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.
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Affiliation(s)
- Kunjing Qu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Guangpeng Ren
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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Bai Z, Wu Y, Cai W, Zheng Y, Hui T, Yue C, Sun J, Wang Y, Wang Z. High-throughput analysis of lncRNA in cows with naturally infected Staphylococcus aureus mammary gland. Anim Biotechnol 2023; 34:2166-2174. [PMID: 35649423 DOI: 10.1080/10495398.2022.2077744] [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] [Indexed: 11/01/2022]
Abstract
LncRNA (long non-coding RNA) is an RNA molecule with a length between 200 and 100,000 nt. It does not encode proteins and is involved in a variety of intracellular processes, becoming a research hotspot of genetics. To identify key lncRNAs associated with dairy mastitis, we collected mammary epithelial tissue samples of Normal disease-free Holstein cows (HCN) and unhealthy Holstein cows with Staphylococcus aureus (HCU) and performed RNA sequencing (RNA-seq) on the samples. A total of 270 differentially expressed lncRNAs and 500 differentially expressed mRNAs were identified by high-throughput sequencing and bioinformatics analysis. Furthermore, Hydrolase activity is the most enriched in GO, and ErbB signaling pathway is significantly enriched in KEGG. In addition, through qPCR validation of 5 candidate lncRNAs in HCN and HCU, four differentially expressed lncRNAs MSTRG.498, MSTRG57.1, MSTRG.41.1 and MSTRG 124.1 were confirmed to have significant differentially expressed in cow mastitis. Also, lncRNA MSTRG.498 and its target gene, SMC4, might directly or indirectly play a role in cow mastitis. The regulatory network of lncRNA-miRNA-mRNA has been inferred from a bioinformatics perspective, which may assist understand the underlying molecular mechanism of lncRNAs involved in regulating mastitis in cows. Our findings will provide meaningful resources for further research on the regulatory function of lncRNAs in cow mastitis.
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Affiliation(s)
- Zhixian Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Zheng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Taiyu Hui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chang Yue
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jiaming Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanru Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Grima N, Liu S, Southwood D, Henden L, Smith A, Lee A, Rowe DB, D'Silva S, Blair IP, Williams KL. RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery. Neuropathol Appl Neurobiol 2023; 49:e12943. [PMID: 37818590 PMCID: PMC10946588 DOI: 10.1111/nan.12943] [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: 06/08/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/12/2023]
Abstract
AIM Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative disease with limited therapeutic options. A key factor limiting the development of effective therapeutics is the lack of disease biomarkers. We sought to assess whether biomarkers for diagnosis, prognosis or cohort stratification could be identified by RNA sequencing (RNA-seq) of ALS patient peripheral blood. METHODS Whole blood RNA-seq data were generated for 96 Australian sporadic ALS (sALS) cases and 48 healthy controls (NCBI GEO accession GSE234297). Differences in sALS-control gene expression, transcript usage and predicted leukocyte proportions were assessed, with pathway analysis used to predict the activity state of biological processes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms were applied to search for diagnostic and prognostic gene expression patterns. Unsupervised clustering analysis was employed to determine whether sALS patient subgroups could be detected. RESULTS Two hundred and forty-five differentially expressed genes were identified in sALS patients relative to controls, with enrichment of immune, metabolic and stress-related pathways. sALS patients also demonstrated switches in transcript usage across a small set of genes. We established a classification model that distinguished sALS patients from controls with an accuracy of 78% (sensitivity: 79%, specificity: 75%) using the expression of 20 genes. Clustering analysis identified four patient subgroups with gene expression signatures and immune cell proportions reflective of distinct peripheral effects. CONCLUSIONS Our findings suggest that peripheral blood RNA-seq can identify diagnostic biomarkers and distinguish molecular subtypes of sALS patients however, its prognostic value requires further investigation.
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Affiliation(s)
- Natalie Grima
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Sidong Liu
- Centre for Health InformaticsFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dean Southwood
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Lyndal Henden
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Andrew Smith
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Albert Lee
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dominic B. Rowe
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Susan D'Silva
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Ian P. Blair
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Kelly L. Williams
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
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Guo Y, Zhu C, Tian Z. Overexpression of KvCHX Enhances Salt Tolerance in Arabidopsis thaliana Seedlings. Curr Issues Mol Biol 2023; 45:9692-9708. [PMID: 38132451 PMCID: PMC10741925 DOI: 10.3390/cimb45120605] [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: 10/27/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The CHX (cation/H+ exchanger) family plays an important role in the transmembrane transport of cation/H+ in plants. The aim of this study was to identify and functionally analyze the KvCHX gene in the halophyte Kosteletzkya virginica to investigate its role in regulating the K+/Na+ ratio under salinity tolerance. Based on a partial gene sequence of EST from K. virginica, the full-length DNA sequence of the KvCHX gene was obtained using genome walking technology. Structural analysis and phylogenetic relationship analysis showed that the KvCHX gene was closely related to the AtCHX17 gene. The KvCHX overexpression vector was successfully constructed and transformed into Arabidopsis via floral dipping. Arabidopsis seedlings overexpressing KvCHX showed an enhanced tolerance to salt stress compared with wild-type plants. Transgenic Arabidopsis seedlings grew better under K+ deficiency than WT. The results showed that KvCHX could promote the uptake of K+, increase the ratio of K+/Na+, and promote the growth of plants under K+ deficiency and treatment with NaCl solution. KvCHX is involved in K+ transport and improves plant salt tolerance by coordinating K+ acquisition and homeostasis.
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Affiliation(s)
- Yuqi Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (C.Z.)
| | - Chengrong Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (C.Z.)
| | - Zengyuan Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Abubakar AS, Wu Y, Chen F, Zhu A, Chen P, Chen K, Qiu X, Huang X, Zhao H, Chen J, Gao G. Comprehensive Analysis of WUSCEL-Related Homeobox Gene Family in Ramie ( Boehmeria nivea) Indicates Its Potential Role in Adventitious Root Development. BIOLOGY 2023; 12:1475. [PMID: 38132301 PMCID: PMC10740585 DOI: 10.3390/biology12121475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
A WUSCHEL-related homeobox (WOX) gene family has been implicated in promoting vegetative organs to embryonic transition and maintaining plant embryonic stem cell identity. Using genome-wide analysis, we identified 17 candidates, WOX genes in ramie (Boehmeria nivea). The genes (BnWOX) showed highly conserved homeodomain regions typical of WOX. Based on phylogenetic analysis, they were classified into three distinct groups: modern, intermediate, and ancient clades. The genes displayed 65% and 35% collinearities with their Arabidopsis thaliana and Oryza sativa ortholog, respectively, and exhibited similar motifs, suggesting similar functions. Furthermore, four segmental duplications (BnWOX10/14, BnWOX13A/13B, BnWOX9A/9B, and BnWOX6A/Maker00021031) and a tandem-duplicated pair (BnWOX5/7) among the putative ramie WOX genes were obtained, suggesting that whole-genome duplication (WGD) played a role in WOX gene expansion. Expression profiling analysis of the genes in the bud, leaf, stem, and root of the stem cuttings revealed higher expression levels of BnWOX10 and BnWOX14 in the stem and root and lower in the leaf consistent with the qRT-PCR analysis, suggesting their direct roles in ramie root formation. Analysis of the rooting characteristics and expression in the stem cuttings of sixty-seven different ramie genetic resources showed a possible involvement of BnWOX14 in the adventitious rooting of ramie. Thus, this study provides valuable information on ramie WOX genes and lays the foundation for further research.
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Affiliation(s)
- Aminu Shehu Abubakar
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China; (A.S.A.); (F.C.)
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- Department of Agronomy, Bayero University Kano, PMB 3011, Kano 700241, Nigeria
| | - Yongmei Wu
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China; (A.S.A.); (F.C.)
| | - Fengming Chen
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China; (A.S.A.); (F.C.)
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xiaojun Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Xiaoyu Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Haohan Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- Key Laboratory of Biological and Processing for Bast Fiber Crops, Changsha 410221, China
| | - Gang Gao
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China; (A.S.A.); (F.C.)
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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England SJ, Rusnock AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells. Neural Dev 2023; 18:8. [PMID: 38017520 PMCID: PMC10683209 DOI: 10.1186/s13064-023-00176-w] [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: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. METHODS To identify candidate members of V0v gene regulatory networks, we FAC-sorted wild-type and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. RESULTS Our data reveal two molecularly distinct subtypes of zebrafish V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuron expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. CONCLUSIONS This study identifies two molecularly distinct subsets of zebrafish V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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Affiliation(s)
| | | | - Amra Mujcic
- Biology Department, Syracuse University, Syracuse, NY, USA
| | | | - Sarah de Jager
- Physiology, Development and Neuroscience Department, Cambridge University, Cambridge, UK
| | | | - José L Juárez-Morales
- Biology Department, Syracuse University, Syracuse, NY, USA
- Programa de IxM-CONAHCYT, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), La Paz, Baja California Sur, México
| | | | - Ginny Grieb
- Biology Department, Syracuse University, Syracuse, NY, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY, USA
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Li Y, Wu Y, Yang Z, Shi R, Zhang L, Feng Z, Wei G, Chou M. The Rpf107 gene, a homolog of LOR, is required for the symbiotic nodulation of Robinia pseudoacacia. PLANTA 2023; 259:6. [PMID: 38001306 DOI: 10.1007/s00425-023-04280-3] [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: 07/18/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023]
Abstract
MAIN CONCLUSION Rpf107 is involved in the infection process of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The LURP-one related (LOR) protein family plays a pivotal role in mediating plant defense responses against both biotic and abiotic stresses. However, our understanding of its function in the symbiotic interaction between legumes and rhizobia remains limited. Here, Rpf107, a homolog of LOR, was identified in Robinia pseudoacacia (black locust). The subcellular localization of Rpf107 was analyzed, and its function was investigated using RNA interference (RNAi) and overexpression techniques. The subcellular localization assay revealed that Rpf107 was mainly distributed in the plasma membrane and nucleus. Rpf107 silencing prevented rhizobial infection and hampered plant growth. The number of infected cells in the nitrogen fixation zone of the Rpf107-RNAi nodules was also noticeably lower than that in the control nodules. Notably, Rpf107 silencing resulted in bacteroid degradation and the premature aging of nodules. In contrast, the overexpression of Rpf107 delayed the senescence of nodules and prolonged the nitrogen-fixing ability of nodules. These results demonstrate that Rpf107 was involved in the infection of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The findings reveal that a member of the LOR protein family plays a role in leguminous root nodule symbiosis, which is helpful to clarify the functions of plant LOR protein family and fully understand the molecular mechanisms underlying legume-rhizobium symbiosis.
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Affiliation(s)
- Yuanli Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yuanyuan Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
- Xiangyang Public Inspection and Testing Center, No.69, Taiziwan Road, Xiangyang, 441000, Hubei Province, People's Republic of China
| | - Ziyi Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
| | - Rui Shi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lu Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
| | - Zhao Feng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China
| | - Minxia Chou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, People's Republic of China.
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Khan A, Shah Z, Ali S, Ahmad N, Iqbal M, Ullah A, Ayub F. Genome wide identification, structural characterization and phylogenetic analysis of High-Affinity potassium (HAK) ion transporters in common bean (Phaseolus vulgaris L.). BMC Genom Data 2023; 24:66. [PMID: 37964195 PMCID: PMC10648387 DOI: 10.1186/s12863-023-01163-0] [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: 03/03/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND High-Affinity Potassium ions represent one of the most important and large group of potassium transporters. Although HAK genes have been studied in a variety of plant species, yet, remain unexplored in common bean. RESULTS In the current study, 20 HAK genes were identified in common bean genome. Super-family "K_trans" domain was found in all PvHAK genes. Signals for localization of PvHAK proteins were detected in cell membrane. Fifty three HAKs genes, across diverse plant species, were divided into 5 groups based on sequential homology. Twelve pairs of orthologs genes were found in various plant species. PvHAKs genes were distributed unequally on 7 chromosomes with maximum number (7) mapped on chromosome 2 while only 1 PvHAK found on each chromosome 1, 4, and 6. Tandem gene duplication was witnessed in 2 paralog pairs while 1 pair exhibited segmental gene duplication. Five groups were made in PvHAK gene family based on Phylogeny. Maximum PvHAKs (10) were detected in Group-V while group-II composed of only 1 PvHAK gene. Variation was witnessed in number and size of motifs, and structure of PvHAKs associated with different groups. Light and hormone responsive elements contributed 57 and 24% share, respectively, to cis regulatory elements. qRT-PCR based results revealed significant increase in expression of all 4 PvHAK genes under low-potassium stress. CONCLUSION The current study provides valuable information for further functional characterization and uncovering the molecular mechanism associated with Potassium transportation in plants.
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Affiliation(s)
- Afrasyab Khan
- Department of Biotechnology, University of Science and Technology, Bannu, 28100, Pakistan
| | - Zamarud Shah
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Nisar Ahmad
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, 21300, Pakistan
| | - Maaz Iqbal
- Institute of Biotechnology and Genetic Engineering, University of Agriculture, Peshawar, 25130, Pakistan
| | - Arif Ullah
- Department of Biotechnology, University of Science and Technology, Bannu, 28100, Pakistan
| | - Firdous Ayub
- Department of Computer Science, Women University Swabi, Swabi, 23430, Pakistan
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Rankins DR, Herrera MJ, Christensen MP, Chen A, Hood NZ, Heras J, German DP. When digestive physiology doesn't match "diet": Lumpenus sagitta (Stichaeidae) is an "omnivore" with a carnivorous gut. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111508. [PMID: 37625480 DOI: 10.1016/j.cbpa.2023.111508] [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: 03/31/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
What an animal ingests and what it digests can be different. Thus, we examined the nutritional physiology of Lumpenus sagitta, a member of the family Stichaeidae, to better understand whether it could digest algal components like its better studied algivorous relatives. Although L. sagitta ingests considerable algal content, we found little evidence of algal digestion. This fish species has a short gut that doesn't show positive allometry with body size, low amylolytic activity that actually decreases as the fish grow, no ontogenetic changes in digestive enzyme gene expression, elevated N-acetyl-glucosaminidase activity (indicative of chitin breakdown), and an enteric microbial community that is consistent with carnivory and differs from members of its family that consume and digest algae. Hence, we are left concluding that L. sagitta is not capable of digesting the algae it consumes, and instead, are likely targeting epibionts on the algae itself, and other invertebrates consumed with the algae. Our study expands the coverage of dietary and digestive information for the family Stichaeidae, which is becoming a model for fish digestive physiology and genomics, and shows the power of moving beyond gut content analyses to better understand what an animal can actually digest and use metabolically.
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Affiliation(s)
- Daniel R Rankins
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA.
| | - Michelle J Herrera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Michelle P Christensen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Alisa Chen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Newton Z Hood
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Joseph Heras
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
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50
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Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023; 49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [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: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
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Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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