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Zeng Z, Ni J, Huang Z, Tan Q. Expression and functional analysis of Fushi Tarazu transcription factor 1 (FTZ-F1) in the regulation of steroid hormones during the gonad development of Fujian Oyster, Crassostrea angulata. Comp Biochem Physiol A Mol Integr Physiol 2024; 295:111668. [PMID: 38797241 DOI: 10.1016/j.cbpa.2024.111668] [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: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Crassostrea angulata, a major shellfish cultivated in Southern China, has experienced a notable surge in commercial value in recent years. Understanding the molecular mechanisms governing their reproductive processes holds significant implications for advancing aquaculture practices. In this study, we cloned the orphan nuclear receptor gene, Fushi Tarazu transcription factor 1 (FTZ-F1), of C. angulata and investigated its functional role in the gonadal development. The full-length cDNA of FTZ-F1 spans 2357 bp and encodes a protein sequence of 530 amino acids. Notably, the amino acid sequence of FTZ-F1 in C. angulata shares remarkable similarity with its homologues in other species, particularly in the DNA-binding region (>90%) and ligand-binding region (>44%). In C. angulata, the highest expression level of FTZ-F1 was observed in the ovary, exhibiting more than a 200-fold increase during the maturation stage compared to the initiation stage (P < 0.001). Specifically, FTZ-F1 was mainly expressed in the follicular cells surrounding the oocytes of C. angulata. Upon inhibiting FTZ-F1 gene expression in C. angulata through RNA interference (RNAi), a substantial reduction in the expression of genes involved in the synthesis of sex steroids in the gonads, including 3β-HSD, Cyp17, and follistatin, was observed. In addition, estradiol (E2) and testosterone (T) levels also showed a decrease upon FTZ-F1 silencing, resulting in a delayed gonadal development. These results indicate that FTZ-F1 acts as a steroidogenic factor, participating in the synthesis and regulation of steroid hormones and thus playing an important role in the reproductive and endocrine systems within oysters.
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Affiliation(s)
- Zhen Zeng
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medical College, Xiamen 361023, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Jianbin Ni
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Qianglai Tan
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medical College, Xiamen 361023, China.
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2
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Pelagalli C, Sera DJ, DeGiorgis JA, Cornely K. Mycobacteriophage maravista: a cluster F1 phage discovered on Cape Cod, Massachusetts. Microbiol Resour Announc 2024:e0050224. [PMID: 38860805 DOI: 10.1128/mra.00502-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Mycobacterium virus Maravista, a member of the family Gracegardnervirianae and species Cheoctovirus, is an F1 cluster phage that infects Mycobacterium smegmatis mc²155. The Maravista genome has 61.3% GC content, is 60,140 bp in length, and encodes 104 putative genes. Maravista encodes two putative glycosyltransferases, suggesting glycosylation of its capsid protein.
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Affiliation(s)
- Charles Pelagalli
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Debbie-Jacobs Sera
- Department of Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
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Nikitenko ED, Borisenko IE, Anisenko AN, Vortsepneva EV. Transcriptomic sequence dataset of a potential new model species for studying biomineralization Onchidoris muricata (Nudibranchia, Gastropoda, Mollusca). Data Brief 2024; 54:110526. [PMID: 38799714 PMCID: PMC11127168 DOI: 10.1016/j.dib.2024.110526] [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: 03/19/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Onchidoris muricata is a widespread shell-less species of nudibranch molluscs, which has unique for Gastropoda skeletal elements - subepidermal calcite spicules. The general and fine morphology of the spicules, as well as their maturation process in ontogenesis, have been studied in detail by authors. The uniqueness of spicules lies in their intracellular formation and location under the ectodermal epithelium, which is more typical for deuterostomes. We present O. muricata as a potentially new model species for studying calcification of intracellular protein structure. A total of 96 individuals were collected in the Kandalaksha Bay of the White Sea, both manually and by scuba diving. All individuals were divided into three groups based on morphological characteristics such as specimens' size, spicule condition etc. This division suggests the existence of three stages in postembryonic ontogenesis of O. muricata reflecting the maturation of the spicule complex. Total RNA samples were isolated from three size groups of molluscs in three biological replicates. Libraries were prepared from the polyadenylated RNA fraction and sequenced at NovaSeq6000 (Illumina), yielding a total of 112.8 Gb of 150 bp paired-end reads, corresponding to almost 1,000-fold coverage of the transcriptome. Representative transcriptome assembled de novo with Trinity. In addition to obtaining the transcriptome sequences of O. muricata, differential expression analysis was also performed for these three size groups. This allows us to trace the dynamics of molecular and biological processes during the life of a mollusc. The obtained data can then be used as a reference transcriptome for closely related species, to study specific expressed genes, to identify various unique sequences, including protein-coding ones, to understand biological processes, including biomineralization and much more.
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Affiliation(s)
- Ekaterina D. Nikitenko
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Leninskye Gory 1/12, Moscow 119234, Russian Federation
| | - Ilya E. Borisenko
- Embryology Department, Saint-Petersburg State University, University Embankment, 7/9, St. Petersburg 199034, Russian Federation
| | - Andrey N. Anisenko
- Chemistry Department, Lomonosov Moscow State University, Leninskye Gory 1/10, Moscow 119234, Russian Federation
| | - Elena V. Vortsepneva
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Leninskye Gory 1/12, Moscow 119234, Russian Federation
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Zhao B, Cai J, Zhang X, Li J, Bao Z, Chen Y, Wu X. Single nucleotide polymorphisms in the KRT82 promoter region modulate irregular thickening and patchiness in the dorsal skin of New Zealand rabbits. BMC Genomics 2024; 25:458. [PMID: 38730432 PMCID: PMC11088042 DOI: 10.1186/s12864-024-10370-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND While rabbits are used as models in skin irritation tests, the presence of irregular patches and thickening on the dorsal skin can affect precise evaluation. In this study, genes associated with patchiness or non-patchiness on the dorsal skin of New Zealand rabbits were investigated to identify potential regulators of the patchiness phenotype. RESULTS The results showed that parameters associated with hair follicles (HFs), such as HF density, skin thickness, and HF depth, were augmented in rabbits with the patchiness phenotype relative to the non-patchiness phenotype. A total of 592 differentially expressed genes (DEGs) were identified between the two groups using RNA-sequencing. These included KRT72, KRT82, KRT85, FUT8, SOX9, and WNT5B. The functions of the DEGs were investigated by GO and KEGG enrichment analyses. A candidate gene, KRT82, was selected for further molecular function verification. There was a significant positive correlation between KRT82 expression and HF-related parameters, and KRT82 overexpression and knockdown experiments with rabbit dermal papilla cells (DPCs) showed that it regulated genes related to skin and HF growth and development. Investigation of single nucleotide polymorphisms (SNPs) in the exons and promoter region of KRT82 identified four SNPs in the promoter region but none in the exons. The G.-631G > T, T.-696T > C, G.-770G > T and A.-873 A > C alleles conformed to the Hardy - Weinberg equilibrium, and three identified haplotypes showed linkage disequilibrium. Luciferase reporter assays showed that the core promoter region of KRT82 was located in the - 600 to - 1200 segment, in which the four SNPs were located. CONCLUSIONS The morphological characteristics of the patchiness phenotype were analyzed in New Zealand rabbits and DEGs associated with this phenotype were identified by RNA-sequencing. The biological functions of the gene KRT82 associated with this phenotype were analyzed, and four SNPs were identified in the promoter region of the gene. These findings suggest that KRT82 may be a potential biomarker for the breeding of experimental New Zealand rabbits.
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Affiliation(s)
- Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jiawei Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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Liu H, Li X, Yin Z, Hu J, Xie L, Wu H, Han S, Li B, Zhang H, Li C, Li L, Zhang F, Tan G. Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility. PeerJ 2024; 12:e17370. [PMID: 38737737 PMCID: PMC11086307 DOI: 10.7717/peerj.17370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/18/2024] [Indexed: 05/14/2024] Open
Abstract
Cysteine-rich receptor-like kinases (CRKs) play many important roles during plant development, including defense responses under both biotic and abiotic stress, reactive oxygen species (ROS) homeostasis, callose deposition and programmed cell death (PCD). However, there are few studies on the involvement of the CRK family in male sterility due to heat stress in wheat (Triticum aestivum L.). In this study, a genome-wide characterization of the CRK family was performed to investigate the structural and functional attributes of the wheat CRKs in anther sterility caused by heat stress. A total of 95 CRK genes were unevenly distributed on 18 chromosomes, with the most genes distributed on chromosome 2B. Paralogous homologous genes with Ka/Ks ratios less than 1 may have undergone strong purifying selection during evolution and are more functionally conserved. The collinearity analysis results of CRK genes showed that wheat and Arabidopsis (A. thaliana), foxtail millet, Brachypodium distachyon (B. distachyon), and rice have three, 12, 15, and 11 pairs of orthologous genes, respectively. In addition, the results of the network interactions of genes and miRNAs showed that five miRNAs were in the hub of the interactions map, namely tae-miR9657b-5p, tae-miR9780, tae-miR9676-5p, tae-miR164, and tae-miR531. Furthermore, qRT-PCR validation of the six TaCRK genes showed that they play key roles in the development of the mononuclear stage anthers, as all six genes were expressed at highly significant levels in heat-stressed male sterile mononuclear stage anthers compared to normal anthers. We hypothesized that the TaCRK gene is significant in the process of high-temperature-induced sterility in wheat based on the combination of anther phenotypes, paraffin sections, and qRT-PCR data. These results improve our understanding of their relationship.
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Affiliation(s)
- Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
- Field Observation and Research Station of Green Agriculture in Dancheng County, Dancheng, Henan Province, China
- Engineering Technology Research Center of Crop Molecular Breeding and Cultivation in Henan Province, Zhoukou, Henan Province, China
| | - Xiaoyi Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Zehui Yin
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Junmin Hu
- Jiaozuo Seed Management Station, Jiaozuo, Henan Province, China
| | - Liuyong Xie
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Huanhuan Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Shuying Han
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Bing Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Huifang Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Chaoqiong Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
- Field Observation and Research Station of Green Agriculture in Dancheng County, Dancheng, Henan Province, China
- Engineering Technology Research Center of Crop Molecular Breeding and Cultivation in Henan Province, Zhoukou, Henan Province, China
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
- Field Observation and Research Station of Green Agriculture in Dancheng County, Dancheng, Henan Province, China
| | - Guangxuan Tan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan Province, China
- Engineering Technology Research Center of Crop Molecular Breeding and Cultivation in Henan Province, Zhoukou, Henan Province, China
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Umezawa A, Matsumoto M, Handa H, Nakazawa K, Miyagawa M, Seifert GJ, Takahashi D, Fushinobu S, Kotake T. Cytosolic UDP-L-arabinose synthesis by bifunctional UDP-glucose 4-epimerases in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38678521 DOI: 10.1111/tpj.16779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024]
Abstract
L-Arabinose (L-Ara) is a plant-specific sugar found in cell wall polysaccharides, proteoglycans, glycoproteins, and small glycoconjugates, which play physiologically important roles in cell proliferation and other essential cellular processes. L-Ara is synthesized as UDP-L-arabinose (UDP-L-Ara) from UDP-xylose (UDP-Xyl) by UDP-Xyl 4-epimerases (UXEs), a type of de novo synthesis of L-Ara unique to plants. In Arabidopsis, the Golgi-localized UXE AtMUR4 is the main contributor to UDP-L-Ara synthesis. However, cytosolic bifunctional UDP-glucose 4-epimerases (UGEs) with UXE activity, AtUGE1, and AtUGE3 also catalyze this reaction. For the present study, we first examined the physiological importance of bifunctional UGEs in Arabidopsis. The uge1 and uge3 mutants enhanced the dwarf phenotype of mur4 and further reduced the L-Ara content in cell walls, suggesting that bifunctional UGEs contribute to UDP-L-Ara synthesis. Through the introduction of point mutations exchanging corresponding amino acid residues between AtUGE1 with high UXE activity and AtUGE2 with low UXE activity, two mutations that increase relative UXE activity of AtUGE2 were identified. The crystal structures of AtUGE2 in complex forms with NAD+ and NAD+/UDP revealed that the UDP-binding domain of AtUGE2 has a more closed conformation and smaller sugar-binding site than bacterial and mammalian UGEs, suggesting that plant UGEs have the appropriate size and shape for binding UDP-Xyl and UDP-L-Ara to exhibit UXE activity. The presented results suggest that the capacity for cytosolic synthesis of UDP-L-Ara was acquired by the small sugar-binding site and several mutations of UGEs, enabling diversified utilization of L-Ara in seed plants.
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Affiliation(s)
- Akira Umezawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Mayuko Matsumoto
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Hiroto Handa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Konatsu Nakazawa
- Department of Biochemistry and Molecular Biology, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Megumi Miyagawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Georg J Seifert
- Institute of Plant Biotechnology and Cell biology, University of Natural Resources and Life Science, Muthgasse 18, A-1190, Vienna, Austria
| | - Daisuke Takahashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Toshihisa Kotake
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
- Green Bioscience Research Center, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
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Kuhn CK, Stenzel U, Berndt S, Liebscher I, Schöneberg T, Horn S. The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples. Nucleic Acids Res 2024; 52:3823-3836. [PMID: 38421639 DOI: 10.1093/nar/gkae145] [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: 09/27/2023] [Revised: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
Alternative splicing and multiple transcription start and termination sites can produce a diverse repertoire of mRNA transcript variants from a given gene. While the full picture of the human transcriptome is still incomplete, publicly available RNA datasets have enabled the assembly of transcripts. Using publicly available deep sequencing data from 927 human samples across 48 tissues, we quantified known and new transcript variants, provide an interactive, browser-based application Splice-O-Mat and demonstrate its relevance using adhesion G protein-coupled receptors (aGPCRs) as an example. On average, 24 different transcript variants were detected for each of the 33 human aGPCR genes, and several dominant transcript variants were not yet annotated. Variable transcription starts and complex exon-intron structures encode a flexible protein domain architecture of the N- and C termini and the seven-transmembrane helix domain (7TMD). Notably, we discovered the first GPCR (ADGRG7/GPR128) with eight transmembrane helices. Both the N- and C terminus of this aGPCR were intracellularly oriented, anchoring the N terminus in the plasma membrane. Moreover, the assessment of tissue-specific transcript variants, also for other gene classes, in our application may change the evaluation of disease-causing mutations, as their position in different transcript variants may explain tissue-specific phenotypes.
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Affiliation(s)
- Christina Katharina Kuhn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Udo Stenzel
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Sandra Berndt
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
- Department of Biochemistry, School of Medicine, University of Global Health Equity (UGHE), PO Box 6955 Kigali, Rwanda
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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Xu L, Yue XL, Li HZ, Jian SL, Shu WS, Cui L, Xu XW. Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7087-7098. [PMID: 38651173 DOI: 10.1021/acs.est.4c02881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- Collge of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Xiao-Lan Yue
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Shu-Ling Jian
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Wen-Sheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, P. R. China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, P. R. China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
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9
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Wang W, Xu L, Jiang G, Li Z, Bi YH, Zhou ZG. Characterization of a novel γ-type carbonic anhydrase, Sjγ-CA2, in Saccharina japonica: Insights into carbon concentration mechanism in macroalgae. Int J Biol Macromol 2024; 263:130506. [PMID: 38423426 DOI: 10.1016/j.ijbiomac.2024.130506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Carbonic anhydrase (CA) is a crucial component of CO2-concentrating mechanism (CCM) in macroalgae. In Saccharina japonica, an important brown seaweed, 11 CAs, including 5 α-, 3 β-, and 3 γ-CAs, have been documented. Among them, one α-CA and one β-CA were localized in the periplasmic space, one α-CA was found in the chloroplast, and one γ-CA was situated in mitochondria. Notably, the known γ-CAs have predominantly been identified in mitochondria. In this study, we identified a chloroplastic γ-type CA, Sjγ-CA2, in S. japonica. Based on the reported amino acid sequence of Sjγ-CA2, the epitope peptide for monoclonal antibody production was selected as 165 Pro-305. After purification and specificity identification, anti-SjγCA2 monoclonal antibody was employed in immunogold electron microscopy. The results illustrated that Sjγ-CA2 was localized in the chloroplasts of both gametophytes and sporophytes of S. japonica. Subsequently, immunoprecipitation coupled with LC-MS/MS analysis revealed that Sjγ-CA2 mainly interacted with photosynthesis-related proteins. Moreover, the first 65 amino acids at N-terminal of Sjγ-CA2 was identified as the chloroplast transit peptide by the transient expression of GFP-SjγCA2 fused protein in tabacco. Real-time PCR results demonstrated an up-regulation of the transcription of Sjγ-CA2 gene in response to high CO2 concentration. These findings implied that Sjγ-CA2 might contribute to minimizing the leakage of CO2 from chloroplasts and help maintaining a high concentration of CO2 around Rubisco.
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Affiliation(s)
- Wen Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ling Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Gang Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Zhi Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yan-Hui Bi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| | - Zhi-Gang Zhou
- International Research Center for Marine Biosciences Conferred By Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
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10
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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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11
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Sun S, Zhao B, Li J, Zhang X, Yao S, Bao Z, Cai J, Yang J, Chen Y, Wu X. Regulation of Hair Follicle Growth and Development by Different Alternative Spliceosomes of FGF5 in Rabbits. Genes (Basel) 2024; 15:409. [PMID: 38674344 PMCID: PMC11049220 DOI: 10.3390/genes15040409] [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: 03/05/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
This study investigated the regulatory effect of alternative spliceosomes of the fibroblast growth factor 5 (FGF5) gene on hair follicle (HF) growth and development in rabbits. The FGF5 alternative spliceosomes (called FGF5-X1, FGF5-X2, FGF5-X3) were cloned. The overexpression vector and siRNA of spliceosomes were transfected into dermal papilla cells (DPCs) to analyze the regulatory effect on DPCs. The results revealed that FGF5-X2 and FGF5-X3 overexpression significantly decreased LEF1 mRNA expression (p < 0.01). FGF5-X1 overexpression significantly reduced CCND1 expression (p < 0.01). FGF5-X1 and FGF5-X2 possibly downregulated the expression level of FGF2 mRNA (p < 0.05), and FGF5-X3 significantly downregulated the expression level of FGF2 mRNA (p < 0.01). The FGF5 alternative spliceosomes significantly downregulated the BCL2 mRNA expression level in both cases (p < 0.01). FGF5-X1 and FGF5-X2 significantly increased TGFβ mRNA expression (p < 0.01). All three FGF5 alternative spliceosomes inhibited DPC proliferation. In conclusion, the expression profile of HF growth and development-related genes can be regulated by FGF5 alternative spliceosomes, inhibiting the proliferation of DPCs and has an influence on the regulation of HF growth in rabbits. This study provides insights to further investigate the mechanism of HF development in rabbits via FGF5 regulation.
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Affiliation(s)
- Shaoning Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Shuyu Yao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jiawei Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Jie Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.S.); (B.Z.); (J.L.); (X.Z.); (S.Y.); (Z.B.); (J.C.); (J.Y.); (Y.C.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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12
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León-García F, García-Laynes F, Estrada-Tapia G, Monforte-González M, Martínez-Estevez M, Echevarría-Machado I. In Silico Analysis of Glutamate Receptors in Capsicum chinense: Structure, Evolution, and Molecular Interactions. PLANTS (BASEL, SWITZERLAND) 2024; 13:812. [PMID: 38592787 PMCID: PMC10975470 DOI: 10.3390/plants13060812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Plant glutamate receptors (GLRs) are integral membrane proteins that function as non-selective cation channels, involved in the regulation of developmental events crucial in plants. Knowledge of these proteins is restricted to a few species and their true agonists are still unknown in plants. Using tomato SlGLRs, a search was performed in the pepper database to identify GLR sequences in habanero pepper (Capsicum chinense Jacq.). Structural, phylogenetic, and orthology analysis of the CcGLRs, as well as molecular docking and protein interaction networks, were conducted. Seventeen CcGLRs were identified, which contained the characteristic domains of GLR. The variation of conserved residues in the M2 transmembrane domain between members suggests a difference in ion selectivity and/or conduction. Also, new conserved motifs in the ligand-binding regions are reported. Duplication events seem to drive the expansion of the species, and these were located in the evolution by using orthologs. Molecular docking analysis allowed us to identify differences in the agonist binding pocket between CcGLRs, which suggest the existence of different affinities for amino acids. The possible interaction of some CcGLRs with proteins leads to suggesting specific functions for them within the plant. These results offer important functional clues for CcGLR, probably extrapolated to other Solanaceae.
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Affiliation(s)
| | | | | | | | | | - Ileana Echevarría-Machado
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Calle 43, #130, x 32 and 34, Mérida 97205, Yucatán, Mexico; (F.L.-G.); (M.M.-G.); (M.M.-E.)
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13
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Wang Y, Ruan L, Li R. GPI-anchored Gas1 protein regulates cytosolic proteostasis in budding yeast. G3 (BETHESDA, MD.) 2024; 14:jkad263. [PMID: 38289859 PMCID: PMC10917523 DOI: 10.1093/g3journal/jkad263] [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: 06/10/2023] [Accepted: 11/01/2023] [Indexed: 02/01/2024]
Abstract
The decline in protein homeostasis (proteostasis) is a hallmark of cellular aging and aging-related diseases. Maintaining a balanced proteostasis requires a complex network of molecular machineries that govern protein synthesis, folding, localization, and degradation. Under proteotoxic stress, misfolded proteins that accumulate in cytosol can be imported into mitochondria for degradation through the "mitochondrial as guardian in cytosol" (MAGIC) pathway. Here, we report an unexpected role of Gas1, a cell wall-bound glycosylphosphatidylinositol (GPI)-anchored β-1,3-glucanosyltransferase in the budding yeast, in differentially regulating MAGIC and ubiquitin-proteasome system (UPS). Deletion of GAS1 inhibits MAGIC but elevates protein ubiquitination and UPS-mediated protein degradation. Interestingly, we found that the Gas1 protein exhibits mitochondrial localization attributed to its C-terminal GPI anchor signal. But this mitochondria-associated GPI anchor signal is not required for mitochondrial import and degradation of misfolded proteins through MAGIC. By contrast, catalytic inactivation of Gas1 via the gas1-E161Q mutation inhibits MAGIC but not its mitochondrial localization. These data suggest that the glucanosyltransferase activity of Gas1 is important for regulating cytosolic proteostasis.
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Affiliation(s)
- Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore
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14
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Yang H, Li Q, Stroup EK, Wang S, Ji Z. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nat Commun 2024; 15:1932. [PMID: 38431639 PMCID: PMC10908861 DOI: 10.1038/s41467-024-46240-9] [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: 07/18/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
Studies have revealed dozens of functional peptides in putative 'noncoding' regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs). Here, we comprehensively annotate genome-wide translated ORFs across five eukaryotes (human, mouse, zebrafish, worm, and yeast) by analyzing ribosome profiling data. We develop a logistic regression model named PepScore based on ORF features (expected length, encoded domain, and conservation) to calculate the probability that the encoded peptide is stable in humans. Systematic ectopic expression validates PepScore and shows that stable complex-associating microproteins can be encoded in 5'/3' untranslated regions and overlapping coding regions of mRNAs besides annotated noncoding RNAs. Stable noncanonical proteins follow conventional rules and localize to different subcellular compartments. Inhibition of proteasomal/lysosomal degradation pathways can stabilize some peptides especially those with moderate PepScores, but cannot rescue the expression of short ones with low PepScores suggesting they are directly degraded by cellular proteases. The majority of human noncanonical peptides with high PepScores show longer lengths but low conservation across species/mammals, and hundreds contain trait-associated genetic variants. Our study presents a statistical framework to identify stable noncanonical peptides in the genome and provides a valuable resource for functional characterization of noncanonical translation during development and disease.
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Affiliation(s)
- Haiwang Yang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Qianru Li
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emily K Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Sheng Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA.
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15
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Broadbent LM, Rothnie AJ, Simms J, Bill RM. Classifying tetraspanins: A universal system for numbering residues and a proposal for naming structural motifs and subfamilies. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184265. [PMID: 38154528 DOI: 10.1016/j.bbamem.2023.184265] [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: 09/21/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
All tetraspanins have four transmembrane domains (TMs). The large extracellular loop (LEL) that connects the third and fourth TMs contains multiple secondary structures together with the family's signature Cys-Cys-Gly motif. These intriguing membrane proteins are involved in diverse and incompletely understood cellular processes including cell adhesion, tissue differentiation, immune cell maturation and host-parasite interactions. Here we present a classification system that accurately describes the position of each amino acid within its primary sequence based on both sequence and topological conservation of the TMs and LEL. This builds on the numbering systems that have been used in the G protein-coupled receptor (GPCR) field for nearly three decades and which have aided the understanding of GPCR structure/activity relationships and ligand interactions. The high-resolution structures of the tetraspanins CD81, CD9, CD53 and Tspan15 were used to validate the structural relevance of our new tetraspanin classification system. Modelling of all tetraspanin LELs highlighted flexibility in LEL disulfide bonding across the family and suggests that the structural arrangement of tetraspanin LELs is more complex than previously thought. We therefore propose a new subfamily naming system that addresses this added complexity and facilitates the systematic classification of human tetraspanins, shedding light on all structural motifs within the family. We anticipate that our universal tetraspanin classification system will enable progress in defining how sequence and structure inform function.
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Affiliation(s)
- Luke M Broadbent
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| | - Alice J Rothnie
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - John Simms
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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16
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Bayramova E, Petrova D, Marchenkov A, Morozov A, Galachyants Y, Zakharova Y, Bedoshvili Y, Likhoshway Y. Differential Expression of Stress Adaptation Genes in a Diatom Ulnaria acus under Different Culture Conditions. Int J Mol Sci 2024; 25:2314. [PMID: 38396992 PMCID: PMC10888605 DOI: 10.3390/ijms25042314] [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: 01/16/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Diatoms are a group of unicellular eukaryotes that are essential primary producers in aquatic ecosystems. The dynamic nature of their habitat necessitates a quick and specific response to various stresses. However, the molecular mechanisms of their physiological adaptations are still underexplored. In this work, we study the response of the cosmopolitan freshwater diatom Ulnaria acus (Bacillariophyceae, Fragilariophycidae, Licmophorales, Ulnariaceae, Ulnaria) in relation to a range of stress factors, namely silica deficiency, prolonged cultivation, and interaction with an algicidal bacterium. Fluorescent staining and light microscopy were used to determine the physiological state of cells under these stresses. To explore molecular reactions, we studied the genes involved in the stress response-type III metacaspase (MC), metacaspase-like proteases (MCP), death-specific protein (DSP), delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH12), and glutathione synthetase (GSHS). We have described the structure of these genes, analyzed the predicted amino acid sequences, and measured their expression dynamics in vitro using qRT-PCR. We demonstrated that the expression of UaMC1, UaMC3, and UaDSP increased during the first five days of silicon starvation. On the seventh day, it was replaced with the expression of UaMC2, UaGSHS, and UaALDH. After 45 days of culture, cells stopped growing, and the expression of UaMC1, UaMC2, UaGSHS, and UaDSP increased. Exposure to an algicidal bacterial filtrate induced a higher expression of UaMC1 and UaGSHS. Thus, we can conclude that these proteins are involved in diatoms' adaptions to environmental changes. Further, these data show that the molecular adaptation mechanisms in diatoms depend on the nature and exposure duration of a stress factor.
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Affiliation(s)
| | | | | | | | | | | | - Yekaterina Bedoshvili
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia; (E.B.); (D.P.); (A.M.); (A.M.); (Y.G.); (Y.Z.); (Y.L.)
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17
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Kaur A, Yadav VG, Pawar SV, Sembi JK. Insights to Phenylalanine Ammonia Lyase (PAL) and Secondary Metabolism in Orchids: An in silico Approach. Biochem Genet 2024; 62:413-435. [PMID: 37358673 DOI: 10.1007/s10528-023-10428-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 06/27/2023]
Abstract
The phenylalanine ammonia lyase (PAL) catalyses the first step of phenylpropanoid metabolic pathway which leads to the biosynthesis of a diverse group of secondary metabolites. Orchids serve as a rich source of metabolites and the availability of genome or transcriptome for selected orchid species provides an opportunity to analyse the PAL genes in orchids. In the present study, 21 PAL genes were characterized using bioinformatics tools in nine orchid species (Apostasia shenzhenica, Cypripedium formosanum, Dendrobium catenatum, Phalaenopsis aphrodite, Phalaenopsis bellina, Phalaenopsis equestris, Phalaenopsis lueddemanniana, Phalaenopsis modesta and Phalaenopsis schilleriana). Multiple sequence alignment confirmed the presence of PAL-specific conserved domains (N-terminal, MIO, core, shielding and C-terminal domain). All these proteins were predicted to be hydrophobic in nature and to have cytoplasmic localisation. Structural modelling depicted the presence of alpha helices, extended strands, beta turns and random coils in their structure. Ala-Ser-Gly triad known for substrate binding and catalysis of MIO-domain was found to be completely conserved in all the proteins. Phylogenetic study showed that the PALs of pteridophytes, gymnosperms and angiosperms clustered together in separate clades. Expression profiling showed tissue-specific expression for all the 21 PAL genes in the various reproductive and vegetative tissues which suggested their diverse role in growth and development. This study provides insights to the molecular characterization of PAL genes which may help in developing biotechnological strategies to enhance the synthesis of phenylpropanoids in orchids and other heterologous systems for pharmaceutical applications.
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Affiliation(s)
- Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Vikramaditya G Yadav
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
| | - Sandip V Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Jaspreet K Sembi
- Department of Botany, Panjab University, Chandigarh, 160014, India.
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18
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You C, Miao S, Xie Z, Lin S, Wang S, Chen C, Lin L, Huang Y, Zhou M, Dong Y, Li Y, Zhuang P. Cloning, tissue specificity and regulation of expression of genes of four key enzymes related to long-chain polyunsaturated fatty acids (LC-PUFA) biosynthesis by ambient salinity during embryogenesis in the marine teleost Siganus guttatus. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110903. [PMID: 37717849 DOI: 10.1016/j.cbpb.2023.110903] [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: 06/14/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
The rabbitfish Siganus canaliculatus was the first marine teleost reported to possess long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic ability, and the related molecular mechanisms have been well clarified. Here, we investigated the LC-PUFA biosynthesis capability of the congeneric rabbitfish S. guttatus. First, cDNAs of genes for four key enzymes related to LC-PUFA biosynthesis, namely Δ6Δ5 fatty acyl desaturase (fads2) (1335 bp; 445 aa), Δ4 fads2 (1335 bp; 445 aa), and elongation of very long chain fatty acid proteins (elovl5) (873 bp; 291 aa) and elovl4 (906 bp; 302 aa) were cloned from the liver of S. guttatus. The Δ6Δ5 fads2, Δ4 fads2 and elovl5 genes showed high expression in brain, liver, spleen, gallbladder, and intestine but relatively low expression in eye, whereas the elovl4 gene showed specific and high expression in eye. During embryogenesis, mRNA expression of Δ4 fads2 and elovl4 was detected from 8 h post-fertilization (hpf) and then maintained a high level to 24 hpf, while mRNA expression of Δ6Δ5 fads2 and elovl5 reached a peak at 14 hpf but then declined. In addition, ambient salinity (32 ppt and 20 ppt) exerted some regulatory influence on the expression of the four genes during embryogenesis. The levels of C18 PUFA precursors and, especially, PUFA and DHA of the embryos, decreased from 17 hpf to 24 hpf. These results suggested that S. guttatus, similar to the congeneric S. canaliculatus, would have capability for LC-PUFA biosynthesis, which is still not activated at the fertilized egg stage.
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Affiliation(s)
- Cuihong You
- Innovative Institute of Animal Healthy Breeding, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510222, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China
| | - Shuangshuang Miao
- Innovative Institute of Animal Healthy Breeding, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510222, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China
| | - Zhiyong Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China
| | - Siyuan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China
| | - Shuqi Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China
| | - Cuiying Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China
| | - Li Lin
- Innovative Institute of Animal Healthy Breeding, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510222, Guangdong, China
| | - Yanhua Huang
- Innovative Institute of Animal Healthy Breeding, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510222, Guangdong, China
| | - Meng Zhou
- Innovative Institute of Animal Healthy Breeding, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510222, Guangdong, China
| | - Yewei Dong
- Innovative Institute of Animal Healthy Breeding, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510222, Guangdong, China.
| | - Yuanyou Li
- College of Marine Sciences & University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on MBCE, South China Agricultural University, Guangzhou 510642, China.
| | - Ping Zhuang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
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19
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Nielsen H. Protein Sorting Prediction. Methods Mol Biol 2024; 2715:27-63. [PMID: 37930519 DOI: 10.1007/978-1-0716-3445-5_2] [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: 11/07/2023]
Abstract
Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global property-based, and homology-based prediction. In this chapter, the strengths and drawbacks of each of these approaches are described through many examples of methods that predict secretion, integration into membranes, or subcellular locations in general. The aim of this chapter is to provide a user-level introduction to the field with a minimum of computational theory.
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Affiliation(s)
- Henrik Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
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20
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Zhu M, Li X. Genome-wide identification of the glutamate receptor-like gene family in Vanilla planifolia and their response to Fusarium oxysporum infection. PLANT SIGNALING & BEHAVIOR 2023; 18:2204654. [PMID: 37096589 PMCID: PMC10132242 DOI: 10.1080/15592324.2023.2204654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glutamate receptor-like genes (GLRs) are essential for plant growth and development and for coping with environmental (biological and non-biological) stresses. In this study, 13 GLR members were identified in the Vanilla planifolia genome and attributed to two subgroups (Clade I and Clade III) based on their physical relationships. Cis-acting element analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated the GLR gene regulation's complexity and their functional diversity. Expression analysis revealed a relatively higher and more general expression pattern of Clade III members compared to the Clade I subgroup in tissues. Most GLRs showed significant differences in expression during Fusarium oxysporum infection. This suggested that GLRs play a critical role in the response of V. planifolia to pathogenic infection. These results provide helpful information for further functional research and crop improvement of VpGLRs.
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Affiliation(s)
- Miao Zhu
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China
| | - Xinran Li
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China
- CONTACT Xinran Li School of Biological Science and Technology, Liupanshui normal University, No.288 Minghu Road, Liupanshui, Guizhou, China
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21
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Mosqueda J, Hernández-Silva DJ, Vega-López MA, Vega-Rojas LJ, Beltrán R, Velasco-Elizondo A, Ramírez-Estudillo MDC, Fragoso-Saavedra M, Pérez-Almeida C, Hernández J, Melgoza-González EA, Hinojosa-Trujillo D, Mercado-Uriostegui MÁ, Mejía-López AS, Rivera-Ballesteros C, García-Gasca T. Evaluation of the humoral and mucosal immune response of a multiepitope vaccine against COVID-19 in pigs. Front Immunol 2023; 14:1276950. [PMID: 38179057 PMCID: PMC10765521 DOI: 10.3389/fimmu.2023.1276950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction This study evaluated the immune response to a multiepitope recombinant chimeric protein (CHIVAX) containing B- and T-cell epitopes of the SARS-CoV-2 spike's receptor binding domain (RBD) in a translational porcine model for pre-clinical studies. Methods We generated a multiepitope recombinant protein engineered to include six coding conserved epitopes from the RBD domain of the SARS-CoV-2 S protein. Pigs were divided into groups and immunized with different doses of the protein, with serum samples collected over time to determine antibody responses by indirect ELISA and antibody titration. Peptide recognition was also analyzed by Western blotting. A surrogate neutralization assay with recombinant ACE2 and RBDs was performed. Intranasal doses of the immunogen were also prepared and tested on Vietnamese minipigs. Results When the immunogen was administered subcutaneously, it induced specific IgG antibodies in pigs, and higher doses correlated with higher antibody levels. Antibodies from immunized pigs recognized individual peptides in the multiepitope vaccine and inhibited RBD-ACE2 binding for five variants of concern (VOC). Comparative antigen delivery methods showed that both, subcutaneous and combined subcutaneous/intranasal approaches, induced specific IgG and IgA antibodies, with the subcutaneous approach having superior neutralizing activity. CHIVAX elicited systemic immunity, evidenced by specific IgG antibodies in the serum, and local mucosal immunity, indicated by IgA antibodies in saliva, nasal, and bronchoalveolar lavage secretions. Importantly, these antibodies demonstrated neutralizing activity against SARS-CoV-2 in vitro. Discussion The elicited antibodies recognized individual epitopes on the chimeric protein and demonstrated the capacity to block RBD-ACE2 binding of the ancestral SARS-CoV-2 strain and four VOCs. The findings provide proof of concept for using multiepitope recombinant antigens and a combined immunization protocol to induce a neutralizing immune response against SARS-CoV-2 in the pig translational model for preclinical studies.
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Affiliation(s)
- Juan Mosqueda
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Diego Josimar Hernández-Silva
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Marco Antonio Vega-López
- Centro de Investigación y de Estudios Avanzados (CINVESTAV) del Instituto Politécnico Nacional, Departamento de Infectómica y Patogénesis Molecular, Laboratorio de Inmunobiología de las Mucosas, Ciudad de México, Mexico
| | - Lineth J. Vega-Rojas
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Rolando Beltrán
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Andrés Velasco-Elizondo
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - María del Carmen Ramírez-Estudillo
- Centro de Investigación y de Estudios Avanzados (CINVESTAV) del Instituto Politécnico Nacional, Departamento de Infectómica y Patogénesis Molecular, Laboratorio de Inmunobiología de las Mucosas, Ciudad de México, Mexico
| | - Mario Fragoso-Saavedra
- Centro de Investigación y de Estudios Avanzados (CINVESTAV) del Instituto Politécnico Nacional, Departamento de Infectómica y Patogénesis Molecular, Laboratorio de Inmunobiología de las Mucosas, Ciudad de México, Mexico
| | - Chyntia Pérez-Almeida
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Mexico
| | - Edgar A. Melgoza-González
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Mexico
| | - Diana Hinojosa-Trujillo
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Mexico
| | - Miguel Ángel Mercado-Uriostegui
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Alma Susana Mejía-López
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Carlos Rivera-Ballesteros
- Immunology and Vaccines Laboratory, Facultad de Ciencias Naturales, Universidad Autonoma de Queretaro, Carretera a Chichimequillas, Santiago de Querétaro, Querétaro, Mexico
| | - Teresa García-Gasca
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, Mexico
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22
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Danneskiold-Samsøe NB, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ. AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.531341. [PMID: 36993313 PMCID: PMC10055078 DOI: 10.1101/2023.03.16.531341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Secreted proteins play crucial roles in paracrine and endocrine signaling; however, identifying novel ligand-receptor interactions remains challenging. Here, we benchmarked AlphaFold as a screening approach to identify extracellular ligand-binding pairs using a structural library of single-pass transmembrane receptors. Key to the approach is the optimization of AlphaFold input and output for screening ligands against receptors to predict the most probable ligand-receptor interactions. Importantly, the predictions were performed on ligand-receptor pairs not used for AlphaFold training. We demonstrate high discriminatory power and a success rate of close to 90 % for known ligand-receptor pairs and 50 % for a diverse set of experimentally validated interactions. These results demonstrate proof-of-concept of a rapid and accurate screening platform to predict high-confidence cell-surface receptors for a diverse set of ligands by structural binding prediction, with potentially wide applicability for the understanding of cell-cell communication.
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Affiliation(s)
- Niels Banhos Danneskiold-Samsøe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, University of Copenhagen, Denmark
| | - Deniz Kavi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Silas Boye Nissen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Lianna W. Wat
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Laetitia Coassolo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Meng Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Katrin J. Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
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23
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Almanaa TN. Design of a novel multi-epitopes vaccine against Escherichia fergusonii: a pan-proteome based in- silico approach. Front Immunol 2023; 14:1332378. [PMID: 38143752 PMCID: PMC10739491 DOI: 10.3389/fimmu.2023.1332378] [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: 11/02/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Escherichia fergusonii a gram-negative rod-shaped bacterium in the Enterobacteriaceae family, infect humans, causing serious illnesses such as urinary tract infection, cystitis, biliary tract infection, pneumonia, meningitis, hemolytic uremic syndrome, and death. Initially treatable with penicillin, antibiotic misuse led to evolving resistance, including resistance to colistin, a last-resort drug. With no licensed vaccine, the study aimed to design a multi-epitope vaccine against E. fergusonii. The study started with the retrieval of the complete proteome of all known strains and proceeded to filter the surface exposed virulent proteins. Seventeen virulent proteins (4 extracellular, 4 outer membranes, 9 periplasmic) with desirable physicochemical properties were identified from the complete proteome of known strains. Further, these proteins were processed for B-cell and T-cell epitope mapping. Obtained epitopes were evaluated for antigenicity, allergenicity, solubility, MHC-binding, and toxicity and the filtered epitopes were fused by specific linkers and an adjuvant into a vaccine construct. Structure of the vaccine candidate was predicted and refined resulting in 78.1% amino acids in allowed regions and VERIFY3D score of 81%. Vaccine construct was docked with TLR-4, MHC-I, and MHC-II, showing binding energies of -1040.8 kcal/mol, -871.4 kcal/mol, and -1154.6 kcal/mol and maximum interactions. Further, molecular dynamic simulation of the docked complexes was carried out resulting in a significant stable nature of the docked complexes (high B-factor and deformability values, lower Eigen and high variance values) in terms of intermolecular binding conformation and interactions. The vaccine was also reported to stimulate a variety of immunological pathways after administration. In short, the designed vaccine revealed promising predictions about its immune protective potential against E. fergusonii infections however experimental validation is needed to validate the results.
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Affiliation(s)
- Taghreed N. Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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24
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Rangra S, Chakraborty R, Hasija Y, Aggarwal KK. A cystatin C similar protein from Musa acuminata that inhibits cathepsin B involved in rheumatoid arthritis using in silico approach and in vitro cathepsin B inhibition by protein extract. J Biomol Struct Dyn 2023; 41:10985-10998. [PMID: 37097972 DOI: 10.1080/07391102.2023.2203234] [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: 09/01/2022] [Accepted: 12/10/2022] [Indexed: 04/26/2023]
Abstract
Rheumatoid arthritis (RA) is an auto-immune disease that affects the synovial lining of the joints, causes synovitis and culminates to joint destruction. Cathepsin B is responsible for digesting unwanted proteins in extracellular matrix but its hyper expression could implicate in pathological diseases like RA. Available treatments for RA are classified into non-steroidal anti-inflammatory drugs (NSAIDs), disease-modifying anti-rheumatic drugs (DMARDs), and steroids, but the severe side effects associated with these drugs is one of concerns and cannot be ignored. Thus, any alternative therapy with minimum or no side effects would be a cornerstone. In our in silico studies a cystatin C similar protein (CCSP) has been identified from Musa acuminata that could effectively inhibit the cathepsin B activity. In silico and molecular dynamics studies showed that the identified CCSP and cathepsin B complex has binding energy -66.89 kcal/mol as compared to cystatin C - cathepsin B complex with binding energy of -23.38 kcal/mol. These results indicate that CCSP from Musa acuminata has better affinity towards cathepsin B as compared to its natural inhibitor cystatin C. Hence, CCSP may be suggested as an alternative therapeutic in combating RA by inhibiting its one of the key proteases cathepsin B. Further, in vitro experiments with fractionated protein extracts from Musa sp. peel inhibited cathepsin B to 98.30% at 300 µg protein concentration and its IC50 was found to be 45.92 µg indicating the presence of cathepsin B inhibitor(s) in protein extract of peel which was further confirmed by reverse zymography.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sabita Rangra
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - Kamal Krishan Aggarwal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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25
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Gidden Z, Oi C, Johnston EJ, Konieczna Z, Bhaskar H, Mendive-Tapia L, de Moliner F, Rosser SJ, Mochrie SGJ, Vendrell M, Horrocks MH, Regan L. Imaging Proteins Sensitive to Direct Fusions Using Transient Peptide-Peptide Interactions. NANO LETTERS 2023; 23:10633-10641. [PMID: 37916770 PMCID: PMC10683072 DOI: 10.1021/acs.nanolett.3c03780] [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: 10/03/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
Fluorescence microscopy enables specific visualization of proteins in living cells and has played an important role in our understanding of the protein subcellular location and function. Some proteins, however, show altered localization or function when labeled using direct fusions to fluorescent proteins, making them difficult to study in live cells. Additionally, the resolution of fluorescence microscopy is limited to ∼200 nm, which is 2 orders of magnitude larger than the size of most proteins. To circumvent these challenges, we previously developed LIVE-PAINT, a live-cell super-resolution approach that takes advantage of short interacting peptides to transiently bind a fluorescent protein to the protein-of-interest. Here, we successfully use LIVE-PAINT to image yeast membrane proteins that do not tolerate the direct fusion of a fluorescent protein by using peptide tags as short as 5-residues. We also demonstrate that it is possible to resolve multiple proteins at the nanoscale concurrently using orthogonal peptide interaction pairs.
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Affiliation(s)
- Zoe Gidden
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
| | - Curran Oi
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Emily J. Johnston
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- Centre
for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
| | - Zuzanna Konieczna
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Haresh Bhaskar
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Lorena Mendive-Tapia
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
- Centre
for
Inflammation Research, The University of
Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Fabio de Moliner
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
- Centre
for
Inflammation Research, The University of
Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Susan J. Rosser
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- Centre
for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
| | - Simon G. J. Mochrie
- Department
of Physics, Yale University, New Haven, Connecticut 06520, United States
- Integrated
Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Marc Vendrell
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
- Centre
for
Inflammation Research, The University of
Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Mathew H. Horrocks
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Lynne Regan
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- Centre
for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
- Integrated
Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
- Institute
of Quantitative Biology, Biochemistry and Biotechnology, Edinburgh, EH9 3FF, U.K.
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26
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Mizaeva T, Alieva K, Zulkarneev E, Kurpe S, Isakova K, Matrosova S, Borvinskaya E, Sukhovskaya I. Antibacterial Activity of Rainbow Trout Plasma: In Vitro Assays and Proteomic Analysis. Animals (Basel) 2023; 13:3565. [PMID: 38003182 PMCID: PMC10668809 DOI: 10.3390/ani13223565] [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: 10/09/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The objective of this study was to investigate the bactericidal activity of blood plasma from cultured rainbow trout obtained from two different fish farms. Plasma from trout naturally infected with the bacterial pathogen Flavobacterium psychrophilum was found to inhibit the growth of Aeromonas hydrophila in vitro. Incubation of A. hydrophila in bacteriostatic trout plasma resulted in agglutination and growth retardation, without causing massive damage to the cell membrane. The proteome of the plasma with high antimicrobial activity revealed an abundance of high-density apolipoproteins, some isoforms of immunoglobulins, complement components C1q and C4, coagulation factors, lectins, periostin, and hemoglobin. Analysis of trout proteins retained on A. hydrophila cells revealed the presence of fish immunoglobulins, lectins, and complement components on bacteria whose growth was inhibited, although the native membrane attack complex of immunised trout plasma did not assemble effectively, resulting in a weak bactericidal effect. Furthermore, this study examined the bacterial response to trout plasma and suggested that the protein synthesis pathway was the target of antimicrobial proteins from fish blood. Taken together, these findings illustrate the advantages of the affinity approach for understanding the role of plasma proteins in host defence against pathogens.
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Affiliation(s)
- Toita Mizaeva
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia; (T.M.); (K.A.)
| | - Kalimat Alieva
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia; (T.M.); (K.A.)
| | - Eldar Zulkarneev
- Plague Control Center, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 119121 Moscow, Russia;
| | - Stanislav Kurpe
- Institute of Biochemistry after H.Buniatyan National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
| | - Kseniya Isakova
- Northern Water Problems Institute of the Karelian Research Centre of the Russian Academy of Sciences, 185000 Petrozavodsk, Republic of Karelia, Russia;
| | - Svetlana Matrosova
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University, 185000 Petrozavodsk, Republic of Karelia, Russia;
| | | | - Irina Sukhovskaya
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University, 185000 Petrozavodsk, Republic of Karelia, Russia;
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, 185000 Petrozavodsk, Republic of Karelia, Russia
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27
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Shen Y, Jiang H, Canario AV, Chen T, Liu Y, Yang G, Meng X, Zhao J, Chen X. The fusion gene hsf5-rnf43 in Nile tilapia: A potential regulator in the maintenance of testis function and sexual differentiation. iScience 2023; 26:108284. [PMID: 38026183 PMCID: PMC10679895 DOI: 10.1016/j.isci.2023.108284] [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: 06/06/2023] [Revised: 08/27/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
We identified that the genes heat shock transcription factor 5 (hsf5) and ring finger protein 43 (rnf43) happened fusion in Nile tilapia (Oreochromis niloticus), called hsf5-rnf43, and provided the characteristic and functional analysis of hsf5-rnf43 gene in fish for the first time. Analysis of spatiotemporal expression showed that hsf5-rnf43 was specifically expressed in the testis and located in primary spermatocytes of adult Nile tilapia and gradually increased during testis development from 5 to 180 days after hatching. We also found DNA methylation regulated sex-biased expression of hsf5-rnf43 in the early development of Nile tilapia, and was affected by high temperature during the thermosensitive period of Nile tilapia sex differentiation. Therefore, we first reported that the fusion gene hsf5-rnf43 was sex-biased expressed in the testis regulated by DNA methylation and affected by high temperature, which may be involved in the maintenance of testis function and sex differentiation of Nile tilapia.
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Affiliation(s)
- Yawei Shen
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Hewei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Adelino V.M. Canario
- CCMAR/CIMAR Centre for Marine Sciences, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Tiantian Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yufei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Guokun Yang
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Xiaolin Meng
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Jinliang Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaowu Chen
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
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28
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Cleary KE, Pelagalli C, Cassford M, Berry N, Aguas E, Kim B, deCarvalho T, Jacobs-Sera D, Caruso SM, Cornely K. Genome sequence of Streptomyces BM cluster phage Frankenweenie. Microbiol Resour Announc 2023; 12:e0059223. [PMID: 37830805 PMCID: PMC10652959 DOI: 10.1128/mra.00592-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023] Open
Abstract
Frankenweenie is a newly isolated bacteriophage that infects Streptomyces scabiei RL-34. Frankenweenie was discovered in Gaithersburg, MD, and has 366 genes comprising a 200,048-bp genome. Frankenweenie is grouped in cluster BM and is predicted to possess a unique tailspike protein that potentially widens its host range.
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Affiliation(s)
- Katherine E. Cleary
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Charles Pelagalli
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marly Cassford
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Nathan Berry
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Elizabeth Aguas
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Brandon Kim
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Tagide deCarvalho
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
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29
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Vaidya K, Rodrigues G, Gupta S, Devarajan A, Yeolekar M, Madhusudhan MS, Kamat SS. Identification of sequence determinants for the ABHD14 enzymes. Proteins 2023. [PMID: 37974539 DOI: 10.1002/prot.26632] [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: 06/12/2023] [Revised: 10/14/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Over the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on their protein sequences and available biochemical studies, enzymes with similar catalytic mechanisms have been clustered together into an enzyme superfamily. Typically, enzymes within a superfamily have similar overall three-dimensional structures, conserved catalytic residues, but large variations in substrate recognition sites and residues to accommodate the diverse biochemical reactions that are catalyzed within the superfamily. The serine hydrolases are an excellent example of such an enzyme superfamily. Based on known enzymatic activities and protein sequences, they are split almost equally into the serine proteases and metabolic serine hydrolases. Within the metabolic serine hydrolases, there are two outlying members, ABHD14A and ABHD14B, that have high sequence similarity, but their biological functions remained cryptic till recently. While ABHD14A still lacks any functional annotation to date, we recently showed that ABHD14B functions as a lysine deacetylase in mammals. Given their high sequence similarity, automated databases often wrongly assign ABHD14A and ABHD14B as the same enzyme, and therefore, annotating functions to them in various organisms has been problematic. In this article, we present a bioinformatics study coupled with biochemical experiments, which identifies key sequence determinants for both ABHD14A and ABHD14B, and enable better classification for them. In addition, we map these enzymes on an evolutionary timescale and provide a much-wanted resource for studying these interesting enzymes in different organisms.
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Affiliation(s)
- Kaveri Vaidya
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Golding Rodrigues
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Sonali Gupta
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Archit Devarajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Mihika Yeolekar
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - M S Madhusudhan
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
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Elalouf A, Kedarya T, Elalouf H, Rosenfeld A. Computational design and evaluation of mRNA- and protein-based conjugate vaccines for influenza A and SARS-CoV-2 viruses. J Genet Eng Biotechnol 2023; 21:120. [PMID: 37966525 PMCID: PMC10651613 DOI: 10.1186/s43141-023-00574-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Israel confirmed the first case of "flurona"-a co-infection of seasonal flu (IAV) and SARS-CoV-2 in an unvaccinated pregnant woman. This twindemic has been confirmed in multiple countries and underscores the importance of managing respiratory viral illnesses. RESULTS The novel conjugate vaccine was designed by joining four hemagglutinin, three neuraminidase, and four S protein of B-cell epitopes, two hemagglutinin, three neuraminidase, and four S proteins of MHC-I epitopes, and three hemagglutinin, nine neuraminidase, and five S proteins of MHC-II epitopes with linkers and adjuvants. The constructed conjugate vaccine was found stable, non-toxic, non-allergic, and antigenic with 0.6466 scores. The vaccine contained 14.87% alpha helix, 29.85% extended strand, 9.64% beta-turn, and 45.64% random coil, which was modeled to a 3D structure with 94.7% residues in the most favored region of the Ramachandran plot and Z-score of -3.33. The molecular docking of the vaccine with TLR3 represented -1513.9 kcal/mol of binding energy with 39 hydrogen bonds and 514 non-bonded contacts, and 1.582925e-07 of eigenvalue complex. Immune stimulation prediction showed the conjugate vaccine could activate T and B lymphocytes to produce high levels of Th1 cytokines and antibodies. CONCLUSION The in silico-designed vaccine against IAV and SARS-CoV-2 showed good population coverage and immune response with predicted T- and B-cell epitopes, favorable molecular docking, Ramachandran plot results, and good protein expression. It fulfilled safety criteria, indicating potential for preclinical studies and experimental clinical trials.
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Affiliation(s)
- Amir Elalouf
- Department of Management, Bar-Ilan University, 5290002, Ramat Gan, Israel.
| | - Tomer Kedarya
- Department of Management, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Hadas Elalouf
- Information Science Department, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Ariel Rosenfeld
- Information Science Department, Bar-Ilan University, 5290002, Ramat Gan, Israel
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Hongo Y, Hano T, Yamaguchi H, Tomaru Y. Transcriptional responses of the marine diatom Chaetoceros tenuissimus to phosphate deficiency. Gene 2023; 884:147695. [PMID: 37549856 DOI: 10.1016/j.gene.2023.147695] [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: 06/07/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The planktonic diatom Chaetoceros tenuissimus sometimes forms blooms in coastal surface waters where dissolved inorganic phosphorus (P) is typically deficient. To understand the molecular mechanisms for survival under P-deficient conditions, we compared whole transcripts and metabolites with P-sufficient conditions using stationary growth cells. Under P-deficient conditions, cell numbers and photosynthetic activities decreased as cells entered the stationary growth phase, with downregulation of transcripts related to the Calvin cycle and glycolysis/gluconeogenesis. Therefore, metabolites varied across nutritional conditions. Alkaline phosphatase, phosphodiesterase, phytase, phosphate transporter, and transcription factor genes were drastically upregulated under dissolved inorganic P deficiency. Genes related to phospholipid degradation and nonphospholipid synthesis were also upregulated. These results indicate that C. tenuissimus rearranges its membrane composition from phospholipids to nonphospholipids to conserve phosphate. To endure in P-deficient conditions, C. tenuissimus modifies its gene responses, suggesting a potential survival strategy in nature.
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Affiliation(s)
- Yuki Hongo
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan.
| | - Takeshi Hano
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
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32
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Alsubaiyel AM, Bukhari SI. Computational exploration and design of a multi-epitopes vaccine construct against Chlamydia psittaci. J Biomol Struct Dyn 2023:1-17. [PMID: 37897717 DOI: 10.1080/07391102.2023.2268173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
Chlamydia psittaci is an intracellular pathogen and causes variety of deadly infections in humans. Antibiotics are effective against C. psittaci however high percentage of resistant strains have been reported in recent times. As there is no licensed vaccine, we used in-silico techniques to design a multi-epitopes vaccine against C. psittaci. Following a step-wise protocol, the proteome of available 26 strains was retrieved and filtered for subcellular localized proteins. Five proteins were selected (2 extracellular and 3 outer membrane) and were further analyzed for B-cell and T-cell epitopes prediction. Epitopes were further checked for antigenicity, solubility, stability, toxigenicity, allergenicity, and adhesive properties. Filtered epitopes were linked via linkers and the 3D structure of the designed vaccine construct was predicted. Binding of the designed vaccine with immune receptors: MHC-I, MHC-II, and TLR-4 was analyzed, which resulted in docking energy scores of -4.37 kcal/mol, -0.20 kcal/mol and -22.38 kcal/mol, respectively. Further, the docked complexes showed stable dynamics with a maximum value of vaccine-MHC-I complex (7.8 Å), vaccine-MHC-II complex (6.2 Å) and vaccine-TLR4 complex (5.2 Å). As per the results, the designed vaccine construct reported robust immune responses to protect the host against C. psittaci infections. In the study, the C. psittaci proteomes were considered in pan-genome analysis to extract core proteins. The pan-genome analysis was conducted using bacterial pan-genome analysis (BPGA) software. The core proteins were checked further for non-redundant proteins using a CD-Hit server. Surface localized proteins were investigated using PSORTb v 3.0. The surface proteins were BLASTp against Virulence Factor Data Base (VFDB) to predict virulent factors. Antigenicity prediction of the shortlisted proteins was further done using VAXIGEN v 2.0. The epitope mapping was done using the immune epitope database (IEDB). A multi-epitopes vaccine was built and a 3D structure was generated using 3Dprot online server. The docking analysis of the designed vaccine with immune receptors was carried out using PATCHDOCK. Molecular dynamics and post-simulation analyses were carried out using AMBER v20 to decipher the dynamics stability and intermolecular binding energies of the docked complexes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amal M Alsubaiyel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Sarah I Bukhari
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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33
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Xie Y, Shi L, Cheng K, Li Y, Yu S. Host Recognition and Specific Infection of Endomelanconiopsis endophytica during Early Infection. J Fungi (Basel) 2023; 9:1040. [PMID: 37888296 PMCID: PMC10607883 DOI: 10.3390/jof9101040] [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: 09/27/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of Endomelanconiopsis endophytica strain LS29, a host-specific pathogen of the common subtropical tree Castanopsis fissa. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of E. endophytica on C. fissa during early infection, we found that E. endophytica repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plant, but most of them showed a significantly opposing expression regulation trend after 24 hpi, indicating that 24 hpi represents a key time point between host recognition and specific infection. Furthermore, a comparison of isoenzymes showed that only a few effectors were identified as specific effectors, which were involved in hydrolyzing the compounds of the plant cell wall and releasing fatty acids during the early infection of C. fissa. Our results determined host recognition timing and identified a specific catalog of effectors, which are crucial for revealing the molecular mechanism of host-specific pathogenesis.
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Affiliation(s)
- Yan Xie
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liuqing Shi
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Keke Cheng
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yang Li
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Naranjo-Galvis CA, McLeod R, Gómez-Marín JE, de-la-Torre A, Rocha-Roa C, Cardona N, Sepúlveda-Arias JC. Genetic Variations in the Purinergic P2X7 Receptor Are Associated with the Immune Response to Ocular Toxoplasmosis in Colombia. Microorganisms 2023; 11:2508. [PMID: 37894166 PMCID: PMC10609425 DOI: 10.3390/microorganisms11102508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 10/29/2023] Open
Abstract
Ocular toxoplasmosis (OT) is characterized by inflammation within the eye and is the most recognized clinical manifestation of toxoplasmosis. The objective of this study was to identify new single-nucleotide polymorphisms (SNPs) in the P2RX7 gene that may have significance in the immune response to OT in Colombian patients. A case-control study was conducted to investigate the associations between SNPs (rs1718119 and rs2230912) in the P2RX7 gene and OT in 64 Colombian patients with OT and 64 controls. Capillary electrophoresis was used to analyze the amplification products, and in silico algorithms were employed to predict deleterious SNPs. Stability analysis of amino acid changes indicated that both mutations could lead to decreased protein structure stability. A nonsynonymous SNP, Gln460Arg, located in the long cytoplasmic tail of the receptor, showed a significant association with OT (Bonferroni correction (BONF) = 0.029; odds ratio OR = 3.46; confidence interval CI: 1.05 to 11.39), while no significant association between rs1718119 and OT risk was observed. Based on the 3D structure analysis of the P2RX7 protein trimer, it is hypothesized that an increase in the flexibility of the cytoplasmic domain of this receptor could alter its function. This SNP could potentially serve as a biomarker for identifying Colombian patients at risk of OT.
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Affiliation(s)
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences and Pediatrics (Infectious Diseases), The University of Chicago, Chicago, IL 60637, USA
| | - Jorge Enrique Gómez-Marín
- Grupo GEPAMOL, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia 630001, Colombia
| | - Alejandra de-la-Torre
- Grupo GEPAMOL, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia 630001, Colombia
- Grupo de Investigación en Neurociencias (NeURos), Neurovitae Research Center, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá 110111, Colombia
| | - Cristian Rocha-Roa
- Grupo GEPAMOL, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia 630001, Colombia
| | - Néstor Cardona
- Grupo GEPAMOL, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia 630001, Colombia
- Facultad de Odontología, Universidad Antonio Nariño, Armenia 630004, Colombia
| | - Juan Carlos Sepúlveda-Arias
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
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35
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Lee SJ, Kim J, Choi EK, Jo E, Cho M, Kim JH, Park H. A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus. Sci Data 2023; 10:657. [PMID: 37752129 PMCID: PMC10522714 DOI: 10.1038/s41597-023-02561-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: 06/22/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023] Open
Abstract
The blackfin Icefish (Chaenocephalus aceratus) belongs to the family Channichthyidae and the suborder Notothenioidei which lives in the Antarctic. We corrected the mis-scaffolds in the previous linkage map results by Hi-C analysis to obtain improved results for chromosome-level genome assembly. The final assembly analysis resulted in a total of 3,135 scaffolds, a genome size of 1,065.72 Mb, and an N50 of 33.46 Mb. 820.24 Mb, representing 88.88% of the total genome, is anchored to 24 chromosomes. The final gene set of 38,024 genes, including AFGPs, was annotated using RNA evidence, proteins, and ab-initio predictions. The complete percentage of BUSCO analysis is 92.7%. In this study, we aim to contribute to the study of polar fishes by improving the genome sequences of the blackfin icefish with the AFGP genes belonging to the Notothenoidei.
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Affiliation(s)
- Seung Jae Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Jinmu Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Eun Kyung Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Euna Jo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Minjoo Cho
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Jeong-Hoon Kim
- Korea Polar Research Institute (KOPRI), Yeonsu-gu, Incheon, Korea
| | - Hyun Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.
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36
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Fakhri AM, Warner MH, DeGiorgis JA, Cornely K. Mycobacteriophage Rita: a cluster F1 phage discovered in North Easton, Massachusetts. Microbiol Resour Announc 2023; 12:e0051023. [PMID: 37638726 PMCID: PMC10508093 DOI: 10.1128/mra.00510-23] [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: 06/13/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Mycobacteriophage Rita infects Mycobacterium smegmatis mc2155 and was isolated from a soil sample collected in North Easton, Massachusetts. Assigned to cluster F1 based on sequence similarity to other phages in the same cluster, Rita has a 58,771 bp genome and encodes 104 genes. Rita is 98% similar to phage Bipolar.
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Affiliation(s)
- Anna M. Fakhri
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marcie H. Warner
- Department of Natural Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
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37
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Xie Q, On Lee S, Vissamsetti N, Guo S, Johnson ME, Fried SD. Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface. Angew Chem Int Ed Engl 2023; 62:e202305178. [PMID: 37469298 DOI: 10.1002/anie.202305178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/28/2023] [Accepted: 07/18/2023] [Indexed: 07/21/2023]
Abstract
Protein-based biomaterials have played a key role in tissue engineering, and additional exciting applications as self-healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production of various fibrous proteins from microbes have been demonstrated; however, the resulting proteins typically must then be purified and processed by humans to form usable fibers and materials. Here, we show that the Gram-positive bacterium Bacillus subtilis can be programmed to secrete silk through its translocon via an orthogonal signal peptide/peptidase pair. Surprisingly, we discover that this translocation mechanism drives the silk proteins to assemble into fibers spontaneously on the cell surface, in a process we call secretion-catalyzed assembly (SCA). Secreted silk fibers form self-healing hydrogels with minimal processing. Alternatively, the fibers retained on the membrane provide a facile route to create engineered living materials from Bacillus cells. This work provides a blueprint to achieve autonomous assembly of protein biomaterials in useful morphologies directly from microbial factories.
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Affiliation(s)
- Qi Xie
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Sea On Lee
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Nitya Vissamsetti
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Sikao Guo
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Margaret E Johnson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 21218, Baltimore, MD, USA
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38
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Jiang H, Zhang Z. Immune response in influenza virus infection and modulation of immune injury by viral neuraminidase. Virol J 2023; 20:193. [PMID: 37641134 PMCID: PMC10463456 DOI: 10.1186/s12985-023-02164-2] [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: 02/10/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Influenza A viruses cause severe respiratory illnesses in humans and animals. Overreaction of the innate immune response to influenza virus infection results in hypercytokinemia, which is responsible for mortality and morbidity. The influenza A virus surface glycoprotein neuraminidase (NA) plays a vital role in viral attachment, entry, and virion release from infected cells. NA acts as a sialidase, which cleaves sialic acids from cell surface proteins and carbohydrate side chains on nascent virions. Here, we review progress in understanding the role of NA in modulating host immune response to influenza virus infection. We also discuss recent exciting findings targeting NA protein to interrupt influenza-induced immune injury.
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Affiliation(s)
- Hongyu Jiang
- The People's Hospital of Dayi Country, Chengdu, Sichuan, China
- Inflammation and Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China
| | - Zongde Zhang
- The People's Hospital of Dayi Country, Chengdu, Sichuan, China.
- Inflammation and Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China.
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39
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Zhang G, Han L, Li Z, Chen Y, Li Q, Wang S, Shi H. Screening of immunogenic proteins and evaluation of vaccine candidates against Mycoplasma synoviae. NPJ Vaccines 2023; 8:121. [PMID: 37582795 PMCID: PMC10427712 DOI: 10.1038/s41541-023-00721-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023] Open
Abstract
Mycoplasma synoviae (M. synoviae) is a serious avian pathogen that causes significant economic losses to chicken and turkey producers worldwide. The currently available live attenuated and inactivated vaccines provide limited protection. The objective of this study was to identify potential subunit vaccine candidates using immunoproteomics and reverse vaccinology analyses and to evaluate their preliminary protection. Twenty-four candidate antigens were identified, and five of them, namely RS01790 (a putative sugar ABC transporter lipoprotein), BMP (a substrate-binding protein of the BMP family ABC transporter), GrpE (a nucleotide exchange factor), RS00900 (a putative nuclease), and RS00275 (an uncharacterized protein), were selected to evaluate their immunogenicity and preliminary protection. The results showed that all five antigens had good immunogenicity, and they were localized on the M. synoviae cell membrane. The antigens induced specific humoral and cellular immune responses, and the vaccinated chickens exhibited significantly greater body weight gain and lower air sac lesion scores and tracheal mucosal thicknesses. Additionally, the vaccinated chickens had lower M. synoviae loads in throat swabs than non-vaccinated chickens. The protective effect of the RS01790, BMP, GrpE, and RS00900 vaccines was better than that of the RS00275 vaccine. In conclusion, our study demonstrates the potential of subunit vaccines as a new approach to developing M. synoviae vaccines, providing new ideas for controlling the spread of M. synoviae worldwide.
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Affiliation(s)
- Guihua Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Lejiabao Han
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Zewei Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yifei Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Shifeng Wang
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611-0880, USA
| | - Huoying Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University (JIRLAAPS), Yangzhou, China.
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40
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Li R, Ma XY, Zhang YJ, Zhang YJ, Zhu H, Shao SN, Zhang DD, Klosterman SJ, Dai XF, Subbarao KV, Chen JY. Genome-wide identification and analysis of a cotton secretome reveals its role in resistance against Verticillium dahliae. BMC Biol 2023; 21:166. [PMID: 37542270 PMCID: PMC10403859 DOI: 10.1186/s12915-023-01650-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: 03/20/2023] [Accepted: 06/13/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND The extracellular space between the cell wall and plasma membrane is a battlefield in plant-pathogen interactions. Within this space, the pathogen employs its secretome to attack the host in a variety of ways, including immunity manipulation. However, the role of the plant secretome is rarely studied for its role in disease resistance. RESULTS Here, we examined the secretome of Verticillium wilt-resistant Gossypium hirsutum cultivar Zhongzhimian No.2 (ZZM2, encoding 95,327 predicted coding sequences) to determine its role in disease resistance against the wilt causal agent, Verticillium dahliae. Bioinformatics-driven analyses showed that the ZZM2 genome encodes 2085 secreted proteins and that these display disequilibrium in their distribution among the chromosomes. The cotton secretome displayed differences in the abundance of certain amino acid residues as compared to the remaining encoded proteins due to the localization of these putative proteins in the extracellular space. The secretome analysis revealed conservation for an allotetraploid genome, which nevertheless exhibited variation among orthologs and comparable unique genes between the two sub-genomes. Secretome annotation strongly suggested its involvement in extracellular stress responses (hydrolase activity, oxidoreductase activity, and extracellular region, etc.), thus contributing to resistance against the V. dahliae infection. Furthermore, the defense response genes (immunity marker NbHIN1, salicylic acid marker NbPR1, and jasmonic acid marker NbLOX4) were activated to varying degrees when Nicotina benthamiana leaves were agro-infiltrated with 28 randomly selected members, suggesting that the secretome plays an important role in the immunity response. Finally, gene silencing assays of 11 members from 13 selected candidates in ZZM2 displayed higher susceptibility to V. dahliae, suggesting that the secretome members confer the Verticillium wilt resistance in cotton. CONCLUSIONS Our data demonstrate that the cotton secretome plays an important role in Verticillium wilt resistance, facilitating the development of the resistance gene markers and increasing the understanding of the mechanisms regulating disease resistance.
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Affiliation(s)
- Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Xi-Yue Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ye-Jing Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - He Zhu
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
- The Cotton Research Center of Liaoning Academy of Agricultural Sciences, National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, Liaoning Provincial Institute of Economic Crops, Liaoyang, 111000, China
| | - Sheng-Nan Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis c/o United States Agricultural Research Station, Salinas, CA, USA.
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Wu Y, Zhang B, Liu S, Zhao Z, Ren W, Chen L, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Han F, Zhang Y. A Whole-Genome Assembly for Hyaloperonospora parasitica, A Pathogen Causing Downy Mildew in Cabbage ( Brassica oleracea var. capitata L.). J Fungi (Basel) 2023; 9:819. [PMID: 37623590 PMCID: PMC10456066 DOI: 10.3390/jof9080819] [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: 05/25/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Hyaloperonospora parasitica is a global pathogen that can cause leaf necrosis and seedling death, severely threatening the quality and yield of cabbage. However, the genome sequence and infection mechanisms of H. parasitica are still unclear. Here, we present the first whole-genome sequence of H. parasitica isolate BJ2020, which causes downy mildew in cabbage. The genome contains 4631 contigs and 9991 protein-coding genes, with a size of 37.10 Mb. The function of 6128 genes has been annotated. We annotated the genome of H. parasitica strain BJ2020 using databases, identifying 2249 PHI-associated genes, 1538 membrane transport proteins, and 126 CAZy-related genes. Comparative analyses between H. parasitica, H.arabidopsidis, and H. brassicae revealed dramatic differences among these three Brassicaceae downy mildew pathogenic fungi. Comprehensive genome-wide clustering analysis of 20 downy mildew-causing pathogens, which infect diverse crops, elucidates the closest phylogenetic affinity between H. parasitica and H. brassicae, the causative agent of downy mildew in Brassica napus. These findings provide important insights into the pathogenic mechanisms and a robust foundation for further investigations into the pathogenesis of H. parasitica BJ2020.
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Affiliation(s)
- Yuankang Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Bin Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Shaobo Liu
- China Vegetable Biotechnology (Shouguang) Co., Ltd., Shouguang 262700, China; (S.L.); (Z.Z.)
| | - Zhiwei Zhao
- China Vegetable Biotechnology (Shouguang) Co., Ltd., Shouguang 262700, China; (S.L.); (Z.Z.)
| | - Wenjing Ren
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Li Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
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Chen Y, Li S, Huang X, Wang C, Pan Y, Xiang Q, Feng Z, Fei L, Wu Y, Ruan Z, An Y, Chen Y. Tetraspan MS4A6D is a coreceptor of MHC class II antigen (MHC-II) that promotes macrophages-derived inflammation. Mol Immunol 2023; 160:121-132. [PMID: 37429063 DOI: 10.1016/j.molimm.2023.07.003] [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: 01/04/2023] [Revised: 05/18/2023] [Accepted: 07/02/2023] [Indexed: 07/12/2023]
Abstract
Our previous research demonstrated that the tetraspan MS4A6D is an adapter of VSIG4 that controls NLRP3 inflammasome activation (Sci Adv. 2019: eaau7426); however, the expression, distribution and biofunction of MS4A6D are still poorly understood. Here, we showed that MS4A6D is restricted to mononuclear phagocytes and that its gene transcript is controlled by the transcription factor NK2 homeobox-1 (NKX2-1). Ms4a6d-deficient (Ms4a6d-/-) mice showed normal macrophage development but manifested a greater survival advantage against endotoxin (lipopolysaccharide) challenge. Mechanistically, MS4A6D homodimers crosslinked with MHC class II antigen (MHC-II) to form a surface signaling complex under acute inflammatory conditions. MHC-II occupancy triggered Tyr241 phosphorylation in MS4A6D, leading to activation of SYK-CREB signaling cascades, further resulting in augmenting the transcription of proinflammatory genes (Il1b, Il6 and Tnfa) and amplifying the secretion of mitochondrial reactive oxygen species (mtROS). Deletion of Tyr241 or interruption of Cys237-mediated MS4A6D homodimerization in macrophages alleviated inflammation. Importantly, both Ms4a6dC237G and Ms4a6dY241G mutation mice phenocopied Ms4a6d-/- animals to prevent endotoxin lethality, highlighting MS4A6D as a novel target for treating macrophage-associated disorders.
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Affiliation(s)
- Yue Chen
- Institute of Medicine, Southwest University, Chongqing 400033, China
| | - Sirui Li
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China
| | - Xiaoyong Huang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China
| | - Chenhui Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China; Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yue Pan
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China
| | - Qun Xiang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China; Chongqing International Institute for Immunology, Chongqing 400026, China
| | - Zeqing Feng
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China; Chongqing International Institute for Immunology, Chongqing 400026, China
| | - Lei Fei
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China
| | - Zhihua Ruan
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400038, China.
| | - Yunfei An
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, China.
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Guo WH, Zhu YJ, Haimiti G, Xie XR, Niu C, Li M, Shi J, Yin ZW, Yu MK, Ding JB, Zhang FB. Bioinformatics-based design of a fusion vaccine with CTLA-4 variable region to combat Brucella. Braz J Med Biol Res 2023; 56:e12938. [PMID: 37493775 PMCID: PMC10361638 DOI: 10.1590/1414-431x2023e12938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Brucellosis has become a global zoonotic disease, seriously endangering the health of people all over the world. Vaccination is an effective strategy for protection against Brucella infection in livestock in developed countries. However, current vaccines are pathogenic to humans and pregnant animals, which limits their use. Therefore, it is very important to improve the safety and immune protection of Brucella vaccine. In this study, different bioinformatics approaches were carried out to predict the physicochemical properties, T/B epitope, and tertiary structure of Omp2b and Omp31. Then, these two proteins were sequentially linked, and the Cytotoxic T lymphocyte associated antigen-4 (CTLA-4) variable region was fused to the N-terminal of the epitope sequence. In addition, molecular docking was performed to show that the structure of the fusion protein vaccine had strong affinity with B7 (B7-1, B7-2). This study showed that the designed vaccine containing CTLA-4 had high potency against Brucella, which could provide a reference for the future development of efficient brucellosis vaccines.
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Affiliation(s)
- W H Guo
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Y J Zhu
- Department of Reproductive Assistance, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - G Haimiti
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - X R Xie
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - C Niu
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - M Li
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - J Shi
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Z W Yin
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - M K Yu
- School of Life Science and Technology, Southeast University, Nanjing, China
| | - J B Ding
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - F B Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Chen C, Dong S, Yu Z, Qiao Y, Li J, Ding X, Li R, Lin J, Bayer EA, Liu YJ, Cui Q, Feng Y. Essential autoproteolysis of bacterial anti-σ factor RsgI for transmembrane signal transduction. SCIENCE ADVANCES 2023; 9:eadg4846. [PMID: 37418529 PMCID: PMC10328401 DOI: 10.1126/sciadv.adg4846] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/06/2023] [Indexed: 07/09/2023]
Abstract
Autoproteolysis has been discovered to play key roles in various biological processes, but functional autoproteolysis has been rarely reported for transmembrane signaling in prokaryotes. In this study, an autoproteolytic effect was discovered in the conserved periplasmic domain of anti-σ factor RsgIs from Clostridium thermocellum, which was found to transmit extracellular polysaccharide-sensing signals into cells for regulation of the cellulosome system, a polysaccharide-degrading multienzyme complex. Crystal and NMR structures of periplasmic domains from three RsgIs demonstrated that they are different from all known proteins that undergo autoproteolysis. The RsgI-based autocleavage site was located at a conserved Asn-Pro motif between the β1 and β2 strands in the periplasmic domain. This cleavage was demonstrated to be essential for subsequent regulated intramembrane proteolysis to activate the cognate SigI, in a manner similar to that of autoproteolysis-dependent activation of eukaryotic adhesion G protein-coupled receptors. These results indicate the presence of a unique prevalent type of autoproteolytic phenomenon in bacteria for signal transduction.
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Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoli Yu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yichen Qiao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renmin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Edward A. Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8499000, Israel
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Zhang W, Yang Q, Yang L, Li H, Zhou W, Meng J, Hu Y, Wang L, Kang R, Li H, Ding S, Li G. High-Quality Nuclear Genome and Mitogenome of Bipolaris sorokiniana LK93, a Devastating Pathogen Causing Wheat Root Rot. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:452-456. [PMID: 36802869 DOI: 10.1094/mpmi-09-22-0196-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Bipolaris sorokiniana, one of the most devastating hemibiotrophic fungal pathogens, causes root rot, crown rot, leaf blotching, and black embryos of gramineous crops worldwide, posing a serious threat to global food security. However, the host-pathogen interaction mechanism between B. sorokiniana and wheat remains poorly understood. To facilitate related studies, we sequenced and assembled the genome of B. sorokiniana LK93. Nanopore long reads and next generation sequencing short reads were applied in the genome assembly, and the final 36.4-Mb genome assembly contains 16 contigs with the contig N50 of 2.3 Mb. Subsequently, we annotated 11,811 protein-coding genes. Of these, 10,620 were functional genes, 258 of which were identified as secretory proteins, including 211 predicted effectors. Additionally, the 111,581-bp mitogenome of LK93 was assembled and annotated. The LK93 genomes presented in this study will facilitate research in the B. sorokiniana-wheat pathosystem for better control of crop diseases. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Wanying Zhang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qun Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyang Li
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Wenqing Zhou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaxing Meng
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yanfeng Hu
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Limin Wang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Ruijiao Kang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Honglian Li
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Shengli Ding
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Guotian Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
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Wang G, Yin H, Zhao T, Yang D, Jia S, Qiao C. De novo transcriptome assembly of Aureobasidium melanogenum CGMCC18996 to analyze the β-poly(L-malic acid) biosynthesis pathway under the CaCO3 addition. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Saikat ASM. Computational approaches for molecular characterization and structure-based functional elucidation of a hypothetical protein from Mycobacterium tuberculosis. Genomics Inform 2023; 21:e25. [PMID: 37415455 PMCID: PMC10326535 DOI: 10.5808/gi.23001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 07/08/2023] Open
Abstract
Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.
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Affiliation(s)
- Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
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Wang Y, Ruan L, Li R. GPI-anchored Gas1 protein regulates cytosolic proteostasis in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542479. [PMID: 37292646 PMCID: PMC10245992 DOI: 10.1101/2023.05.26.542479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Decline in protein homeostasis (proteostasis) is a hallmark of cellular aging and aging-related diseases. Maintaining a balanced proteostasis requires a complex network of molecular machineries that govern protein synthesis, folding, localization, and degradation. Under proteotoxic stress, misfolded proteins that accumulate in cytosol can be imported into mitochondria for degradation via 'mitochondrial as guardian in cytosol' (MAGIC) pathway. Here we report an unexpected role of yeast Gas1, a cell wall-bound glycosylphosphatidylinositol (GPI)-anchored β-1,3-glucanosyltransferase, in differentially regulating MAGIC and ubiquitin-proteasome system (UPS). Deletion of Gas1 inhibits MAGIC but elevates polyubiquitination and UPS-mediated protein degradation. Interestingly, we found that Gas1 exhibits mitochondrial localization attributed to its C-terminal GPI anchor signal. But this mitochondria-associated GPI anchor signal is not required for mitochondrial import and degradation of misfolded proteins via MAGIC. By contrast, catalytic inactivation of Gas1 via the gas1E161Q mutation inhibits MAGIC but not its mitochondrial localization. These data suggest that the glucanosyltransferase activity of Gas1 is important for regulating cytosolic proteostasis.
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Affiliation(s)
- Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine; Baltimore, MD 21287, USA
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore 117411, Singapore
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Wang Q, Dicke M, Haverkamp A. Sympatric Pieris butterfly species exhibit a high conservation of chemoreceptors. Front Cell Neurosci 2023; 17:1155405. [PMID: 37252192 PMCID: PMC10210156 DOI: 10.3389/fncel.2023.1155405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sensory processes have often been argued to play a central role in the selection of ecological niches and in the formation of new species. Butterflies are among the best studied animal groups with regards to their evolutionary and behavioral ecology and thereby offer an attractive system to investigate the role of chemosensory genes in sympatric speciation. We focus on two Pieris butterflies with overlapping host-plant ranges: P. brassicae and P. rapae. Host-plant choice in lepidopterans is largely based on their olfactory and gustatory senses. Although the chemosensory responses of the two species have been well characterized at the behavioral and physiological levels, little is known about their chemoreceptor genes. Here, we compared the chemosensory genes of P. brassicae and P. rapae to investigate whether differences in these genes might have contributed to their evolutionary separation. We identified a total of 130 and 122 chemoreceptor genes in the P. brassicae genome and antennal transcriptome, respectively. Similarly, 133 and 124 chemoreceptors were identified in the P. rapae genome and antennal transcriptome. We found some chemoreceptors being differentially expressed in the antennal transcriptomes of the two species. The motifs and gene structures of chemoreceptors were compared between the two species. We show that paralogs share conserved motifs and orthologs have similar gene structures. Our study therefore found surprisingly few differences in the numbers, sequence identities and gene structures between the two species, indicating that the ecological differences between these two butterflies might be more related to a quantitative shift in the expression of orthologous genes than to the evolution of novel receptors as has been found in other insects. Our molecular data supplement the wealth of behavioral and ecological studies on these two species and will thereby help to better understand the role of chemoreceptor genes in the evolution of lepidopterans.
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Andov B, Boulaflous-Stevens A, Pain C, Mermet S, Voisin M, Charrondiere C, Vanrobays E, Tutois S, Evans DE, Kriechbaumer V, Tatout C, Graumann K. In Depth Topological Analysis of Arabidopsis Mid-SUN Proteins and Their Interaction with the Membrane-Bound Transcription Factor MaMYB. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091787. [PMID: 37176845 PMCID: PMC10180911 DOI: 10.3390/plants12091787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Mid-SUN proteins are a neglected family of conserved type III membrane proteins of ancient origin with representatives in plants, animals, and fungi. Previous higher plant studies have associated them with functions at the nuclear envelope and the endoplasmic reticulum (ER). In this study, high-resolution confocal light microscopy is used to explore the localisation of SUN3 and SUN4 in the perinuclear region, to explore topology, and to study the role of mid-SUNs on endoplasmic reticulum morphology. The role of SUN3 in the ER is reinforced by the identification of a protein interaction between SUN3 and the ER membrane-bound transcription factor maMYB. The results highlight the importance of mid-SUNs as functional components of the ER and outer nuclear membrane.
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Affiliation(s)
- Bisa Andov
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | | | - Charlotte Pain
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Sarah Mermet
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Maxime Voisin
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Camille Charrondiere
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Sylvie Tutois
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - David E Evans
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Verena Kriechbaumer
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christophe Tatout
- CNRS, Inserm, GReD Clermont-Ferrand, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Katja Graumann
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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