1
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Chu LC, Christopoulou N, McCaughan H, Winterbourne S, Cazzola D, Wang S, Litvin U, Brunon S, Harker PJ, McNae I, Granneman S. pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data. Life Sci Alliance 2024; 7:e202402787. [PMID: 39079742 PMCID: PMC11289467 DOI: 10.26508/lsa.202402787] [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: 04/22/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologies, is difficult to quantify as experimental approaches for validating the results are generally low throughput. To address this, we introduce pyRBDome, a pipeline for enhancing RNA-binding proteome data in silico. It aligns the experimental results with RNA-binding site (RBS) predictions from distinct machine-learning tools and integrates high-resolution structural data when available. Its statistical evaluation of RBDome data enables quick identification of likely genuine RNA-binders in experimental datasets. Furthermore, by leveraging the pyRBDome results, we have enhanced the sensitivity and specificity of RBS detection through training new ensemble machine-learning models. pyRBDome analysis of a human RBDome dataset, compared with known structural data, revealed that although UV-cross-linked amino acids were more likely to contain predicted RBSs, they infrequently bind RNA in high-resolution structures. This discrepancy underscores the limitations of structural data as benchmarks, positioning pyRBDome as a valuable alternative for increasing confidence in RBDome datasets.
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Affiliation(s)
- Liang-Cui Chu
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Niki Christopoulou
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Hugh McCaughan
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sophie Winterbourne
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Davide Cazzola
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
| | - Shichao Wang
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Ulad Litvin
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Salomé Brunon
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France
| | - Patrick Jb Harker
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Cancer Biomarker Centre, University of Manchester, Manchester, UK
| | - Iain McNae
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sander Granneman
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
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2
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Pal AK, Gandhivel VHS, Nambiar AB, Shivaprasad PV. Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler. Nat Commun 2024; 15:7807. [PMID: 39242590 DOI: 10.1038/s41467-024-52239-z] [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: 09/01/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024] Open
Abstract
Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small RNAs (sRNAs) mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in the sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its likely paternal imprinted nature. These important features are modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines, we observe defects in endosperm development and a loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms are also dependent on OsCLSY3. We observed that many imprinted genes and seed development-associated genes are under the control of OsCLSY3. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.
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Affiliation(s)
- Avik Kumar Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Vivek Hari-Sundar Gandhivel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Amruta B Nambiar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India.
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3
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Reyes-Herrera PH, Delgadillo-Duran DA, Flores-Gonzalez M, Mueller LA, Cristancho MA, Barrero LS. Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region. G3 (BETHESDA, MD.) 2024; 14:jkae139. [PMID: 39058924 DOI: 10.1093/g3journal/jkae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/05/2024] [Indexed: 07/28/2024]
Abstract
Potato (Solanum tuberosum) is an essential crop for food security and is ranked as the third most important crop worldwide for human consumption. The Diacol Capiro cultivar holds the dominant position in Colombian cultivation, primarily catering to the food processing industry. This highly heterozygous, autotetraploid cultivar belongs to the Andigenum group and it stands out for its adaptation to a wide variety of environments spanning altitudes from 1,800 to 3,200 meters above sea level. Here, a chromosome-scale assembly, referred to as DC, is presented for this cultivar. The assembly was generated by combining circular consensus sequencing with proximity ligation Hi-C for the scaffolding and represents 2.369 Gb with 48 pseudochromosomes covering 2,091 Gb and an anchor rate of 88.26%. The reference genome metrics, including an N50 of 50.5 Mb, a BUSCO (Benchmarking Universal Single-Copy Orthologue) score of 99.38%, and an Long Terminal Repeat Assembly Index score of 13.53, collectively signal the achieved high assembly quality. A comprehensive annotation yielded a total of 154,114 genes, and the associated BUSCO score of 95.78% for the annotated sequences attests to their completeness. The number of predicted NLR (Nucleotide-Binding and Leucine-Rich-Repeat genes) was 2107 with a large representation of NBARC (for nucleotide binding domain shared by Apaf-1, certain R gene products, and CED-4) containing domains (99.85%). Further comparative analysis of the proposed annotation-based assembly with high-quality known potato genomes, showed a similar genome metrics with differences in total gene numbers related to the ploidy status. The genome assembly and annotation of DC presented in this study represent a valuable asset for comprehending potato genetics. This resource aids in targeted breeding initiatives and contributes to the creation of enhanced, resilient, and more productive potato varieties, particularly beneficial for countries in Latin America.
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Affiliation(s)
- Paula H Reyes-Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Bogotá, Cundinamarca 250047, Colombia
| | - Diego A Delgadillo-Duran
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Bogotá, Cundinamarca 250047, Colombia
| | | | | | - Marco A Cristancho
- Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá 111711, Colombia
| | - Luz Stella Barrero
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Bogotá, Cundinamarca 250047, Colombia
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4
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Singh D, Dwivedi S, Singh N, Trivedi PK. HY5 and COP1 function antagonistically in the regulation of nicotine biosynthesis in Nicotiana tabacum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108916. [PMID: 39002305 DOI: 10.1016/j.plaphy.2024.108916] [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: 03/06/2024] [Revised: 05/30/2024] [Accepted: 07/04/2024] [Indexed: 07/15/2024]
Abstract
Nicotine constitutes approximately 90% of the total alkaloid content in leaves within the Nicotiana species, rendering it the most prevalent alkaloid. While the majority of genes responsible for nicotine biosynthesis express in root tissue, the influence of light on this process through shoot-to-root mobile ELONGATED HYPOCOTYL 5 (HY5) has been recognized. CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), a key regulator of light-associated responses, known for its role in modulating HY5 accumulation, remains largely unexplored in its relationship to light-dependent nicotine accumulation. Here, we identified NtCOP1, a COP1 homolog in Nicotiana tabacum, and demonstrated its ability to complement the cop1-4 mutant in Arabidopsis thaliana at molecular, morphological, and biochemical levels. Through the development of NtCOP1 overexpression (NtCOP1OX) plants, we observed a significant reduction in nicotine and flavonol content, inversely correlated with the down-regulation of nicotine and phenylpropanoid pathway. Conversely, CRISPR/Cas9-based knockout mutant plants (NtCOP1CR) exhibited an increase in nicotine levels. Further investigations, including yeast-two hybrid assays, grafting experiments, and Western blot analyses, revealed that NtCOP1 modulates nicotine biosynthesis by targeting NtHY5, thereby impeding its transport from shoot-to-root. We conclude that the interplay between HY5 and COP1 functions antagonistically in the light-dependent regulation of nicotine biosynthesis in tobacco.
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Affiliation(s)
- Deeksha Singh
- Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shambhavi Dwivedi
- Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Nivedita Singh
- Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India
| | - Prabodh Kumar Trivedi
- Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India; CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Kushwah AS, Dixit H, Upadhyay V, Verma SK, Prasad R. The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates. Proteins 2024; 92:1097-1112. [PMID: 38666709 DOI: 10.1002/prot.26696] [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: 07/05/2023] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.
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Affiliation(s)
- Ankita Singh Kushwah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, North Campus, Delhi, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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6
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Rothmann-Meyer W, Naidoo K, de Waal PJ. Spirocerca lupi draft genome, vaccine and anthelmintic targets. Mol Biochem Parasitol 2024; 259:111632. [PMID: 38834134 DOI: 10.1016/j.molbiopara.2024.111632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Spirocerca lupi is a parasitic nematode affecting predominantly domestic dogs. It causes spirocercosis, a disease that is often fatal. The assembled draft genome of S. lupi consists of 13,627 predicted protein-coding genes and is approximately 150 Mb in length. Several known anthelmintic gene targets such as for β-Tubulin, glutamate, and GABA receptors as well as known vaccine gene targets such as cysteine protease inhibitor and cytokines were identified in S. lupi by comparing orthologs of C. elegans anthelmintic gene targets as well as orthologs to known vaccine candidates. New anthelmintic targets were predicted through an inclusion-exclusion strategy and new vaccine targets were predicted through an immunoinformatics approach. New anthelminthic targets include DNA-directed RNA polymerases, chitin synthase, polymerases, and other enzymes. New vaccine targets include cuticle collagens. These gene targets provide a starting platform for new drug identification and vaccine design.
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Affiliation(s)
- Wiekolize Rothmann-Meyer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa; Thermo Fisher Scientific, Hybrid Field Application Scientist & Field Service Engineer, South Africa
| | - Pamela J de Waal
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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7
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Rede JE, Breitbart M, Lundquist C, Nagasaki K, Hewson I. Diverse RNA viruses discovered in multiple seagrass species. PLoS One 2024; 19:e0302314. [PMID: 39196976 PMCID: PMC11356395 DOI: 10.1371/journal.pone.0302314] [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: 08/25/2023] [Accepted: 04/01/2024] [Indexed: 08/30/2024] Open
Abstract
Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.
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Affiliation(s)
- Jordan E. Rede
- Department of Microbiology, Cornell University, Ithaca, NY, United States of America
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States of America
| | - Carolyn Lundquist
- National Institute of Water and Atmospheric Research, Hamilton, New Zealand
- School of Environment, The University of Auckland, Auckland, New Zealand
| | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, United States of America
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8
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Fu Y, Yu S, Li J, Lao Z, Yang X, Lin Z. DeepMineLys: Deep mining of phage lysins from human microbiome. Cell Rep 2024; 43:114583. [PMID: 39110597 DOI: 10.1016/j.celrep.2024.114583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024] Open
Abstract
Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.
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Affiliation(s)
- Yiran Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Shuting Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianfeng Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Zisha Lao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
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Hoshino M, Cossard G, Haas FB, Kane EI, Kogame K, Jomori T, Wakimoto T, Glemin S, Coelho SM. Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality. Nat Ecol Evol 2024:10.1038/s41559-024-02490-w. [PMID: 39152327 DOI: 10.1038/s41559-024-02490-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/18/2024] [Indexed: 08/19/2024]
Abstract
Sexual reproduction is widespread, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of eukaryotic taxa. The molecular changes underpinning the switch to asexuality remain elusive, particularly in organisms with haploid sexual systems. Here we explore independent events of loss of sex in the brown alga Scytosiphon, examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that asexual females ('Amazons') lose ability to produce sex pheromone and, consequently, are incapable of attracting males, whereas they gain rapid parthenogenic development from large, unfertilized eggs. These phenotypic changes are accompanied by convergent changes in gene expression. Decay of female functions, rather than relaxation of sexual antagonism, may be a dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we show that haploid purifying selection plays a key role in limiting the accumulation of deleterious alleles in Amazons, and we identify an autosomal locus associated with the Amazon phenotype. The sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.
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Affiliation(s)
- Masakazu Hoshino
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Research Center for Inland Seas, Kobe University, Rokkodai 1-1, Nadaku, Kobe, Japan
| | - Guillaume Cossard
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Emma I Kane
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | - Sylvain Glemin
- Laboratoire ECOBIO (Ecosystèmes, biodiversité, évolution), UMR 6553, CNRS, Université de Rennes, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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Wang L, Zhao Z, Li H, Pei D, Ma Q, Huang Z, Wang H, Xiao L. Genome-Wide Identification and Molecular Evolutionary History of the Whirly Family Genes in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2024; 13:2243. [PMID: 39204679 PMCID: PMC11359715 DOI: 10.3390/plants13162243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Whirly transcription factors are unique to plants, playing pivotal roles in managing leaf senescence and DNA repair. While present in various species, their identification in Brassica napus L. (B. napus) and their differences during hybridization and polyploidy has been elusive. Addressing this, our study delves into the functional and evolutionary aspects of the Whirly gene family during the emergence of B. napus, applying bioinformatics and comparative genomics. We identified six Whirly genes in B. napus. In Brassica rapa L. (B. rapa), three Whirly genes were identified, while four were found in Brassica oleracea L. (B. oleracea). The results show that the identified Whirly genes not only have homology but also share the same chromosomal positions. Phylogenetic analysis indicates that Whirly genes in monocots and dicots exhibit high conservation. In the evolutionary process, the Whirly gene family in B. napus experienced events of intron/exon loss. Collinearity insights point to intense purifying selection post-duplication. Promoter regions housed diverse cis-acting elements linked to photoresponse, anaerobic initiation, and methyl jasmonate responsiveness. Notably, elements tied to abscisic acid signaling and meristem expression were prominent in diploid ancestors but subdued in tetraploid B. napus. Tissue-specific expression unveiled analogous patterns within subfamily genes. Subsequent qRT-PCR analysis spotlighted BnAWHY1b's potential significance in abiotic stress response, particularly drought. These findings can be used as theoretical foundations to understand the functions and effects of the Whirly gene family in B. napus, providing references for the molecular mechanism of gene evolution between this species and its diploid ancestors.
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Affiliation(s)
- Long Wang
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Zhi Zhao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Huaxin Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Damei Pei
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Qianru Ma
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Lu Xiao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
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11
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Kant R, Khan MS, Chopra M, Saluja D. Artificial intelligence-driven reverse vaccinology for Neisseria gonorrhoeae vaccine: Prioritizing epitope-based candidates. Front Mol Biosci 2024; 11:1442158. [PMID: 39193221 PMCID: PMC11347834 DOI: 10.3389/fmolb.2024.1442158] [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: 06/01/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
Neisseria gonorrhoeae is the causative agent of the sexually transmitted disease gonorrhea. The increasing prevalence of this disease worldwide, the rise of antibiotic-resistant strains, and the difficulties in treatment necessitate the development of a vaccine, highlighting the significance of preventative measures to control and eradicate the infection. Currently, there is no widely available vaccine, partly due to the bacterium's ability to evade natural immunity and the limited research investment in gonorrhea compared to other diseases. To identify distinct vaccine candidates, we chose to focus on the uncharacterized, hypothetical proteins (HPs) as our initial approach. Using the in silico method, we first carried out a comprehensive assessment of hypothetical proteins of Neisseria gonorrhoeae, encompassing assessments of physicochemical properties, cellular localization, secretary pathways, transmembrane regions, antigenicity, toxicity, and prediction of B-cell and T-cell epitopes, among other analyses. Detailed analysis of all HPs resulted in the functional annotation of twenty proteins with a great degree of confidence. Further, using the immuno-informatics approach, the prediction pipeline identified one CD8+ restricted T-cell epitope, seven linear B-cell epitopes, and seven conformational B-cell epitopes as putative epitope-based peptide vaccine candidates which certainly require further validation in laboratory settings. The study accentuates the promise of functional annotation and immuno-informatics in the systematic design of epitope-based peptide vaccines targeting Neisseria gonorrhoeae.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence (IoE), University of Delhi, Delhi, India
| | - Mohd. Shoaib Khan
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence (IoE), University of Delhi, Delhi, India
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12
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Lau KJX, Selvaraj P, Muralishankar V, Chen CY, Muruganantham S, Naqvi NI. Draft genome sequence of Penicillium citrinum B9, a plant growth-promoting symbiont from barley rhizosphere. Microbiol Resour Announc 2024; 13:e0035424. [PMID: 38967472 PMCID: PMC11320902 DOI: 10.1128/mra.00354-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
Penicillium citrinum strain B9 is a plant growth-promoting fungus isolated from Barley (Hordeum vulgare) rhizosphere. We report the first draft genome of P. citrinum B9 assembled using single-molecule real-time sequencing and Illumina reads. The assembled genome spans 31.3 Mb comprising nine contigs and 10,106 protein-encoding genes.
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Affiliation(s)
- Kenny J. X. Lau
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Poonguzhali Selvaraj
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Vayutha Muralishankar
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Cheng-Yen Chen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Sahanna Muruganantham
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
| | - Naweed I. Naqvi
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, Singapore
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13
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Morikawa S, Verdonk C, John E, Lenzo L, Sbaraini N, Turo C, Li H, Jiang D, Chooi YH, Tan KC. The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum. BMC Microbiol 2024; 24:299. [PMID: 39127645 PMCID: PMC11316297 DOI: 10.1186/s12866-024-03454-7] [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: 02/05/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion of the P. nodorum VeA ortholog, PnVeA, resulted in growth abnormalities including pigmentation, abolished asexual sporulation and highly reduced virulence on wheat. Comparative RNA-Seq and RT-PCR analyses revealed that the deletion of PnVeA also decoupled the expression of major necrotrophic effector genes. In addition, the deletion of PnVeA resulted in an up-regulation of four predicted secondary metabolite (SM) gene clusters. Using liquid-chromatography mass-spectrometry, it was observed that one of the SM gene clusters led to an accumulation of the mycotoxin alternariol. PnVeA is essential for asexual sporulation, full virulence, secondary metabolism and necrotrophic effector regulation.
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Affiliation(s)
- Shota Morikawa
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Callum Verdonk
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Evan John
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Leon Lenzo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Nicolau Sbaraini
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Chala Turo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Hang Li
- School of Molecular Sciences, University of Western Australia, Perth, Australia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - David Jiang
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia.
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14
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Yoda T, Matsuhashi A, Matsushita A, Shibagaki S, Sasakura Y, Aoki K, Hosokawa M, Tsuda S. Uncovering Endolysins against Methicillin-Resistant Staphylococcus aureus Using a Microbial Single-Cell Genome Database. ACS Infect Dis 2024; 10:2679-2689. [PMID: 38906534 PMCID: PMC11320564 DOI: 10.1021/acsinfecdis.4c00039] [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: 01/14/2024] [Revised: 04/18/2024] [Accepted: 05/22/2024] [Indexed: 06/23/2024]
Abstract
Endolysins, peptidoglycan hydrolases derived from bacteriophages (phages), are being developed as a promising alternative to conventional antibiotics. To obtain highly active endolysins, a diverse library of these endolysins is vital. We propose here microbial single-cell genome sequencing as an efficient tool to discover dozens of previously unknown endolysins, owing to its culture-independent sequencing method. As a proof of concept, we analyzed and recovered endolysin genes within prophage regions of Staphylococcus single-amplified genomes in human skin microbiome samples. We constructed a library of chimeric endolysins by shuffling domains of the natural endolysins and performed high-throughput screening against Staphylococcus aureus. One of the lead endolysins, bbst1027, exhibited desirable antimicrobial properties, such as rapid bactericidal activity, no detectable resistance development, and in vivo efficacy. We foresee that this endolysin discovery pipeline is in principle applicable to any bacterial target and boost the development of novel antimicrobial agents.
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Affiliation(s)
- Takuya Yoda
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Ayumi Matsuhashi
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Ai Matsushita
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Shohei Shibagaki
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Yukie Sasakura
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Kazuteru Aoki
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Department
of Life Science and Medical Bioscience, Waseda University, 2-2
Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Research
Organization for Nano and Life Innovation, Waseda University, 513
Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Institute
for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Soichiro Tsuda
- bitBiome,
Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
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15
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Guo S, Liu P, Tang Y, Chen J, Zhang T, Liu H. Identification and expression profiles of olfactory-related genes in the antennal transcriptome of Graphosoma rubrolineatum (Hemiptera: Pentatomidae). PLoS One 2024; 19:e0306986. [PMID: 39106289 DOI: 10.1371/journal.pone.0306986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/26/2024] [Indexed: 08/09/2024] Open
Abstract
Graphosoma rubrolineatum (Hemiptera: Pentatomidae) is an important pest of vegetables and herbs (e.g., Umbelliferae and Cruciferae) in China, Siberia, Korea, and Japan. Insects are highly dependent on their olfactory system to detect odorants. However, no molecular-mediated olfactory genes in G. rubrolineatum have yet been identified. In this study, we first established the antennal transcriptome of G. rubrolineatum and identified 189 candidate olfactory genes, including 31 odorant-binding proteins (OBPs), 15 chemosensory proteins (CSPs), four sensory neuron membrane proteins (SNMPs),94 odorant receptors (ORs), 23 ionotropic receptors (IRs), and 22 gustatory receptors (GRs). Additionally, phylogenetic trees were constructed for olfactory genes between G. rubrolineatum and other hemipteran insects. We also detected the expression profiles of ten OBPs, five CSPs, two SNMPs, five ORs, four IRs, and four GRs by real-time quantitative PCR. The results revealed that most genes (GrubOBP1/11/31, GrubCSP3/8, GrubSNMP1a/1b, GrubOrco/OR9/11/13, GrubGR1/4/22, GrubIR25/75h/76b/GluR1) were highly expressed in the antennae, GrubOBP13/31 and GrubCSP4/11/12 were highly expressed in the legs, while GrubOBP20 and GrubGR19 were highly expressed in the wings. Our results will enrich the gene inventory of G. rubrolineatum and provide further insight into the molecular chemosensory mechanisms of G. rubrolineatum.
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Affiliation(s)
- Shibao Guo
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Panjing Liu
- Plant Protection Institute, HAAFS/Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, Baoding, P. R. China
- IPM Innovation Center of Hebei Province/International Science and Technology Joint Research Center on IPM of Hebei Province, Baoding, China
| | - Yin Tang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junhua Chen
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Tao Zhang
- Plant Protection Institute, HAAFS/Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, Baoding, P. R. China
- IPM Innovation Center of Hebei Province/International Science and Technology Joint Research Center on IPM of Hebei Province, Baoding, China
| | - Hongmin Liu
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, China
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16
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Wang Y, Cui T, Niu K, Ma H. Integrated proteomics, transcriptomics, and metabolomics offer novel insights into Cd resistance and accumulation in Poa pratensis. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134727. [PMID: 38824780 DOI: 10.1016/j.jhazmat.2024.134727] [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: 03/15/2024] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 06/04/2024]
Abstract
Kentucky bluegrass (Poa pratensis L., KB) demonstrates superior performance in both cadmium (Cd) accumulation and tolerance; however, the regulatory mechanisms and detoxification pathways in this species remain unclear. Therefore, phenotype, root ultrastructure, cell wall components, proteomics, transcriptomics, and metabolomics were analyzed under the hydroponic system to investigate the Cd tolerance and accumulation mechanisms in the Cd-tolerant KB variety 'Midnight (M)' and the Cd-sensitive variety 'Rugby II (R)' under Cd stress. The M variety exhibited higher levels of hydroxyl and carboxyl groups as revealed by Fourier transform infrared spectroscopy spectral analysis. Additionally, a reduced abundance of polysaccharide degradation proteins was observed in the M variety. The higher abundance of glutathione S-transferase and content of L-cysteine-glutathione disulfide and oxidized glutathione in the M variety may contribute to better performance of the M variety under Cd stress. Additionally, the R variety had an enhanced content of carboxylic acids and derivatives, increasing the Cd translocation capacity. Collectively, the down-regulation of cell wall polysaccharide degradation genes coupled with the up-regulation of glutathione metabolism genes enhances the tolerance to Cd stress in KB. Additionally, lignification of the endodermis and the increase in carboxylic acids and derivatives play crucial roles in the redistribution of Cd in KB.
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Affiliation(s)
- Yong Wang
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-US. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu 730070, China
| | - Ting Cui
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-US. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu 730070, China
| | - Kuiju Niu
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-US. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu 730070, China
| | - Huiling Ma
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-US. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu 730070, China.
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17
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Dong Y, Li T, Hou Y, Wilson K, Wang X, Su C, Li Y, Ren G, Xu P. Densovirus infection facilitates plant-virus transmission by an aphid. THE NEW PHYTOLOGIST 2024; 243:1539-1553. [PMID: 39021237 DOI: 10.1111/nph.19908] [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: 04/05/2024] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
The interactions among plant viruses, insect vectors, and host plants have been well studied; however, the roles of insect viruses in this system have largely been neglected. We investigated the effects of MpnDV infection on aphid and PVY transmission using bioassays, RNA interference (RNAi), and GC-MS methods and green peach aphid (Myzus persicae (Sulzer)), potato virus Y (PVY), and densovirus (Myzus persicae nicotianae densovirus, MpnDV) as model systems. MpnDV increased the activities of its host, promoting population dispersal and leading to significant proliferation in tobacco plants by significantly enhancing the titer of the sesquiterpene (E)-β-farnesene (EβF) via up-regulation of expression levels of the MpFPPS1 gene. The proliferation and dispersal of MpnDV-positive individuals were faster than that of MpnDV-negative individuals in PVY-infected tobacco plants, which promoted the transmission of PVY. These results combined showed that an insect virus may facilitate the transmission of a plant virus by enhancing the locomotor activity and population proliferation of insect vectors. These findings provide novel opportunities for controlling insect vectors and plant viruses, which can be used in the development of novel management strategies.
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Affiliation(s)
- Yonghao Dong
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Tong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Yuanyuan Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YW, UK
| | - Xiufang Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Chenyu Su
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yunhe Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences and College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Guangwei Ren
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Pengjun Xu
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
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18
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Cossío-Bayúgar R, Miranda-Miranda E, Aguilar-Díaz H, Narváez-Padilla V, Reynaud E. Transcriptomic dataset of the development and maturation of the Rhipicephalus microplus ovary. Data Brief 2024; 55:110661. [PMID: 39049973 PMCID: PMC11267085 DOI: 10.1016/j.dib.2024.110661] [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: 03/20/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024] Open
Abstract
To conduct differential gene expression analysis, ovaries from the cattle tick Rhipicephalus microplus were dissected at three distinct developmental stages (preingurgitated, immature ingurgitated, and mature ingurgitated). Additionally, undissected intact mature males and complete ingurgitated female ticks without ovaries (carcasses) were also collected to serve as reference samples for analysis. To perform total RNA purification, tissue from ten individuals representing each of the five previously described conditions was pooled. mRNA was isolated from the purified total RNA using the oligo (dT) method. Following fragmentation, double stranded cDNA was synthesized and ligated to sequencing adapters. Suitable-sized fragments were subsequently used for PCR amplification. Libraries were analyzed and quantified using an Agilent 2100 Bioanalyzer and an ABI StepOnePlus Real-Time PCR System. A total of 45.64 Gb bases were sequenced using the Illumina HiSeq sequencing platform. After assembling the samples and correcting for abundance, we obtained 82,877 unigenes. The total length, average length, N50, and GC content of the unigenes were 89,754,828 bp,1,082 bp,2,068 bp and 49.04 % respectively. For functional annotation, the unigenes were aligned with 7 functional databases. The number of unigenes identified in the functional databases were as follows: 32,518 (NR:39.24 %), 10,259 (NT:12.38 %), 23,624 (Swissprot:28.50 %), 22,203 (KOG:26.79 %), 25,072 (KEGG:30.25 %), 17,435(GO:21.04 %), and 23,220 (InterPro:28.02 %). Unigene candidate coding regions (CDS) among the unigenes were predicted using TransDecoder software and 42,143 CDS were detected. We also detected 10,522 simple sequence repeats (SSRs) distributed on 8,126 unigenes, and predicted 4,672 transcription factors (TF) coding unigenes. Our data can be used to identify genes that are important for male and female tick and arachnid reproduction and tick general physiology.
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Affiliation(s)
- Raquel Cossío-Bayúgar
- Centro Nacional de Investigaciones Disciplinarias en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP). Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
| | - Estefan Miranda-Miranda
- Centro Nacional de Investigaciones Disciplinarias en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP). Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
| | - Hugo Aguilar-Díaz
- Centro Nacional de Investigaciones Disciplinarias en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP). Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
| | - Verónica Narváez-Padilla
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca, 62209, Mexico
| | - Enrique Reynaud
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos. Av. Universidad 2001, Chamilpa, Cuernavaca, 62209, Mexico
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19
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Wang H, Chen M, Wei X, Xia R, Pei D, Huang X, Han B. Computational tools for plant genomics and breeding. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1579-1590. [PMID: 38676814 DOI: 10.1007/s11427-024-2578-6] [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: 02/05/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024]
Abstract
Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along the central dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advances further revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic prediction and selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rational design of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.
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Affiliation(s)
- Hai Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Mengjiao Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
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20
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Walt HK, Jordan HR, Meyer F, Hoffmann FG. Detection of Known and Novel Virus Sequences in the Black Solider Fly and Expression of Host Antiviral Pathways. Viruses 2024; 16:1219. [PMID: 39205193 PMCID: PMC11359925 DOI: 10.3390/v16081219] [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: 05/09/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
The mass rearing of animals in close quarters can be highly conducive to microbe transmission, including pathogens. This has been shown multiple times in the case of important industrial insects such as crickets, silkworms, and honeybees. One industrial insect of increasing importance is the black soldier fly (Diptera: Hermetia illucens), as it can convert organic waste into high-quality protein and fatty acids. Along with this, they take up far less space than traditional protein sources, as millions of black soldier flies can be reared in a relatively small facility. Because of this, there is a growing interest in the pathogens that could impact black soldier fly-rearing efforts. So far, only three black soldier fly-associated viruses have been identified. We used metatranscriptomic sequencing to survey black soldier fly guts, frass, and diet for viruses. We detected sequences from two novel viruses. One, which we name Hermetia illucens sigma-like virus 1, is phylogenetically related to viruses of the genus Sigmavirus, which have been highly studied in Drosophila. The other novel virus, which we name Hermetia illucens inse-like virus 1, is the second double-stranded RNA virus of the order Ghabrivirales described in the black soldier fly, and groups within a new family of insect viruses called the Inseviridae. We also detected two black soldier fly-associated viruses previously identified by our group: BSF nairo-like virus 1 and BSF uncharacterized bunyavirus-like 1. Consistent with our previous study, these two viruses are found primarily in frass samples and occur together more often than expected at random. When analyzing host transcription, we found significant differences in gene expression for eight candidate antiviral genes in the black soldier fly when comparing samples with and without viral sequences. Our results suggest that black soldier fly-virus interactions are ongoing, and they could be of interest to black soldier fly producers.
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Affiliation(s)
- Hunter K. Walt
- Department of Biochemistry, Nutrition and Health Promotion, Mississippi State University, Mississippi State, MS 39762, USA; (H.K.W.); (F.M.)
| | - Heather R. Jordan
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA;
| | - Florencia Meyer
- Department of Biochemistry, Nutrition and Health Promotion, Mississippi State University, Mississippi State, MS 39762, USA; (H.K.W.); (F.M.)
| | - Federico G. Hoffmann
- Department of Biochemistry, Nutrition and Health Promotion, Mississippi State University, Mississippi State, MS 39762, USA; (H.K.W.); (F.M.)
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
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21
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Seldeslachts A, Maurstad MF, Øyen JP, Undheim EAB, Peigneur S, Tytgat J. Exploring oak processionary caterpillar induced lepidopterism (Part 1): unveiling molecular insights through transcriptomics and proteomics. Cell Mol Life Sci 2024; 81:311. [PMID: 39066932 PMCID: PMC11335235 DOI: 10.1007/s00018-024-05330-z] [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: 03/28/2024] [Revised: 05/30/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Lepidopterism, a skin inflammation condition caused by direct or airborne exposure to irritating hairs (setae) from processionary caterpillars, is becoming a significant public health concern. Recent outbreaks of the oak processionary caterpillar (Thaumetopoea processionea) have caused noteworthy health and economic consequences, with a rising frequency expected in the future, exacerbated by global warming promoting the survival of the caterpillar. Current medical treatments focus on symptom relief due to the lack of an effective therapy. While the source is known, understanding the precise causes of symptoms remain incomplete understood. In this study, we employed an advanced method to extract venom from the setae and identify the venom components through high-quality de novo transcriptomics, venom proteomics, and bioinformatic analysis. A total of 171 venom components were identified, including allergens, odorant binding proteins, small peptides, enzymes, enzyme inhibitors, and chitin biosynthesis products, potentially responsible for inflammatory and allergic reactions. This work presents the first comprehensive proteotranscriptomic database of T. processionea, contributing to understanding the complexity of lepidopterism. Furthermore, these findings hold promise for advancing therapeutic approaches to mitigate the global health impact of T. processionea and related caterpillars.
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Affiliation(s)
- Andrea Seldeslachts
- Toxicology and Pharmacology, Department Pharmaceutical and Pharmacological Sciences, KU Leuven , Leuven, Vlaams-Brabant, Belgium
| | - Marius F Maurstad
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jan Philip Øyen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Division of biotechnology and plant health & viruses, bacteria and nematodes in forestry, agriculture and horticulture, Norwegian Institute of Bioeconomy Research (NIBIO), Oslo, Norway
| | | | - Steve Peigneur
- Toxicology and Pharmacology, Department Pharmaceutical and Pharmacological Sciences, KU Leuven , Leuven, Vlaams-Brabant, Belgium.
| | - Jan Tytgat
- Toxicology and Pharmacology, Department Pharmaceutical and Pharmacological Sciences, KU Leuven , Leuven, Vlaams-Brabant, Belgium.
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22
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Terui R, Berger SE, Sambel LA, Song D, Chistol G. Single-molecule imaging reveals the mechanism of bidirectional replication initiation in metazoa. Cell 2024; 187:3992-4009.e25. [PMID: 38866019 PMCID: PMC11283366 DOI: 10.1016/j.cell.2024.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]
Abstract
Metazoan genomes are copied bidirectionally from thousands of replication origins. Replication initiation entails the assembly and activation of two CMG helicases (Cdc45⋅Mcm2-7⋅GINS) at each origin. This requires several replication firing factors (including TopBP1, RecQL4, and DONSON) whose exact roles are still under debate. How two helicases are correctly assembled and activated at each origin is a long-standing question. By visualizing the recruitment of GINS, Cdc45, TopBP1, RecQL4, and DONSON in real time, we uncovered that replication initiation is surprisingly dynamic. First, TopBP1 transiently binds to the origin and dissociates before the start of DNA synthesis. Second, two Cdc45 are recruited together, even though Cdc45 alone cannot dimerize. Next, two copies of DONSON and two GINS simultaneously arrive at the origin, completing the assembly of two CMG helicases. Finally, RecQL4 is recruited to the CMG⋅DONSON⋅DONSON⋅CMG complex and promotes DONSON dissociation and CMG activation via its ATPase activity.
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Affiliation(s)
- Riki Terui
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Scott E Berger
- Biophysics Program, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Larissa A Sambel
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Dan Song
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Gheorghe Chistol
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA; Biophysics Program, Stanford School of Medicine, Stanford, CA 94305, USA; Cancer Biology Program, Stanford School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA; BioX Interdisciplinary Institute, Stanford School of Medicine, Stanford, CA 94305, USA.
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23
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Bi Y, An H, Chi Z, Xu Z, Deng Y, Ren Y, Wang R, Lu X, Guo J, Hu R, Virolle MJ, Xu D. The acetyltransferase SCO0988 controls positively specialized metabolism and morphological differentiation in the model strains Streptomyces coelicolor and Streptomyces lividans. Front Microbiol 2024; 15:1366336. [PMID: 39113837 PMCID: PMC11303876 DOI: 10.3389/fmicb.2024.1366336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Streptomycetes are well-known antibiotic producers possessing in their genomes numerous silent biosynthetic pathways that might direct the biosynthesis of novel bio-active specialized metabolites. It is thus of great interest to find ways to enhance the expression of these pathways to discover most needed novel antibiotics. In this study, we demonstrated that the over-expression of acetyltransferase SCO0988 up-regulated the production of specialized metabolites and accelerated sporulation of the weak antibiotic producer, Streptomyces lividans and that the deletion of this gene had opposite effects in the strong antibiotic producer, Streptomyces coelicolor. The comparative analysis of the acetylome of a S. lividans strain over-expressing sco0988 with that of the original strain revealed that SCO0988 acetylates a broad range of proteins of various pathways including BldKB/SCO5113, the extracellular solute-binding protein of an ABC-transporter involved in the up-take of a signal oligopeptide of the quorum sensing pathway. The up-take of this oligopeptide triggers the "bald cascade" that regulates positively specialized metabolism, aerial mycelium formation and sporulation in S. coelicolor. Interestingly, BldKB/SCO5113 was over-acetylated on four Lysine residues, including Lys425, upon SCO0988 over-expression. The bald phenotype of a bldKB mutant could be complemented by native bldKB but not by variant of bldKB in which the Lys425 was replaced by arginine, an amino acid that could not be acetylated or by glutamine, an amino acid that is expected to mimic acetylated lysine. Our study demonstrated that Lys425 was a critical residue for BldKB function but was inconclusive concerning the impact of acetylation of Lys425 on BldKB function.
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Affiliation(s)
- Yunwen Bi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Hao An
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Zhewei Chi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Zhongheng Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Yuan Deng
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Yuxian Ren
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Rui Wang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Xinyi Lu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Jia Guo
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Ren Hu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, Gif-sur-Yvette, France
| | - Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
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24
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Goeckeritz CZ, Grabb C, Grumet R, Iezzoni AF, Hollender CA. Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4428-4452. [PMID: 38602443 PMCID: PMC11263489 DOI: 10.1093/jxb/erae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/10/2024] [Indexed: 04/12/2024]
Abstract
Understanding the process of Prunus species floral development is crucial for developing strategies to manipulate bloom time and prevent crop loss due to climate change. Here, we present a detailed examination of flower development from initiation until bloom for early- and late-blooming sour cherries (Prunus cerasus) from a population segregating for a major bloom time QTL on chromosome 4. Using a new staging system, we show floral buds from early-blooming trees were persistently more advanced than those from late-blooming siblings. A genomic DNA coverage analysis revealed the late-blooming haplotype of this QTL, k, is located on a subgenome originating from the late-blooming P. fruticosa progenitor. Transcriptome analyses identified many genes within this QTL as differentially expressed between early- and late-blooming trees during the vegetative-to-floral transition. From these, we identified candidate genes for the late bloom phenotype, including multiple transcription factors homologous to Reproductive Meristem B3 domain-containing proteins. Additionally, we determined that the basis of k in sour cherry is likely separate from candidate genes found in sweet cherry-suggesting several major regulators of bloom time are located on Prunus chromosome 4.
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Affiliation(s)
- Charity Z Goeckeritz
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Chloe Grabb
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Amy F Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
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25
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Zhu ZS, Bu SH, Liu JX, Niu C, Wang L, Yuan H, Zhang L, Song Y. Label-free-based proteomics analysis reveals differential proteins of sheep, goat and cow milk. J Dairy Sci 2024:S0022-0302(24)01002-6. [PMID: 39004124 DOI: 10.3168/jds.2024-24998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
Regarding the limited information on species protein differences between sheep, goat, and cow milk, the differentially expressed proteins in sheep, goat, and cow milk and their functional differences are analyzed using label-free proteomics technology to identify potential biomarkers. 770 proteins and 2914 peptide segments were identified. The statistical analysis showed significant differences in the relative abundances of the 74 proteins among the sheep, goat, and cow milk. CSN3 and LALBA can be used as potential biomarkers for goat milk, XDH can be used as potential biomarkers for cow milk, and CTSB and BPIFB1 can be used as potential biomarkers for sheep milk. The functional analysis using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes showed that these significantly different proteins were enriched by different pathways including thyroid hormone synthesis and glycerol phospholipid metabolism. The data revealed differences in the amounts and physiological functions of the milk proteins of different species, which may provide an important basis for research on the nutritional composition of dairy products and adulteration identification technology.
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Affiliation(s)
- Z S Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - S H Bu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - J X Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - C Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - L Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - H Yuan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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26
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Lu YT, Wu YY, Li YN, Zheng WY, Liu WZ. Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis. Arch Microbiol 2024; 206:342. [PMID: 38967823 DOI: 10.1007/s00203-024-04069-2] [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: 01/08/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.
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Affiliation(s)
- Yi-Ting Lu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Yi-Yi Wu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Ya-Nan Li
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
- Department of Pharmaceutical Laboratory, Anhui Sunhere Pharmaceutical Excipients Co., Ltd, Huainan, Anhui Province, 232000, China
| | - Wei-Yi Zheng
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
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27
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Rahuman S, N S J, Sebastian W, Varghese E, P K A. Tidings from the Tides-De novo transcriptome assembly of the endemic estuarine bivalve Villorita cyprinoides. Sci Data 2024; 11:723. [PMID: 38956059 PMCID: PMC11219770 DOI: 10.1038/s41597-024-03541-4] [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: 02/23/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
The Indian black clam Villorita cyprinoides Gray, 1825, is an economically valuable estuarine bivalve that faces challenges from multiple stressors and anthropogenic pressures. However, limited genomic resources have hindered molecular investigations into the impact of these stressors on clam populations. Here, we have generated the first transcriptomic reference datasets for V. cyprinoides to address this knowledge gap. A total of 25,040,592 and 22,486,217 million Illumina paired-end reads generated from two individuals were assembled using Trinity and rnaSPAdes. From the 47,607 transcripts identified as Coding Domain Sequences, 37,487 returned positive BLAST hits against six different databases. Additionally, a total of 14,063 Single Sequence Repeats were identified using GMATA. This study significantly enhances the genetic understanding of V. cyprinoides, a potential candidate for aquaculture that supports the livelihoods of many people dependent on small-scale fisheries. The data generated provides insights into broader genealogical connections within the family Cyrenidae through comparative transcriptomics. Furthermore, this transcriptional profile serves as baseline data for future studies in toxicological and conservation genetics.
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Affiliation(s)
- Summaya Rahuman
- Indian Council of Agricultural Research - Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India
- Mangalore University, Mangalagangotri, Mangalore, 574 199, Karnataka, India
| | - Jeena N S
- Indian Council of Agricultural Research - Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India.
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology, Kochi, 682508, Kerala, India
| | - Eldho Varghese
- Indian Council of Agricultural Research - Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India
| | - Asokan P K
- Indian Council of Agricultural Research - Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India
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28
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Dong J, Qiu L, Zhou X, Liu S. Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana. Mol Ecol 2024; 33:e17414. [PMID: 38801184 DOI: 10.1111/mec.17414] [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: 07/07/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non-genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central-peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation-with-gene-flow models generate the heterogeneous genome landscapes. These elements weight differently between central-island and other central-peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low-recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non-uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana.
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Affiliation(s)
- Jiangxing Dong
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lifei Qiu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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29
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Ahmed MH, Samia NSN, Singh G, Gupta V, Mishal MFM, Hossain A, Suman KH, Raza A, Dutta AK, Labony MA, Sultana J, Faysal EH, Alnasser SM, Alam P, Azam F. An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus. J Biomol Struct Dyn 2024; 42:5288-5307. [PMID: 37519185 DOI: 10.1080/07391102.2023.2239921] [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: 04/02/2023] [Accepted: 06/09/2023] [Indexed: 08/01/2023]
Abstract
A worrying new outbreak of Monkeypox (Mpox) in humans is caused by the Mpox virus (MpoxV). The pathogen has roughly 28 hypothetical proteins of unknown structure, function, and pathogenicity. Using reliable bioinformatics tools, we attempted to analyze the MpoxV genome, identify the role of hypothetical proteins (HPs), and design a potential candidate vaccine. Out of 28, we identified seven hypothetical proteins using multi-server validation with high confidence for the occurrence of conserved domains. Their physical, chemical, and functional characterizations, including molecular weight, theoretical isoelectric point, 3D structures, GRAVY value, subcellular localization, functional motifs, antigenicity, and virulence factors, were performed. We predicted possible cytotoxic T cell (CTL), helper T cell (HTL) and linear and conformational B cell epitopes, which were combined in a 219 amino acid multiepitope vaccine with human β defensin as a linker. This multi-epitopic vaccine was structurally modelled and docked with toll-like receptor-3 (TLR-3). The dynamical stability of the vaccine-TLR-3 docked complexes exhibited stable interactions based on RMSD and RMSF tests. Additionally, the modelled vaccine was cloned in-silico in an E. coli host to check the appropriate expression of the final vaccine built. Our results might conform to an immunogenic and safe vaccine, which would require further experimental validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Hridoy Ahmed
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Nure Sharaf Nower Samia
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Dhaka, Bangladesh
| | - Gagandeep Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi CCRAS, Ministry of Ayush, India
| | - Vandana Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, New Delhi, India
| | | | - Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Adnan Raza
- Bioscience department, COMSATS University of Islamabad, Islamabad, Pakistan
| | - Amit Kumar Dutta
- Department of Microbiology, University of Rajshahi, Rajshahi, Bangladesh
| | - Moriom Akhter Labony
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Jakia Sultana
- Department of Botany, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Sulaiman Mohammed Alnasser
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
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30
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Zheng X, Ali ZM, Lim PK, Mutwil M, Wang Y. Comparative transcriptome database for Camellia sinensis reveals genes related to the cold sensitivity and albino mechanism of 'Anji Baicha'. PHYSIOLOGIA PLANTARUM 2024; 176:e14474. [PMID: 39139072 DOI: 10.1111/ppl.14474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 08/15/2024]
Abstract
Tea, a globally popular beverage, contains various beneficial secondary metabolites. Tea plants (Camellia sinensis) exhibit diverse genetic traits across cultivars, impacting yield, adaptability, morphology, and secondary metabolite composition. Many tea cultivars have been the subject of much research interest, which have led to the accumulation of publicly available RNA-seq data. As such, it has become possible to systematically summarize the characteristics of different cultivars at the transcriptomic level, identify functional genes, and infer gene functions through co-expression analysis. Here, the transcriptomes of 9 tea cultivars were assembled, and comparative analysis was conducted on the coding sequences of 13 cultivars. To give access to this data, we present TeaNekT (https://teanekt.sbs.ntu.edu.sg/), a web resource that facilitates the prediction of gene functions of various tea cultivars. We used TeaNekT to perform a cross-cultivar comparison of co-expressed gene clusters and tissue-specific gene expression. We observed that 'Anji Baicha' possesses the highest number of cultivar-specific genes and the second-highest number of expanded genes. These genes in 'Anji Baicha' tend to be enriched in functions associated with cold stress response, chloroplast thylakoid structure, and nitrogen metabolism. Notably, we identified three significantly expanded homologous genes in 'Anji Baicha' encoding the ICE1, SIZ1, and MAPKK2, which are closely associated with the cold sensitivity of 'Anji Baicha'. Additionally, one significantly expanded homologous gene in 'Anji Baicha' encoding regulatory factor RIQ may play a crucial role in the abnormal chloroplast structure and absence of thylakoid membranes in 'Anji Baicha'.
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Affiliation(s)
- Xinghai Zheng
- Tea Research Institute, Zhejiang University, Hangzhou, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore
| | - Zahin Mohd Ali
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore
| | - Yuefei Wang
- Tea Research Institute, Zhejiang University, Hangzhou, China
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Kim N, Ma J, Kim W, Kim J, Belenky P, Lee I. Genome-resolved metagenomics: a game changer for microbiome medicine. Exp Mol Med 2024; 56:1501-1512. [PMID: 38945961 PMCID: PMC11297344 DOI: 10.1038/s12276-024-01262-7] [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: 12/13/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 07/02/2024] Open
Abstract
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.
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Affiliation(s)
- Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Wonjong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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Ebrahimikondori H, Sutherland D, Yanai A, Richter A, Salehi A, Li C, Coombe L, Kotkoff M, Warren RL, Birol I. Structure-aware deep learning model for peptide toxicity prediction. Protein Sci 2024; 33:e5076. [PMID: 39196703 PMCID: PMC11193153 DOI: 10.1002/pro.5076] [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: 01/09/2024] [Revised: 04/26/2024] [Accepted: 05/28/2024] [Indexed: 08/30/2024]
Abstract
Antimicrobial resistance is a critical public health concern, necessitating the exploration of alternative treatments. While antimicrobial peptides (AMPs) show promise, assessing their toxicity using traditional wet lab methods is both time-consuming and costly. We introduce tAMPer, a novel multi-modal deep learning model designed to predict peptide toxicity by integrating the underlying amino acid sequence composition and the three-dimensional structure of peptides. tAMPer adopts a graph-based representation for peptides, encoding ColabFold-predicted structures, where nodes represent amino acids and edges represent spatial interactions. Structural features are extracted using graph neural networks, and recurrent neural networks capture sequential dependencies. tAMPer's performance was assessed on a publicly available protein toxicity benchmark and an AMP hemolysis data we generated. On the latter, tAMPer achieves an F1-score of 68.7%, outperforming the second-best method by 23.4%. On the protein benchmark, tAMPer exhibited an improvement of over 3.0% in the F1-score compared to current state-of-the-art methods. We anticipate tAMPer to accelerate AMP discovery and development by reducing the reliance on laborious toxicity screening experiments.
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Affiliation(s)
- Hossein Ebrahimikondori
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Bioinformatics Graduate ProgramUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Darcy Sutherland
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Public Health LaboratoryBritish Columbia Centre for Disease ControlVancouverBritish ColumbiaCanada
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Anat Yanai
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Public Health LaboratoryBritish Columbia Centre for Disease ControlVancouverBritish ColumbiaCanada
| | - Amelia Richter
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Public Health LaboratoryBritish Columbia Centre for Disease ControlVancouverBritish ColumbiaCanada
| | - Ali Salehi
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Public Health LaboratoryBritish Columbia Centre for Disease ControlVancouverBritish ColumbiaCanada
| | - Chenkai Li
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Bioinformatics Graduate ProgramUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Monica Kotkoff
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - René L. Warren
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences CentreBC Cancer AgencyVancouverBritish ColumbiaCanada
- Public Health LaboratoryBritish Columbia Centre for Disease ControlVancouverBritish ColumbiaCanada
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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Lee NK, Uhler KM, Yoon PJ, Santos-Cortez RLP. Clinical Genetic Testing for Hearing Loss: Implications for Genetic Counseling and Gene-Based Therapies. Biomedicines 2024; 12:1427. [PMID: 39062005 PMCID: PMC11274279 DOI: 10.3390/biomedicines12071427] [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: 02/26/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 07/28/2024] Open
Abstract
Genetic factors contribute significantly to congenital hearing loss, with non-syndromic cases being more prevalent and genetically heterogeneous. Currently, 150 genes have been associated with non-syndromic hearing loss, and their identification has improved our understanding of auditory physiology and potential therapeutic targets. Hearing loss gene panels offer comprehensive genetic testing for hereditary hearing loss, and advancements in sequencing technology have made genetic testing more accessible and affordable. Currently, genetic panel tests available at a relatively lower cost are offered to patients who face financial barriers. In this study, clinical and audiometric data were collected from six pediatric patients who underwent genetic panel testing. Known pathogenic variants in MYO15A, GJB2, and USH2A were most likely to be causal of hearing loss. Novel pathogenic variants in the MYO7A and TECTA genes were also identified. Variable hearing phenotypes and inheritance patterns were observed amongst individuals with different pathogenic variants. The identification of these variants contributes to the continually expanding knowledge base on genetic hearing loss and lays the groundwork for personalized treatment options in the future.
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Affiliation(s)
- Nam K. Lee
- Department of Otolaryngology—Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin M. Uhler
- Department of Physical Medicine and Rehabilitation, Children’s Hospital Colorado, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Patricia J. Yoon
- Department of Otolaryngology—Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology—Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Dangoudoubiyam S, Norris JK, Namasivayam S, de Paula Baptista R, Cannes do Nascimento N, Camp J, Schardl CL, Kissinger JC, Howe DK. Temporal gene expression during asexual development of the apicomplexan Sarcocystis neurona. mSphere 2024; 9:e0011124. [PMID: 38809064 PMCID: PMC11332336 DOI: 10.1128/msphere.00111-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
Asexual replication in the apicomplexan Sarcocystis neurona involves two main developmental stages: the motile extracellular merozoite and the sessile intracellular schizont. Merozoites invade host cells and transform into schizonts that undergo replication via endopolygeny to form multiple (64) daughter merozoites that are invasive to new host cells. Given that the capabilities of the merozoite vary significantly from the schizont, the patterns of transcript levels throughout the asexual lifecycle were determined and compared in this study. RNA-Seq data were generated from extracellular merozoites and four intracellular schizont development time points. Of the 6,938 genes annotated in the S. neurona genome, 6,784 were identified in the transcriptome. Of these, 4,111 genes exhibited significant differential expression between the merozoite and at least one schizont development time point. Transcript levels were significantly higher for 2,338 genes in the merozoite and 1,773 genes in the schizont stages. Included in this list were genes encoding the secretory pathogenesis determinants (SPDs), which encompass the surface antigen and SAG-related sequence (SAG/SRS) and the secretory organelle proteins of the invasive zoite stage (micronemes, rhoptries, and dense granules). As anticipated, many of the S. neurona SPD gene transcripts were abundant in merozoites. However, several SPD transcripts were elevated in intracellular schizonts, suggesting roles unrelated to host cell invasion and the initial establishment of the intracellular niche. The hypothetical genes that are potentially unique to the genus Sarcocystis are of particular interest. Their conserved expression patterns are instructive for future investigations into the possible functions of these putative Sarcocystis-unique genes. IMPORTANCE The genus Sarcocystis is an expansive clade within the Apicomplexa, with the species S. neurona being an important cause of neurological disease in horses. Research to decipher the biology of S. neurona and its host-pathogen interactions can be enhanced by gene expression data. This study has identified conserved apicomplexan orthologs in S. neurona, putative Sarcocystis-unique genes, and gene transcripts abundant in the merozoite and schizont stages. Importantly, we have identified distinct clusters of genes with transcript levels peaking during different intracellular schizont development time points, reflecting active gene expression changes across endopolygeny. Each cluster also has subsets of transcripts with unknown functions, and investigation of these seemingly Sarcocystis-unique transcripts will provide insights into the interesting biology of this parasite genus.
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Affiliation(s)
- Sriveny Dangoudoubiyam
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Jamie K. Norris
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Sivaranjani Namasivayam
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Rodrigo de Paula Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Naila Cannes do Nascimento
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Joseph Camp
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | | | - Jessica C. Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Daniel K. Howe
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
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Liu Z, Yang F, Deng C, Wan H, Tang H, Feng J, Wang Q, Yang N, Li J, Yang W. Chromosome-level assembly of the synthetic hexaploid wheat-derived cultivar Chuanmai 104. Sci Data 2024; 11:670. [PMID: 38909086 PMCID: PMC11193762 DOI: 10.1038/s41597-024-03527-2] [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: 03/01/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024] Open
Abstract
Synthetic hexaploid wheats (SHWs) are effective genetic resources for transferring agronomically important genes from wild relatives to common wheat (Triticum aestivum L.). Dozens of reference-quality pseudomolecule assemblies of hexaploid wheat have been generated, but none is reported for SHW-derived cultivars. Here, we generated a chromosome-scale assembly for the SHW-derived cultivar 'Chuanmai 104' based on PacBio HiFi reads and chromosome conformation capture sequencing. The total assembly size was 14.81 Gb with a contig N50 length of 58.25 Mb. A BUSCO analysis yielded a completeness score of 99.30%. In total, repetitive elements comprised 81.36% of the genome and 122,554 high-confidence protein-coding gene models were predicted. In summary, the first chromosome-level assembly for a SHW-derived cultivar presents a promising outlook for the study and utilization of SHWs in wheat improvement, which is essential to meet the global food demand.
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Affiliation(s)
- Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Fan Yang
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Cao Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Hao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Junyan Feng
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China.
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China.
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.
- Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Chengdu, China.
- Key Laboratory of Tianfu Seed Industry Innovation, Chengdu, China.
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Wang L, Zhao Z, Li H, Pei D, Huang Z, Wang H, Xiao L. Genome-Wide Identification of NDPK Family Genes and Expression Analysis under Abiotic Stress in Brassica napus. Int J Mol Sci 2024; 25:6795. [PMID: 38928501 PMCID: PMC11203525 DOI: 10.3390/ijms25126795] [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: 04/17/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The NDPK gene family is an important group of genes in plants, playing a crucial role in regulating energy metabolism, growth, and differentiation, cell signal transduction, and response to abiotic stress. However, our understanding of the NDPK gene family in Brassica napus L. remains limited. This paper systematically analyzes the NDPK gene family in B. napus, particularly focusing on the evolutionary differences within the species. In this study, sixteen, nine, and eight NDPK genes were identified in B. napus and its diploid ancestors, respectively. These genes are not only homologous but also highly similar in their chromosomal locations. Phylogenetic analysis showed that the identified NDPK proteins were divided into four clades, each containing unique motif sequences, with most NDPKs experiencing a loss of introns/exons during evolution. Collinearity analysis revealed that the NDPK genes underwent whole-genome duplication (WGD) events, resulting in duplicate copies, and most of these duplicate genes were subjected to purifying selection. Cis-acting element analysis identified in the promoters of most NDPK genes elements related to a light response, methyl jasmonate response, and abscisic acid response, especially with an increased number of abscisic acid response elements in B. napus. RNA-Seq results indicated that NDPK genes in B. napus exhibited different expression patterns across various tissues. Further analysis through qRT-PCR revealed that BnNDPK genes responded significantly to stress conditions such as salt, drought, and methyl jasmonate. This study enhances our understanding of the NDPK gene family in B. napus, providing a preliminary theoretical basis for the functional study of NDPK genes and offering some references for further revealing the phenomenon of polyploidization in plants.
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Affiliation(s)
- Long Wang
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (L.W.); (Z.Z.); (H.L.); (D.P.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Zhi Zhao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (L.W.); (Z.Z.); (H.L.); (D.P.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Huaxin Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (L.W.); (Z.Z.); (H.L.); (D.P.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Damei Pei
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (L.W.); (Z.Z.); (H.L.); (D.P.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China;
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Lu Xiao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (L.W.); (Z.Z.); (H.L.); (D.P.)
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
- Key Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, Xining 810016, China
- Qinghai Spring Rape Engineering Research Center, Xining 810016, China
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Chen H, Yu S, Zhang X, Gao Y, Wang H, Li Y, He D, Jia W. Comparative proteomics reveals that fatty acid metabolism is involved in myocardial adaptation to chronic hypoxic injury. PLoS One 2024; 19:e0305571. [PMID: 38885281 PMCID: PMC11182518 DOI: 10.1371/journal.pone.0305571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
Congenital heart disease (CHD) is the most serious form of heart disease, and chronic hypoxia is the basic physiological process underlying CHD. Some patients with CHD do not undergo surgery, and thus, they remain susceptible to chronic hypoxia, suggesting that some protective mechanism might exist in CHD patients. However, the mechanism underlying myocardial adaptation to chronic hypoxia remains unclear. Proteomics was used to identify the differentially expressed proteins in cardiomyocytes cultured under hypoxia for different durations. Western blotting assays were used to verify protein expression. A Real-Time Cell Analyzer (RTCA) was used to analyze cell growth. In this study, 3881 proteins were identified by proteomics. Subsequent bioinformatics analysis revealed that proteins were enriched in regulating oxidoreductase activity. Functional similarity cluster analyses showed that chronic hypoxia resulted in proteins enrichment in the mitochondrial metabolic pathway. Further KEGG analyses found that the proteins involved in fatty acid metabolism, the TCA cycle and oxidative phosphorylation were markedly upregulated. Moreover, knockdown of CPT1A or ECI1, which is critical for fatty acid degradation, suppressed the growth of cardiomyocytes under chronic hypoxia. The results of our study revealed that chronic hypoxia activates fatty acid metabolism to maintain the growth of cardiomyocytes.
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Affiliation(s)
- Hu Chen
- Department of Cardiothoracic Surgery, School of Clinical Medicine and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Shiran Yu
- Department of Cardiothoracic Surgery, School of Clinical Medicine and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
- Department of Thoracic Surgery, The Third Affiliated Hospital of Chengdu Medical College, Pidu District People’s Hospital, Chengdu, China
| | - Xiaoyun Zhang
- Department of Cardiology, Pengzhou People’s Hospital, Pengzhou, China
| | - Yujie Gao
- Department of Stomatology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Hongqi Wang
- Department of Cardiothoracic Surgery, School of Clinical Medicine and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yuankun Li
- Department of Cardiothoracic Surgery, School of Clinical Medicine and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Dongsheng He
- Department of Cardiothoracic Surgery, School of Clinical Medicine and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Weikun Jia
- Department of Cardiothoracic Surgery, School of Clinical Medicine and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
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Fu Z, Gong X, Hu Z, Wei B, Zhang H. Unveiling biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2. BMC Genomics 2024; 25:603. [PMID: 38886660 PMCID: PMC11181645 DOI: 10.1186/s12864-024-10501-0] [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: 04/20/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND A growing number of studies have demonstrated that the polar regions have the potential to be a significant repository of microbial resources and a potential source of active ingredients. Genome mining strategy plays a key role in the discovery of bioactive secondary metabolites (SMs) from microorganisms. This work highlighted deciphering the biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2 by a combination of whole genome analysis and antiSMASH as well as feature-based molecular networking (MN) in the Global Natural Products Social Molecular Networking (GNPS). RESULTS In this study, a high-quality whole genome sequence of an Arctic marine strain MNP-2, with a size of 34.9 Mb was successfully obtained. Its total number of genes predicted by BRAKER software was 13,218, and that of non-coding RNAs (rRNA, sRNA, snRNA, and tRNA) predicted by using INFERNAL software was 204. AntiSMASH results indicated that strain MNP-2 harbors 56 biosynthetic gene clusters (BGCs), including 18 NRPS/NRPS-like gene clusters, 10 PKS/PKS-like gene clusters, 8 terpene synthse gene clusters, 5 indole synthase gene clusters, 10 hybrid gene clusters, and 5 fungal-RiPP gene clusters. Metabolic analyses of strain MNP-2 grown on various media using GNPS networking revealed its great potential for the biosynthesis of bioactive SMs containing a variety of heterocyclic and bridge-ring structures. For example, compound G-8 exhibited a potent anti-HIV effect with an IC50 value of 7.2 nM and an EC50 value of 0.9 nM. Compound G-6 had excellent in vitro cytotoxicities against the K562, MCF-7, Hela, DU145, U1975, SGC-7901, A549, MOLT-4, and HL60 cell lines, with IC50 values ranging from 0.10 to 3.3 µM, and showed significant anti-viral (H1N1 and H3N2) activities with IC50 values of 15.9 and 30.0 µM, respectively. CONCLUSIONS These findings definitely improve our knowledge about the molecular biology of genus A. sydowii and would effectively unveil the biosynthetic potential of strain MNP-2 using genomics and metabolomics techniques.
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Affiliation(s)
- Zhiyang Fu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Xiangzhou Gong
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Zhe Hu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Bin Wei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, 310014, Hangzhou, China.
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Wang Q, Zhang J, Liu C, Ru C, Qian Q, Yang M, Yan S, Liu W, Wang G. Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis in Bactrocera dorsalis. Front Physiol 2024; 15:1384426. [PMID: 38952867 PMCID: PMC11215311 DOI: 10.3389/fphys.2024.1384426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
Alternative splicing is an essential post-transcriptional regulatory mechanism that diversifies gene function by generating multiple protein isoforms from a single gene and act as a crucial role in insect environmental adaptation. Olfaction, a key sense for insect adaptation, relies heavily on the antennae, which are the primary olfactory organs expressing most of the olfactory genes. Despite the extensive annotation of olfactory genes within insect antennal tissues facilitated by high-throughput sequencing technology advancements, systematic analyses of alternative splicing are still relatively less. In this study, we focused on the oriental fruit fly (Bactrocera dorsalis), a significant pest of fruit crops. We performed a detailed analysis of alternative splicing in its antennae by utilizing the full-length transcriptome of its antennal tissue and the insect's genome. The results revealed 8600 non-redundant full-length transcripts identified in the oriental fruit fly antennal full-length transcriptome, spanning 4,145 gene loci. Over 40% of these loci exhibited multiple isoforms. Among these, 161 genes showed sex-biased isoform switching, involving seven different types of alternative splicing. Notably, events involving alternative transcription start sites (ATSS) and alternative transcription termination sites (ATTS) were the most common. Of all the genes undergoing ATSS and ATTS alternative splicing between male and female, 32 genes were alternatively spliced in protein coding regions, potentially affecting protein function. These genes were categorized based on the length of the sex-biased isoforms, with the highest difference in isoform fraction (dIF) associated with the ATSS type, including genes such as BdorABCA13, BdorCAT2, and BdorTSN3. Additionally, transcription factor binding sites for doublesex were identified upstream of both BdorABCA13 and BdorCAT2. Besides being expressed in the antennal tissues, BdorABCA13 and BdorCAT2 are also expressed in the mouthparts, legs, and genitalia of both female and male adults, suggesting their functional diversity. This study reveals alternative splicing events in the antennae of Bactrophora dorsalis from two aspects: odorant receptor genes and other types of genes expressed in the antennae. This study not only provides a research foundation for understanding the regulation of gene function by alternative splicing in the oriental fruit fly but also offers new insights for utilizing olfaction-based behavioral manipulation techniques to manage this pest.
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Affiliation(s)
- Qi Wang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jie Zhang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chenhao Liu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chuanjian Ru
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Qian Qian
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Minghuan Yang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Shanchun Yan
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Wei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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40
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Huang YZ, Liu Y, Zhu R, Ma X, Xin S, Zhu B, Dong XP. Multi-omics Analysis of Volatile Flavor Components in Pacific Chub and Spanish Mackerel during Freezing using GC-MS-O. Food Chem 2024; 443:138534. [PMID: 38320377 DOI: 10.1016/j.foodchem.2024.138534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/15/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024]
Abstract
This study employed gas chromatography-mass spectrometry with olfactory (GC-MS-O) and multi-omics methods to investigate the changes in volatile flavor compounds during the freezing process of Pacific chub mackerel (Scomber japonicus) from Japan and China, and Spanish mackerel (Scomberomorus niphonius). A total of 18 volatile flavor compounds were identified, and significant differences in volatile flavor components were observed among samples frozen for 1 week, 1 year, and 2 years. The results of the Partial least squares regression (PLSR) indicated that the fishy odor was correlated with independent variables such as fatty acids (FA 22:4, FA 28:6, FA 24:4), differentially expressed genes (Gene.2425 (NDUFA5), Gene.38 (GPX1), and Gene.2844 (DAD1)). Classification and regression tree (CART) analysis revealed that the peak area values of fatty acids (FA 22:5, FA 20:4) and fatty acid esters of hydroxy fatty acids (FAHFA 18:0/22:3) were the main differentiating factors for fishy odor perception.
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Affiliation(s)
- Yi-Zhen Huang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Academy of Food Interdisciplinary Science, Dalian Technology Innovation Center for Chinese Prepared Food, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Yu Liu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Academy of Food Interdisciplinary Science, Dalian Technology Innovation Center for Chinese Prepared Food, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Rui Zhu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Academy of Food Interdisciplinary Science, Dalian Technology Innovation Center for Chinese Prepared Food, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Xiaoxiao Ma
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Academy of Food Interdisciplinary Science, Dalian Technology Innovation Center for Chinese Prepared Food, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Songlin Xin
- Sichuan Tourism University, no.459, Hongling Road, Longquanyi District, Chengdu 610100, Sichuan Province, China
| | - Beiwei Zhu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Academy of Food Interdisciplinary Science, Dalian Technology Innovation Center for Chinese Prepared Food, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Xiu-Ping Dong
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Academy of Food Interdisciplinary Science, Dalian Technology Innovation Center for Chinese Prepared Food, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
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41
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Alami MM, Shu S, Liu S, Ouyang Z, Zhang Y, Lv M, Sang Y, Gong D, Yang G, Feng S, Mei Z, Xie DY, Wang X. Chromosome-scale genome assembly of medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family. Sci Data 2024; 11:610. [PMID: 38866889 PMCID: PMC11169364 DOI: 10.1038/s41597-024-03315-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 06/14/2024] Open
Abstract
Tinospora sagittata (Oliv.) Gagnep. is an important medicinal tetraploid plant in the Menispermaceae family. Its tuber, Radix Tinosporae, used in traditional Chinese medicine, is rich in diterpenoids and benzylisoquinoline alkaloids (BIAs). To enhance our understanding of medicinal compounds' biosynthesis and Menispermaceae's evolution, we herein report assembling a high-quality chromosome-scale genome with both PacBio HiFi and Illumina sequencing technologies. PacBio Sequel II generated 2.5 million circular consensus sequencing (CCS) reads, and a hybrid assembly strategy with Illumina sequencing resulted in 4483 contigs. The assembled genome size was 2.33 Gb, consisting of 4070 scaffolds (N50 = 42.06 Mb), of which 92.05% were assigned to 26 pseudochromosomes. T. sagittata's chromosomal-scale genome assembly, the first species in Menispermaceae, aids Menispermaceae evolution and T. sagittata's secondary metabolites biosynthesis understanding.
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Affiliation(s)
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sanbo Liu
- China Resources Sanjiu (Huangshi) Pharmaceutical Co., Ltd., Huangshi, 435000, Hubei, China
| | - Zhen Ouyang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yipeng Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meijia Lv
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yonghui Sang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dalin Gong
- China Resources Sanjiu (Huangshi) Pharmaceutical Co., Ltd., Huangshi, 435000, Hubei, China
| | - Guozheng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengqiu Feng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhinan Mei
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xuekui Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Shahidi P, Bahramnejad B, Vafaee Y, Dastan D, Heidari P. Isolation and Characterization of Phenylalanine Ammonia Lyase ( PAL) Genes in Ferula pseudalliacea: Insights into the Phenylpropanoid Pathway. Genes (Basel) 2024; 15:771. [PMID: 38927707 PMCID: PMC11203166 DOI: 10.3390/genes15060771] [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: 04/12/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Phenylalanine ammonia lyase (PAL) is a key enzyme regulating the biosynthesis of the compounds of the phenylpropanoid pathway. This study aimed to isolate and characterize PAL genes from Ferula pseudalliacea Rech.f. (Apiales: Apiaceae) to better understand the regulation of metabolite production. Three PAL gene isoforms (FpPAL1-3) were identified and cloned using the 3'-RACE technique and confirmed by sequencing. Bioinformatics analysis revealed important structural features, such as phosphorylation sites, physicochemical properties, and evolutionary relationships. Expression analysis by qPCR demonstrated the differential transcription profiles of each FpPAL isoform across roots, stems, leaves, flowers, and seeds. FpPAL1 showed the highest expression in stems, FpPAL2 in roots and flowers, and FpPAL3 in flowers. The presence of three isoforms of PAL in F. pseudalliacea, along with the diversity of PAL genes and their tissue-specific expression profiles, suggests that complex modes of regulation exist for phenylpropanoid biosynthesis in this important medicinal plant. The predicted interaction network revealed associations with key metabolic pathways, emphasizing the multifaceted roles of these PAL genes. In silico biochemical analyses revealed the hydrophilicity of the FpPAL isozyme; however, further analysis of substrate specificity and enzyme kinetics can clarify the specific role of each FpPAL isozyme. These comprehensive results increase the understanding of PAL genes in F. pseudalliacea, helping to characterize their contributions to secondary metabolite biosynthesis.
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Affiliation(s)
- Pegah Shahidi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Bahman Bahramnejad
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Yavar Vafaee
- Department of Horticultural Sciences, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Dara Dastan
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran;
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
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43
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Yan X, Shi G, Sun M, Shan S, Chen R, Li R, Wu S, Zhou Z, Li Y, Liu Z, Hu Y, Liu Z, Soltis PS, Zhang J, Soltis DE, Ning G, Bao M. Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree). Proc Natl Acad Sci U S A 2024; 121:e2319679121. [PMID: 38830106 PMCID: PMC11181145 DOI: 10.1073/pnas.2319679121] [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: 11/18/2023] [Accepted: 04/25/2024] [Indexed: 06/05/2024] Open
Abstract
Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus × acerifolia (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of Platanus and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of Platanus genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that P. × acerifolia (2n = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; Platanus does not seem to share any WGD with other Proteales or with core eudicots. Each P. × acerifolia subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The P. × acerifolia genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in P. × acerifolia has undergone an expansion compared to other noncore eudicots, mainly via the WGD events. Sub-/neo-functionalization of duplicated genes provided the genetic basis underlying the unique flowering-time regulation in P. × acerifolia. The P. × acerifolia reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering-time regulation in angiosperms.
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Affiliation(s)
- Xu Yan
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Gehui Shi
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Miao Sun
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL32611
| | - Runzhou Chen
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Runhui Li
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Songlin Wu
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Zheng Zhou
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Yuhan Li
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | | | - Yonghong Hu
- Shanghai Chenshan Botanical Garden, Shanghai201602, China
| | - Zhongjian Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou350002, China
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL32611
- Biodiversity Institute, University of Florida, Gainesville, FL32611
- Genetics Institute, University of Florida, Gainesville, FL32608
| | - Jiaqi Zhang
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL32611
- Biodiversity Institute, University of Florida, Gainesville, FL32611
- Genetics Institute, University of Florida, Gainesville, FL32608
- Department of Biology, University of Florida, Gainesville, FL32611
| | - Guogui Ning
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
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Sanz-Gaitero M, De Maesschalck V, Patel A, Longin H, Van Noort V, Rodriguez-Rubio L, van Ryne M, Danis-Wlodarczyk K, Drulis-Kawa Z, Mesnage S, van Raaij M, Lavigne R. Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:53-62. [PMID: 39119210 PMCID: PMC11304755 DOI: 10.1089/phage.2023.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Background Endolysins are phage-encoded lytic enzymes that degrade bacterial peptidoglycan at the end of phage lytic cycles to release new phage particles. These enzymes are being explored as an alternative to small-molecule antibiotics. Methods The crystal structure of KTN6 Gp46 was determined and compared with a ColabFold model. Cleavage specificity was examined using a peptidoglycan digest and reversed-phase high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS). Results The structure of KTN6 Gp46 could be determined at 1.4 Å resolution, and key differences in loops of the putative peptidoglycan binding domain were identified in comparison with its closest known homologue, the endolysin of phage SPN1S. Reversed-phase HPLC/MS analysis of the reaction products following peptidoglycan digestion confirmed the muramidase activity of Gp46, consistent with structural predictions. Conclusion These insights into the structure and function of endolysins further expand the toolbox for endolysin engineering and explore their potential in enzyme-based antibacterial design strategies.
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Affiliation(s)
- Marta Sanz-Gaitero
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Ankur Patel
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Hannelore Longin
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium
| | - Vera Van Noort
- Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium
| | | | | | - Katarzyna Danis-Wlodarczyk
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Stephane Mesnage
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Mark van Raaij
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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45
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Secci-Petretto G, Weiss S, Gomes-Dos-Santos A, Persat H, Machado AM, Vasconcelos I, Castro LFC, Froufe E. A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus. Genetica 2024; 152:71-81. [PMID: 38888686 PMCID: PMC11199216 DOI: 10.1007/s10709-024-00210-7] [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: 01/15/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.
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Affiliation(s)
- Giulia Secci-Petretto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Steven Weiss
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
| | - Henri Persat
- Société Française d'Ichthyologie, Muséum National d'Histoire Naturelle Paris, France, 57 Rue Cuvier CP26, 75005, Paris, France
| | - André M Machado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Inês Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
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Xia Z, Fan W, Liu D, Chen Y, Lv J, Xu M, Zhang M, Ren Z, Chen X, Wang X, Li L, Zhu P, Liu C, Song Z, Huang C, Wang X, Wang S, Zhao A. Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content. HORTICULTURE RESEARCH 2024; 11:uhae120. [PMID: 38919559 PMCID: PMC11197311 DOI: 10.1093/hr/uhae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/14/2024] [Indexed: 06/27/2024]
Abstract
Understanding the intricate regulatory mechanisms underlying the anthocyanin content (AC) in fruits and vegetables is crucial for advanced biotechnological customization. In this study, we generated high-quality haplotype-resolved genome assemblies for two mulberry cultivars: the high-AC 'Zhongsang5801' (ZS5801) and the low-AC 'Zhenzhubai' (ZZB). Additionally, we conducted a comprehensive analysis of genes associated with AC production. Through genome-wide association studies (GWAS) on 112 mulberry fruits, we identified MaVHAG3, which encodes a vacuolar-type H+-ATPase G3 subunit, as a key gene linked to purple pigmentation. To gain deeper insights into the genetic and molecular processes underlying high AC, we compared the genomes of ZS5801 and ZZB, along with fruit transcriptome data across five developmental stages, and quantified the accumulation of metabolic substances. Compared to ZZB, ZS5801 exhibited significantly more differentially expressed genes (DEGs) related to anthocyanin metabolism and higher levels of anthocyanins and flavonoids. Comparative analyses revealed expansions and contractions in the flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) genes, resulting in altered carbon flow. Co-expression analysis demonstrated that ZS5801 displayed more significant alterations in genes involved in late-stage AC regulation compared to ZZB, particularly during the phase stage. In summary, our findings provide valuable insights into the regulation of mulberry fruit AC, offering genetic resources to enhance cultivars with higher AC traits.
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Affiliation(s)
- Zhongqiang Xia
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Wei Fan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Duanyang Liu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Yuane Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Jing Lv
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Mengxia Xu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Meirong Zhang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Zuzhao Ren
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xuefei Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xiujuan Wang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Liang Li
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Panpan Zhu
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China
| | - Zhiguang Song
- Chongqing Sericulture Science and Technology Research Institute, Chongqing.400715, China
| | - Chuanshu Huang
- Chongqing Sericulture Science and Technology Research Institute, Chongqing.400715, China
| | - Xiling Wang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Shuchang Wang
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Aichun Zhao
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
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Gao J, Lu C, Wei Y, Xie Q, Jin J, Li J, Yang F, Zhu G. Phosphorylation of 399S at CsHsp70 of Cymbidium sinense is essential to maintain chlorophyll stability. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108518. [PMID: 38744085 DOI: 10.1016/j.plaphy.2024.108518] [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: 11/18/2023] [Revised: 02/08/2024] [Accepted: 03/08/2024] [Indexed: 05/16/2024]
Abstract
The Chinese orchids symbolise nobility and gentility in China, and the variation of leaf color makes Cymbidium sinense more diversified and valuable. However, its color variations especially at the protein level still remain largely unexplored. In this study, the proteomics and phosphoproteomics of Cymbidium sinense leaf color variation mutants were studied. A total of 1059 differentially abundant proteins (DAPs) and 1127 differentially abundant phosphorylation sites belonging to 644 phosphoproteins (DAPPs) were identified in the yellow section of leaf variegation mutant of Cymbidium sinense (MY) compared with the green section (MG). Moreover, 349 co-expressing proteins were found in both omics' datasets, while only 26 proteins showed the same expression patterns in the two omics. The interaction network analysis of kinases and phosphatases showed that DAPs and DAPPs in photosynthesis, response to hormones, pigment metabolic process, phosphorylation, glucose metabolic process, and dephosphorylation might contribute to leaf color variation. The abundance of 28 Hsps and 28 phosphorylation sites belonging to 10 Hsps showed significant differences between MG and MY. CsHsp70 was selected to explore the function in Cymbidium sinense leaf variegation. The results showed CsHsp70 is essential for maintaining photosynthetic pigment content and the 399S phosphorylation site is crucial to the function of CsHsp70. Collectively, our findings construct a comprehensive coverage of protein and protein phosphorylation in leaf variegation of C. sinense, providing valuable insights into its formation mechanisms.
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Affiliation(s)
- Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Qi Xie
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
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Shi XF, Zhang JL, Liu K, Wang L, Wang HP, Wu HY. Detection of serum major histocompatibility complex I (HLA-1) and β2-microglobulin (β2M) in pre-eclampsia using isobaric tags for relative and absolute quantitation (iTRAQ). Int J Gynaecol Obstet 2024; 165:1072-1084. [PMID: 38149341 DOI: 10.1002/ijgo.15312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
OBJECTIVE The purpose of this preliminary investigation into the pathogenesis of pre-eclampsia was to screen the differential proteins in the serum of pregnant women with normal pregnancy and early-onset pre-eclampsia using isobaric tags for relative and absolute quantitation (iTRAQ), so as to identify serum biomarkers for the early diagnosis of pre-eclampsia. METHODS We examined the peripheral serum of 58 normal pregnant women and 42 pregnant women with early-onset pre-eclampsia using iTRAQ; the differentially expressed proteins were screened for bioinformatics analysis; and the expression of candidate proteins human leukocyte antigen-1 (HLA-1) and β2-microglobulin (β2M) in placental tissues was detected using western blot. RESULTS We identified a total of 63 differential proteins in the serum of patients from the normal control group and the pre-eclampsia group, and this included 24 up-regulated proteins and 39 down-regulated proteins. The western blot results of placental tissue showed reduced HLA-1 expression (1.12 ± 0.23) in the placenta in the pre-eclampsia group as compared with the normal control group (1.34 ± 0.22). Consistent with the results observed in the serum, β2M in the placenta in the pre-eclampsia group was significantly elevated (1.05 ± 0.47) in comparison with the normal group (0.75 ± 0.33) (P < 0.05). CONCLUSION In this study, we found that iTRAQ technology was useful for identifying differentially expressed proteins in the peripheral serum of pregnant women with pre-eclampsia, and that HLA-1 and β2M, which may be involved in the occurrence of pre-eclampsia, show promise as predictive markers of pre-eclampsia.
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Affiliation(s)
- Xu-Feng Shi
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Jing-Li Zhang
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Kan Liu
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Li Wang
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Huan-Ping Wang
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hai-Ying Wu
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
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Mukhopadhyay S, Garvetto A, Neuhauser S, Pérez-López E. Decoding the Arsenal: Protist Effectors and Their Impact on Photosynthetic Hosts. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:498-506. [PMID: 38551366 DOI: 10.1094/mpmi-11-23-0196-cr] [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: 06/22/2024]
Abstract
Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes, and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, which makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionizing the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools like AlphaFold2 enable structure-based function prediction of effector candidates with divergent protein sequences. In turn, this allows us to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts. [Formula: see text] Copyright © 2024 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)
- Soham Mukhopadhyay
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- L'Institute EDS, Université Laval, Quebec City, Quebec, Canada
| | - Andrea Garvetto
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Edel Pérez-López
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- L'Institute EDS, Université Laval, Quebec City, Quebec, Canada
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Wang H, Fang T, Li X, Xie Y, Wang W, Hu T, Kudrna D, Amombo E, Yin Y, Fan S, Gong Z, Huang Y, Xia C, Zhang J, Wu Y, Fu J. Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2068-2084. [PMID: 38531629 DOI: 10.1111/tpj.16729] [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: 05/18/2023] [Revised: 02/06/2024] [Accepted: 03/09/2024] [Indexed: 03/28/2024]
Abstract
Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.
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Affiliation(s)
- Huan Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao City, Shandong Province, 266109, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Tilin Fang
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Yan Xie
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province, 430074, China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Tao Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, Gansu Province, 730020, China
| | - David Kudrna
- School of Plant Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Erick Amombo
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Zhiyun Gong
- Agricultural Department, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Yicheng Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chunjiao Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Jinmin Fu
- College of Grassland Science, Qingdao Agricultural University, Qingdao City, Shandong Province, 266109, China
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
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