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Frontiers in microbiology
2023;14 1243371.

Comparative genomic analysis reveals differential genomic characteristics and featured genes between rapid- and slow-growing .

Menglu Zhang, Peihan Wang, Cuidan Li, Ofir Segev, Jie Wang, Xiaotong Wang, Liya Yue, Xiaoyuan Jiang, Yongjie Sheng, Asaf Levy, Chunlai Jiang, Fei Chen
Author Information
  1. Menglu Zhang: National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China.
  2. Peihan Wang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  3. Cuidan Li: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  4. Ofir Segev: Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
  5. Jie Wang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  6. Xiaotong Wang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  7. Liya Yue: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  8. Xiaoyuan Jiang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  9. Yongjie Sheng: Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China.
  10. Asaf Levy: Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
  11. Chunlai Jiang: National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China.
  12. Fei Chen: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
PMID: 37808319 DOI: 10.3389/fmicb.2023.1243371

Abstract

Introduction: (NTM) is a major category of environmental bacteria in nature that can be divided into rapidly growing (RGM) and slowly growing (SGM) based on their distinct growth rates. To explore differential molecular mechanisms between RGM and SGM is crucial to understand their survival state, environmental/host adaptation and pathogenicity. Comparative genomic analysis provides a powerful tool for deeply investigating differential molecular mechanisms between them. However, large-scale comparative genomic analysis between RGM and SGM is still uncovered.
Methods: In this study, we screened 335 high-quality, non-redundant NTM genome sequences covering 187 species from 3,478 online NTM genomes, and then performed a comprehensive comparative genomic analysis to identify differential genomic characteristics and featured genes/protein domains between RGM and SGM.
Results: Our findings reveal that RGM has a larger genome size, more genes, lower GC content, and more featured genes/protein domains in metabolism of some main substances (e.g. carbohydrates, amino acids, nucleotides, ions, and coenzymes), energy metabolism, signal transduction, replication, transcription, and translation processes, which are essential for its rapid growth requirements. On the other hand, SGM has a smaller genome size, fewer genes, higher GC content, and more featured genes/protein domains in lipid and secondary metabolite metabolisms and cellular defense mechanisms, which help enhance its genome stability and environmental adaptability. Additionally, orthogroup analysis revealed the important roles of bacterial division and bacteriophage associated genes in RGM and secretion system related genes for better environmental adaptation in SGM. Notably, PCoA analysis of the top 20 genes/protein domains showed precision classification between RGM and SGM, indicating the credibility of our screening/classification strategies.
Discussion: Overall, our findings shed light on differential underlying molecular mechanisms in survival state, adaptation and pathogenicity between RGM and SGM, show the potential for our comparative genomic pipeline to investigate differential genes/protein domains at whole genomic level across different bacterial species on a large scale, and provide an important reference and improved understanding of NTM.

Keywords

adaptive evolution comparative genomics growth rate non-tuberculous mycobacteria (NTM) rapidly growing mycobacteria (RGM) slowly growing mycobacteria (SGM) toxin-antitoxin

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Journal Article
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Word Cloud

Created with Highcharts 10.0.0RGMSGMgenomicdifferentialanalysisNTMgenes/proteindomainsgenesgrowingmechanismscomparativegenomefeaturedenvironmentalgrowthmolecularadaptationmycobacteriarapidlyslowlysurvivalstatepathogenicityComparativespeciescharacteristicsfindingssizeGCcontentmetabolismimportantbacterialIntroduction:majorcategorybacterianaturecandividedbaseddistinctratesexplorecrucialunderstandenvironmental/hostprovidespowerfultooldeeplyinvestigatingHoweverlarge-scalestilluncoveredMethods:studyscreened335high-qualitynon-redundantsequencescovering1873478onlinegenomesperformedcomprehensiveidentifyResults:reveallargerlowermainsubstancesegcarbohydratesaminoacidsnucleotidesionscoenzymesenergysignaltransductionreplicationtranscriptiontranslationprocessesessentialrapidrequirementshandsmallerfewerhigherlipidsecondarymetabolitemetabolismscellulardefensehelpenhancestabilityadaptabilityAdditionallyorthogrouprevealedrolesdivisionbacteriophageassociatedsecretionsystemrelatedbetterNotablyPCoAtop20showedprecisionclassificationindicatingcredibilityscreening/classificationstrategiesDiscussion:Overallshedlightunderlyingshowpotentialpipelineinvestigatewholelevelacrossdifferentlargescaleprovidereferenceimprovedunderstandingrevealsrapid-slow-growingadaptiveevolutiongenomicsratenon-tuberculoustoxin-antitoxin

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