Comparative genomic analysis reveals differential genomic characteristics and featured genes between rapid- and slow-growing non-tuberculous mycobacteria

Frontiers in Microbiology

Microbiology

Xiaoyuan Jiang¹  Cuidan Li¹  Xiaotong Wang¹  Liya Yue¹  Peihan Wang²  Jie Wang²  Fei Chen³  Asaf Levy⁴  Ofir Segev⁴  Yongjie Sheng⁵  Chunlai Jiang⁶  Menglu Zhang⁶ 

[1] CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;University of Chinese Academy of Sciences, Beijing, China;CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;University of Chinese Academy of Sciences, Beijing, China;Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China;State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China;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;Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China;National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China;

关键词: non-tuberculous mycobacteria;    mycobacteria;    mycobacteria;    growth rate;    adaptive evolution;    comparative genomics;    toxin-antitoxin;   

DOI  :  10.3389/fmicb.2023.1243371

 received in 2023-07-03, accepted in 2023-09-05,  发布年份 2023

来源: Frontiers

【 摘 要 】

IntroductionNon-tuberculous mycobacteria (NTM) is a major category of environmental bacteria in nature that can be divided into rapidly growing mycobacteria (RGM) and slowly growing mycobacteria (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.MethodsIn 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.ResultsOur 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.DiscussionOverall, 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.

【 授权许可】

Unknown   
Copyright © 2023 Zhang, Wang, Li, Segev, Wang, Wang, Yue, Jiang, Sheng, Levy, Jiang and Chen.