Predicting Mycoplasma tissue and host specificity from genome sequences

Author:

Zondervan Niels A.ORCID,dos Santos Vitor A. P. MartinsORCID,Suarez-Diez MariaORCID

Abstract

AbstractTo gain insights into the genotype-phenotype relationships in Mycoplasmas, we set to investigate which Mycoplasma proteins are most predictive of tissue and host trophism and to which functional groups of proteins they belong. We retrieved and annotated 430 Mycoplasma genomes and combined their genome information with data on which host and tissue these Mycoplasmas were isolated from. We assessed clustering of Mycoplasma strains from a wide range of hosts and tissues based on different functional groups of proteins. Additionally, we assessed clustering using only a subset of M. pneumoniae strains based on different functional groups of proteins. We found that proteins belonging to the Gene Ontology (GO) Biological process group ‘Interspecies interaction between organisms’ proteins are most important for predicting the pathogenesis of Mycoplasma strains whereas for M. pneumoniae, those belonging to ‘Quorum sensing’ and ‘Biofilm formation’ proteins are most important for predicting pathogenesis.Two Random Forest Classifiers were trained to accurately predicts host and tissue specificity based on only 12 proteins. For Mycoplasma host specificity CTP synthase complex, magnesium transporter MgtE, and glycine cleavage system are most important for correctly classifying Mycoplasma strains that infect humans, including opportunistic zoonotic strains. For tissue specificity, we found that a) known virulence and adhesions factor Methionine sulphate reductase MetA is predictive of urinary tract infecting Mycoplasmas; b) an extra cytoplasmic thiamine binding lipoprotein is most predictive of gastro-intestinal infecting Mycoplasmas; c) a type I restriction endonuclease is most predictive of respiratory infecting Mycoplasmas, and; d) a branched-chain amino acid transport system is most predictive for blood infecting Mycoplasmas. These findings can aid in predicting host and tissue specific pathogenicity of Mycoplasmas as well as provide insight in which proteins are important for specific host and tissue adaptations. Furthermore, these results underscore the usefulness of deploying genome-wide methodologies for gaining insights into pathogenicity from genome sequences.

Publisher

Cold Spring Harbor Laboratory

Reference41 articles.

1. Microbial Minimalism

2. Extreme genome reduction in symbiotic bacteria

3. Essential genes of a minimal bacterium

4. Consolidation alters motor sequence-specific distributed representations

5. Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life;Front. Cell. Infect. Microbiol,2017

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3