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Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter.
Wang, Liang; Yang, Jianye; Xu, Yaping; Piao, Xue; Lv, Jichang.
Afiliação
  • Wang L; 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Con
  • Yang J; 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Con
  • Xu Y; 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Con
  • Piao X; 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Con
  • Lv J; 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Con
Curr Genomics ; 20(2): 115-123, 2019 Feb.
Article em En | MEDLINE | ID: mdl-31555062
ABSTRACT

BACKGROUND:

Proteins may have none, single, double, or multiple domains, while a single domain may appear in multiple proteins. Their distribution patterns may have impacts on bacterial physi-ology and lifestyle.

Objective:

This study aims to understand how domains are distributed and duplicated in bacterial prote-omes, in order to better understand bacterial physiology and lifestyles.

METHODS:

In this study, we used 16712 Hidden Markov Models to screen 944 bacterial reference prote-omes versus a threshold E-value<0.001. The number of non-redundant domains and duplication rates of redundant domains for each species were calculated. The unique domains, if any, were also identified for each species. In addition, the properties of no-domain proteins were investigated in terms of physico-chemical properties.

RESULTS:

The increasing number of non-redundant domains for a bacterial proteome follows the trend of an asymptotic function. The domain duplication rate is positively correlated with proteome size and in-creases more rapidly. The high percentage of single-domain proteins is more associated with small pro-teome size. For each proteome, unique domains were also obtained. Moreover, no-domain proteins show differences with the other three groups for several physicochemical properties analysed in this study.

CONCLUSION:

The study confirmed that a low domain duplication rate and a high percentage of single-domain proteins are more likely to be associated with bacterial host-dependent or restricted niche-adapted lifestyle. In addition, the unique lifestyle and physiology were revealed based on the analysis of species-specific domains and core domain interactions or co-occurrences.
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2019 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2019 Tipo de documento: Article