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基因组岛与家畜相关金黄色葡萄球菌基因组的进化。

Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes.

机构信息

Department of Animal Behaviour and Physiology, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.

Research Intern, Dr. Praveen K. Lab, Centre for Ecological Sciences, Indian Institute of Science, Bengaluru 560012, Karnataka, India.

出版信息

Biosci Rep. 2020 Nov 27;40(11). doi: 10.1042/BSR20202287.

DOI:10.1042/BSR20202287
PMID:33185245
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7689654/
Abstract

BACKGROUND

Genomic Islands (GIs) are commonly believed to be relics of horizontal transfer and associated with specific metabolic capacities, including virulence of the strain. Horizontal gene transfer (HGT) plays a vital role in the acquisition of GIs and the evolution and adaptation of bacterial genomes.

OBJECTIVE

The present study was designed to predict the GIs and role of HGT in evolution of livestock-associated Staphylococcus aureus (LA-SA).

METHODS

GIs were predicted with two methods namely, Ensemble algorithm for Genomic Island Detection (EGID) tool, and Seq word Sniffer script. Functional characterization of GI elements was performed with clustering of orthologs. The putative donor predictions of GIs was done with the aid of the pre_GI database.

RESULTS

The present study predicted a pan of 46 GIs across the LA-SA genomes. Functional characterization of GI sequences revealed few unique results like the presence of metabolic operons like leuABCD and folPK genes in GIs and showed the importance of GIs in the adaptation to the host niche. The developed framework for GI donor prediction results revealed Rickettsia and Mycoplasma as the major donors of GI elements.

CONCLUSIONS

The role of GIs during the evolutionary race of LA-SA could be concluded from the present study. Niche adaptation of LA-SA enhanced presumably due to these GIs. Future studies could focus on the evolutionary relationships between Rickettsia and Mycoplasma sp. with S. aureus and also the evolution of Leucine/Isoleucine mosaic operon (leuABCD).

摘要

背景

基因岛（GI）通常被认为是水平转移的遗迹，与特定的代谢能力有关，包括菌株的毒力。水平基因转移（HGT）在 GI 的获取以及细菌基因组的进化和适应中起着至关重要的作用。

目的

本研究旨在预测与牲畜相关的金黄色葡萄球菌（LA-SA）进化过程中的基因岛和 HGT 的作用。

方法

使用两种方法预测基因岛，即基因组岛检测的集成算法（EGID）工具和 Seq word Sniffer 脚本。通过同源聚类对 GI 元件进行功能特征分析。借助预 GI 数据库对 GI 的假定供体进行预测。

结果

本研究预测了 LA-SA 基因组中存在的 46 个基因岛。GI 序列的功能特征分析揭示了一些独特的结果，例如在 GI 中存在代谢操纵子，如 leuABCD 和 folPK 基因，并显示了 GI 在适应宿主小生境中的重要性。GI 供体预测框架的结果表明，立克次体和支原体是 GI 元件的主要供体。

结论

从本研究可以得出，基因岛在 LA-SA 的进化竞争中发挥了作用。LA-SA 的小生境适应能力增强可能归因于这些基因岛。未来的研究可以集中于立克次体和支原体与金黄色葡萄球菌之间的进化关系，以及亮氨酸/异亮氨酸镶嵌操纵子（leuABCD）的进化。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/ebe99708e797/bsr-40-bsr20202287-g5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/cdf4e5119695/bsr-40-bsr20202287-g1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/290d1d9e81f4/bsr-40-bsr20202287-g2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/5c23e78b6634/bsr-40-bsr20202287-g3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/b7e51b40af79/bsr-40-bsr20202287-g4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/ebe99708e797/bsr-40-bsr20202287-g5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/cdf4e5119695/bsr-40-bsr20202287-g1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/290d1d9e81f4/bsr-40-bsr20202287-g2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/5c23e78b6634/bsr-40-bsr20202287-g3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/b7e51b40af79/bsr-40-bsr20202287-g4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/175b/7689654/ebe99708e797/bsr-40-bsr20202287-g5.jpg

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