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采用分析和比较基因组学方法，预测南极洲志贺氏菌 PAMC28760 全基因组中的致病性海藻糖酶基因。

analysis and a comparative genomics approach to predict pathogenic trehalase genes in the complete genome of Antarctica Shigella sp. PAMC28760.

机构信息

Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea.

Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.

出版信息

Virulence. 2022 Dec;13(1):1502-1514. doi: 10.1080/21505594.2022.2117679.

DOI:10.1080/21505594.2022.2117679
PMID:36040103
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9450901/
Abstract

Although four species (. , , and ) have been reported, . sp. PAMC 28760, an Antarctica isolate, is the only one with a complete genome deposited in NCBI database as an uncharacterized isolate. Because it is the world's driest, windiest, and coldest continent, Antarctica provides an unfavourable environment for microorganisms. Computational analysis of genomic sequences of four species and our uncategorized Antarctica isolates sp. PAMC28760 was performed using MP3 (offline version) program to predict trehalase encoding genes as a pathogenic or non-pathogenic form. Additionally, we employed RAST and Prokka (offline version) annotation programs to determine locations of periplasmic () and cytoplasmic () trehalase genes in studied genomes. Our results showed that only 56 out of 134 strains had two different trehalase genes ( and ). It was revealed that the gene tends to be prevalent in species. In addition, both and genes were present in our strain . sp. PAMC28760. The main objective of this study was to predict the prevalence of two different trehalase genes ( and ) in the complete genome of sp. PAMC28760 and other complete genomes of species. Till date, it is the first study to show that two types of trehalase genes are involved in species, which could offer insight on how the bacteria use accessible carbohydrate like glucose produced from the trehalose degradation pathway, and importance of periplasmic trehalase involvement in bacterial virulence.

摘要

尽管已经报道了 4 个物种（ 、 、 和 ），但仅有南极洲分离株. sp. PAMC 28760 具有完整基因组，并作为未分类分离株存入 NCBI 数据库。由于南极洲是世界上最干燥、多风且最冷的大陆，因此为微生物提供了不利的环境。使用 MP3（离线版）程序对 4 个. 物种和我们未分类的南极洲分离株. sp. PAMC28760 的基因组序列进行计算分析，以预测海藻糖酶编码基因是作为致病或非致病形式存在。此外，我们还采用了 RAST 和 Prokka（离线版）注释程序来确定研究基因组中周质（ ）和细胞质（ ）海藻糖酶基因的位置。我们的结果表明，134 株菌株中仅有 56 株具有两个不同的海藻糖酶基因（ 和 ）。结果表明， 基因在. 物种中更为普遍。此外，我们的菌株. sp. PAMC28760 同时存在 和 基因。本研究的主要目的是预测. sp. PAMC28760 的完整基因组以及其他. 物种的完整基因组中两种不同的海藻糖酶基因（ 和 ）的流行情况。迄今为止，这是首次表明两种类型的海藻糖酶基因参与了. 物种，这可以深入了解细菌如何利用可利用的碳水化合物（如来自海藻糖降解途径的葡萄糖），以及周质海藻糖酶参与细菌毒力的重要性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/bd4d7a851bed/KVIR_A_2117679_F0007_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/c27d887c3d74/KVIR_A_2117679_F0001_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/1e5b540feb39/KVIR_A_2117679_F0002_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/e8aeb149c531/KVIR_A_2117679_F0003_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/252a6b2b38fe/KVIR_A_2117679_F0004_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/2f6bbe7e2b22/KVIR_A_2117679_F0005_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/18e896021cf3/KVIR_A_2117679_F0006_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/bd4d7a851bed/KVIR_A_2117679_F0007_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/c27d887c3d74/KVIR_A_2117679_F0001_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/1e5b540feb39/KVIR_A_2117679_F0002_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/e8aeb149c531/KVIR_A_2117679_F0003_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/252a6b2b38fe/KVIR_A_2117679_F0004_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/2f6bbe7e2b22/KVIR_A_2117679_F0005_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/18e896021cf3/KVIR_A_2117679_F0006_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f20f/9450901/bd4d7a851bed/KVIR_A_2117679_F0007_OC.jpg

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