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对铜绿假单胞菌和结核分枝杆菌不稳定区域的综合研究。

Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis.

机构信息

Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, People's Republic of China.

University of Hong Kong Shenzhen Research Institute, Shenzhen Hi-Tech Industrial Park, Nanshan District, Shenzhen, People's Republic of China.

出版信息

Biomed Eng Online. 2018 Nov 20;17(Suppl 1):133. doi: 10.1186/s12938-018-0563-8.

DOI:10.1186/s12938-018-0563-8
PMID:30458797
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6245595/
Abstract

BACKGROUND

Pseudomonas aeruginosa is a common bacterium which is recognized for its association with hospital-acquired infections and its advanced antibiotic resistance mechanisms. Tuberculosis, one of the major causes of mortality, is initiated by the deposition of Mycobacterium tuberculosis. Accessory sequences shared by a subset of strains of a species play an important role in a species' evolution, antibiotic resistance and infectious potential.

RESULTS

Here, with a multiple sequence aligner, we segmented 25 P. aeruginosa genomes and 28 M. tuberculosis genomes into core blocks (include sequences shared by all the input genomes) and dispensable blocks (include sequences shared by a subset of the input genomes), respectively. For each input genome, we then constructed a scaffold consisting of its core and dispensable blocks sorted by blocks' locations on the chromosomes. Consecutive dispensable blocks on these scaffold formed instable regions. After a comprehensive study of these instable regions, three characteristics of instable regions are summarized: instable regions were short, site specific and varied in different strains. Three DNA elements (directed repeats (DRs), transposons and integrons) were then studied to see whether these DNA elements are associated with the variation of instable regions. A pipeline was developed to search for DR pairs on the flank of every instable sequence. 27 DR pairs in P. aeruginosa strains and 6 pairs in M. tuberculosis strains were found to exist in the instable regions. On the average, 14% and 12% of instable regions in P. aeruginosa strains covered transposase genes and integrase genes, respectively. In M. tuberculosis strains, an average of 43% and 8% of instable regions contain transposase genes and integrase genes, respectively.

CONCLUSIONS

Instable regions were short, site specific and varied in different strains for both P. aeruginosa and M. tuberculosis. Our experimental results showed that DRs, transposons and integrons may be associated with variation of instable regions.

摘要

背景

铜绿假单胞菌是一种常见的细菌，它与医院获得性感染及其先进的抗生素耐药机制有关。结核病是主要的死亡原因之一，由结核分枝杆菌的沉积引发。物种的一部分菌株共享的辅助序列在物种的进化、抗生素耐药性和感染潜力中起着重要作用。

结果

在这里，我们使用多序列比对器，将 25 株铜绿假单胞菌和 28 株结核分枝杆菌基因组分别划分为核心块（包含所有输入基因组共享的序列）和可分配块（包含部分输入基因组共享的序列）。对于每个输入基因组，我们构建了一个由其核心和可分配块组成的支架，这些块按染色体上的位置排序。这些支架上的连续可分配块形成不稳定区域。在对这些不稳定区域进行全面研究后，总结了不稳定区域的三个特征：不稳定区域较短、位置特异性和在不同菌株中变化。然后研究了三个 DNA 元件（直接重复序列 (DRs)、转座子和整合子），以确定这些 DNA 元件是否与不稳定区域的变化有关。开发了一个管道来搜索每个不稳定序列侧翼的 DR 对。在铜绿假单胞菌菌株中发现了 27 对 DR 对，在结核分枝杆菌菌株中发现了 6 对 DR 对，它们存在于不稳定区域中。平均而言，铜绿假单胞菌菌株中 14%和 12%的不稳定区域分别覆盖转座酶基因和整合酶基因。在结核分枝杆菌菌株中，不稳定区域分别含有 43%和 8%的转座酶基因和整合酶基因。

结论

铜绿假单胞菌和结核分枝杆菌的不稳定区域在不同菌株中均较短、位置特异性和变化。我们的实验结果表明，DRs、转座子和整合子可能与不稳定区域的变化有关。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/670224032d1f/12938_2018_563_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/45392d3113ec/12938_2018_563_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/31fa3063db00/12938_2018_563_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/3c7d92fa1d6d/12938_2018_563_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/8f1538b5e977/12938_2018_563_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/cab71aed4aaf/12938_2018_563_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/f87a776be40f/12938_2018_563_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/6c7760025a82/12938_2018_563_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/091db76a2dcd/12938_2018_563_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/670224032d1f/12938_2018_563_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/45392d3113ec/12938_2018_563_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/31fa3063db00/12938_2018_563_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/3c7d92fa1d6d/12938_2018_563_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/8f1538b5e977/12938_2018_563_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/cab71aed4aaf/12938_2018_563_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/f87a776be40f/12938_2018_563_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/6c7760025a82/12938_2018_563_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/091db76a2dcd/12938_2018_563_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72fe/6245595/670224032d1f/12938_2018_563_Fig9_HTML.jpg

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