Suppr超能文献

鸭疫里默氏菌Yb2株全基因组序列分析及全基因组毒力基因鉴定

Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2.

作者信息

Wang Xiaolan, Ding Chan, Wang Shaohui, Han Xiangan, Yu Shengqing

机构信息

Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, People's Republic of China.

Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, People's Republic of China

出版信息

Appl Environ Microbiol. 2015 Aug;81(15):5093-102. doi: 10.1128/AEM.00828-15. Epub 2015 May 22.

Abstract

Riemerella anatipestifer is a well-described pathogen of waterfowl and other avian species that can cause septicemic and exudative diseases. In this study, we sequenced the complete genome of R. anatipestifer strain Yb2 and analyzed it against the published genomic sequences of R. anatipestifer strains DSM15868, RA-GD, RA-CH-1, and RA-CH-2. The Yb2 genome contains one circular chromosome of 2,184,066 bp with a 35.73% GC content and no plasmid. The genome has 2,021 open reading frames that occupy 90.88% of the genome. A comparative genomic analysis revealed that genome organization is highly conserved among R. anatipestifer strains, except for four inversions of a sequence segment in Yb2. A phylogenetic analysis found that the closest neighbor of Yb2 is RA-GD. Furthermore, we constructed a library of 3,175 mutants by random transposon mutagenesis, and 100 mutants exhibiting more than 100-fold-attenuated virulence were obtained by animal screening experiments. Southern blot analysis and genetic characterization of the mutants led to the identification of 49 virulence genes. Of these, 25 encode cytoplasmic proteins, 6 encode cytoplasmic membrane proteins, 4 encode outer membrane proteins, and the subcellular localization of the remaining 14 gene products is unknown. The functional classification of orthologous-group clusters revealed that 16 genes are associated with metabolism, 6 are associated with cellular processing and signaling, and 4 are associated with information storage and processing. The functions of the other 23 genes are poorly characterized or unknown. This genome-wide study identified genes important to the virulence of R. anatipestifer.

摘要

鸭疫里默氏菌是一种已被充分描述的水禽和其他禽类病原体,可引起败血性和渗出性疾病。在本研究中,我们对鸭疫里默氏菌Yb2菌株的全基因组进行了测序,并将其与已发表的鸭疫里默氏菌DSM15868、RA-GD、RA-CH-1和RA-CH-2菌株的基因组序列进行了分析。Yb2基因组包含一条2,184,066 bp的环状染色体,GC含量为35.73%,无质粒。该基因组有2,021个开放阅读框,占基因组的90.88%。比较基因组分析表明,除Yb2中一个序列片段的四处倒位外,鸭疫里默氏菌菌株间的基因组结构高度保守。系统发育分析发现,Yb2最接近的亲缘菌株是RA-GD。此外,我们通过随机转座子诱变构建了一个包含3,175个突变体的文库,并通过动物筛选实验获得了100个毒力降低100倍以上的突变体。对这些突变体进行Southern印迹分析和遗传特征鉴定,确定了49个毒力基因。其中,25个编码细胞质蛋白,6个编码细胞质膜蛋白,4个编码外膜蛋白,其余14个基因产物的亚细胞定位未知。直系同源簇的功能分类显示,16个基因与代谢相关,6个与细胞加工和信号传导相关,4个与信息存储和加工相关。其他23个基因的功能特征不明确或未知。这项全基因组研究确定了对鸭疫里默氏菌毒力重要的基因。

相似文献

1
Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2.
Appl Environ Microbiol. 2015 Aug;81(15):5093-102. doi: 10.1128/AEM.00828-15. Epub 2015 May 22.
2
The Riemerella anatipestifer AS87_01735 Gene Encodes Nicotinamidase PncA, an Important Virulence Factor.
Appl Environ Microbiol. 2016 Sep 16;82(19):5815-23. doi: 10.1128/AEM.01829-16. Print 2016 Oct 1.
3
Characterization and cross-protection evaluation of M949_1603 gene deletion Riemerella anatipestifer mutant RA-M1.
Appl Microbiol Biotechnol. 2015 Dec;99(23):10107-16. doi: 10.1007/s00253-015-6848-y. Epub 2015 Aug 13.
6
Complete genome sequence of Riemerella anatipestifer reference strain.
J Bacteriol. 2012 Jun;194(12):3270-1. doi: 10.1128/JB.00366-12.
7
Riemerella anatipestifer gene AS87_08785 encodes a functional component, GldK, of the type IX secretion system.
Vet Microbiol. 2019 Apr;231:93-99. doi: 10.1016/j.vetmic.2019.03.006. Epub 2019 Mar 8.
8
Genome-wide mining of potential virulence-associated genes in Riemerella anatipestifer using random transposon mutagenesis.
Vet Microbiol. 2016 Jun 30;189:52-8. doi: 10.1016/j.vetmic.2016.04.014. Epub 2016 Apr 26.
9
Development of signature-tagged mutagenesis in Riemerella anatipestifer to identify genes essential for survival and pathogenesis.
Vet Microbiol. 2020 Nov;250:108857. doi: 10.1016/j.vetmic.2020.108857. Epub 2020 Sep 19.
10
The M949_1556 gene plays a role on the bacterial antigenicity and pathogenicity of Riemerella anatipestifer.
Vet Microbiol. 2015 May 15;177(1-2):193-200. doi: 10.1016/j.vetmic.2015.03.003. Epub 2015 Mar 14.

引用本文的文献

1
Genome-Wide Analysis Reveals that PhoP Regulates Pathogenicity in Riemerella anatipestifer.
Microbiol Spectr. 2022 Oct 26;10(5):e0188322. doi: 10.1128/spectrum.01883-22. Epub 2022 Oct 5.
2
Riemerella anatipestifer AS87_RS02955 Acts as a Virulence Factor and Displays Endonuclease Activity.
Appl Environ Microbiol. 2022 Oct 11;88(19):e0127622. doi: 10.1128/aem.01276-22. Epub 2022 Sep 15.
3
Identification of novel biofilm genes in avian pathogenic Escherichia coli by Tn5 transposon mutant library.
World J Microbiol Biotechnol. 2022 Jun 11;38(8):130. doi: 10.1007/s11274-022-03314-4.
5
Riemerella anatipestifer T9SS Effector SspA Functions in Bacterial Virulence and Defending Natural Host Immunity.
Appl Environ Microbiol. 2022 Jun 14;88(11):e0240921. doi: 10.1128/aem.02409-21. Epub 2022 May 16.
8
Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands.
Funct Integr Genomics. 2020 May;20(3):307-320. doi: 10.1007/s10142-019-00715-x. Epub 2019 Oct 25.
10
Interplay Between the Phenotype and Genotype, and Efflux Pumps in Drug-Resistant Strains of .
Front Microbiol. 2018 Oct 1;9:2136. doi: 10.3389/fmicb.2018.02136. eCollection 2018.

本文引用的文献

1
The AS87_04050 gene is involved in bacterial lipopolysaccharide biosynthesis and pathogenicity of Riemerella anatipestifer.
PLoS One. 2014 Oct 10;9(10):e109962. doi: 10.1371/journal.pone.0109962. eCollection 2014.
2
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
3
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
4
Rfam 11.0: 10 years of RNA families.
Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3.
5
Identification of the genes involved in Riemerella anatipestifer biofilm formation by random transposon mutagenesis.
PLoS One. 2012;7(6):e39805. doi: 10.1371/journal.pone.0039805. Epub 2012 Jun 29.
6
A TonB-dependent outer membrane receptor of Pseudomonas fluorescens: virulence and vaccine potential.
Arch Microbiol. 2012 Sep;194(9):795-802. doi: 10.1007/s00203-012-0812-3. Epub 2012 Apr 12.
7
Molecular characterization of the antimicrobial resistance of Riemerella anatipestifer isolated from ducks.
Vet Microbiol. 2012 Aug 17;158(3-4):376-83. doi: 10.1016/j.vetmic.2012.03.005. Epub 2012 Mar 13.
8
Biotin synthase: insights into radical-mediated carbon-sulfur bond formation.
Biochim Biophys Acta. 2012 Nov;1824(11):1213-22. doi: 10.1016/j.bbapap.2012.01.010. Epub 2012 Jan 28.
9
Immunoproteomics analysis of whole cell bacterial proteins of Riemerella anatipestifer.
Vet Microbiol. 2012 Jun 15;157(3-4):428-38. doi: 10.1016/j.vetmic.2012.01.009. Epub 2012 Jan 17.
10
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. doi: 10.1093/nar/gkr1060. Epub 2011 Nov 16.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验