Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

被引:32
|
作者
Tekedar, Hasan C. [1 ]
Karsi, Attila [1 ]
Reddy, Joseph S. [2 ]
Nho, Seong W. [1 ]
Kalindamar, Safak [1 ]
Lawrence, Mark L. [1 ]
机构
[1] Mississippi State Univ, Coll Vet Med, Mississippi State, MS 39762 USA
[2] Mayo Clin, Dept Hlth Sci Res, Jacksonville, FL 32224 USA
来源
FRONTIERS IN MICROBIOLOGY | 2017年 / 8卷
基金
美国农业部;
关键词
Flavobacterium columnare; comparative genomics analysis; fish health; denitrification; RNA-Seq; GLIDING MOTILITY; PATHOGENICITY ISLANDS; INSERTION SEQUENCES; SECRETION SYSTEMS; FLEXIBACTER-COLUMNARIS; KYOTO ENCYCLOPEDIA; VIRULENCE FACTORS; IRON ACQUISITION; II SECRETION; UREA CYCLE;
D O I
10.3389/fmicb.2017.00588
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Flavobacterium columnare is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of F columnare and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of F columnare strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other Flavobacterium genomes. In this analysis, we identified predicted proteins whose functions indicate F columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of F columnare ATCC 49512 with nitrate supplementation was detected experimentally. F columnare ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other Flavobacterium species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in F columnare along with F johnsoniae and F branchiophilum. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of F columnare ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.
引用
收藏
页数:21
相关论文
共 50 条
  • [21] Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum
    Castillo, Daniel
    Christiansen, Roi Hammershaimb
    Dalsgaard, Inger
    Madsen, Lone
    Espejo, Romilio
    Middelboe, Mathias
    PLOS ONE, 2016, 11 (04):
  • [22] Molecular typing of isolates of the fish pathogen, Flavobacterium columnare, by single-strand conformation polymorphism analysis
    Olivares-Fuster, Oscar
    Shoemaker, Craig A.
    Klesius, Phillip H.
    Arias, Covadonga R.
    FEMS MICROBIOLOGY LETTERS, 2007, 269 (01) : 63 - 69
  • [23] Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp Strain MED134
    Gonzalez, Jose M.
    Pinhassi, Jarone
    Fernandez-Gomez, Beatriz
    Coll-Llado, Montserrat
    Gonzalez-Velazquez, Monica
    Puigbo, Pere
    Jaenicke, Sebastian
    Gomez-Consarnau, Laura
    Fernandez-Guerra, Antoni
    Goesmann, Alexander
    Pedros-Alio, Carlos
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2011, 77 (24) : 8676 - 8686
  • [24] Transcriptome analysis of head kidney and liver in grass carp (Ctenopharyngodon idella) symptomatically or asymptomatically infected with Flavobacterium columnare
    Jin, Yong
    Li, Nan
    Chen, Shan Nan
    Lu, Yi Shan
    Gan, Zhen
    Nie, Pin
    FISH & SHELLFISH IMMUNOLOGY, 2025, 161
  • [25] Transcriptomic analysis of the head kidney of Topmouth culter (Culter alburnus) infected with Flavobacterium columnare with an emphasis on phagosome pathway
    Zhao, Lijuan
    Tu, Jiagang
    Zhang, Yulei
    Wang, Jinfu
    Yang, Ling
    Wang, Weimin
    Wu, Zaohe
    Meng, Qinglei
    Lin, Li
    FISH & SHELLFISH IMMUNOLOGY, 2016, 57 : 413 - 418
  • [26] Deciphering the Molecular Basis for Attenuation of Flavobacterium columnare Strain Fc1723 Used as Modified Live Vaccine against Columnaris Disease
    Cai, Wenlong
    Arias, Covadonga R.
    VACCINES, 2021, 9 (11)
  • [27] Improved pulsed-field gel electrophoresis procedure for the analysis of Flavobacterium columnare isolates previously affected by DNA degradation
    Soto, Esteban
    Mauel, Michael
    Lawrence, Mark
    VETERINARY MICROBIOLOGY, 2008, 128 (1-2) : 207 - 212
  • [28] Molecular characteristics, polymorphism and expression analysis of mhc II in yellow catfish(pelteobagrus fulvidraco)responding to Flavobacterium columnare infection
    Wang, Bingchao
    Zhu, Fangzheng
    Shi, Zechao
    Huang, Zhenyu
    Sun, Ruhan
    Wang, Qingchao
    Gang, Ouyang
    Ji, Wei
    FISH & SHELLFISH IMMUNOLOGY, 2022, 125 : 90 - 100
  • [29] Complementary DNA sequences of the constant regions of T-cell antigen receptors α, β and γ in mandarin fish, Siniperca chuatsi Basilewsky, and their transcriptional changes after stimulation with Flavobacterium columnare
    Tian, J. Y.
    Qi, Z. T.
    Wu, N.
    Chang, M. X.
    Nie, P.
    JOURNAL OF FISH DISEASES, 2014, 37 (02) : 89 - 101
  • [30] Expression profiling analysis of immune-related genes in channel catfish (Ictalurus punctatus) skin mucus following Flavobacterium columnare challenge
    Ren, Yichao
    Zhao, Honggang
    Su, Baofeng
    Peatman, Eric
    Li, Chao
    FISH & SHELLFISH IMMUNOLOGY, 2015, 46 (02) : 537 - 542