Charakterystyka porównawcza nowo odkrytych bakteriofagów phD2B i En2 zakażających Enterobacter nimipressuralis
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2015-06-15
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Comparative characterization of two novel bacteriophages phD2B and En2 infecting Enterobacter nimipressuralis
Abstract
Bakteriofagi należą do najbardziej rozpowszechnionych i zróżnicowanych cząstek biologicznych występujących w ekosystemach.
W trakcie badań, z ekosystemów wodnych wyizolowano, zidentyfikowano i scharakteryzowano dwa nieznane dotychczas bakteriofagi zakażające Enterobacter nimipressuralis – bakterie zaangażowaną w procesy patogenezy roślin. Nowo odkryte bakteriofagi phD2B i En2, są pierwszymi wirusami, zakażającymi bakterie z gatunku E. nimipressuralis.
W genomie bakteriofaga phD2B zidentyfikowano 49 genów, a w genomie faga En2 292 genów kodujących białka i 8 genów tRNA oraz poznano funkcje, niektórych genów. Ustalono pozycje taksonomiczne fagów i zaliczono faga phD2B do rodzaju SP6-like, a En2 do rodzaju T4-like. W kolejnym etapie analiz prześledzono rearanżacje genomów phD2B i En2 oraz potwierdzono pozycje taksonomiczne stosując metody filogenetyki molekularnej. W genomie faga phD2B odkryto nietypową cechę - obecność intronu w genie kodującym dużą podjednostkę terminazy. Potwierdzono aktywność białek enzymatycznych o potencjale aplikacyjnym, zaangażowanych w degradację peptydoglikanu. Uzyskane metodą spektrometrii mas dane, pozwoliły na potwierdzenie ekspresji 84% genów faga phD2B oraz 37% genów faga En2. Ponadto analiza proteomiczna kapsydów badanych wirusów wskazuje na obecność nieznanych białek mogących pełnić rolę w strukturze kapsydów.
Bacteriophages are the most abundant biological entities in the world. They can be found wherever bacteria are present and play the crucial role in virtually all natural communities. During investigation, two novel phages infecting Enterobacter nimipressuralis were characterized. These new phages (phD2B and En2) are the first known viruses infecting E. nimipressuralis – a plant pathogen, associated with the wetwood disease. The aim of the study was to characterize of the phages’ morphology, organization of their genomes and gain insight into the phages’ proteomes. Based on the morphology, phage phD2B was classified as podovirus, while phage En2 belongs to the Myoviridae family. The examination of the phages’ genomes revealed 49 predicted CDS in the phD2B genome and 292 CDS and 8 tRNA in the En2 genome. The taxonomic positions, evolutionary relationships and genomic rearrangements of both phages were analyzed. An interesting feature of the phD2B genome was the identification of the large terminase subunit gene containing an intron. Proteomic analysis confirmed the expression of 84% and 37% predicted genes in the genomes of phD2B and En2, respectively. Also, the activity of the enzymes involved in the peptidoglycan degradation, which can be potentially useful, was determined. The virion proteomics, revealed unknown proteins which can be important in the functioning of capsid.
Bacteriophages are the most abundant biological entities in the world. They can be found wherever bacteria are present and play the crucial role in virtually all natural communities. During investigation, two novel phages infecting Enterobacter nimipressuralis were characterized. These new phages (phD2B and En2) are the first known viruses infecting E. nimipressuralis – a plant pathogen, associated with the wetwood disease. The aim of the study was to characterize of the phages’ morphology, organization of their genomes and gain insight into the phages’ proteomes. Based on the morphology, phage phD2B was classified as podovirus, while phage En2 belongs to the Myoviridae family. The examination of the phages’ genomes revealed 49 predicted CDS in the phD2B genome and 292 CDS and 8 tRNA in the En2 genome. The taxonomic positions, evolutionary relationships and genomic rearrangements of both phages were analyzed. An interesting feature of the phD2B genome was the identification of the large terminase subunit gene containing an intron. Proteomic analysis confirmed the expression of 84% and 37% predicted genes in the genomes of phD2B and En2, respectively. Also, the activity of the enzymes involved in the peptidoglycan degradation, which can be potentially useful, was determined. The virion proteomics, revealed unknown proteins which can be important in the functioning of capsid.
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Keywords
bakteriofagi, bacteriophages, genomika, genomic, proteomika, proteomic, enterobacter, enterobacter