Czajkowski Robert
Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
Front Microbiol. 2019 Feb 14;10:138. doi: 10.3389/fmicb.2019.00138. eCollection 2019.
Soft Rot (SRP; spp. and spp., formerly known as pectinolytic spp.) are necrotrophic bacterial pathogens infecting a large number of plant species worldwide, including agriculturally-important crops. Despite the SRP importance in agriculture, little is known about the bacteriophages infecting them, and even less about the prophages present in their genomes. Prophages are recognized as factors underlying bacterial virulence, genomic diversification and ecological fitness that contribute to the novel phenotypic properties of bacterial hosts. Likewise, they are recognized as a driving force of bacterial evolution. In this study, 57 complete genomes of spp. and spp. deposited in NCBI GenBank, were analyzed for the presence of prophage-like elements. Viral sequences were discovered in 95% of bacterial genomes analyzed with the use of PHASTER, PhiSpy, and manual curation of the candidate sequences using NCBI BLAST. In total 37 seemingly intact and 48 putatively defective prophages were found. The 37 seemingly intact prophages (27 sequences in spp. genomes and 10 sequences in spp. genomes) were annotated using RAST. Analysis of the prophage genes encoding viral structural proteins allowed classification of these prophages into different families of the order (tailed bacteriophages) with the SRP prophages of the family (81% of found prophages) being the most abundant. The phylogenetic relationships between prophages were analyzed using amino acid sequences of terminase large subunit (gene ), integrase (gene ), holin (gene ), and lysin (gene ). None of these markers however proved fully useful for clear phylogenetic separation of prophages of SRP into distinct clades. Comparative analyses of prophage proteomes revealed six clusters: five present in spp. and one within spp. When screened for the presence of bacterial genes in the genomes of intact prophages, only one prophage did not contain any ORFs of bacterial origin, the other prophages contained up to 23 genes acquired from bacterial hosts. The bacterial genes present in prophages could possibly affect fitness and virulence of their hosts. The implication of prophage presence in the genomes of spp. and spp. is discussed.
软腐病菌（SRP；[多种菌属]，以前称为果胶分解菌属）是坏死营养型细菌病原体，在全球感染大量植物物种，包括具有重要农业意义的作物。尽管软腐病菌在农业中很重要，但关于感染它们的噬菌体知之甚少，对其基因组中存在的原噬菌体了解更少。原噬菌体被认为是细菌毒力、基因组多样化和生态适应性的潜在因素，这些因素有助于细菌宿主产生新的表型特性。同样，它们被认为是细菌进化的驱动力。在本研究中，对NCBI GenBank中存放的[多种菌属]的57个完整基因组进行分析，以寻找类原噬菌体元件的存在情况。使用PHASTER、PhiSpy并通过NCBI BLAST对候选序列进行人工筛选，在95%分析的细菌基因组中发现了病毒序列。总共发现了37个看似完整的和48个推定有缺陷的原噬菌体。使用RAST对37个看似完整的原噬菌体（[某种菌属]基因组中有27个序列，[另一种菌属]基因组中有10个序列）进行注释。对编码病毒结构蛋白的原噬菌体基因进行分析，可将这些原噬菌体分类到[噬菌体目]的不同科中，其中[某一科]的SRP原噬菌体（占发现原噬菌体的81%）最为丰富。使用末端酶大亚基（基因[具体名称]）、整合酶（基因[具体名称]）、孔蛋白（基因[具体名称]）和溶菌酶（基因[具体名称]）的氨基酸序列分析原噬菌体之间的系统发育关系。然而，这些标记物均未被证明对将SRP原噬菌体清晰地系统发育分离到不同进化枝中完全有用。对原噬菌体蛋白质组的比较分析揭示了六个簇：五个存在于[某种菌属]中，一个存在于[另一种菌属]中。在完整原噬菌体基因组中筛选细菌基因的存在情况时，只有一个原噬菌体不包含任何细菌来源的开放阅读框，其他原噬菌体包含多达23个从细菌宿主获得的基因。原噬菌体中存在的细菌基因可能会影响其宿主的适应性和毒力。本文讨论了原噬菌体存在于[多种菌属]基因组中的意义。
