Bioinformatic survey of CRISPR loci across 15 Serratia species

IF 3.9 3区 生物学 Q2 MICROBIOLOGY MicrobiologyOpen Pub Date : 2023-03-02 DOI:10.1002/mbo3.1339
Maria Scrascia, Roberta Roberto, Pietro D'Addabbo, Yosra Ahmed, Francesco Porcelli, Marta Oliva, Carla Calia, Angelo Marzella, Carlo Pazzani
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Abstract

The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins (CRISPR–Cas) system of prokaryotes is an adaptative immune defense mechanism to protect themselves from invading genetic elements (e.g., phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order of Enterobacterales). For some genera, data on CRISPR–Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high-quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotica, and ureilytica. Apart from subtypes I-E and I-F1 which had previously been identified in marcescens, we report that of I-C and the I-E unique locus 1, I-E*, and I-F1 unique locus 1. Analysis of the genomic contexts for CRISPR loci revealed mdtN-phnP as the region mostly shared (grimesii, inhibens, marcescens, nematodiphila, plymuthica, rubidaea, and Serratia sp.). Three new contexts detected in genomes of rubidaea and fonticola (puu genes-mnmA) and rubidaea (osmE-soxG and ampC-yebZ) were also found. The plasmid and/or phage origin of spacers was also established.

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15种沙雷氏菌CRISPR基因座的生物信息学调查
原核生物的簇状规则间隔短回文重复序列和crispr相关蛋白(CRISPR-Cas)系统是一种适应性免疫防御机制,用于保护自身免受入侵遗传元件(如噬菌体和质粒)的侵害。描述这些原核生物系统遗传组织的研究主要报道了肠杆菌科(现在重组为肠杆菌目)。对于某些属,CRISPR-Cas系统的数据仍然很差,例如在沙雷氏菌(现在是耶尔森科的一部分)的情况下,数据仅限于marcescens物种的几个基因组。本研究描述了在146个沙雷氏菌全基因组和336个高质量序列中检测到CRISPR位点,这些序列可用于ficaria、fonticola、grimesii、inhibens、liquefaciens、marcesens、nematodiphila、odorifera、oryzae、plymuthica、proteomaculans、quinivorans、rubidaea、symbiotica和ureilytica。除了先前在粘质系中发现的I-E和I-F1亚型外,我们还报道了I-C和I-E独特位点1、I-E*和I-F1独特位点1的亚型。CRISPR基因座的基因组背景分析显示,mdtN-phnP是主要共享的区域(grimesii, inhibens, marcescens, nematodiphila, plymuthica, rubidaea和Serratia sp.)。此外,还发现了3个新基因背景(puu基因- mnma)和3个新基因背景(osmE-soxG和ampC-yebZ)。也确定了间隔物的质粒和/或噬菌体来源。
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来源期刊
MicrobiologyOpen
MicrobiologyOpen MICROBIOLOGY-
CiteScore
8.00
自引率
0.00%
发文量
78
审稿时长
20 weeks
期刊介绍: MicrobiologyOpen is a peer reviewed, fully open access, broad-scope, and interdisciplinary journal delivering rapid decisions and fast publication of microbial science, a field which is undergoing a profound and exciting evolution in this post-genomic era. The journal aims to serve the research community by providing a vehicle for authors wishing to publish quality research in both fundamental and applied microbiology. Our goal is to publish articles that stimulate discussion and debate, as well as add to our knowledge base and further the understanding of microbial interactions and microbial processes. MicrobiologyOpen gives prompt and equal consideration to articles reporting theoretical, experimental, applied, and descriptive work in all aspects of bacteriology, virology, mycology and protistology, including, but not limited to: - agriculture - antimicrobial resistance - astrobiology - biochemistry - biotechnology - cell and molecular biology - clinical microbiology - computational, systems, and synthetic microbiology - environmental science - evolutionary biology, ecology, and systematics - food science and technology - genetics and genomics - geobiology and earth science - host-microbe interactions - infectious diseases - natural products discovery - pharmaceutical and medicinal chemistry - physiology - plant pathology - veterinary microbiology We will consider submissions across unicellular and cell-cluster organisms: prokaryotes (bacteria, archaea) and eukaryotes (fungi, protists, microalgae, lichens), as well as viruses and prions infecting or interacting with microorganisms, plants and animals, including genetic, biochemical, biophysical, bioinformatic and structural analyses. The journal features Original Articles (including full Research articles, Method articles, and Short Communications), Commentaries, Reviews, and Editorials. Original papers must report well-conducted research with conclusions supported by the data presented in the article. We also support confirmatory research and aim to work with authors to meet reviewer expectations. MicrobiologyOpen publishes articles submitted directly to the journal and those referred from other Wiley journals.
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