Cargando…
Bioinformatic survey of CRISPR loci across 15 Serratia species
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 o...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981886/ https://www.ncbi.nlm.nih.gov/pubmed/37186230 http://dx.doi.org/10.1002/mbo3.1339 |
_version_ | 1784900203210342400 |
---|---|
author | Scrascia, Maria Roberto, Roberta D'Addabbo, Pietro Ahmed, Yosra Porcelli, Francesco Oliva, Marta Calia, Carla Marzella, Angelo Pazzani, Carlo |
author_facet | Scrascia, Maria Roberto, Roberta D'Addabbo, Pietro Ahmed, Yosra Porcelli, Francesco Oliva, Marta Calia, Carla Marzella, Angelo Pazzani, Carlo |
author_sort | Scrascia, Maria |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9981886 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-99818862023-03-04 Bioinformatic survey of CRISPR loci across 15 Serratia species Scrascia, Maria Roberto, Roberta D'Addabbo, Pietro Ahmed, Yosra Porcelli, Francesco Oliva, Marta Calia, Carla Marzella, Angelo Pazzani, Carlo Microbiologyopen Original Articles 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. John Wiley and Sons Inc. 2023-03-02 /pmc/articles/PMC9981886/ /pubmed/37186230 http://dx.doi.org/10.1002/mbo3.1339 Text en © 2022 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Articles Scrascia, Maria Roberto, Roberta D'Addabbo, Pietro Ahmed, Yosra Porcelli, Francesco Oliva, Marta Calia, Carla Marzella, Angelo Pazzani, Carlo Bioinformatic survey of CRISPR loci across 15 Serratia species |
title | Bioinformatic survey of CRISPR loci across 15 Serratia species |
title_full | Bioinformatic survey of CRISPR loci across 15 Serratia species |
title_fullStr | Bioinformatic survey of CRISPR loci across 15 Serratia species |
title_full_unstemmed | Bioinformatic survey of CRISPR loci across 15 Serratia species |
title_short | Bioinformatic survey of CRISPR loci across 15 Serratia species |
title_sort | bioinformatic survey of crispr loci across 15 serratia species |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981886/ https://www.ncbi.nlm.nih.gov/pubmed/37186230 http://dx.doi.org/10.1002/mbo3.1339 |
work_keys_str_mv | AT scrasciamaria bioinformaticsurveyofcrisprlociacross15serratiaspecies AT robertoroberta bioinformaticsurveyofcrisprlociacross15serratiaspecies AT daddabbopietro bioinformaticsurveyofcrisprlociacross15serratiaspecies AT ahmedyosra bioinformaticsurveyofcrisprlociacross15serratiaspecies AT porcellifrancesco bioinformaticsurveyofcrisprlociacross15serratiaspecies AT olivamarta bioinformaticsurveyofcrisprlociacross15serratiaspecies AT caliacarla bioinformaticsurveyofcrisprlociacross15serratiaspecies AT marzellaangelo bioinformaticsurveyofcrisprlociacross15serratiaspecies AT pazzanicarlo bioinformaticsurveyofcrisprlociacross15serratiaspecies |