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Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea
Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis,...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606334/ https://www.ncbi.nlm.nih.gov/pubmed/37895260 http://dx.doi.org/10.3390/genes14101911 |
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author | Ullah, Numan Yang, Naisu Guan, Zhongxia Xiang, Kuilin Wang, Yali Diaby, Mohamed Chen, Cai Gao, Bo Song, Chengyi |
author_facet | Ullah, Numan Yang, Naisu Guan, Zhongxia Xiang, Kuilin Wang, Yali Diaby, Mohamed Chen, Cai Gao, Bo Song, Chengyi |
author_sort | Ullah, Numan |
collection | PubMed |
description | Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins. |
format | Online Article Text |
id | pubmed-10606334 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-106063342023-10-28 Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea Ullah, Numan Yang, Naisu Guan, Zhongxia Xiang, Kuilin Wang, Yali Diaby, Mohamed Chen, Cai Gao, Bo Song, Chengyi Genes (Basel) Article Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins. MDPI 2023-10-06 /pmc/articles/PMC10606334/ /pubmed/37895260 http://dx.doi.org/10.3390/genes14101911 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Ullah, Numan Yang, Naisu Guan, Zhongxia Xiang, Kuilin Wang, Yali Diaby, Mohamed Chen, Cai Gao, Bo Song, Chengyi Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea |
title | Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea |
title_full | Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea |
title_fullStr | Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea |
title_full_unstemmed | Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea |
title_short | Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea |
title_sort | comparative analysis and phylogenetic insights of cas14-homology proteins in bacteria and archaea |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606334/ https://www.ncbi.nlm.nih.gov/pubmed/37895260 http://dx.doi.org/10.3390/genes14101911 |
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