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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,...

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Autores principales: Ullah, Numan, Yang, Naisu, Guan, Zhongxia, Xiang, Kuilin, Wang, Yali, Diaby, Mohamed, Chen, Cai, Gao, Bo, Song, Chengyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
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.
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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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