Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities

Oscar Salgado; Sergio Guajardo-Leiva; Ana Moya-Beltrán; Carla Barbosa; Christina Ridley; Javier Tamayo-Leiva; Raquel Quatrini; Francisco J M Mojica; Beatriz Díez

doi:10.3389/fmicb.2022.1069452

Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities

Front Microbiol. 2022 Dec 2:13:1069452. doi: 10.3389/fmicb.2022.1069452. eCollection 2022.

Authors

Oscar Salgado^{1

2}, Sergio Guajardo-Leiva^{3

4}, Ana Moya-Beltrán⁵, Carla Barbosa^{1

6

7}, Christina Ridley¹, Javier Tamayo-Leiva¹, Raquel Quatrini^{5

8}, Francisco J M Mojica⁹, Beatriz Díez^{1

10

11}

Affiliations

¹ Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile.
² Núcleo de Ciencias Naturales y Exactas, Universidad Adventista de Chile, Chillán, Chile.
³ Departamento de Microbiología, Universidad de Talca, Talca, Chile.
⁴ Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile.
⁵ Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile.
⁶ Departamento de Geología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile.
⁷ Centro de Excelencia en Geotermia de Los Andes (CEGA-Fondap), Santiago, Chile.
⁸ Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.
⁹ Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
¹⁰ Center for Climate and Resilience Research (CR)2, Santiago, Chile.
¹¹ Millennium Institute Center for Genome Regulation (CGR), Santiago, Chile.

Abstract

The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42-80°C, pH 6-9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.

Keywords: CRISPR-Cas; Cas1; casposase; hot spring; phylogenomic.

Grants and funding

This work was financed in part by FONDECYT regular N° 1190998 (ANID) and Iniciativa de Investigación UnACh 2021-157-Unach. OS and JT-L were supported in part by ANID National Doctoral Scholarship (Beca de Doctorado Nacional ANID) N° 21172022 and 21171048, respectively. SG-L was supported by ANID FONDECYT Postdoctoral N° 3210547. AM-B and RQ were supported by Centro Ciencia and Vida, FB210008, Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia de ANID, and FONDECYT regular N° 1221035 (ANID). FJMM acknowledged research support by the Conselleria d’Innovació, Universitats, Ciència i Societat Digital from Generalitat Valenciana, research project PROMETEO/2021/057. BD acknowledged the Millennium Institute Center for Genome Regulation, Project ICN2021-044 supported by the ANID Millennium Scientific Initiative (Chile).