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Lookup NU author(s): Dr Maria Del Carmen Montero-CalasanzORCiD
This is the authors' accepted manuscript of an article that has been published in its final definitive form by Oxford University Press, 2020.
For re-use rights please refer to the publisher's terms and conditions.
Motivation: A small amount of research is focused on investigation of rhodopsins in cultivated bacteria isolated from non-aquatic environments. Furthermore, the abundance of these proteins in strains from hot and arid habitats was not reported previously. Since there is an insignificant amount of such isolates, the enigmatic role of the rhodopsins in dry ecological niches is still poorly understood. The members of the family Geodermatophilaceae could be used as interesting objects to search for new rhodopsin genes that will provide novel insights into versatility and importance of these proteins in non-aquatic conditions. Results: This is the first report of the abundance of different rhodopsins in cultivated bacteria isolated from hot and arid ecological niches. A total of 31 rhodopsin genes were identified in 51 analyzed genomes of strains belonging to the family Geodermatophilaceae. Overall, 88% of the strains harbouring rhodopsins are isolated from non-aquatic environments. It was found that 82% of strains belonging to the genus Geodermatophilus have at least one gene as compared to 38% of strains of other genera which contain rhodopsins. Analysis of key amino acids revealed two types of the studied proteins: DTE type (putative proton pump) and NDQ type (putative sodium pump). Proton pumps were divided into two subtypes (DTEW and DTEF) according to phylogenetic analysis and the presence of highly conserved tryptophan or phenylalanine at position 182. Among all studied rhodopsins DTEF subtype is the most unique one, identified only in this family.
Author(s): Tarlachkov SV, Shevchuk TV, Montero-Calasanz MdC, Starodumova IP
Publication type: Article
Publication status: Published
Journal: Bioinformatics
Year: 2020
Volume: 36
Issue: 6
Pages: 1668–1672
Print publication date: 15/03/2020
Online publication date: 11/11/2019
Acceptance date: 10/11/2019
Date deposited: 10/12/2019
ISSN (print): 1367-4803
ISSN (electronic): 1460-2059
Publisher: Oxford University Press
URL: https://doi.org/10.1093/bioinformatics/btz840
DOI: 10.1093/bioinformatics/btz840
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