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Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa an...

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Autores principales: Balabanova, Larissa, Nedashkovskaya, Olga, Otstavnykh, Nadezhda, Isaeva, Marina, Kolpakova, Oksana, Pentehina, Iuliia, Seitkalieva, Aleksandra, Noskova, Yulia, Stepochkina, Varvara, Son, Oksana, Tekutyeva, Liudmila
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9966250/
https://www.ncbi.nlm.nih.gov/pubmed/36835570
http://dx.doi.org/10.3390/ijms24044158
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author Balabanova, Larissa
Nedashkovskaya, Olga
Otstavnykh, Nadezhda
Isaeva, Marina
Kolpakova, Oksana
Pentehina, Iuliia
Seitkalieva, Aleksandra
Noskova, Yulia
Stepochkina, Varvara
Son, Oksana
Tekutyeva, Liudmila
author_facet Balabanova, Larissa
Nedashkovskaya, Olga
Otstavnykh, Nadezhda
Isaeva, Marina
Kolpakova, Oksana
Pentehina, Iuliia
Seitkalieva, Aleksandra
Noskova, Yulia
Stepochkina, Varvara
Son, Oksana
Tekutyeva, Liudmila
author_sort Balabanova, Larissa
collection PubMed
description Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4′-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.
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spelling pubmed-99662502023-02-26 Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity Balabanova, Larissa Nedashkovskaya, Olga Otstavnykh, Nadezhda Isaeva, Marina Kolpakova, Oksana Pentehina, Iuliia Seitkalieva, Aleksandra Noskova, Yulia Stepochkina, Varvara Son, Oksana Tekutyeva, Liudmila Int J Mol Sci Article Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4′-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific. MDPI 2023-02-19 /pmc/articles/PMC9966250/ /pubmed/36835570 http://dx.doi.org/10.3390/ijms24044158 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
Balabanova, Larissa
Nedashkovskaya, Olga
Otstavnykh, Nadezhda
Isaeva, Marina
Kolpakova, Oksana
Pentehina, Iuliia
Seitkalieva, Aleksandra
Noskova, Yulia
Stepochkina, Varvara
Son, Oksana
Tekutyeva, Liudmila
Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity
title Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity
title_full Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity
title_fullStr Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity
title_full_unstemmed Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity
title_short Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity
title_sort computational insight into intraspecies distinctions in pseudoalteromonas distincta: carotenoid-like synthesis traits and genomic heterogeneity
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9966250/
https://www.ncbi.nlm.nih.gov/pubmed/36835570
http://dx.doi.org/10.3390/ijms24044158
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