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

• Published in: International journal of molecular sciences Vol. 24; no. 4; p. 4158
• Main Authors: Balabanova, Larissa, Nedashkovskaya, Olga, Otstavnykh, Nadezhda, Isaeva, Marina, Kolpakova, Oksana, Pentehina, Iuliia, Seitkalieva, Aleksandra, Noskova, Yulia, Stepochkina, Varvara, Son, Oksana, Tekutyeva, Liudmila
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 19-02-2023; MDPI
• Subjects: Alginates; Alginic acid; Annotations; Aromatic compounds; Bacteria; Biosynthesis; biosynthetic gene clusters; Biotechnology; Carotenoids; Carotenoids - metabolism; Carrageenan; Computer applications; Ecophysiology; Environmental conditions; Esterification; Folic acid; Gene clusters; Genes; Genomes; Genomics; Glycosylation; Heterogeneity; Invertebrates; marine bacteria; Metabolic pathways; Metabolism; Metabolites; Microbiota; pan-genome; Pathogens; Phenotype; phenotype variability; Phenotypes; Phosphatase; phylogenomic relationships; Phylogeny; Pigmentation; Pigments; Polysaccharides; Pseudoalteromonas; Pseudoalteromonas - genetics; Resorcinol; Secondary metabolites; Survivability; Virulence; Vitamin B12; biosynthetic gene clusters; phylogenomic relationships; Pseudoalteromonas; metabolic reconstruction; pan-genome; marine bacteria; phenotype variability; metabolic pathways; aryl polyene hybrid
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24044158

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
and an inability to use common molecular markers make their identification within the genus
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
, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics.
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.