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Int J Mol Sci
2023 Feb 19;244:. doi: 10.3390/ijms24044158.
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Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity.
Balabanova L
,
Nedashkovskaya O
,
Otstavnykh N
,
Isaeva M
,
Kolpakova O
,
Pentehina I
,
Seitkalieva A
,
Noskova Y
,
Stepochkina V
,
Son O
,
Tekutyeva L
.
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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.
075-11-2021-065 the Ministry of Science and Higher Education of the Russian Federation within the framework of Decree of the Government of the Russian Federation № 218
Al Khudary,
Pseudoalteromonas arctica sp. nov., an aerobic, psychrotolerant, marine bacterium isolated from Spitzbergen.
2008, Pubmed
Al Khudary,
Pseudoalteromonas arctica sp. nov., an aerobic, psychrotolerant, marine bacterium isolated from Spitzbergen.
2008,
Pubmed
Asnicar,
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.
2020,
Pubmed
Balabanova,
Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology.
2021,
Pubmed
Bankevich,
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
2012,
Pubmed
Bauer,
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.
2017,
Pubmed
Bertelli,
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
2017,
Pubmed
Bohn,
Carotenoids, Chronic Disease Prevention and Dietary Recommendations.
2017,
Pubmed
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed
Bornstein,
LibSBML: an API library for SBML.
2008,
Pubmed
Bosi,
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.
2017,
Pubmed
Botas,
Genetic Engineering in Combination with Semi-Synthesis Leads to a New Route for Gram-Scale Production of the Immunosuppressive Natural Product Brasilicardin A.
2021,
Pubmed
Buglak,
Autoxidation and photooxidation of tetrahydrobiopterin: a theoretical study.
2021,
Pubmed
Bäumgen,
Marine Polysaccharides: Occurrence, Enzymatic Degradation and Utilization.
2021,
Pubmed
CAZypedia Consortium,
Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes.
2018,
Pubmed
Casillo,
Structural Elucidation of a Novel Lipooligosaccharide from the Antarctic Bacterium OMVs Producer Shewanella sp. HM13.
2019,
Pubmed
Celedón,
Natural Pigments of Bacterial Origin and Their Possible Biomedical Applications.
2021,
Pubmed
Chattopadhyay,
Mechanism of bacterial adaptation to low temperature.
2006,
Pubmed
Chau,
A Pseudoalteromonas Clade with Remarkable Biosynthetic Potential.
2021,
Pubmed
Chen,
Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses.
2020,
Pubmed
Chidwick,
Reconstitution and optimisation of the biosynthesis of bacterial sugar pseudaminic acid (Pse5Ac7Ac) enables preparative enzymatic synthesis of CMP-Pse5Ac7Ac.
2021,
Pubmed
Chiu,
Mechanisms and Impact of Symbiotic Phosphate Acquisition.
2019,
Pubmed
El-Naggar,
Bioproduction, characterization, anticancer and antioxidant activities of extracellular melanin pigment produced by newly isolated microbial cell factories Streptomyces glaucescens NEAE-H.
2017,
Pubmed
Feng,
Isolation of 5'-O-sulfamyladenosine and related 3'-O-β-glucosylated adenosines from the nucleocidin producer Streptomyces calvus.
2021,
Pubmed
Gelius-Dietrich,
Sybil--efficient constraint-based modelling in R.
2013,
Pubmed
Grammbitter,
An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments.
2019,
Pubmed
Gurevich,
QUAST: quality assessment tool for genome assemblies.
2013,
Pubmed
Halder,
Structural and Functional Properties, Biosynthesis, and Patenting Trends of Bacterial Succinoglycan: A Review.
2017,
Pubmed
He,
Chemical Structure, Biological Roles, Biosynthesis and Regulation of the Yellow Xanthomonadin Pigments in the Phytopathogenic Genus Xanthomonas.
2020,
Pubmed
Hettle,
Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species.
2019,
Pubmed
Ivanova,
Reclassification of Alteromonas distincta Romanenko et al. 1995 as Pseudoalteromonas distincta comb. nov.
2000,
Pubmed
Johnston,
Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation.
2021,
Pubmed
Kalyaanamoorthy,
ModelFinder: fast model selection for accurate phylogenetic estimates.
2017,
Pubmed
Karp,
The BioCyc collection of microbial genomes and metabolic pathways.
2019,
Pubmed
Kaval,
Ethanolamine Utilization in Bacteria.
2018,
Pubmed
Kearse,
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
2012,
Pubmed
Khorshidian,
An Overview of Antimicrobial Activity of Lysozyme and Its Functionality in Cheese.
2022,
Pubmed
Kim,
Functional expression and extension of staphylococcal staphyloxanthin biosynthetic pathway in Escherichia coli.
2012,
Pubmed
Kim,
PubChem in 2021: new data content and improved web interfaces.
2021,
Pubmed
Koch,
Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii.
2020,
Pubmed
Li,
Co-production of Xylooligosaccharides and Xylose From Poplar Sawdust by Recombinant Endo-1,4-β-Xylanase and β-Xylosidase Mixture Hydrolysis.
2020,
Pubmed
Liang,
Carotenoids biosynthesis and cleavage related genes from bacteria to plants.
2018,
Pubmed
Maoka,
Carotenoids as natural functional pigments.
2020,
Pubmed
Matsuyama,
Pseudoalteromonas shioyasakiensis sp. nov., a marine polysaccharide-producing bacterium.
2014,
Pubmed
Meier-Kolthoff,
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
2013,
Pubmed
Meier-Kolthoff,
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.
2019,
Pubmed
Metwally,
Optimization and multiple in vitro activity potentials of carotenoids from marine Kocuria sp. RAM1.
2022,
Pubmed
,
Echinobase
Mikkola,
Nucleotide Sugars in Chemistry and Biology.
2020,
Pubmed
Munoz-Munoz,
An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.
2017,
Pubmed
Nedashkovkaya,
Genome-Based Classification of Strain 16-SW-7, a Marine Bacterium Capable of Converting B Red Blood Cells, as Pseudoalteromonas distincta and Proposal to Reclassify Pseudoalteromonas paragorgicola as a Later Heterotypic Synonym of Pseudoalteromonas distincta.
2021,
Pubmed
Nguyen,
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
2015,
Pubmed
Norsigian,
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power.
2022,
Pubmed
Okie,
Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment.
2020,
Pubmed
Page,
Roary: rapid large-scale prokaryote pan genome analysis.
2015,
Pubmed
Parks,
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
2015,
Pubmed
Parrilli,
The art of adapting to extreme environments: The model system Pseudoalteromonas.
2021,
Pubmed
Pavoncello,
Degradation of Exogenous Fatty Acids in Escherichia coli.
2022,
Pubmed
Perret,
A novel acyl-CoA beta-transaminase characterized from a metagenome.
2011,
Pubmed
Richter,
Shifting the genomic gold standard for the prokaryotic species definition.
2009,
Pubmed
Rodriguez-Concepcion,
A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health.
2018,
Pubmed
Sawabe,
Assignment of Alteromonas elyakovii KMM 162T and five strains isolated from spot-wounded fronds of Laminaria japonica to Pseudoalteromonas elyakovii comb. nov. and the extended description of the species.
2000,
Pubmed
Schöner,
Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids.
2016,
Pubmed
Schöner,
Identification and biosynthesis of a novel xanthomonadin-dialkylresorcinol-hybrid from Azoarcus sp. BH72.
2014,
Pubmed
Seemann,
Prokka: rapid prokaryotic genome annotation.
2014,
Pubmed
Shi,
Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria.
2022,
Pubmed
Siziya,
Antioxidant Potential and Capacity of Microorganism-Sourced C30 Carotenoids-A Review.
2022,
Pubmed
Srinivasan,
Insights into the role of bacteria in vitamin A biosynthesis: Future research opportunities.
2019,
Pubmed
Stamatakis,
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
2014,
Pubmed
Sullivan,
Easyfig: a genome comparison visualizer.
2011,
Pubmed
Takemura,
Heterologous production of novel and rare C30-carotenoids using Planococcus carotenoid biosynthesis genes.
2021,
Pubmed
Tatusova,
NCBI prokaryotic genome annotation pipeline.
2016,
Pubmed
Tenconi,
Production of Prodiginines Is Part of a Programmed Cell Death Process in Streptomyces coelicolor.
2018,
Pubmed
Tran-Ly,
Microbial production of melanin and its various applications.
2020,
Pubmed
Veaudor,
Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications.
2019,
Pubmed
Vázquez-Rosas-Landa,
Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.
2020,
Pubmed
Wang,
Facile Synthesis of Sugar Nucleotides from Common Sugars by the Cascade Conversion Strategy.
2022,
Pubmed
Wang,
Facile and Stereo-Selective Synthesis of UDP-α-D-xylose and UDP-β-L-arabinose Using UDP-Sugar Pyrophosphorylase.
2018,
Pubmed
Wang,
Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence.
2018,
Pubmed
Wood,
Regulation of tyrosinase by tetrahydropteridines and H2O2.
2004,
Pubmed
Xu,
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
2019,
Pubmed
Yoon,
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
2017,
Pubmed
Zhang,
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
2018,
Pubmed
Zimmermann,
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.
2021,
Pubmed
da Silva Filho,
Comparative Analysis of Genomic Island Prediction Tools.
2018,
Pubmed
van der Beek,
Streptococcal dTDP-L-rhamnose biosynthesis enzymes: functional characterization and lead compound identification.
2019,
Pubmed