Conserved insertions in protein sequences for molecular studies in the genus Rhodomicrobium
Keywords:
Rhodomicrobium; identificación; marcadores moleculares; indeles.Abstract
The genus Rhodomicrobium comprises species with agricultural and environmental importance. However, few investigations have been conducted to identify molecular markers that could be used to distinguish members of Rhodomicrobium from other groups of bacteria. Conserved signature indels (insertions and deletions) in protein sequences are useful for evolutionary and taxonomic studies in bacteria. Homologous sequences of the proteins NAD+ dependent DNA ligase and Serine-tRNA synthetase were obtained from the UniprotKB/Swiss-Prot database and aligned using MUSCLE programme. Phylogenomic analysis was performed through the Maximum Likelihood method with RAxML. Insertions were identified which support the monophyly of this genus and confirm that Rhodomicrobium lacus forms a sister group of R. vannielii and R. udaipurense. Thus, the insertions analyzed constitute important molecular markers for taxonomic and evolutionary studies in Rhodomicrobium, and also for future biochemical or functional studies in those enzymes.
References
Hördt, A. y otros. “Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria”. Frontiers in Microbiology. 2020, 11, p. 468. https://doi.org/10.3389/fmicb.2020.00468 2. Parte, A. C. “LPSN–List of Prokaryotic names with Standing in Nomenclature (bacterio. net), 20 years on”. International Journal of Systematic and Evolutionary Microbiology. 2018, 68(6), 1825-1829. https://doi.org/10.1099/ ijsem.0.002786
Tushar, L.; Sasikala, C.; Ramana, C. V. “Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis”. DNA Research. 2014, 21(6), 639-647. https://doi.org/10.1093/dnares/dsu026
Conners, E. M.; Davenport, E. J.; Bose, A. “Revised Draft Genome Sequences of Rhodomicrobium vannielii ATCC 17100 and Rhodomicrobium udaipurense JA643”. Microbiology resource announcements. 2021, 10(13), p. e00022-21. https://doi.org/10.1128/MRA.00022-21 5. Suresh, G.; Kumar, D.; Uppada, J.; Ch. S.; Ramana, Ch. V. “Rhodomicrobium lacus sp. nov., an alkalitolerant bacterium isolated from Umiam lake, Shillong, India”. International Journal of Systematic and Evolutionary Microbiology. 2020, 70(1), 662-667. https://doi.org/10.1099/ijsem.0.003813
Gupta, R. “Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin’s views on classification”. FEMS Microbiology Reviews. 2016, 40(4), 520–553. https://doi.org/10.1093/femsre/fuw011
The UniProt Consortium. “UniProt: the universal protein knowledgebase in 2021”. Nucleic Acids Research. 2021, 49 (D1), D480-D489. https://doi.org/10.1093/nar/gkaa1100
Altschul, S. F. y otros. “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”. Nucleic Acids Research. 1997, 25, 3389-3402. https://doi.org/10.1093/nar/25.17.3389 9. Pearson, W. R. “An introduction to sequence similarity (“homology”) searching”. Current Protocols in Bioinformatics. 2013, 42(1), p. 3.1. 1-3.1.8 https://doi.org/10.1002/0471250953.bi0301s42 10. Edgar, R. C. “MUSCLE: multiple sequence alignment with high accuracy and high throughput”. Nucleic Acids Research. 2004, 32(5), 1792-1797. https://doi.org/10.1093/nar/gkh340
Olson, R. D. y otros. “Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR”. Nucleic Acids Research. 2022, 1, D678-D689. https://doi.org/10.1093/nar/gkac1003
Kozlov, A. M. y otros. “RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference”. Bioinformatics, 2019, 35(21), 4453-4455. https://doi.org/10.1093/bioinformatics/btz305
Stamatakis, A. “How many bootstrap replicates are necessary?”. Journal of Computational Biology, 2010, 17(3), 337-354. https://doi.org/10.1089/cmb.2009.0179
Gupta, R. S. “Applications of genome sequences for discovering characteristics that are unique to different groups of organisms and provide insights into evolutionary relationships”. Frontiers in Genetics. 2016, 7, p. 27. https://doi.org/10.3389/fgene.2016.00027 15. Gupta, R. y otros. “SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics”. Journal of Biological Chemistry. 2020, 295(33), 11742-11753. https://doi.org/10.1074/jbc.RA120.014873
Khadka, B.; Persaud, D.; Gupta, R. S. “Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles”. Microorganisms. 2020, 8(1), p. 59. https://doi:10.3390/microorganisms8010059 17. Hu, T. y otros. “Succession of diazotroph community and functional gene response to inoculating swine manure compost with a lignocellulose-degrading consortium”. Bioresource Technology, 2021, 337, p. 125469. https://doi.org/10.1016/j.biortech.2021.125469
Braun, B.; Künzel, S.; Schröder, J.; Szewzyk, U. “Draft genome sequence of strain R_RK_3, an iron-depositing isolate of the genus Rhodomicrobium, isolated from a dewatering well of an opencast mine”. Genome Announcements. 2017, 5(34), p. e00864-17. https://doi.org/10.1128/genomeA.00864-17
Adeolu, M. y otros. “Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.”. International Journal of Systematic and Evolutionary Microbiology. 2016, 66(12), 5575-5599. https://doi.org/10.1099/ijsem.0.001485
Cutiño Jiménez, A. M.; Menck, C. F. M.; Cambas, Y. T.; Díaz-Pérez, J. C. “Protein signatures to identify the different genera within the Xanthomonadaceae family”. Brazilian Journal of Microbiology. 2020, 51(4), 1515-1526. https://doi.org/10.1007/s42770-020-00304-2
Naushad, S. y otros. “A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives”. Antonie Van Leeuwenhoek. 2015, 107(2), 467-485. https://doi: 10.1007/s10482-014-0344-8
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