Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer
Jazyk angličtina Země Anglie, Velká Británie Médium print
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
34908127
PubMed Central
PMC8715522
DOI
10.1093/gbe/evab280
PII: 6462190
Knihovny.cz E-zdroje
- Klíčová slova
- Tepidimonas taiwanensis, Oxford Nanopore Technologies, alkaline protease, functional annotation, hybrid assembly, polyhydroxyalkanoates,
- MeSH
- bakteriální proteiny MeSH
- Burkholderiales * genetika MeSH
- endopeptidasy MeSH
- polyhydroxyalkanoáty * genetika MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- alkaline protease MeSH Prohlížeč
- bakteriální proteiny MeSH
- endopeptidasy MeSH
- polyhydroxyalkanoáty * MeSH
Tepidimonas taiwanensis is a moderately thermophilic, Gram-negative, rod-shaped, chemoorganoheterotrophic, motile bacterium. The alkaline protease producing type strain T. taiwanensis LMG 22826T was recently reported to also be a promising producer of polyhydroxyalkanoates (PHAs)-renewable and biodegradable polymers representing an alternative to conventional plastics. Here, we present its first complete genome sequence which is also the first complete genome sequence of the whole species. The genome consists of a single 2,915,587-bp-long circular chromosome with GC content of 68.75%. Genome annotation identified 2,764 genes in total while 2,634 open reading frames belonged to protein-coding genes. Although functional annotation of the genome and division of genes into Clusters of Orthologous Groups (COGs) revealed a relatively high number of 694 genes with unknown function or unknown COG, the majority of genes were assigned a function. Most of the genes, 406 in total, were involved in energy production and conversion, and amino acid transport and metabolism. Moreover, particular key genes involved in the metabolism of PHA were identified. Knowledge of the genome in connection with the recently reported ability to produce bioplastics from the waste stream of wine production makes T. taiwanensis LMG 22826T, an ideal candidate for further genome engineering as a bacterium with high biotechnological potential.
Department of Informatics Institute of Bioinformatics Ludwig Maximilians Universität München Germany
Department of Internal Medicine Hematology and Oncology University Hospital Brno Czech Republic
Zobrazit více v PubMed
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. PubMed
Arndt D, et al.2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44(W1):W16–W21. PubMed PMC
Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM.. 2016. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genomics 17(1):356. PubMed PMC
Bolger AM, Lohse M, Usadel B.. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. PubMed PMC
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J.. 2021. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 38(12):5825–5829. PubMed PMC
Chan PP, Lowe TM.. 2019. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol. 1962:1. PubMed PMC
Chen GQ, Jiang XR.. 2018. Next generation industrial biotechnology based on extremophilic bacteria. Curr Opin Biotechnol. 50:94–100. PubMed
Chen TL, Chou YJ, Chen WM, Arun B, Young CC.. 2006. Tepidimonas taiwanensis sp. nov., a novel alkaline-protease-producing bacterium isolated from a hot spring. Extremophiles 10(1):35–40. PubMed
Couvin D, et al.2018. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 46(W1):W246–W251. PubMed PMC
Covarrubias PC, et al.2018. Occurrence, integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex. Res Microbiol. 169(10):628–637. PubMed
Engel LS, Hill JM, Caballero AR, Green LC, O’Callaghan RJ.. 1998. Protease IV, a unique extracellular protease and virulence factor from Pseudomonas aeruginosa. J Biol Chem. 273(27):16792–16797. PubMed
Gasteiger E, et al.2003. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31(13):3784–3788. PubMed PMC
Gupta R, Beg QK, Khan S, Chauhan B.. 2002. An overview on fermentation, downstream processing and properties of microbial alkaline proteases. Appl Microbiol Biotechnol. 60:4. 60:381–395. PubMed
Huerta-Cepas J, et al.2019. EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47(D1):D309–D314. PubMed PMC
Kanaya S, Yamada Y, Kudo Y, Ikemura T.. 1999. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238(1):143–155. PubMed
Kanehisa M, Goto S.. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28(1):27–30. PubMed PMC
Kawashima N, Yagi T, Kojima K.. 2019. How do bioplastics and fossil-based plastics play in a circular economy? Macromol Mater Eng. 304(9):1900383.
Koller M. 2018. A review on established and emerging fermentation schemes for microbial production of polyhydroxyalkanoate (PHA) biopolyesters. Fermentation 4(2):30.
Kolmogorov M, Yuan J, Lin Y, Pevzner PA.. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 37(5):540–546. PubMed
Kourilova X, et al.2021. Biotechnological conversion of grape pomace to poly(3-hydroxybutyrate) by moderately thermophilic bacterium Tepidimonas taiwanensis. Bioengineering 8(10):141. PubMed PMC
Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B.. 2019. MinIONQC: fast and simple quality control for MinION sequencing data. Bioinformatics 35(3):523–525. PubMed PMC
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100. PubMed PMC
Li H, Durbin R.. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760. PubMed PMC
Luo H, Zhang CT, Gao F.. 2014. Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Front Microbiol. 5:482. PubMed PMC
Meier-Kolthoff JP, Göker M.. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 10:1–10. PubMed PMC
Muhammadi S, Afzal M, Hameed S.. 2015. Bacterial polyhydroxyalkanoates-eco-friendly next generation plastic: production, biocompatibility, biodegradation, physical properties and applications. Green Chem Lett Rev.8:56–77.
Obruca S, Sedlacek P, Koller M, Kucera D, Pernicova I.. 2018. Involvement of polyhydroxyalkanoates in stress resistance of microbial cells: biotechnological consequences and applications. Biotechnol Adv. 36(3):856–870. PubMed
Rocha EPC. 2004. Codon usage bias from tRNA’s point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 14(11):2279–2286. PubMed PMC
Sabapathy PC, et al.2020. Recent developments in polyhydroxyalkanoates (PHAs) production – A review. Bioresour Technol. 306:123132. PubMed
Shogren R, Wood D, Orts W, Glenn G.. 2019. Plant-based materials and transitioning to a circular economy. Sust Prod Consump. 19:194–215.
Song W, et al.2019. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic Acids Res. 47(W1):W74–W80. PubMed PMC
Stothard P, Wishart DS.. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21(4):537–539. PubMed
Taboada B, Estrada K, Ciria R, Merino E.. 2018. Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics 34(23):4118–4120. PubMed PMC
Tatusova T, et al.2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44(14):6614–6624. PubMed PMC
Vaser R, Sović I, Nagarajan N, Šikić M.. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27(5):737–746. PubMed PMC
Walker BJ, et al.2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9(11):e112963. PubMed PMC
Yosef I, Goren MG, Qimron U.. 2012. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40(12):5569–5576. PubMed PMC