Draft genome sequence of Psychrobacter nivimaris LAMA 639 and its biotechnological potential.

Autor:	Staloch BEK; School of Sea, Science and Technology, University of Vale do Itajaí (UNIVALI), 88302-202, Itajaí-SC, Brazil., Niero H; Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), 13083-100, Campinas-SP, Brazil.; Faculty of Pharmaceutical Sciences, University of Campinas (UNICAMP), 13083-871 Campinas-SP, Brazil., Freitas RC; School of Sea, Science and Technology, University of Vale do Itajaí (UNIVALI), 88302-202, Itajaí-SC, Brazil., Ballone P; Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), 13083-100, Campinas-SP, Brazil.; Institute of Biology, University of Campinas (UNICAMP), 13083-862 Campinas-SP, Brazil., Rodrigues-Costa F; Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), 13083-100, Campinas-SP, Brazil.; Institute of Biology, University of Campinas (UNICAMP), 13083-862 Campinas-SP, Brazil., Trivella DBB; Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), 13083-100, Campinas-SP, Brazil., Dessen A; Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), 13083-100, Campinas-SP, Brazil.; Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS) F-38044, Grenoble, France., Silva MACD; School of Sea, Science and Technology, University of Vale do Itajaí (UNIVALI), 88302-202, Itajaí-SC, Brazil., Lima AOS; School of Sea, Science and Technology, University of Vale do Itajaí (UNIVALI), 88302-202, Itajaí-SC, Brazil.
Jazyk:	angličtina
Zdroj:	Data in brief [Data Brief] 2022 Feb 05; Vol. 41, pp. 107927. Date of Electronic Publication: 2022 Feb 05 (Print Publication: 2022).
DOI:	10.1016/j.dib.2022.107927
Abstrakt:	Bacteria of the genus Psychrobacter are known for their psychrophilic characteristics, being extremophilic organisms capable of surviving and reproducing in hostile environments of low temperature and high pressure. Among many of the genus characteristics, there is the ability to produce enzymes and molecules of industrial biotechnology importance, such as pigments and proteins related to heavy metal bioremediation. The bacterium strain Psychrobacter nivimaris LAMA 639 was isolated from sediments from the Walvis Ridge ocean crest at a depth of 4.400 m (33.40 S 2.35 E). It is a nonmotile, halotolerant, cream-colored gram-negative aerobic bacterium. Its cultivation was performed in marine agar plates and inoculated into test tubes with NaCl at an optimal temperature of 30 °C and with shaking at 100 rpm. Genome extraction was performed with the DNeasy Blood & Tissue Kit (QIAGEN®). Sequencing was performed by Macrogen using the NovaSeq® 6000 platform (Illumina) applying the whole genome shotgun (WGS) method. Thereafter, 14.712.526 reads of 151 bp were generated, totaling 2.2 G bp with a GC content of 42.9%. Assembly and mapping were performed with a CLC Genomics Workbench. The best assembly considered was the one with the lowest number of contigs and the highest base length pair. The assemblies were evaluated using QUAST, and the best resulting variant was selected for annotation. Genome annotation was performed with RAST and PATRIC; the antiSMASH tool was used for secondary metabolites; NaPDoS was used for domains; and three-dimensional structural prediction of relevant proteins was performed using Phyre2. Annotation with ClassicRAST generated 2,891 coding sequences (CDSs) distributed in 402 subsystems. Annotation with PATRIC generated 2,896 coding sequences, among them 776 hypothetical proteins. The antiSMASH tool visualized a beta-lactone cluster in contig 06. In the search for natural products with NaPDoS, two ketosynthase domains were identified. The search for relevant proteins was performed using the AMFEP list as a criterion. From these data, 34 possible enzymes with biotechnological potential were found. Finally, the organism is presented as a new reference regarding the potential of deep-sea marine bacteria, demonstrating that, from the annotated and cured genome, it is possible to find in its genetic repertory products of interest for biotechnological applications. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article. (© 2022 The Author(s). Published by Elsevier Inc.)
Databáze:	MEDLINE
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