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

Author(s)

Staloch, Brendon Egon Kormann ; Niero, Henrique ; de Freitas, Robert Cardoso ; Ballone, Patricia ; Rodrigues-Costa, Fernanda ; Trivella, Daniela Barretto Barbosa ; Dessen, Andrea ; da Silva, Marcus Adonai Castro ; Lima, Andre Oliveira de Souza

• Document type: Journal article
• Source: DATA IN BRIEF; v. 41, p. 11-pg., 2022-04-01.

Abstract

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 degrees C and with shaking at 100 rpm. Genome extraction was performed with the DNeasy Blood & Tissue Kit (QIAGEN (R)). Sequencing was performed by Macrogen using the NovaSeq (R) 60 0 0 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 anti SMASH 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. (C) 2022 The Author(s). Published by Elsevier Inc. (AU)

• FAPESP's process: 14/10753-9 - Bioprospecting and rational design for the discovery of next generation proteasome inhibitors
• Grantee: Daniela Barretto Barbosa Trivella
• Support Opportunities: Regular Research Grants
• FAPESP's process: 17/12436-9 - ANTIBIO-BAC: exploring the bacterial cell wall as a target for novel antibiotherapies
• Grantee: Andrea Dessen de Souza e Silva
• Support Opportunities: Research Projects - SPEC Program
• FAPESP's process: 15/19906-5 - Identification of new antibacterial agents in libraries of natural products
• Grantee: Fernanda Rodrigues da Costa
• Support Opportunities: Scholarships in Brazil - Doctorate