Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium

• Published in: 3 Biotech Vol. 10; no. 4; p. 175
• Main Authors: Kumaran, Selvapravin, Ngo, Anna Christina R., Schultes, Fabian Peter Josef, Tischler, Dirk
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01-04-2020; Springer Nature B.V
• Subjects: Agriculture; Amino acid sequence; Annotations; Azo dyes; Azoreductase; Bioinformatics; Biomaterials; Biotechnology; Cancer Research; Carbon sources; Chemistry; Chemistry and Materials Science; Degradation; Dyes; Flavin; Gene sequencing; Genes; Genome Reports; Genomes; High-performance liquid chromatography; Kocuria; NAD; Nucleotide sequence; Phylogeny; rRNA 16S; Stem Cells; tRNA; Biodegradation; Dye degradation; Soil bacteria; Azo dye; Azoreductase
• ISSN: 2190-572X; 2190-5738
• DOI: 10.1007/s13205-020-2136-3

In the present study, we report the draft genome of soil isolate DP-K7 that has the potential to degrade methyl red. The 16S rRNA gene sequencing and whole-genome analysis exposed that the bacterial strain DP-K7 belongs to the species
Kocuria indica
. The genome annotation of the strain DP-K7 through the bioinformatics tool “Prokka” showed that the genome contains 3,010,594 bp with 69.01% GC content. The genome comprises 57 contigs including 2 rRNA genes, 47 tRNA genes, and 2754 CDS. The plate and broth assay showed that the strain DP-K7 has the potential to utilize methyl red as the sole carbon source for growth. Indeed, the RP-HPLC analysis proved that the strain DP-K7 is capable of degrading methyl red. The genome BLAST against a characterized azoreductase (AzoB—
Xenophilus azovorans
KF46F) revealed the presence of two azoreductase-like genes (
azoKi-1
and
azoKi-2
). The phylogenetic analysis of the primary amino acid sequence of characterized azoreductases suggested that AzoKi-1 and AzoKi-2 belong to members of the clade IV azoreductase, which are flavin-independent. The multiple sequence alignment of AzoKi-1 and AzoKi-2 with flavin-independent azoreductases showed the presence of NAD(P)H binding like motif (GxxGxxG). In addition, other genes coding for dye degrading enzymes (SodC, SodA, KatA, KatE, and DyP2) were also found in the genome supporting that the strain
K. indica
DP-K7 is a potential azo dye degrader.