Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors

Abstract

Dermacoccus abyssi strain MT1.1^T is a piezotolerant actinobacterium that was isolated from Mariana Trench sediment collected at a depth of 10898 m. The organism was found to produce ten dermacozines (A‒J) that belonged to a new phenazine family and which displayed various biological activities such as radical scavenging and cytotoxicity. Here, we report on the isolation and identification of a new dermacozine compound, dermacozine M, the chemical structure of which was determined using 1D and 2D-NMR, and high resolution MS. A whole genome sequence of the strain contained six secondary metabolite-biosynthetic gene clusters (BGCs), including one responsible for the biosynthesis of a family of phenazine compounds. A pathway leading to the biosynthesis of dermacozines is proposed. Bioinformatic analyses of key stress-related genes provide an insight into how the organism adapted to the environmental conditions that prevail in the deep-sea.

Keywords: Dermacoccus abyssi MT1.1T; Mariana Trench; biosynthetic gene clusters; dermacozines; genome sequencing.

Figure 1

Chemical structures of D. abyssi dermacozines (1–11).

Figure 2

Selected COSY (), NOESY (), and HMBC (HC) correlations.

Figure 3

Dermacozine M: (a) Conformers obtained from the conformational search; (b) Theoretical UV spectra.

Figure 4

(A) Genetic organization of a putative phenazine gene cluster present in the genome of D. abyssi MT1.1^T; (B) Comparison of the putative phenazine gene clusters from D. abyssi MT1.1^T with characterized homologous gene clusters found in the genome of other bacteria.

Figure 5

Proposed biosynthetic pathways for the synthesis of dermacozines by D. abyssi MT1.1^T.