Genome Sequence of the Cycloprodigiosin-Producing Bacterial Strain Pseudoalteromonas rubra ATCC 29570^T

Abstract

The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome of a cycloprodigiosin-producing bacterial strain, Pseudoalteromonas rubra ATCC 29570^T. Analysis revealed a probable cycloprodigiosin biosynthetic cluster, providing a good model for the study of cycloprodigiosin synthesis and regulation.

GENOME ANNOUNCEMENT

Prodiginines are a family of tripyrrole red pigments which have antifungal, antibacterial, antiprotozoal, antimalarial, immunosuppressive, and anticancer activities (16). Prodiginines can be divided into four structural classes (16): prodigiosin/undecylprodigiosin, butyl-meta-cycloheptylprodiginine, cycloprodigiosin, and cyclononylprodigiosin. The prodigiosin/undecylprodigiosin biosynthetic (pig) cluster has been studied in Serratia sp. ATCC 39006 (17), Serratia marcescens ATCC 274 (9), and Hahella chejuensisi KCTC 2396 (10), and the prodigiosin/undecylprodigiosin and butyl-meta-cycloheptylprodiginine biosynthetic (red) cluster has been studied in Streptomyces coelicolor strain A3(2) (3, 5–7, 13, 15). However, biosynthetic gene clusters for cycloprodigiosin and cyclononylprodigiosin have not been reported.

The genus Pseudoalteromonas (Gammaproteobacteria, Alteromonadales, Alteromonadaceae) is a group of wide-spreading marine bacteria, and many species of the genus have been shown to be able to produce series of bioactive compounds (2). Studies have shown that Pseudoalteromonas denitrificans (11) and Pseudoalteromonas rubra (8) can produce cycloprodigiosin. To uncover the biosynthetic gene cluster for cycloprodigiosin, we sequenced the genome of the type strain of P. rubra, ATCC 29570^T.

The genome of strain ATCC 29570^T was sequenced using Illumina Solexa technology (1). A 500-bp Illumina paired-end library produced 6,666,668 reads (read length, 90 bp) totaling 600 Mb, which represents 101 times the average genome coverage. Solexa paired-end reads were then assembled using SOAPdenovo, version 1.05 (12), resulting in 64 contigs (>500 bp). The protein-coding open reading frames (ORFs) were predicted using Glimmer, version 3.02 (4), and were annotated using the Swiss-Prot, NCBI nr, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (14). A comprehensive annotation and comparative genome analysis are under way.

The size of the P. rubra ATCC 29570^T genome is 5.97 Mb, larger than that of all other sequenced Pseudoalteromonas genomes except that of P. luteoviolacea 2ta16 (6.36 Mb) (https://moore.jcvi.org/moore/). The G+C content is 47.80%, higher than that of all other sequenced Pseudoalteromonas genomes.

The genome contains 5,195 protein-coding ORFs. A BLASTP search against the pig gene cluster in H. chejuensisi KCTC 2396 revealed a probable cycloprodigiosin biosynthetic gene cluster (13 ORFs) in the ATCC 29570^T genome. The first 11 ORFs encode proteins with high amino acid identity (43% to 60%) to their homologs in H. chejuensisi KCTC 2396. However, the amino acid sequence identities of the last two ORFs to their homologs were much lower (31% to 33%). This cluster represents the first reported biosynthetic cluster for cycloprodigiosin. In addition, the genome sequence of P. rubra ATCC 29570^T provides a good resource for the study of bioactive compounds produced by the Pseudoalteromonas genus.

Nucleotide sequence accession number.

The data for the genome sequence of P. rubra ATCC 29570^T were deposited in GenBank under accession number AHCD00000000.