Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

Abstract

The production of pentabromopseudilin and related brominated compounds by Pseudoalteromonas spp. has recently been linked to the bmp biosynthetic gene cluster. This study explored the distribution and evolutionary history of this gene cluster in the genus Pseudoalteromonas. A phylogeny of the genus revealed numerous clades that do not contain type strains, suggesting considerable species level diversity has yet to be described. Comparative genomics revealed four distinct versions of the gene cluster distributed among 19 of the 101 Pseudoalteromonas genomes examined. These were largely localized to the least inclusive clades containing the Pseudoalteromonas luteoviolacea and Pseudoalteromonas phenolica type strains and show clear evidence of gene and gene cluster loss in certain lineages. Bmp gene phylogeny is largely congruent with the Pseudoalteromonas species phylogeny, suggesting vertical inheritance within the genus. However, the gene cluster is found in three different genomic environments suggesting either chromosomal rearrangement or multiple acquisition events. Bmp conservation within certain lineages suggests the encoded products are highly relevant to the ecology of these bacteria.

Fig. 1

The bmp gene cluster and its products. A. Five versions of the bmp gene cluster have been identified: four in Pseudoalteromonas spp. (A, C-E) and one in M. mediterranea MMB-1 (B). Hash marks indicate an ~150 bp insertion in bmp1 (version C). The small molecule products detected from each version are indicated. B. Bmp functional roles in the biosynthesis of brominated natural products.

Fig. 2

Pseudoalteromonas species phylogeny and bmp gene cluster distribution. A maximum likelihood phylogeny generated from concatenated 16S, gyrB, pyrH, recA and rpoD nucleotide sequences. The three least inclusive clades containing the bmp cluster are highlighted in color. Lettered brackets (A, C, D and E) indicate the version of the bmp cluster. The 42 type strains are indicated in bold italics and the 17 strains isolated as part of this study by CN prefixes followed by country of origin (USA or Fiji) and source (SW = seawater, PT = plankton tow, GA = green alga, RA = red alga, BA = brown alga). Squares indicate bmp distribution (filled = present, empty = absent) and bmp version (fully filled = version A, half-filled = partial BCG). Method of detection (GM = genome sequence or PCR) indicated. Filled triangles indicate the detection of pentabromopseudilin, half-filled triangles indicate the detection of tetrabromopyrrole but not pentabromopseudolin and empty triangles indicate that no compounds associated with the bmp gene cluster were detected. Roman numerals (as designated in Fig. 3) indicate 17 candidate new species identified based on coherence between 95% ANI groupings and the species phylogeny.

Fig. 3

ANI analysis. Average nucleotide identity of 91 Pseudoalteromonas genome sequences. The vertical dashed line specifies 95% ANI and the grey circles designate ANI species groupings. Strain names are followed by clade designations (from Fig. 2) and the 28 ANI groups (95%) that lack type strains indicated by Roman numerals (I–XXVIII). Coloured blocks correspond to sub-clade designations (from Fig. 2). The distribution of the 10 genes in the bmp gene cluster are displayed on the right with the version of the gene cluster (from Fig. 1) indicated on the right. Hash marks indicate an ~150 bp insertion in bmp1.

Fig. 4

Bmp gene phylogeny. A. Concatenated maximum likelihood phylogeny of bmp gene sequences. B. Concatenated maximum likelihood phylogenies of 16S, gyrB, pyrH, recA and rpoD sequences derived from the 19 Pseudoalteromonas and one M. mediterranea strain (MMB-1) that contain the bmp gene cluster. The bmp gene tree is rooted based on the species phylogeny while the species tree is rooted with MMB-1. Type strains are indicated by species names.

Fig. 5

Genomic environment of the bmp gene cluster. A. The species phylogeny is contrasted with conservation of the bmp gene cluster (red) and surrounding genomic environments (grey). Strain names are followed by the version of the gene cluster (A, C, D or E) and candidate ANI species identifiers. Opacity indicates percent sequence identity with anything below 50% not shown. B. A high level of sequence identity is observed in the bmp gene cluster between two distantly related strains (HI1 and P. phenolica) but not in the surrounding genomic environment. C. Strain A757 (bmp version D) reveals a partial loss of the bmp gene cluster.

Fig. 6.

Evolutionary history of the bmp gene cluster in Pseudoalteromonas. A. Inferred ancestral gene clusters are mapped onto a condensed species phylogeny (animated from Fig. 2). The distribution of each gene (coloured lines) is indicated based on presence or absence in that lineage (truncated or missing lines = absence). B. Versions of the gene cluster (A, C, D or E) observed in relation to the tree with evolutionary events indicated as maintenance, loss or modification. Losses include complete or partial deletion of the gene cluster. An insertion in bmp1 is the only modification observed (indicated with a star). Percent sequence identities between homologues indicated.