Revised Genome Sequence of the Purple Photosynthetic Bacterium Blastochloris viridis.

Blastochloris viridis is a unique anaerobic, phototrophic purple bacterium that produces bacteriochlorophyll b. Here we report an improved genome sequence of Blastochloris viridis DSM133, which is instrumental to the studies of photosynthesis, metabolic versatility, and genetic engineering of this microorganism.

GENOME ANNOUNCEMENT

Blastochloris (formerly Rhodopseudomonas) viridis is a Gram-negative purple nonsulfur photosynthetic bacterium that preferentially grows photohetrotrophically. The photosynthetic machinery of B. viridis has been extensively studied, comprising solely a single light-harvesting complex surrounding a photosynthetic reaction center (forming an RC-LH1 core complex) (1), as well as cytochrome bc1 and ATPase. Unlike many of the other photosynthetic bacteria, B. viridis uniquely produces bacteriochlorophyll b (2, 3). The reaction center has been determined using X-ray crystallography (4). The organization of RC-LH1 core complexes in the photosynthetic membrane has been characterized using atomic force microscopy (5, 6). Recently, the genome sequence of B. viridis has been reported (Data Bank of Japan accession number AP014854) (7). However, sequence analysis shows that the published genome sequence contains two large sequence segments (over 136 kbp with 130 open reading frames) that are originally from a cyanobacterium, Geminocystis sp. strain NIES-3709 (8), likely due to contaminations during genomic DNA preparation. Here, we report the revised complete genome sequence of B. viridis DSM133 and improved annotation.

Genomic DNA from B. viridis DSM133 was extracted using phenol-chloroform standard procedure. Whole-genome sequencing was performed with the Pacific Bioscience RS II platform using P6C4 chemistry by the Centre for Genomic Research, University of Liverpool. A total of 22,943 reads-of-insert were generated with an N50 length of 2.719, giving 89.1-fold coverage of the genome. The complete chromosome, without gaps, was assembled/polished using HGAP (9) and annotated using PROKKA 1.7.2 (10). Comparative analysis between sequenced genomes was performed and visualized using the Artemis comparison tool (11).

The genome of B. viridis DSM133 consists of a single circular chromosome containing 3,723,225 bp with 3,260 predicted open reading frames, 53 tRNA genes, and 9 rRNA operons. The average length of each coding sequence is 971 bp, with a total coding percentage of 85%. The genome has a G+C content of 67.9%. The photosynthetic apparatus is encoded by a number of genes organized in a photosynthesis gene cluster. Six of these genes, pufBALMC and puhA, encode the RC-LH1 core complex (light-harvesting protein β and α subunits and reaction center L, M, and H subunits, respectively). Bacteriochlorophyll biosynthesis is encoded by a gene cluster (bchPGFNBHLMIDCXYZ). Another gene cluster, petABC, encodes the cytochrome bc1. A single gene (cycA) encodes cytochrome c2 that is a soluble electron carrier between cytochrome bc1 and the photosynthetic reaction center. The F0F1-ATPase is encoded by two gene operons, atpHAGDC for the F1 sector and atpIBEXF for the F0 sector. In addition, there are carbon fixation-related genes for ribulose bisphosphate carboxylase (RuBisCO) (cbbL, cbxSC), RuBisCO expression protein (cbbX), RuBisCO-like protein 2 (rlp2), and carbonic anhydrase (cynT).

The number of endogenous plasmids in purple bacteria varies between species: no plasmid found in B. viridis; one plasmid identified in Rhodopseudomonas palustris CGA009 (12) and Rhodobacter capsulatus SB1003 (13); two plasmids in Rhodobacter sphaeroides WS8N (14), KD131 (15), and Rhodovulum sulfidophilum W4 (16); five plasmids in R. sphaeroides 2.4.1 (17) and ATCC 17025 (18).

Nucleotide sequence accession number.

The revised complete genome sequence of Blastochloris viridis DSM133 has been deposited at DDBJ/ENA/GenBank under the accession number LN907867.