DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1T

Abstract

This paper describes the DNA sequence of the photosynthesis region of Rhodobacter sphaeroides 2.4.1 (T). The photosynthesis gene cluster is located within a approximately 73 kb Ase I genomic DNA fragment containing the puf, puhA, cycA and puc operons. A total of 65 open reading frames (ORFs) have been identified, of which 61 showed significant similarity to genes/proteins of other organisms while only four did not reveal any significant sequence similarity to any gene/protein sequences in the database. The data were compared with the corresponding genes/ORFs from a different strain of R.sphaeroides and Rhodobacter capsulatus, a close relative of R. sphaeroides. A detailed analysis of the gene organization in the photosynthesis region revealed a similar gene order in both species with some notable differences located to the pucBAC = cycA region. In addition, photosynthesis gene regulatory protein (PpsR, FNR, IHF) binding motifs in upstream sequences of a number of photosynthesis genes have been identified and shown to differ between these two species. The difference in gene organization relative to pucBAC and cycA suggests that this region originated independently of the photosynthesis gene cluster of R.sphaeroides.

Unsuspected diversity among marine aerobic anoxygenic phototrophs

“…2). Clones 65D09 and 29C02 are similar in their photosynthetic operon organization (data not shown), and when compared with both a-or b-proteobacterial (Rhodobacter sphaeroides 13 and Rubrivivax gelatinosus 14 , respectively) operon organization, more closely resemble the bproteobacterial operon (Fig. 2).…”

“…BAC clone 60D04, which is related to a-3 proteobacteria (on the basis of pufM sequences), also differs signi®cantly in gene arrangement from any other photosynthetic operon organization reported to date. It most closely resembles the photosynthetic operons from Rhodobacter capsulatus 8 and R. sphaeroides 13,15 , in both organization and gene content (it contains the bchIDO and crtD genes, which are missing in R. gelatinosus 14 and BAC clones 29C02 and 65D09). The superoperonal gene arrangement, crtEF±bchCXYZ±puf and bchFNBHLM±lhaA±puhA 13±17 , found in R. sphaeroides, R. capsulatus and R. gelatinosus are conserved among the naturally occurring planktonic bacterial genomes (Fig.…”

The cyanobacterial genome core and the origin of photosynthesis

“…It is generally believed that the evolution of photosynthetic genes was accompanied by their dissemination by way of LGT between different groups of bacteria (12,26,30,31,56). This idea is supported by the apparent presence of nonphotosynthetic representatives in all of these phyla, except for Cyanobacteria; by the fact that the photosynthesis-related proteins are often encoded on a single contiguous chromosomal region (superoperon) (20,57); by several phylogenetic analyses (8,11,58); and by the observation that photosynthetic genes can be transduced by cyanophages (59).…”

Generalized approach to the regulation and integration of gene expression

“…Sequence analyses of the < 67 kb PS gene cluster (puf to hemN) of R. sphaeroides 2.4.1 (Choudhary and Kaplan, 2000) reveals the bch genes to be clustered into four transcriptional units (Fig. 1C).…”