The Rhodobacter Capsulatus Genome Project

Haselkorn, Robert; Fonstein, Michael; Kogan, Yakov; Kumar, Vivek; Maltsev, Natalia; Pačes, Jan; Milgram, Arthur J.; Pačes, Václav; Vlček, Čestmı́r

doi:10.1007/978-1-4615-4827-0_49

Cited by 13 publications

(16 citation statements)

References 8 publications

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“…The resulting library contained 1,536 clones with an average insert size of 23.5 kb. On the basis of comparison to the genome sizes of R. sphaeroides and R. capsulatus, which are ϳ4.5 and 3.6 Mb, respectively, we estimate that our library represents five-to six-times coverage of the SW2 genome (24,35).…”

Section: Methodsmentioning

confidence: 99%

The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003

2007

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In this study, we circumvented this problem by taking a heterologous-complementation approach to identify a three-gene operon (the foxEYZ operon) from Rhodobacter sp. strain SW2 that confers enhanced light-dependent Fe(II) oxidation activity when expressed in its genetically tractable relative Rhodobacter capsulatus SB1003. The first gene in this operon, foxE, encodes a c-type cytochrome with no significant similarity to other known proteins. Expression of foxE alone confers significant light-dependent Fe(II) oxidation activity on SB1003, but maximal activity is achieved when foxE is expressed with the two downstream genes foxY and foxZ. In SW2, the foxE and foxY genes are cotranscribed in the presence of Fe(II) and/or hydrogen, with foxZ being transcribed only in the presence of Fe(II). Sequence analysis predicts that foxY encodes a protein containing the redox cofactor pyrroloquinoline quinone and that foxZ encodes a protein with a transport function. Future biochemical studies will permit the localization and function of the Fox proteins in SW2 to be determined.

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Section: Methodsmentioning

confidence: 99%

The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003

2007

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“…The clustering of photosynthesis genes into a PGC was first described in Rhodobacter capsulatus (previously Rhodopseudomonas capsulata) (17)(18)(19). The PGCs are a typical feature in most purple phototrophic bacteria (20)(21)(22) and heliobacteria (23), but are not present in other chlorophototrophic lineages.…”

Section: Significancementioning

confidence: 99%

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Zeng

Feng

Medová

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

222

253

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Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyllbased phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.anoxygenic photosynthesis | horizontal gene transfer | bacterial pigments | aerobic photoheterotroph | fluorescence imaging system

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“…A portion of the R. capsulatus genome sequence was described previously (21,53), and the complete annotated sequence is now available (GenBank accession no. CP001312 and CP001313; http://rhodo.img.cas.cz/).…”

mentioning

confidence: 99%

Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus

Mercer

Callister²,

Lipton³

et al. 2010

J Bacteriol

Self Cite

102

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The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in Caulobacter crescentus has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in R. capsulatus shares a high degree of sequence similarity with the C. crescentus protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and ctrA mutant cultures to identify the genes dysregulated by the loss of CtrA in R. capsulatus. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of ϳ6% of genes in the R. capsulatus genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral ctrA gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.The purple nonsulfur bacterium Rhodobacter capsulatus is a model organism for various aspects of bacterial physiology, such as bioenergetics and N 2 fixation, and also engages in an unusual mechanism of genetic exchange, carried out by a bacteriophage-like element called the R. capsulatus gene transfer agent (RcGTA) (34, 56). The production of RcGTA is maximal in the stationary phase of growth of R. capsulatus cultures (49) and is regulated by at least 2 distinct signaling systems, one through quorum sensing of a long chain acyl-homoserine lactone (43) and the other involving the response regulator protein CtrA (30).The CtrA protein was first characterized for Caulobacter crescentus (41), where it is essential for viability and acts as a master regulator of the cell cycle (reviewed in reference 45), controlling at least 25% (144 of 553) of the genes involved in cell cycle progression (31). Despite sharing remarkable sequence identity (71%) with the CtrA protein from C. crescentus, the R. capsulatus protein has a very different role because it is not essential and does not appear to be involved in cell cycle processes. One function of CtrA in common to the two species is the regulation of expression of genes that encode the flagellum (29, 41). The ctrA genes of Sinorhizobium meliloti (3), Brucella abortus (6), and Ruegeria sp. strain TM1040 (36) have also been studied. Similarly to C. crescentus and R. capsulatus CtrA, Ruegeria CtrA controls motility (36). A search of the GenBank database reveals that convincing homologs which share Ͼ50% identity with the C. crescen...

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The Rhodobacter Capsulatus Genome Project

Cited by 13 publications

References 8 publications

The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003

The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus

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