Abstract
Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in freshwater ponds, sewage ditches, activated sludge, and food processing wastewater. There have not been many studies on photosynthetic betaproteobacteria. Here we announce the complete genome sequence of the best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC 100245).
GENOME ANNOUNCEMENT
The cells of the purple nonsulfur bacterium Rubrivivax gelatinosus (8, 4) have an ovoid shape and are motile by means of flagella. Photoheterotrophy is their preferred mode of growth under laboratory conditions. Aerobic growth and fermentative growth are also possible. R. gelatinosus utilizes a diverse array of different carbon sources, including hydrolyzed starch and gelatin, because of the peculiar hydrolyzing enzymes it produces. R. gelatinosus is capable of carbon and nitrogen fixation.
R. gelatinosus IL-144 (NBRC 100245) was isolated from food wastewater in Nagano, Japan (2). The total genome consisted of a single circular chromosome of 5,043,253 bp with 71.24% G+C content in which 4,706 protein-encoding genes were predicted. The genome contains many genes that encode alternate or redundant systems, including three sets of 16S-23S-5S rRNA operons. Both polar (fla) and lateral (laf) flagellin genes with 47 methyl-accepting chemosensory transducer genes as chemotaxis genes were also predicted. The name gelatinosus is derived from its ability to liquefy gelatin. This phenotype could be ascribed to the presence of six genes that possibly encode putative extracellular serine proteases and two genes for oligopeptidases. The genome contained the genes required for the complete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in addition to a pentose phosphate pathway and a tricarboxylic acid cycle. Two sets of the nitrogenase structural gene cluster nifHDK were predicted. The genes for NiFe-hydrogenase, cooLXH, found in the genome of R. gelatinosus strain CBS, were absent from the R. gelatinosus IL-144 genome (7). In purple photosynthetic bacteria, genes that encode the enzymes required for the biosynthesis of bacteriochlorophyll and carotenoids have been known to form a large cluster called the photosynthetic gene cluster (PGC). R. gelatinosus also has the PGC, which has been suspected to be obtained by horizontal gene transfer from ancestral species of the alphaproteobacterium (3, 5). Four genes that encode bacteriochlorophyll biosynthesis enzymes, bchI, -D, -E, and -J, were found outside the PGC, and they show high levels of sequence identity with those genes of alphaproteobacteria. Recently R. gelatinosus was shown to have denitrification, in addition to photosynthesis, ability under anaerobic conditions (6). This is supported by the presence of the gene cluster responsible for nitrite, nitric oxide, and nitrous oxide reduction (nir, nor, and nos). This implies that R. gelatinosus can reduce NO2− to N2 gas but cannot use NO3− as a substrate for the denitrification pathway. In support of its facultative anaerobic metabolism, genes possibly coding for three different terminal oxidases, cytochrome aa3- and cbb3-type cytochrome c oxidases and cytochrome bd-type quinol oxidase, were found, as shown in R. gelatinosus strain S1 (1). Further analysis of the R. gelatinosus IL-144 genome will provide insights into the molecular mechanism of photosynthesis and the metabolic versatility of betaproteobacteria and also processes of acquisition and adaptation of new metabolisms derived from convergent evolution or horizontal gene transfer.
Nucleotide sequence accession number.
The complete genome sequence determined in this study has been deposited in the DDBJ/EMBL/GenBank database under accession no. AP012320.
ACKNOWLEDGMENT
This work was supported by PRESTO of the Japan Science and Technology Agency (K.V.P.N.).
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