Difference between revisions of "Roseobacter denitrificans"
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[[image:Table1rd.|none|thumb||General features of ''R. denitrificans'' genome]]
[[image:Chromosomerd.|none|thumb|250px|Circular representation of ''R. denitrificans'' OCh 114 chromosome'']]
Revision as of 20:21, 28 August 2007
A Microbial Biorealm page on the genus Roseobacter denitrificans
Higher order taxa
Bacteria, Proteobacteria, Alphaproteobacteria, Rhodobacterales, Rhodobacteraceae, Roseobacter
Roseobacter denitrificans sp. OCh114 (previously called Erythrobacter sp. OCh114)
Description and significance
Roseobacter denitrificans is a purple aerobic anyoxygenic phototrophic (AAP) bacterium that dwells free-living in lakes and ocean surface waters, soils and even near deep sea hydrothermal vents. It was isolated from the surfaces of green seaweeds of the coastal marine sediments in Australia, using proteinase K treatment followed by phenol extraction. Members of the Roseobacter clade are widespread and abundant in such marine environments, having diverse metabolisms. The purple proteobacteria in particular, are the only known organisms to capture light energy to enhance growth requiring the presence of oxygen yet do not produce oxygen themselves. It grows photoautotrophically only at low oxygen levels, while at higher oxygen levels, the photosynthetic apparatus is down-regulated, resulting in chemotrophic growth using organic carbon.
The highly adaptive AAPs compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas CO2. The marine AAP species R. denitrificans grows not only photoheterotrophically in the presence of oxygen and light but also anaerobically in the dark using nitrate or trimethylamine N-oxide as an electron acceptor. It is the most studied AAP for this reason and is one of the main model organisms to study aerobic phototrophic bacteria.
The importances of the bacterium's genome sequence are for the following reasons: 1) The evolutionary genesis of photosynthesis genes - it is a marine bacterium, and so may be representative of the globally huge population of aerobic phototrophic bacteria and help narrow their true evolutionary position by whole genome comparisons; 2) Pathways of carbon dioxide fixation and production - in understanding the processes for its autotrophic CO2 production and the key genes involved in AAP CO2 fixation pathways. As the only aerobic phototrophic bacterium capable of anaerobic growth with use of nitrate as a terminal electron acceptor, it can also be used to facilitate subsequent studies of the effects of oxygen on photosynthetic and other metabolic processes; 3) Light and oxygen signal transduction in gene expression - offering an opportunity, through bioinformatic approaches, to use the AAP's exaggerated responses to study of both light- and oxygen-responsive pathways and mechanisms that are difficult to study in other species.
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated. Include a picture or two (with sources) if you can find them.
The genome sequence of Roseobacter denitrificans sp OCh 114 was completed in 2006 by a team in Arizona State University as the first AAP sequenced. R. denitrificans contains a circular chromosome of 4,133,097 bp and four plasmids. Nearly half of the genes in the largest plasmid (pTB1) share a high degree of similarity to genes in plasmid pSD25 from Ruegeria sp. isolate PR1b and the Ti plasmid from Agrobacterium tumefaciens strain C58. The conservation of many DNA integration and transfer proteins, plasmid replication proteins, and inverted repeats imply that R. denitrificans plasmid pTB1 may also promote lateral gene transfer. This possibility is especially interesting considering the propensity of R. denitrificans to associate with higher organisms. The genome of R. denitrificans additionally lacks genes that code for known photosynthetic carbon fixation pathways, with most notably missing the genes for Calvin cycle enzymes ribulose bisphosphate carboxylase (RuBisCO) and phosphoribukolkinase.
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Does it have any plasmids? Are they important to the organism's lifestyle?
Cell structure and metabolism
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
There are no known pathological effects of this bacterium on humans.
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
Application to Biotechnology
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
Enter summaries of the most recent research here--at least three required
1) Fleischman D and Kramer D (1998) Photosynthetic rhizobia. Biochim Biophys Acta 1364: 17-36.
2) Swingley W.D., Sadekar S., Mastrian S.D., Matthies H.J., Hao J., Ramos H., Acharya C.R., Conrad A.L., Taylor H.L., Dejesa L.C., Shah M.K., O'Huallachain M.E., Lince M.T., Blankenship R.E., Beatty J.T., Touchman J.W. ; "The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism"; J. Bacteriol. 189:683-690 (2007)
4) Candela, M., E. Zaccherini, and D. Zannoni. 2001. Respiratory electron transport and light-induced energy transduction in membranes from the aerobic photosynthetic bacterium Roseobacter denitrificans. Arch. Microbiol. 175:168-177
6) Kolber, Z. S., F. G. Plumley, A. S. Lang, J. T. Beatty, R. E. Blankenship, C. L. VanDover, C. Vetriani, M. Koblizek, C. Rathgeber, and P. G. Falkowski. 2001. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292:2492-2495
7) Schwarze C, Carluccio AV, Venturoli G & Labahn A (2000) Photo-induced cyclic electron transfer involving cytochrome bc1 complex and reaction center in the obligate aerobic phototroph Roseobacter denitrificans. Eur J Biochem 267: 422–433
8) Goodner, B., G. Hinkle, S. Gattung, N. Miller, M. Blanchard, B. Qurollo, B. S. Goldman, Y. Cao, M. Askenazi, C. Halling, L. Mullin, K. Houmiel, J. Gordon, M. Vaudin, O. Iartchouk, A. Epp, F. Liu, C. Wollam, M. Allinger, D. Doughty, C. Scott, C. Lappas, B. Markelz, C. Flanagan, C. Crowell, J. Gurson, C. Lomo, C. Sear, G. Strub, C. Cielo, and S. Slater. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-2328
Edited by student of Rachel Larsen