Pelagibacter ubique: Difference between revisions

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'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=335992&lvl=3&lin=f&keep=1&srchmode=1&unlock ''Candidatus Pelagibacter ubique'' HTCC1062 Taxonomy]'''
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''Pelagibacter ubique''
''Pelagibacter ubique''
Equivalent Names:
    Pelagibacter ubique HTCC1062
    Candidatus Pelagibacter ubique strain HTCC1062
    SAR11


==Description and significance==
==Description and significance==
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.
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.
Include a picture or two (with sources) if you can find them.
''Pelagibacter ubique'', strain HTCC1062, is significantly known to be one of smallest and simplest, self-replicating, and free living cell. It is part of the SAR11 clade, which are small, heterotrophic alphaproteobacteria, which is ~25% of all microbial plankton cells. ''P. ubique'' has a coastal, ocean surface ecotype (6). When combined, this clade weighs more than the weight of all fish present in the sea. As the first cultivated member of SAR11 clade (the most successful clade of organisms), ''P. ubique'' is completely sequenced and has the smallest genome for any free living organism, as well as the smallest number of predicted open reading frames (ORF) (3). Differing from bacteria and archaea, which have small genomes as well, ''P. ubique'' has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. Also, it has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins (9). In other words, ''P. ubique'' has no duplicate gene copies, no viral genes, and no junk DNA (14).
''P. ubique'' is rod or crescent shaped, with a length of 0.37-0.89 μm and an average cell diamter of 0.12-0.20 μm (8). The size range is due to natural variation associated with cell division. An average cell size after cell division is about 0.4 × 0.2μm^2, with the cell volume of 0.01 μm^3 (8). The genome of ''P. ubique'' is 1,308,759 bp, constituting 30% of the cell volume (9).


==Genome structure==
==Genome structure==
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(8) Giovannoni, S.J., Rappe, M. S., Connan, S. A., and Vergin, K. L. [http://www.mcb.oregonstate.edu/giovannoni/publications/subpublication/nature00917_r.pdf Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.] Nature 418 (8 August 2002): 630-631.  
(8) Giovannoni, S.J., Rappe, M. S., Connan, S. A., and Vergin, K. L. [http://www.mcb.oregonstate.edu/giovannoni/publications/subpublication/nature00917_r.pdf Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.] Nature 418 (8 August 2002): 630-631.  


(9) Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., Bibbs, L., Eads, J., Richardson, T.H., Noordewier, M., Rappe, M.S., Short, J., Carrington, J.C., and Mathur, E.J. [www.sciencemag.org Genome Streamlining in a Cosmopolitan Oceanic Bacterium.] Science 309 (19 August 2005): 1242-1245.
(9) Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., Bibbs, L., Eads, J., Richardson, T.H., Noordewier, M., Rappe, M.S., Short, J., Carrington, J.C., and Mathur, E.J. [http://www.sciencemag.org Genome Streamlining in a Cosmopolitan Oceanic Bacterium.] Science 309 (19 August 2005): 1242-1245.


(10) Genomics: GTL. U.S. Department of Energy Office of Science. Systems for Biology for Energy and Environment: Genomes to Life Contractor-Grantee Workschop 2005. [http://genomicsgtl.energy.gov/pubs/2005abstracts/html/file71.shtml Microbial Genomics - ''Pelagibacter ubique'': A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium.] February 2005. Accessed 26 August 2007.
(10) Genomics: GTL. U.S. Department of Energy Office of Science. Systems for Biology for Energy and Environment: Genomes to Life Contractor-Grantee Workschop 2005. [http://genomicsgtl.energy.gov/pubs/2005abstracts/html/file71.shtml Microbial Genomics - ''Pelagibacter ubique'': A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium.] February 2005. Accessed 26 August 2007.

Revision as of 07:10, 29 August 2007

A Microbial Biorealm page on the genus Pelagibacter ubique

Pelagibacter ubique. Image courtesy of Office of Biological & Environmental Research

.

Classification

Higher order taxa

Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; SAR11 cluster; Candidatus Pelagibacter; Candidatus Pelagibacter ubique

Species

NCBI: Candidatus Pelagibacter ubique HTCC1062 Taxonomy

Pelagibacter ubique

Equivalent Names:

    Pelagibacter ubique HTCC1062 
    Candidatus Pelagibacter ubique strain HTCC1062 
    SAR11


Description and significance

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.

Pelagibacter ubique, strain HTCC1062, is significantly known to be one of smallest and simplest, self-replicating, and free living cell. It is part of the SAR11 clade, which are small, heterotrophic alphaproteobacteria, which is ~25% of all microbial plankton cells. P. ubique has a coastal, ocean surface ecotype (6). When combined, this clade weighs more than the weight of all fish present in the sea. As the first cultivated member of SAR11 clade (the most successful clade of organisms), P. ubique is completely sequenced and has the smallest genome for any free living organism, as well as the smallest number of predicted open reading frames (ORF) (3). Differing from bacteria and archaea, which have small genomes as well, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. Also, it has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins (9). In other words, P. ubique has no duplicate gene copies, no viral genes, and no junk DNA (14).

P. ubique is rod or crescent shaped, with a length of 0.37-0.89 μm and an average cell diamter of 0.12-0.20 μm (8). The size range is due to natural variation associated with cell division. An average cell size after cell division is about 0.4 × 0.2μm^2, with the cell volume of 0.01 μm^3 (8). The genome of P. ubique is 1,308,759 bp, constituting 30% of the cell volume (9).

Genome structure

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.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

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?

Current Research

Enter summaries of the most recent research here--at least three required

References

(1) Cascio, Jamais. World Changing. Genetic Efficiency and the Carbon Cycle. 19 August 2005. Accessed 26 August 2007.

(2) Comprehensive Microbial Resource. Candidatus Pelagibacter ubique HTCC1062 Genome Page. Last updated 27 September 2006. Accessed 26 August 2007.

(3) European Bioinfomatics Institute. Bacteria Genomes - CANDIDATUS PELAGIBACTER UBIQUE. Accessed 26 August 2007.

(4) Giovannoni, Stephen. Oregon State University. Giovannoni Lab: SAR 11. Accessed 26 August 2007.

(5) Giovannoni, Stephen, and Douglas Barofsky, comps. U.S. Department of Energy. Biological and Environmental Research - PNNL Proteomics. Biological Applications - Organisms: Pelagibacter ubique. Last updated May 2007. Accessed 26 August 2007.

(6) Giovannoni, S.J., Bibbs, L., Cho, J.-C., Stapels, M.D., Desiderio, R., Vergin, K.L., Rappe, M.S., Laney, S., Wilhelm, L.J., Tripp, H.J., Mathur, E.J., and Barofsky, D.F. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438 (3 November 2005): 82-85.

(7) Giovannoni S.J., Morris, R. M., Rappe, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., and Carlson, C. A. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420 (December 2002): 806-810.

(8) Giovannoni, S.J., Rappe, M. S., Connan, S. A., and Vergin, K. L. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418 (8 August 2002): 630-631.

(9) Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., Bibbs, L., Eads, J., Richardson, T.H., Noordewier, M., Rappe, M.S., Short, J., Carrington, J.C., and Mathur, E.J. Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Science 309 (19 August 2005): 1242-1245.

(10) Genomics: GTL. U.S. Department of Energy Office of Science. Systems for Biology for Energy and Environment: Genomes to Life Contractor-Grantee Workschop 2005. Microbial Genomics - Pelagibacter ubique: A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium. February 2005. Accessed 26 August 2007.

(11) Kyoto Encyclopedia of Genes and Genomes. Candidatus Pelagibacter ubique. Accessed 26 August 2007.

(12) Monterey Bay Aquarium Research Institute (MBARI). Giovannoni, Stephen. Pelagibacter ubique: A Perfect engineering solution? Seminar: Pacific Forum. 15 April 2005. Accessed 26 August 2007.

(13) National Library of Medicine (NLM) and National Institutes of Health (NIH). National Center for Biotechnology Information (NCBI): Pelagibacter ubique. Accessed 26 August 2007.

(14) Pease, Roland. BBC News. Ocean bug has 'smallest genome'. Last updated 19 August 2005. Accessed 26 August 2007.

Edited by Liza Dizon, student of Rachel Larsen