Difference between revisions of "Halorhodospira halophila"

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(Description and significance)
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This halophilic organism was first isolated from a salt lake mud [5] and has been determined to have several functions: production of organic solutes glycine betaine, ectoine, and trehalose to help balance osmotic pressure, as well as the oxidization of sulfide to sulfur (which later would be further oxidized into sulfate). [2] This has resulted in the use of ''Halorhodospira halophila'' for research on topics from a photobiological ability to produce hydrogen gas to effects on sulfur.
 
This halophilic organism was first isolated from a salt lake mud [5] and has been determined to have several functions: production of organic solutes glycine betaine, ectoine, and trehalose to help balance osmotic pressure, as well as the oxidization of sulfide to sulfur (which later would be further oxidized into sulfate). [2] This has resulted in the use of ''Halorhodospira halophila'' for research on topics from a photobiological ability to produce hydrogen gas to effects on sulfur.
  
One important aspect is the production of the bacterial photoreceptor PYP (photoactive yellow protein) within ''Halorhodospira halophila''. PYP is a blue-light sensor found in ''Halorhodospira halophila'' that has great significance towards protein research and biotechnology. Photoactive proteins are generally accepted as "model systems for studying protein signal state formation." [4]  
+
One important aspect is the production of the bacterial photoreceptor PYP (photoactive yellow protein) within ''Halorhodospira halophila''. PYP is a blue-light sensor found in ''Halorhodospira halophila'' that has great significance towards protein research and biotechnology. Photoactive proteins are generally accepted as "model systems for studying protein signal state formation." As a small protein, PYP provides for an 'attractive model system for exploring how a chromophore and protein interact to sense light and send a biological signal." [4]  
  
 
''Halorhodospira halophila'' has one major strain (DSM244/SL1) whose genome has been sequenced. But two other strains are recognized: BN9624 and BN9630. [1]
 
''Halorhodospira halophila'' has one major strain (DSM244/SL1) whose genome has been sequenced. But two other strains are recognized: BN9624 and BN9630. [1]
  
 
==Genome structure==
 
==Genome structure==
The gene sequence of <I>Halorhodospira halophila S1</I>, the only listed organism of the species has been fully determined. Genome sequencing of <I>Halorhodospira halophila S1</I> was completed in January 2007 by the [http://genome.jgi-psf.org/draft_microbes/halha/halha.info.html Department of Energy Joint Genome Institute]. The genome is 2,678,452 nucleotides long (1,339,226 base pairs) and is made up of circular DNA. There are 2493 genes, 2407 which are protein coding, as well as 55 structural RNAs. There is no current information on plasmids related to this species.
+
The gene sequence of <I>Halorhodospira halophila S1</I> is the only listed strain of the species that has fully been sequenced. Genome sequencing of <I>Halorhodospira halophila S1</I> was completed in January 2007 by the [http://genome.jgi-psf.org/draft_microbes/halha/halha.info.html Department of Energy Joint Genome Institute]. The genome is 2,678,452 nucleotides long (1,339,226 base pairs) and is made up of circular DNA. There are 2493 genes, 2407 which are protein coding, as well as 55 structural RNAs and 31 pseudo genes. The GC content of strain S1 is 67.9%. There is no current information on plasmids related to this species. [6]
 +
 
 +
While not all strains of ''Halorhodospira halophila'' have been sequenced, there is still some information on their similarity to related species. ''Halorhodospira neutriphila'', displayed in the photo on the right, has a 94.6% similarity to strain DSM 244. Meanwhile, similarities with strains BN 9624 and BN 9630 are 91.4% and 90.7% respectively.
  
 
==Cell structure and metabolism==
 
==Cell structure and metabolism==
<I>Halorhodospira halophila</I> is known as a "purple sulfur bacterium", whose structure consists of two membranes as well as the presence of flagella. One important part of <I>Halorhodospira halophila</I> and subject to recent research has been the Photoactive Yellow Protein (PYP), a 14kDa cytoplasmic photoreceptor protein. It generates hydrogen gas during photoautotrophic growth as a byproduct of a nitrogenase reaction.  
+
<I>Halorhodospira halophila</I> is known as a "purple sulfur bacterium", whose structure consists of two membranes as well as the presence of flagella. [2] Its size is about ~4Mb. [7]
 +
 
 +
''Halorhodospira halophila'' is capable of a large number of metabolic pathways such as glycolysis, the citrate cylce, amino acid metabolism, and more. A full list of these pathways and their individual maps can be found at the [http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=kegg&keywords=halorhodospira+halophila KEGG Pathway Database for Halorhodospira halophila]. [8]
 +
 
 +
One important part of <I>Halorhodospira halophila</I> (and subject to recent research) is the generation of Photoactive Yellow Protein (PYP), a 14kDa cytoplasmic photoreceptor protein, which is an important protein for current research.
  
 +
''Halorhodospira halophila'' also has a potential role of hydrogen production through the nitrogen fixation of nitrogenase, which will be further explained below.
  
 
==Ecology==
 
==Ecology==
 +
''Halorhodospira halophila''
 +
 
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
 
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
  
 
==Pathology==
 
==Pathology==
 
At this time, <I> Halorhodospira halophila </I> causes no known diseases.
 
At this time, <I> Halorhodospira halophila </I> causes no known diseases.
 
How does this organism cause disease?  Human, animal, plant hosts?  Virulence factors, as well as patient symptoms.
 
  
 
==Application to Biotechnology==
 
==Application to Biotechnology==
 +
As will be explained below, current research has speculated that ''Halorhodospira halophila'' could play a strong role in nitrogen fixation through its byproduct hydrogen generating capabilities. Research in this field can aide in the use of the organism in photobiological hydrogen generation to develop new fuel cells as a possible "next-generation fuel source". [9]
 
Does this organism produce any useful compounds or enzymes?  What are they and how are they used?
 
Does this organism produce any useful compounds or enzymes?  What are they and how are they used?
  
 
==Current Research==
 
==Current Research==
 +
===Designation of ''Halorhodospira'' as a separate genus===
 +
Recent studies of the sequences of the 16sRNA gene have been able to provide details and data into the ''Ectothiorhodospira'' genus and the different species within, helping to distinguish <I>Halorhodospira</I> and reassigning it as a separate genus category. Within the ''Ectothiorhodospira'' genus, three organisms with an extremely halophilic nature showed enough difference to warrant reclassification: ''Halorhodospira halophila'', ''Halorhodospira halochloris'', and ''Halorhodospira abdelmalekii.''[10]
  
Enter summaries of the most recent research here--at least three required
+
[http://www.springerlink.com/content/7b3j189vdcl1aryl/ The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses]
  
Some of the recent research on <I>Halorhodospira halophila</I> includes focusing on it's photobiological ability to produce hydrogen gas and the potential applications of this.
+
===Photobiological hydrogen generation===
 +
Some of the recent research on <I>Halorhodospira halophila</I> includes focusing on it's photobiological ability to produce hydrogen gas and the potential applications of this. Through the nitrogen fixation process in photosynthetic bacteria involving nitrogenase, hydrogen generation typically results as a byproduct. However, most of the studies of photobiological hydrogen production has been with purple non-sulfur bacteria. Current research is looking into the hydrogen production capabilities specific to purple sulfur bacteria. Purple sulfur bacteria are preferable for hydrogen generation because they are "complete photoautotrophs and can be cultivated in minimal culture media." Additionally, ''Halorhodospira halophila's" capability to withstand high pH and salt environments is a benefit since seawater could be "used directly as a culture medium". Current research, as shown by the paper below, shows that ''Halorhodospira halophila'' is capable of generating a substantial amount of hydrogen, and thus is a viable candidate for helping in the production of renewable energy sources in the future. [9]
  
 
[http://www.jstage.jst.go.jp/article/jbb/101/3/263/_pdf Cloning and Characterization of nif Structural and Regulatory Genes in the Purple Sulfur Bacterium, Halorhodospira halophila]
 
[http://www.jstage.jst.go.jp/article/jbb/101/3/263/_pdf Cloning and Characterization of nif Structural and Regulatory Genes in the Purple Sulfur Bacterium, Halorhodospira halophila]
 
Recent studies of the sequences of the 16sRNA gene have been able to provide details and data into the Ectothiorhodospira genus and the different species within, helping to distinguish <I>Halorhodospira</I> and reassigning it as a separate genus category due to it's extremely halophilic nature.
 
 
[http://www.springerlink.com/content/7b3j189vdcl1aryl/ The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses]
 
  
 
==References==
 
==References==
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5. [http://www.dsmz.de/microorganisms/html/strains/strain.dsm000244.html "''DSM 244 - Halorhodospira halophila''" ''DSMZ.com''. German Collection of Microorganisms and Cell Cultures. 2004. June 2007.]
 
5. [http://www.dsmz.de/microorganisms/html/strains/strain.dsm000244.html "''DSM 244 - Halorhodospira halophila''" ''DSMZ.com''. German Collection of Microorganisms and Cell Cultures. 2004. June 2007.]
 +
 +
6. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=20280 "''Halorhodospira halophila SL1, complete genome''". ''NCBI.com''. National Center for Biotechnology Information. January 2007. June 2007.]
 +
 +
7. [http://microbialgenomics.energy.gov/announcement/seq2005.shtml "''Microbial Genome Sequencing List, 2005''". ''Genomics.energy.gov''. US Department of Energy Microbial Genome Program. 2005. June 2007.]
 +
 +
8. [http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=kegg&keywords=halorhodospira+halophila "''KEGG Pathway Database for Halorhodospira halophila''". ''Kyoto Encyclopedia of Genes and Genomes''. April 2007. June 2007.]
 +
 +
9. [http://www.jstage.jst.go.jp/article/jbb/101/3/263/_pdf Hisayoshi Tsuihiji, Yoichi Yamazaki, Hironari Kamikubo, Yasushi Imamoto and Mikio Kataoka: “Cloning and Characterization of nif Structural and Regulatory Genes in the Purple Sulfur Bacterium, Halorhodospira halophila”. J. BIOSCI. BIOENG., Vol. 101, 263-270 (2006).
 +
 +
10. [http://www.springerlink.com/content/7b3j189vdcl1aryl/ Imhoff, J.F. and Suling, Jorg. "''The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses''". ''Archives of Microbiology''. Springerlink. 19 February, 2004. June 2007.]
  
 
Edited by student Kent Lee of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
 
Edited by student Kent Lee of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano

Revision as of 16:29, 8 June 2007

A Microbial Biorealm page on the genus Halorhodospira halophila

Classification

Higher order taxa

Superkingdom: Bacteria;

Phylum: Proteobacteria;

Class: Gammaproteobacteria;

Order: Chromatiales;

Family: Ectothiorhodospiraceae;

Genus: Halorhodospira;

Species: Halorhodospira halophila


NCBI

Species

Halorhodospira halophila

NCBI: Taxonomy

Strains

Halorhodospira halophila DSM 244/S1

Halorhodospira halophila BN9624

Halorhodospira halophila BN9630

Description and significance

(a)Halorhodospira neutriphila species similar to Halorhodospira halophila, with negative staining to show polar flagella. Bar, 1µm. (b) Ultrathin section of Halorhodospira neutriphila showing intracellular stacks of lamellar membranes and envelopes of the Gram-negative type. Bar, 0·5 µm. Photos from the International Journal of Systematic and Evolutionary Microbiology.

Halorhodospira halophila (formerly Ectothiorhodospira halophila) is an extremely halophilic purple bacterium that was formally a member of the Ectothiorhodospira genus until recently reclassified. Phylogenetically, Halorhodospira halohila is associated within the gamma subdivision of the phylum Proteobacteria and is known to be phototrophic and Gram-negative. It is considered to be “one of the most halophilic eubacteria known.” [2] Its halophilic nature allows for it to be present in conditions that often have been thought to be too harsh for bacteria, and it is found proliferating in saturated salts such as crystallizer ponds (a hypersaline environment where sodium chloride precipitates) that have a salinity of 25% or higher. This importantly shows that harsh environments once thought to be exclusive to archaea actually contain bacteria as well. [3]

This halophilic organism was first isolated from a salt lake mud [5] and has been determined to have several functions: production of organic solutes glycine betaine, ectoine, and trehalose to help balance osmotic pressure, as well as the oxidization of sulfide to sulfur (which later would be further oxidized into sulfate). [2] This has resulted in the use of Halorhodospira halophila for research on topics from a photobiological ability to produce hydrogen gas to effects on sulfur.

One important aspect is the production of the bacterial photoreceptor PYP (photoactive yellow protein) within Halorhodospira halophila. PYP is a blue-light sensor found in Halorhodospira halophila that has great significance towards protein research and biotechnology. Photoactive proteins are generally accepted as "model systems for studying protein signal state formation." As a small protein, PYP provides for an 'attractive model system for exploring how a chromophore and protein interact to sense light and send a biological signal." [4]

Halorhodospira halophila has one major strain (DSM244/SL1) whose genome has been sequenced. But two other strains are recognized: BN9624 and BN9630. [1]

Genome structure

The gene sequence of Halorhodospira halophila S1 is the only listed strain of the species that has fully been sequenced. Genome sequencing of Halorhodospira halophila S1 was completed in January 2007 by the Department of Energy Joint Genome Institute. The genome is 2,678,452 nucleotides long (1,339,226 base pairs) and is made up of circular DNA. There are 2493 genes, 2407 which are protein coding, as well as 55 structural RNAs and 31 pseudo genes. The GC content of strain S1 is 67.9%. There is no current information on plasmids related to this species. [6]

While not all strains of Halorhodospira halophila have been sequenced, there is still some information on their similarity to related species. Halorhodospira neutriphila, displayed in the photo on the right, has a 94.6% similarity to strain DSM 244. Meanwhile, similarities with strains BN 9624 and BN 9630 are 91.4% and 90.7% respectively.

Cell structure and metabolism

Halorhodospira halophila is known as a "purple sulfur bacterium", whose structure consists of two membranes as well as the presence of flagella. [2] Its size is about ~4Mb. [7]

Halorhodospira halophila is capable of a large number of metabolic pathways such as glycolysis, the citrate cylce, amino acid metabolism, and more. A full list of these pathways and their individual maps can be found at the KEGG Pathway Database for Halorhodospira halophila. [8]

One important part of Halorhodospira halophila (and subject to recent research) is the generation of Photoactive Yellow Protein (PYP), a 14kDa cytoplasmic photoreceptor protein, which is an important protein for current research.

Halorhodospira halophila also has a potential role of hydrogen production through the nitrogen fixation of nitrogenase, which will be further explained below.

Ecology

Halorhodospira halophila

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

Pathology

At this time, Halorhodospira halophila causes no known diseases.

Application to Biotechnology

As will be explained below, current research has speculated that Halorhodospira halophila could play a strong role in nitrogen fixation through its byproduct hydrogen generating capabilities. Research in this field can aide in the use of the organism in photobiological hydrogen generation to develop new fuel cells as a possible "next-generation fuel source". [9] Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

Designation of Halorhodospira as a separate genus

Recent studies of the sequences of the 16sRNA gene have been able to provide details and data into the Ectothiorhodospira genus and the different species within, helping to distinguish Halorhodospira and reassigning it as a separate genus category. Within the Ectothiorhodospira genus, three organisms with an extremely halophilic nature showed enough difference to warrant reclassification: Halorhodospira halophila, Halorhodospira halochloris, and Halorhodospira abdelmalekii.[10]

The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses

Photobiological hydrogen generation

Some of the recent research on Halorhodospira halophila includes focusing on it's photobiological ability to produce hydrogen gas and the potential applications of this. Through the nitrogen fixation process in photosynthetic bacteria involving nitrogenase, hydrogen generation typically results as a byproduct. However, most of the studies of photobiological hydrogen production has been with purple non-sulfur bacteria. Current research is looking into the hydrogen production capabilities specific to purple sulfur bacteria. Purple sulfur bacteria are preferable for hydrogen generation because they are "complete photoautotrophs and can be cultivated in minimal culture media." Additionally, Halorhodospira halophila's" capability to withstand high pH and salt environments is a benefit since seawater could be "used directly as a culture medium". Current research, as shown by the paper below, shows that Halorhodospira halophila is capable of generating a substantial amount of hydrogen, and thus is a viable candidate for helping in the production of renewable energy sources in the future. [9]

Cloning and Characterization of nif Structural and Regulatory Genes in the Purple Sulfur Bacterium, Halorhodospira halophila

References

1. Hirschler-Rea, Anges, et al. "Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns: description of Halorhodospira neutriphila sp. nov. and emendation of the genus Halorhodospira". International Journal of Systematic and Evolutional Microbiology. International Union of Microbiological Sciences. 2003. June 2007.

2. "HAMAP: Halorhodospira halophila (strain DSM 244 / SL1) (Ectothiorhodospira halophila (strain DSM 244 / SL1)) complete proteome". ExPASy Proteomics Server. Swiss Institute of Bioinformatics. 2007. June 2007.

3. Anton, Josefa et al. "'Extremely Halophilic Bacteria in Crystallizer Ponds from Solar Salterns". Applied and Environmental Microbiology. American Society for Microbiology. July 2000. June 2007.

4. Van Wilderen, L.J. et al. "Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein". PNAS.com. Proceedings of the National Academy of Sciences of the United States of America. 2 October 2006. June 2007.

5. "DSM 244 - Halorhodospira halophila" DSMZ.com. German Collection of Microorganisms and Cell Cultures. 2004. June 2007.

6. "Halorhodospira halophila SL1, complete genome". NCBI.com. National Center for Biotechnology Information. January 2007. June 2007.

7. "Microbial Genome Sequencing List, 2005". Genomics.energy.gov. US Department of Energy Microbial Genome Program. 2005. June 2007.

8. "KEGG Pathway Database for Halorhodospira halophila". Kyoto Encyclopedia of Genes and Genomes. April 2007. June 2007.

9. [http://www.jstage.jst.go.jp/article/jbb/101/3/263/_pdf Hisayoshi Tsuihiji, Yoichi Yamazaki, Hironari Kamikubo, Yasushi Imamoto and Mikio Kataoka: “Cloning and Characterization of nif Structural and Regulatory Genes in the Purple Sulfur Bacterium, Halorhodospira halophila”. J. BIOSCI. BIOENG., Vol. 101, 263-270 (2006).

10. Imhoff, J.F. and Suling, Jorg. "The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses". Archives of Microbiology. Springerlink. 19 February, 2004. June 2007.

Edited by student Kent Lee of Rachel Larsen and Kit Pogliano