Halobacterium NRC-1: Difference between revisions

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{{CZ:Biol_201:_General_Microbiology/EZnotice}}
{{Taxobox
| color = pink
| name =  ''Halobacterium sp. NRC-1''
| image = Halobacterium sp..jpg
| regnum = Archaea
| phylum = Euryarchaeota
| classis = Halobacteria
| ordo =  Halobacteriales
| familia = Halobacteriaceae
| genus =  Halobacterium
| species = Halobacterium sp. NRC-1
| binomial = ''Halobacterium sp. NRC-1''
| binomial_authority = 
}}
==Description and Significance==
''Halobacterium sp. NRC-1'' is a non-pathogenic, halophilic [[archaea]] which thrives all over the world in high salt environments, including salt production facilities, brine inclusions in salt crystals, natural lakes and ponds, and salt marshes.  Prior to 1990 ''H. NRC-1'' was classified as an [[archeabacterium]] under the [[prokaryote]] kingdom in the [[two-empire]] system which consisted of [[eukaryote]]s and [[prokaryote]]s.  Since 1990 the [[prokaryote]]s were split into [[bacteria]] and [[archaea]] due to their different evolutionary paths and biochemical differences.<ref>{{Cite journal
| issn = 0146-0749
| volume = 58
| issue = 1
| pages = 1-9
| last = Woese
| first = C R
| title = There must be a prokaryote somewhere: microbiology's search for itself
| journal = Microbiological Reviews
| accessdate = 2009-04-28
| date = 1994-03
| url = http://www.ncbi.nlm.nih.gov/pubmed/8177167
}}</ref>
Like all [[archaea]] ''H. NRC-1'' has no [[nucleus]] or [[organelles]] within the cell, and like other [[archaea]], have evolved many metabolic pathways to allow it to survive in extreme environments.<ref name=ArchaeaWiki>{{Cite web
| title = Archaea - Wikipedia, the free encyclopedia
| accessdate = 2009-04-26
| url = http://en.wikipedia.org/wiki/Archaea
}}</ref>
''Halobacterium sp. NRC-1'' is motile using both [[flagella]] and gas vesicles, and respond to their environment by moving toward or away from chemicals in a process called [[chemotaxis]]. Additionally, they can move toward or away from light in a process called [[phototaxis]] by utilizing their sensory [[Bacteriorhodopsin|rhodopsins]].  Phototaxis is an advantageous abilty for halobacteria because it enables them to swim away from the high levels of ultra violet and ionizing radiation that they are exposed to on a daily basis. 
''Halobacterium sp. NRC-1'' reproduce by binary fission and grow best in a 42 degree Celsius aerobic high salt environment. 
''Halobacterium sp. NRC-1'' is very easy to culture in the lab and its genome has been completely mapped.  Whole-genome [[DNA microarray]]s are available to investigate gene expression.  This makes it an excellent model microorganism for research in basic cellular processes, gene expression and as well as for teaching.
==Genome structure==
The genome of ''Halobacterium sp. NRC-1'' was published in 2000. Since that time scientists have done extensive research to gain insights into both its extremophilic abilities as well as its biological processes.  In order to survive in its environment, ''H. NRC-1'' has developed amazing capabilities to repair its own genome, one being a precise base excision repair system.  Homologous [[recombination]] plays an important role in [[DNA]] repair as well. Its ability to repair its chromosomes after extensive damage is only exceeded by the extremely radiation resistant [[Deinococcus radiodurans]]bacterium.<ref name=UVRad>{{Cite journal
| doi = 10.1186/1746-1448-1-3
| issn = 1746-1448
| volume = 1
| issue = 1
| pages = 3
| last = McCready
| first = Shirley
| coauthors = Jochen Muller, Ivan Boubriak, Brian Berquist, Wooi Ng, Shiladitya DasSarma
| title = UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1
| journal = Saline Systems
| accessdate = 2009-04-18
| date = 2005
| url = http://www.salinesystems.org/content/1/1/3
}}</ref> In fact, ''H. NRC-1'' was found to display a significant number of unique homologs with this bacterium, which suggests that they might have been acquired through [[lateral gene transfer]].<ref name=GenomeSeq>{{Cite journal
| doi = VL  - 97
| volume = 97
| issue = 22
| pages = 12176-12181
| last = Ng
| first = Wailap Victor, et al.
| title = Genome sequence of Halobacterium species NRC-1
| journal = Proceedings of the National Academy of Sciences of the United States of America
| accessdate = 2009-04-18
| date = 2000-10-24
| url = http://www.pnas.org/content/97/22/12176.abstract
}}</ref>
This microorganism also displays other types of defense mechanisms. In combination with its saline environment which provides some protection from UV radiation, the proteins that are produced by ''H. NRC-1'' were found to be highly acidic.  This low pH helps the proteins resist the denaturing effects of the high concentration of salts that surrounds it.<ref name=PhysResponse>{{Cite journal
| doi = 10.1007/s00792-005-0437-4
| volume = 9
| issue = 3
| pages = 219-227
| last = Kottemann
| first = Molly
| coauthors = Adrienne Kish, Chika Iloanusi, Sarah Bjork, Jocelyne DiRuggiero
| title = Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation
| journal = Extremophiles
| accessdate = 2009-04-28
| date = 2005-06-01
| url = http://dx.doi.org/10.1007/s00792-005-0437-4
}}</ref>
<ref name=PostGenome>{{Cite journal
| doi = 10.1186/1746-1448-2-3
| issn = 1746-1448
| volume = 2
| issue = 1
| pages = 3
| last = DasSarma
| first = Shiladitya
| coauthors = Brian Berquist, James Coker, Priya DasSarma, Jochen Muller
| title = Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1
| journal = Saline Systems
| accessdate = 2009-04-18
| date = 2006
| url = http://www.salinesystems.org/content/2/1/3
}}</ref>
''Halobacterium sp. NRC-1'' contains the smallest [[genome]] to date among the halophiles.<ref name=PostGenome/>
It is 2,571,010 bp in size, and is composed of a large GC-rich chromosome (2,014,239 bp, 68 % G+C), and two smaller extrachromosomal [[replicon]]s, pNRC100 (191,346 bp) and pNRC200 (365,425 bp), with 58–59 % G+C composition.  The large chromosome contains 2,111 genes, pNRC200 contains 374, and pNRC100 contains 197.  Of the 2,682 genes in the genome, only 1,658 coded for proteins that had significant matches to the [[genome database]].  A significantly smaller fraction of the genes on pNRC200 and pNRC100 matched to genes of known function in the databases.  The genes on the large chromosome had a 45% match rate, while pNRC200 had a 32% match rate and pNRC100 had only 26% of it's genome match up to genes of known function.  52 [[RNA]] genes have also been identified.  Interestingly, about 40 genes that are located on the small [[replicons]], pNRC100 and pNRC200, code for functions likely to be essential or important for cell livelihood  (e.g. [[thioredoxin]] and [[thioredoxin reductase]], a [[cytochrome oxidase]], a [[DNA]] [[polymerase]], multiple [[TATA]]-binding proteins (TBP) and transcription factor B (TFB) transcription factors, and the only [[arginyl-tRNA synthetase]] in the genome. In fact, these two [[replicon]]s share 145,428 base pairs of identical DNA.<ref name=GenomeSeq/>
After the publication of ''Halobacterium sp. NRC-1''s complete genome, the mapping of another closely related microorganism, [[Halobacterium H. Salinarum]], was published as well.  Interestingly, genomic comparisons between these two [[halophiles]] showed that the large chromosomes were virtually identical to one another while the smaller [[replicons]] carried different genes.<ref name=ModelOrganism>{{Cite journal
| doi = 10.1099/mic.0.28504-0
| volume = 152
| issue = 3
| pages = 585-590
| last = Soppa
| first = Jorg
| title = From genomes to function: haloarchaea as model organisms
| journal = Microbiology
| accessdate = 2009-04-18
| date = 2006-03-01
| url = http://mic.sgmjournals.org/cgi/content/abstract/152/3/585
}}</ref>
This information has cast new light on how the species differ from each other and the role of [[replicons]] in these organisms.  While much of the published literature on ''Halobacterium sp. NRC-1'' refers to the smaller genetic elements as replicons or megaplasmids, their characteristics don't really fit the definition of these terms.  [[Replicon]]s are considered to be exact copies of specific sequences of an original DNA or RNA genome, or even a whole copy of the original genome.  Plasmids are referred to as being small extra chromosomal [[DNA]] elements that carry relatively few genes that code for genetic information that is not essential to an organism's biological processes. Considering that the genetic information carried on these [[replicon]]s not only code for information that is essential to the organism's survival, but also contain nucleotide sequences that are not identical to that of it's larger chromosome, scientists are beginning to refer to them as "minichromosomes" rather than megaplasmids or replicons.<ref name=PostGenome/>
==Cell structure and metabolism==
''Halobacterium sp.NRC-1'' is a rod shaped [[aerobic]] [[chemoorganotroph]] which uses organic molecules as its source of energy, carbon and electrons.  This halophile possesses [[facultative anaerobic]] and phototrophic capabilities as well.  Research has shown that it is unable to metabolize sugars, but instead rely on amino acids that are eventually  [[catabolize]]d by the citric acid cycle during [[aerobic respiration]].  It survives on the remains of less halophilic organisms that have [[lysed]] due to the overwhelming amounts of salt in the environment. Outside of their natural environment, cells are cultured best in a [[complex medium]]. A [[minimal medium]] described for ''Halobacterium'' includes all but 5 of the 20 [[amino acid]]s for growth.<ref name=GenomeSeq/>
This microorganism has been studied extensively and has been shown to contain some of the usual features found in halophilic archaea, for example, an [[S-layer glycoprotein]], [[ether-linked lipids]], and [[purple membrane]].<ref name=UnderstandAdapt>{{Cite journal
| doi = 10.1101/gr.190201
| issn = 1088-9051
| volume = 11
| issue = 10
| pages = 1641-50
| last = Kennedy
| first = S P
| coauthors = W V Ng, S L Salzberg, L Hood, S DasSarma
| title = Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence
| journal = Genome Research
| accessdate = 2009-04-18
| date = 2001-10
| url = http://www.ncbi.nlm.nih.gov/pubmed/11591641
}}</ref>
This purple membrane consists of the light-driven ion transporters [[bacteriorhodopsin]] and [[halorhodopsin]], and the [[phototaxis]] receptors, sensory [[rhodopsin]]s I and II.<ref name=GenomeSeq/> In order to survive in low oxygen environments, ''Halobacterium sp. NRC-1'' increases its production of [[Bacteriorhodopsin]], which is a unique protein that can use light as an energy source, much like [[chlorophyll]] can in [[cyanobacteria]] and phototrophic [[eukaryotes]].  When the [[retinal]] in [[Bacteriorhodopsin]] absorbs light, it results in a series of conformational changes that translocates  protons through the cell's membrane into the [[periplasmic]] space.  This light driven proton pumping generates an electrochemical proton  gradient which is then used to power the synthesis of [[ATP]].  This phototrophic capability is particularly useful to ''Halobacterium sp. NRC-1'' as oxygen is not very soluble in concentrated salt solutions. In addition to its ability to use light as an energy source, it is also capable of anaerobic respiration using [[dimethyl sulfoxide]] ([[DMSO]]) and [[trimethylamine-N-oxide]] ([[TMAO]]) as terminal electron acceptors.  [[Arginine]] [[fermentation]] can also be used for anaerobic energy production as well.<ref name=GeneAnaerobic>{{Cite journal
| doi = 10.1128/JB.187.5.1659-1667.2005
| volume = 187
| issue = 5
| pages = 1659–1667
| last = Müller
| first = Jochen A.
| coauthors = Shiladitya DasSarma
| title = Genomic Analysis of Anaerobic Respiration in the Archaeon Halobacterium sp. Strain NRC-1: Dimethyl Sulfoxide and Trimethylamine N-Oxide as Terminal Electron Acceptors
| journal = Journal of Bacteriology
| accessdate = 2009-04-18
| date = 2005-03
| url = http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1064022
}}</ref>
''Halobacterium sp. NRC-1'' is also classified as an obligate [[halophilic]] microorganism which has adapted to be able to grow in conditions of extremely high salinity, up to 10 times that of seawater.<ref name=GenomeSeq/> 
In order to survive under these conditions it maintains a very high concentration of salts internally in the form of KCl to enable it to remain isotonic to its preferred environment.<ref>{{Cite journal
| doi = 10.1186/1746-1448-3-6
| issn = 1746-1448
| volume = 3
| issue = 1
| pages = 6
| last = Coker
| first = James
| coauthors = Priya DasSarma, Jeffrey Kumar, Jochen Muller, Shiladitya DasSarma
| title = Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-1: responses to changes in salinity and temperature
| journal = Saline Systems
| accessdate = 2009-04-18
| date = 2007
| url = http://www.salinesystems.org/content/3/1/6
}} </ref>
[[Halorhodopsin]] plays a very important role in helping to maintain the osmotic balance within the cell. This membrane protein acts as a light driven pump by transporting chloride and potassium ions into the cell.  [[Halorhodopsin]] saves the organism a large amount of metabolic energy by using the energy of the yellow light that it captures to fuel the movement of these ions.<ref name=Halorhodopsin>{{Cite journal
| issn = 0959-440X
| volume = 8
| issue = 4
| pages = 489-500
| last = Oesterhelt
| first = D
| title = The structure and mechanism of the family of retinal proteins from halophilic archaea
| journal = Current Opinion in Structural Biology
| accessdate = 2009-04-26
| date = 1998-08
| url = http://www.ncbi.nlm.nih.gov/pubmed/9729742
}}</ref>
==Ecology==
==Ecology==
[[Image: ISS007-E-13002.jpg|right|thumb|350px|-Image ISS007-E-13002 from the ISS of the Great Salt Lake showing purple tint due to ''halobacterium'' presence and increased [[bacteriorhodopsin]] production due to high salt concentration. Image courtesy of the Image Science & Analysis Laboratory, NASA Johnson Space Center]]  
[[Image: ISS007-E-13002.jpg|right|thumb|350px|-Image ISS007-E-13002 from the ISS of the Great Salt Lake showing purple tint due to ''halobacterium'' presence and increased [[bacteriorhodopsin]] production due to high salt concentration. Image courtesy of the Image Science & Analysis Laboratory, NASA Johnson Space Center]]  
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There are not many other organisms that can survive in these high salt environments, in fact one of its primary sources of food is the [[amino acid]]s of other organisms which have [[lyse]]d due to the high salt concentration in this environment.  Brine shrimp are one of a few other organisms that can survive the high salt concentration, and they feed almost exclusively on the halobacteria.  In addition to rhodopsin, ''Halobacterium NRC-1''  produce carotenoids, which are red organic pigments that can also serve as antioxidants.  The flamingo, whose pink color comes exclusively from the carotenoids in its diet (it doesn't have the ability to produce these pigments naturally ) feed on the brine shrimp (who are capable of producing these pigments). These same brine shrimp have fed on the carotenoid producing halobacteria.  So interestingly enough, these small organisms, the brine shrimp and the halobacteria, are the ones responsible for the flamingos beautiful pink coloring.
There are not many other organisms that can survive in these high salt environments, in fact one of its primary sources of food is the [[amino acid]]s of other organisms which have [[lyse]]d due to the high salt concentration in this environment.  Brine shrimp are one of a few other organisms that can survive the high salt concentration, and they feed almost exclusively on the halobacteria.  In addition to rhodopsin, ''Halobacterium NRC-1''  produce carotenoids, which are red organic pigments that can also serve as antioxidants.  The flamingo, whose pink color comes exclusively from the carotenoids in its diet (it doesn't have the ability to produce these pigments naturally ) feed on the brine shrimp (who are capable of producing these pigments). These same brine shrimp have fed on the carotenoid producing halobacteria.  So interestingly enough, these small organisms, the brine shrimp and the halobacteria, are the ones responsible for the flamingos beautiful pink coloring.
==Application to Biotechnology==
''Halobacterium NRC-1'' can easily be analyzed just by placing it in a [[hypotonic]] solution.  Due to the higher salt concentration within the microorganism in comparison to it's less salinic environment, water will flow into the cell following its concentration gradient, causing the cell to swell and and undergo lysis.  This explosion releases this microorganism's proteins, which then can be used by researchers for genetic analysis.  ''Halobacterium sp. NRC-1'' was one of the first [[Archaea]] to have its genome fully mapped and published.  Since that time several more species have been successfully mapped and a few others partially mapped.  This allows scientists to analyze the properties of halobacterium [[in silico]] to determine the activity of genes.  Transformation tools have also been developed to create loss-of-function mutants which aid in research.  Mutant strains of ''Halobacterium sp. NRC-1'' are experimentally designed to carry inoperative [[knockout genes]] which alter this organism's normal cellular processes.  Scientists can then infer the function of the mutated gene by comparing the physical and biochemical characteristics of the original ''Halobacterium sp. NRC-1'' with the characteristics of the new mutant.  These gene knockouts are making it possible to analyze this organism's ability to withstand extreme environmental conditions, including high levels of radiation, severe temperature changes, and fluctuations in oxygen levels. <ref name=ModelOrganism/>
The ability of this organism to be easily cultured along with these advanced research tools make ''Halobacterium sp. NRC-1'' an ideal model for the testing of gene functions.
In addition, ''Halobacterium sp. NRC-1'' is an ideal study tool because it is an [[extremophile]], it exists in environments that are very unfriendly toward life.  This makes it very useful for studying many biological questions especially those involved with adaptation and survival in extreme environments.  In fact, much research is being done to investigate whether or not ''halobacterium'' could be potential candidates for extraterrestrial life, such as on Mars or Europa.  Recent research has shown that ''Halobacterium sp. NRC-1'' can not only survive at temperatures far below its optimal growth temperature, but continue to reproduce as well.<ref name=ExtremeHalo>{{citation
| contribution =Survival and growth of Halobacterium sp. NRC-1 following incubation at -15&deg;C, freezing or freeze-drying, and the protective effect of cations
| volume = 545
| pages = 311-312
| last = Weidler
| first = Gerhard
| coauthors = Stefan Leunko, Helga Stan-Lotter
| title = Third European Workshop on Exo-Astrobiology
| accessdate = 2009-04-18
| date = 2004-03-01
| url = http://adsabs.harvard.edu/abs/2004ESASP.545..311W
}}</ref>
==Current Research==
<big>'''Survival and growth of Halobacterium sp. NRC-1 following incubation at -15&deg;C, freezing or freezedrying, and the protective effect of cations.'''</big>
The [[extremophillic]] properties and biological responses of Halobacteruim NRC-1 are currently being investigated to test the organism's survival potential in the harsh environmental conditions that exist on Mars.  The recent discoveries that [[meterorites]] from Mars contain a mineral form of sodium chloride as well as the isolation of halophilic archaea from ancient rock salt has led scientists to believe that the existence of Halobacterium sp. NRC-1 in a Martian environment is quite possible.  Halobacterium are known to be slightly thermophilic organisms, showing optimum growth at 40 degrees [[Celcius]].  In this experiment, cells of ''Halobacterium sp. NRC-1'' were freeze dried and suspended in buffers containing specific cations, including Mg++,Ca++,or K+. Results showed that NRC-1 was still capable of slow, yet steady growth at the extremely low temperature of -15 degrees [[Celcius]]. All of the cations appeared to show protective qualities during the freeze drying, with K+ being the most effective. The conditions of the the Martian environment include very low temperatures and low water availabilty. Scientists will continue to research NRC-1's ability to survive in such inhospitable environments such as the one on Mars. Hopefully, these future findings will  provide us some further insight in our search for life beyond our planet.<ref name=ExtremeHalo/>
<big>'''Functional Genomics of Thioredoxins in ''Halobacterium sp. NRC-1''.'''</big>
This project addresses the functions of an ancient protein family in Archaea that occupy extreme environments. Some of these proteins may play roles similar to those of comparable proteins in other living organisms, and thus may tell us about functions that evolved in the last universal common ancestor of life. Others may have evolved as the Archaea began to occupy specialized and often extreme environments. This project also addresses the emergence of proto-metabolic networks that supplied the precursors for the RNA World.<ref>{{Cite web
| title = Library of Resources « NASA Astrobiology
| accessdate = 2009-04-18
| url = http://astrobiology.nasa.gov/nai/library-of-resources/annual-reports/2008/cub/projects/functional-genomics-of-thioredoxins-in-halobacterium-sp-nrc-1/
}}</ref>
<big>'''Recombinant gas vesicles from Halobacterium sp. displaying SIV peptides demonstrate biotechnology potential as a pathogen peptide delivery vehicle'''</big>
''Halobacterium sp. NRC-1'' is also playing a significant role in the advancement of immunological biotechnology.  Recent experimental findings show that recombinant gas vesicles from a mutant strain of ''Halobacterium sp. NRC-1'' have the potential to serve as [[antigen]] display/delivery systems.  [[DNA]] segments of an [[SIV]] gene were inserted into a specific site on a GvpC gene (gas vesicle protein C) in the ''Halobacterium''.  The  gene was successfully taking up by the microorganism and recombination had been accomplished.  Subsequently, the gas vesicles began to express the new recombinant/pathogenic proteins at their surface.  Mice were then immunized with these antigen presenting [[SIV]] recombinant gas vesicles.  [[Antibody]] production was monitored, and an increased level of [[humoral]] response was observed.  After a 12 week period, a booster shot was given.  43 weeks after the booster shot was administered, an elevated number of antibodies still remained and was recorded. Research showed that this increased production of antibodies was long lived even in the absence of an [[adjuvant]], and immunologic memory had been proven.  These results indicate that the gas vesicles of ''Halobacterium sp. NRC-1'' show  great potential in their possible roles as immunizing agents.<ref name=Recombinant>{{Cite journal
| doi = 10.1186/1472-6750-8-9
| volume = 8
| pages = 9
| last = Sremac
| first = Marinko
| coauthors = Elizabeth S Stuart
| title = Recombinant gas vesicles from Halobacterium sp. displaying SIV peptides demonstrate biotechnology potential as a pathogen peptide delivery vehicle
| journal = BMC Biotechnology
| accessdate = 2009-04-30
| date = 2008
| url = http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2270826
}}</ref>
==References==
{{reflist|1}}

Revision as of 10:51, 4 May 2009

Ecology

-Image ISS007-E-13002 from the ISS of the Great Salt Lake showing purple tint due to halobacterium presence and increased bacteriorhodopsin production due to high salt concentration. Image courtesy of the Image Science & Analysis Laboratory, NASA Johnson Space Center

Halobacterium NRC-1 is one of many strains of halobacterium which thrive in extremely high salinity environments such as salt lakes, salt marshes and salt drying ponds. Their optimal temperature for reproduction is 42°C. Often these highly saline bodies of water will be tinted red or purple. It is the red/purple color of the bacteriorhodopsins that give the purple color you often see in these highly saline environments. Bacteriorhodopsin consists of a photosensitive protein pigment called retinal. This protein pigment is responsible for NRC-1's colorful properties. The more saline the environment the more colorful the water will be because halobacterium increase their production of bacteriorhodopsin in response to drops in oxygen which is less soluble in saline solutions.

There are not many other organisms that can survive in these high salt environments, in fact one of its primary sources of food is the amino acids of other organisms which have lysed due to the high salt concentration in this environment. Brine shrimp are one of a few other organisms that can survive the high salt concentration, and they feed almost exclusively on the halobacteria. In addition to rhodopsin, Halobacterium NRC-1 produce carotenoids, which are red organic pigments that can also serve as antioxidants. The flamingo, whose pink color comes exclusively from the carotenoids in its diet (it doesn't have the ability to produce these pigments naturally ) feed on the brine shrimp (who are capable of producing these pigments). These same brine shrimp have fed on the carotenoid producing halobacteria. So interestingly enough, these small organisms, the brine shrimp and the halobacteria, are the ones responsible for the flamingos beautiful pink coloring.

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