Difference between revisions of "Thermobifida fusca"

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{{Curated}}
 
==Classification==
 
==Classification==
  
 
===Higher order taxa===
 
===Higher order taxa===
  
cellular organisms; Bacteria; Firmicutes; ''Bacilli; Bacillales; Bacillaceae; Bacillus; Bacillus licheniformis''
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cellular organisms; Bacteria; Actinobacteria; ''Actinobacteridae; Actinomycetales; Streptosporangineae; Nocardiopsaceae; Thermobifida; fusca''
  
===Genus===  
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===Species===  
  
  
''Jannaschia''
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''Thermobifida fusca'' strain YX
  
 
==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.
 
Include a picture or two (with sources) if you can find them.
 
  
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''Thermobifida fusca'', formerly known as ''Thermomonaspora fusca'', is a rod shaped, thermophilic organism found in decaying organic matter and is a major degrader of plant cell wall (1, 2).  Its preferred habitat are compost heaps, rotting hay, manure piles, or mushroom growth medium because these are self-heated organic materials that can reach ''Thermobifida fusca’s'' growth temperature of 55ºC (2).  The genus Thermobifida is comprised of 2 members, the other being ''Thermobifida alba'' (1).  Both members of the genus are acid fast, Gram-positive aerobic organisms (1).  It is important to map out the entire genome of this organism because of its biotechnological uses.  The organism produces multiple extracellular enzymes including cellulases that are responsible for the decomposition of cellulose and lignocellulose residues, which are important for the breakdown of agricultural and urban wastes (1).
  
''Bacillus licheniformis'' is a bacterium that is commonly found in soil and bird feathers. Birds that tend to stay on the ground more than the air (i.e. sparrows) and on the water (i.e. ducks) are common carriers of this bacterium; it is mostly found around the bird's chest area and back plumage.
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[[Image:Thefu.gif|thumb|none|300px|''Thermobifida fusca'' Acknowledgement: David B. Wilson]]
  
''Bacillus licheniformis'' is part of the subtilis group along with ''Bacillus subtilis'' and ''Bacillus pumilus''. These bacteria are commonly known to cause food poisoning and food spoilage. ''Bacillus licheniformis'' also is known for contaminating dairy products. Food borne outbreaks usually involve cases of cooked meats and vegetables, raw milk, and industrially produced baby food contaminated with ''Bacillus licheniformis''.
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==Genome structure==
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''Thermobifida fusca'' “has a single circular chromosome of 3,642,249 bp predicted to encode 3,110 proteins and 65 RNA species with a coding density of 85%” (4). There are also other enzymes such as glycosyl hydrolases as well as cellulases and xylanases that are necessary for the degradation of plant cell walls (4). ''T. fusca'' has a 67.5% G-C content which is expected for an organism that can survive in high temperatures and a wide pH range from 4 to 10 (2).
  
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==Cell structure and metabolism==
 +
Actinomycetes generally grow as branched aerial hyphae which help the organism in the penetration and degradation of insoluble substrates such as lignocellulose (1).  ''Thermobifida fusca'' do not have flagella or pili. Their cell wall contains two teichoic acids made of poly(glycerol phosphate) (6). “Cell-wall analysis revealed the presence of meso-diaminopimelic acid, but no other characteristic amino acids or sugars in the murein.” (3)  It also has an endospore, which help it to survive in the rough environment for long periods of time (1).
  
==Genome structure==
+
==Ecology==
Describe the size and content of the genomeHow many chromosomes?  Circular or linear? Other interesting features?  What is known about its sequence?
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''Thermobifida fusca'' is usually in the “presence of abundant plant materials and other bio-polymer substrates of natural origin.” (1) ''T. fusca'' contributes to the environment by decomposing organic matter such as rotting hay, compost, manure or urban waste piles. There are also other thermophilic actinomycetes that share its natural habitat (1).
Does it have any plasmids?  Are they important to the organism's lifestyle?
 
  
''Bacillus Licheniformis'' is a Gram positive, thermophillic bacterium. Its optimal growth temperature is 50°C, but it can also survive at much higher temperatures. Its optimal temperature for
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==Pathology==
 +
The actinobacterium produces spores that can be allergenic in humans and cause a respiratory condition called farmer’s lung disease and mushroom worker’s disease (2).  Farmer’s lung disease and mushroom worker’s disease are examples of hypersensitivity pneumonitis, an inflammation of the alveoli within the lungs caused by inhaled organic dusts. These diseases usually develop in agricultural workers who breathe in large amounts of actinomycete spores (1).
  
 +
==Application to Biotechnology==
 +
''Thermobifida fusca'' produces multiple extracellular enzymes including cellulases that are responsible for the decomposition of cellulose and lignocellulose residues, which make up the bulk of agricultural and urban wastes (1).  ''T. fusca'' is important for waste remediation because they can degrade all major plant cell wall polymers except lignin and pectin (2).  The cellulose-decomposing capabilities of this organism are of importance in establishing safe biotechnological processes (1).  There is also good potential for use in the wood and paper industry (1). Cellulases are being studied for their “thermostability, broad pH range (4-10), and high activity.” (2)
  
==Cell structure and metabolism==
+
==Current Research==
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.
 
  
 +
1) David B. Wilson has been studying ''Thermobifida fusca'' cellulose degrading proteins for 25 years.  Six extracellular cellulases and an intracellular beta- glucosidase used by ''T. fusca'' for cellulose degradation have been purified and characterized (7).  He also “cloned and sequenced the structural genes encoding these enzymes, and helped to determine the 3-dimensional structures of two of the cellulase catalytic domains.” (7)
  
==Ecology==
+
2) David B. Wilson’s research helped to determine the “mechanism of a novel class of cellulase, family 9 processive endoglucanases” (7).  He helped show that there were two types of exocellulases. One type attacked the non-reducing ends of cellulose and the other type attacked the reducing ends (7).  Research on the regulation of ''T. fusca'' cellulase have shown that “cellobiose is the inducer and that cellulase synthesis is repressed by any good carbon source.” (7)
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
 
  
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3) Transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems have been researched (4).  “''T. fusca'' possesses two protein secretion systems: the sec general secretion system and the twin-arginine translocation system.” (4)  The twin-arginine translocation system may mediate the secretion of cellulases (4). “''T. fusca'' has extensive transport systems for import of carbohydrates coupled to transcriptional regulators controlling the expression of the transporters and glycosylhydrolases.” (4)
  
==Pathology==
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==References==
How does this organism cause disease?  Human, animal, plant hosts?  Virulence factors, as well as patient symptoms.
 
  
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1) DOE Joint Genome Institute, Thermobifida fusca YX project,
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Website:
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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&d
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opt=Overview&list_uids=94
  
==Application to Biotechnology==
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2) JGI Finished Genome, 2005.
Does this organism produce any useful compounds or enzymes?  What are they and how are they used?
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Website: http://genome.jgi-psf.org/finished_microbes/thefu/thefu.home.html
  
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3) Jozsef Kukolya, Thermobifida International Journal of Systematic and Evolutionary
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Microbiology, Thermobifia cellulolytica sp. nov., a novel lignocellulose-
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decomposing actinomycete, 2002.
  
==Current Research==
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4) Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, DiBartolo G, Martinez M, Lapidus A, Lucas S, Copeland A, Richardson P, Wilson DB, Kyrpides N.,
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Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida
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fusca YX., J Bacteriol. 2007 Mar;189(6):2477-86. Epub 2007 Jan 5. 47):14094-100.
  
Enter summaries of the most recent research here--at least three required
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5) McGrath CE, Wilson DB., Characterization of a Thermobifida fusca beta-1,3-
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glucanase (Lam81A) with a potential role in plant biomass degradation.,
 +
Biochemistry. 2006 Nov 28;45(
  
 +
6) Potekhina NV, Shashkov AS, Evtushenko LI, Naumova IB., [Teichoic acids in the cell
 +
walls of Microbispora mesophila Ac-1953t and Thermobifida fusca Ac-1952t],
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Mikrobiologiia. 2003 Mar-Apr;72(2):189-93. Russian.
  
==References==
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7) Wilson DB., Studies of Thermobifida fusca plant cell wall degrading enzymes., Chem
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]
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Rec. 2004;4(2):72-82.
  
  
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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=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''
 
|}
 
|}
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KMG

Latest revision as of 15:22, 7 July 2011

This is a curated page. Report corrections to Microbewiki.

Classification

Higher order taxa

cellular organisms; Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptosporangineae; Nocardiopsaceae; Thermobifida; fusca

Species

Thermobifida fusca strain YX

Description and significance

Thermobifida fusca, formerly known as Thermomonaspora fusca, is a rod shaped, thermophilic organism found in decaying organic matter and is a major degrader of plant cell wall (1, 2). Its preferred habitat are compost heaps, rotting hay, manure piles, or mushroom growth medium because these are self-heated organic materials that can reach Thermobifida fusca’s growth temperature of 55ºC (2). The genus Thermobifida is comprised of 2 members, the other being Thermobifida alba (1). Both members of the genus are acid fast, Gram-positive aerobic organisms (1). It is important to map out the entire genome of this organism because of its biotechnological uses. The organism produces multiple extracellular enzymes including cellulases that are responsible for the decomposition of cellulose and lignocellulose residues, which are important for the breakdown of agricultural and urban wastes (1).

Thermobifida fusca Acknowledgement: David B. Wilson

Genome structure

Thermobifida fusca “has a single circular chromosome of 3,642,249 bp predicted to encode 3,110 proteins and 65 RNA species with a coding density of 85%” (4). There are also other enzymes such as glycosyl hydrolases as well as cellulases and xylanases that are necessary for the degradation of plant cell walls (4). T. fusca has a 67.5% G-C content which is expected for an organism that can survive in high temperatures and a wide pH range from 4 to 10 (2).

Cell structure and metabolism

Actinomycetes generally grow as branched aerial hyphae which help the organism in the penetration and degradation of insoluble substrates such as lignocellulose (1). Thermobifida fusca do not have flagella or pili. Their cell wall contains two teichoic acids made of poly(glycerol phosphate) (6). “Cell-wall analysis revealed the presence of meso-diaminopimelic acid, but no other characteristic amino acids or sugars in the murein.” (3) It also has an endospore, which help it to survive in the rough environment for long periods of time (1).

Ecology

Thermobifida fusca is usually in the “presence of abundant plant materials and other bio-polymer substrates of natural origin.” (1) T. fusca contributes to the environment by decomposing organic matter such as rotting hay, compost, manure or urban waste piles. There are also other thermophilic actinomycetes that share its natural habitat (1).

Pathology

The actinobacterium produces spores that can be allergenic in humans and cause a respiratory condition called farmer’s lung disease and mushroom worker’s disease (2). Farmer’s lung disease and mushroom worker’s disease are examples of hypersensitivity pneumonitis, an inflammation of the alveoli within the lungs caused by inhaled organic dusts. These diseases usually develop in agricultural workers who breathe in large amounts of actinomycete spores (1).

Application to Biotechnology

Thermobifida fusca produces multiple extracellular enzymes including cellulases that are responsible for the decomposition of cellulose and lignocellulose residues, which make up the bulk of agricultural and urban wastes (1). T. fusca is important for waste remediation because they can degrade all major plant cell wall polymers except lignin and pectin (2). The cellulose-decomposing capabilities of this organism are of importance in establishing safe biotechnological processes (1). There is also good potential for use in the wood and paper industry (1). Cellulases are being studied for their “thermostability, broad pH range (4-10), and high activity.” (2)

Current Research

1) David B. Wilson has been studying Thermobifida fusca cellulose degrading proteins for 25 years. Six extracellular cellulases and an intracellular beta- glucosidase used by T. fusca for cellulose degradation have been purified and characterized (7). He also “cloned and sequenced the structural genes encoding these enzymes, and helped to determine the 3-dimensional structures of two of the cellulase catalytic domains.” (7)

2) David B. Wilson’s research helped to determine the “mechanism of a novel class of cellulase, family 9 processive endoglucanases” (7). He helped show that there were two types of exocellulases. One type attacked the non-reducing ends of cellulose and the other type attacked the reducing ends (7). Research on the regulation of T. fusca cellulase have shown that “cellobiose is the inducer and that cellulase synthesis is repressed by any good carbon source.” (7)

3) Transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems have been researched (4). “T. fusca possesses two protein secretion systems: the sec general secretion system and the twin-arginine translocation system.” (4) The twin-arginine translocation system may mediate the secretion of cellulases (4). “T. fusca has extensive transport systems for import of carbohydrates coupled to transcriptional regulators controlling the expression of the transporters and glycosylhydrolases.” (4)

References

1) DOE Joint Genome Institute, Thermobifida fusca YX project, Website: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&d opt=Overview&list_uids=94

2) JGI Finished Genome, 2005. Website: http://genome.jgi-psf.org/finished_microbes/thefu/thefu.home.html

3) Jozsef Kukolya, Thermobifida International Journal of Systematic and Evolutionary Microbiology, Thermobifia cellulolytica sp. nov., a novel lignocellulose- decomposing actinomycete, 2002.

4) Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, DiBartolo G, Martinez M, Lapidus A, Lucas S, Copeland A, Richardson P, Wilson DB, Kyrpides N., Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX., J Bacteriol. 2007 Mar;189(6):2477-86. Epub 2007 Jan 5. 47):14094-100.

5) McGrath CE, Wilson DB., Characterization of a Thermobifida fusca beta-1,3- glucanase (Lam81A) with a potential role in plant biomass degradation., Biochemistry. 2006 Nov 28;45(

6) Potekhina NV, Shashkov AS, Evtushenko LI, Naumova IB., [Teichoic acids in the cell walls of Microbispora mesophila Ac-1953t and Thermobifida fusca Ac-1952t], Mikrobiologiia. 2003 Mar-Apr;72(2):189-93. Russian.

7) Wilson DB., Studies of Thermobifida fusca plant cell wall degrading enzymes., Chem Rec. 2004;4(2):72-82.


Edited by Michael Zhang, student of Rachel Larsen and Kit Pogliano at UCSD.

NCBI: Taxonomy

KMG