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MetaCyc Pathway: cellulose and hemicellulose degradation (cellulolosome)

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/Assimilation Carbohydrates Degradation Polysaccharides Degradation Cellulose Degradation
Degradation/Utilization/Assimilation Polymeric Compounds Degradation Polysaccharides Degradation Cellulose Degradation
Metabolic Clusters
Superpathways

Some taxa known to possess this pathway include ? : Acetivibrio cellulolyticus , Clostridium acetobutylicum , Clostridium cellulovorans , Pseudobacteroides cellulosolvens , Ruminiclostridium thermocellum , Ruminiclostridium thermocellum ATCC 27405 , Ruminococcus albus , [Clostridium] cellulolyticum , [Clostridium] josui , [Clostridium] papyrosolvens

Expected Taxonomic Range: Bacteria

Summary:
The strictly anaerobic, thermophilic bacterium Ruminiclostridium thermocellum is the microorganism with the fastest documented growth rate on the recalcitrant substrate crystalline cellulose [Lynd02]. Unlike fungal cellulases, Ruminiclostridium thermocellum is able to completely solubilize crystalline forms of cellulose such as cotton and avicel [Johnson82]. The organism achieves this remarkable ability by forming very large extracellular multi-enzyme complexes, known as cellulosomes. The complex has a diameter of 18 nm and a mass in excess of 2000 kDa [Shoham99]. Similar complexes are formed by related Clostridia (such as Clostridium acetobutylicum, [Clostridium] cellulolyticum, Clostridium cellulovorans, [Clostridium] josui and [Clostridium] papyrosolvens) and other anaerobic cellulose-degrading bacteria, such as Acetivibrio cellulolyticus, Pseudobacteroides cellulosolvens and Ruminococcus albus [Bayer08].

Although these bacteria cannot readily utilize carbohydrates other than cellodextrins [Demain05], the cellulosome contains not just endo- and exo-cellulases but also a number of hemicellulolytic enzymes, including xylanases, non-glucanolytic polysaccharide hydrolases and lyases, feruloyl esterases etc. The function of the non-cellulolytic enzymes is presumably the unwrapping of the cellulose crystals from the covering matrix of lignin, pectin and hemicellulose.

The cellulosome is a modular complex. The center of the complex consists of a central non-catalytic protein known as the scaffoldin (CipA), which binds up to nine catalytic subunits [Wu88]. The attachment of each catalytic subunit is mediated by the interaction of its type I dockerin domain with one of the nine type I cohesin domains of CipA [Kruus95].

CipA is, in turn, bound to the cell surface by the interaction of its type II dockerin domain with the type II cohesin domain of one of three S-layer anchor proteins, SdbA, Orf2p, or OlpB [Bayer98]. Each of these anchor proteins contains a C-terminal S-layer homology module that mediates attachment to the bacterial cell surface, and a different number of type II cohesin modules capable of binding CipA molecules. Thus different anchoring scaffoldins form cellulosome complexes of differing sizes. The smallest one, anchoring scaffoldin SdbA, contains one cohesin domain, and thus binds one CipA molecule along with the nine catalytic units bound to it. The medium size anchoring scaffoldin Orf2p contains two cohesin domains and thus binds two CipA molecules and forms complexes with 18 catalytic units. The most abundant anchor protein is anchoring scaffoldin OlpB, which contains seven cohesin domains and forms complexes of up to 63 catalytic units.

In addition to nine type I cohesin domains and a type II dockerin domain, the CipA scaffoldin also contains a type III cellulose-binding module for attachment of the complex to cellulose [Gerngross93]. Many of the catalytic units also contain carbohydrate-binding domains with differing specificities.

The exact composition of the cellulosomes depend on growth rate and the nature of substrates available. A 2007 experiment that compared the protein components of cellulosomes formed under conditions of growth on either β-D-cellobiose or avicel found significant differences [Gold07a]. Over 70 proteins that possess type I dockerin modules have been identified in the genome of Ruminiclostridium thermocellum ATCC 27405 [Pinheiro09].

Variants: cellulose degradation I (cellulosome) , cellulose degradation II (fungi)

Credits:
Created 04-Apr-2011 by Caspi R , SRI International


References

Bayer08: Bayer EA, Lamed R, White BA, Flint HJ (2008). "From cellulosomes to cellulosomics." Chem Rec 8(6);364-77. PMID: 19107866

Bayer98: Bayer EA, Shimon LJ, Shoham Y, Lamed R (1998). "Cellulosomes-structure and ultrastructure." J Struct Biol 124(2-3);221-34. PMID: 10049808

Demain05: Demain AL, Newcomb M, Wu JH (2005). "Cellulase, clostridia, and ethanol." Microbiol Mol Biol Rev 69(1);124-54. PMID: 15755956

Gerngross93: Gerngross UT, Romaniec MP, Kobayashi T, Huskisson NS, Demain AL (1993). "Sequencing of a Clostridium thermocellum gene (cipA) encoding the cellulosomal SL-protein reveals an unusual degree of internal homology." Mol Microbiol 8(2);325-34. PMID: 8316083

Gold07a: Gold ND, Martin VJ (2007). "Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis." J Bacteriol 189(19);6787-95. PMID: 17644599

Johnson82: Johnson EA, Sakajoh M, Halliwell G, Madia A, Demain AL (1982). "Saccharification of Complex Cellulosic Substrates by the Cellulase System from Clostridium thermocellum." Appl Environ Microbiol 43(5);1125-32. PMID: 16346009

Kruus95: Kruus K, Lua AC, Demain AL, Wu JH (1995). "The anchorage function of CipA (CelL), a scaffolding protein of the Clostridium thermocellum cellulosome." Proc Natl Acad Sci U S A 92(20);9254-8. PMID: 7568112

Lynd02: Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002). "Microbial cellulose utilization: fundamentals and biotechnology." Microbiol Mol Biol Rev 66(3);506-77, table of contents. PMID: 12209002

Pinheiro09: Pinheiro BA, Gilbert HJ, Sakka K, Fernandes VO, Prates JA, Alves VD, Bolam DN, Ferreira LM, Fontes CM (2009). "Functional insights into the role of novel type I cohesin and dockerin domains from Clostridium thermocellum." Biochem J 424(3);375-84. PMID: 19758121

Shoham99: Shoham Y, Lamed R, Bayer EA (1999). "The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides." Trends Microbiol 7(7);275-81. PMID: 10390637

Wu88: Wu, J.H.D., Orme-Johnson, W.H., Demain, A.L. (1988). "Two components of an extracellular protein aggregate of Clostridium thermocellum together degrade crystalline cellulose." Biochemistry 27:1703-1709.

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Ahsan96: Ahsan MM, Kimura T, Karita S, Sakka K, Ohmiya K (1996). "Cloning, DNA sequencing, and expression of the gene encoding Clostridium thermocellum cellulase CelJ, the largest catalytic component of the cellulosome." J Bacteriol 178(19);5732-40. PMID: 8824619

Ahsan97: Ahsan M, Matsumoto M, Karita S, Kimura T, Sakka K, Ohmiya K (1997). "Purification and characterization of the family J catalytic domain derived from the Clostridium thermocellum endoglucanase CelJ." Biosci Biotechnol Biochem 61(3);427-31. PMID: 9095547

Arai03: Arai T, Araki R, Tanaka A, Karita S, Kimura T, Sakka K, Ohmiya K (2003). "Characterization of a cellulase containing a family 30 carbohydrate-binding module (CBM) derived from Clostridium thermocellum CelJ: importance of the CBM to cellulose hydrolysis." J Bacteriol 185(2);504-12. PMID: 12511497

Blum00: Blum DL, Kataeva IA, Li XL, Ljungdahl LG (2000). "Feruloyl esterase activity of the Clostridium thermocellum cellulosome can be attributed to previously unknown domains of XynY and XynZ." J Bacteriol 182(5);1346-51. PMID: 10671457

Faulds91: Faulds CB, Williamson G (1991). "The purification and characterization of 4-hydroxy-3-methoxycinnamic (ferulic) acid esterase from Streptomyces olivochromogenes." J Gen Microbiol 137(10);2339-45. PMID: 1663152

Fontes95: Fontes CM, Hazlewood GP, Morag E, Hall J, Hirst BH, Gilbert HJ (1995). "Evidence for a general role for non-catalytic thermostabilizing domains in xylanases from thermophilic bacteria." Biochem J 307 ( Pt 1);151-8. PMID: 7717969

Fry93: Fry, S. C., York, W. S., Albersheim, P., et al (1993). "An unambiguous nomenclature for xyloglucan-derived oligosaccharides." Physiol Plant 89, 1-3.

Grepinet88: Grepinet O, Chebrou MC, Beguin P (1988). "Purification of Clostridium thermocellum xylanase Z expressed in Escherichia coli and identification of the corresponding product in the culture medium of C. thermocellum." J Bacteriol 170(10);4576-81. PMID: 3139631

Grepinet88a: Grepinet O, Chebrou MC, Beguin P (1988). "Nucleotide sequence and deletion analysis of the xylanase gene (xynZ) of Clostridium thermocellum." J Bacteriol 170(10);4582-8. PMID: 3139632

Hayashi97: Hayashi H, Takagi KI, Fukumura M, Kimura T, Karita S, Sakka K, Ohmiya K (1997). "Sequence of xynC and properties of XynC, a major component of the Clostridium thermocellum cellulosome." J Bacteriol 179(13);4246-53. PMID: 9209040

Hayashi99: Hayashi H, Takehara M, Hattori T, Kimura T, Karita S, Sakka K, Ohmiya K (1999). "Nucleotide sequences of two contiguous and highly homologous xylanase genes xynA and xynB and characterization of XynA from Clostridium thermocellum." Appl Microbiol Biotechnol 51(3);348-57. PMID: 10222584

Kimura00: Kimura T, Suzuki H, Furuhashi H, Aburatani T, Morimoto K, Karita S, Sakka K, Ohmiya K (2000). "Molecular cloning, overexpression, and purification of a major xylanase from Aspergillus oryzae." Biosci Biotechnol Biochem 64(12);2734-8. PMID: 11210150

Kimura03: Kimura T, Mizutani T, Sakka K, Ohmiya K (2003). "Stable expression of a thermostable xylanase of Clostridium thermocellum in cultured tobacco cells." J Biosci Bioeng 95(4);397-400. PMID: 16233426

Kimura03a: Kimura T, Mizutani T, Tanaka T, Koyama T, Sakka K, Ohmiya K (2003). "Molecular breeding of transgenic rice expressing a xylanase domain of the xynA gene from Clostridium thermocellum." Appl Microbiol Biotechnol 62(4);374-9. PMID: 12684848

Kishino09: Kishino Y, Sugihara Y, Jindou S, Sakka M, Inagaki M, Kimura T, Sakka K (2009). "Unusual binding properties of the dockerin module of Clostridium thermocellum endoglucanase CelJ (Cel9D-Cel44A)." FEMS Microbiol Lett 300(2);249-55. PMID: 19811541

Kitago07: Kitago Y, Karita S, Watanabe N, Kamiya M, Aizawa T, Sakka K, Tanaka I (2007). "Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum." J Biol Chem 282(49);35703-11. PMID: 17905739

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Lerouxel06: Lerouxel O, Cavalier DM, Liepman AH, Keegstra K (2006). "Biosynthesis of plant cell wall polysaccharides - a complex process." Curr Opin Plant Biol 9(6);621-30. PMID: 17011813

Madson03: Madson M, Dunand C, Li X, Verma R, Vanzin GF, Caplan J, Shoue DA, Carpita NC, Reiter WD (2003). "The MUR3 gene of Arabidopsis encodes a xyloglucan galactosyltransferase that is evolutionarily related to animal exostosins." Plant Cell 15(7);1662-70. PMID: 12837954

Millet85: Millet, J., Petre, D., Beguin, P., Raynaud, O., Aubert, J. P. (1985). "Cloning of ten distinct DNA fragments of Clostridium thermocellum coding for cellulases (Endoglucanases, cellobiohydrolases, cellulolytic genes)." FEMS Microbiology Letters 29:145-149.

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Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, biocyc14.