Introduction
Protein sequences originating from complete genomes and that can be assigned to CAZy families are listed in the links below. The only genomes that are consistently surveyed in the CAZy database are those released by the NCBI as regular entries in the daily releases of GenBank. In a very limited number of cases, we have included data from RefSeq genomes.
The collection of carbohydrate-active enzymes encoded by the genome of an organism ("CAZome") provides an insight into the nature and extent of the metabolism of complex carbohydrates of the species. The CAZomes of free living organisms typically correspond to 1-5% of the predicted coding sequences. Extremely reduced CAZomes are characteristic of species with a strict intracellular parasitic lifestyle. Because of the massive chemical, structural and functional variability of carbohydrates, CAZome analyses and comparisons highlight significant differences between species.
Although often useful, the simple assignment of a protein sequence to a CAZy family does not constitute a refined functional prediction for genomic annotation. For the later task, we are developping a CAZy-based annotation methodology, which takes into account protein modularity, family and subfamily assignment, relatedness to experimentally characterized enzymes and expertise in the varying substrate specificity of carbohydrate-active enzymes. This methodology, which results in coherent, expert and comparable sets of annotations, is applied to novel genomes and metagenomes on a collaborative basis.
Our published work on CAZymes in genomes and metagenomes
[32] Ma et al (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367-373 [PMID: 20237561].
[31] Ventura et al. (2009) The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet 5(12) e1000785 [PMID: 20041198].
[30] Coleman et al (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5, e1000618 [PMID: 19714214].
[29] Yang et al (2009) The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PloS One 4, e6085 [PMID: 19568419].
[28] Worden et al (2009) The genomes of Micromonas: global reporters in marine environments. Science 324, 268-272 [PMID: 19359590].
[27] Turnbaugh et al (2009) A core gut microbiome in obese and lean twins. Nature 457, 480-484 [PMID: 19043404].
[26] McBride et al (2009) Novel features of the polysaccharide digesting gliding bacterium Flavobacterium johnsoniae revealed by genome sequence analysis. Appl. Environm. Microbiol. 75, 6864-6875 [PMID: 19717629].
[25] Berg Miller M, Antonopoulos DA, Berg ME, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA (2009) Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 4, e6650. [PMID: 19680555].
[24] Mahowald et al (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. USA 106, 5859-5864 [PMID: 19321416].
[23] Ward et al (2009) Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl. Environ. Microbiol. 75, 2046-2056 [PMID: 19201974].
[22] Brulc et al (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc. Natl. Acad. Sci. USA 106, 1948-1953 [PMID: 19181843].
[21] Martinez et al (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA 106, 1954-1959 [PMID: 19193860].
[20] Coutinho et al (2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet. Biol. 46, S161-S169 [PMID: 19618505].
[19] Wortman et al (2009) The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet. Biol. 46, S2-S13 [PMID: 19146970].
[18] Martin et al (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452, 88-92 [PMID: 18322534].
[17] Lozupone C, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI & Knight R. (2008) The convergence of carbohydrate active gene repertoires in human gut microbes. Proc. Natl. Acad. Sci. USA, 105, 15076-15081 [PMID: 18806222].
[16] Abad et al (2008) Genome sequence of the metazoan plant-specific nematode Meloidogyne incognita. Nature Biotechnol. 26, 909-915. [PMID: 18660804].
[15] Deboy et al (2008) Insights into plant cell-wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J. Bacteriol. 190, 5455-5463 [PMID: 18556790].
[14] Weiner et al (2008) Complete genome sequence of the complex carbohydrate-degrading marine bacterium Saccharophagus degradans strain 2-40T. PLoS Genet., 4(5):e1000087. [PMID: 18516288].
[13] Martinez et al (2008) Genome sequence analysis of the cellulolytic fungus Trichoderma reesei (syn. Hypocrea jecorina) reveals a surprisingly limited inventory of carbohydrate-active enzymes. Nature Biotechnol. 26, 553-560. [PMID: 18454138].
[12] Espagne et al (2008) The genome sequence of the model Ascomycete fungus Podospora anserina. Genome Biol. 9:R77 (doi:10.1186/gb-2008-9-5-r77) [PMID: 18460219].
[11] Pel et al (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnol. 25, 221-231 [PMID: 17259976].
[10] Xu et al (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology 5, e156 [PMID: 17579514].
[9] Samuel et al (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl. Acad. Sci. USA 104, 10643-10648. [PMID: 17563350].
[8] Xie et al (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl. Environm. Microbiol. 73, 3536-3546. [PMID: 17400776].
[7] Geisler-Lee et al (2006) Poplar Carbohydrate-Active Enzymes (CAZymes). Gene identification and expression analyses. Plant Physiol 140, 946-962. [PMID: 16415215].
[6] Tuskan et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313, 1596-1604 [PMID: 16973872].
[5] West CM, van der Wel H, Coutinho P M, Henrissat B (2005) Glycosyltransferase genomics in Dictyostelium discoideum (2005) In Dictyostelium Genomics. W.F. Loomis & A. Kuspa, eds., Horizon Scientific Press 235-264.
[4] Martinez et al (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnol 22 695-700 [PMID: 15122302].
[3] Coutinho, P.M., Stam, M., Blanc, E. & Henrissat, B. (2003) Why so many carbohydrate-active enzymes related genes in plants ? Trends Plant Sci. 8, 563-565 [PMID: 14659702].
[2] Henrissat B, Deleury E, Coutinho P M (2002) Glycogen metabolism loss : a common marker of parasitic behaviour in bacteria ? Trends Genet 18 437-440 [PMID: 12175798].
[1] Henrissat B, Coutinho P M, Davies GJ (2001) A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol Biol 47 55-72 [PMID: 11554480].