Lignocellulose degradation mechanisms across the Tree of Life

Lombard, 2014, The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res, 42, D490, 10.1093/nar/gkt1178

Busk, 2014, Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in Nature, PLoS One, 9, e114138, 10.1371/journal.pone.0114138

Payne, 2015, Fungal cellulases, Chem Rev, 115, 1308, 10.1021/cr500351c

van den Brink, 2011, Fungal enzyme sets for plant polysaccharide degradation, Appl Microbiol Biotechnol, 91, 1477, 10.1007/s00253-011-3473-2

Eichinger, 2005, The genome of the social amoeba Dictyostelium discoideum, Nature, 435, 43, 10.1038/nature03481

King, 2010, Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes, Proc Natl Acad Sci U S A, 107, 5345, 10.1073/pnas.0914228107

Bayer, 2004, The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides, Annu Rev Microbiol, 58, 521, 10.1146/annurev.micro.57.030502.091022

Brunecky, 2013, Revealing Nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA, Science, 342, 1513, 10.1126/science.1244273

Ekborg, 2007, CelAB a multifunctional cellulase encoded by Teredinibacter turnerae T7902(T), a culturable symbiont isolated from the wood-boring marine bivalve Lyrodus pedicellatus, Appl Environ Microbiol, 73, 7785, 10.1128/AEM.00876-07

Vaaje-Kolstad, 2010, An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides, Science, 330, 219, 10.1126/science.1192231

Beeson, 2015, Cellulose degradation by polysaccharide monooxygenases, Annu Rev Biochem, 84, 923, 10.1146/annurev-biochem-060614-034439

Agger, 2014, Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation, Proc Natl Acad Sci U S A, 111, 6287, 10.1073/pnas.1323629111

Kjaergaard, 2014, Spectroscopic and computational insight into the activation of O-2 by the mononuclear Cu center in polysaccharide monooxygenases, Proc Natl Acad Sci U S A, 111, 8797, 10.1073/pnas.1408115111

Arantes, 2014, Current understanding of brown-rot fungal degradation mechanisms: a review, 147

Bugg, 2011, Pathways for degradation of lignin in bacteria and fungi, Nat Prod Rep, 28, 1883, 10.1039/c1np00042j

Pollegioni, 2015, Lignin-degrading enzymes, FEBS J, 282, 1190, 10.1111/febs.13224

Floudas, 2012, The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes, Science, 336, 1715, 10.1126/science.1221748

Brune, 2014, Symbiotic digestion of lignocellulose in termite guts, Nat Rev Microbiol, 12, 168, 10.1038/nrmicro3182

Distel, 2011, Molecular phylogeny of Pholadoidea Lamarck, 1809 supports a single origin for xylotrophy (wood feeding) and xylotrophic bacterial endosymbiosis in Bivalvia, Mol Phylogenet Evol, 61, 245, 10.1016/j.ympev.2011.05.019

Simmons, 2014, Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw, Biotechnol Biofuels, 7, 495, 10.1186/s13068-014-0180-0

Scharf, 2015, Omic research in termites: an overview and a roadmap, Front Genet, 6, 76, 10.3389/fgene.2015.00076

Boucias, 2013, The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition, Mol Ecol, 22, 1836, 10.1111/mec.12230

Mikaelyan, 2014, The fibre-associated cellulolytic bacterial community in the hindgut of wood-feeding higher termites (Nasutitermes spp.), Environ Microbiol, 16, 2711, 10.1111/1462-2920.12425

Ahmad, 2011, Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase, Biochemistry, 50, 5096, 10.1021/bi101892z

Brown, 2012, Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium, ACS Chem Biol, 7, 2074, 10.1021/cb300383y

Rahmanpour, 2015, Characterisation of Dyp-type peroxidases from Pseudomonas fluorescens Pf-5: oxidation of Mn(II) and polymeric lignin by Dyp1B, Arch Biochem Biophys, 574, 93, 10.1016/j.abb.2014.12.022

Majumdar, 2014, Roles of small laccases from Streptomyces in lignin degradation, Biochemistry, 53, 4047, 10.1021/bi500285t

Gall, 2014, Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp strain SYK-6 beta-aryl etherase pathway, J Biol Chem, 289, 8656, 10.1074/jbc.M113.536250

Salvachua, 2015, Towards lignin consolidated bioprocessing: simultaneous lignin depolymerisation and product generation by bacteria, Green Chem, 10.1039/C5GC01165E

de Gannes, 2013, Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing, Bioresour Technol, 133, 573, 10.1016/j.biortech.2013.01.138

Tian, 2014, Occurrence of lignin degradation genotypes and phenotypes among prokaryotes, Appl Microbiol Biotechnol, 98, 9527, 10.1007/s00253-014-6142-4

Graham, 2011, Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment, Nat Commun, 2, 375, 10.1038/ncomms1373

Kataoka, 2014, A new crystal form of a hyperthermophilic endocellulase, Acta Crystallogr F Struct Biol Commun, 70, 878, 10.1107/S2053230X14010930

Bjordal, 2012, Evaluation of microbial degradation of shipwrecks in the Baltic Sea, Int Biodeterior Biodegr, 70, 126, 10.1016/j.ibiod.2012.01.012

Pedersen, 2015, Bacterial and abiotic decay in waterlogged archaeological Picea abies (L.) Karst studied by confocal Raman imaging and ATR-FTIR spectroscopy, Holzforschung, 69, 103, 10.1515/hf-2014-0024

Fagervold, 2014, Microbial communities in sunken wood are structured by wood-boring bivalves and location in a submarine canyon, PLoS One, 9, e96248, 10.1371/journal.pone.0096248

Kunii, 2014, A Dictyostelium cellobiohydrolase orthologue that affects developmental timing, Dev Genes Evol, 224, 25, 10.1007/s00427-013-0460-x

Blifernez-Klassen, 2012, Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii, Nat Commun, 3, 1, 10.1038/ncomms2210

Toulza, 2010, Gene expression in proliferating cells of the dinoflagellate Alexandrium catenella (Dinophyceae), Appl Environ Microbiol, 76, 4521, 10.1128/AEM.02345-09

Blackman, 2014, Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome, BMC Genomics, 15, 785, 10.1186/1471-2164-15-785

Riley, 2014, Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi, Proc Natl Acad Sci U S A, 111, 9923, 10.1073/pnas.1400592111

Busk, 2015, Classification of fungal and bacterial lytic polysaccharide monooxygenases, BMC Genomics, 16, 368, 10.1186/s12864-015-1601-6

Eastwood, 2011, The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi, Science, 333, 762, 10.1126/science.1205411

Shelomi, 2014, Endogenous cellulase enzymes in the stick insect (Phasmatodea) gut, J Insect Physiol, 60, 25, 10.1016/j.jinsphys.2013.10.007

Tsuji, 2013, Comprehensive enzymatic analysis of the cellulolytic system in digestive fluid of the sea hare Aplysia kurodai. Efficient glucose release from sea lettuce by synergistic action of 45kDa endoglucanase and 210kDa beta-glucosidase, PLoS One, 8, e65418, 10.1371/journal.pone.0065418

Bui, 2015, Endogenous cellulase production in the leaf litter foraging mangrove crab Parasesarma erythodactyla, Comp Biochem Physiol B Biochem Mol Biol, 179, 27, 10.1016/j.cbpb.2014.09.004

Kostanjsek, 2010, Endogenous origin of endo-beta-1,4-glucanase in common woodlouse Porcellio scaber (Crustacea Isopoda), J Comp Physiol B Biochem Syst Environ Physiol, 180, 1143, 10.1007/s00360-010-0485-7

Nozaki, 2009, The contribution of endogenous cellulase to the cellulose digestion in the gut of earthworm (Pheretima hilgendorfi: Megascolecidae), Soil Biol Biochem, 41, 762, 10.1016/j.soilbio.2009.01.016

Betcher, 2012, Microbial distribution and abundance in the digestive system of five shipworm species (Bivalvia: Teredinidae), PLoS One, 7, e45309, 10.1371/journal.pone.0045309

O’Connor, 2014, Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk, Proc Natl Acad Sci U S A, 111, E5096, 10.1073/pnas.1413110111

Lechene, 2007, Quantitative imaging of nitrogen fixation by individual bacteria within animal cells, Science, 317, 1563, 10.1126/science.1145557

Sakamoto, 2009, Putative endogenous xylanase from brackish-water clam Corbicula japonica, Comp Biochem Physiol B Biochem Mol Biol, 154, 85, 10.1016/j.cbpb.2009.05.007

Koenig, 2013, The cellulolytic system of the termite gut, Appl Microbiol Biotechnol, 97, 7943, 10.1007/s00253-013-5119-z

Jaenicke, 2009, Is activated hemocyanin instead of phenoloxidase involved in immune response in woodlice?, Dev Comp Immunol, 33, 1055, 10.1016/j.dci.2009.05.005

Allardyce, 2008, Purification and characterisation of endo-beta-1,4-glucanase and laminarinase enzymes from the gecarcinid land crab Gecarcoidea anatalis and the aquatic crayfish Cherax destructor, J Exp Biol, 211, 2275, 10.1242/jeb.017657

Tsukagoshi, 2014, Structural and biochemical analyses of glycoside hydrolase family 26 beta-mannanase from a symbiotic protist of the termite Reticulitermes speratus, J Biol Chem, 289, 10843, 10.1074/jbc.M114.555383

Zheng, 2015, Population structure of endomicrobia in single host cells of termite gut flagellates (Trichonympha spp.), Microb Environ, 30, 92, 10.1264/jsme2.ME14169

Poulsen, 2014, Complementary symbiont contributions to plant decomposition in a fungus-farming termite, Proc Natl Acad Sci U S A, 111, 14500, 10.1073/pnas.1319718111

Kern, 2013, Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance, Proc Natl Acad Sci U S A, 110, 10189, 10.1073/pnas.1301502110

Vispo, 1995, The digestive tract and digestive function in the North American porcupine and beaver, Can J Zool, 73, 967, 10.1139/z95-113

Zhu, 2011, Evidence of cellulose metabolism by the giant panda gut microbiome, Proc Natl Acad Sci U S A, 108, 17714, 10.1073/pnas.1017956108

Xue, 2015, The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations, mBio, 6, e00022-15, 10.1128/mBio.00022-15

McDonald, 2012, Phylogenetic analysis of microbial communities in different regions of the gastrointestinal tract in Panaque nigrolineatus, a wood-eating fish, PLoS One, 7, e48018, 10.1371/journal.pone.0048018

McDonald, 2015, Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus, ISME J, 65

Blumer-Schuette, 2015, Discrete and structurally unique proteins (Tapirins) mediate attachment of extremely thermophilic caldicellulosiruptor species to cellulose, J Biol Chem, 290, 10645, 10.1074/jbc.M115.641480

Resch, 2013, Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction, Energy Environ Sci, 6, 1858, 10.1039/c3ee00019b

Eibinger, 2014, Cellulose surface degradation by a lytic polysaccharide monooxygenase and its effect on cellulase hydrolytic efficiency, J Biol Chem, 289, 35929, 10.1074/jbc.M114.602227

Li, 2013, Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active enzymes, Biotechnol Biofuels, 6, 94, 10.1186/1754-6834-6-94

Larkin, 2007, ClustalW and ClustalX version 2, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404

Robert, 2014, Deciphering key features in protein structures with the new ENDscript server, Nucleic Acids Res, 42, W320, 10.1093/nar/gku316

Biasini, 2014, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Res, 42, W252, 10.1093/nar/gku340

Knott, 2014, The mechanism of cellulose hydrolysis by a two-step, retaining cellobiohydrolase elucidated by structural and transition path sampling studies, J Am Chem Soc, 136, 321, 10.1021/ja410291u

Li, 2012, DelPhi: a comprehensive suite for DelPhi software and associated resources, BMC Biophys, 4, 9, 10.1186/2046-1682-5-9

Arantes, 2012, Peculiarities of brown-rot fungi and biochemical Fenton reaction with regard to their potential as a model for bioprocessing biomass, Appl Microbiol Biotechnol, 94, 323, 10.1007/s00253-012-3954-y