Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel-from systems biology to synthetic design

Current Opinion in Biotechnology

Volumn 27, Issue , 2014, Pages 195-203

  Xie, Shangxian ^a   Syrenne, Ryan ^a,b   Sun, Su ^a   Yuan, Joshua S ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCONVERSION; BIOMASS; BIOPRODUCTS; CELLULOSIC ETHANOL; COST BENEFIT ANALYSIS; COST EFFECTIVENESS; ENZYMES; LIGNOCELLULOSIC BIOMASS; MICROORGANISMS; PLANTS (BOTANY);

'OMICS' TECHNOLOGIES; ADVANCED BIOFUELS; BIOMASS CONVERSION; DEGRADING ENZYMES; FUNCTIONAL RELEVANCE; MECHANISM ANALYSIS; RECENT RESEARCHES; SYNTHETIC DESIGN;

BIOFUELS;

BIOFUEL;

BIODEGRADATION; BIOENGINEERING; BIOMASS CONVERSION; BROWN ROT FUNGUS; CELL STRUCTURE; CHEMICAL ANALYSIS; CHEMICAL PROCEDURES; CHEMICAL STRUCTURE; CONCENTRATION (PARAMETERS); ENZYME ASSAY; EXPERIMENTAL DESIGN; FUNGUS IDENTIFICATION; HIGH THROUGHPUT SCREENING; MOLECULAR EVOLUTION; MOLECULAR MODEL; NATURAL BIOMASS UTILIZATION SYSTEM; NONHUMAN; PLANT CELL; PRIORITY JOURNAL; REVIEW; RUMINANT STOMACH; SINGLE CELL ANALYSIS; SYSTEMS BIOLOGY; WHITE ROT FUNGUS;

ANIMALS; BACTERIA; BIOFUELS; BIOMASS; CELL WALL; COMPUTATIONAL BIOLOGY; DIGESTIVE SYSTEM; FUNGI; ISOPTERA; LIGNIN; PLANT CELLS; RUMINANTS; SYSTEMS BIOLOGY;

EID: 84896276495     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.02.007     Document Type: Review

References (70)

1. Ragauskas A.J., Williams C.K., Davison B.H., Britovsek G., Cairney J., Eckert C.A., Frederick W.J., Hallett J.P., Leak D.J., Liotta C.L., et al. The path forward for biofuels and biomaterials. Science 2006, 311:484-489.
2. Yuan J.S., Wang X., Stewart C.N. Biomass feedstock: diversity as a solution. Biofuels 2011, 2:491-493.
3. Yuan J.S., Tiller K.H., Al-Ahmad H., Stewart N.R., Stewart C.N. Plants to power: bioenergy to fuel the future. Trends Plant Sci 2008, 13:421-429.
4. Ding S.-Y., Liu Y.-S., Zeng Y., Himmel M.E., Baker J.O., Bayer E.A. How does plant cell wall nanoscale architecture correlate with enzymatic digestibility?. Science 2012, 338:1055-1060.
5. Xu Z., Zhang D., Hu J., Zhou X., Ye X., Reichel K.L., Stewart N.R., Syrenne R.D., Yang X., Gao P., et al. Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. BMC Bioinform 2009, 8:1471-2105.
6. Shi W., Xie S., Chen X., Sun S., Zhou X., Liu L., Gao P., Kyrpides N.C., No E.-G., Yuan J.S. Comparative genomic analysis of the endosymbionts of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PLoS Genet 2013, 9:e1003131.
7. Shi W., Ding S.-Y., Yuan J.S. Comparison of insect gut cellulase and xylanase activity across different insect species with distinct food sources. Bioenerg Res 2011, 4:1-10.
8. Hess M., Sczyrba A., Egan R., Kim T.-W., Chokhawala H., Schroth G., Luo S., Clark D.S., Chen F., Zhang T., et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011, 331:463-467.
9. Warnecke F., Luginbuhl P., Ivanova N., Ghassemian M., Richardson T.H., Stege J.T., Cayouette M., McHardy A.C., Djordjevic G., Aboushadi N., et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007, 450:560-565.
10. Quinlan R.J., Sweeney M.D., Lo Leggio L., Otten H., Poulsen J.C., Johansen K.S., Krogh K.B., Jorgensen C.I., Tovborg M., Anthonsen A., et al. Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. Proc Natl Acad Sci U S A 2011, 108:15079-15084.
11. Aachmann F.L., Sorlie M., Skjak-Braek G., Eijsink V.G., Vaaje-Kolstad G. NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions. Proc Natl Acad Sci U S A 2012, 109:18779-18784.
12. Geib S.M., Filley T.R., Hatcher P.G., Hoover K., Carlson J.E., Jimenez-Gasco Mdel M., Nakagawa-Izumi A., Sleighter R.L., Tien M. Lignin degradation in wood-feeding insects. Proc Natl Acad Sci U S A 2008, 105:12932-12937.
13. Floudas D., Binder M., Riley R., Barry K., Blanchette R.A., Henrissat B., Martínez A.T., Otillar R., Spatafora J.W., Yadav J.S., et al. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 2012, 336:1715-1719.
14. Shi Y., Chai L., Tang C., Yang Z., Zhang H., Chen R., Chen Y., Zheng Y. Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8. Biotechnol Biofuels 2013, 6:1.
15. Ke J., Sun J.-Z., Nguyen H.D., Singh D., Lee K.C., Beyenal H., Chen S.-L. In-situ oxygen profiling and lignin modification in guts of wood-feeding termites. Insect Sci 2010, 17:277-290.
16. Scharf M.E., Karl Z.J., Sethi A., Boucias D.G. Multiple levels of synergistic collaboration in termite lignocellulose digestion. PLoS ONE 2011, 6.
17. Kersten P., Cullen D. Extracellular oxidative systems of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol 2007, 44:77-87.
18. Aanen D.K., Eggleton P., Rouland-Lefevre C., Guldberg-Froslev T., Rosendahl S., Boomsma J.J. The evolution of fungus-growing termites and their mutualistic fungal symbionts. Proc Natl Acad Sci U S A 2002, 99:14887-14892.
19. Taprab Y., Johjima T., Maeda Y., Moriya S., Trakulnaleamsai S., Noparatnaraporn N., Ohkuma M., Kudo T. Symbiotic fungi produce laccases potentially involved in phenol degradation in fungus combs of fungus-growing termites in Thailand. Appl Environ Microbiol 2005, 71:7696-7704.
20. Bugg T.D., Ahmad M., Hardiman E.M., Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 2011, 28:1883-1896.
21. Martinez D., Berka R.M., Henrissat B., Saloheimo M., Arvas M., Baker S.E., Chapman J., Chertkov O., Coutinho P.M., Cullen D., et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 2008, 26:553-560.
22. Coutinho P.M., Andersen M.R., Kolenova K., vanKuyk P.A., Benoit I., Gruben B.S., Trejo-Aguilar B., Visser H., van Solingen P., Pakula T., et al. Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol 2009, 46:S161-S169.
23. Tian C., Beeson W.T., Iavarone A.T., Sun J., Marletta M.A., Cate J.H., Glass N.L. Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proc Natl Acad Sci U S A 2009, 106:22157-22162.
24. Pel H.J., de Winde J.H., Archer D.B., Dyer P.S., Hofmann G., Schaap P.J., Turner G., de Vries R.P., Albang R., Albermann K., et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 2007, 25:221-231.
25. Levasseur A., Drula E., Lombard V., Coutinho P.M., Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuel 2013, 6:41.
26. Martinez A.T., Ruiz-Duenas F.J., Martinez M.J., Del Rio J.C., Gutierrez A. Enzymatic delignification of plant cell wall: from nature to mill. Curr Opin Biotechnol 2009, 20:348-357.
27. Levasseur A., Piumi F., Coutinho P.M., Rancurel C., Asther M., Delattre M., Henrissat B., Pontarotti P., Asther M., Record E. FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genet Biol 2008, 45:638-645.
28. ten Have R., Teunissen P.J. Oxidative mechanisms involved in lignin degradation by white-rot fungi. Chem Rev 2001, 101:3397-3413.
29. Martinez D., Challacombe J., Morgenstern I., Hibbett D., Schmoll M., Kubicek C.P., Ferreira P., Ruiz-Duenas F.J., Martinez A.T., Kersten P., et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A 2009, 106:1954-1959.
30. Hori C., Gaskell J., Igarashi K., Samejima M., Hibbett D.S., Henrissat B., Cullen D. Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay. Mycologia 2013.
31. Vanden Wymelenberg A., Gaskell J., Mozuch M., Sabat G., Ralph J., Skyba O., Mansfield S.D., Blanchette R.A., Martinez D., Grigoriev I., et al. Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol 2010, 76:3599-3610.
32. Ryu J.S., Shary S., Houtman C.J., Panisko E.A., Korripally P., St John F.J., Crooks C., Siika-Aho M., Magnuson J.K., Hammel K.E. Proteomic and functional analysis of the cellulase system expressed by Postia placenta during brown rot of solid wood. Appl Environ Microbiol 2011, 77:7933-7941.
33. Martinez D., Larrondo L.F., Putnam N., Gelpke M.D.S., Huang K., Chapman J., Helfenbein K.G., Ramaiya P., Detter J.C., Larimer F., et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 2004, 22:695-700.
34. MacDonald J., Doering M., Canam T., Gong Y., Guttman D.S., Campbell M.M., Master E.R. Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood. Appl Environ Microbiol 2011, 77:3211-3218.
35. Bugg T.D., Ahmad M., Hardiman E.M., Singh R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol 2011, 22:394-400.
36. Peralta-Yahya P.P., Zhang F., del Cardayre S.B., Keasling J.D. Microbial engineering for the production of advanced biofuels. Nature 2012, 488:320-328.
37. Bayer E.A., Lamed R., White B.A., Flint H.J. From cellulosomes to cellulosomics. Chem Rec 2008, 8:364-377.
38. Doi R.H., Kosugi A. Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat Rev Micro 2004, 2:541-551.
39. de Souza B.W.R. Microbial Degradation of Lignocellulosic Biomass 2013, InTech.
40. Wilson D.B. Microbial diversity of cellulose hydrolysis. Curr Opin Microbiol 2011, 14:259-263.
41. Masai E., Katayama Y., Fukuda M. Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem 2007, 71:1-15.
42. Pieper D.H. Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 2005, 67:170-191.
43. Ausec L., Zakrzewski M., Goesmann A., Schlüter A., Mandic-Mulec I. Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. PLoS ONE 2011, 6:e25724.
44. Jing D., Wang J. Controlling the simultaneous production of laccase and lignin peroxidase from Streptomyces cinnamomensis by medium formulation. Biotechnol Biofuel 2012, 5:15.
45. Jing D. Improving the simultaneous production of laccase and lignin peroxidase from Streptomyces lavendulae by medium optimization. Bioresour Technol 2010, 101:7592-7597.
46. McLeod M.P., Warren R.L., Hsiao W.W., Araki N., Myhre M., Fernandes C., Miyazawa D., Wong W., Lillquist A.L., Wang D., et al. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 2006, 103:15582-15587.
47. Yam K., Geize R., Eltis L. Catabolism of aromatic compounds and steroids by Rhodococcus. Biology of Rhodococcus 2010, 133-169. Springer, Berlin Heidelberg. H.M. Alvarez (Ed.).
48. Davis J.R., Brown B.L., Page R., Sello J.K. Study of PcaV from Streptomyces coelicolor yields new insights into ligand-responsive MarR family transcription factors. Nucleic Acids Res 2013, 41:3888-3900.
49. Iwagami S.G., Yang K., Davies J. Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065. Appl Environ Microbiol 2000, 66:1499-1508.
50. Koike S., Kobayashi Y. Fibrolytic rumen bacteria: their ecology and functions. Asian Austral J Anim 2009, 22:131-138.
51. Flint H.J., Bayer E.A., Rincon M.T., Lamed R., White B.A. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Micro 2008, 6:121-131.
52. Jami E., Mizrahi I. Composition and similarity of bovine rumen microbiota across individual animals. PLoS ONE 2012, 7:e33306.
53. Sylvester J.T., Karnati S.K., Yu Z., Morrison M., Firkins J.L. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J Nutr 2004, 134:3378-3384.
54. McCutcheon J.P., McDonald B.R., Moran N.A. Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci U S A 2009, 106:15394-15399.
55. Taupp M., Mewis K., Hallam S.J. The art and design of functional metagenomic screens. Curr Opin Biotechnol 2011, 22:465-472.
56. Pope P.B., Mackenzie A.K., Gregor I., Smith W., Sundset M.A., McHardy A.C., Morrison M., Eijsink V.G.H. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS ONE 2012, 7:e38571.
57. Findley S.D., Mormile M.R., Sommer-Hurley A., Zhang X.C., Tipton P., Arnett K., Porter J.H., Kerley M., Stacey G. Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases. Appl Environ Microbiol 2011, 77:8106-8113.
58. Shi W., Syrenne R., Sun J.-Z., Yuan J.S. Molecular approaches to study the insect gut symbiotic microbiota at the 'omics' age. Insect Sci 2010, 17:199-219.
59. Burnum K.E., Callister S.J., Nicora C.D., Purvine S.O., Hugenholtz P., Warnecke F., Scheffrahn R.H., Smith R.D., Lipton M.S. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J 2011, 5:161-164.
60. Watanabe H., Noda H., Tokuda G., Lo N. A cellulase gene of termite origin. Nature 1998, 394:330-331.
61. Sun J.-Z., Scharf M.E. Exploring and integrating cellulolytic systems of insects to advance biofuel technology. Insect Sci 2010, 17:163-165.
62. Tartar A., Wheeler M.M., Zhou X., Coy M.R., Boucias D.G., Scharf M.E. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. Biotechnol Biofuel 2009, 2:25.
63. Rubin E.M. Genomics of cellulosic biofuels. Nature 2008, 454:841-845.
64. Eastwood D.C., Floudas D., Binder M., Majcherczyk A., Schneider P., Aerts A., Asiegbu F.O., Baker S.E., Barry K., Bendiksby M., et al. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 2011, 333:762-765.
65. Fernandez-Fueyo E., Ruiz-Duenas F.J., Ferreira P., Floudas D., Hibbett D.S., Canessa P., Larrondo L.F., James T.Y., Seelenfreund D., Lobos S., et al. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A 2012, 109:5458-5463.
66. Suzuki H., MacDonald J., Syed K., Salamov A., Hori C., Aerts A., Henrissat B., Wiebenga A., vanKuyk P., Barry K., et al. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics 2012, 13:444.
67. He S., Ivanova N., Kirton E., Allgaier M., Bergin C., Scheffrahn R.H., Kyrpides N.C., Warnecke F., Tringe S.G., Hugenholtz P. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS ONE 2013, 8:e61126.
68. Ishii N., Tomita M. Multi-omics data-driven systems biology of E. coli. Systems Biology and Biotechnology of Escherichia coli 2009, 41-57. Springer, Netherlands. S. Lee (Ed.).
69. Yuki M., Moriya S., Inoue T., Kudo T. Transcriptome analysis of the digestive organs of Hodotermopsis sjostedti, a lower termite that hosts mutualistic microorganisms in its hindgut. Zool Sci 2008, 25:401-406.
70. Hongoh Y. Toward the functional analysis of uncultivable, symbiotic microorganisms in the termite gut. Cell Mol Life Sci 2011, 68:1311-1325.