Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199

Biotechnology for Biofuels

Volumn 9, Issue 1, 2016, Pages

  López Mondéjar, Rubén ^a   Zühlke, Daniela ^b   Větrovský, Tomáš ^a   Becher, Dörte ^b   Riedel, Katharina ^b   Baldrian, Petr ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

CAZyme; Cellulose; Glycosyl hydrolase; Hemicellulose; Paenibacillus; Plant biomass

Indexed keywords

AGRICULTURAL WASTES; BINS; BIOMASS; CARBOHYDRATES; CRYSTALLINE MATERIALS; ENZYME ACTIVITY; ENZYMES; GENES; HYDROLASES; LIGNIN; PROTEINS; STRAW;

CAZYME; GLYCOSYL HYDROLASES; HEMICELLULOSE; PAENIBACILLUS; PLANT BIOMASS;

CELLULOSE;

BACTERIUM; BIODEGRADATION; BIOMASS; CELLULOSE; DECOMPOSITION; ENZYME ACTIVITY; GENOME; PROTEIN;

BIOMASS; CELLULOSE; HEMICELLULOSES; PLANTS;

BACTERIA (MICROORGANISMS); PAENIBACILLUS; TRITICUM AESTIVUM;

EID: 84969248474     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/s13068-016-0518-x     Document Type: Article

References (65)

1. Van Dyk JS, Pletschke BI. A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes-factors affecting enzymes, conversion and synergy. Biotechnol Adv. 2012;30:1458-80.
2. Himmel ME, Xu Q, Luo Y, Ding S, Lamed R, Bayer EA. Microbial enzyme systems for biomass conversion: emerging paradigms. Biofuels. 2010;1:323-41.
3. Zhou Y, Pope PB, Li S, Wen B, Tan F, Cheng S, Chen J, Yang J, Liu F, Lei X, et al. Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community. Sci Rep. 2014;4:5288.
4. Rakotoarivonina H, Hermant B, Monthe N, Rémond C. The hemicellulolytic enzyme arsenal of Thermobacillus xylanilyticus depends on the composition of biomass used for growth. Microb Cell Fact. 2012;11:159.
5. Song HY, Lim HK, Kim DR, Lee KI, Hwang IT. A new bi-modular endo-beta-1,4-xylanase KRICT PX-3 from whole genome sequence of Paenibacillus terrae HPL-003. Enzyme Microb Technol. 2014;54:1-7.
6. Lombard V. Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490-5.
7. Brumm PJ. Bacterial genomes: what they teach us about cellulose degradation. Biofuels. 2013;4:669-81.
8. Koeck DE, Pechtl A, Zverlov VV, Schwarz WH. Genomics of cellulolytic bacteria. Curr Opin Biotechnol. 2014;29:171-83.
9. Sukharnikov LO, Cantwell BJ, Podar M, Zhulin IB. Cellulases: ambiguous nonhomologous enzymes in a genomic perspective. Trends Biotechnol. 2011;29:473-9.
10. Dos Santos Castro L, Ramos Pedersoli W, Campos Antoniêto AC, Stecca Steindorff A, Silva-Rocha R, Martinez-Rossi NM, Rossi A, Brown NA, Goldman GH, Faça VM, et al. Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses. Biotechnol Biofuels. 2014;7:41.
11. Mori T, Kamei I, Hirai H, Kondo R. Identification of novel glycosyl hydrolases with cellulolytic activity against crystalline cellulose from metagenomic libraries constructed from bacterial enrichment cultures. SpringerPlus. 2014;3:365.
12. Maki M, Leung KT, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci. 2009;5:500-16.
13. Yang JK, Zhang JJ, Yu HY, Cheng JW, Miao LH. Community composition and cellulase activity of cellulolytic bacteria from forest soils planted with broad-leaved deciduous and evergreen trees. Appl Microbiol Biotechnol. 2014;98:1449-58.
14. Gastelum-Arellanez A, Paredes-Lopez O, Olalde-Portugal V. Extracellular endoglucanase activity from Paenibacillus polymyxa BEb-40: production, optimization and enzymatic characterization. World J Microbiol Biotechnol. 2014;30:2953-65.
15. Mihajlovski KR, Carević MB, Dević ML, Šiler-Marinković S, Rajilić-Stojanović MD, Dimitrijević-Branković S. Lignocellulosic waste material as substrate for Avicelase production by a new strain of Paenibacillus chitinolyticus CKS1. Inter Biodeter Biodegr. 2015;104:426-34.
16. Hwang IT, Lim HK, Song HY, Cho SJ, Chang JS, Park NJ. Cloning and characterization of a xylanase, KRICT PX1 from the strain Paenibacillus sp. HPL-001. Biotechnol Adv. 2010;28:594-601.
17. Park IH, Chang J, Lee YS, Fang SJ, Choi YL. Gene cloning of endoglucanase Cel5A from cellulose-degrading Paenibacillus xylanilyticus KJ-03 and purification and characterization of the recombinant enzyme. Protein J. 2012;31:238-45.
18. Pason P, Kosugi A, Waeonukul R, Tachaapaikoon C, Ratanakhanokchai K, Arai T, Murata Y, Nakajima J, Mori Y. Purification and characterization of a multienzyme complex produced by Paenibacillus curdlanolyticus B-6. Appl Microbiol Biotechnol. 2010;85:573-80.
19. van Dyk JS, Sakka M, Sakka K, Pletschke BI. Identification of endoglucanases, xylanases, pectinases and mannanases in the multi-enzyme complex of Bacillus licheniformis SVD1. Enzyme Microb Technol. 2010;47:112-8.
20. Baldrian P, López-Mondéjar R. Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol. 2014;98:1531-7.
21. Berlemont R, Martiny AC. Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol. 2013;79:1545-54.
22. Mba Medie F, Davies GJ, Drancourt M, Henrissat B. Genome analyses highlight the different biological roles of cellulases. Nat Rev Microbiol. 2012;10:227-34.
23. Wilson DB. Processive and nonprocessive cellulases for biofuel production - lessons from bacterial genomes and structural analysis. Appl Microbiol Biotechnol. 2012;93:497-502.
24. Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG. Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces. Sci Rep. 1030;2013:3.
25. Maqbool A, Horler RS, Muller A, Wilkinson AJ, Wilson KS, Thomas GH. The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity. Biochem Soc Trans. 2015;43:1011-7.
26. Harris PV, Xu F, Kreel NE, Kang C, Fukuyama S. New enzyme insights drive advances in commercial ethanol production. Curr Opin Chem Biol. 2014;19:162-70.
27. Chua P, Yoo H-S, Gan HM, Lee S-M. Draft genome sequences of two cellulolytic Paenibacillus sp. strains, MAEPY1 and MAEPY2, from Malaysian landfill leachate. Genome Announc. 2014;2:e00065-14.
28. Dhar H, Swarnkar MK, Gulati A, Singh AK, Kasana RC. Draft genome sequence of a cellulase-producing psychrotrophic Paenibacillus strain, IHB B 3415, isolated from the cold environment of the Western Himalayas, India. Genome Announc. 2015;3:e01581-14.
29. Yuki M, Oshima K, Suda W, Oshida Y, Kitamura K, Iida T, Hattori M, Ohkuma M. Draft genome sequence of Paenibacillus pini JCM 16418T, isolated from the rhizosphere of pine tree. Genome Announc. 2014;2:e00210-4.
30. Shin SH, Kim S, Kim JY, Song HY, Cho SJ, Kim DR, Lee KI, Lim HK, Park NJ, Hwang IT, Yang KS. Genome sequence of Paenibacillus terrae HPL-003, a xylanase-producing bacterium isolated from soil found in forest residue. J Bacteriol. 2012;194:1266.
31. Eastman AW, Heinrichs DE, Yuan Z. Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. BMC Genom. 2014;15:851.
32. Adams AS, Jordan MS, Adams SM, Suen G, Goodwin LA, Davenport KW, Currie CR, Raffa KF. Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. ISME J. 2011;5:1323-31.
33. Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL 2nd, Westpheling J, Hettich R, Giannone R, et al. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res. 2011;39:3240-54.
34. Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JB, Martiny AC. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Front Microbiol. 2014;5:639.
35. Wilson DB. Microbial diversity of cellulose hydrolysis. Curr Opin Microbiol. 2011;14:259-63.
36. Sanchez MM, Irwin DC, Pastor FI, Wilson DB, Diaz P. Synergistic activity of Paenibacillus sp. BP-23 cellobiohydrolase Cel48C in association with the contiguous endoglucanase Cel9B and with endo- or exo-acting glucanases from Thermobifida fusca. Biotechnol Bioeng. 2004;87:161-9.
37. Berger E, Zhang D, Zverlov VV, Schwarz WH. Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically. FEMS Microbiol Lett. 2007;268:194-201.
38. Vardakou M, Katapodis P, Topakas E, Kekos D, Macris BJ, Christakopoulos P. Synergy between enzymes involved in the degradation of insoluble wheat flour arabinoxylan. Innov Food Sci Emerg. 2004;5:107-12.
39. Ozdemir I, Blumer-Schuette SE, Kelly RM. S-layer homology domain proteins Csac-0678 and Csac-2722 are implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol. 2012;78:768-77.
40. Chow V, Kim YS, Rhee MS, Sawhney N. St John FJ, Nong G, Rice JD, Preston JF: A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2. Appl Environ Microbiol. 2016;82:1789-98.
41. Fukuda M, Watanabe S, Yoshida S, Itoh H, Itoh Y, Kamio Y, Kaneko J. Cell surface xylanases of the glycoside hydrolase family 10 are essential for xylan utilization by Paenibacillus sp. W-61 as generators of xylo-oligosaccharide inducers for the xylanase genes. J Bacteriol. 2010;192:2210-9.
42. Waeonukul R, Kyu KL, Sakka K, Ratanakhanokchai K. Effect of Carbon Sources on the Induction of Xylanolytic-Cellulolytic Multienzyme Complexes in Paenibacillus curdlanolyticus Strain B-6. Biosci Biotechnol Biochem. 2008;72:321-8.
43. Wegmann U, Louis P, Goesmann A, Henrissat B, Duncan SH, Flint HJ. Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans. Environ Microbiol. 2014;16:2879-90.
44. Nataf Y, Bahari L, Kahel-Raifer H, Borovok I, Lamed R, Bayer EA, Sonenshein AL, Shoham Y. Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors. Proc Natl Acad Sci USA. 2010;107:18646-51.
45. Zhang H, Hutcheson SW. Complex expression of the cellulolytic transcriptome of Saccharophagus degradans. Appl Environ Microbiol. 2011;77:5591-6.
46. Xu C, Huang R, Teng L, Wang D, Hemme CL, Borovok I, He Q, Lamed R, Bayer EA, Zhou J, Xu J. Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. Biotechnol Biofuels. 2013;6:73.
47. Yokoyama H, Yamashita T, Morioka R, Ohmori H. Extracellular secretion of noncatalytic plant cell wall-binding proteins by the cellulolytic thermophile Caldicellulosiruptor bescii. J Bacteriol. 2014;196:3784-92.
48. Šnajdr J, Cajthaml T, Valášková V, Merhautová V, Petranková M, Spetz P, Leppanen K, Baldrian P. Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition. FEMS Microbiol Ecol. 2011;75:291-303.
49. Šnajdr J, Valášková V. Merhautová Vr, Herinková J, Cajthaml T, Baldrian P: Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil. Soil Biol Biochem. 2008;40:2068-75.
50. López-Mondéjar R, Voříšková J, Větrovský T, Baldrian P. The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics. Soil Biol Biochem. 2015;87:43-50.
51. Valášková V, Šnajdr J, Bittner B, Cajthaml T, Merhautová V, Hofrichter M, Baldrian P. Production of lignocellulose-degrading enzymes and degradation of leaf litter by saprotrophic basidiomycetes isolated from a Quercus petraea forest. Soil Biol Biochem. 2007;39:2651-60.
52. Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acids techniques in bacterial systematics. Chichester: Wiley; 1991. p. 115-47.
53. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012;62:716-21.
54. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821-9.
55. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. BMC Genom. 2008;9:75.
56. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014;42:D206-14.
57. Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40:W445-51.
58. Grube M, Cernava T, Soh J, Fuchs S, Aschenbrenner I, Lassek C, Wegner U, Becher D, Riedel K, Sensen CW, Berg G. Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. ISME J. 2015;9:412-24.
59. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn M. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2006;5:2339-47.
60. Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003;34:374-8.
61. Schneider T, Schmid E, de Castro JV Jr, Cardinale M, Eberl L, Grube M, Berg G, Riedel K. Structure and function of the symbiosis partners of the lung lichen (Lobaria pulmonaria L. Hoffm.) analyzed by metaproteomics. Proteomics. 2011;11:2752-6.
62. Edgar RC. MUSCLE: multiple sequence alignment with high accurance and high throughput. Nucleic Acids Res. 2004;32:1792-7.
63. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307-21.
64. Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, et al. ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination. Nat Biotechnol. 2014;30:223-6.
65. Burton RA, Gidley MJ, Fincher GB. Heterogeneity in the chemistry, structure and function of plant cell walls. Nat Chem Biol. 2010;6:724-32.