Genomic and transcriptomic analysis of carbohydrate utilization by Paenibacillus sp. JDR-2: systems for bioprocessing plant polysaccharides

Sawhney, Neha; Crooks, Casey; Chow, Virginia; Preston, James F.; St John, Franz J.

doi:10.1186/s12864-016-2436-5

Genomic and transcriptomic analysis of carbohydrate utilization by Paenibacillus sp. JDR-2: systems for bioprocessing plant polysaccharides

Journal Article · Tue Feb 23 23:00:00 EST 2016 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-016-2436-5· OSTI ID:1618544

Sawhney, Neha; Crooks, Casey; Chow, Virginia; Preston, James F.; St John, Franz J.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618544

Alternate ID(s):: OSTI ID: 1626796

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 17; ISSN 1471-2164

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (50)

Catalytic Properties ofBacillus megaterium Amylase David, M. -H.; Günther, H.; Röper, H. Starch - Stärke, Vol. 39, Issue 12 https://doi.org/10.1002/star.19870391208	journal	January 1987
Chemistry of Cereal Grains Koehler, Peter; Wieser, Herbert Handbook on Sourdough Biotechnology https://doi.org/10.1007/978-1-4614-5425-0_2	book	October 2012
Substrate competition and specificity at the active site of amylopullulanase from Clostridium thermohydrosulfuricum Mathupala, Saroj; Saha, Badal C.; Zeikus, J. Gregory Biochemical and Biophysical Research Communications, Vol. 166, Issue 1 https://doi.org/10.1016/0006-291X(90)91920-N	journal	January 1990
Molecular characterization of a dimeric intracellular maltogenic amylase of Bacillus subtilis SUH4-2 Cho, Hee-Yeon; Kim, Young-Wan; Kim, Tae-Jip Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1478, Issue 2 https://doi.org/10.1016/S0167-4838(00)00037-6	journal	May 2000
Structural features and biological activity of an acidic polysaccharide complex from Mahonia aquifolium (Pursh) Nutt Kardoova, A. Carbohydrate Polymers, Vol. 57, Issue 2 https://doi.org/10.1016/j.carbpol.2004.04.016	journal	August 2004
Construction and characterization of recombinant Bacillus subtilis JY123 able to transport xylose efficiently Park, Yong-Cheol; Jun, Soo Young; Seo, Jin-Ho Journal of Biotechnology, Vol. 161, Issue 4 https://doi.org/10.1016/j.jbiotec.2012.07.192	journal	November 2012
Molecular aspects of cereal β-glucan functionality: Physical properties, technological applications and physiological effects Lazaridou, A.; Biliaderis, C. G. Journal of Cereal Science, Vol. 46, Issue 2 https://doi.org/10.1016/j.jcs.2007.05.003	journal	September 2007
Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex Smith, Steven P.; Bayer, Edward A. Current Opinion in Structural Biology, Vol. 23, Issue 5 https://doi.org/10.1016/j.sbi.2013.09.002	journal	October 2013
Microbial Strategies for the Depolymerization of Glucuronoxylan: Leads to Biotechnological Applications of Endoxylanases Preston, James F.; Hurlbert, Jason C.; Rice, John D. ACS Symposium Series https://doi.org/10.1021/bk-2003-0855.ch012	book	August 2003
Cellulosomes: plant-cell-wall-degrading enzyme complexes Doi, Roy H.; Kosugi, Akihiko Nature Reviews Microbiology, Vol. 2, Issue 7 https://doi.org/10.1038/nrmicro925	journal	July 2004
Carbohydrate-binding modules: fine-tuning polysaccharide recognition Boraston, Alisdair B.; Bolam, David N.; Gilbert, Harry J. Biochemical Journal, Vol. 382, Issue 3 https://doi.org/10.1042/BJ20040892	journal	September 2004
Cellulose utilization by Clostridium thermocellum: Bioenergetics and hydrolysis product assimilation Zhang, Y. -H. P.; Lynd, L. R. Proceedings of the National Academy of Sciences, Vol. 102, Issue 20 https://doi.org/10.1073/pnas.0408734102	journal	May 2005
Structure of Surface Layer Homology (SLH) Domains from Bacillus anthracis Surface Array Protein Kern, Justin; Wilton, Rosemarie; Zhang, Rongguang Journal of Biological Chemistry, Vol. 286, Issue 29 https://doi.org/10.1074/jbc.M111.248070	journal	May 2011
Crystal Structures of the Laminarinase Catalytic Domain from Thermotoga maritima MSB8 in Complex with Inhibitors : ESSENTIAL RESIDUES FOR β-1,3- and β-1,4-GLUCAN SELECTION Jeng, Wen-Yih; Wang, Nai-Chen; Lin, Cheng-Tse Journal of Biological Chemistry, Vol. 286, Issue 52 https://doi.org/10.1074/jbc.M111.271213	journal	November 2011
Multiple Regulatory Mechanisms Control the Expression of the Geobacillus stearothermophilus Gene for Extracellular Xylanase Shulami, Smadar; Shenker, Ofer; Langut, Yael Journal of Biological Chemistry, Vol. 289, Issue 37 https://doi.org/10.1074/jbc.M114.592873	journal	July 2014
Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima Chhabra, Swapnil R.; Shockley, Keith R.; Conners, Shannon B. Journal of Biological Chemistry, Vol. 278, Issue 9 https://doi.org/10.1074/jbc.M211748200	journal	December 2002
Nucleotide sequence of an amylase gene from Bacillus megaterium Metz, Raymond J.; Allen, Larry N.; Cao, Tin M. Nucleic Acids Research, Vol. 16, Issue 11 https://doi.org/10.1093/nar/16.11.5203	journal	January 1988
The Pfam protein families database Bateman, Alex; Coin, Lachlan; Durbin, Richard Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141 https://doi.org/10.1093/nar/gkh121	journal	January 2004
CDD: a conserved domain database for interactive domain family analysis Marchler-Bauer, A.; Anderson, J. B.; Derbyshire, M. K. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl951	journal	January 2007
NCBI BLAST: a better web interface Johnson, M.; Zaretskaya, I.; Raytselis, Y. Nucleic Acids Research, Vol. 36, Issue Web Server https://doi.org/10.1093/nar/gkn201	journal	May 2008
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
Genes encoding xylan and -glucan hydrolysing enzymes in Bacillus subtilis: characterization, mapping and construction of strains deficient in lichenase, cellulase and xylanase Wolf, M.; Geczi, A.; Simon, O. Microbiology, Vol. 141, Issue 2 https://doi.org/10.1099/13500872-141-2-281	journal	February 1995
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing Benjamini, Yoav; Hochberg, Yosef Journal of the Royal Statistical Society: Series B (Methodological), Vol. 57, Issue 1 https://doi.org/10.1111/j.2517-6161.1995.tb02031.x	journal	January 1995
GH51 Arabinofuranosidase and Its Role in the Methylglucuronoarabinoxylan Utilization System in Paenibacillus sp. Strain JDR-2 Sawhney, Neha; Preston, James F. Applied and Environmental Microbiology, Vol. 80, Issue 19 https://doi.org/10.1128/AEM.01684-14	journal	July 2014
Aldouronate Utilization in Paenibacillus sp. Strain JDR-2: Physiological and Enzymatic Evidence for Coupling of Extracellular Depolymerization and Intracellular Metabolism Nong, Guang; Rice, John D.; Chow, Virginia Applied and Environmental Microbiology, Vol. 75, Issue 13 https://doi.org/10.1128/AEM.02354-08	journal	April 2009
Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus sp. Strain JDR-2 Sawhney, Neha; Crooks, Casey; St. John, Franz Applied and Environmental Microbiology, Vol. 81, Issue 4 https://doi.org/10.1128/AEM.03523-14	journal	December 2014
A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2 Chow, Virginia; Kim, Young Sik; Rhee, Mun Su Applied and Environmental Microbiology, Vol. 82, Issue 6 https://doi.org/10.1128/AEM.03526-15	journal	January 2016
S-Layer Homology Domain Proteins Csac_0678 and Csac_2722 Are Implicated in Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Ozdemir, Inci; Blumer-Schuette, Sara E.; Kelly, Robert M. Applied and Environmental Microbiology, Vol. 78, Issue 3 https://doi.org/10.1128/AEM.07031-11	journal	December 2011
Paenibacillus sp. Strain JDR-2 and XynA1: a Novel System for Methylglucuronoxylan Utilization StJohn, F. J.; Rice, J. D.; Preston, J. F. Applied and Environmental Microbiology, Vol. 72, Issue 2 https://doi.org/10.1128/AEM.72.2.1496-1506.2006	journal	February 2006
Maltose and Maltodextrin Utilization by Bacillus subtilis Schönert, Stefan; Seitz, Sabine; Krafft, Holger Journal of Bacteriology, Vol. 188, Issue 11 https://doi.org/10.1128/JB.00213-06	journal	June 2006
The L-Arabinan Utilization System of Geobacillus stearothermophilus Shulami, S.; Raz-Pasteur, A.; Tabachnikov, O. Journal of Bacteriology, Vol. 193, Issue 11 https://doi.org/10.1128/JB.00222-11	journal	April 2011
The thuEFGKAB Operon of Rhizobia and Agrobacterium tumefaciens Codes for Transport of Trehalose, Maltitol, and Isomers of Sucrose and Their Assimilation through the Formation of Their 3-Keto Derivatives Ampomah, O. Y.; Avetisyan, A.; Hansen, E. Journal of Bacteriology, Vol. 195, Issue 17 https://doi.org/10.1128/JB.00478-13	journal	June 2013
Global View of the Clostridium thermocellum Cellulosome Revealed by Quantitative Proteomic Analysis Gold, N. D.; Martin, V. J. J. Journal of Bacteriology, Vol. 189, Issue 19 https://doi.org/10.1128/JB.00882-07	journal	July 2007
Structure, Function, and Regulation of the Aldouronate Utilization Gene Cluster from Paenibacillus sp. Strain JDR-2 Chow, Virginia; Nong, Guang; Preston, James F. Journal of Bacteriology, Vol. 189, Issue 24 https://doi.org/10.1128/JB.01141-07	journal	October 2007
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 Fukuda, Mutsumi; Watanabe, Seiji; Yoshida, Shigeki Journal of Bacteriology, Vol. 192, Issue 8 https://doi.org/10.1128/JB.01406-09	journal	February 2010
Are the Surface Layer Homology Domains Essential for Cell Surface Display and Glycosylation of the S-Layer Protein from Paenibacillus alvei CCM 2051T? Janesch, B.; Messner, P.; Schaffer, C. Journal of Bacteriology, Vol. 195, Issue 3 https://doi.org/10.1128/JB.01487-12	journal	November 2012
Regulation of Pectate Lyase Synthesis in Pseudomonas fluorescens and Erwinia carotovora Zucker, Milton; Hankin, Lester Journal of Bacteriology, Vol. 104, Issue 1 https://doi.org/10.1128/JB.104.1.13-18.1970	journal	January 1970
Cloning, sequencing, and expression of the gene encoding a large S-layer-associated endoxylanase from Thermoanaerobacterium sp. strain JW/SL-YS 485 in Escherichia coli. Liu, S. Y.; Gherardini, F. C.; Matuschek, M. Journal of bacteriology, Vol. 178, Issue 6 https://doi.org/10.1128/JB.178.6.1539-1547.1996	journal	January 1996
Maltose Metabolism in the Hyperthermophilic Archaeon Thermococcus litoralis: Purification and Characterization of Key Enzymes Xavier, Karina B.; Peist, Ralf; Kossmann, Marina Journal of Bacteriology, Vol. 181, Issue 11 https://doi.org/10.1128/JB.181.11.3358-3367.1999	journal	June 1999
The Glucuronic Acid Utilization Gene Cluster from Bacillus stearothermophilus T-6 Shulami, Smadar; Gat, Orit; Sonenshein, Abraham L. Journal of Bacteriology, Vol. 181, Issue 12 https://doi.org/10.1128/JB.181.12.3695-3704.1999	journal	June 1999
Functional Characterization of a Novel Xylanase from a Corn Strain of Erwinia chrysanthemi Hurlbert, J. C.; Preston, J. F. Journal of Bacteriology, Vol. 183, Issue 6 https://doi.org/10.1128/JB.183.6.2093-2100.2001	journal	March 2001
Microbial Cellulose Utilization: Fundamentals and Biotechnology Lynd, L. R.; Weimer, P. J.; van Zyl, W. H. Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577 https://doi.org/10.1128/MMBR.66.3.506-577.2002	journal	September 2002
Cell-Surface-Anchoring Role of N-Terminal Surface Layer Homology Domains of Clostridium cellulovorans EngE Kosugi, Akihiko; Murashima, Koichiro; Tamaru, Yutaka Journal of Bacteriology, Vol. 184, Issue 4 https://doi.org/10.1128/jb.184.4.884-888.2002	journal	February 2002
CONSTITUTION OF A 4- O -METHYLGLUCURONOXYLAN FROM THE WOOD OF TREMBLING ASPEN (POPULUS TREMULOIDES MICHX.) Jones, J. K. N.; Purves, C. B.; Timell, T. E. Canadian Journal of Chemistry, Vol. 39, Issue 5 https://doi.org/10.1139/v61-131	journal	May 1961
Recombinant production and biochemical characterization of a hyperthermostable α-glucan/maltodextrin phosphorylase from Pyrococcus furiosus Mizanur, Rahman M.; Griffin, Amanda K. K.; Pohl, Nicola L. Archaea, Vol. 2, Issue 3 https://doi.org/10.1155/2008/549759	journal	January 2008
PePPER: a webserver for prediction of prokaryote promoter elements and regulons de Jong, Anne; Pietersma, Hilco; Cordes, Martijn BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-299	journal	January 2012
Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellumto utilize hemicellulose and unpretreated plant material Izquierdo, Javier A.; Pattathil, Sivakumar; Guseva, Anna Biotechnology for Biofuels, Vol. 7, Issue 1 https://doi.org/10.1186/s13068-014-0136-4	journal	November 2014
Cloning, Sequencing, and Expression of the Gene Encoding the Clostridium stercorarium Xylanase C in Escherichia coli Ali, Mursheda K.; Fukumura, Masayuki; Sakano, Katsushi Bioscience, Biotechnology, and Biochemistry, Vol. 63, Issue 9 https://doi.org/10.1271/bbb.63.1596	journal	January 1999
Cloning, Sequencing, and Expression of the Gene Encoding a Cell-bound Multi-domain Xylanase from Clostridium josui , and Characterization of the Translated Product Feng, Jia-Xun; Karita, Shuichi; Fujino, Emi Bioscience, Biotechnology, and Biochemistry, Vol. 64, Issue 12 https://doi.org/10.1271/bbb.64.2614	journal	January 2000
Complete genome sequence of Paenibacillus sp. strain JDR-2 Chow, Virginia; Nong, Guang; St. John, Franz J. Standards in Genomic Sciences, Vol. 6, Issue 1 https://doi.org/10.4056/sigs.2374349	journal	March 2012

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