Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum

Journal of Industrial Microbiology and Biotechnology

Volumn 38, Issue 7, 2011, Pages 825-832

  Bahari, Liat ^a   Gilad, Yuval ^a   Borovok, Ilya ^b   Kahel Raifer, Hamutal ^b   Dassa, Bareket ^a   Nataf, Yakir ^c   Shoham, Yuval ^c   Lamed, Raphael ^b   Bayer, Edward A ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

^c TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

Anti sigma factor; Carbohydrate binding module (CBM); Family 24 sigma factor; Glycoside hydrolase (GH); RsgI

Indexed keywords

CELLULOSE; GLUTAMIC ACID; GLUTAMINE; GLYCOSIDASE; RSGI6-GH10; RSI24C-GH5; UNCLASSIFIED DRUG; XYLAN;

ARTICLE; BIOINFORMATICS; CATALYSIS; CLOSTRIDIUM THERMOCELLUM; ENZYME ACTIVITY; ENZYMIC BIOSENSOR; HYDROLYSIS; NUCLEOTIDE SEQUENCE; PROTEIN CARBOHYDRATE INTERACTION; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CARBOHYDRATE METABOLISM; CELLULOSE; CELLULOSOMES; CLOSTRIDIUM THERMOCELLUM; CONSERVED SEQUENCE; GLYCOSIDE HYDROLASES; HYDROLYSIS; SIGMA FACTOR; XYLANS;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM THERMOCELLUM;

EID: 80051799611     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-010-0848-9     Document Type: Article

References (33)

1. R Lamed E Setter EA Bayer 1983 Characterization of a cellulose-binding, cellulase-containing complex in Clostridium thermocellum J Bacteriol 156 828 836 6195146 1:CAS:528:DyaL2cXjt1Cm (Pubitemid 14202591)
2. R Lamed E Setter R Kenig EA Bayer 1983 The cellulosome-a discrete cell surface organelle of Clostridium thermocellum which exhibits separate antigenic, cellulose-binding and various cellulolytic activities Biotechnol Bioeng Symp 13 163 181 1:CAS:528:DyaL2MXlvV2ktg%3D%3D (Pubitemid 14102885)
3. EA Bayer J-P Belaich Y Shoham R Lamed 2004 The cellulosomes: multi-enzyme machines for degradation of plant cell wall polysaccharides Annu Rev Microbiol 58 521 554 15487947 10.1146/annurev.micro.57.030502.091022 1:CAS:528: DC%2BD2cXhtVejsr3M (Pubitemid 39551996)
4. TW Dror A Rolider EA Bayer R Lamed Y Shoham 2005 Regulation of major cellulosomal endoglucanases of Clostridium thermocellum differs from that of a prominent cellulosomal xylanase J Bacteriol 187 2261 2266 15774868 10.1128/JB.187.7.2261-2266.2005 1:CAS:528:DC%2BD2MXjt1Kru7k%3D (Pubitemid 40389124)
5. ND Gold VJ Martin 2007 Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis J Bacteriol 189 6787 6795 17644599 10.1128/JB.00882-07 1:CAS:528:DC%2BD2sXhtFKmsL%2FF (Pubitemid 47525422)
6. B Raman C Pan GB Hurst M Rodriguez CK McKeown PK Lankford NF Samatova JR Mielenz 2009 Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis PLoS ONE 4 e5271 19384422 10.1371/journal.pone.0005271
7. H Kahel-Raifer S Jindou L Bahari Y Nataf Y Shoham EA Bayer I Borovok R Lamed 2010 The unique set of putative membrane-associated anti-σ factors in Clostridium thermocellum suggests a novel extracellular carbohydrate-sensing mechanism involved in gene regulation FEMS Microbiol Lett 308 84 93 20487018 10.1111/j.1574-6968.2010.01997.x 1:CAS:528:DC%2BC3cXotFGqtrY%3D
8. BL Cantarel PM Coutinho C Rancurel T Bernard V Lombard B Henrissat 2009 The Carbohydrate-Active Enzymes database (CAZy): an expert resource for glycogenomics Nucl Acids Res 37 D233 D238 18838391 10.1093/nar/gkn663 1:CAS:528:DC%2BD1cXhsFejtL7K
9. R Lamed R Kenig E Setter EA Bayer 1985 Major characteristics of the cellulolytic system of Clostridium thermocellum coincide with those of the purified cellulosome Enzyme Microb Technol 7 37 41 10.1016/0141-0229(85)90008-0 1:CAS:528:DyaL2MXptFyrsw%3D%3D (Pubitemid 15028119)
10. Demishtein A, Karpol A, Barak Y, Lamed R, Bayer EA (2010) Characterization of a dockerin-based affinity tag: application for purification of a broad variety of target proteins. J Mol Recogit (in press)
11. GL Miller 1959 Use of dinitrosalicylic acid reagent for determination of reducing sugar Anal Biochem 31 426 428 1:CAS:528:DyaG1MXmtFKiuw%3D%3D
12. H Lineweaver D Burk 1934 The determination of enzyme dissociation constants J Am Chem Soc 56 658 666 10.1021/ja01318a036 1:CAS:528: DyaA2cXisF2ltg%3D%3D
13. S Moraïs Y Barak J Caspi Y Hadar R Lamed Y Shoham DB Wilson EA Bayer 2010 Contribution of a xylan-binding module to the degradation of a complex cellulosic substrate by designer cellulosomes Appl Environ Microbiol 76 3787 3796 20400556 10.1128/AEM.00266-10
14. RD Finn J Tate J Mistry PC Coggill SJ Sammut H-R Hotz G Ceric K Forslund SR Eddy ELL Sonnhammer A Bateman 2008 The Pfam protein families database Nucl Acids Res 36 D281 D288 18039703 10.1093/nar/gkm960 1:CAS:528: DC%2BD1cXhtVWiu7c%3D (Pubitemid 351149737)
15. S Hunter R Apweiler TK Attwood A Bairoch A Bateman D Binns P Bork U Das L Daugherty L Duquenne RD Finn J Gough D Haft N Hulo D Kahn E Kelly A Laugraud I Letunic D Lonsdale R Lopez M Madera J Maslen C McAnulla J McDowall J Mistry A Mitchell N Mulder D Natale C Orengo AF Quinn JD Selengut CJA Sigrist M Thimma PD Thomas F Valentin D Wilson CH Wu C Yeats 2009 InterPro: the integrative protein signature database Nucl Acids Res 37 D211 D215 18940856 10.1093/nar/gkn785 1:CAS:528:DC%2BD1cXhsFejtL%2FF
16. DG Higgins JD Thompson TJ Gibson 1996 Using CLUSTAL for multiple sequence alignments Methods Enzymol 266 383 402 8743695 10.1016/S0076-6879(96)66024-8 1:CAS:528:DyaK28Xltl2nt7w%3D (Pubitemid 26165878)
17. Coutinho PM, Henrissat B (1999) Carbohydrate-active enzymes: an integrated database approach. In: Gilbert HJ, Davies GJ, Henrissat B, Svensson B (eds) Recent advances in carbohydrate bioengineering. R Soc Chem, Cambridge, pp 3-12
18. B Henrissat A Bairoch 1993 New families in the classification of glycosyl hydrolases based on amino acid sequence similarities Biochem J 293 781 788 8352747 1:CAS:528:DyaK3sXmt1Sgu70%3D (Pubitemid 23244564)
19. G Davies B Henrissat 1995 Structures and mechanisms of glycosyl hydrolases Structure 3 853 859 8535779 10.1016/S0969-2126(01)00220-9 1:CAS:528:DyaK2MXotlWktrY%3D
20. B Henrissat I Callebaut S Fabrega P Lehn J-P Mornon G Davies 1995 Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases Proc Natl Acad Sci USA 92 7090 7094 7624375 10.1073/pnas.92.15.7090 1:CAS:528:DyaK2MXntVSkur4%3D
21. B Henrissat G Davies 1997 Structural and sequence-based classification of glycoside hydrolases Curr Opin Struct Biol 7 637 644 9345621 10.1016/S0959-440X(97)80072-3 1:CAS:528:DyaK2sXmvVGgtb8%3D (Pubitemid 27472582)
22. AM MacLeod T Lindhorst SG Withers RA Warren 1994 The acid/base catalyst in the exoglucanase/xylanase from Cellulomonas fimi is glutamic acid 127: evidence from detailed kinetic studies of mutants Biochemistry 33 6371 6376 7910761 10.1021/bi00186a042 1:CAS:528:DyaK2cXksFejsL4%3D (Pubitemid 24190794)
23. D Tull SG Withers NR Gilkes DG Kilburn RA Warren R Aebersold 1991 Glutamic acid 274 is the nucleophile in the active site of a "retaining" exoglucanase from Cellulomonas fimi J Biol Chem 266 15621 15625 1678739 1:CAS:528:DyaK3MXmt1Ojs7c%3D (Pubitemid 21907700)
24. T Collins C Gerday G Feller 2005 Xylanases, xylanase families and extremophilic xylanases FEMS Microbiol Rev 29 3 23 15652973 10.1016/j.femsre. 2004.06.005 1:CAS:528:DC%2BD2MXkvFeiug%3D%3D (Pubitemid 40103579)
25. MT Cottrell L Yu DL Kirchman 2005 Sequence and expression analyses of Cytophaga-like hydrolases in a western Arctic metagenomic library and the Sargasso Sea Appl Environ Microbiol 71 8506 8513 16332841 10.1128/AEM.71.12. 8506-8513.2005 1:CAS:528:DC%2BD2MXhtlehtbrP (Pubitemid 41803982)
26. V Ducros M Czjzek A Belaich C Gaudin H-P Fierobe J-P Belaich GJ Davies R Haser 1995 Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5 Structure 3 939 949 8535787 10.1016/S0969-2126(01)00228-3 1:CAS:528:DyaK2MXotlWkt7g%3D
27. AB Boraston DN Bolam HJ Gilbert GJ Davies 2004 Carbohydrate-binding modules: fine-tuning polysaccharide recognition Biochem J 382 769 781 15214846 10.1042/BJ20040892 1:CAS:528:DC%2BD2cXntlOrsL8%3D (Pubitemid 39312891)
28. D Guillén S Sánchez R Rodríguez-Sanoja 2010 Carbohydrate-binding domains: multiplicity of biological roles Appl Microbiol Biotechnol 85 1241 1249 19908036 10.1007/s00253-009-2331-y
29. E Bonnin S Daviet JF Sorensen O Sibbesen A Goldson N Juge L Saulnier 2006 Behaviour of family 10 and 11 xylanases towards arabinoxylans with varying structure J Sci Food and Agr 86 1618 1622 10.1002/jsfa.2501 1:CAS:528: DC%2BD28XoslaitL8%3D
30. J Beaugrand G Chambat VW Wong F Goubet C Rémond G Paës S Benamrouche P Debeire M O'Donohue B Chabbert 2004 Impact and efficiency of GH10 and GH11 thermostable endoxylanases on wheat bran and alkali-extractable arabinoxylans Carbohydr Res 339 2529 2540 15476714 10.1016/j.carres.2004.08.012 1:CAS:528:DC%2BD2cXotlSrt74%3D (Pubitemid 39346069)
31. FM Dias A Goyal HJ Gilbert AMP Jose LM Ferreira CM Fontes 2004 The N-terminal family 22 carbohydrate-binding module of xylanase 10B of Clostridium themocellum is not a thermostabilizing domain FEMS Microbiol Lett 238 71 78 15336405 1:CAS:528:DC%2BD2cXntFWrtbY%3D (Pubitemid 39164533)
32. AC Fernandes CM Fontes HJ Gilbert GP Hazlewood TH Fernandes LMA Ferreira 1999 Homologous xylanases from Clostridium thermocellum: evidence for bi-functional activity, synergism between xylanase catalytic modules and the presence of xylan-binding domains in enzyme complexes Biochem J 342 105 110 10432306 10.1042/0264-6021:3420105 1:CAS:528:DyaK1MXmtVaktbc%3D (Pubitemid 29410855)
33. A Khasin I Alchanati Y Shoham 1993 Purification and characterization of a thermostable xylanase from Bacillus stearothermophilus T-6 Appl Environ Microbiol 59 1725 1730 8328796 1:CAS:528:DyaK3sXkvV2lurk%3D (Pubitemid 23171540)