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Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum.

Grinberg IR, Yaniv O, de Ora LO, Muñoz-Gutiérrez I, Hershko A, Livnah O, Bayer EA, Borovok I, Frolow F, Lamed R, Voronov-Goldman M.

Proteins. 2019 Jun 4. doi: 10.1002/prot.25753. [Epub ahead of print]


Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex.

Wei Z, Chen C, Liu YJ, Dong S, Li J, Qi K, Liu S, Ding X, Ortiz de Ora L, Muñoz-Gutiérrez I, Li Y, Yao H, Lamed R, Bayer EA, Cui Q, Feng Y.

Nucleic Acids Res. 2019 Jun 20;47(11):5988-5997. doi: 10.1093/nar/gkz355.


RGD-modified dihydrolipoamide dehydrogenase as a molecular bridge for enhancing the adhesion of bone forming cells to titanium dioxide implant surfaces.

Dayan A, Lamed R, Benayahu D, Fleminger G.

J Biomed Mater Res A. 2019 Mar;107(3):545-551. doi: 10.1002/jbm.a.36570. Epub 2018 Nov 25.


Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia.

Ortiz de Ora L, Lamed R, Liu YJ, Xu J, Cui Q, Feng Y, Shoham Y, Bayer EA, Muñoz-Gutiérrez I.

Sci Rep. 2018 Jul 23;8(1):11036. doi: 10.1038/s41598-018-29245-5.


Assembly of Synthetic Functional Cellulosomal Structures onto the Cell Surface of Lactobacillus plantarum, a Potent Member of the Gut Microbiome.

Stern J, Moraïs S, Ben-David Y, Salama R, Shamshoum M, Lamed R, Shoham Y, Bayer EA, Mizrahi I.

Appl Environ Microbiol. 2018 Apr 2;84(8). pii: e00282-18. doi: 10.1128/AEM.00282-18. Print 2018 Apr 15.


Pan-Cellulosomics of Mesophilic Clostridia: Variations on a Theme.

Dassa B, Borovok I, Lombard V, Henrissat B, Lamed R, Bayer EA, Moraïs S.

Microorganisms. 2017 Nov 18;5(4). pii: E74. doi: 10.3390/microorganisms5040074.


How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium (Ruminiclostridium) thermocellum DSM 1313?

Yoav S, Barak Y, Shamshoum M, Borovok I, Lamed R, Dassa B, Hadar Y, Morag E, Bayer EA.

Biotechnol Biofuels. 2017 Sep 18;10:222. doi: 10.1186/s13068-017-0909-7. eCollection 2017.


Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system.

Zhivin O, Dassa B, Moraïs S, Utturkar SM, Brown SD, Henrissat B, Lamed R, Bayer EA.

Biotechnol Biofuels. 2017 Sep 7;10:211. doi: 10.1186/s13068-017-0898-6. eCollection 2017.


Modular Organization of the Thermobifida fusca Exoglucanase Cel6B Impacts Cellulose Hydrolysis and Designer Cellulosome Efficiency.

Setter-Lamed E, Moraïs S, Stern J, Lamed R, Bayer EA.

Biotechnol J. 2017 Oct;12(10). doi: 10.1002/biot.201700205. Epub 2017 Sep 28.


Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions.

Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CM, Bayer EA.

Sci Rep. 2017 Feb 10;7:42355. doi: 10.1038/srep42355.


Revisiting the Regulation of the Primary Scaffoldin Gene in Clostridium thermocellum.

Ortiz de Ora L, Muñoz-Gutiérrez I, Bayer EA, Shoham Y, Lamed R, Borovok I.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03088-16. doi: 10.1128/AEM.03088-16. Print 2017 Apr 15.


Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Utturkar SM, Bayer EA, Borovok I, Lamed R, Hurt RA, Land ML, Klingeman DM, Elias D, Zhou J, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Brown SD.

Genome Announc. 2016 Sep 29;4(5). pii: e01043-16. doi: 10.1128/genomeA.01043-16.


Adaptor Scaffoldins: An Original Strategy for Extended Designer Cellulosomes, Inspired from Nature.

Stern J, Moraïs S, Lamed R, Bayer EA.

MBio. 2016 Apr 5;7(2):e00083. doi: 10.1128/mBio.00083-16.


Decoding Biomass-Sensing Regulons of Clostridium thermocellum Alternative Sigma-I Factors in a Heterologous Bacillus subtilis Host System.

Muñoz-Gutiérrez I, Ortiz de Ora L, Rozman Grinberg I, Garty Y, Bayer EA, Shoham Y, Lamed R, Borovok I.

PLoS One. 2016 Jan 5;11(1):e0146316. doi: 10.1371/journal.pone.0146316. eCollection 2016.


Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603.

Dassa B, Utturkar S, Hurt RA, Klingeman DM, Keller M, Xu J, Reddy YH, Borovok I, Rozman Grinberg I, Lamed R, Zhivin O, Bayer EA, Brown SD.

Genome Announc. 2015 Sep 24;3(5). pii: e01022-15. doi: 10.1128/genomeA.01022-15.


Reassembly and co-crystallization of a family 9 processive endoglucanase from its component parts: structural and functional significance of the intermodular linker.

Petkun S, Rozman Grinberg I, Lamed R, Jindou S, Burstein T, Yaniv O, Shoham Y, Shimon LJ, Bayer EA, Frolow F.

PeerJ. 2015 Sep 15;3:e1126. doi: 10.7717/peerj.1126. eCollection 2015.


Three cellulosomal xylanase genes in Clostridium thermocellum are regulated by both vegetative SigA (σ(A)) and alternative SigI6 (σ(I6)) factors.

Sand A, Holwerda EK, Ruppertsberger NM, Maloney M, Olson DG, Nataf Y, Borovok I, Sonenshein AL, Bayer EA, Lamed R, Lynd LR, Shoham Y.

FEBS Lett. 2015 Oct 7;589(20 Pt B):3133-40. doi: 10.1016/j.febslet.2015.08.026. Epub 2015 Aug 29.


Significance of relative position of cellulases in designer cellulosomes for optimized cellulolysis.

Stern J, Kahn A, Vazana Y, Shamshoum M, Moraïs S, Lamed R, Bayer EA.

PLoS One. 2015 May 29;10(5):e0127326. doi: 10.1371/journal.pone.0127326. eCollection 2015.


Clostridium clariflavum: Key Cellulosome Players Are Revealed by Proteomic Analysis.

Artzi L, Morag E, Barak Y, Lamed R, Bayer EA.

MBio. 2015 May 19;6(3):e00411-15. doi: 10.1128/mBio.00411-15.


Standalone cohesin as a molecular shuttle in cellulosome assembly.

Voronov-Goldman M, Yaniv O, Gul O, Yoffe H, Salama-Alber O, Slutzki M, Levy-Assaraf M, Jindou S, Shimon LJ, Borovok I, Bayer EA, Lamed R, Frolow F.

FEBS Lett. 2015 Jun 22;589(14):1569-76. doi: 10.1016/j.febslet.2015.04.013. Epub 2015 Apr 17.


Ruminococcal cellulosome systems from rumen to human.

Ben David Y, Dassa B, Borovok I, Lamed R, Koropatkin NM, Martens EC, White BA, Bernalier-Donadille A, Duncan SH, Flint HJ, Bayer EA, Moraïs S.

Environ Microbiol. 2015 Sep;17(9):3407-26. doi: 10.1111/1462-2920.12868. Epub 2015 May 7.


Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface.

Slutzki M, Reshef D, Barak Y, Haimovitz R, Rotem-Bamberger S, Lamed R, Bayer EA, Schueler-Furman O.

J Biol Chem. 2015 May 29;290(22):13654-66. doi: 10.1074/jbc.M115.651208. Epub 2015 Apr 1.


Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome.

Rozman Grinberg I, Yin G, Borovok I, Berg Miller ME, Yeoman CJ, Dassa B, Yu Z, Mizrahi I, Flint HJ, Bayer EA, White BA, Lamed R.

FEMS Microbiol Lett. 2015 Jan;362(3):1-10. doi: 10.1093/femsle/fnu047. Epub 2014 Dec 22.


Insights into a type III cohesin-dockerin recognition interface from the cellulose-degrading bacterium Ruminococcus flavefaciens.

Weinstein JY, Slutzki M, Karpol A, Barak Y, Gul O, Lamed R, Bayer EA, Fried DB.

J Mol Recognit. 2015 Mar;28(3):148-54. doi: 10.1002/jmr.2380. Epub 2015 Jan 30.


Elaborate cellulosome architecture of Acetivibrio cellulolyticus revealed by selective screening of cohesin-dockerin interactions.

Hamberg Y, Ruimy-Israeli V, Dassa B, Barak Y, Lamed R, Cameron K, Fontes CM, Bayer EA, Fried DB.

PeerJ. 2014 Oct 30;2:e636. doi: 10.7717/peerj.636. eCollection 2014.


Revisiting the NMR solution structure of the Cel48S type-I dockerin module from Clostridium thermocellum reveals a cohesin-primed conformation.

Chen C, Cui Z, Xiao Y, Cui Q, Smith SP, Lamed R, Bayer EA, Feng Y.

J Struct Biol. 2014 Nov;188(2):188-93. doi: 10.1016/j.jsb.2014.09.006. Epub 2014 Sep 28.


Biomass utilization by gut microbiomes.

White BA, Lamed R, Bayer EA, Flint HJ.

Annu Rev Microbiol. 2014;68:279-96. doi: 10.1146/annurev-micro-092412-155618. Epub 2014 Jun 16. Review.


Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.

Dassa B, Borovok I, Ruimy-Israeli V, Lamed R, Flint HJ, Duncan SH, Henrissat B, Coutinho P, Morrison M, Mosoni P, Yeoman CJ, White BA, Bayer EA.

PLoS One. 2014 Jul 3;9(7):e99221. doi: 10.1371/journal.pone.0099221. eCollection 2014.


Structural characterization of a novel autonomous cohesin from Ruminococcus flavefaciens.

Voronov-Goldman M, Levy-Assaraf M, Yaniv O, Wisserman G, Jindou S, Borovok I, Bayer EA, Lamed R, Shimon LJ, Frolow F.

Acta Crystallogr F Struct Biol Commun. 2014 Apr;70(Pt 4):450-6. doi: 10.1107/S2053230X14004051. Epub 2014 Mar 25.


Insights into enhanced thermostability of a cellulosomal enzyme.

Stern J, Anbar M, Moraïs S, Lamed R, Bayer EA.

Carbohydr Res. 2014 May 7;389:78-84. doi: 10.1016/j.carres.2014.01.014. Epub 2014 Jan 27.


Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-σI factors.

Yaniv O, Fichman G, Borovok I, Shoham Y, Bayer EA, Lamed R, Shimon LJ, Frolow F.

Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):522-34. doi: 10.1107/S139900471302926X. Epub 2014 Jan 31.


Cellulosomics of the cellulolytic thermophile Clostridium clariflavum.

Artzi L, Dassa B, Borovok I, Shamshoum M, Lamed R, Bayer EA.

Biotechnol Biofuels. 2014 Jul 1;7:100. doi: 10.1186/1754-6834-7-100. eCollection 2014.


A combined cell-consortium approach for lignocellulose degradation by specialized Lactobacillus plantarum cells.

Moraïs S, Shterzer N, Lamed R, Bayer EA, Mizrahi I.

Biotechnol Biofuels. 2014 Jul 24;7:112. doi: 10.1186/1754-6834-7-112. eCollection 2014.


A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates.

Vazana Y, Barak Y, Unger T, Peleg Y, Shamshoum M, Ben-Yehezkel T, Mazor Y, Shapiro E, Lamed R, Bayer EA.

Biotechnol Biofuels. 2013 Dec 16;6(1):182. doi: 10.1186/1754-6834-6-182.


Intramolecular clasp of the cellulosomal Ruminococcus flavefaciens ScaA dockerin module confers structural stability.

Slutzki M, Jobby MK, Chitayat S, Karpol A, Dassa B, Barak Y, Lamed R, Smith SP, Bayer EA.

FEBS Open Bio. 2013 Sep 25;3:398-405. doi: 10.1016/j.fob.2013.09.006. eCollection 2013.


Draft Genome Sequence of the Cellulolytic Bacterium Clostridium papyrosolvens C7 (ATCC 700395).

Zepeda V, Dassa B, Borovok I, Lamed R, Bayer EA, Cate JH.

Genome Announc. 2013 Sep 12;1(5). pii: e00698-13. doi: 10.1128/genomeA.00698-13.


Structure of a family 3a carbohydrate-binding module from the cellulosomal scaffoldin CipA of Clostridium thermocellum with flanking linkers: implications for cellulosome structure.

Yaniv O, Morag E, Borovok I, Bayer EA, Lamed R, Frolow F, Shimon LJ.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jul;69(Pt 7):733-7. doi: 10.1107/S174430911301614X. Epub 2013 Jun 27.


Establishment of a simple Lactobacillus plantarum cell consortium for cellulase-xylanase synergistic interactions.

Moraïs S, Shterzer N, Grinberg IR, Mathiesen G, Eijsink VG, Axelsson L, Lamed R, Bayer EA, Mizrahi I.

Appl Environ Microbiol. 2013 Sep;79(17):5242-9. doi: 10.1128/AEM.01211-13. Epub 2013 Jun 28.


Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007.

Vodovnik M, Duncan SH, Reid MD, Cantlay L, Turner K, Parkhill J, Lamed R, Yeoman CJ, Miller ME, White BA, Bayer EA, Marinšek-Logar R, Flint HJ.

PLoS One. 2013 Jun 4;8(6):e65333. doi: 10.1371/journal.pone.0065333. Print 2013.


Structure and regulation of the cellulose degradome in Clostridium cellulolyticum.

Xu C, Huang R, Teng L, Wang D, Hemme CL, Borovok I, He Q, Lamed R, Bayer EA, Zhou J, Xu J.

Biotechnol Biofuels. 2013 May 8;6(1):73. doi: 10.1186/1754-6834-6-73.


Atypical cohesin-dockerin complex responsible for cell surface attachment of cellulosomal components: binding fidelity, promiscuity, and structural buttresses.

Salama-Alber O, Jobby MK, Chitayat S, Smith SP, White BA, Shimon LJ, Lamed R, Frolow F, Bayer EA.

J Biol Chem. 2013 Jun 7;288(23):16827-38. doi: 10.1074/jbc.M113.466672. Epub 2013 Apr 11.


Crystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases.

Levy-Assaraf M, Voronov-Goldman M, Rozman Grinberg I, Weiserman G, Shimon LJ, Jindou S, Borovok I, White BA, Bayer EA, Lamed R, Frolow F.

PLoS One. 2013;8(2):e56138. doi: 10.1371/journal.pone.0056138. Epub 2013 Feb 14.


Deconstruction of lignocellulose into soluble sugars by native and designer cellulosomes.

Moraïs S, Morag E, Barak Y, Goldman D, Hadar Y, Lamed R, Shoham Y, Wilson DB, Bayer EA.

MBio. 2012 Dec 11;3(6). pii: e00508-12. doi: 10.1128/mBio.00508-12.


Indirect ELISA-based approach for comparative measurement of high-affinity cohesin-dockerin interactions.

Slutzki M, Barak Y, Reshef D, Schueler-Furman O, Lamed R, Bayer EA.

J Mol Recognit. 2012 Nov;25(11):616-22. doi: 10.1002/jmr.2178.


Paradigmatic status of an endo- and exoglucanase and its effect on crystalline cellulose degradation.

Moraïs S, Barak Y, Lamed R, Wilson DB, Xu Q, Himmel ME, Bayer EA.

Biotechnol Biofuels. 2012 Oct 24;5(1):78. doi: 10.1186/1754-6834-5-78.


Crystallization and preliminary X-ray characterization of a type III cohesin-dockerin complex from the cellulosome system of Ruminococcus flavefaciens.

Salama-Alber O, Gat Y, Lamed R, Shimon LJ, Bayer EA, Frolow F.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Sep 1;68(Pt 9):1116-9. doi: 10.1107/S1744309112033088. Epub 2012 Aug 31.


Affinity electrophoresis as a method for determining substrate-binding specificity of carbohydrate-active enzymes for soluble polysaccharides.

Moraïs S, Lamed R, Bayer EA.

Methods Mol Biol. 2012;908:119-27. doi: 10.1007/978-1-61779-956-3_12.


Bacterial cadherin domains as carbohydrate binding modules: determination of affinity constants to insoluble complex polysaccharides.

Fraiberg M, Borovok I, Weiner RM, Lamed R, Bayer EA.

Methods Mol Biol. 2012;908:109-18. doi: 10.1007/978-1-61779-956-3_11.


A simple method for determining specificity of carbohydrate-binding modules for purified and crude insoluble polysaccharide substrates.

Yaniv O, Jindou S, Frolow F, Lamed R, Bayer EA.

Methods Mol Biol. 2012;908:101-7. doi: 10.1007/978-1-61779-956-3_10.


A single mutation reforms the binding activity of an adhesion-deficient family 3 carbohydrate-binding module.

Yaniv O, Petkun S, Shimon LJ, Bayer EA, Lamed R, Frolow F.

Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):819-28. doi: 10.1107/S0907444912013133. Epub 2012 Jun 15.


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