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1,240 results on '"Bayer, Edward A."'

1. Phylogenomics and genetic analysis of solvent-producing Clostridium species.

Author

Jensen, Rasmus, Schulz, Frederik, Roux, Simon, Klingeman, Dawn, Mitchell, Wayne, Udwary, Daniel, Moraïs, Sarah, Reynoso, Vinicio, Winkler, James, Nagaraju, Shilpa, De Tissera, Sashini, Shapiro, Nicole, Ivanova, Natalia, Reddy, T, Mizrahi, Itzhak, Utturkar, Sagar, Bayer, Edward, Woyke, Tanja, Mouncey, Nigel, Jewett, Michael, Simpson, Séan, Köpke, Michael, Jones, David, and Brown, Steven

Subjects
Clostridium, Phylogeny, Genome, Bacterial, Solvents, Fermentation
Abstract

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

Published
2024

10. Unique Fn3‐like biosensor in σI/anti‐σI factors for regulatory expression of major cellulosomal scaffoldins in Pseudobacteroides cellulosolvens.

Author

Dong, Sheng, Chen, Chao, Li, Jie, Liu, Ya‐Jun, Bayer, Edward A., Lamed, Raphael, Mizrahi, Itzhak, Cui, Qiu, and Feng, Yingang

Abstract

Lignocellulolytic clostridia employ multiple pairs of alternative σ/anti‐σ (SigI/RsgI) factors to regulate cellulosomal components for substrate‐specific degradation of cellulosic biomass. The current model has proposed that RsgIs use a sensor domain to bind specific extracellular lignocellulosic components and activate cognate SigIs to initiate expression of corresponding cellulosomal enzyme genes, while expression of scaffoldins can be initiated by several different SigIs. Pseudobacteroides cellulosolvens contains the most complex known cellulosome system and the highest number of SigI–RsgI regulons yet discovered. However, the function of many RsgI sensor domains and their relationship with the various enzyme types are not fully understood. Here, we report that RsgI4 from P. cellulosolvens employs a C‐terminal module that bears distant similarity to the fibronectin type III (Fn3) domain and serves as the sensor domain. Substrate‐binding analysis revealed that the Fn3‐like domain of RsgI4 represents a novel carbohydrate‐binding module (CBM) that binds to a wide range of polysaccharide types. Structure determination further revealed that the Fn3‐like domain belongs to the type B group of CBMs with a predicted concave face for substrate binding. Promoter sequence analysis of cellulosomal genes revealed that SigI4 is responsible for cellulosomal regulation of major scaffoldins rather than enzymes, consistent with the broad substrate specificity of the RsgI4 sensor domain. Notably, scaffoldins are invariably required as cellulosome components regardless of the substrate type. These findings suggest that the intricate cellulosome system of P. cellulosolvens comprises a more elaborate regulation mechanism than other bacteria and thus expands the paradigm of cellulosome regulation. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Undefined cellulase formulations hinder scientific reproducibility

Author

Himmel, Michael E, Abbas, Charles A, Baker, John O, Bayer, Edward A, Bomble, Yannick J, Brunecky, Roman, Chen, Xiaowen, Felby, Claus, Jeoh, Tina, Kumar, Rajeev, McCleary, Barry V, Pletschke, Brett I, Tucker, Melvin P, Wyman, Charles E, and Decker, Stephen R

Subjects
Biological Sciences, Industrial Biotechnology, Cellulase, Cellulose, Biofuels, Assays, Commercial cellulase formulations, Chemical Engineering, Biochemistry and cell biology, Industrial biotechnology
Abstract

In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparations may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.

Published
2017

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

Author

Utturkar, Sagar M, Bayer, Edward A, Borovok, Ilya, Lamed, Raphael, Hurt, Richard A, Land, Miriam L, Klingeman, Dawn M, Elias, Dwayne, Zhou, Jizhong, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, TBK, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, and Brown, Steven D

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Infection
Abstract

We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Published
2016

29. Bacterial Adhesion

Author

Ofek, Itzhak, Bayer, Edward A., Abraham, Soman N., Rosenberg, Eugene, editor, DeLong, Edward F., editor, Lory, Stephen, editor, Stackebrandt, Erko, editor, and Thompson, Fabiano, editor

Published
2013
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34. Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch‐degrader Ruminococcus bromii

Author

Mukhopadhya, Indrani, Moraïs, Sarah, Laverde‐Gomez, Jenny, Sheridan, Paul O., Walker, Alan W., Kelly, William, Klieve, Athol V., Ouwerkerk, Diane, Duncan, Sylvia H., Louis, Petra, Koropatkin, Nicole, Cockburn, Darrell, Kibler, Ryan, Cooper, Philip J., Sandoval, Carlos, Crost, Emmanuelle, Juge, Nathalie, Bayer, Edward A., and Flint, Harry J.

Published
2018
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41. Impact of scaffoldin mechanostability on cellulosomal activity

Author

CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Educación, Cultura y Deporte (España), Galera-Prat, Albert [0000-0002-6334-3428], Bayer, Edward A. [0000-0001-7749-5150], Carrión-Vázquez, Mariano Sixto [0000-0001-7319-406X], Galera-Prat, Albert, Vera, Andrés M., Moraïs, Sarah, Vazana, Yael, Bayer, Edward A., Carrión-Vázquez, Mariano Sixto, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Educación, Cultura y Deporte (España), Galera-Prat, Albert [0000-0002-6334-3428], Bayer, Edward A. [0000-0001-7749-5150], Carrión-Vázquez, Mariano Sixto [0000-0001-7319-406X], Galera-Prat, Albert, Vera, Andrés M., Moraïs, Sarah, Vazana, Yael, Bayer, Edward A., and Carrión-Vázquez, Mariano Sixto

Abstract

Lignocellulose is the most abundant renewable carbon source in the biosphere. However, the main bottleneck in its conversion to produce second generation biofuels is the saccharification step: the hydrolysis of lignocellulosic material into soluble fermentable sugars. Some anaerobic bacteria have developed an extracellular multi-enzyme complex called the cellulosome that efficiently degrades cellulosic substrates. Cellulosome complexes rely on enzyme-integrating scaffoldins that are large non-catalytic scaffolding proteins comprising several cohesin modules and additional functional modules that mediate the anchoring of the complex to the cell surface and the specific binding to its cellulosic substrate. It was proposed that mechanical forces may affect the cohesins positioned between the cell- and cellulose-anchoring points in the so-called connecting region. Consequently, the mechanical resistance of cohesins within the scaffoldin is of great importance, both to understand cellulosome function and as a parameter of industrial interest, to better mimic natural complexes through the use of the established designer cellulosome technology. Here we study how the mechanical stability of cohesins in a scaffoldin affects the enzymatic activity of a cellulosome. We found that when a cohesin of low mechanical stability is positioned in the connecting region of a scaffoldin, the activity of the resulting cellulosome is reduced as opposed to a cohesin of higher mechanical stability. This observation directly relates mechanical stability of the scaffoldin-borne cohesins to cellulosome activity and provides a rationale for the design of artificial cellulosomes for industrial applications, by incorporating mechanical stability as a new industrial parameter in the biotechnology toolbox.

Published
2020

45. Nanoscale resolution of microbial fiber degradation in action

Author

Tatli, Meltem; https://orcid.org/0000-0003-3632-6208, Moraïs, Sarah; https://orcid.org/0000-0001-9026-2386, Tovar-Herrera, Omar E, Bomble, Yannick J; https://orcid.org/0000-0001-7624-8000, Bayer, Edward A, Medalia, Ohad; https://orcid.org/0000-0003-0994-2937, Mizrahi, Itzhak; https://orcid.org/0000-0001-6636-8818, Tatli, Meltem; https://orcid.org/0000-0003-3632-6208, Moraïs, Sarah; https://orcid.org/0000-0001-9026-2386, Tovar-Herrera, Omar E, Bomble, Yannick J; https://orcid.org/0000-0001-7624-8000, Bayer, Edward A, Medalia, Ohad; https://orcid.org/0000-0003-0994-2937, and Mizrahi, Itzhak; https://orcid.org/0000-0001-6636-8818

Abstract

The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation of the canonical Clostridium thermocellum system to comprehend how microbes build and use their cellulosomal machinery at these nanometer scales. Degradation of cellulose, the most abundant organic polymer on Earth, is instrumental to the global carbon cycle. We reveal that bacterial cells form 'cellulosome capsules' driven by catalytic product-dependent dynamics, which can increase the rate of hydrolysis. Biosynthesis of this energetically costly machinery and cell growth are decoupled at the single-cell level, hinting at a division-of-labor strategy through phenotypic heterogeneity. This novel observation highlights intrapopulation interactions as key to understanding rates of fiber degradation.

Published
2022

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