James C. Hayes’s scientific contributions


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Publications (1)


Fig 1.  Neighbor-joining tree of C. phytofermentans and related taxa within the class Clostridia based on 16S rRNA gene sequences.
Taxa with sequenced genomes are marked with an asterisk. Cluster numbers correspond to the cluster system of Collins et al. [68]. Bootstrap values were determined for 1,000 replicates.
Table 1.  General features of the genome of C. phytofermentans.
Fig 2.  Fermentation products on different growth substrates.
(A) Fermentation products during growth on 2% (w/v) cellobiose. Data are an average of two samples; error bars represent range. (B) Ethanol produced on a variety of substrates expressed as the molar percentage of non-gaseous products. All substrates were present at a concentration of 1% (w/v) except where otherwise indicated. The particle size of insoluble substrates was reduced by grinding; the substrates were not otherwise pre-treated. Fermentation products were measured after obvious growth ceased (3–5 days) at 30°C. In most cases, substrate conversion was incomplete.
Fig 3. Comparative analysis of AraC transcriptional regulators, glycoside hydrolases (GH), and ABC transporters among selected sequenced clostridial genomes. (A) A conceptual illustration of how GH (blue), ABC transporters (purple) and AraC regulators (red) may work together. (B) Number of AraC transcriptional regulators per genome. (C) Number of GH domains per genome. Organisms having both GH48 and GH9 are marked with two asterisks, and organisms having GH9 alone are marked with one asterisk. (D) Number of putative ABC transporters per genome. doi:10.1371/journal.pone.0118285.g003 
Fig 3.  Comparative analysis of AraC transcriptional regulators, glycoside hydrolases (GH), and ABC transporters among selected sequenced clostridial genomes.
(A) A conceptual illustration of how GH (blue), ABC transporters (purple) and AraC regulators (red) may work together. (B) Number of AraC transcriptional regulators per genome. (C) Number of GH domains per genome. Organisms having both GH48 and GH9 are marked with two asterisks, and organisms having GH9 alone are marked with one asterisk. (D) Number of putative ABC transporters per genome.

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Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels
  • Article
  • Full-text available

June 2015

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452 Reads

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17 Citations

PLOS ONE

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Maddalena V. Coppi

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James C. Hayes

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[...]

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Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.

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Citations (1)


... The overabundance of Cazymes is not necessarily related to high enzymatic activity, as it depends on the genomic context such as the possible presence of a promoter (Williams-Rhaesa et al. 2018), operon (Chakraborty et al. 2021). Indeed, Clostridia phytofermentas, which is a very good lignocellulolytic degrader (Tolonen et al. 2011) and expresses several high lignocellulolytic enzymatic activities (Petit et al. 2015), secreted approximately 80 Cazymes (among the 161 present in its genome) in silico, which confirms that a very high abundance of Cazymes does not necessarily indicate excellent enzymatic activity. ...

Reference:

Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels