E-GEOD-52494 - Population level analysis of evolved mutations underlying improvements in plant cellulose and hemicellulose fermentation by Clostridium phytofermentans

Status
Released on 20 November 2013, last updated on 3 June 2014
Organism
Clostridium phytofermentans
Samples (4)
Array (1)
Protocols (6)
Description
The complexity of the plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by C. phytofermentans and identify molecular mechanisms that may overcome these limitations. Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end 100bp paired end reads were generated per population resulting in ~300 fold coverage of each site in the genome. A mixture of alleles fixed in the population down to frequencies of 5% could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Protein structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane proteins and the ATPase binding protein. Experimental evolution was effective in identifying molecular constraints on the rate of cellulose and hemicellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates. Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose. Microarray analysis was performed on 1 time point from the evolved lines and the initial founder
Experiment type
transcription profiling by array 
Contacts
Jeffrey L Blanchard <jeffb@bio.umass.edu>, Anna Lipzen, Jeffrey Blanchard, Joel Martin, Lynmarie Thompson, Stephen Godin, Supratim Mukherjee, Wendy Schackwitz
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-52494.idf.txt
Sample and data relationshipE-GEOD-52494.sdrf.txt
Raw data (1)E-GEOD-52494.raw.1.zip
Processed data (1)E-GEOD-52494.processed.1.zip
Array designA-GEOD-7481.adf.txt
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