Microbial solvent formation revisited by comparative genome analysis

Abstract

BackgroundMicrobial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for the chemical and biofuel industry. However, biological synthesis suffers from high substrate costs and competition from chemical synthesis supported by the low price of crude oil. To render the biotechnological production economically viable again, improvements in microbial and fermentation performance are necessary. However, no comprehensive comparisons of respective species and strains used and their specific abilities exist today.ResultsThe genomes of a total 30 saccharolytic Clostridium strains, representative of the species Clostridium acetobutylicum, C. aurantibutyricum, C. beijerinckii, C. diolis, C. felsineum, C. pasteurianum, C. puniceum, C. roseum, C. saccharobutylicum, and C. saccharoperbutylacetonicum, have been determined; 10 of them completely, and compared to 14 published genomes of other solvent-forming clostridia. Two major groups could be differentiated and several misclassified species were detected.ConclusionsOur findings represent a comprehensive study of phylogeny and taxonomy of clostridial solvent producers that highlights differences in energy conservation mechanisms and substrate utilization between strains, and allow for the first time a direct comparison of sequentially selected industrial strains at the genetic level. Detailed data mining is now possible, supporting the identification of new engineering targets for improved solvent production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0742-z) contains supplementary material, which is available to authorized users.

The Butanol Producing Microbe Clostridium beijerinckii NCIMB 14988 Manipulated Using Forward and Reverse Genetic Tools

“…In common with all known C. beijerinckii , Clostridium puniceum , C. saccharobutylicum and Clostridium saccharoperbutylacetonicum , the ctfAB genes of C. beijerinckii NCIMB 14988 reside in a type II sol operon, starting with the ald gene LF65_04317 (aldehyde dehydrogenase). In an attempt to utilise the promoter of this operon, 246 bp of the region upstream of the ald RBS was inserted upstream of the ctfAB genes (with their native RBS) in chromosomal complementation plasmid pMTL‐GL7C‐P ald ‐ ctfAB .…”

“…The roadmap enables the targeted introduction of point mutations into the genome. Analysis of historical industrial butanol producing strains suggests that the amino‐acid substitution M122I in the phosphate butyryltransferase ( ptb ) enzyme (Figure a) results in a reduced activity . Compared to other Clostridium spp.…”

“…Clearly the selection method used is specific for C. beijerinckii , and could prove useful to others who wish to isolate new representatives of this species. Here we were able to derive a complete sequence of the genome using PacBio sequencing, making it the sixth representative of C. beijerinckii for which a closed genome is available …”

“…The saccharolytic mesophiles Clostridium beijerinckii , Clostridium acetobutylicum , and Clostridium saccharobutylicum are able to convert sugar into the solvents acetone, butanol and ethanol, with industrial scale acetone production widespread during the early twentieth century . After the demise of commercial Clostridium fermentations in the latter part of the 20th century due to reduced oil prices, Clostridium strains are again being commercialized by companies such as LanzaTech and Green Biologics Ltd. As genome sequences of saccharolytic Clostridium strains have become available, historical isolates, including those used in industrial acetone‐butanol‐ethanol (ABE) fermentations, have been reclassified, often as C. beijerinckii …”

Self-Synchronized Oscillatory Metabolism of Clostridium pasteurianum in Continuous Culture

“…Most of the genes of C. pasteurianum associated with the enzymes in the glycerol oxidative and reduction pathways have been recently identified [4,16,17], however the regulation of glycerol metabolism is still not well understood. Genetic tools have been developed for engineering C. pasteurianum [15,[18][19][20].…”