Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Whitham, Jason M.; Moon, Ji-Won; Rodriguez, Jr., Miguel; Engle, Nancy L.; Klingeman, Dawn M.; Rydzak, Thomas; Abel, Malaney M.; Tschaplinski, Timothy J.; Guss, Adam M.; Brown, Steven D.

doi:10.1186/s13068-018-1095-y

Title: Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Journal Article · Thu Apr 05 00:00:00 EDT 2018 · Biotechnology for Biofuels

DOI:https://doi.org/10.1186/s13068-018-1095-y· OSTI ID:1618721

Whitham, Jason M.; Moon, Ji-Won; Rodriguez, Jr., Miguel; Engle, Nancy L.; Klingeman, Dawn M.; Rydzak, Thomas; Abel, Malaney M.; Tschaplinski, Timothy J.; Guss, Adam M.; Brown, Steven D.

Background: Clostridium (Ruminiclostridium) thermocellum is a model fermentative anaerobic thermophile being studied and engineered for consolidated bioprocessing of lignocellulosic feedstocks into fuels and chemicals. Engineering efforts have resulted in significant improvements in ethanol yields and titers although further advances are required to make the bacterium industry-ready. For instance, fermentations at lower pH could enable co-culturing with microbes that have lower pH optima, augment productivity, and reduce buffering cost. C. thermocellum is typically grown at neutral pH, and little is known about its pH limits or pH homeostasis mechanisms. To better understand C. thermocellum pH homeostasis we grew strain LL1210 (C. thermocellum DSM1313 Δhpt ΔhydG Δldh Δpfl Δpta-ack), currently the highest ethanol producing strain of C. thermocellum, at different pH values in chemostat culture and applied systems biology tools.Results: Clostridium thermocellum LL1210 was found to be growth-limited below pH 6.24 at a dilution rate of 0.1 h^-1. F1F0-ATPase gene expression was upregulated while many ATP-utilizing enzymes and pathways were downregulated at pH 6.24. These included most flagella biosynthesis genes, genes for chemotaxis, and other motility-related genes (> 50) as well as sulfate transport and reduction, nitrate transport and nitrogen fixation, and fatty acid biosynthesis genes. Clustering and enrichment of differentially expressed genes at pH values 6.48, pH 6.24 and pH 6.12 (washout conditions) compared to pH 6.98 showed inverse differential expression patterns between the F1F0-ATPase and genes for other ATP-utilizing enzymes. At and below pH 6.24, amino acids including glutamate and valine; long-chain fatty acids, their iso-counterparts and glycerol conjugates; glycolysis intermediates 3-phosphoglycerate, glucose 6-phosphate, and glucose accumulated intracellularly. Glutamate was 267 times more abundant in cells at pH 6.24 compared to pH 6.98, and intercellular concentration reached 1.8 μmol/g pellet at pH 5.80 (stopped flow).Conclusions: Clostridium thermocellum LL1210 can grow under slightly acidic conditions, similar to limits reported for other strains. This foundational study provides a detailed characterization of a relatively acid-intolerant bacterium and provides genetic targets for strain improvement. Future studies should examine adding gene functions used by more acid-tolerant bacteria for improved pH homeostasis at acidic pH values.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: BESC; AC05-00OR22725

OSTI ID:: 1618721

Alternate ID(s):: OSTI ID: 1435276

Journal Information:: Biotechnology for Biofuels, Journal Name: Biotechnology for Biofuels Vol. 11 Journal Issue: 1; ISSN 1754-6834

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: Netherlands

Language:: English

Citation Metrics:

Cited by: 14 works

Citation information provided by
Web of Science

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MOESM1 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105350 The current record is supplemented by this dataset	dataset	April 2018
MOESM1 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105350.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM2 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105371.v1 The current record is supplemented by this dataset	dataset	April 2018
MOESM3 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105389.v1 The current record is supplemented by this dataset	dataset	April 2018
MOESM4 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105407.v1 The current record is supplemented by this figure	figure	April 2018
MOESM5 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105419 The current record is supplemented by this dataset	dataset	April 2018
MOESM6 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105431.v1 The current record is supplemented by this dataset	dataset	April 2018
MOESM7 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/M9.FIGSHARE.6105437 The current record is supplemented by this dataset	dataset	April 2018
MOESM7 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105437.v1 The current record is supplemented by this dataset	dataset	April 2018
MOESM8 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105446.v1 The current record is supplemented by this dataset	dataset	April 2018
Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics [Supplemental Data] Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/M9.FIGSHARE.C.4061360 The current record is supplemented by this dataset	dataset	April 2018
Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics [Supplemental Data] Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.c.4061360.v1 The current record is supplemented by this collection	collection	April 2018
MOESM3 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105389 The current record is supplemented by this dataset	dataset	April 2018
MOESM4 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105407 The current record is supplemented by this figure	figure	April 2018
MOESM5 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105419.v1 The current record is supplemented by this figure	figure	April 2018
MOESM8 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics Whitham, Jason; Moon, Ji-Won; Rodriguez, Miguel https://doi.org/10.6084/m9.figshare.6105446 The current record is supplemented by this dataset	dataset	April 2018