Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose

Aklujkar, Muktak; Leang, Ching; Shrestha, Pravin M.; Shrestha, Minita; Lovley, Derek R.

doi:10.1038/s41598-017-12712-w

Title: Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H₂ and CO₂ compared to organotrophic growth with fructose

Journal Article · Fri Oct 13 00:00:00 EDT 2017 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-017-12712-w· OSTI ID:1419439

Aklujkar, Muktak ^[1]; Leang, Ching ^[2]; Shrestha, Pravin M. ^[3]; Shrestha, Minita ^[4]; Lovley, Derek R. ^[5]

Univ. of Massachusetts, Amherst, MA (United States); Univ. of Nevada, Reno, NV (United States)
Univ. of Massachusetts, Amherst, MA (United States); LanzaTech, Skokie, IL (United States)
Univ. of Massachusetts, Amherst, MA (United States); Univ. of California, Berkeley, CA (United States). Energy Biosciences Inst.
Univ. of Massachusetts, Amherst, MA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
Univ. of Massachusetts, Amherst, MA (United States)

Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H₂), carbon dioxide (CO₂), and carbon monoxide (CO), or with H₂ and CO₂. Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H₂/CO₂ was compared by RNA-Seq. Upregulated genes with both syngas and H₂/CO₂ (compared to fructose) point to the urea cycle, uptake and degradation of peptides and amino acids, response to sulfur starvation, potentially NADPH-producing pathways involving (S)-malate and ornithine, quorum sensing, sporulation, and cell wall remodeling, suggesting a global and multicellular response to lithotrophic conditions. With syngas, the upregulated (R)-lactate dehydrogenase gene represents a route of electron transfer from ferredoxin to NAD. With H₂/CO₂, flavodoxin and histidine biosynthesis genes were upregulated. Downregulated genes corresponded to an intracytoplasmic microcompartment for disposal of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several cytoplasmic and membrane-associated redox-active protein genes were differentially regulated. In conclusion, the transcriptomic profiles of C. ljungdahlii in lithotrophic and organotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide biofuel and commodity chemical production with this species.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Advanced Research Projects Agency - Energy (ARPA-E); US Department of the Navy, Office of Naval Research (ONR)

Grant/Contract Number:: AC02-05CH11231; AR0000159; N000141310549

OSTI ID:: 1419439

Journal Information:: Scientific Reports, Vol. 7, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 20 works

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Title: Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose

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Title: Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H₂ and CO₂ compared to organotrophic growth with fructose