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Title: Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H 2 and CO 2 compared to organotrophic growth with fructose

Abstract

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 (H 2), carbon dioxide (CO 2), and carbon monoxide (CO), or with H 2 and CO 2. Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H 2/CO 2 was compared by RNA-Seq. Upregulated genes with both syngas and H 2/CO 2 (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 H 2/CO 2, 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,more » observations that may guide biofuel and commodity chemical production with this species.« less

Authors:
 [1];  [2];  [3];  [4];  [5]
  1. Univ. of Massachusetts, Amherst, MA (United States); Univ. of Nevada, Reno, NV (United States)
  2. Univ. of Massachusetts, Amherst, MA (United States); LanzaTech, Skokie, IL (United States)
  3. Univ. of Massachusetts, Amherst, MA (United States); Univ. of California, Berkeley, CA (United States). Energy Biosciences Inst.
  4. Univ. of Massachusetts, Amherst, MA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
  5. Univ. of Massachusetts, Amherst, MA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Advanced Research Projects Agency - Energy (ARPA-E); US Department of the Navy, Office of Naval Research (ONR)
OSTI Identifier:
1419439
Grant/Contract Number:  
AC02-05CH11231; AR0000159; N000141310549
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bacterial genomics; Gene expression profiling

Citation Formats

Aklujkar, Muktak, Leang, Ching, Shrestha, Pravin M., Shrestha, Minita, and Lovley, Derek R. Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose. United States: N. p., 2017. Web. doi:10.1038/s41598-017-12712-w.
Aklujkar, Muktak, Leang, Ching, Shrestha, Pravin M., Shrestha, Minita, & Lovley, Derek R. Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose. United States. doi:10.1038/s41598-017-12712-w.
Aklujkar, Muktak, Leang, Ching, Shrestha, Pravin M., Shrestha, Minita, and Lovley, Derek R. Fri . "Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose". United States. doi:10.1038/s41598-017-12712-w. https://www.osti.gov/servlets/purl/1419439.
@article{osti_1419439,
title = {Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose},
author = {Aklujkar, Muktak and Leang, Ching and Shrestha, Pravin M. and Shrestha, Minita and Lovley, Derek R.},
abstractNote = {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.},
doi = {10.1038/s41598-017-12712-w},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Fri Oct 13 00:00:00 EDT 2017},
month = {Fri Oct 13 00:00:00 EDT 2017}
}

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Works referenced in this record:

Electrosynthesis of Organic Compounds from Carbon Dioxide Is Catalyzed by a Diversity of Acetogenic Microorganisms
journal, March 2011

  • Nevin, Kelly P.; Hensley, Sarah A.; Franks, Ashley E.
  • Applied and Environmental Microbiology, Vol. 77, Issue 9, p. 2882-2886
  • DOI: 10.1128/AEM.02642-10

Mapping and quantifying mammalian transcriptomes by RNA-Seq
journal, May 2008

  • Mortazavi, Ali; Williams, Brian A.; McCue, Kenneth
  • Nature Methods, Vol. 5, Issue 7, p. 621-628
  • DOI: 10.1038/nmeth.1226

Clostridium ljungdahlii represents a microbial production platform based on syngas
journal, July 2010

  • Kopke, M.; Held, C.; Hujer, S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 29, p. 13087-13092
  • DOI: 10.1073/pnas.1004716107