Applied Microbiology and Biotechnology

, Volume 99, Issue 5, pp 2313–2327 | Cite as

Relating mRNA and protein biomarker levels in a Dehalococcoides and Methanospirillum-containing community

  • Annette R. Rowe
  • Cresten B. Mansfeldt
  • Gretchen L. Heavner
  • Ruth E. Richardson
Applied microbial and cell physiology
First Online:
Received:
Revised:
Accepted:

Abstract

To better understand the quantitative relationships between messenger RNA (mRNA) and protein biomarkers relevant to bioremediation, we quantified and compared respiration-associated gene products in an anaerobic syntrophic community. Respiration biomarkers for Dehalococcoides, an organohalide reducer, and Methanospirillum, a hydrogenotrophic methanogen, were quantified via qRT-PCR for mRNA and multiple reaction monitoring (MRM) of proteotypic peptides for protein. mRNA transcripts of the Dehalococcoides reductive dehalogenases PceA, TceA, and DMC1545, and hydrogenase HupL, as well as the Methanospirillum oxidoreductases MvrD and FrcA were shown to be similarly regulated with respect to their temporal responses to substrate addition. However, MvrD was two orders of magnitude lower in mRNA abundance. Per cell, Dehalococcoides protein biomarkers quantified were more abundant than Methanospirillum proteins. Comparing mRNA with protein abundance, poor correlations were observed between mRNA transcript levels and the net protein produced. For example, Dehalococcoides HupL and TceA transcripts were similarly abundant though TceA was far more abundant at the protein level (167 ± 121 vs. 1095 ± 337 proteins per cell, respectively). In Methanospirillum, MvrD maintained comparable per-cell protein abundance to FrcA (42 ± 14 vs. 60 ± 1 proteins per cell, respectively) despite the significantly lower transcript levels. Though no variability in protein decay rates was observed, the mRNA translation rate quantified for TceA was greater than the other Dehalococcoides targets monitored. These data suggest that there is considerable variation in the relationship between mRNA abundance and protein production both across transcripts within an organism and across organisms. This highlights the importance of empirically based studies for interpreting biomarker levels in environmentally relevant organisms.

Keywords

Biomarker Transcription Protein synthesis Organochlorine respiration Methanogenesis 
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Notes

Acknowledgments

We gratefully acknowledge services of the Cornell Proteomics and Mass Spectrometry core facility (Celeste Ptak and Sheng Zhang). Graduate research funding was provided by the National Science Foundation NSF Graduate Research Fellowship (Annette Rowe). Research funds were provided from the NSF CBET Program (CBET-0731169), the Department of Defense Army Research Office (W911NF-07-10249) and an NSF-IGERT funded Biogeochemistry and Environmental Biocomplexity small grant program (DGE 0221658). Metaproteome samples quantified with NSAF were analyzed through the Environmental Molecular Sciences Lab Users Program at the Pacific Northwest National Lab (Proposal 40006). Special thanks to Mike Wilkins for his valued input and technical assistance.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

253_2014_6220_MOESM1_ESM.pdf (201 kb)
ESM 1 (PDF 200 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Annette R. Rowe
    • 1
    • 3
  • Cresten B. Mansfeldt
    • 2
  • Gretchen L. Heavner
    • 2
  • Ruth E. Richardson
    • 2
  1. 1.Field of Microbiology, 220 Hollister HallCornell UniversityIthacaUSA
  2. 2.Civil and Environmental Engineering, 220 Hollister HallCornell UniversityIthacaUSA
  3. 3.Los AngelesUSA

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