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Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers.

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Title: Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers.
Authors: Rowe, Annette R.1, Heavner, Gretchen L.2, Mansfeldt, Cresten B.2, Wemer, Jeffrey J.3, Richardson, Ruth E.2 rer26@cornell.edu
Source: Environmental Science & Technology. 9/4/2012, Vol. 46 Issue 17, p9388-9397. 10p.
Subjects: Biomarkers, Vinyl chloride, Dehalococcoides, Microbial respiration, Bacterial protein analysis, Messenger RNA, Dehalogenases, Hydrogenase, Bioremediation, Electrophiles
Abstract: Molecular biomarkers could provide critical insight into myriad in situ microbial activities. In this study we explore correlations of both mRNA and protein biomarkers with chloroethene respiration rate in Dehalococcoides. In a series of continuously fed dechlorinating mixed-culture microcosm experiments (n = 26), we varied respiratory substrates, substrate ratios and feeding rates. Transcript levels for most biomarkers were responsive down to 0.01× the culture's maximum respiration rate. The dehalogenase TceA and the Ni-Fe hydrogenase HupL transcripts were positively correlated (Pearson's r of 0.89 and 0.88, respectively) with respiration rates on log-log plots between 1.5 and 280 μeeq/L-hr for mRNA abundances of 107 to 1010 transcripts/mL (0.07-230 transcripts/genome). These trends were independent of the types of chloroethene or electron donors fed. Other mRNA target levels plateaued or declined at respiration rates above 5 μeeq/L-hr. Using both relative and absolute protein quantification methods, we found that per-genome protein abundances of most targeted biomarkers did not statistically change over the experimental time frames. However, quantified enzyme levels allowed us to calculate in vivo enzyme-specific rate constants (kcat) for the dehalogenases PceA and TceA: 400 and 22 substrate molecules/enzyme-sec, respectively. Overall, these data support the promise of both mRNA and protein biomarkers for estimating process rates through either empirical (mRNA-based) or kinetic (protein-based) models, but they require follow-up studies in other cultures and at active remediation sites. [ABSTRACT FROM AUTHOR]
Copyright of Environmental Science & Technology is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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DbLabel: Engineering Source
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  Data: Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers.
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  Data: <searchLink fieldCode="AR" term="%22Rowe%2C+Annette+R%2E%22">Rowe, Annette R.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Heavner%2C+Gretchen+L%2E%22">Heavner, Gretchen L.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Mansfeldt%2C+Cresten+B%2E%22">Mansfeldt, Cresten B.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Wemer%2C+Jeffrey+J%2E%22">Wemer, Jeffrey J.</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Richardson%2C+Ruth+E%2E%22">Richardson, Ruth E.</searchLink><relatesTo>2</relatesTo><i> rer26@cornell.edu</i>
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Science+%26+Technology%22">Environmental Science & Technology</searchLink>. 9/4/2012, Vol. 46 Issue 17, p9388-9397. 10p.
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  Data: <searchLink fieldCode="DE" term="%22Biomarkers%22">Biomarkers</searchLink><br /><searchLink fieldCode="DE" term="%22Vinyl+chloride%22">Vinyl chloride</searchLink><br /><searchLink fieldCode="DE" term="%22Dehalococcoides%22">Dehalococcoides</searchLink><br /><searchLink fieldCode="DE" term="%22Microbial+respiration%22">Microbial respiration</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+protein+analysis%22">Bacterial protein analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Messenger+RNA%22">Messenger RNA</searchLink><br /><searchLink fieldCode="DE" term="%22Dehalogenases%22">Dehalogenases</searchLink><br /><searchLink fieldCode="DE" term="%22Hydrogenase%22">Hydrogenase</searchLink><br /><searchLink fieldCode="DE" term="%22Bioremediation%22">Bioremediation</searchLink><br /><searchLink fieldCode="DE" term="%22Electrophiles%22">Electrophiles</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: Molecular biomarkers could provide critical insight into myriad in situ microbial activities. In this study we explore correlations of both mRNA and protein biomarkers with chloroethene respiration rate in Dehalococcoides. In a series of continuously fed dechlorinating mixed-culture microcosm experiments (n = 26), we varied respiratory substrates, substrate ratios and feeding rates. Transcript levels for most biomarkers were responsive down to 0.01× the culture's maximum respiration rate. The dehalogenase TceA and the Ni-Fe hydrogenase HupL transcripts were positively correlated (Pearson's r of 0.89 and 0.88, respectively) with respiration rates on log-log plots between 1.5 and 280 μeeq/L-hr for mRNA abundances of 107 to 1010 transcripts/mL (0.07-230 transcripts/genome). These trends were independent of the types of chloroethene or electron donors fed. Other mRNA target levels plateaued or declined at respiration rates above 5 μeeq/L-hr. Using both relative and absolute protein quantification methods, we found that per-genome protein abundances of most targeted biomarkers did not statistically change over the experimental time frames. However, quantified enzyme levels allowed us to calculate in vivo enzyme-specific rate constants (kcat) for the dehalogenases PceA and TceA: 400 and 22 substrate molecules/enzyme-sec, respectively. Overall, these data support the promise of both mRNA and protein biomarkers for estimating process rates through either empirical (mRNA-based) or kinetic (protein-based) models, but they require follow-up studies in other cultures and at active remediation sites. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Environmental Science & Technology is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
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      – Type: doi
        Value: 10.1021/es300996c
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      – Code: eng
        Text: English
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        PageCount: 10
        StartPage: 9388
    Subjects:
      – SubjectFull: Biomarkers
        Type: general
      – SubjectFull: Vinyl chloride
        Type: general
      – SubjectFull: Dehalococcoides
        Type: general
      – SubjectFull: Microbial respiration
        Type: general
      – SubjectFull: Bacterial protein analysis
        Type: general
      – SubjectFull: Messenger RNA
        Type: general
      – SubjectFull: Dehalogenases
        Type: general
      – SubjectFull: Hydrogenase
        Type: general
      – SubjectFull: Bioremediation
        Type: general
      – SubjectFull: Electrophiles
        Type: general
    Titles:
      – TitleFull: Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers.
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            NameFull: Rowe, Annette R.
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            NameFull: Heavner, Gretchen L.
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            NameFull: Mansfeldt, Cresten B.
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            NameFull: Wemer, Jeffrey J.
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              M: 09
              Text: 9/4/2012
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              Y: 2012
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              Value: 46
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