Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Abstract
© 2016 International Society for Microbial Ecology All rights reserved. Previous studies on enhanced biological phosphorus removal (EBPR) have focused on reconstructing genomic blueprints for the model polyphosphate-accumulating organism Candidatus Accumulibacter phosphatis. Here, a time series metatranscriptome generated from enrichment cultures of Accumulibacter was used to gain insight into anerobic/aerobic metabolism and regulatory mechanisms within an EBPR cycle. Co-expressed gene clusters were identified displaying ecologically relevant trends consistent with batch cycle phases. Transcripts displaying increased abundance during anerobic acetate contact were functionally enriched in energy production and conversion, including upregulation of both cytoplasmic and membrane-bound hydrogenases demonstrating the importance of transcriptional regulation to manage energy and electron flux during anerobic acetate contact. We hypothesized and demonstrated hydrogen production after anerobic acetate contact, a previously unknown strategy for Accumulibacter to maintain redox balance. Genes involved in anerobic glycine utilization were identified and phosphorus release after anerobic glycine contact demonstrated, suggesting that Accumulibacter routes diverse carbon sources to acetyl-CoA formation via previously unrecognized pathways. A comparative genomics analysis of sequences upstream of co-expressed genes identified two statistically significant putative regulatory motifs. One palindromic motif was identified upstream of genes involved in PHA synthesis and acetate activation and is hypothesized to be amore »
- Authors:
-
[2];
- Univ. of Wisconsin, Madison, WI (United States)
- U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1346927
- Alternate Identifier(s):
- OSTI ID: 1379256
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 4; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
Citation Formats
Oyserman, Ben O., Noguera, Daniel R., del Rio, Tijana Glavina, Tringe, Susannah G., and McMahon, Katherine D. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. United States: N. p., 2015.
Web. doi:10.1038/ismej.2015.155.
Oyserman, Ben O., Noguera, Daniel R., del Rio, Tijana Glavina, Tringe, Susannah G., & McMahon, Katherine D. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. United States. https://doi.org/10.1038/ismej.2015.155
Oyserman, Ben O., Noguera, Daniel R., del Rio, Tijana Glavina, Tringe, Susannah G., and McMahon, Katherine D. Tue .
"Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis". United States. https://doi.org/10.1038/ismej.2015.155. https://www.osti.gov/servlets/purl/1346927.
@article{osti_1346927,
title = {Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis},
author = {Oyserman, Ben O. and Noguera, Daniel R. and del Rio, Tijana Glavina and Tringe, Susannah G. and McMahon, Katherine D.},
abstractNote = {© 2016 International Society for Microbial Ecology All rights reserved. Previous studies on enhanced biological phosphorus removal (EBPR) have focused on reconstructing genomic blueprints for the model polyphosphate-accumulating organism Candidatus Accumulibacter phosphatis. Here, a time series metatranscriptome generated from enrichment cultures of Accumulibacter was used to gain insight into anerobic/aerobic metabolism and regulatory mechanisms within an EBPR cycle. Co-expressed gene clusters were identified displaying ecologically relevant trends consistent with batch cycle phases. Transcripts displaying increased abundance during anerobic acetate contact were functionally enriched in energy production and conversion, including upregulation of both cytoplasmic and membrane-bound hydrogenases demonstrating the importance of transcriptional regulation to manage energy and electron flux during anerobic acetate contact. We hypothesized and demonstrated hydrogen production after anerobic acetate contact, a previously unknown strategy for Accumulibacter to maintain redox balance. Genes involved in anerobic glycine utilization were identified and phosphorus release after anerobic glycine contact demonstrated, suggesting that Accumulibacter routes diverse carbon sources to acetyl-CoA formation via previously unrecognized pathways. A comparative genomics analysis of sequences upstream of co-expressed genes identified two statistically significant putative regulatory motifs. One palindromic motif was identified upstream of genes involved in PHA synthesis and acetate activation and is hypothesized to be a phaR binding site, hence representing a hypothetical PHA modulon. A second motif was identified ~35 base pairs (bp) upstream of a large and diverse array of genes and hence may represent a sigma factor bind ing site. This analysis provides a basis and framework for further investigations into Accumulibacter metabolism and the reconstruction of regulatory networks in uncultured organisms.},
doi = {10.1038/ismej.2015.155},
journal = {The ISME Journal},
number = 4,
volume = 10,
place = {United States},
year = {Tue Nov 10 00:00:00 EST 2015},
month = {Tue Nov 10 00:00:00 EST 2015}
}
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- Polónia, Ana Rita Moura; Cleary, Daniel Francis Richard; Coelho, Francisco José Riso da Costa
- Marine Biology Research, Vol. 14, Issue 6
The proteome of Tetrasphaera elongata is adapted to changing conditions in wastewater treatment plants
posted_content, April 2019
- Herbst, Florian-Alexander; Dueholm, Morten S.; Wimmer, Reinhard
- Proteomes
A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems
journal, April 2017
- Stokholm-Bjerregaard, Mikkel; McIlroy, Simon J.; Nierychlo, Marta
- Frontiers in Microbiology, Vol. 8