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Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis

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. Amore » second motif was identified ~35 base pairs (bp) upstream of a large and diverse array of genes and hence may represent a sigma factor binding site. As a result, this analysis provides a basis and framework for further investigations into Accumulibacter metabolism and the reconstruction of regulatory networks in uncultured organisms.« less
Authors:
 [1] ;  [1] ;  [2] ; ORCiD logo [2] ;  [1]
  1. Univ. of Wisconsin, Madison, WI (United States)
  2. U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
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
Research Org:
Dept. of Energy Joint Genome Inst., Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
OSTI Identifier:
1346927
Alternate Identifier(s):
OSTI ID: 1379256

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., 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. doi:10.1038/ismej.2015.155.
Oyserman, Ben O., Noguera, Daniel R., del Rio, Tijana Glavina, Tringe, Susannah G., and McMahon, Katherine D.. 2015. "Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis". United States. doi: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 = {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 binding site. As a result, 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 = {2015},
month = {11}
}

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Mapping and quantifying mammalian transcriptomes by RNA-Seq
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