Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome
Abstract
Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate how the microbiome responds to recurring change. Meta-transcriptomic analysis revealed a dramatic disconnect between the relative DNA abundance and gene expression within the metagenome-assembled genomes (MAGs) of community members, suggesting the importance of transcriptional regulation in this microbiome. To explore how community members responded to cyclic aeration via transcriptional regulation, we searched for homologs of the catabolite repressor protein/fumarate and nitrate reductase regulatory protein (CRP/FNR) family of transcription factors (TFs) within the MAGs. Using phylogenetic analyses, evaluation of sequence conservation in important amino acid residues, and prediction of genes regulated by TFs in the MAGs, we identified homologs of the oxygen-sensing FNR in Nitrosomonas and Rhodocyclaceae, nitrogen-sensing dissimilative nitrate respiration regulator that responds to nitrogen species (DNR) in Rhodocyclaceae, and nitrogen-sensing nitrite and nitric oxide reductase regulator that responds to nitrogen species (NnrR) in Nitrospira MAGs. Our data also predict that CRP/FNR homologs in Ignavibacteria, Flavobacteriales, and Saprospiraceae MAGs sense carbon availability. In addition, a CRP/FNR homolog inmore »
- Authors:
-
[1];
[2];
[5];
[6];
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA, Carollo Engineers, Inc., Broomfield, Colorado, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA, Carollo Engineers, Inc., San Diego, California, USA
- Madison Metropolitan Sewerage District, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA, Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF)
- OSTI Identifier:
- 1825345
- Alternate Identifier(s):
- OSTI ID: 1852641
- Grant/Contract Number:
- SC0018409; CBET-1435661
- Resource Type:
- Published Article
- Journal Name:
- mSystems
- Additional Journal Information:
- Journal Name: mSystems Journal Volume: 6 Journal Issue: 5; Journal ID: ISSN 2379-5077
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; microbiology; bioinformatics; metagenomics; metatranscriptomics; microbiome; transcription factors; wastewater treatment
Citation Formats
Beach, Natalie K., Myers, Kevin S., Owen, Brian R., Seib, Matt, Donohue, Timothy J., Noguera, Daniel R., and Lindemann, ed., Stephen R. Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome. United States: N. p., 2021.
Web. doi:10.1128/mSystems.00906-21.
Beach, Natalie K., Myers, Kevin S., Owen, Brian R., Seib, Matt, Donohue, Timothy J., Noguera, Daniel R., & Lindemann, ed., Stephen R. Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome. United States. https://doi.org/10.1128/mSystems.00906-21
Beach, Natalie K., Myers, Kevin S., Owen, Brian R., Seib, Matt, Donohue, Timothy J., Noguera, Daniel R., and Lindemann, ed., Stephen R. Tue .
"Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome". United States. https://doi.org/10.1128/mSystems.00906-21.
@article{osti_1825345,
title = {Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome},
author = {Beach, Natalie K. and Myers, Kevin S. and Owen, Brian R. and Seib, Matt and Donohue, Timothy J. and Noguera, Daniel R. and Lindemann, ed., Stephen R.},
abstractNote = {Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate how the microbiome responds to recurring change. Meta-transcriptomic analysis revealed a dramatic disconnect between the relative DNA abundance and gene expression within the metagenome-assembled genomes (MAGs) of community members, suggesting the importance of transcriptional regulation in this microbiome. To explore how community members responded to cyclic aeration via transcriptional regulation, we searched for homologs of the catabolite repressor protein/fumarate and nitrate reductase regulatory protein (CRP/FNR) family of transcription factors (TFs) within the MAGs. Using phylogenetic analyses, evaluation of sequence conservation in important amino acid residues, and prediction of genes regulated by TFs in the MAGs, we identified homologs of the oxygen-sensing FNR in Nitrosomonas and Rhodocyclaceae, nitrogen-sensing dissimilative nitrate respiration regulator that responds to nitrogen species (DNR) in Rhodocyclaceae, and nitrogen-sensing nitrite and nitric oxide reductase regulator that responds to nitrogen species (NnrR) in Nitrospira MAGs. Our data also predict that CRP/FNR homologs in Ignavibacteria, Flavobacteriales, and Saprospiraceae MAGs sense carbon availability. In addition, a CRP/FNR homolog in a Brocadia MAG was most closely related to CRP TFs known to sense carbon sources in well-studied organisms. However, we predict that in autotrophic Brocadia, this TF most likely regulates a diverse set of functions, including a response to stress during the cyclic aerobic/anoxic conditions. Overall, this analysis allowed us to define a meta-regulon of the PNA microbiome that explains functions and interactions of the most active community members.},
doi = {10.1128/mSystems.00906-21},
journal = {mSystems},
number = 5,
volume = 6,
place = {United States},
year = {2021},
month = {10}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1128/mSystems.00906-21
https://doi.org/10.1128/mSystems.00906-21
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Induction of ammonia monooxygenase and hydroxylamine oxidoreductase mRNAs by ammonium in Nitrosomonas europaea
journal, May 1996
- Sayavedra‐Soto, Luis A.; Hommes, Norman G.; Russell, Sterling A.
- Molecular Microbiology, Vol. 20, Issue 3
Performance of a Full-Scale Sidestream DEMON® Deammonification Installation
journal, January 2013
- Nifong, Andrea; Nelson, Andy; Johnson, Chandler
- Proceedings of the Water Environment Federation, Vol. 2013, Issue 13
Anvi’o: an advanced analysis and visualization platform for ‘omics data
journal, January 2015
- Eren, A. Murat; Esen, Özcan C.; Quince, Christopher
- PeerJ, Vol. 3
Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes
journal, June 2018
- Taboada, Blanca; Estrada, Karel; Ciria, Ricardo
- Bioinformatics, Vol. 34, Issue 23
The regulation of bacterial transcription initiation
journal, January 2004
- Browning, Douglas F.; Busby, Stephen J. W.
- Nature Reviews Microbiology, Vol. 2, Issue 1
Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron
journal, October 2016
- Schwalm, Nathan D.; Townsend, Guy E.; Groisman, Eduardo A.
- mBio, Vol. 7, Issue 5
Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm
journal, March 2001
- Gieseke, Armin; Purkhold, Ulrike; Wagner, Michael
- Applied and Environmental Microbiology, Vol. 67, Issue 3
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB
journal, March 2016
- Doğan, Tunca; MacDougall, Alistair; Saidi, Rabie
- Bioinformatics, Vol. 32, Issue 15
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
journal, January 2004
- Laslett, Dean; Canback, Bjorn
- Nucleic Acids Research, Vol. 32, Issue 1, p. 11-16
The FNR family of transcriptional regulators
journal, January 1994
- Spiro, Stephen
- Antonie van Leeuwenhoek, Vol. 66, Issue 1-3
The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms
journal, January 2011
- Giardina, Giorgio; Castiglione, Nicoletta; Caruso, Manuela
- Biochemical Society Transactions, Vol. 39, Issue 1
Cytochrome cbb3 oxidase and bacterial microaerobic metabolism
journal, August 2002
- Pitcher, R. S.; Brittain, T.; Watmugh, N. J.
- Biochemical Society Transactions, Vol. 30, Issue 4
Identification, Functional Studies, and Genomic Comparisons of New Members of the NnrR Regulon in Rhodobacter sphaeroides
journal, February 2010
- Hartsock, Angela; Shapleigh, James P.
- Journal of Bacteriology, Vol. 192, Issue 4
Activating Transcription in Bacteria
journal, October 2012
- Lee, David J.; Minchin, Stephen D.; Busby, Stephen J. W.
- Annual Review of Microbiology, Vol. 66, Issue 1
Defining bacterial regulons using ChIP-seq
journal, September 2015
- Myers, Kevin S.; Park, Dan M.; Beauchene, Nicole A.
- Methods, Vol. 86
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000
- Kanehisa, Minoru; Goto, Susumu
- Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor
journal, February 2020
- Townsend, Guy E.; Han, Weiwei; Schwalm, Nathan D.
- mBio, Vol. 11, Issue 1
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
journal, February 2010
- Bullard, James H.; Purdom, Elizabeth; Hansen, Kasper D.
- BMC Bioinformatics, Vol. 11, Issue 1
Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping
journal, October 2020
- Lawson, Christopher E.; Nuijten, Guylaine H. L.; de Graaf, Rob M.
- The ISME Journal, Vol. 15, Issue 3
Cyclic AMP-Dependent Catabolite Repression Is the Dominant Control Mechanism of Metabolic Fluxes under Glucose Limitation in Escherichia coli
journal, April 2008
- Nanchen, Annik; Schicker, Alexander; Revelles, Olga
- Journal of Bacteriology, Vol. 190, Issue 7
Anammox bacteria: from discovery to application
journal, April 2008
- Kuenen, J. Gijs
- Nature Reviews Microbiology, Vol. 6, Issue 4
Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
journal, March 2016
- Jewell, Talia N. M.; Karaoz, Ulas; Brodie, Eoin L.
- The ISME Journal, Vol. 10, Issue 9
Identification of the CRP regulon using in vitro and in vivo transcriptional profiling
journal, October 2004
- Zheng, D.
- Nucleic Acids Research, Vol. 32, Issue 19
N-oxide sensing and denitrification: the DNR transcription factors
journal, January 2006
- Rinaldo, S.; Giardina, G.; Brunori, M.
- Biochemical Society Transactions, Vol. 34, Issue 1
Common principles and best practices for engineering microbiomes
journal, September 2019
- Lawson, Christopher E.; Harcombe, William R.; Hatzenpichler, Roland
- Nature Reviews Microbiology, Vol. 17, Issue 12
PRODORIC: prokaryotic database of gene regulation
journal, January 2003
- Munch, R.
- Nucleic Acids Research, Vol. 31, Issue 1
Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome
journal, November 2005
- Grainger, D. C.; Hurd, D.; Harrison, M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 49
Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs
journal, December 2003
- Körner, Heinz; Sofia, Heidi J.; Zumft, Walter G.
- FEMS Microbiology Reviews, Vol. 27, Issue 5
Bradyrhizobium japonicum NnrR, a Denitrification Regulator, Expands the FixLJ-FixK2 Regulatory Cascade
journal, July 2003
- Mesa, Socorro; Bedmar, Eulogio J.; Chanfon, Astrid
- Journal of Bacteriology, Vol. 185, Issue 13
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks
journal, January 2013
- Ravcheev, Dmitry A.; Godzik, Adam; Osterman, Andrei L.
- BMC Genomics, Vol. 14, Issue 1
A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
journal, July 2010
- Lucker, S.; Wagner, M.; Maixner, F.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 30
metaSPAdes: a new versatile metagenomic assembler
journal, March 2017
- Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton
- Genome Research, Vol. 27, Issue 5
Unusual Heme Binding Properties of the Dissimilative Nitrate Respiration Regulator, a Bacterial Nitric Oxide Sensor
journal, November 2012
- Rinaldo, Serena; Castiglione, Nicoletta; Giardina, Giorgio
- Antioxidants & Redox Signaling, Vol. 17, Issue 9
Characterization of two ammonia-oxidizing bacteria isolated from reactors operated with low dissolved oxygen concentrations
journal, May 2007
- Park, H. -D.; Noguera, D. R.
- Journal of Applied Microbiology, Vol. 102, Issue 5
An Anaerobic-Type α-Ketoglutarate Ferredoxin Oxidoreductase Completes the Oxidative Tricarboxylic Acid Cycle of Mycobacterium tuberculosis
journal, November 2009
- Baughn, Anthony D.; Garforth, Scott J.; Vilchèze, Catherine
- PLoS Pathogens, Vol. 5, Issue 11
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system
journal, March 2016
- Speth, Daan R.; in ’t Zandt, Michiel H.; Guerrero-Cruz, Simon
- Nature Communications, Vol. 7, Issue 1
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Strategies of Nitrosomonas europaea 19718 to counter low dissolved oxygen and high nitrite concentrations
journal, January 2010
- Yu, Ran; Chandran, Kartik
- BMC Microbiology, Vol. 10, Issue 1
Metabolic network analysis reveals microbial community interactions in anammox granules
journal, May 2017
- Lawson, Christopher E.; Wu, Sha; Bhattacharjee, Ananda S.
- Nature Communications, Vol. 8, Issue 1
The Monofunctional Glycosyltransferase of Escherichia coli Localizes to the Cell Division Site and Interacts with Penicillin-Binding Protein 3, FtsW, and FtsN
journal, March 2008
- Derouaux, Adeline; Wolf, Benoît; Fraipont, Claudine
- Journal of Bacteriology, Vol. 190, Issue 5
ProDeGe: a computational protocol for fully automated decontamination of genomes
journal, June 2015
- Tennessen, Kristin; Andersen, Evan; Clingenpeel, Scott
- The ISME Journal, Vol. 10, Issue 1
Transcriptional Regulation by cAMP and Its Receptor Protein
journal, June 1993
- Kolb, A.; Busby, S.; Buc, H.
- Annual Review of Biochemistry, Vol. 62, Issue 1
Candidatus Accumulibacter phosphatis clades enriched under cyclic anaerobic and microaerobic conditions simultaneously use different electron acceptors
journal, October 2016
- Camejo, Pamela Y.; Owen, Brian R.; Martirano, Joseph
- Water Research, Vol. 102
Reconstruction of the Core and Extended Regulons of Global Transcription Factors
journal, July 2010
- Dufour, Yann S.; Kiley, Patricia J.; Donohue, Timothy J.
- PLoS Genetics, Vol. 6, Issue 7
cAMP Receptor Protein from Escherichia coli as a Model of Signal Transduction in Proteins – A Review
journal, January 2009
- Fic, E.; Bonarek, P.; Gorecki, A.
- Journal of Molecular Microbiology and Biotechnology, Vol. 17, Issue 1
Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding
journal, June 2013
- Myers, Kevin S.; Yan, Huihuang; Ong, Irene M.
- PLoS Genetics, Vol. 9, Issue 6
Regulators of bacterial responses to nitric oxide
journal, March 2007
- Spiro, Stephen
- FEMS Microbiology Reviews, Vol. 31, Issue 2
Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014
- Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
- Nucleic Acids Research, Vol. 43, Issue D1
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
journal, July 1999
- Hertz, G. Z.; Stormo, G. D.
- Bioinformatics, Vol. 15, Issue 7
Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome
journal, November 2018
- Scarborough, Matthew J.; Lawson, Christopher E.; Hamilton, Joshua J.
- mSystems, Vol. 3, Issue 6
CooA, a paradigm for gas sensing regulatory proteins
journal, January 2005
- Roberts, G.; Kerby, R.; Youn, H.
- Journal of Inorganic Biochemistry, Vol. 99, Issue 1
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
journal, October 2012
- Kopylova, Evguenia; Noé, Laurent; Touzet, Hélène
- Bioinformatics, Vol. 28, Issue 24
Site-directed mutagenesis of NnrR: a transcriptional regulator of nitrite and nitric oxide reductase in Rhodobacter sphaeroides
journal, December 2003
- Laratta, William P.; Shapleigh, James P.
- FEMS Microbiology Letters, Vol. 229, Issue 2
The inhibition of the Anammox process: A review
journal, July 2012
- Jin, Ren-Cun; Yang, Guang-Feng; Yu, Jin-Jin
- Chemical Engineering Journal, Vol. 197
Accelerated Profile HMM Searches
journal, October 2011
- Eddy, Sean R.
- PLoS Computational Biology, Vol. 7, Issue 10
HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014
- Anders, S.; Pyl, P. T.; Huber, W.
- Bioinformatics, Vol. 31, Issue 2
Binning metagenomic contigs by coverage and composition
journal, September 2014
- Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino
- Nature Methods, Vol. 11, Issue 11
A complete domain-to-species taxonomy for Bacteria and Archaea
journal, April 2020
- Parks, Donovan H.; Chuvochina, Maria; Chaumeil, Pierre-Alain
- Nature Biotechnology
Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions
journal, September 2017
- Keene, Natalie A.; Reusser, Steve R.; Scarborough, Matthew J.
- Water Research, Vol. 121
Positive FNR-like control of anaerobic arginine degradation and nitrate respiration in Pseudomonas aeruginosa.
journal, January 1991
- Galimand, M.; Gamper, M.; Zimmermann, A.
- Journal of Bacteriology, Vol. 173, Issue 5
Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms
journal, May 2021
- Wang, Yubo; Gao, Han; Wells, George
- Environmental Microbiology, Vol. 23, Issue 6
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
Transcription activation in bacteria: ancient and modern
journal, April 2019
- Busby, Stephen J. W.
- Microbiology, Vol. 165, Issue 4
The role of Fe–S proteins in sensing and regulation in bacteria
journal, April 2003
- Kiley, Patricia J.; Beinert, Helmut
- Current Opinion in Microbiology, Vol. 6, Issue 2
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Iron-containing transcription factors and their roles as sensors
journal, April 2011
- Fleischhacker, Angela S.; Kiley, Patricia J.
- Current Opinion in Chemical Biology, Vol. 15, Issue 2
Asymmetric cross-regulation between the nitrate-responsive NarX-NarL and NarQ-NarP two-component regulatory systems from Escherichia coli K-12
journal, January 2010
- Noriega, Chris E.; Lin, Hsia-Yin; Chen, Li-Ling
- Molecular Microbiology, Vol. 75, Issue 2
The transcription of the cbb operon in Nitrosomonas europaea
journal, June 2004
- Wei, Xueming; Sayavedra-Soto, Luis A.; Arp, Daniel J.
- Microbiology, Vol. 150, Issue 6
Low-Dissolved-Oxygen Nitrifying Systems Exploit Ammonia-Oxidizing Bacteria with Unusually High Yields
journal, November 2011
- Bellucci, Micol; Ofiţeru, Irina D.; Graham, David W.
- Applied and Environmental Microbiology, Vol. 77, Issue 21
Clustering gene expression time series data using an infinite Gaussian process mixture model
journal, January 2018
- McDowell, Ian C.; Manandhar, Dinesh; Vockley, Christopher M.
- PLOS Computational Biology, Vol. 14, Issue 1
CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation
journal, August 2015
- Dangel, Andrew W.; Tabita, F. Robert
- Journal of Bacteriology, Vol. 197, Issue 22
Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons: P. aeruginosa Anr and Dnr regulon
journal, November 2009
- Trunk, Katharina; Benkert, Beatrice; Quäck, Nicole
- Environmental Microbiology, Vol. 12, Issue 6
PhyloSift: phylogenetic analysis of genomes and metagenomes
journal, January 2014
- Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric
- PeerJ, Vol. 2
Modulation of Anaerobic Energy Metabolism of Bacillus subtilis by arfM ( ywiD )
journal, December 2001
- Marino, Marco; Ramos, Hugo Cruz; Hoffmann, Tamara
- Journal of Bacteriology, Vol. 183, Issue 23
Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons
journal, December 2015
- Beauchene, Nicole A.; Myers, Kevin S.; Chung, Dongjun
- mBio, Vol. 6, Issue 6
IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins : Positive regulation of the
journal, May 2006
- Yeo, Won-Sik; Lee, Joon-Hee; Lee, Kyung-Chang
- Molecular Microbiology, Vol. 61, Issue 1
Regulation of Pseudomonas aeruginosa hemF and hemN by the dual action of the redox response regulators Anr and Dnr
journal, August 1998
- Rompf, Alexandra; Hungerer, Christoph; Hoffmann, Tamara
- Molecular Microbiology, Vol. 29, Issue 4
IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli
journal, May 2006
- Giel, Jennifer L.; Rodionov, Dmitry; Liu, Mingzhu
- Molecular Microbiology, Vol. 60, Issue 4
New Regulatory Gene That Contributes to Control of Bacteroides thetaiotaomicron Starch Utilization Genes
journal, December 2001
- Cho, Kyu Hong; Cho, Diedre; Wang, Gui-Rong
- Journal of Bacteriology, Vol. 183, Issue 24
Integrated Omic Analyses Provide Evidence that a “Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
journal, January 2019
- Camejo, Pamela Y.; Oyserman, Ben O.; McMahon, Katherine D.
- mSystems, Vol. 4, Issue 1
Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks
journal, January 2013
- Matsui, Motomu; Tomita, Masaru; Kanai, Akio
- Genome Biology and Evolution, Vol. 5, Issue 2
Effect of organic matter on the performance and N 2 O emission of a granular sludge anammox reactor
journal, January 2018
- Jia, Mingsheng; Castro-Barros, Celia M.; Winkler, Mari K. H.
- Environmental Science: Water Research & Technology, Vol. 4, Issue 7
Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster
journal, December 1998
- Kiley, Patricia J.; Beinert, Helmut
- FEMS Microbiology Reviews, Vol. 22, Issue 5
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
journal, January 2005
- Rodionov, Dmitry A.; Dubchak, Inna L.; Arkin, Adam P.
- PLoS Computational Biology, Vol. 1, Issue 5
Mode of Selectivity in Cyclic AMP Receptor Protein-Dependent Promoters in Escherichia coli
journal, January 1996
- Pyles, Erica A.; Lee, J. Ching
- Biochemistry, Vol. 35, Issue 4
Mapping genome-wide transcription-factor binding sites using DAP-seq
journal, July 2017
- Bartlett, Anna; O'Malley, Ronan C.; Huang, Shao-shan Carol
- Nature Protocols, Vol. 12, Issue 8
Evaluation of COD effect on anammox process and microbial communities in the anaerobic baffled reactor (ABR)
journal, September 2016
- Chen, Chongjun; Sun, Faqian; Zhang, Haiqing
- Bioresource Technology, Vol. 216