Domain architectures of σ54-dependent transcriptional activators
David J. Studholme,Ray Dixon +1 more
Reads0
Chats0
TLDR
The σ54 subunit is a unique sigma subunit required for promoter recognition and initiation of transcription by the bacterial RNAP that resembles the enhancer-binding proteins (EBPs) found in eukaryotic systems, and for this reason such activators are known as bacterial EBPs.Abstract:
Transcription is the key control point for regulation of numerous cellular activities. Bacteria regulate levels of gene expression by using transcription factors that modulate the recruitment of RNA polymerase (RNAP) to promoter elements in the DNA. Many bacteria also control gene expression by using a second class of transcription factor that uses energy from nucleotide hydrolysis to actively promote transcription initiation.
The sigma (σ) subunit is required for promoter recognition and initiation of transcription by the bacterial RNAP. Typically a bacterial cell may contain several alternative σ subunits with differing sequence specificities that direct the RNAP holoenzyme to different sets of promoters. The σ54 subunit (also known as RpoN, NtrA, and σN) is unique (42) in that it shares no detectable homology with any of the other known sigma factors (e.g., σ70 and σ28). σ54-RNAP binds to specific promoter sites, with the consensus DNA sequence YTGGCACGrNNNTTGCW (6), to form a transcriptionally inactive closed complex consisting of holoenzyme bound to double-stranded DNA. In contrast to σ70-RNAP bound at its cognate promoter sites, σ54-RNAP is unable to spontaneously isomerize from a closed complex to a transcriptionally competent open complex (11, 72). To proceed with initiation of transcription, the closed complex must participate in an interaction with a transcriptional activator, involving nucleotide hydrolysis. This transcriptional activator is usually bound at least 100 bp upstream of the promoter site, and DNA looping is required for the activator to contact the closed complex and catalyze formation of the open promoter complex. In this respect the activator resembles the enhancer-binding proteins (EBPs) found in eukaryotic systems, and for this reason such activators are known as bacterial EBPs.
From a protein structural point of view, EBPs share in common a σ54 interaction module (Pfam accession number PF00158) but typically have at least one additional domain (Fig. (Fig.1).1). In nearly all of those investigated so far, there is a DNA-binding domain containing a helix-turn-helix sequence motif, enabling the protein to bind to specific DNA enhancer elements upstream of σ54-dependent promoters (44, 47, 52, 56, 72). One exception to this scenario was recently reported (30), where Pseudomonas aeruginosa FleQ can activate transcription while bound in the downstream vicinity of the promoter.
FIG. 1.
Major domain architectures of bacterial EBPs. Examples of each of the known domain organizations found in bacterial EBPs are given. Sequences are identified by SwissProt/trEMBL accession numbers, except for XAC3643, TTE0180, and {"type":"entrez-protein","attrs":{"text":"CPE23358","term_id":"896862659","term_text":"CPE23358"}} ...
Although the physiological advantages conferred by the σ54-EBP mode of transcription are not yet clear, activation of σ54-dependent transcription is highly regulated by environmental cues through regulatory modules in the EBPs and in some cases by interactions with other regulatory proteins. Sensory modules in EBPs include CheY-like response regulator domains, PAS domains, GAF domains, PRD modules, and V4R domains, often represented within an N-terminal region (Fig. (Fig.1).1). These sequence features are described in more detail later in this article. Intriguingly, recent complete genome sequences have revealed some unusual EBPs containing regions of homology to other signal transduction domains and enzymes. With the large number of complete bacterial genomes now available, and with the importance of accurate annotation of future sequence data, we feel that it is timely to survey the variety of domain architectures found in these important proteins.read more
Citations
More filters
Journal ArticleDOI
How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria
TL;DR: The known protein phosphorylation-related regulatory functions of the PTS are summarized, which shows that the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
Journal ArticleDOI
Genetic regulation of biological nitrogen fixation
Ray Dixon,Daniel Kahn +1 more
TL;DR: The ability of microorganisms to use nitrogen gas as the sole nitrogen source and engage in symbioses with host plants confers many ecological advantages, but also incurs physiological penalties because the process is oxygen sensitive and energy dependent.
Journal ArticleDOI
Evolution of sensory complexity recorded in a myxobacterial genome
Barry S. Goldman,William C. Nierman,William C. Nierman,Dale Kaiser,Steven C. Slater,Steven C. Slater,Anthony S. Durkin,Jonathan A. Eisen,Catherine M. Ronning,W. B. Barbazuk,M. Blanchard,C. Field,Conrad Halling,Gregory Hinkle,O. Iartchuk,H. S. Kim,Chris Mackenzie,Ramana Madupu,Nancy M. Miller,Alla Shvartsbeyn,Steven A. Sullivan,Mark Vaudin,Roger C. Wiegand,Heidi B. Kaplan +23 more
TL;DR: It is suggested that gene duplication and divergence were major contributors to genomic expansion from its progenitor, and families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.
Journal ArticleDOI
The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription
Matthew J. Bush,Ray Dixon +1 more
TL;DR: A comprehensive and detailed summary of recent advances in understanding of how bacterial enhancer binding proteins function is presented, paying particular attention to the importance of σ54 to the bacterial cell and its unique role in regulating transcription.
Journal ArticleDOI
A non-haem iron centre in the transcription factor NorR senses nitric oxide
TL;DR: The mechanism of NorR reveals an unprecedented biological role for a non-haem mononitrosyl–iron complex in NO sensing, and contains a mononuclear non- haem iron centre, which reversibly binds NO.
References
More filters
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
The Complete Genome Sequence of Escherichia coli K-12
Frederick R. Blattner,Guy Plunkett,Craig A. Bloch,Nicole T. Perna,Valerie Burland,Monica Riley,Julio Collado-Vides,Jeremy D. Glasner,Christopher K. Rode,George F. Mayhew,Jason Gregor,Nelson Wayne Davis,Heather A. Kirkpatrick,Michael A. Goeden,Debra J. Rose,Bob Mau,Ying Shao +16 more
TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Journal ArticleDOI
The complete genome sequence of the gastric pathogen Helicobacter pylori
Jean-F. Tomb,Owen White,Anthony R. Kerlavage,Rebecca A. Clayton,Granger G. Sutton,Robert D. Fleischmann,Karen A. Ketchum,Hans-Peter Klenk,Steven R. Gill,Brian Dougherty,Karen E. Nelson,John Quackenbush,Lixin Zhou,Ewen F. Kirkness,Scott N. Peterson,Brendan J. Loftus,Delwood Richardson,Robert J. Dodson,Hanif Khalak,Anna Glodek,Keith McKenney,Lisa M. Fitzegerald,Norman H. Lee,Mark Raymond Adams,Erin Hickey,Douglas E. Berg,Jeanine D. Gocayne,Teresa Utterback,Jeremy Peterson,Jenny M. Kelley,Matthew D. Cotton,J. Weidman,Claire Fujii,Cheryl Bowman,Larry Watthey,Erik Wallin,William S. Hayes,Mark Borodovsky,Peter D. Karp,Hamilton O. Smith,Claire M. Fraser,J. Craig Venter +41 more
TL;DR: Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification, and consistent with its restricted niche, it has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity.
Journal ArticleDOI
Two-component signal transduction
TL;DR: Detailed analyses of a relatively small number of representative proteins provide a foundation for understanding this large family of signaling proteins, which consists of two conserved components, a histidine protein kinase and a response regulator protein.
Journal ArticleDOI
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
Alm Richard A,Lo-See L. Ling,Donald T. Moir,Benjamin L. King,Eric D. Brown,Peter Doig,Douglas R. Smith,Brian Noonan,Braydon C. Guild,Boudewijn L. deJonge,Gilles Carmel,Peter J. Tummino,Anthony Caruso,Maria Uria-Nickelsen,Debra M. Mills,Cameron Ives,Rene Gibson,David Merberg,Scott D. Mills,Qin Jiang,Diane E. Taylor,Gerald F. Vovis,Trevor J. Trust +22 more
TL;DR: The overall genomic organization, gene order and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite similar, and it is found that H. pylori was believed to exhibit a large degree of genomic and allelic diversity, but this is the first such genomic comparison.