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The mechanism for RNA recognition by ANTAR regulators of gene expression.

Ramesh A, DebRoy S, Goodson JR, Fox KA, Faz H, Garsin DA, Winkler WC - PLoS Genet. (2012)

Bottom Line: The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination.Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management.These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.

ABSTRACT
ANTAR proteins are widespread bacterial regulatory proteins that have RNA-binding output domains and utilize antitermination to control gene expression at the post-initiation level. An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. Using this system, we present genetic and biochemical evidence of a general mechanism of antitermination used by ANTARs, including details of the antiterminator structure. The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination. The ANTAR protein dimerizes and associates with its substrate RNA in response to signal-induced phosphorylation. Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management. These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism.

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Distribution of ANTAR-containing proteins according to their domain organization (Pfam: PF03861).The bar graph shows the number of ANTAR proteins for each of 17 domain architectures that have been identified. The latter are schematically represented to the right of the bar graph.
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pgen-1002666-g001: Distribution of ANTAR-containing proteins according to their domain organization (Pfam: PF03861).The bar graph shows the number of ANTAR proteins for each of 17 domain architectures that have been identified. The latter are schematically represented to the right of the bar graph.

Mentions: Another important family of proteins with putative RNA-binding activity contains the AmiR and NasR Transcriptional Antiterminator Regulator domain (ANTAR) [4]. The ANTAR domain is composed of three helices with five strictly conserved residues (three alanines, one alanine/serine and one aromatic residue) that are exposed in the three-helical structure [5]. Sequence homology based searches have predicted more than 1100 occurrences of the ANTAR domain, widely distributed across at least 644 bacterial species (Figure 1; http://pfam.sanger.ac.uk/; Pfam: PF03861). ANTAR-containing proteins typically occur as multi-domain proteins. A significant class of ANTAR proteins appear to possess an N-terminal domain that resembles a pseudo-receiver domain capable of protein-protein interactions [5]. This class of proteins may therefore regulate gene-expression via interactions with a modulator protein, which itself may possess signal-sensing function. For example, the ANTAR protein AmiR from Pseudomonas aeruginosa dimerizes upon binding two molecules of its negative regulator AmiC. Under inducing conditions AmiC binds a small amide compound, allowing association of AmiR with the 5′ leader of the appropriate target mRNA. This has been hypothesized to prevent formation of an intrinsic terminator. However, the molecular mechanism of antitermination, including the AmiR RNA recognition determinants, has yet to be revealed [6]–[7].


The mechanism for RNA recognition by ANTAR regulators of gene expression.

Ramesh A, DebRoy S, Goodson JR, Fox KA, Faz H, Garsin DA, Winkler WC - PLoS Genet. (2012)

Distribution of ANTAR-containing proteins according to their domain organization (Pfam: PF03861).The bar graph shows the number of ANTAR proteins for each of 17 domain architectures that have been identified. The latter are schematically represented to the right of the bar graph.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369931&req=5

pgen-1002666-g001: Distribution of ANTAR-containing proteins according to their domain organization (Pfam: PF03861).The bar graph shows the number of ANTAR proteins for each of 17 domain architectures that have been identified. The latter are schematically represented to the right of the bar graph.
Mentions: Another important family of proteins with putative RNA-binding activity contains the AmiR and NasR Transcriptional Antiterminator Regulator domain (ANTAR) [4]. The ANTAR domain is composed of three helices with five strictly conserved residues (three alanines, one alanine/serine and one aromatic residue) that are exposed in the three-helical structure [5]. Sequence homology based searches have predicted more than 1100 occurrences of the ANTAR domain, widely distributed across at least 644 bacterial species (Figure 1; http://pfam.sanger.ac.uk/; Pfam: PF03861). ANTAR-containing proteins typically occur as multi-domain proteins. A significant class of ANTAR proteins appear to possess an N-terminal domain that resembles a pseudo-receiver domain capable of protein-protein interactions [5]. This class of proteins may therefore regulate gene-expression via interactions with a modulator protein, which itself may possess signal-sensing function. For example, the ANTAR protein AmiR from Pseudomonas aeruginosa dimerizes upon binding two molecules of its negative regulator AmiC. Under inducing conditions AmiC binds a small amide compound, allowing association of AmiR with the 5′ leader of the appropriate target mRNA. This has been hypothesized to prevent formation of an intrinsic terminator. However, the molecular mechanism of antitermination, including the AmiR RNA recognition determinants, has yet to be revealed [6]–[7].

Bottom Line: The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination.Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management.These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.

ABSTRACT
ANTAR proteins are widespread bacterial regulatory proteins that have RNA-binding output domains and utilize antitermination to control gene expression at the post-initiation level. An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. Using this system, we present genetic and biochemical evidence of a general mechanism of antitermination used by ANTARs, including details of the antiterminator structure. The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination. The ANTAR protein dimerizes and associates with its substrate RNA in response to signal-induced phosphorylation. Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management. These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism.

Show MeSH