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Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay.

Kolesnikova O, Back R, Graille M, Séraphin B - Nucleic Acids Res. (2013)

Bottom Line: In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA).We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein.This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum.

View Article: PubMed Central - PubMed

Affiliation: Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France, Ecole Polytechnique, Laboratoire de Biochimie, CNRS UMR7654, 91128 Palaiseau Cedex, France and Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), CNRS, UMR8619, Bat 430, Université Paris Sud, 91405 Orsay Cedex, France.

ABSTRACT
In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA). We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein. This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum. Functional analyses indicate that the ability of Edc3 to interact with Rps28 is not required for its general function and for its role in the regulation of the YRA1 pre-mRNA decay. In contrast, this interaction appears to be exclusively required for the auto-regulatory mechanism controlling the RPS28B mRNA decay. These observations suggest a plausible model for the evolutionary appearance of a Rps28 binding motif in Edc3.

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Related in: MedlinePlus

Localization of a new conserved motif in yeast Edc3 protein. Upper part: Domain architecture of Saccharomycetaceae Edc3 protein composed of an Lsm domain, a FDF motif and an YjeF-N domain. Numbers above the schematic representation of the protein indicate the amino acid positions of domain boundaries for the S. cerevisiae protein. Lower part: Amino acid alignment of Edc3 proteins from several Saccharomycetaceae species encompassing the RB motif. The RB motif is often preceded by an acidic region that is not absolutely conserved.
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gkt607-F1: Localization of a new conserved motif in yeast Edc3 protein. Upper part: Domain architecture of Saccharomycetaceae Edc3 protein composed of an Lsm domain, a FDF motif and an YjeF-N domain. Numbers above the schematic representation of the protein indicate the amino acid positions of domain boundaries for the S. cerevisiae protein. Lower part: Amino acid alignment of Edc3 proteins from several Saccharomycetaceae species encompassing the RB motif. The RB motif is often preceded by an acidic region that is not absolutely conserved.

Mentions: Amino acid sequence of Edc3 from different species (S.cerevisiae, Human, Mouse and Drosophila) were reported to share significant conservation (25). This early analysis was improved with the identification of three conserved motifs and domains: Lsm, FDF and YjeF-N. The availability of additional putative Edc3 sequences deduced from genome-sequencing projects lead us to perform new Edc3 sequence alignments. Although confirming the conservation of the Lsm domain, FDF motif and YjeF-N domain, those revealed the presence of a conserved region located between the FDF motif and the YjeF-N domain in Edc3 proteins from various Saccharomycetaceae species, but not from the other subdivisions of the Saccharomycetales phylum or more divergent species (Figure 1). This correlated with the previous report of the presence of a conserved hairpin in the 3′ UTR of the RPS28B mRNA in the former group of organisms (19). This additional conserved region of Edc3, which corresponds to amino acids 209–222 of the S.cerevisiae protein, is hereafter referred to as the RB motif (for Rps28 binding motif). The presence of this motif in a specific subset of Edc3 proteins suggested that it could be involved in the auto-regulatory feedback loop that controls the stability of the RPS28B mRNA, for example by mediating interaction with Rps28 or facilitating interaction of the latter with the hairpin structure present in the RPS28B mRNA 3′ UTR.Figure 1.


Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay.

Kolesnikova O, Back R, Graille M, Séraphin B - Nucleic Acids Res. (2013)

Localization of a new conserved motif in yeast Edc3 protein. Upper part: Domain architecture of Saccharomycetaceae Edc3 protein composed of an Lsm domain, a FDF motif and an YjeF-N domain. Numbers above the schematic representation of the protein indicate the amino acid positions of domain boundaries for the S. cerevisiae protein. Lower part: Amino acid alignment of Edc3 proteins from several Saccharomycetaceae species encompassing the RB motif. The RB motif is often preceded by an acidic region that is not absolutely conserved.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814365&req=5

gkt607-F1: Localization of a new conserved motif in yeast Edc3 protein. Upper part: Domain architecture of Saccharomycetaceae Edc3 protein composed of an Lsm domain, a FDF motif and an YjeF-N domain. Numbers above the schematic representation of the protein indicate the amino acid positions of domain boundaries for the S. cerevisiae protein. Lower part: Amino acid alignment of Edc3 proteins from several Saccharomycetaceae species encompassing the RB motif. The RB motif is often preceded by an acidic region that is not absolutely conserved.
Mentions: Amino acid sequence of Edc3 from different species (S.cerevisiae, Human, Mouse and Drosophila) were reported to share significant conservation (25). This early analysis was improved with the identification of three conserved motifs and domains: Lsm, FDF and YjeF-N. The availability of additional putative Edc3 sequences deduced from genome-sequencing projects lead us to perform new Edc3 sequence alignments. Although confirming the conservation of the Lsm domain, FDF motif and YjeF-N domain, those revealed the presence of a conserved region located between the FDF motif and the YjeF-N domain in Edc3 proteins from various Saccharomycetaceae species, but not from the other subdivisions of the Saccharomycetales phylum or more divergent species (Figure 1). This correlated with the previous report of the presence of a conserved hairpin in the 3′ UTR of the RPS28B mRNA in the former group of organisms (19). This additional conserved region of Edc3, which corresponds to amino acids 209–222 of the S.cerevisiae protein, is hereafter referred to as the RB motif (for Rps28 binding motif). The presence of this motif in a specific subset of Edc3 proteins suggested that it could be involved in the auto-regulatory feedback loop that controls the stability of the RPS28B mRNA, for example by mediating interaction with Rps28 or facilitating interaction of the latter with the hairpin structure present in the RPS28B mRNA 3′ UTR.Figure 1.

Bottom Line: In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA).We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein.This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum.

View Article: PubMed Central - PubMed

Affiliation: Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France, Ecole Polytechnique, Laboratoire de Biochimie, CNRS UMR7654, 91128 Palaiseau Cedex, France and Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), CNRS, UMR8619, Bat 430, Université Paris Sud, 91405 Orsay Cedex, France.

ABSTRACT
In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA). We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein. This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum. Functional analyses indicate that the ability of Edc3 to interact with Rps28 is not required for its general function and for its role in the regulation of the YRA1 pre-mRNA decay. In contrast, this interaction appears to be exclusively required for the auto-regulatory mechanism controlling the RPS28B mRNA decay. These observations suggest a plausible model for the evolutionary appearance of a Rps28 binding motif in Edc3.

Show MeSH
Related in: MedlinePlus