Determinants of substrate specificity in RNA-dependent nucleotidyl transferases

Martín, Georges; Doublié, Sylvie; Keller, Walter

doi:10.1016/j.bbagrm.2007.12.003

Cited by 22 publications

(21 citation statements)

References 70 publications

(126 reference statements)

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“…It should be noted that CCA transferase (CCAtr) activity in several organisms such as Synechocystis sp., Deinococcus radiodurans and Aquifex aeolicus is split between two enzymes, one that adds -CC and the other that adds a terminal -A (Tomita and Weiner, 2002). Although it is difficult to assign an activity to a Class II NTR based on primary sequence, several informatic and experimental approaches (Betat et al, 2004;Cho et al, 2007;Martin and Keller, 2007;Martin et al, 2008) identified Glu193 in Bacillus stearothermophilus as a residue in the PAP domain that allows discrimination between CCAtrs and PAPs. In CCAtrs this residue is Glu, but is variable in other family members.…”

Section: Resultsmentioning

confidence: 99%

Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase

et al. 2009

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SUMMARYThe polyadenylation-stimulated RNA degradation pathway takes place in plant and algal organelles, yet the identities of the enzymes that catalyze the addition of the tails remain to be clarified. In a search for the enzymes responsible for adding poly(A) tails in Chlamydomonas and Arabidopsis organelles, reverse genetic and biochemical approaches were employed. The involvement of candidate enzymes including members of the nucleotidyltransferase (Ntr) family and polynucleotide phosphorylase (PNPase) was examined. For several of the analyzed nuclear-encoded proteins, mitochondrial localization was established and possible dual targeting to mitochondria and chloroplasts could be predicted. We found that certain members of the Ntr family, when expressed in bacteria, displayed poly(A) polymerase (PAP) activity and partially complemented an Escherichia coli strain lacking the endogenous PAP1 enzyme. Other Ntr proteins appeared to be specific for tRNA maturation. When the expression of PNPase was down-regulated by RNAi in Chlamydomonas, very few poly(A) tails were detected in chloroplasts for the atpB transcript, suggesting that this enzyme may be solely responsible for chloroplast polyadenylation activity in this species. Depletion of PNPase did not affect the number or sequence of mitochondrial mRNA poly(A) tails, where unexpectedly we found, in addition to polyadenylation, poly(U)-rich tails. Together, our results identify several Ntr-PAPs and PNPase in organelle polyadenylation, and reveal novel poly(U)-rich sequences in Chlamydomonas mitochondria.

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Section: Resultsmentioning

confidence: 99%

Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase

et al. 2009

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“…The sidewalls of the cleft are lined by the β-sheet of the catalytic domain and by helices α5-α6 of the central domain, whereas helix α4 lines the bottom. The cleft harbors the active site: Strands β2 and β5 of the catalytic domain provide the three conserved aspartic acids that mediate the chemical reaction characteristic of nucleotidyl transferases (25,35) (Fig. 2A).…”

Section: Resultsmentioning

confidence: 99%

Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3

Nakel

Bonneau

Eckmann

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The Caenorhabditis elegans germ-line development defective (GLD)-2–GLD-3 complex up-regulates the expression of genes required for meiotic progression. GLD-2–GLD-3 acts by extending the short poly(A) tail of germ-line–specific mRNAs, switching them from a dormant state into a translationally active state. GLD-2 is a cytoplasmic noncanonical poly(A) polymerase that lacks the RNA-binding domain typical of the canonical nuclear poly(A)-polymerase Pap1. The activity of C. elegans GLD-2 in vivo and in vitro depends on its association with the multi-K homology (KH) domain-containing protein, GLD-3, a homolog of Bicaudal-C. We have identified a minimal polyadenylation complex that includes the conserved nucleotidyl-transferase core of GLD-2 and the N-terminal domain of GLD-3, and determined its structure at 2.3-Å resolution. The structure shows that the N-terminal domain of GLD-3 does not fold into the predicted KH domain but wraps around the catalytic domain of GLD-2. The picture that emerges from the structural and biochemical data are that GLD-3 activates GLD-2 both indirectly by stabilizing the enzyme and directly by contributing positively charged residues near the RNA-binding cleft. The RNA-binding cleft of GLD-2 has distinct structural features compared with the poly(A)-polymerases Pap1 and Trf4. Consistently, GLD-2 has distinct biochemical properties: It displays unusual specificity in vitro for single-stranded RNAs with at least one adenosine at the 3′ end. GLD-2 thus appears to have evolved specialized nucleotidyl-transferase properties that match the 3′ end features of dormant cytoplasmic mRNAs.

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“…Trf4p/5p belongs to a family of ribonucleotide transferases in the Pol ß superfamily of nucleotidyl transferases (10,11). It consists of N-and C-terminal sequences that have little predicted secondary structure, a catalytic domain similar in sequence to several Pol ß members with known structures, and an adjacent "central domain," which shares a short nucleotide recognition motif hx(I/L/V)(E/Q)(E/D/N)PhxxxxNxx (h, hydrophobic; x, any residue) with so-called noncanonical Pol β RNA polymerases.…”

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confidence: 99%

Structure and function of the polymerase core of TRAMP, a RNA surveillance complex

Hamill¹,

Wolin

Reinisch³

2010

Proc. Natl. Acad. Sci. U.S.A.

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The Trf4p/Air2p/Mtr4p polyadenylation (TRAMP) complex recognizes aberrant RNAs in Saccharomyces cerevisiae and targets them for degradation. A TRAMP subcomplex consisting of a noncanonical poly(A) RNA polymerase in the Pol ß superfamily of nucleotidyl transferases, Trf4p, and a zinc knuckle protein, Air2p, mediates initial substrate recognition. Trf4p and related eukaryotic poly(A) and poly(U) polymerases differ from other characterized enzymes in the Pol ß superfamily both in sequence and in the lack of recognizable nucleic acid binding motifs. Here we report, at 2.7-Å resolution, the structure of Trf4p in complex with a fragment of Air2p comprising two zinc knuckle motifs. Trf4p consists of a catalytic and central domain similar in fold to those of other noncanonical Pol β RNA polymerases, and the two zinc knuckle motifs of Air2p interact with the Trf4p central domain. The interaction surface on Trf4p is highly conserved across eukaryotes, providing evidence that the Trf4p/Air2p complex is conserved in higher eukaryotes as well as in yeast and that the TRAMP complex may also function in RNA surveillance in higher eukaryotes. We show that Air2p, and in particular sequences encompassing a zinc knuckle motif near its N terminus, modulate Trf4p activity, and we present data supporting a role for this zinc knuckle in RNA binding. Finally, we show that the RNA 3′ end plays a role in substrate recognition.protein-RNA interactions | RNA quality control T he vast majority of transcripts from eukaryotic genomes do not encode proteins. These transcripts include precursors to noncoding RNAs, such as transfer and ribosomal RNAs, small nuclear and nucleolar RNAs, microRNAs, siRNAs, and piRNAs. These noncoding RNAs often fold into intricate three-dimensional structures that are critical for subsequent processing and for assembling with proteins to form ribonucleoprotein complexes. In addition, genomic sequencing experiments in both yeast and mammals have revealed the existence of a large number of short-lived noncoding transcripts that initiate near RNA polymerase II promoters.

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Determinants of substrate specificity in RNA-dependent nucleotidyl transferases

Cited by 22 publications

References 70 publications

Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase

Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase

Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3

Structure and function of the polymerase core of TRAMP, a RNA surveillance complex

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