Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen

Fuchs, Gabriele; Stein, Adam J.; Fu, Chao; Reinisch, Karin M; Wolin, Sandra L.

doi:10.1038/nsmb1156

Cited by 67 publications

(136 citation statements)

References 30 publications

Supporting

Mentioning

132

Contrasting

Order By: Relevance

“…g447800.t1.2) that show remarkable sequence similarity to the bacterial Rsr and to the human Ro 60-kD autoantigen but are not predicted to be targeted to the chloroplast (Stein et al, 2005) (Supplemental Data Set 4 and Supplemental Figure 4F). Intriguingly, both in bacteria and in humans, these proteins are known to act as cofactors to increase the association of exonucleases with misfolded RNA substrates during stress (Chen et al, 2005;Stein et al, 2005;Fuchs et al, 2006;Wolin and Wurtmann, 2006). We found that the Cre17.g725750.t1.1 transcript is also upregulated under high light (Supplemental Figure 4F).…”

Section: Depletion Of Clpp Affects Chloroplast and Cytosolic Rna Metamentioning

confidence: 52%

Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

et al. 2014

View full text Add to dashboard Cite

Plastid protein homeostasis is critical during chloroplast biogenesis and responses to changes in environmental conditions. Proteases and molecular chaperones involved in plastid protein quality control are encoded by the nucleus except for the catalytic subunit of ClpP, an evolutionarily conserved serine protease. Unlike its Escherichia coli ortholog, this chloroplast protease is essential for cell viability. To study its function, we used a recently developed system of repressible chloroplast gene expression in the alga Chlamydomonas reinhardtii. Using this repressible system, we have shown that a selective gradual depletion of ClpP leads to alteration of chloroplast morphology, causes formation of vesicles, and induces extensive cytoplasmic vacuolization that is reminiscent of autophagy. Analysis of the transcriptome and proteome during ClpP depletion revealed a set of proteins that are more abundant at the protein level, but not at the RNA level. These proteins may comprise some of the ClpP substrates. Moreover, the specific increase in accumulation, both at the RNA and protein level, of small heat shock proteins, chaperones, proteases, and proteins involved in thylakoid maintenance upon perturbation of plastid protein homeostasis suggests the existence of a chloroplast-to-nucleus signaling pathway involved in organelle quality control. We suggest that this represents a chloroplast unfolded protein response that is conceptually similar to that observed in the endoplasmic reticulum and in mitochondria.

show abstract

Section: Depletion Of Clpp Affects Chloroplast and Cytosolic Rna Metamentioning

confidence: 52%

Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

et al. 2014

View full text Add to dashboard Cite

show abstract

“…2B). Given the presence of at least 2 functionally important and distinct RNA binding surfaces, which can be filled simultaneously (8,53), Hfq is qualitatively similar to the small RNA quality control protein Ro, which also uses separate surfaces to bind its multiple RNA ligands (54). (A-R-N-N ) Tracts.…”

Section: Resultsmentioning

confidence: 99%

Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

Link

Valentin‐Hansen

Brennan

2009

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

321

451

View full text Add to dashboard Cite

show abstract

“…RNA ends have also been found to be recognition elements for other proteins involved in noncoding RNA processing and/or surveillance, including T455 I175 S176 V374 I377 D177 N371 I366 E378 D367 D365 R360 T363 P359 H358 E381 N386 K444 R441 M357 Y403 V402 F404 G388 V392 L382 F354 D391 D390 L394 I308 V146 I144 Y143 A142 R141 W140 R135 I139 L198 N197 F193 S191 N197 the eukaryotic proteins La and Ro (19,20), which both bind nascent transcripts, as well as the bacterial RNase T and RNase R (21,22). Sequences at the 3′ end may be one mechanism for recognizing such transcripts.…”

Section: N-terminal Zinc Knuckle Of Air2p Modulates Trf4p Activity Onmentioning

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.

View full text Add to dashboard Cite

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.

show abstract

Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen

Cited by 67 publications

References 30 publications

Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control

Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

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

Contact Info

Product

Resources

About