Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand

Williams‐Carrier, Rosalind; Kroeger, Tiffany; Barkan, Alice

doi:10.1261/rna.1077708

Cited by 101 publications

(108 citation statements)

References 38 publications

(65 reference statements)

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“…Several PPR proteins have been shown to bind specifically in vitro to their genetically defined RNA targets (17,20,(35)(36)(37). Although structures are not available for PPR/RNA complexes, current data support a modular 1-repeat 1 nucleotide recognition mechanism that is reminiscent of the Puf/RNA interaction (18,38).…”

Section: Discussionmentioning

confidence: 84%

“…The product was digested with Sal I and Bam HI and cloned into pMAL-TEV. maltose binding protein-HCF107 was expressed in E. coli, purified by amylose affinity chromatography, and cleaved with TEV protease, and the untagged protein was then purified on a gel filtration column as described previously for PPR5 (36), except that the lysis and dialysis buffers contained 400 mM NaCl and did not include CHAPS detergent.…”

Section: Methodsmentioning

confidence: 99%

“…The 31-mers used to test sequence nonspecific binding to various nucleic acid forms (Fig. 1A) were of the same sequence and prepared in the same manner as those used previously (36). The nonspecific oligonucleotide used in Fig.…”

Section: Methodsmentioning

confidence: 99%

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RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression

Hammani

Cook

Barkan

2012

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

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The half-a-tetratricopeptide repeat (HAT) motif is a helical repeat motif found in proteins that influence various aspects of RNA metabolism, including rRNA biogenesis, RNA splicing, and polyadenylation. This functional association with RNA suggested that HAT repeat tracts might bind RNA. However, RNA binding activity has not been reported for any HAT repeat tract, and recent literature has emphasized a protein binding role. In this study, we show that a chloroplast-localized HAT protein, HCF107, is a sequence-specific RNA binding protein. HCF107 consists of 11 tandem HAT repeats and short flanking regions that are also predicted to form helical hairpins. The minimal HCF107 binding site spans ∼11 nt, consistent with the possibility that HAT repeats bind RNA through a modular one repeat-1 nt mechanism. Binding of HCF107 to its native RNA ligand in the psbH 5′ UTR remodels local RNA structure and protects the adjacent RNA from exonucleases in vitro. These activities can account for the RNA stabilizing, RNA processing, and translational activation functions attributed to HCF107 based on genetic data. We suggest that analogous activities contribute to the functions of HAT domains found in ribonucleoprotein complexes in the nuclear-cytosolic compartment.helical repeat protein | plastid | pentatricopeptide repeat T he half-a-tetratricopeptide (HAT) motif is a helical repeat motif that has been functionally linked to RNA because of its presence exclusively in complexes that influence RNA metabolism (1). Examples of HAT domain proteins include Utp6, which is involved in nuclear pre-rRNA processing, Prp6, which is involved in nuclear pre-mRNA splicing, and CstF-77, which is involved in pre-mRNA cleavage and polyadenylation. The HAT motif is related to the tetratricopeptide repeat (TPR), a degenerate 34-aa motif that forms a pair of antiparallel α-helices (reviewed in ref.2). TPR motifs are typically found in tandem arrays, which stack to form a broad surface that binds protein ligands. Crystal structures of CstF-77 confirmed that HAT repeat tracts adopt a TPR-like structure (3, 4). The possibility that HAT repeat tracts might bind RNA has been suggested (1, 5-7), but the notion that HAT repeat tracts serve as a scaffold for binding other proteins dominates recent literature (3,(8)(9)(10)). This view is reflected by the annotation of the HAT motif at InterPro, which states only that "the repeats may be involved in protein-protein interactions" (http://www.ebi. ac.uk/interpro/IEntry?ac=IPR003107).Although TPR, HEAT, and several other helical repeat motifs form protein binding surfaces, similar structures have been shown to bind nucleic acids. Puf and pentatricopeptide repeat (PPR) motifs have been shown to bind RNA (reviewed in refs. 11 and 12), and mTERF, ALK, and TAL repeat motifs have been shown to bind DNA (reviewed in refs. 13 and 14). Thus, it seemed quite plausible that the presence of HAT domains exclusively in ribonucleoprotein complexes reflects the fact that HAT repeat tracts interact directly with RNA. In this ...

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Section: Discussionmentioning

confidence: 84%

Section: Methodsmentioning

confidence: 99%

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RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression

Hammani

Cook

Barkan

2012

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

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“…The only positive patch is found in the base of the PPR domain closest to the active site, including side chains from the interior-facing helices and connecting loops. The PPR domain could interact directly with pre-tRNA through contacts between this positive patch and the negative phosphodiester backbone, recognition of the tertiary fold of tRNA, and/or interactions with conserved nucleobases of tRNA, as proposed for other PPR domains (16).…”

Section: Resultsmentioning

confidence: 95%

Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5′ processing

Howard¹,

Lim²,

Fierke

et al. 2012

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

110

235

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Ribonuclease P (RNase P) catalyzes the maturation of the 5′ end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.catalytic mechanism | magnesium | molecular recognition A ccording to the RNA world hypothesis, RNA played dual roles as carrier of genetic information and catalyst in a prebiotic world. However, over eons of evolution, proteins with their expanded 20-aa alphabet and greater structural and functional complexity took over many RNA-based functions. Structural insights into this evolutionary transition are limited because of the lack of examples of RNA and protein macromolecules that perform the same biological function in nature. One notable exception is ribonuclease P (RNase P) that catalyzes maturation of the 5′ end of tRNA across all domains of life. Until recently, all known RNase P enzymes included a catalytic RNA component. The discovery of a protein-only RNase P [proteinacous RNase P (PRORP)] from human mitochondria and Arabidopsis thaliana has dramatically shifted this paradigm (1-3). These enzymes represent a unique class of metallonucleases and are conserved among many eukaroytes (1, 2). A. thaliana encodes three PRORP enzymes (PRORP1, -2, and -3) that catalyze pretRNA processing (2). PRORP1 localizes to the mitochondria and chloroplast whereas PRORP2 and PRORP3 localize to the nucleus (2), suggesting that protein-based enzymes catalyze pretRNA maturation in these cellular locations (2, 3). To gain mechanistic and evolutionary insights into the PRORP...

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“…19,20 PPR tracks organize highly specific interaction domains, which preferentially associate with single-stranded RNAs. 21 Functional characterization of Arabidopsis (Arabidopsis thaliana), maize (Zea mays), rice (Oryza sativa), and Physcomitrella patens mutants has revealed the plethoric roles played by PPR proteins in organellar gene expression. These proteins were shown to participate in most RNA processing and expression steps including gene transcription, RNA stabilization, 5' and 3' RNA cleavage, intron splicing, RNA editing, and mRNA translation.…”

Section: Rf-ppr Genes Impede Specifically the Expression Or The Accummentioning

confidence: 99%

The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes

Dahan¹,

Mireau²

2013

RNA Biology

125

110

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Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand

Cited by 101 publications

References 38 publications

RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression

RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression

Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5′ processing

The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes

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