Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA

Abstract Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5′-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNAPhe at 2.85 Å resolution. The PPR domain of PRORP1 bound to the structurally conserved elbow of tRNA and recognized conserved structural features of tRNAs using mechanisms that are different from the established single-stranded RNA recognition mode of PPR motifs. The PRORP1 PPR domain-tRNAPhe structure revealed a conformational change of the PPR domain upon tRNA binding and moreover demonstrated the need for pronounced overall flexibility in the PRORP1 enzyme conformation for substrate recognition and catalysis. The PRORP1 PPR motifs have evolved strategies for protein-tRNA interaction analogous to tRNA recognition by the RNA component of ribonucleoprotein RNase P and other catalytic RNAs, indicating convergence on a common solution for tRNA substrate recognition.

Download Full-text

Partial characterization of an RNA component that copurifies with Saccharomyces cerevisiae RNase P

Molecular and Cellular Biology ◽

10.1128/mcb.9.6.2536-2543.1989 ◽

1989 ◽

Vol 9 (6) ◽

pp. 2536-2543

Author(s):

J Y Lee ◽

D R Engelke

Keyword(s):

Saccharomyces Cerevisiae ◽

Secondary Structure ◽

Schizosaccharomyces Pombe ◽

Rnase P ◽

Partial Characterization ◽

Rna Sequences ◽

Extensive Sequence ◽

Sequence Similarities

Saccharomyces cerevisiae cellular RNase P is composed of both protein and RNA components that are essential for activity. The isolated holoenzyme contains a highly structured RNA of 369 nucleotides that has extensive sequence similarities to the 286-nucleotide RNA associated with Schizosaccharomyces pombe RNase P but bears little resemblance to the analogous RNA sequences in procaryotes or S. cerevisiae mitochondria. Even so, the predicted secondary structure of S. cerevisiae RNA is strikingly similar to the bacterial phylogenetic consensus rather than to previously predicted structures of other eucaryotic RNase P RNAs.

Download Full-text

tRNA recognition, processing, and disease: Hypotheses around an unorthodox type of RNase P in human mitochondria

Mitochondrion ◽

10.1016/j.mito.2009.03.008 ◽

2009 ◽

Vol 9 (4) ◽

pp. 284-288 ◽

Cited By ~ 18

Author(s):

Johann Holzmann ◽

Walter Rossmanith

Keyword(s):

Rnase P ◽

Trna Recognition

Download Full-text

Triplet Analysis That Identifies Unpaired Regions of Functional RNAs

Journal of Nucleic Acids ◽

10.4061/2011/471843 ◽

2011 ◽

Vol 2011 ◽

pp. 1-6

Author(s):

Junji Kawakami ◽

Yoshie Yamaguchi ◽

Naoki Sugimoto

Keyword(s):

Consensus Sequence ◽

Structural Features ◽

Analysis Method ◽

Primary Sequence ◽

Rna Sequences ◽

Unpaired Region ◽

Novel Method ◽

Functional Rnas ◽

Hiv 1

We developed a novel method for analyzing RNA sequences, deemed triplet analysis, and applied the method in anin vitroRNA selection experiment in which HIV-1 Tat was the target. Aptamers are nucleic acids that bind a desired target (bait), and to date, many aptamers have been identified byin vitroselection from enough concentrated libraries in which many RNAs had an obvious consensus primary sequence after sufficient cycles of the selection. Therefore, the higher-order structural features of the aptamers that are indispensable for interaction with the bait must be determined by additional investigation of the aptamers. In contrast, our triplet analysis enabled us to extract important information on functional primary and secondary structure from minimally concentrated RNA libraries. As a result, by using our method, an important unpaired region that is similar to the bulge of TAR was readily predicted from a partially concentrated library in which no consensus sequence was revealed by a conventional sequence analysis. Moreover, our analysis method may be used to assess a variety of structural motifs with desired function.

Download Full-text

RNase P RNA mediated cleavage: Substrate recognition and catalysis

Biochimie ◽

10.1016/j.biochi.2007.05.009 ◽

2007 ◽

Vol 89 (10) ◽

pp. 1183-1194 ◽

Cited By ~ 63

Author(s):

L KIRSEBOM

Keyword(s):

Substrate Recognition ◽

Rnase P

Download Full-text

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

PLoS Genetics ◽

10.1371/journal.pgen.1002910 ◽

2012 ◽

Vol 8 (8) ◽

pp. e1002910 ◽

Cited By ~ 297

Author(s):

Alice Barkan ◽

Margarita Rojas ◽

Sota Fujii ◽

Aaron Yap ◽

Yee Seng Chong ◽

...

Keyword(s):

Amino Acid ◽

Rna Recognition ◽

Pentatricopeptide Repeat ◽

Repeat Proteins ◽

Amino Acid Code ◽

Pentatricopeptide Repeat Proteins

Download Full-text

Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA

Communications Chemistry ◽

10.1038/s42004-020-00400-2 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Yukiko Kamiya ◽

Tadashi Satoh ◽

Atsuji Kodama ◽

Tatsuya Suzuki ◽

Keiji Murayama ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Crystal Structures ◽

Prebiotic Chemistry ◽

Basic Research ◽

Structural Features ◽

Helical Structures ◽

Base Pairs ◽

Triplex Structure ◽

Rna And Dna

Abstract Xeno nucleic acids, which are synthetic analogues of natural nucleic acids, have potential for use in nucleic acid drugs and as orthogonal genetic biopolymers and prebiotic precursors. Although few acyclic nucleic acids can stably bind to RNA and DNA, serinol nucleic acid (SNA) and L-threoninol nucleic acid (L-aTNA) stably bind to them. Here we disclose crystal structures of RNA hybridizing with SNA and with L-aTNA. The heteroduplexes show unwound right-handed helical structures. Unlike canonical A-type duplexes, the base pairs in the heteroduplexes align perpendicularly to the helical axes, and consequently helical pitches are large. The unwound helical structures originate from interactions between nucleobases and neighbouring backbones of L-aTNA and SNA through CH–O bonds. In addition, SNA and L-aTNA form a triplex structure via C:G*G parallel Hoogsteen interactions with RNA. The unique structural features of the RNA-recognizing mode of L-aTNA and SNA should prove useful in nanotechnology, biotechnology, and basic research into prebiotic chemistry.

Download Full-text

A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52.

Molecular and Cellular Biology ◽

10.1128/mcb.17.5.2649 ◽

1997 ◽

Vol 17 (5) ◽

pp. 2649-2657 ◽

Cited By ~ 49

Author(s):

H Shi ◽

B E Hoffman ◽

J T Lis

Keyword(s):

Rna Binding ◽

Rna Recognition ◽

Loop Structure ◽

Hairpin Loop ◽

Structural Element ◽

Rna Sequences ◽

Sr Protein ◽

Rna Recognition Motifs ◽

Splicing Regulators ◽

Recognition Motifs

B52, also known as SRp55, is a member of the Drosophila melanogaster SR protein family, a group of nuclear proteins that are both essential splicing factors and specific splicing regulators. Like most SR proteins, B52 contains two RNA recognition motifs in the N terminus and a C-terminal domain rich in serine-arginine dipeptide repeats. Since B52 is an essential protein and is expected to play a role in splicing a subset of Drosophila pre-mRNAs, its function is likely to be mediated by specific interactions with RNA. To investigate the RNA-binding specificity of B52, we isolated B52-binding RNAs by selection and amplification from a pool of random RNA sequences by using full-length B52 protein as the target. These RNAs contained a conserved consensus motif that constitutes the core of a secondary structural element predicted by energy minimization. Deletion and substitution mutations defined the B52-binding site on these RNAs as a hairpin loop structure covering about 20 nucleotides, which was confirmed by structure-specific enzymatic probing. Finally, we demonstrated that both RNA recognition motifs of B52 are required for RNA binding, while the RS domain is not involved in this interaction.

Download Full-text

RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis

Nucleic Acids Research ◽

10.1093/nar/gki828 ◽

2005 ◽

Vol 33 (16) ◽

pp. 5120-5132 ◽

Cited By ~ 11

Author(s):

E. Sharin

Keyword(s):

Substrate Recognition ◽

Rnase P ◽

Trna Substrate

Download Full-text

Cytosolic Hsp70 and co-chaperones constitute a novel system for tRNA import into the nucleus

eLife ◽

10.7554/elife.04659 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 10

Author(s):

Akira Takano ◽

Takuya Kajita ◽

Makoto Mochizuki ◽

Toshiya Endo ◽

Tohru Yoshihisa

Keyword(s):

Saccharomyces Cerevisiae ◽

Quality Control ◽

Nuclear Import ◽

Nuclear Export ◽

Substrate Recognition ◽

Structural Features ◽

Nuclear Accumulation ◽

Nucleotide Binding Domain ◽

Trna Import ◽

Trna Binding

tRNAs are unique among various RNAs in that they shuttle between the nucleus and the cytoplasm, and their localization is regulated by nutrient conditions. Although nuclear export of tRNAs has been well documented, the import machinery is poorly understood. Here, we identified Ssa2p, a major cytoplasmic Hsp70 in Saccharomyces cerevisiae, as a tRNA-binding protein whose deletion compromises nuclear accumulation of tRNAs upon nutrient starvation. Ssa2p recognizes several structural features of tRNAs through its nucleotide-binding domain, but prefers loosely-folded tRNAs, suggesting that Ssa2p has a chaperone-like activity for RNAs. Ssa2p also binds Nup116, one of the yeast nucleoporins. Sis1p and Ydj1p, cytoplasmic co-chaperones for Ssa proteins, were also found to contribute to the tRNA import. These results unveil a novel function of the Ssa2p system as a tRNA carrier for nuclear import by a novel mode of substrate recognition. Such Ssa2p-mediated tRNA import likely contributes to quality control of cytosolic tRNAs.

Download Full-text