Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes

Esakova, Olga; Perederina, Anna; Quan, Chao; Schmitt, Michael N.; Krasilnikov, Andrey S.

doi:10.1261/rna.1106408

Cited by 32 publications

(79 citation statements)

References 63 publications

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“…Others have suggested that this conserved GARAR element may form a pentaloop, P8 [38]. However, the P8 structure was not detected by holoenzyme footprinting analyses in vitro [39]. In our analysis, the P8 region was found to interact with proteins, suggesting that the conformation of P8 may change when it is bound by an RBP in vivo.…”

Section: Rbp Binding Facilitates Rna Secondary Structure Conformationcontrasting

confidence: 66%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical non-coding RNAs (ncRNAs) and ~11% of long ncRNAs (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responses. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. . Many mRNAs are regulated by one or more RBPs as co-regulators. In Saccharomyces cerevisiae, there are approximately 600 annotated and predicted RBPs, but relatively few of them have been systematically studied to determine their regulatory targets [5]. In addition to mRNAs, numerous non-coding RNAs (ncRNAs) are targets of RBPs [6,7]. Previous studies revealed that RNAs were regulated by many RBPs post-transcriptionally [8]. It is widely accepted that altering the expression of RBPs will change cellular physiology profoundly. Studies using animal models have revealed that RBPs are involved in many human diseases, such as neurologic disorders and cancers [9]. Although the mechanisms that confer the specificity of RBP-RNA interaction are poorly understood, it is clear that this specificity is determined by both the primary sequence and secondary structure of the target RNA [10,11]. The secondary structures recognized by some RBPs are known. For example, the SAM domain of the yeast post-transcriptional regulator Vts1p recognizes the shape of the SRE of the RNA ligand [12].Currently, the most direct and powerful approach to profiling RBP-RNA interactions is UV crosslinking and immunoprecipitation (CLIP) of RNA-protein complexes,

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Section: Rbp Binding Facilitates Rna Secondary Structure Conformationcontrasting

confidence: 66%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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“…enzyme (Esakova et al 2008), which indicate that the eP15 loop is not involved in interactions with proteins, as are the results of mutational studies (Shadel et al 2000;Li et al 2004), which indicate that the terminal part of the eP15 stem is not essential for the function of RNase MRP.…”

Section: Resultsmentioning

confidence: 90%

“…We generated two yeast strains, each containing a TAP tag (Rigaut et al 1999) attached to the carboxyl terminus of RNase MRP/P protein component Pop4 Esakova et al 2008) plus a His 6 tag attached to the carboxyl terminus of either Pop5 or Rpp1. Active RNase MRP was purified from both yeast strains using established protocols Esakova et al 2008); the TAP tag was used as the purification handle. Following purification, RNase MRP was subjected to UV irradiation.…”

Section: Resultsmentioning

confidence: 99%

“…RNase MRP (as a z1:1 mix with RNase P) was purified from S. cerevisiae strains EK-Pop5 and EK-Rpp1 using tandem affinity purification (Rigaut et al 1999) and following a protocol described in Salinas et al (2005) and Esakova et al (2008). Strains EK-Pop5 and EK-Rpp1 were based on yeast strain YSW1 ), a generous gift from Mark Schmitt.…”

Section: Purification Of Rnase Mrp Holoenzymementioning

confidence: 99%

“…1A,B; for a recent review, see Esakova and Krasilnikov 2010). Footprinting studies of RNase MRP and RNase P holoenzymes suggest that the catalytic domain of RNase P and the corresponding domain of RNase MRP have similar structural organizations (Esakova et al 2008). The differences in the substrate specificities of RNases MRP and P (Esakova et al 2011) are likely to be due to the divergence in parts of their RNA components (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP

Perederina

Khanova

Quan

et al. 2011

RNA

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Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding site corresponds to the protein binding site in bacterial RNase P RNA. Structural and evolutionary roles of the Pop5/Rpp1 heterodimer in RNases P and MRP are discussed.

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Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus on coordinated action of endo‐ and exoribonucleases

2017

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Edited by Michael IbbaProper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo-and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.Keywords: endoribonuclease; exoribonuclease; pre-rRNA processing; ribosome biogenesis; RNA quality control; RNA trimming Ribosome biosynthesis is a multistep process that includes several tightly controlled events -ribosomal DNA (rDNA) transcription, processing of rRNA precursors into mature molecules, accompanied by binding of ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs), and the final assembly of all Abbreviations CD, catalytic domain; dsRBD, double-stranded RNA-binding domain; ETS, external transcribed spacer; ITS, internal transcribed spacer; LSU, large ribosome subunit (60S); miRNA, microRNA; mRNA, messenger RNA; MRP RNA, noncoding RNA component of the RNase MRP; mTOR, mammalian target of rapamycin; nt(s), nucleotide(s); PIN domain, PilT N-terminal domain; Pol I/II/III, RNA polymerase I/II/III; prerRNA, ribosomal RNA precursor; RBF, ribosome biogenesis factor; RMRP, RNase MRP (mitochondrial RNA processing ribonuclease); RNase, ribonuclease; RNB domain, RNase II domain; RNP, ribonucleoprotein; RP, ribosomal protein; rRNA, ribosomal RNA; siRNA, short interfering RNA; snoRNA, small nucleolar RNA; snoRNP, small nucleolar ribonucleoprotein; snRNA, small nuclear RNA; SSU, small ribosome subunit (40S); TRAMP4 or TRAMP5, Trf4/Air/Mtr4 or Trf5/Air/Mtr4 polyadenylation complex; tRNA, transfer RNA.

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Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes

Cited by 32 publications

References 63 publications

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus on coordinated action of endo‐ and exoribonucleases

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