scholarly journals Structural basis of RNA processing by human mitochondrial RNase P

2021 ◽  
Author(s):  
Arjun Bhatta ◽  
Christian Dienemann ◽  
Patrick Cramer ◽  
Hauke S. Hillen
Keyword(s):  
Rna Processing ◽  
Rnase P ◽  
Structural Basis ◽  
Rna Cleavage ◽  
Anticodon Loop ◽  
Mitochondrial Trna ◽  
Transfer Rnas ◽  
Protein Subunits ◽  
Mitochondrial Transcripts ◽  
Unique Mechanism

AbstractHuman mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria.

scholarly journals Yeast mitochondrial RNase P RNA synthesis is altered in an RNase P protein subunit mutant: insights into the biogenesis of a mitochondrial RNA-processing enzyme.

1996 ◽  
Vol 16 (7) ◽  
pp. 3429-3436 ◽  
Author(s):  
V Stribinskis ◽  
G J Gao ◽  
P Sulo ◽  
Y L Dang ◽  
N C Martin
Keyword(s):  
Rna Processing ◽  
Mitochondrial Protein ◽  
Rnase P ◽  
Mitochondrial Rna ◽  
Wild Type ◽  
Protein Subunit ◽  
Mitochondrial Trna ◽  
P Deficiency ◽  
F Gene ◽  
P Protein

Rpm2p is a protein subunit of Saccharomyces cerevisiae yeast mitochondrial RNase P, an enzyme which removes 5' leader sequences from mitochondrial tRNA precursors. Precursor tRNAs accumulate in strains carrying a disrupted allele of RPM2. The resulting defect in mitochondrial protein synthesis causes petite mutants to form. We report here that alteration in the biogenesis of Rpm1r, the RNase P RNA subunit, is another consequence of disrupting RPM2. High-molecular-weight transcripts accumulate, and no mature Rpm1r is produced. Transcript mapping reveals that the smallest RNA accumulated is extended on both the 5' and 3' ends relative to mature Rpm1r. This intermediate and other longer transcripts which accumulate are also found as low-abundance RNAs in wild-type cells, allowing identification of processing events necessary for conversion of the primary transcript to final products. Our data demonstrate directly that Rpm1r is transcribed with its substrates, tRNA met f and tRNAPro, from a promoter located upstream of the tRNA met f gene and suggest that a portion also originates from a second promoter, located between the tRNA met f gene and RPM1. We tested the possibility that precursors accumulate because the RNase P deficiency prevents the removal of the downstream tRNAPro. Large RPM1 transcripts still accumulate in strains missing this tRNA. Thus, an inability to process cotranscribed tRNAs does not explain the precursor accumulation phenotype. Furthermore, strains with mutant RPM1 genes also accumulate precursor Rpm1r, suggesting that mutations in either gene can lead to similar biogenesis defects. Several models to explain precursor accumulation are presented.

Modified Oligonucleotides for Guiding RNA Cleavage Using Bacterial RNase P

2018 ◽  
Vol 52 (6) ◽  
pp. 905-912 ◽  
Author(s):  
D. S. Novopashina ◽  
A. S. Nazarov ◽  
M. A. Vorobjeva ◽  
M. S. Kuprushkin ◽  
A. S. Davydova ◽  
...  
Keyword(s):  
Rnase P ◽  
Rna Cleavage ◽  
Modified Oligonucleotides

scholarly journals A screening platform to monitor RNA processing and protein-RNA interactions in ribonuclease P uncovers a small molecule inhibitor

2019 ◽  
Vol 47 (12) ◽  
pp. 6425-6438 ◽  
Author(s):  
Ezequiel-Alejandro Madrigal-Carrillo ◽  
Carlos-Alejandro Díaz-Tufinio ◽  
Hugo-Aníbal Santamaría-Suárez ◽  
Marcelino Arciniega ◽  
Alfredo Torres-Larios
Keyword(s):  
Rna Processing ◽  
Rnase P ◽  
Ribonuclease P ◽  
Binding Assays ◽  
Antibiotic Development ◽  
Processing Enzymes ◽  
P Protein ◽  
Molecule Inhibitor ◽  
Screening Platform ◽  
Dynamics Simulations

AbstractRibonucleoprotein (RNP) complexes and RNA-processing enzymes are attractive targets for antibiotic development owing to their central roles in microbial physiology. For many of these complexes, comprehensive strategies to identify inhibitors are either lacking or suffer from substantial technical limitations. Here, we describe an activity-binding-structure platform for bacterial ribonuclease P (RNase P), an essential RNP ribozyme involved in 5′ tRNA processing. A novel, real-time fluorescence-based assay was used to monitor RNase P activity and rapidly identify inhibitors using a mini-helix and a pre-tRNA-like bipartite substrate. Using the mini-helix substrate, we screened a library comprising 2560 compounds. Initial hits were then validated using pre-tRNA and the pre-tRNA-like substrate, which ultimately verified four compounds as inhibitors. Biolayer interferometry-based binding assays and molecular dynamics simulations were then used to characterize the interactions between each validated inhibitor and the P protein, P RNA and pre-tRNA. X-ray crystallographic studies subsequently elucidated the structure of the P protein bound to the most promising hit, purpurin, and revealed how this inhibitor adversely affects tRNA 5′ leader binding. This integrated platform affords improved structure-function studies of RNA processing enzymes and facilitates the discovery of novel regulators or inhibitors.

scholarly journals Transcription initiation and RNA processing of a yeast mitochondrial tRNA gene cluster

1987 ◽  
Vol 15 (18) ◽  
pp. 7381-7394 ◽  
Author(s):  
Rémy Borodonné ◽  
Guy Dirheimer ◽  
Robert P. Martin
Keyword(s):  
Gene Cluster ◽  
Rna Processing ◽  
Transcription Initiation ◽  
Trna Gene ◽  
Mitochondrial Trna ◽  
Mitochondrial Trna Gene

scholarly journals RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme

Cell ◽  
2008 ◽  
Vol 135 (3) ◽  
pp. 462-474 ◽  
Author(s):  
Johann Holzmann ◽  
Peter Frank ◽  
Esther Löffler ◽  
Keiryn L. Bennett ◽  
Christopher Gerner ◽  
...  
Keyword(s):  
Rnase P ◽  
Mitochondrial Trna ◽  
Trna Processing ◽  
Processing Enzyme

scholarly journals Basic Domains Target Protein Subunits of the RNase MRP Complex to the Nucleolus Independently of Complex Association

2001 ◽  
Vol 12 (11) ◽  
pp. 3680-3689 ◽  
Author(s):  
Hans van Eenennaam ◽  
Annemarie van der Heijden ◽  
Rolf J. R. J. Janssen ◽  
Walther J. van Venrooij ◽  
Ger J. M. Pruijn
Keyword(s):  
Protein Composition ◽  
Rnase P ◽  
Nucleolar Localization ◽  
Rrna Processing ◽  
Protein Subunits ◽  
Trna Processing ◽  
Rnase Mrp ◽  
Human Rnase ◽  
The Difference ◽  
Active Transport Process

The RNase MRP and RNase P ribonucleoprotein particles both function as endoribonucleases, have a similar RNA component, and share several protein subunits. RNase MRP has been implicated in pre-rRNA processing and mitochondrial DNA replication, whereas RNase P functions in pre-tRNA processing. Both RNase MRP and RNase P accumulate in the nucleolus of eukaryotic cells. In this report we show that for three protein subunits of the RNase MRP complex (hPop1, hPop4, and Rpp38) basic domains are responsible for their nucleolar accumulation and that they are able to accumulate in the nucleolus independently of their association with the RNase MRP and RNase P complexes. We also show that certain mutants of hPop4 accumulate in the Cajal bodies, suggesting that hPop4 traverses through these bodies to the nucleolus. Furthermore, we characterized a deletion mutant of Rpp38 that preferentially associates with the RNase MRP complex, giving a first clue about the difference in protein composition of the human RNase MRP and RNase P complexes. On the basis of all available data on nucleolar localization sequences, we hypothesize that nucleolar accumulation of proteins containing basic domains proceeds by diffusion and retention rather than by an active transport process. The existence of nucleolar localization sequences is discussed.

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