RNase P enzymes

Howard, Michael J.; Liu, Xin; Lim, Wan Hsin; Klemm, Bradley P.; Fierke, Carol A.; Koutmos, Markos; Engelke, David R.

doi:10.4161/rna.24513

Cited by 36 publications

(24 citation statements)

References 48 publications

(50 reference statements)

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“…We found that all of the aspartate to alanine mutants are unable to cleave (nu)pre-tRNA Gly 8:1 in our single turnover assays (Table 3), and some of these mutants have significantly weaker substrate affinity than the wild type enzyme (Supplemental Table 2) 6 . The H445A PRORP2 mutant reduced the k obs value measured in cleavage assays by approximately 50-fold relative to the wild type protein.…”

Section: Resultsmentioning

confidence: 83%

“…Furthermore, the single turnover rate constants that we measure for PRORP2 cleaving (nu)pre-tRNA Gly substrates are comparable with previously published rate constants for PRORP1 catalyzing cleavage of (mt)pre-tRNAs under the same conditions 8; 12 . However these activities are at least 10-fold lower than that of bacterial and yeast RNA based RNase P 6 .…”

Section: Discussionmentioning

confidence: 84%

“…In some Eukaryotes, such as land plants, PRORPs have entirely taken over the role of “ribozyme-based” RNase Ps 4; 5; 6; 9 . Despite their essential nature 9 to date only a single PRORP, the A. thaliana PRORP1 localized to mitochondria and chloroplast, has been characterized biochemically and structurally 4; 6; 8; 12; 15 . To broadly understand how PRORPs function, our work here is the first structure and function study of a nuclear localized PRORP, A. thaliana PRORP2.…”

Section: Discussionmentioning

confidence: 99%

“…However, a second form of the enzyme, called p rotein o nly RN ase P (PRORP), comprised solely of protein and lacking an RNA component has been discovered in Eukaryotes 3; 4; 5 . It is noteworthy that none of the known protein components of the “ribozyme-based” RNase P have any homology to PRORPs 6 . Beyond the bioinformatic identification of PRORPs in a wide variety of organisms 3; 7; 8 little is known about how they recognize substrates.…”

Section: Introductionmentioning

confidence: 99%

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Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5′ End Processing Enzymes

Karasik

Shanmuganathan

Howard

et al. 2016

Journal of Molecular Biology

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Protein-only RNase Ps (PRORPs) are a recently discovered class of RNA processing enzymes that catalyze maturation of the 5′ end of precursor tRNAs (pre-tRNAs) in Eukaryotes. PRORPs are found in the nucleus and/or organelles of most eukaryotic organisms. Arabidopsis thaliana is a representative organism that contains PRORP enzymes (PRORP1, PRORP2, PRORP3) in both its nucleus and organelles; PRORP2 and 3 localize to the nucleus, PRORP1 to the chloroplast and the mitochondria. Apart from their identification, almost nothing is known about the structure and function of PRORPs that act in the nucleus. Here we use a combination of biochemical assays and X-ray crystallography to characterize A. thaliana PRORP2. We solved the crystal structure of PRORP2 (3.2 Å) revealing an overall V-shaped protein and conserved metallonuclease active site structure. Our biochemical studies indicate that PRORP2 requires Mg2+ for catalysis and catalyzes the maturation of nuclear encoded substrates up to 10-fold faster than mitochondrial encoded precursor nad6 t-element under single turnover conditions. We also demonstrate that PRORP2 preferentially binds pre-tRNAs containing short 5′ leaders and 3′ trailers; however, leader and trailer length do not significantly alter the observed rate constants of PRORP2 in single turnover cleavage assays. Our data provide a biochemical and structural framework to begin understanding how nuclear localized PRORPs recognize and cleave their substrates.

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Section: Resultsmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5′ End Processing Enzymes

Karasik

Shanmuganathan

Howard

et al. 2016

Journal of Molecular Biology

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“…This result has been interpreted as a clue for the presence of an RNP RNase P enzyme in plant nuclei 67 . Since the downregulation of POP1 in planta resulted in decreased RNase MRP activity and did not affect RNase P activity, 62 we believe that the results instead reflect the presence of both PRORP and RNase MRP in the immunoprecipitated fraction, i.e., that the two enzymes might be present in a single complex in planta as also proposed by Krehan, et al 66 …”

Section: Identification At the Molecular Level Of Protein-only Rnase Pmentioning

confidence: 83%

PPR proteins shed a new light on RNase P biology

et al. 2013

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A fast growing number of studies identify pentatricopeptide repeat (PPR) proteins as major players in gene expression processes. Among them, a subset of PPR proteins called PRORP possesses RNase P activity in several eukaryotes, both in nuclei and organelles. RNase P is the endonucleolytic activity that removes 5′ leader sequences from tRNA precursors and is thus essential for translation. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins, although some evidence implied that some eukaryotes or cellular compartments did not use RNA for RNase P activity. The characterization of PRORP reveals a two-domain enzyme, with an N-terminal domain containing multiple PPR motifs and assumed to achieve target specificity and a C-terminal domain holding catalytic activity. The nature of PRORP interactions with tRNAs suggests that ribonucleoprotein and protein-only RNase P enzymes share a similar substrate binding process.

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Mitochondrial Genome Evolution

Bernt

Machné²,

Sahyoun

et al. 2013

Encyclopedia of Life Sciences

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Mitochondria are membrane‐enclosed organelles present in most eukaryotic cells that generate most of the cell's adenosine triphosphate (ATP) supply. Derived from a proteobacterial ancestor, mitochondria harbour their own, drastically reduced genome. Starting from a prokaryote‐like ancestral state encoding a complete ribosomal ribonucleic acid (rRNA) operon, a complete set of transfer RNAs (tRNAs) required for translation, and key enzymes of the respiratory chain as well as some ribosomal proteins, the mitogenome has been dramatically restructured and further reduced in many of the eukaryotic lineages. The loss and transfer to the nucleus of mitochondrial genes is a common trend in most phyla, in particular in Metazoa and Alveolata. In extreme, phylogenetically dispersed cases, often associated with parasitic or anaerobic life styles, mitochondria have been transformed to the so‐called mitosomes or hydrogenosomes devoid of their own genetic material. Ancestrally a single circular deoxyribonucleic acid (DNA) , mitogenomes have evolved to complex, fragmented architectures in particular in Euglenozoa. Key Concepts: Mitochondria have an endosymbiotic origin deriving from a proteobacterial ancestor. Various evolutionary mechanisms operate on mitochondrial genomes. Mitochondrial genomes have developed very diverse properties during eukaryote evolution. Mitogenomic gene content declines in most eukaryotic lineages by horizontal transfer to the nuclear genome. Complex idiosyncratic genome organisations have independently evolved in several eukaryotic phyla.

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RNase P enzymes

Cited by 36 publications

References 48 publications

Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5′ End Processing Enzymes

Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5′ End Processing Enzymes

PPR proteins shed a new light on RNase P biology

Mitochondrial Genome Evolution

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