A surprisingly large RNase P RNA in <i>Candida glabrata</i>

Kachouri, Rym; Stribinskis, Vilius; Zhu, Yun; Ramos, Kenneth S.; Westhof, Éric; Li, Yong

doi:10.1261/rna.2130705

Cited by 27 publications

(27 citation statements)

References 44 publications

(46 reference statements)

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“…41 RNase P. Ascomycete mitochondrial RNase P RNAs are, on the other hand, highly reduced in size and lack most of the sequence and structural elements conserved in other RNase P RNAs. [42][43][44][45] The human (and presumably other metazoans) mitochondrial RNase P lacks the RNA subunit entirely; the RNase P catalytic function has been replaced by a Rube Goldberg triad of unrelated proteins. 46,47 The secondary structure of RNase P RNAs from primitive plastids are similar to those of cyanobacteria, from which they derive.…”

Section: Eukaryotic Rnase P Rnasmentioning

confidence: 99%

The RNase P family

Ellis¹,

Brown²

2009

RNA Biology

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Ribonuclease P (RNase P) is a ribonucleoprotein comprised of a catalytic RNA subunit and one or several protein subunits. RNase P is best known for its role in 5'-processing of tRNA precursors. RNase P enzymes from almost all forms of life, including protein-synthesizing organelles, contain an RNase P with a conserved, homologous RNA. Five distinct structure classes of RNase P RNAs have been identified in bacteria and archaea; eukaryotic RNase P RNAs are not yet sufficiently well surveyed for structure classes to be defined. Here we will examine the structure variations in RNase P RNAs in bacteria, archaea, eukaryotes, plastids and mitochondria with special emphasis on the functional roles these unique secondary structures perform.

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Section: Eukaryotic Rnase P Rnasmentioning

confidence: 99%

The RNase P family

Ellis¹,

Brown²

2009

RNA Biology

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“…Helix numbering follows their putative homology with bacterial structures (Haas et al 1994). The PRNA structure model is derived from (Kachouri et al 2005), while the insertions are shown with arrows.…”

Section: Catalytic Domain Of Mrp Rnamentioning

confidence: 99%

“…The eP8 and eP9 helicesa re ubiquitous components of eukaryotic PRNAs (Frank et al2000;Kachouri et al 2005;Marquez et al 2005;Piccinellie ta l. 2005). Basedo n sequence analysis, an equivalent helix in the MRP RNAi s the helix that preservesasignificant number of nucleotides fromits counterpartinthe PRNA.This criterion led to the identificationofthe helices P8 and P9 in the MRP RNA of Encephalitozoon cuniculi (Fig.3 A), where the P8 in the MRP RNA is 100% identical to the P8 in the PR NA, and theP9s have four nucleotidesconserved in theterminalloop (Fig.3A).…”

Section: The Specificity Domain Of Mrp Rnamentioning

confidence: 99%

“…1). Some unusually large sequences, like the putative extremely large MRP RNAs from Candida albicans and Candida dubliniensis (Piccinelli et al2 005) and the large PR NA from Candida glabrata still under investigation ( Kachouri et al 2005), as well as MRP RNAf rom Candida tropicalis, Debaryomyces hansenii, Pichia guilliermondii ,and Yarrowialipolytica,were not included in Figure 1. Beyond the conserved regions (CR I, CR IV, CR V), the MRP RNAs within hemiascomycetesare conserved in P1, P2, P3a, and ymP5 helices (Fig.1 ).…”

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confidence: 99%

“…If the ymP7 stem is equivalent to the P10/P11 stem of PR NA, and if there is aP 7-like stem in MRP RNA, both MRP RNA and PR NA will possessthe cruciform structure (P7, P8, P9, and P10/11 in PR NA;a nd P7-like, ymP5, ymP6, and ymP7 in MRP RNA), which is well defined as the specificity domaino f PR NA (Chen and Pace 1997;Massire et al 1998). Subsequently, the two-domain structurem odel of bacterial PRNA (Chen and Pace 1997;Massire et al1998) could be well applied to that of MRP RNA in additiont o the eukaryotic PRNA (Kachouri et al 2005). However, the formation of aP 7-like structure is not required for the essential functiono fR Nase MRP and may not be in the active complex (Walker et al 2005).…”

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confidence: 99%

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Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

Zhu

Stribinskis

Ramos

et al. 2006

RNA

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RNase MRP is ae ukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase Pi saubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5 9 termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata,t he internal loop of helix P3 is 100% conserved between MRP and PR NAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of PRNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and PRNA, such as those from Dictyostelium discoideum.These conserved nucleotides between the MRP and PR NAs strongly support the hypothesis that the MRP RNA is derived from the PR NA molecule in early eukaryote evolution.Keywords: specificity domain; catalytic domain; RNase MRP RNA RNasePandR Nase MRPa re ribonucleoprotein (RNP) complexes participating in cellularR NA processing. RNase Pi saubiquitouse ndoribonucleaset hatc leavesp recursor tRNA (pre-tRNA) transcripts to produce their mature 5 9 termini (Altman1 990; Altmana nd Kirsebom 1999).B acterialR Nase Pc onsistso facatalytic RNA subunit and a protein cofactor,w hilea rchaeal and eukaryotic enzymes haveasingle RNA subunit andm oret hanf ourp roteins (Hartmann and Hartmann2003). RNase MRPisaeukaryotespecific endoribonuclease that has at least two roles: one in themitochondrial compartmentwhere it generates RNA primersfor theinitiationofmitochondrial DNAreplication (Chang and Clayton 1989), and as econd in the nucleolus whereitparticipates in precursorrRNAprocessing (Lygerou et al. 1996). Hemiascomycetes, such as the budding yeast Saccharomyces cerevisiae,havebeenextensively used to study the structureand functionofeukaryotic RNase Pand MRP. The S. cerevisiae RNase Penzyme possessesone RNA (P RNA) and nine integral protein subunits, while RNase MRP has one RNA (MRP RNA) and 10 proteins (Chamberlain et al. 1998;Salinas et al. 2005). Previously, the catalytic domains of these two RNAs havebeen demonstrated to havesimilar secondary structures (Li et al. 2002). Moreover, eight of the associated protein components are identical ( Chamberlain et al. 1998), indicating that these two enzymecomplexes are structurallya nd evolutionally related.Despite structural similarity in the catalytic domains, little sequence homology beyond the P3 and P4 helices of Pa nd MRP RNA has been demonstrated, partially due to limited availability of sequences, especially the MRP RNA sequences. Ar ecent report by Samuelsson and colleagues identified more than 100 new MRP and PR NA sequences frome ukaryotes with completeg enomes equences or whole-genome-shotguns equences (Piccinelli et al. 2005). Some of thesep redictedM RP and PR NA genes from Candida speciesare demonstrated by biochemical methods in our laboratory to be expressed (data not shown). These sequences allowed us to perform ac omprehensive analysis of MRP RNAs and their homolog...

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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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A surprisingly large RNase P RNA in Candida glabrata

Cited by 27 publications

References 44 publications

The RNase P family

The RNase P family

Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

Mitochondrial Genome Evolution

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