Identification of pentatricopeptide repeat proteins in Trypanosoma brucei

Mingler, Melissa K.; Hingst, Andrea M.; Clement, Sandra L.; Yu, Laura E.; Reifur, Larissa; Koslowsky, Donna J.

doi:10.1016/j.molbiopara.2006.06.006

Cited by 40 publications

(43 citation statements)

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“…Hundreds of PPR proteins are found in plants where they are thought to be involved in post-transcriptional gene regulation in organelles by specific binding to mRNA [44]. Recently, 23 conserved members of the PPR family were identified by a genome-wide search in T. brucei, and the down-regulation of one of these proteins had influenced steady-state levels and editing of some of the maxicircle gene transcripts [45]. One of the three PPR proteins present in the 45S complexes (LmjF24.0830) was not found in that work.…”

Section: Discussionmentioning

confidence: 99%

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Maslov

Spremulli

Sharma

et al. 2007

Molecular and Biochemical Parasitology

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A novel type of ribonucleoprotein (RNP) complex has been described from the kinetoplastmitochondria of Leishmania tarentolae. The complex, termed the 45S SSU*, contains the 9S small subunit rRNA but does not contain the 12S large subunit rRNA. This complex is the most stable and abundant mitochondrial RNP complex present in Leishmania. As shown by tandem mass spectrometry, the complex contains at least 39 polypeptides with a combined molecular mass of almost 2.1 MDa. These components include several homologs of small subunit ribosomal proteins (S5, S6, S8 S9, S11, S15, S16, S17, S18, MRPS29); however, most of the polypeptides present are unique. Only a few of them show recognizable motifs, such as protein-protein (coiled-coil, Rhodanese) or protein-RNA (pentatricopeptide repeat) interaction domains. A cryo-electron microscopy examination of the 45S SSU* fraction reveals that 27% of particles represent SSU homodimers arranged in a head-to-tail orientation, while the majority of particles are clearly different and show an asymmetric bilobed morphology. Multiple classes of two-dimensional averages were derived for the asymmetrical particles, probably reflecting random orientations of the particles and difficulties in correlating these views with the known projections of ribosomal complexes. One class of the two-dimensional averages shows an SSU moiety attached to a protein mass or masses in a monosome-like appearance. The combined mass spectrometry and electron microscopy data thus indicate that the majority 45S SSU* particles represents a heterodimeric complex in which the SSU Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access

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Section: Discussionmentioning

confidence: 99%

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Maslov

Spremulli

Sharma

et al. 2007

Molecular and Biochemical Parasitology

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“…Several PPR proteins are encoded in animal and fungal genomes, and ;20 PPR proteins are encoded in trypanosome genomes (Mingler et al, 2006), but the family is greatly expanded in seed plants, with >400 hundred members in Arabidopsis thaliana and rice (Oryza sativa; Lurin et al, 2004). Most of these proteins are predicted to be targeted to chloroplasts or mitochondria, and all but one of the ;15 PPR proteins that have been genetically characterized affect the processing or translation of specific organellar RNAs (Barkan et al, 1994;Manthey and McEwen, 1995;Coffin et al, 1997;Fisk et al, 1999;Ikeda and Gray, 1999;Lown et al, 2001;Mancebo et al, 2001;Auchincloss et al, 2002;Bentolila et al, 2002;Desloire et al, 2003;Hashimoto et al, 2003;Kazama and Toriyama, 2003;Koizuka et al, 2003;Meierhoff et al, 2003;Mili and Pinol-Roma, 2003;Williams and Barkan, 2003;Xu et al, 2004;Yamazaki et al, 2004;Kotera et al, 2005;Prasad et al, 2005;Mingler et al, 2006;Wang et al, 2006); the lone exception, Arabidopsis GRP23, is a nuclear protein that is proposed to regulate transcription (Ding et al, 2006). By extrapolation, it is anticipated that the PPR family plays a central and broad role in modulating gene expression in both mitochondria and chloroplasts.…”

Section: Introductionmentioning

confidence: 99%

A Pentatricopeptide Repeat Protein Facilitates the trans-Splicing of the Maize Chloroplast rps12 Pre-mRNA

et al. 2006

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The pentatricopeptide repeat (PPR) is a degenerate 35-amino acid repeat motif that is widely distributed among eukaryotes. Genetic, biochemical, and bioinformatic data suggest that many PPR proteins influence specific posttranscriptional steps in mitochondrial or chloroplast gene expression and that they may typically bind RNA. However, biological functions have been determined for only a few PPR proteins, and with few exceptions, substrate RNAs are unknown. To gain insight into the functions and substrates of the PPR protein family, we characterized the maize (Zea mays) nuclear gene ppr4, which encodes a chloroplast-targeted protein harboring both a PPR tract and an RNA recognition motif. Microarray analysis of RNA that coimmunoprecipitates with PPR4 showed that PPR4 is associated in vivo with the first intron of the plastid rps12 pre-mRNA, a group II intron that is transcribed in segments and spliced in trans. ppr4 mutants were recovered through a reverse-genetic screen and shown to be defective for rps12 trans-splicing. The observations that PPR4 is associated in vivo with rps12-intron 1 and that it is also required for its splicing demonstrate that PPR4 is an rps12 trans-splicing factor. These findings add trans-splicing to the list of RNA-related functions associated with PPR proteins and suggest that plastid group II trans-splicing is performed by different machineries in vascular plants and algae.

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“…Most PPR proteins have an N-terminal sequence predicted to target the protein to either mitochondria or chloroplasts, followed by an average of z12 tandem PPR motifs and a small amount of non-PPR sequence flanking the PPR tract (Small and Peeters 2000;Delannoy et al 2007). PPR proteins are encoded by small gene families in animals and fungi (z5-10 members), by z20 genes in trypanosomes (Mingler et al 2006;Pusnik et al 2007), and by over 400 genes in plants (Lurin et al 2004;Rivals et al 2006). The biological functions of z20 PPR proteins have been elucidated, including representatives from animals, plants, trypanosomes, and fungi; the vast majority of these localize to mitochondria or chloroplasts and influence specific post-transcriptional steps in gene expression (for review, see Delannoy et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand

Williams‐Carrier

Kroeger²,

Barkan³

2008

RNA

104

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Pentatricopeptide repeat (PPR) proteins are defined by degenerate 35-amino acid repeats that are related to the tetratricopeptide repeat (TPR). Most characterized PPR proteins mediate specific post-transcriptional steps in gene expression in mitochondria or chloroplasts. However, little is known about the structure of PPR proteins or the biochemical mechanisms through which they act. Here we establish features of PPR protein structure and nucleic acid binding activity through in vitro experiments with PPR5, which binds and stabilizes a chloroplast tRNA precursor harboring a group II intron. Recombinant PPR5 was shown to be monomeric by analytical ultracentrifugation and gel filtration. Circular dichroism spectroscopy showed that PPR5 has a high content of a helices, as predicted from the similarity between PPR and TPR motifs. PPR5 and another PPR protein, CRP1, bind with high affinity to single-stranded RNA, but bind poorly to single-stranded DNA or to double-stranded RNA or DNA. A specific PPR5 binding site was identified within its group II intron ligand. The minimal site spans ;45 nucleotides, encompasses two group II intron functional motifs, and overlaps the terminus of an in vivo RNA decay product. These results suggest mechanisms by which PPR5 influences both RNA stability and splicing.

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Identification of pentatricopeptide repeat proteins in Trypanosoma brucei

Cited by 40 publications

References 50 publications

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

A Pentatricopeptide Repeat Protein Facilitates the trans-Splicing of the Maize Chloroplast rps12 Pre-mRNA

Sequence-specific binding of a chloroplast pentatricopeptide repeat protein to its native group II intron ligand

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