Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids.

Feagin, Jean E.; Shaw, Janet M.; Simpson, Larry; Stuart, Kenneth

doi:10.1073/pnas.85.2.539

Cited by 98 publications

(55 citation statements)

References 25 publications

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“…No Shine-Dalgarno sequence or equivalent signal is found upstream of the initiation codon. In contrast to mammalian mitochondria, the first AUG or AUA codon at the 5' end of the mRNA is generally not used as the start codon in trypanosomatid mitochondria [4][5][6][7][8][9]. Non-canonical initiation codons may also be used in some cases [7,[10][11][12][13].…”

Section: Introductionmentioning

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: Introductionmentioning

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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“…These include obligatory trans-splicing of a common nucleotide sequence, the miniexon, onto the 5' ends of all mRNAs (17, 57, 63, 70, 74; reviewed in 11), as well as editing of mitochondrial mRNAs (4,26). An increasing body of data suggests that some protein-coding mRNAs may be synthesized as larger polycistronic precursors, up to 60 kilobases (kb) in length, which are subsequently cleaved and processed into mature mRNAs.…”

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confidence: 99%

Transcriptional mapping of the amplified region encoding the dihydrofolate reductase-thymidylate synthase of Leishmania major reveals a high density of transcripts, including overlapping and antisense RNAs.

Kapler¹,

Beverley²

1989

Mol. Cell. Biol.

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We have examined the transcriptional organization of the R region of the protozoan parasite Leishmania major. This region encodes the bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) and is frequently amplified as a 30-kilobase (kb) extrachromosomal circular DNA in methotrexate-resistant lines. Northern (RNA) blot analysis shows that the R region encodes at least 10 stable cytoplasmic polysomal poly(A)+ RNAs, ranging in size from 1.7 to 13 kb and including the 3.2-kb DHFR-TS mRNA. Transcriptional mapping reveals that these RNAs are closely spaced and collectively cover more than 95% of the 30-kb amplified R region. The organization is complex, including several overlapping RNAs 3' of DHFR-TS and two examples of antisense RNAs 5' of DHFR-TS. The R region RNAs can be grouped into two empirical domains, with eight contiguous RNAs transcribed in the same direction as that of DHFR-TS and two contiguous RNAs transcribed in the orientation opposite to that of DHFR-TS. The two 5'-most RNAs of the DHFR-TS-containing domain overlap the RNAs transcribed from the opposite strand. These data are relevant to models of transcription, including recent studies suggesting polycistronic transcription in trypanosomatids. The abundance of R region RNAs increases uniformly 10-to 15-fold in the amplified R1000-3 line relative to the wild type, and no new RNAs were observed. This suggests that all elements required in cis for DHFR-TS expression are contained within the 30-kb circular DNA. Quantitative analysis reveals that the steady-state DHFR-TS mRNA and protein levels are not growth phase regulated, unlike the monofunctional mouse DHFR. DHFR-TS is developmentally regulated, however, declining about fivefold in lesion amastigotes relative to promastigotes.Trypanosomatid protozoan parasites comprise a group of eucaryotic organisms which use a number of unconventional strategies for gene expression. These include obligatory trans-splicing of a common nucleotide sequence, the miniexon, onto the 5' ends of all mRNAs (17, 57, 63, 70, 74; reviewed in 11), as well as editing of mitochondrial mRNAs (4,26). An increasing body of data suggests that some protein-coding mRNAs may be synthesized as larger polycistronic precursors, up to 60 kilobases (kb) in length, which are subsequently cleaved and processed into mature mRNAs. Evidence supporting this view includes the following: (i) determination of the size of a variant surface glycoprotein gene transcriptional unit by UV inactivation (38); (ii) demonstration of comparable transcription rates for flanking, mRNA-coding, and intergenic regions (30,46,72); and (iii) the identification of a putative polycistronic mRNA precursor (56). Whether this process is ubiquitous and what DNA sequences are involved in transcription initiation and mRNA processing remain to be determined because of the lack of striking sequence homology with consensus eucaryotic elements and the lack of in vitro or in vivo functional assays such as DNA transfection.We have examined the gene encoding ...

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“…RNA editing is posttranscriptional, involving the modification of pre-edited precursor RNAs (16). Editing appears to be functionally important in the correction of a frameshift mutation in the cytochrome oxidase subunit II (COII) mRNA (4), in generation of initiation codons near the 5' ends of cytochrome b (CYb) and maxicircle unidentified reading frame 2 mRNAs (13,14), and in creation of nearly the entire coding regions of the cytochrome oxidase subunit III (COIII), ATPase subunit 6, and NADH dehydrogenase subunit 7 mRNAs (5, 12, 17). The variation in the degree to which different mRNAs are edited is extreme.…”

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confidence: 99%

Specific cleavage of pre-edited mRNAs in trypanosome mitochondrial extracts.

Harris¹,

Decker²,

Sollner‐Webb³

et al. 1992

Mol. Cell. Biol.

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RNA editing in Trypanosoma brucei is a posttranscriptional processing event that results in the addition and deletion of uridine residues within several mitochondrial mRNAs. We have examined reactions involving pre-edited precursor RNAs in vitro. In this study, we report specific cleavage of pre-edited cytochrome b (CYb), cytochrome oxidase subunit II (COII), and cytochrome oxidase subunit III (COIII) mRNAs when incubated with T. brucei mitochondrial extracts. The pre-edited CYb RNA was cleaved near the 3'-most uridine addition sites, within the region where editing would be expected to commence. Pre-edited COII mRNA was similarly cleaved adjacent to its small editing domain, while pre-edited COIII RNA was cleaved at multiple sites in the region where uridine addition and deletion occurs in vivo. In contrast, edited versions of CYb, COII, and COIII RNAs were not cleaved within the editing domains. Such differential cleavage of the edited and pre-edited forms of these mRNAs suggests either a direct involvement in RNA editing or involvement in another aspect of mitochondrial gene expression requiring cleavage of pre-edited RNAs.RNA editing in kinetoplastid mitochondria involves the addition and, to a lesser degree, deletion of uridine (U) residues at defined sites within several mRNAs (reviewed in references 3, 11, and 24). RNA editing is posttranscriptional, involving the modification of pre-edited precursor RNAs (16). Editing appears to be functionally important in the correction of a frameshift mutation in the cytochrome oxidase subunit II (COII) mRNA (4), in generation of initiation codons near the 5' ends of cytochrome b (CYb) and maxicircle unidentified reading frame 2 mRNAs (13,14), and in creation of nearly the entire coding regions of the cytochrome oxidase subunit III (COIII), ATPase subunit 6, and NADH dehydrogenase subunit 7 mRNAs (5, 12, 17). The variation in the degree to which different mRNAs are edited is extreme. For example, COII mRNA has only four U's added, while completely edited COIII mRNA contains 558 added U's and has 40 U's deleted (11).The information required for formation of edited mRNAs from pre-edited precursors is found in small (-70-nucleotide [nt]) guide RNAs (gRNAs) (6). gRNAs from maxicircle (6) and minicircle (21, 26) mitochondrial DNAs exist in the steady-state RNA population, but their precise role in editing is unknown.Based on the structure of gRNA and the presence of mitochondrial terminal uridylyl transferase (TUTase) and RNA ligase activities, Blum et al. (6) proposed the following mechanism for RNA editing. First, a gRNA hybridizes to mRNA sequences 3' to an editing site. An endoribonuclease activity then cleaves the pre-edited RNA once at the site where the complementarity between the pre-edited mRNA and gRNA ends. The TUTase and RNA ligase activities then insert the U residues that are directed by the gRNA and rejoin the RNA chain. Decker and Sollner-Webb (10) more random U additions within defined regions of the pre-edited RNA. Homology between correctly edited seque...

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Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids.

Cited by 98 publications

References 25 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

Transcriptional mapping of the amplified region encoding the dihydrofolate reductase-thymidylate synthase of Leishmania major reveals a high density of transcripts, including overlapping and antisense RNAs.

Specific cleavage of pre-edited mRNAs in trypanosome mitochondrial extracts.

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