RNA editing site recognition in higher plant mitochondria.

RNA editing is a process by which genomically encoded cytidines are converted to uridines in plant mitochondrial transcripts. This conversion usually changes the amino acid specified by a codon and converts an "aberrant" residue to the evolutionarily conserved amino acid. The selection of the edited cytidine is highly specific. The cis-acting sequences for editing site recognition have been examined in ribosomal protein S12 (rps12) transcripts and in transcripts for a second copy of an internal portion of the ribosomal protein S12 (rps12b). rps12b was created by recombination at 7 and 9 nucleotide sequences that included editing sites I and IV of rps12, thus affording an opportunity to study the editing of chimeric transcripts with rearrangement very near C to U editing sites. Rearrangements downstream of editing site IV did not affect the editing of that sequence, while rearrangement upstream of editing site I ablated editing at that cytidine residue. Secondary structure predictions indicated that RNA structure did not correlate with the editing of these substrates. These results taken together with other studies in the literature suggest that RNA editing site recognition is primarily dependent on the 5' flanking RNA sequence.

[1]  J. Vaughn,et al.  RNA editing in Drosophila 4f-rnp gene nuclear transcripts by multiple A-to-G conversions. , 1996, Journal of molecular biology.

[2]  Jacques-Henry Weil,et al.  Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites , 1990, Nucleic Acids Res..

[3]  R. Bock,et al.  Identification of critical nucleotide positions for plastid RNA editing site recognition. , 1997, RNA.

[4]  R. Mulligan,et al.  RNA editing intermediates of cox2 transcripts in maize mitochondria. , 1991, Molecular and cellular biology.

[5]  P. Covello,et al.  On the evolution of RNA editing. , 1993, Trends in genetics : TIG.

[6]  A. Weiner,et al.  A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation , 1986, Cell.

[7]  M. W. Gray,et al.  Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. , 1993, Science.

[8]  Kenneth Stuart,et al.  Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei , 1988, Cell.

[9]  K. Pruitt,et al.  Editing of pre-mRNAs can occur before cis- and trans-splicing in Petunia mitochondria , 1991, Molecular and cellular biology.

[10]  K. Nishikura,et al.  Editing of the GLuR‐B ion channel RNA in vitro by recombinant double‐stranded RNA adenosine deaminase. , 1996, The EMBO journal.

[11]  M. Williams,et al.  Incomplete editing of rps12 transcripts results in the synthesis of polymorphic polypeptides in plant mitochondria. , 1996, The Plant cell.

[12]  James Scott,et al.  Evolutionary origins of apoB mRNA editing: Catalysis by a cytidine deaminase that has acquired a novel RNA-binding motif at its active site , 1995, Cell.

[13]  A. Brennicke,et al.  Regenerating good sense: RNA editing and trans splicing in plant mitochondria. , 1992, Trends in genetics : TIG.

[14]  R. Wolfenden,et al.  Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex. , 1994, Journal of molecular biology.

[15]  K. Yoshinaga,et al.  Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants. , 1996, Nucleic acids research.

[16]  J. Bachellerie,et al.  Guiding ribose methylation of rRNA. , 1997, Trends in biochemical sciences.

[17]  B. Bass,et al.  RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase , 1996, Nature.

[18]  J. Grienenberger,et al.  RNA editing in plant mitochondria , 1993 .

[19]  Z. Kiss-László,et al.  Sequence and structural elements of methylation guide snoRNAs essential for site‐specific ribose methylation of pre‐rRNA , 1998, The EMBO journal.

[20]  Wei Yu,et al.  Evidence for a Site-specific Cytidine Deamination Reaction Involved in C to U RNA Editing of Plant Mitochondria (*) , 1995, The Journal of Biological Chemistry.

[21]  Michael W. Gray,et al.  RNA editing in plant mitochondria , 1989, Nature.

[22]  R. Bock,et al.  In vivo dissection of cis‐acting determinants for plastid RNA editing. , 1996, The EMBO journal.

[23]  G. Igloi,et al.  Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. , 1995, Journal of molecular biology.

[24]  L Simpson,et al.  Guide RNA‐directed uridine insertion RNA editing in vitro. , 1996, The EMBO journal.

[25]  L. Simpson,et al.  Guide RNA-independent and Guide RNA-dependent Uridine Insertion into Cytochrome b mRNA in a Mitochondrial Lysate from Leishmania tarentolae , 1997, The Journal of Biological Chemistry.

[26]  R. Mahendran,et al.  Editing of the mitochondrial small subunit rRNA in Physarum polycephalum. , 1994, The EMBO journal.

[27]  Mark A. Williams,et al.  Editing and translation of ribosomal protein S13 transcripts: unedited translation products are not detectable in maize mitochondria , 1998, Current Genetics.

[28]  Laurie Smith,et al.  The RNA World of the Nucleolus: Two Major Families of Small RNAs Defined by Different Box Elements with Related Functions , 1996, Cell.

[29]  A Araya,et al.  RNA editing in wheat mitochondria proceeds by a deamination mechanism , 1995, FEBS letters.

[30]  Michael W. Gray,et al.  Transcription, processing and editing in plant mitochondria , 1992 .

[31]  D. Kolakofsky,et al.  Paramyxovirus mRNA editing leads to G deletions as well as insertions. , 1994, The EMBO journal.

[32]  A. Brennicke,et al.  RNA editing in bryophytes and a molecular phylogeny of land plants. , 1996, The EMBO journal.

[33]  J. Grienenberger,et al.  Expression of the wheat mitochondrial nad3-rps12 transcription unit: correlation between editing and mRNA maturation. , 1991, The Plant cell.

[34]  L. Simpson,et al.  Sense from nonsense: RNA editing in mitochondria of kinetoplastid protozoa and slime molds , 1995, Cell.

[35]  N. Navaratnam,et al.  Site-specific creation of uridine from cytidine in apolipoprotein B mRNA editing. , 1991, Nucleic acids research.

[36]  Brenda L. Bass,et al.  An unwinding activity that covalently modifies its double-stranded RNA substrate , 1988, Cell.

[37]  G. Schaffner,et al.  Ribozyme, antisense RNA, and antisense DNA inhibition of U7 small nuclear ribonucleoprotein-mediated histone pre-mRNA processing in vitro , 1989, Molecular and cellular biology.

[38]  R. Wilson,et al.  Sequencing, processing, and localization of the petunia CMS-associated mitochondrial protein. , 1994, The Plant journal : for cell and molecular biology.

[39]  Tamás Kiss,et al.  Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs , 1996, Cell.

[40]  J. Morrison,et al.  The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. , 1993, The Journal of biological chemistry.

[41]  T. Innerarity,et al.  Apolipoprotein B mRNA editing. Direct determination of the edited base and occurrence in non-apolipoprotein B-producing cell lines. , 1990, The Journal of biological chemistry.

[42]  Z W Gu,et al.  Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. , 1987, Science.

[43]  A. Weiner,et al.  A compensatory base change in human U2 snRNA can suppress a branch site mutation. , 1989, Genes & development.

[44]  J. Gott,et al.  Accurate and efficient insertional RNA editing in isolated Physarum mitochondria. , 1995, RNA.

[45]  N. Kubo,et al.  Involvement of 5′ flanking sequence for specifying RNA editing sites in plant mitochondria , 1997, FEBS letters.

[46]  V. K. Rajasekhar,et al.  RNA Editing in Plant Mitochondria: [alpha]-Phosphate Is Retained during C-to-U Conversion in mRNAs. , 1993, The Plant cell.

[47]  K. Stuart,et al.  Editing of kinetoplastid mitochondrial mRNAs by uridine addition and deletion generates conserved amino acid sequences and AUG initiation codons , 1988, Cell.

[48]  P. Seeburg,et al.  RNA editing of AMPA receptor subunit GluR-B: A base-paired intron-exon structure determines position and efficiency , 1993, Cell.

[49]  K. Stuart,et al.  RNA Editing: A Mechanism for gRNA-Specified Uridylate Insertion into Precursor mRNA , 1996, Science.

[50]  R. Pease,et al.  A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine , 1987, Cell.

[51]  R. Bock,et al.  Introduction of a heterologous editing site into the tobacco plastid genome: the lack of RNA editing leads to a mutant phenotype. , 1994, The EMBO journal.

[52]  P. Maliga,et al.  Sequences directing C to U editing of the plastid psbL mRNA are located within a 22 nucleotide segment spanning the editing site. , 1996, The EMBO journal.

[53]  M. W. Gray,et al.  RNA editing in plant mitochondria and chloroplasts , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[54]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[55]  R. Benne,et al.  Major transcript of the frameshifted coxll gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA , 1986, Cell.

[56]  K. Stuart,et al.  Direct Visualization of Uridylate Deletion In Vitro Suggests a Mechanism for Kinetoplastid RNA Editing , 1996, Cell.

[57]  José M. Gualberto,et al.  RNA editing in wheat mitochondria results in the conservation of protein sequences , 1989, Nature.