title: Addition of non-genomically encoded nucleotides to the 3'-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA.
abstract: The 3'-termini of maize mitochondrial RNAs were characterized by ligation of an anchor oligonucleotide, reverse transcription and amplification. DNA sequence analysis of cDNA clones for tRNA(Ser) and 18S rRNA confirmed the expected 3'-terminal nucleotides and demonstrated the accuracy and fidelity of the protocol. Analysis of cDNAs for rps12, cox2 and atp9 indicated that non-genomically encoded nucleotides were present at the 3'-terminus. rps12 cDNAs exhibited the highest degree of modification, with 94% of 35 cDNA clones analyzed containing one to four non-genomically encoded C or A residues; 83% of these cDNAs terminated with the trinucleotide CCA. DNA sequence and transcript mapping analyses demonstrated that four positions exhibited modified 3'-termini within a small region of the 3' flank of rps12 transcripts. These transcript termini represented low abundance, truncated forms of rps12 mRNAs which may be intermediates in degradation. cox2 mRNAs are also modified at a truncated position. Sixty percent of the cox2 cDNAs were modified with 1-5 nt that most frequently included A and C residues, but also included a few G and T residues. Non-genomically encoded nucleotides were detected in 27% of the atp9 cDNAs as a single C or A residue.
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Williams
authors.forename: Y
authors.initials: Y
authors.lastname: Johzuka
authors.forename: R M
authors.initials: RM
authors.lastname: Mulligan
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D029681:Arabidopsis Proteins; D001483:Base Sequence; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D008928:Mitochondria / Q000235:genetics*; D025261:Mitochondrial Proton-Translocating ATPases; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics; D011510:Proteolipids / Q000235:genetics; D006180:Proton-Translocating ATPases / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012362:RNA, Transfer, Ser / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; C063668:ATP9 protein, Arabidopsis; D029681:Arabidopsis Proteins; D018076:DNA, Complementary; D010940:Plant Proteins; D011510:Proteolipids; D012333:RNA, Messenger; D018749:RNA, Plant; D012337:RNA, Ribosomal, 18S; D012362:RNA, Transfer, Ser; C103919:Rps12 protein, plant; C111957:cox2 protein, Glycine soja; D003576:Electron Transport Complex IV; D025261:Mitochondrial Proton-Translocating ATPases; D006180:Proton-Translocating ATPases