title: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae.
abstract: BACKGROUND
  The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution.
  
  
  RESULTS
  Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history.
  
  
  CONCLUSIONS
  These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
authors.affiliation: Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA. mbarthet@coastal.edu.|School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia. mbarthet@coastal.edu.
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Barthet
authors.affiliation: Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. kmzl@vt.edu.
authors.forename: Keenan
authors.initials: K
authors.lastname: Moukarzel
authors.affiliation: Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA. knsmith2@g.coastal.edu.
authors.forename: Kayla N
authors.initials: KN
authors.lastname: Smith
authors.affiliation: Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. jaimin1710@gmail.com.
authors.forename: Jaimin
authors.initials: J
authors.lastname: Patel
authors.affiliation: Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. hilukw@vt.edu.
authors.forename: Khidir W
authors.initials: KW
authors.lastname: Hilu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D018387:Codon, Initiator; D007438:Introns; D008969:Molecular Sequence Data; D009713:Nucleotidyltransferases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D029595:Orchidaceae / Q000145:classification / Q000201:enzymology* / Q000235:genetics*; D010802:Phylogeny; D018087:Plastids / Q000201:enzymology* / Q000235:genetics*; D011544:Pseudogenes; D012326:RNA Splicing; D012270:Ribosomes / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D018387:Codon, Initiator; D009713:Nucleotidyltransferases