title: Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control.
abstract: Gene expression in nongreen plastids is largely uncharacterized. To compare gene expression in potato (Solanum tuberosum) tuber amyloplasts and leaf chloroplasts, amounts of transcripts of all plastid genes were determined by hybridization to plastome arrays. Except for a few genes, transcript accumulation was much lower in tubers compared with leaves. Transcripts of photosynthesis-related genes showed a greater reduction in tubers compared with leaves than transcripts of genes for the genetic system. Plastid genome copy number in tubers was 2- to 3-fold lower than in leaves and thus cannot account for the observed reduction of transcript accumulation in amyloplasts. Both the plastid-encoded and the nucleus-encoded RNA polymerases were active in potato amyloplasts. Transcription initiation sites were identical in chloroplasts and amyloplasts, although some differences in promoter utilization between the two organelles were evident. For some intron-containing genes, RNA splicing was less efficient in tubers than in leaves. Furthermore, tissue-specific differences in editing of ndh transcripts were detected. Hybridization of the plastome arrays with RNA extracted from polysomes indicated that, in tubers, ribosome association of transcripts was generally low. Nevertheless, some mRNAs, such as the transcript of the fatty acid biosynthesis gene accD, displayed relatively high ribosome association. Selected nuclear genes involved in plastid gene expression were generally significantly less expressed in tubers than in leaves. Hence, compared with leaf chloroplasts, gene expression in tuber amyloplasts is much lower, with control occurring at the transcriptional, posttranscriptional, and translational levels. Candidate regulatory sequences that potentially can improve plastid (trans)gene expression in amyloplasts have been identified.
authors.affiliation: Consiglio Nazionale delle Ricerche, Istituto di Genetica Vegetale, 80055 Portici, Italy.
authors.forename: Vladimir T
authors.initials: VT
authors.lastname: Valkov
authors.forename: Nunzia
authors.initials: N
authors.lastname: Scotti
authors.forename: Sabine
authors.initials: S
authors.lastname: Kahlau
authors.forename: Daniel
authors.initials: D
authors.lastname: Maclean
authors.forename: Stefania
authors.initials: S
authors.lastname: Grillo
authors.forename: John C
authors.initials: JC
authors.lastname: Gray
authors.forename: Ralph
authors.initials: R
authors.lastname: Bock
authors.forename: Teodoro
authors.initials: T
authors.lastname: Cardi
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics*; D017931:DNA Primers / Q000378:metabolism; D018628:Gene Dosage; D018506:Gene Expression Regulation, Plant; D054628:Genome, Chloroplast / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D018515:Plant Leaves / Q000235:genetics*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D035281:Plant Tubers / Q000235:genetics*; D011132:Polyribosomes / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D014176:Protein Biosynthesis; D017393:RNA Editing / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional; D012326:RNA Splicing / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D011198:Solanum tuberosum / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D017931:DNA Primers; D010940:Plant Proteins; D012333:RNA, Messenger