title: The primary transcriptome of the marine diazotroph Trichodesmium erythraeum IMS101.
abstract: Blooms of the dinitrogen-fixing marine cyanobacterium Trichodesmium considerably contribute to new nitrogen inputs into tropical oceans. Intriguingly, only 60% of the Trichodesmium erythraeum IMS101 genome sequence codes for protein, compared with ~85% in other sequenced cyanobacterial genomes. The extensive non-coding genome fraction suggests space for an unusually high number of unidentified, potentially regulatory non-protein-coding RNAs (ncRNAs). To identify the transcribed fraction of the genome, here we present a genome-wide map of transcriptional start sites (TSS) at single nucleotide resolution, revealing the activity of 6,080 promoters. We demonstrate that T. erythraeum has the highest number of actively splicing group II introns and the highest percentage of TSS yielding ncRNAs of any bacterium examined to date. We identified a highly transcribed retroelement that serves as template repeat for the targeted mutation of at least 12 different genes by mutagenic homing. Our findings explain the non-coding portion of the T. erythraeum genome by the transcription of an unusually high number of non-coding transcripts in addition to the known high incidence of transposable elements. We conclude that riboregulation and RNA maturation-dependent processes constitute a major part of the Trichodesmium regulatory apparatus.
authors.affiliation: University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Pfreundt
authors.affiliation: University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Kopf
authors.affiliation: Bar Ilan University Tel Aviv, Mina and Everard Goodman Faculty of Life Sciences, Israel.
authors.forename: Natalia
authors.initials: N
authors.lastname: Belkin
authors.affiliation: Bar Ilan University Tel Aviv, Mina and Everard Goodman Faculty of Life Sciences, Israel.
authors.forename: Ilana
authors.initials: I
authors.lastname: Berman-Frank
authors.affiliation: University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D000458:Cyanobacteria / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D007438:Introns; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D018626:Retroelements; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D018626:Retroelements