Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA

Abstract

The genome of the unicellular, euryhaline cyanobacterium Synechococcus sp. PCC 7002 encodes about 3200 proteins. Transcripts were detected for nearly all annotated open reading frames by a global transcriptomic analysis by Next-Generation (SOLiD™) sequencing of cDNA. In the cDNA samples sequenced, ∼90% of the mapped sequences were derived from the 16S and 23S ribosomal RNAs and ∼10% of the sequences were derived from mRNAs. In cells grown photoautotrophically under standard conditions [38°C, 1% (v/v) CO2 in air, 250 μmol photons m−2 s−1], the highest transcript levels (up to 2% of the total mRNA for the most abundantly transcribed genes; e.g., cpcAB, psbA, psaA) were generally derived from genes encoding structural components of the photosynthetic apparatus. High-light exposure for 1 h caused changes in transcript levels for genes encoding proteins of the photosynthetic apparatus, Type-1 NADH dehydrogenase complex and ATP synthase, whereas dark incubation for 1 h resulted in a global decrease in transcript levels for photosynthesis-related genes and an increase in transcript levels for genes involved in carbohydrate degradation. Transcript levels for pyruvate kinase and the pyruvate dehydrogenase complex decreased sharply in cells incubated in the dark. Under dark anoxic (fermentative) conditions, transcript changes indicated a global decrease in transcripts for respiratory proteins and suggested that cells employ an alternative phosphoenolpyruvate degradation pathway via phosphoenolpyruvate synthase (ppsA) and the pyruvate:ferredoxin oxidoreductase (nifJ). Finally, the data suggested that an apparent operon involved in tetrapyrrole biosynthesis and fatty acid desaturation, acsF2–ho2–hemN2–desF, may be regulated by oxygen concentration.

Comparative Analysis of 126 Cyanobacterial Genomes Reveals Evidence of Functional Diversity Among Homologs of the Redox-Regulated CP12 Protein

“…In Synechococcus sp. PCC 7002, the ratio of expression of CP12-N-CBS under dark oxic conditions relative to standard growth conditions is 4-fold higher than that of CP12-N/C (Ludwig and Bryant, 2011). Under nitrogen deprivation, Nostoc sp.…”

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

“…Axenic batch cultures of Synechococcus 7002 were routinely grown in modified basal medium A containing: 18 g l -1 NaCl, 0.6 g l -1 KCl, 0.9 g l -1 NH 4 (Stevens and Porter, 1980;Ludwig and Bryant, 2011). The cultivation was carried out at room temperature in 1-L Roux bottles sparged with 2% CO 2 -enriched air under continuous 50 mmol m À 2 s À 1 illumination.…”

Identification and Regulation of Genes for Cobalamin Transport in the Cyanobacterium Synechococcus sp. Strain PCC 7002

“…strain PCC 7002 is a euryhaline, unicellular cyanobacterium that tolerates high light intensities and a wide range of NaCl concentrations (1,2). This organism has one of the highest growth rates among cyanobacteria (1,3) and is naturally transformable (4). Furthermore, the genome of Synechococcus sp.…”

“…Global transcription profiling by high-throughput RNA sequencing (RNA-seq) and characterization of the btu promoter variants with yfp reporter fusions support the presence of a predicted cobalamin riboswitch in the untranslated leader sequence upstream of this newly validated btu operon. (1). Antibiotics at the following concentrations were supplied when required: 50 g of spectinomycin ml -1 , 100 g of kanamycin ml -1 , 20 g of erythromycin ml -1 , and 20 g of gentamicin ml -1 .…”