Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

Abstract

The Chlamydomonas reinhardtii plastid and mitochondrial transcriptomes were surveyed for changes in RNA profiles resulting from growth in 12 culture conditions representing 8 abiotic stimuli. Organellar RNA abundance exhibited marked changes during nutrient stress and exposure to UV light, as revealed by both RNA gel blot and DNA microarray analyses. Of particular note were large increases in tufA and clpP transcript abundance during nutrient limitation. Phosphate and sulfur limitation resulted in the most global, yet opposite, effects on organellar RNA abundance, changes that were dissected further using run-on transcription assays. Removal of sulfate from the culture medium, which is known to reduce photosynthesis, resulted in 2-fold to 10-fold decreases in transcription rates, which were reflected in lower RNA abundance. The decrease in transcriptional activity was completely reversible and recovered to twice the control level after sulfate replenishment. Conversely, phosphate limitation resulted in a twofold to threefold increase in RNA abundance that was found to be a post-transcriptional effect, because it could be accounted for by increased RNA stability. This finding is consistent with the known metabolic slowdown under phosphate stress. Additionally, inhibitor studies suggested that unlike those in higher plants, Chlamydomonas chloroplasts lack a nucleusencoded plastid RNA polymerase. The apparently single type of polymerase could contribute to the rapid and genomewide transcriptional responses observed within the chloroplast.

System Response of Metabolic Networks in Chlamydomonas reinhardtii to Total Available Ammonium

“…Such drastic differences in study parameters can lead to a plethora of systemic responses, but relevance of such data for applications in bioreactors or biofuel production is questionable (37,38). In difference to previous studies on differential gene expression in C. reinhardtii in response to nitrogen stress (13,39,40), we have here followed the biochemical responses to total ammonium availability from lag phase to the entry of stationary phases ensuring that ammonium uptake was not the limiting factor in cellular responses and that cell division remained unaltered. Using mass spectrometry for quantifying cellular responses on the level of protein and metabolite abundances, we show that C. reinhardtii readily responds to the total available ammonium content in its local environment, and that there are a range of biochemical modules that differ in a dynamic manner to cultures grown with "standard" starting ammonium conditions.…”

Evidence for regulatory function of nucleus-encoded factors on mRNA stabilization and translation in the chloroplast

“…Alternatively, they may serve regulatory functions that remain to be determined. Whether variations in their abundance accompanies physiological changes that affect chloroplast gene expression, such as changes in nutrient availability (9), circadian rhythms (10, 11), or gametic differentiation (12), has not been addressed up to now.…”

“…f expression in Chlamydomonas is tightly controlled by nitrogen availability: The abundance of petA mRNA decreases with a concomitant degradation of cyt. b 6 f complex upon nitrogen starvation (9). Wild-type, M-HA, and T-fl cells were cultured in nitrogen-deficient medium for up to 5 days and then transferred to nitrogen-repleted medium for several hours.…”

Paths toward Algal Genomics

“…With the generation of both cDNA and genomic information (Dutcher, 2000;Grossman, 2000;Dent et al, 2001;Lilly et al, 2002;Simpson and Stern, 2002;Grossman et al, 2003;Shrager et al, 2003; http:// genome.jgi-psf.org/chlre2/chlre2.home.html), DNA microarrays and macroarrays have been used to study biological processes in C. reinhardtii (Im et al, 2003;Miura et al, 2004;Yoshioka et al, 2004;Zhang et al, 2004). Furthermore, genome-wide and proteomic approaches are currently being used to understand the dynamics of the photosynthetic apparatus in response to nutrient conditions (Im et al, 2003;Zhang et al, 2004; Y. Wang, Z.…”