Dissecting nitrogen starvation signaling in Chlamydomonas: Insights from arginine-fed transcriptome profiling
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Bibliographic record
Abstract
Nitrogen (N) acquisition from environmental sources is critical for most organisms. In plants and other photosynthetic eukaryotes, the limitation of available N induces global changes in gene expression; yet, the underlying regulatory mechanisms remain largely unknown. Chlamydomonas reinhardtii primarily utilizes inorganic N sources but also thrives on organic N sources like arginine. Our recent characterization of the molecular and physiological responses of arginine-fed Chlamydomonas cultures reveals a stark resemblance to the responses invoked by N starvation. To determine if arginine feeding triggers full-scale N starvation responses in the absence of metabolic N limitation, we compared the transcriptomes of arginine-fed cultures with those of early and late stages of N starvation. Our analysis shows that arginine-fed cells maintain both the N starvation-induced upregulation of N scavenging genes and genome-wide downregulation of genes involved in energy-producing carbon flow during exponential growth. Our study defines the N starvation-triggered gene regulatory network in two tiers: the early response involves N scavenging within the first two hours, and the late response includes the rerouting of energy-producing carbon flow into the biosynthesis of energy storage molecules. This regulation operates independently of growth, allowing cells to balance N and carbon budgets regardless of growth status. Our findings pave the way for future research on the triggers of N starvation responses in photosynthetic eukaryotic organisms and the strategies to enhance the production of starvation-associated high-value products in microalgae. • The genes that are commonly regulated by N-depletion and arginine-feeding compared to N-replete cultures are collected as N starvation-specific genes. • N starvation signal activates N scavenging genes and represses photosynthesis-related genes. • Arginine-fed culture provides a stress-free cell model for bona fide N starvation signaling and responses. • Arginine-fed cells represent N-heterotrophy, where energetic carbon can be redirected to the biosynthesis of carbon storage molecules, such as TAG, at the expense of organic N for growth.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it