Nitrogen acquisition, PEP carboxylase, and cellular pH homeostasis: new views on old paradigms
Bibliographic record
Abstract
ABSTRACT The classic biochemical pH‐stat model of cytosolic pH regulation in plant cells presupposes a pH‐dependent biosynthesis and degradation of organic acids, specifically malic acid, in the cytosol. This model has been used to explain the higher tissue accumulation of organic acids in nitrate (NO3–)‐grown, relative to ammonium (NH4+)‐grown, plants, the result of proposed cytosolic alkalinization by NO3–metabolism, and acidification by NH4+metabolism. Here, a critical examination of the model shows that its key assumptions are fundamentally problematic, particularly in the context of the effects on cellular pH of nitrogen source differences. Specifically, the model fails to account for proton transport accompanying inorganic nitrogen transport, which, if considered, renders the H+production of combined transport and assimilation (although not the accumulation) to be equal for NO3–and NH4+as externally provided N sources. We show that the model's evidentiary basis in total‐tissue mineral ion and organic acid analysis is not directly relevant to subcellular (cytosolic) pH homeostasis, while the analysis of the ionic components of the cytosol is relevant to this process. A literature analysis further shows that the assumed greater activity of the enzyme phosphoenolpyruvate (PEP) carboxylase under nitrate nutrition, which is a key characteristic of the biochemical pH‐stat model as it applies to nitrogen source, is not borne out in numerous instances. We conclude that this model is not tenable in its current state, and propose an alternative model that reaffirms the anaplerotic role of PEP carboxylase within the context of N nutrition, in the production of carbon skeletons for amino acid synthesis.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.007 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.001 | 0.017 |
| Scholarly communication | 0.007 | 0.025 |
| Open science | 0.004 | 0.005 |
| Research integrity | 0.006 | 0.008 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".