Sigma factor based trasnscription#5
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tanbirbhai1212 wants to merge 4 commits intovivarium-collective:sRNA-regulationfrom
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Sigma factor based trasnscription#5tanbirbhai1212 wants to merge 4 commits intovivarium-collective:sRNA-regulationfrom
tanbirbhai1212 wants to merge 4 commits intovivarium-collective:sRNA-regulationfrom
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…ion' into sigma_factor_based_trasnscription # Conflicts: # configs/sigma_competition.json # configs/sigma_competition_stress.json # ecoli/library/sim_data.py
Removed: - Old process drafts: new_transcript_initiation_toy, new_ecoli_transcript_initiation, sigma_factor_competion_model, sigma_factor_model, WC_stationary_genes, RpoS_based_transcript_initiation, Stationary_phse_plotting, stationary_phase_transcript_initiation, oxidative_stress_backup - Old config iterations: ox_stress_base_v5, stress_mauri_klumpp_wcm, etc. - Old analysis files with typos: anaalysis-SIGMA-FACTOR, sigma_fcator_competition_analysis - Duplicate TranscriptInitiationSigma registration (deleted file) Kept (core files): - ecoli/processes/sigma_factor_transcript_initiation.py (5-sigma model) - ecoli/processes/mauri_klumpp_transcript_initiation.py (2-sigma model) - ecoli/processes/oxidative_stress.py (H2O2/OxyR/ppGpp coupling) - ecoli/processes/ppgpp_sustained_stress.py (stress helper) - ecoli/processes/sigma_competition_process.py (drop-in replacement) - configs: coupled_baseline, coupled_h2o2_stress, sigma_factor_wcm, oxidative_stress_wcm, oxidative_stress_challenge_wcm, original_wcm - scripts: coupled_analysis, publication_analysis, oxidative_stress_analysis
… 2006) Adjusted sigma_free_fractions from [1.0, 0.3, 0.02, 0.10, 0.05] to [1.0, 0.02, 0.01, 0.05, 0.02] to match in vivo holoenzyme fractions: σ70: 0.845 (target 0.85, Grigorova et al. 2006 Mol Cell) σ38: 0.044 (target 0.05, Jishage et al. 1996 J Bacteriol) σ32: 0.043 (target 0.05, Grossman et al. 1984 Cell) σ24: 0.044 (target 0.03) σ54: 0.024 (target 0.02) Biological basis for free fractions: σ38: 2% free (98% degraded by ClpXP, Zgurskaya et al. 1997) σ32: 1% free (99% sequestered by DnaK/DnaJ, Guisbert et al. 2004) σ24: 5% free (95% sequestered by RseA, Ades et al. 1999) σ54: 2% free (requires EBP activator, Cannon et al. 1999) Under stress (ppGpp=325µM, RpoS=2000): σ38 rises to 0.82 (Δ=+0.78)
New process: NutrientLimitation (ecoli-nutrient-limitation) Models carbon starvation → stringent response → growth arrest: glucose depletion → uncharged tRNA ↑ → RelA activation → ppGpp synthesis (kcat=15/s, positive feedback from Shyp et al. 2012) → ppGpp accumulates to ~380 µM in 2 min (lit: 200-500 µM) → RNAP active fraction ↓ → rRNA ↓ → growth arrest → RpoS stabilised (ClpXP inhibited by ppGpp) Literature parameters: RelA kcat: 15 s-1 (English et al. 2011 PNAS, with feedback) SpoT kcat: 0.5 s-1 (Xiao et al. 1991 J Biol Chem) Ks_glucose: 4 µM (Kovárová-Kovar & Egli 1998) ppGpp Km (SpoT): 50 µM (Murray & Bremer 1996) RpoS deg rate: 0.006 s-1 (t½=2min, Zgurskaya et al. 1997) Configs: nutrient_baseline.json, nutrient_starvation.json
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