🦠 E. coli Cellular Processes

Programming Framework Analysis - 10 Core Processes

🧬 Detailed Mermaid Flowcharts

Important Note: This document contains detailed E. coli cellular process flowcharts rendered using embedded Mermaid code with detail-preserving configuration to demonstrate the full complexity of bacterial cellular processes as computational programs.

Each flowchart uses the programming framework methodology to model biological processes as computational systems, showing how bacterial cells process information, make decisions, and execute responses through molecular networks that function like biological software.

1. Beta-Galactosidase (Lac Operon)

The classic bacterial gene regulation system demonstrating how E. coli processes environmental lactose and glucose signals through regulatory logic gates to control enzyme production.

graph TD %% Environmental Inputs A[Lactose in Environment] --> B[Lactose Transport] C[Glucose in Environment] --> D[Glucose Transport] E[Low Energy Status] --> F[Energy Stress Signal] %% Lactose Processing B --> G[Lactose Permease LacY] G --> H[Lactose Inside Cell] H --> I[Lactose Availability] %% Regulatory Logic I --> J{Is Lactose Present?} J -->|Yes| K[Lac Repressor Inactive] J -->|No| L[Lac Repressor Active] %% Transcription Control K --> M[Operator Free] L --> N[Transcription Blocked] M --> O[RNA Polymerase Binding] O --> P[Transcription Initiation] %% Enzyme Production P --> Q[Beta-Galactosidase] P --> R[Lactose Permease] P --> S[Galactoside Acetyltransferase] %% Functional Outputs Q --> T[Lactose Hydrolysis] R --> U[Lactose Transport] T --> V[Glucose + Galactose] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#ffd43b,color:#000 style D fill:#ffd43b,color:#000 style F fill:#ffd43b,color:#000 style G fill:#ffd43b,color:#000 style H fill:#74c0fc,color:#fff style I fill:#74c0fc,color:#fff style J fill:#74c0fc,color:#fff style K fill:#ffd43b,color:#000 style L fill:#ffd43b,color:#000 style M fill:#74c0fc,color:#fff style N fill:#74c0fc,color:#fff style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#b197fc,color:#fff style R fill:#b197fc,color:#fff style S fill:#b197fc,color:#fff style T fill:#b197fc,color:#fff style U fill:#b197fc,color:#fff style V fill:#b197fc,color:#fff
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2. Chemotaxis

Bacterial navigation system showing how E. coli processes chemical gradients to direct movement through sophisticated signal processing and motor control.

graph TD %% Environmental Inputs A[Chemical Attractants] --> B[Attractant Detection] C[Chemical Repellents] --> D[Repellent Detection] E[Gradient Changes] --> F[Temporal Sensing] %% Signal Transduction B --> G[CheA Kinase] D --> G F --> G G --> H[CheY Phosphorylation] %% Motor Control H --> I{CheY-P Level?} I -->|High| J[Clockwise Rotation] I -->|Low| K[Counterclockwise Rotation] %% Swimming Behavior J --> L[Tumbling] K --> M[Smooth Swimming] L --> N[Random Direction] M --> O[Straight Movement] %% Adaptation H --> P[CheZ Phosphatase] P --> Q[CheY Dephosphorylation] Q --> R[Signal Termination] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#ffd43b,color:#000 style D fill:#ffd43b,color:#000 style F fill:#ffd43b,color:#000 style G fill:#ffd43b,color:#000 style H fill:#74c0fc,color:#fff style I fill:#74c0fc,color:#fff style J fill:#b197fc,color:#fff style K fill:#b197fc,color:#fff style L fill:#b197fc,color:#fff style M fill:#b197fc,color:#fff style N fill:#b197fc,color:#fff style O fill:#b197fc,color:#fff style P fill:#ffd43b,color:#000 style Q fill:#74c0fc,color:#fff style R fill:#b197fc,color:#fff
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3. SOS Response

DNA damage emergency response system showing how E. coli detects and responds to genetic threats through error detection and repair protocols.

graph TD %% DNA Damage Signals A[UV Radiation] --> B[DNA Damage Detection] C[Chemical Mutagens] --> B D[Replication Stress] --> B %% Damage Recognition B --> E[Single-strand DNA] E --> F[RecA Protein Binding] F --> G[RecA Activation] %% LexA Control G --> H{RecA Active?} H -->|Yes| I[LexA Cleavage] H -->|No| J[LexA Repressor Active] %% SOS Activation I --> K[Operator Sites Free] K --> L[RNA Polymerase Binding] L --> M[SOS Gene Transcription] %% DNA Repair M --> N[UvrA Expression] M --> O[UvrB Expression] M --> P[UvrC Expression] N --> Q[Damage Recognition] O --> Q P --> R[Damage Excision] Q --> R R --> S[DNA Repair Complete] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style D fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style E fill:#74c0fc,color:#fff style F fill:#ffd43b,color:#000 style G fill:#ffd43b,color:#000 style H fill:#74c0fc,color:#fff style I fill:#ffd43b,color:#000 style J fill:#ffd43b,color:#000 style K fill:#74c0fc,color:#fff style L fill:#ffd43b,color:#000 style M fill:#ffd43b,color:#000 style N fill:#ffd43b,color:#000 style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#ffd43b,color:#000 style R fill:#ffd43b,color:#000 style S fill:#b197fc,color:#fff
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4. Tryptophan Biosynthesis

Amino acid production pathway with sophisticated feedback control and transcriptional attenuation showing how E. coli regulates enzyme synthesis based on amino acid availability.

graph TD %% Environmental Inputs A[Tryptophan Availability] --> B[Tryptophan Transport] C[Chorismate Precursor] --> D[Pathway Initiation] E[Energy Status ATP] --> F[Metabolic Readiness] %% Transport and Sensing B --> G[TrpT Transporter] G --> H[Internal Tryptophan] H --> I[Tryptophan Pool] %% Transcriptional Control I --> J{Tryptophan High?} J -->|Yes| K[TrpR Repressor Active] J -->|No| L[TrpR Repressor Inactive] %% Enzyme Production L --> M[trp Operon Transcription] M --> N[TrpE Translation] M --> O[TrpD Translation] M --> P[TrpC Translation] M --> Q[TrpB Translation] M --> R[TrpA Translation] %% Biosynthetic Pathway D --> S[Anthranilate Synthase] S --> T[Anthranilate] T --> U[PRA Formation] U --> V[InGP Formation] V --> W[Tryptophan Synthase] W --> X[Tryptophan Production] %% Feedback Regulation X --> Y[Product Inhibition] Y --> Z[Pathway Slowdown] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#ffd43b,color:#000 style D fill:#ffd43b,color:#000 style F fill:#ffd43b,color:#000 style G fill:#ffd43b,color:#000 style H fill:#74c0fc,color:#fff style I fill:#74c0fc,color:#fff style J fill:#74c0fc,color:#fff style K fill:#ffd43b,color:#000 style L fill:#ffd43b,color:#000 style M fill:#ffd43b,color:#000 style N fill:#ffd43b,color:#000 style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#ffd43b,color:#000 style R fill:#ffd43b,color:#000 style S fill:#ffd43b,color:#000 style T fill:#74c0fc,color:#fff style U fill:#74c0fc,color:#fff style V fill:#74c0fc,color:#fff style W fill:#ffd43b,color:#000 style X fill:#b197fc,color:#fff style Y fill:#ffd43b,color:#000 style Z fill:#b197fc,color:#fff
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5. Iron Homeostasis

Essential metal management system showing how E. coli balances iron acquisition, storage, and toxicity protection through complex regulatory networks.

graph TD %% Environmental Iron Status A[Iron Availability] --> B[Iron Sensing] C[Iron Limitation] --> D[Stress Signal] E[Iron Excess] --> F[Toxicity Risk] %% Iron Transport Systems D --> G[FepA Receptor] D --> H[FhuA Receptor] D --> I[Siderophore Production] %% Iron Uptake G --> J[Outer Membrane Transport] H --> J I --> K[Iron Chelation] K --> L[Fe-Enterobactin] J --> M[Cytoplasmic Iron] %% Fur Regulatory System M --> N{Iron Sufficient?} N -->|Yes| O[Fur-Fe Complex] N -->|No| P[Apo-Fur] O --> Q[Gene Repression] P --> R[Derepression] %% Iron Storage M --> S{Iron Excess?} S -->|Yes| T[Ferritin Induction] S -->|No| U[Normal Storage] T --> V[Iron Sequestration] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style D fill:#74c0fc,color:#fff style F fill:#74c0fc,color:#fff style G fill:#ffd43b,color:#000 style H fill:#ffd43b,color:#000 style I fill:#ffd43b,color:#000 style J fill:#ffd43b,color:#000 style K fill:#ffd43b,color:#000 style L fill:#74c0fc,color:#fff style M fill:#74c0fc,color:#fff style N fill:#74c0fc,color:#fff style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#ffd43b,color:#000 style R fill:#ffd43b,color:#000 style S fill:#74c0fc,color:#fff style T fill:#ffd43b,color:#000 style U fill:#ffd43b,color:#000 style V fill:#b197fc,color:#fff
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6. Heat Shock Response

Temperature stress management system showing how E. coli detects and responds to thermal damage through chaperones and recovery mechanisms.

graph TD %% Temperature Stress A[Temperature Increase] --> B[Protein Unfolding] C[Heat Shock] --> D[Membrane Stress] E[Thermal Damage] --> F[Cellular Stress] %% Stress Detection B --> G[Misfolded Proteins] D --> H[Membrane Disruption] F --> I[Stress Signal] %% Sigma Factor Regulation I --> J[σ32 Activation] J --> K[Heat Shock Promoters] K --> L[HSP Gene Expression] %% DnaK/DnaJ System L --> M[DnaK Chaperone] L --> N[DnaJ Co-chaperone] G --> O[Substrate Recognition] O --> P[Protein-DnaK Complex] P --> Q[Protein Refolding] %% Quality Control Q --> R{Refolding Success?} R -->|Yes| S[Native Protein] R -->|No| T[Repeat Cycle] R -->|Failed| U[Degradation Target] %% Recovery S --> V[Protein Function Restored] V --> W[Cellular Function] W --> X[Temperature Tolerance] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style D fill:#74c0fc,color:#fff style F fill:#74c0fc,color:#fff style G fill:#74c0fc,color:#fff style H fill:#74c0fc,color:#fff style I fill:#74c0fc,color:#fff style J fill:#ffd43b,color:#000 style K fill:#ffd43b,color:#000 style L fill:#ffd43b,color:#000 style M fill:#ffd43b,color:#000 style N fill:#ffd43b,color:#000 style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#ffd43b,color:#000 style R fill:#74c0fc,color:#fff style S fill:#b197fc,color:#fff style T fill:#ffd43b,color:#000 style U fill:#b197fc,color:#fff style V fill:#b197fc,color:#fff style W fill:#b197fc,color:#fff style X fill:#b197fc,color:#fff
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7. Nitrogen Metabolism

Nitrogen assimilation and regulation system showing how E. coli processes various nitrogen sources for amino acid and nucleotide synthesis.

graph TD %% Nitrogen Sources A[Ammonia NH3] --> B[Ammonia Transport] C[Nitrate NO3] --> D[Nitrate Transport] E[Amino Acids] --> F[Amino Acid Transport] %% Transport Systems B --> G[AmtB Transporter] D --> H[NarK Transporter] F --> I[General Amino Acid Permease] %% Nitrogen Assimilation G --> J[NH4+ Pool] H --> K[NO3- Reduction] I --> L[Amino Acid Pool] K --> M[NH4+ Production] M --> J %% Glutamine Synthetase System J --> N{NH4+ Concentration?} N -->|High| O[Direct Assimilation] N -->|Low| P[GlnA Activation] P --> Q[Glutamine Synthetase] Q --> R[Glutamine Formation] %% GOGAT System R --> S[Glutamine Pool] S --> T[GltBD GOGAT] T --> U[2 Glutamate] U --> V[Amino Acid Biosynthesis] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#ffd43b,color:#000 style D fill:#ffd43b,color:#000 style F fill:#ffd43b,color:#000 style G fill:#ffd43b,color:#000 style H fill:#ffd43b,color:#000 style I fill:#ffd43b,color:#000 style J fill:#74c0fc,color:#fff style K fill:#ffd43b,color:#000 style L fill:#74c0fc,color:#fff style M fill:#ffd43b,color:#000 style N fill:#74c0fc,color:#fff style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#ffd43b,color:#000 style R fill:#b197fc,color:#fff style S fill:#74c0fc,color:#fff style T fill:#ffd43b,color:#000 style U fill:#b197fc,color:#fff style V fill:#b197fc,color:#fff
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8. Cell Division

Bacterial cell division machinery showing how E. coli coordinates chromosome segregation, septum formation, and daughter cell separation.

graph TD %% Division Initiation Signals A[Cell Size Critical] --> B[Division Signal] C[DNA Replication Complete] --> D[Chromosome Signal] E[Nutrient Availability] --> F[Growth Signal] %% Cell Cycle Checkpoints B --> G{Size Adequate?} D --> H{DNA Segregated?} F --> I{Resources Available?} G -->|Yes| J[Division Permitted] H -->|Yes| J I -->|Yes| J %% FtsZ Ring Assembly J --> K[FtsZ Polymerization] K --> L[Z-ring Formation] L --> M[FtsZ-ring Positioning] M --> N[Mid-cell Localization] %% Divisome Assembly N --> O[FtsA Recruitment] O --> P[ZipA Recruitment] P --> Q[FtsK Assembly] Q --> R[Divisome Complete] %% Chromosome Segregation D --> S[Chromosome Duplication] S --> T[ParAB System] T --> U[oriC Separation] U --> V[Nucleoid Segregation] %% Peptidoglycan Synthesis R --> W[Septum Initiation] W --> X[FtsW Lipid II Transport] X --> Y[FtsI Transpeptidase] Y --> Z[Peptidoglycan Cross-linking] Z --> AA[Septum Formation] %% Cell Separation AA --> BB[Cell Wall Constriction] BB --> CC[Septum Completion] CC --> DD[Daughter Cell Formation] DD --> EE[Cell Separation] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style D fill:#74c0fc,color:#fff style F fill:#74c0fc,color:#fff style G fill:#74c0fc,color:#fff style H fill:#74c0fc,color:#fff style I fill:#74c0fc,color:#fff style J fill:#ffd43b,color:#000 style K fill:#ffd43b,color:#000 style L fill:#ffd43b,color:#000 style M fill:#ffd43b,color:#000 style N fill:#ffd43b,color:#000 style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#ffd43b,color:#000 style R fill:#ffd43b,color:#000 style S fill:#ffd43b,color:#000 style T fill:#ffd43b,color:#000 style U fill:#ffd43b,color:#000 style V fill:#ffd43b,color:#000 style W fill:#ffd43b,color:#000 style X fill:#ffd43b,color:#000 style Y fill:#ffd43b,color:#000 style Z fill:#ffd43b,color:#000 style AA fill:#ffd43b,color:#000 style BB fill:#ffd43b,color:#000 style CC fill:#ffd43b,color:#000 style DD fill:#b197fc,color:#fff style EE fill:#b197fc,color:#fff
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9. Biofilm Formation

Multicellular community formation system showing how E. coli transitions from planktonic to sessile lifestyle through quorum sensing and matrix production.

graph TD %% Environmental Triggers A[Surface Contact] --> B[Adhesion Signal] C[Nutrient Limitation] --> D[Stress Signal] E[Cell Density] --> F[Quorum Signal] %% Initial Attachment B --> G[Flagellar Contact] G --> H[Surface Recognition] H --> I[Reversible Attachment] I --> J{Surface Suitable?} J -->|Yes| K[Attachment Commitment] J -->|No| L[Detachment] %% Adhesion Mechanisms K --> M[Type I Pili Expression] M --> N[FimA Assembly] N --> O[Mannose-specific Binding] O --> P[Irreversible Attachment] %% Curli Fiber Production P --> Q[csg Operon Activation] Q --> R[CsgA Monomer] Q --> S[CsgB Nucleator] R --> T[Curli Assembly] S --> T T --> U[Amyloid Fibers] U --> V[Strong Adhesion] %% Biofilm Development V --> W[Microcolony Formation] W --> X[Coordinated Development] X --> Y[Cell-Cell Adhesion] Y --> Z[Multilayer Structure] %% Matrix Maturation Z --> AA[EPS Production] AA --> BB[Extracellular DNA] AA --> CC[Protein Secretion] BB --> DD[Matrix Integration] CC --> DD DD --> EE[Biofilm Architecture] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style D fill:#74c0fc,color:#fff style F fill:#74c0fc,color:#fff style G fill:#ffd43b,color:#000 style H fill:#ffd43b,color:#000 style I fill:#ffd43b,color:#000 style J fill:#74c0fc,color:#fff style K fill:#ffd43b,color:#000 style L fill:#b197fc,color:#fff style M fill:#ffd43b,color:#000 style N fill:#ffd43b,color:#000 style O fill:#ffd43b,color:#000 style P fill:#b197fc,color:#fff style Q fill:#ffd43b,color:#000 style R fill:#ffd43b,color:#000 style S fill:#ffd43b,color:#000 style T fill:#ffd43b,color:#000 style U fill:#b197fc,color:#fff style V fill:#b197fc,color:#fff style W fill:#ffd43b,color:#000 style X fill:#ffd43b,color:#000 style Y fill:#ffd43b,color:#000 style Z fill:#b197fc,color:#fff style AA fill:#ffd43b,color:#000 style BB fill:#ffd43b,color:#000 style CC fill:#ffd43b,color:#000 style DD fill:#ffd43b,color:#000 style EE fill:#b197fc,color:#fff
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10. Phage Defense (CRISPR-Cas)

Adaptive immune system showing how E. coli acquires, stores, and uses genetic memory to defend against phage infections through targeted defense responses.

graph TD %% Phage Infection A[Phage Attachment] --> B[DNA Injection] C[Phage Replication] --> D[Foreign DNA Signal] E[Viral Proteins] --> F[Infection Detection] %% Spacer Acquisition B --> G[Cas1-Cas2 Complex] D --> G F --> G G --> H[Foreign DNA Recognition] H --> I[PAM Sequence Identification] I --> J[Protospacer Selection] J --> K[DNA Cleavage] K --> L[Spacer Processing] %% CRISPR Array Integration L --> M[Leader Sequence Targeting] M --> N[Array Integration] N --> O[New Spacer Addition] O --> P[Genetic Memory Storage] P --> Q[Inherited Immunity] %% Transcription and Processing Q --> R[CRISPR Transcription] R --> S[pre-crRNA Synthesis] S --> T[Cas6 Endonuclease] T --> U[crRNA Processing] U --> V[Mature crRNA] V --> W[Guide RNA Ready] %% Surveillance Complex W --> X[Cas3 Recruitment] X --> Y[Cascade Complex] Y --> Z[crRNA Loading] Z --> AA[Surveillance Mode] %% Target Recognition AA --> BB[DNA Scanning] BB --> CC{PAM Present?} CC -->|Yes| DD[PAM Recognition] CC -->|No| EE[Continue Scanning] DD --> FF[R-loop Formation] FF --> GG[Target Validation] %% Sequence Matching GG --> HH{Perfect Match?} HH -->|Yes| II[Target Confirmed] HH -->|No| JJ[Mismatch Detected] II --> KK[Cas3 Activation] KK --> LL[DNA Degradation] %% Immune Response LL --> MM[Phage DNA Destruction] MM --> NN[Infection Clearance] NN --> OO[Cell Survival] OO --> PP[Immunity Acquired] %% Styling - Programming Framework Colors style A fill:#ff6b6b,color:#fff style C fill:#ff6b6b,color:#fff style E fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style D fill:#74c0fc,color:#fff style F fill:#74c0fc,color:#fff style G fill:#ffd43b,color:#000 style H fill:#ffd43b,color:#000 style I fill:#ffd43b,color:#000 style J fill:#ffd43b,color:#000 style K fill:#ffd43b,color:#000 style L fill:#ffd43b,color:#000 style M fill:#ffd43b,color:#000 style N fill:#ffd43b,color:#000 style O fill:#ffd43b,color:#000 style P fill:#ffd43b,color:#000 style Q fill:#b197fc,color:#fff style R fill:#ffd43b,color:#000 style S fill:#b197fc,color:#fff style T fill:#ffd43b,color:#000 style U fill:#ffd43b,color:#000 style V fill:#b197fc,color:#fff style W fill:#b197fc,color:#fff style X fill:#ffd43b,color:#000 style Y fill:#74c0fc,color:#fff style Z fill:#b197fc,color:#fff style AA fill:#b197fc,color:#fff style BB fill:#ffd43b,color:#000 style CC fill:#74c0fc,color:#fff style DD fill:#ffd43b,color:#000 style EE fill:#ffd43b,color:#000 style FF fill:#ffd43b,color:#000 style GG fill:#ffd43b,color:#000 style HH fill:#74c0fc,color:#fff style II fill:#ffd43b,color:#000 style JJ fill:#ffd43b,color:#000 style KK fill:#ffd43b,color:#000 style LL fill:#ffd43b,color:#000 style MM fill:#b197fc,color:#fff style NN fill:#b197fc,color:#fff style OO fill:#b197fc,color:#fff style PP fill:#b197fc,color:#fff
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