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| | <title>E. coli Cellular Processes - Programming Framework Analysis</title> |
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| | <div class="container"> |
| | <div class="header"> |
| | <h1>🦠 E. coli Cellular Processes</h1> |
| | <p>Programming Framework Analysis - 10 Core Processes</p> |
| | </div> |
| | <div class="content"> |
| | <div class="intro"> |
| | <h2>🧬 Detailed Mermaid Flowcharts</h2> |
| | <p><strong>Important Note:</strong> 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.</p> |
| | <p>Each flowchart uses the <strong>programming framework</strong> 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.</p> |
| | </div> |
| | |
| | <div class="toc"> |
| | <h2>📋 Table of Contents - 10 E. coli Processes</h2> |
| | <ul> |
| | <li><a href="#beta-galactosidase">1. Beta-Galactosidase (Lac Operon)</a></li> |
| | <li><a href="#chemotaxis">2. Chemotaxis</a></li> |
| | <li><a href="#sos-response">3. SOS Response</a></li> |
| | <li><a href="#tryptophan">4. Tryptophan Biosynthesis</a></li> |
| | <li><a href="#iron-homeostasis">5. Iron Homeostasis</a></li> |
| | <li><a href="#heat-shock">6. Heat Shock Response</a></li> |
| | <li><a href="#nitrogen">7. Nitrogen Metabolism</a></li> |
| | <li><a href="#cell-division">8. Cell Division</a></li> |
| | <li><a href="#biofilm">9. Biofilm Formation</a></li> |
| | <li><a href="#crispr">10. Phage Defense (CRISPR-Cas)</a></li> |
| | </ul> |
| | </div> |
| | |
| | |
| | <div class="process-item" id="beta-galactosidase"> |
| | <h3>1. Beta-Galactosidase (Lac Operon)</h3> |
| | <p>The classic bacterial gene regulation system demonstrating how E. coli processes environmental lactose and glucose signals through regulatory logic gates to control enzyme production.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="chemotaxis"> |
| | <h3>2. Chemotaxis</h3> |
| | <p>Bacterial navigation system showing how E. coli processes chemical gradients to direct movement through sophisticated signal processing and motor control.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="sos-response"> |
| | <h3>3. SOS Response</h3> |
| | <p>DNA damage emergency response system showing how E. coli detects and responds to genetic threats through error detection and repair protocols.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="tryptophan"> |
| | <h3>4. Tryptophan Biosynthesis</h3> |
| | <p>Amino acid production pathway with sophisticated feedback control and transcriptional attenuation showing how E. coli regulates enzyme synthesis based on amino acid availability.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="iron-homeostasis"> |
| | <h3>5. Iron Homeostasis</h3> |
| | <p>Essential metal management system showing how E. coli balances iron acquisition, storage, and toxicity protection through complex regulatory networks.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="heat-shock"> |
| | <h3>6. Heat Shock Response</h3> |
| | <p>Temperature stress management system showing how E. coli detects and responds to thermal damage through chaperones and recovery mechanisms.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="nitrogen"> |
| | <h3>7. Nitrogen Metabolism</h3> |
| | <p>Nitrogen assimilation and regulation system showing how E. coli processes various nitrogen sources for amino acid and nucleotide synthesis.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="cell-division"> |
| | <h3>8. Cell Division</h3> |
| | <p>Bacterial cell division machinery showing how E. coli coordinates chromosome segregation, septum formation, and daughter cell separation.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="biofilm"> |
| | <h3>9. Biofilm Formation</h3> |
| | <p>Multicellular community formation system showing how E. coli transitions from planktonic to sessile lifestyle through quorum sensing and matrix production.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| |
|
| | |
| | <div class="process-item" id="crispr"> |
| | <h3>10. Phage Defense (CRISPR-Cas)</h3> |
| | <p>Adaptive immune system showing how E. coli acquires, stores, and uses genetic memory to defend against phage infections through targeted defense responses.</p> |
| | <div class="mermaid-container"> |
| | <div class="mermaid"> |
| | 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 |
| | </div> |
| | <div class="color-legend"> |
| | <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| | <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| | <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| | <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| | </div> |
| | </div> |
| | </div> |
| | |
| | <div class="footer"> |
| | <p><strong>Generated using the Programming Framework methodology</strong></p> |
| | <p>These detailed flowcharts demonstrate the full complexity of E. coli cellular processes as computational programs</p> |
| | <p>Each flowchart preserves the intricate detail through optimized Mermaid configuration and shows the computational nature of biological systems</p> |
| | </div> |
| | </div> |
| | </div> |
| | |
| | <script> |
| | mermaid.initialize({ |
| | startOnLoad: true, |
| | theme: 'default', |
| | flowchart: { |
| | useMaxWidth: false, |
| | htmlLabels: true, |
| | curve: 'linear', |
| | nodeSpacing: 30, |
| | rankSpacing: 40, |
| | padding: 10 |
| | }, |
| | themeVariables: { |
| | fontFamily: 'Arial, sans-serif', |
| | fontSize: '14px', |
| | primaryColor: '#ff6b6b', |
| | lineColor: '#333333', |
| | secondaryColor: '#feca57', |
| | tertiaryColor: '#4ecdc4' |
| | } |
| | }); |
| | </script> |
| | </body> |
| | </html> |
