⏰ T7 Phage Time Cascade

graph TD %% Initial Setup A[T7 Infection] --> B[DNA Injection] B --> C[Host RNAP Binding] C --> D[Early Promoter Recognition] D --> E[Class I Gene Transcription] E --> F[0.7 Protein Synthesis] E --> G[1.0 Protein Synthesis] E --> H[1.1 Protein Synthesis] F --> I[Host RNAP Modification] G --> J[Anti-restriction Activity] H --> K[Host Transcription Inhibition] I --> L[Enhanced T7 Transcription] J --> M[DNA Protection] K --> N[Host Gene Shutdown] L --> O[Metabolic Redirection] M --> P[Viral DNA Stability] N --> Q[Resource Reallocation] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#51cf66,color:#fff style C fill:#ffd43b,color:#000 style D fill:#74c0fc,color:#fff style E fill:#51cf66,color:#fff style F fill:#51cf66,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff style I fill:#51cf66,color:#fff style J fill:#51cf66,color:#fff style K fill:#51cf66,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:#b197fc,color:#fff style Q fill:#b197fc,color:#fff

graph TD %% Initial Setup A[Class I Genes Active] --> B[1.0 Protein Accumulation] B --> C[T7 RNAP Gene Transcription] C --> D[T7 RNAP mRNA Synthesis] D --> E[T7 RNAP Translation] E --> F[T7 RNAP Protein] F --> G[T7 RNAP Folding] G --> H[T7 RNAP Activation] H --> I[T7 Promoter Recognition] I --> J[Class II Gene Activation] J --> K[Host RNAP Displacement] K --> L[T7 RNAP Dominance] L --> M[Temporal Control Established] M --> N[Class II Transcription] N --> O[Metabolic Shift] O --> P[Viral Program Initiation] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style C fill:#51cf66,color:#fff style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#ffd43b,color:#000 style G fill:#51cf66,color:#fff style H fill:#ffd43b,color:#000 style I fill:#74c0fc,color:#fff style J fill:#b197fc,color:#fff style K fill:#51cf66,color:#fff style L fill:#b197fc,color:#fff style M fill:#b197fc,color:#fff style N fill:#51cf66,color:#fff style O fill:#b197fc,color:#fff style P fill:#b197fc,color:#fff

graph TD %% Initial Setup A[T7 RNAP Active] --> B[Class II Promoter Binding] B --> C[Host RNAP Displacement] C --> D[Class II Gene Transcription] D --> E[DNA Polymerase Synthesis] D --> F[DNA Ligase Synthesis] D --> G[Endonuclease Synthesis] D --> H[Exonuclease Synthesis] E --> I[Viral DNA Replication Prep] F --> J[DNA Repair Machinery] G --> K[DNA Processing Enzymes] H --> L[DNA Degradation Control] I --> M[Replication Readiness] J --> N[Genome Maintenance] K --> O[DNA Processing] L --> P[Host DNA Degradation] M --> Q[Class III Activation] N --> R[Genome Stability] O --> S[DNA Processing] P --> T[Resource Liberation] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style C fill:#51cf66,color:#fff style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#51cf66,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff 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:#b197fc,color:#fff style N fill:#b197fc,color:#fff style O fill:#b197fc,color:#fff style P fill:#b197fc,color:#fff style Q fill:#b197fc,color:#fff style R fill:#b197fc,color:#fff style S fill:#b197fc,color:#fff style T fill:#b197fc,color:#fff

graph TD %% Initial Setup A[Viral DNA Polymerase] --> B[Origin Recognition] B --> C[Replication Origin Binding] C --> D[DNA Unwinding] D --> E[Primer Synthesis] E --> F[Leading Strand Initiation] F --> G[Lagging Strand Initiation] G --> H[Bidirectional Replication] H --> I[Replication Fork Movement] I --> J[DNA Synthesis] J --> K[Genome Amplification] K --> L[Copy Number Increase] L --> M[Replication Timing Control] M --> N[Class III Gene Activation] N --> O[Late Gene Expression] O --> P[Temporal Coordination] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style C fill:#74c0fc,color:#fff style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#51cf66,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff style I fill:#51cf66,color:#fff style J fill:#51cf66,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:#b197fc,color:#fff

graph TD %% Initial Setup A[Replication Active] --> B[Class III Promoter Activation] B --> C[Late Gene Transcription] C --> D[Structural Protein mRNAs] D --> E[Capsid Protein Synthesis] D --> F[Tail Protein Synthesis] D --> G[Portal Protein Synthesis] D --> H[Scaffold Protein Synthesis] E --> I[Capsid Assembly Prep] F --> J[Tail Assembly Prep] G --> K[Portal Assembly Prep] H --> L[Scaffold Assembly Prep] I --> M[Structural Components Ready] J --> N[Tail Components Ready] K --> O[Portal Components Ready] L --> P[Scaffold Components Ready] M --> Q[Assembly Initiation] N --> R[Assembly Coordination] O --> S[Assembly Coordination] P --> T[Assembly Coordination] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style C fill:#51cf66,color:#fff style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#51cf66,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff 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:#b197fc,color:#fff style N fill:#b197fc,color:#fff style O fill:#b197fc,color:#fff style P fill:#b197fc,color:#fff style Q fill:#b197fc,color:#fff style R fill:#b197fc,color:#fff style S fill:#b197fc,color:#fff style T fill:#b197fc,color:#fff

graph TD %% Initial Setup A[Structural Components] --> B[Capsid Protein Oligomerization] B --> C[Pentamer Formation] C --> D[Hexamer Formation] D --> E[Capsid Shell Assembly] F[Tail Proteins] --> G[Tail Tube Assembly] G --> H[Tail Fiber Attachment] H --> I[Complete Tail Structure] J[Portal Proteins] --> K[Portal Ring Assembly] K --> L[Portal Integration] E --> M[Capsid Shell Complete] I --> N[Tail Structure Complete] L --> O[Portal Structure Complete] M --> P[Assembly Coordination] N --> Q[Assembly Coordination] O --> R[Assembly Coordination] P --> S[Virion Assembly Initiation] Q --> S R --> S %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#51cf66,color:#fff style C fill:#51cf66,color:#fff style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#ff6b6b,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff style I fill:#51cf66,color:#fff style J fill:#ff6b6b,color:#fff style K fill:#51cf66,color:#fff style L fill:#51cf66,color:#fff style M fill:#b197fc,color:#fff style N fill:#b197fc,color:#fff style O fill:#b197fc,color:#fff style P fill:#74c0fc,color:#fff style Q fill:#74c0fc,color:#fff style R fill:#74c0fc,color:#fff style S fill:#b197fc,color:#fff

graph TD %% Initial Setup A[Replicated Genomes] --> B[Packaging Signal Recognition] B --> C[Terminase Complex Assembly] C --> D[DNA Cleavage] D --> E[Genome End Processing] E --> F[Portal Binding] F --> G[DNA Translocation] G --> H[Genome Packaging] H --> I[Capsid Filling] I --> J[Packaging Completion] J --> K[Terminase Release] K --> L[Portal Sealing] L --> M[Packaged Genome] M --> N[Virion Maturation Prep] N --> O[Assembly Quality Control] O --> P[Packaging Success] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style C fill:#ffd43b,color:#000 style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#74c0fc,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff style I fill:#51cf66,color:#fff style J fill:#b197fc,color:#fff style K fill:#51cf66,color:#fff style L fill:#51cf66,color:#fff style M fill:#b197fc,color:#fff style N fill:#b197fc,color:#fff style O fill:#b197fc,color:#fff style P fill:#b197fc,color:#fff

graph TD %% Initial Setup A[Packaged Genome] --> B[Scaffold Protein Removal] B --> C[Capsid Expansion] C --> D[Capsid Stabilization] D --> E[Tail Attachment] E --> F[Virion Assembly] F --> G[Infectivity Acquisition] G --> H[Mature Virion] H --> I[Lysis Timing Check] I --> J{Timing Ready?} J -->|Yes| K[Lysis Activation] J -->|No| L[Timing Wait] K --> M[Lysis Protein Expression] L --> I M --> N[Cell Wall Degradation] N --> O[Cell Lysis] O --> P[Progeny Release] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#51cf66,color:#fff style C fill:#51cf66,color:#fff style D fill:#51cf66,color:#fff style E fill:#51cf66,color:#fff style F fill:#51cf66,color:#fff style G fill:#b197fc,color:#fff style H fill:#b197fc,color:#fff style I fill:#74c0fc,color:#fff style J fill:#74c0fc,color:#fff style K fill:#b197fc,color:#fff style L fill:#74c0fc,color:#fff style M fill:#51cf66,color:#fff style N fill:#51cf66,color:#fff style O fill:#b197fc,color:#fff style P fill:#b197fc,color:#fff

graph TD %% Initial Setup A[Mature Virions] --> B[Lysis Gene Activation] B --> C[Holin Protein Synthesis] C --> D[Holin Accumulation] D --> E[Holin Oligomerization] E --> F[Membrane Channel Formation] F --> G[Endolysin Release] G --> H[Cell Wall Degradation] H --> I[Cell Lysis] I --> J[Progeny Release] J --> K[Infection Cycle Complete] K --> L[Temporal Program Success] L --> M[Optimal Timing Achieved] M --> N[Efficient Progeny Production] N --> O[Infection Success] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#74c0fc,color:#fff style C fill:#51cf66,color:#fff style D fill:#74c0fc,color:#fff style E fill:#51cf66,color:#fff style F fill:#51cf66,color:#fff style G fill:#51cf66,color:#fff style H fill:#51cf66,color:#fff style I fill:#b197fc,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

graph TD %% Initial Setup A[Infection Initiation] --> B[Early Gene Expression] A --> C[Host Takeover] A --> D[Metabolic Redirection] B --> E[T7 RNAP Production] C --> F[Host RNAP Displacement] D --> G[Resource Reallocation] E --> H[Class II Activation] F --> I[Class II Activation] G --> J[Class II Activation] H --> K[DNA Replication] I --> K J --> K K --> L[Class III Activation] L --> M[Structural Assembly] M --> N[DNA Packaging] N --> O[Virion Maturation] O --> P[Lysis Timing] P --> Q[Progeny Release] Q --> R[Temporal Program Success] R --> S[Biological Computing] %% Styling - Biological Color Scheme style A fill:#ff6b6b,color:#fff style B fill:#51cf66,color:#fff style C fill:#51cf66,color:#fff style D fill:#51cf66,color:#fff style E fill:#ffd43b,color:#000 style F fill:#51cf66,color:#fff style G fill:#51cf66,color:#fff style H fill:#b197fc,color:#fff style I fill:#b197fc,color:#fff style J fill:#b197fc,color:#fff style K fill:#51cf66,color:#fff style L fill:#b197fc,color:#fff style M fill:#51cf66,color:#fff style N fill:#51cf66,color:#fff style O fill:#51cf66,color:#fff style P fill:#74c0fc,color:#fff style Q fill:#b197fc,color:#fff style R fill:#b197fc,color:#fff style S fill:#b197fc,color:#fff