Slide 1

Genetics and Evolution: Molecular Basis of Inheritance

  • Topic: Role of Sigma factor in transcription
  • Importance of understanding transcription process
  • Introduction to Sigma factor
  • Function of Sigma factor in RNA synthesis
  • Significance of Sigma factor in regulating gene expression

Slide 2

Transcription: Introduction

  • Definition of transcription
  • Importance of transcription in gene expression
  • Comparison between transcription and DNA replication
  • Key players in the transcription process: RNA polymerase and Sigma factor
  • Types of RNA molecules synthesized during transcription

Slide 3

RNA Polymerase: The Transcription Enzyme

  • Definition of RNA polymerase
  • Structure and subunits of RNA polymerase
  • Role of RNA polymerase in producing RNA from DNA template strand
  • Process of RNA synthesis by RNA polymerase (initiation, elongation, termination)
  • Importance of RNA polymerase in gene expression

Slide 4

Sigma Factor: Overview

  • Definition of Sigma factor
  • Subunit composition of bacterial RNA polymerase holoenzyme
  • Role of Sigma factor in determining promoter specificity
  • Classification of Sigma factors in bacteria
  • Sigma factor function in gamma proteobacteria

Slide 5

Sigma Factor in Transcription Initiation

  • Importance of specificity in transcription initiation
  • Role of Sigma factor in recognizing and binding to promoters
  • Different Sigma factors and their affinity to specific promoters
  • Role of Sigma 70 factor in E. coli transcription initiation
  • Detailed mechanism of Sigma factor-mediated transcription initiation

Slide 6

Sigma Factor in Transcription Elongation

  • Overview of transcription elongation process
  • Role of Sigma factor during transcription elongation
  • Sigma factor dissociation from RNA polymerase during elongation
  • Impact of Sigma factor release on RNA synthesis
  • Regulation of transcription elongation by Sigma factor

Slide 7

Sigma Factor in Transcription Termination

  • Importance of termination in transcription process
  • Role of intrinsic and factor-dependent termination mechanisms
  • Role of Sigma factor in termination processes
  • Detailed mechanism of Sigma factor-mediated termination
  • Impact of Sigma factor on gene expression through termination

Slide 8

Sigma Factor vs. Transcription Factors

  • Definition and role of transcription factors
  • Comparison between Sigma factor and transcription factors
  • Function of Sigma factor in prokaryotic transcription
  • Activities and regulation of transcription factors in eukaryotes
  • Interplay between Sigma factor and transcription factors in gene regulation

Slide 9

Role of Sigma Factor in Gene Expression

  • Overview of gene expression regulation
  • Influence of Sigma factor on gene expression
  • Regulation of Sigma factor activity and abundance
  • Impact of Sigma factor mutations on gene expression
  • Significance of studying Sigma factor in understanding genetics and evolution

Slide 10

Summary

  • Recap of the key points discussed about Sigma factor
  • Importance of Sigma factor in transcription
  • Role of Sigma factor in initiation, elongation, and termination
  • Comparison between Sigma factor and transcription factors
  • Significance of understanding Sigma factor in gene expression regulation

Slide 11

Significance of Sigma Factor in Transcription

  • Required for accurate and efficient RNA synthesis
  • Determines the specificity of RNA polymerase for different promoters
  • Plays a crucial role in regulating gene expression
  • Essential for cell survival and adaptation
  • Can be targeted and manipulated for potential therapeutic applications

Slide 12

Types of Sigma Factors

  • Sigma-70 (σ70) factor: Found in most bacteria, recognizes housekeeping genes
  • Alternative Sigma factors:
    • Sigma-54 (σ54) factor: Involved in nitrogen metabolism in bacteria
    • Sigma-32 (σ32) factor: Regulates heat shock response
    • Sigma-38 (σ38) factor: Associated with starvation stress
  • Each Sigma factor targets specific genes based on promoter sequence

Slide 13

Sigma Factor and Promoter Recognition

  • Promoters contain conserved DNA sequences called -35 and -10 regions
  • Sigma factor recognizes and binds to the -35 and -10 regions of the promoter
  • Binding of Sigma factor to DNA facilitates RNA polymerase binding and initiation
  • Sigma factor controls the timing and efficiency of transcription initiation
  • Specific Sigma factors have different affinities for -35 and -10 regions

Slide 14

Mechanism of Transcription Initiation by Sigma Factor

  • Sigma factor associates with RNA polymerase to form a holoenzyme
  • Holoenzyme searches DNA for the promoter regions
  • When the promoter is recognized, holoenzyme binds to the -35 and -10 regions
  • DNA melts at the transcription start site, forming a transcription bubble
  • RNA synthesis begins with the initiation of phosphodiester bond formation

Slide 15

Sigma Factor and Transcription Elongation

  • During transcription elongation, Sigma factor dissociates from the holoenzyme
  • Sigma factor release allows the elongating RNA polymerase to move smoothly along the DNA template strand
  • Released Sigma factor can associate with another holoenzyme to initiate transcription at a different promoter
  • Sigma factor influences the speed and processivity of the RNA polymerase during elongation
  • Multiple factors coordinate transcription elongation termination

Slide 16

Sigma Factor and Transcription Termination

  • Two mechanisms of transcription termination: intrinsic and factor-dependent
  • In intrinsic termination, RNA polymerase encounters a termination sequence and forms an unstable RNA hairpin structure
  • The hairpin structure triggers RNA polymerase release
  • In factor-dependent termination, additional factors (rho factor) are involved in termination
  • Sigma factor affects the stability and efficiency of transcription termination

Slide 17

Regulation of Sigma Factor Activity

  • Sigma factor activity can be regulated at multiple levels
  • Transcriptional regulation: Control of Sigma factor gene expression
  • Post-translational modification of Sigma factor protein
  • Availability of Sigma factors and competing Sigma factor binding
  • Environmental cues and stress conditions influence Sigma factor activity
  • Dysregulation of Sigma factor activity can lead to various cellular consequences

Slide 18

Impact of Sigma Factor Mutations

  • Mutations in Sigma factor genes can affect gene expression and cell survival
  • Loss-of-function mutations: Reduced or defective Sigma factor activity
  • Gain-of-function mutations: Altered Sigma factor specificity or increased activity
  • Mutations in Sigma factors can lead to phenotypic changes and adaptation
  • Studying Sigma factor mutations helps understand genetic variations and evolution

Slide 19

Sigma Factor and Gene Regulation

  • Sigma factor activity influences overall gene expression in bacteria
  • Different Sigma factors control the expression of genes under specific conditions
  • Sigma factor switch regulates the transition from one gene expression program to another
  • Sigma factor competition and interplay with other transcription factors dictate gene regulation outcomes
  • Complex regulatory networks control gene expression using Sigma factors

Slide 20

Conclusion

  • Sigma factor is a key player in transcription initiation, elongation, and termination
  • Sigma factor determines promoter specificity and controls gene expression
  • Different Sigma factors target specific genes under various environmental conditions
  • Mutations and dysregulation of Sigma factor activity can have profound effects on cells
  • Studying Sigma factor provides insights into genetic and evolutionary processes

Slide 21

Regulation of Sigma Factor Expression

  • Levels of Sigma factor expression are controlled by transcriptional regulation
  • Environmental signals and cellular cues influence Sigma factor gene expression
  • Regulatory proteins and transcription factors modulate Sigma factor promoter activity
  • Positive and negative feedback loops regulate Sigma factor expression
  • Changes in Sigma factor expression levels affect gene expression dynamics

Slide 22

Post-Translational Modifications of Sigma Factor

  • Sigma factors can undergo post-translational modifications
  • Phosphorylation of Sigma factors regulates their activity
  • Phosphorylation is catalyzed by protein kinases
  • Phosphorylated Sigma factors can exhibit altered affinity for promoters
  • Post-translational modifications provide additional layers of Sigma factor regulation

Slide 23

Sigma Factor Competition and Promoter Usage

  • Multiple Sigma factors can compete for binding to RNA polymerase
  • Relative affinity of different Sigma factors dictates promoter usage
  • Promoters with different Sigma factor binding sites result in distinct gene expression patterns
  • Sigma factor competition is influenced by environmental conditions and cellular factors
  • Competing Sigma factors determine the activation or repression of specific gene programs

Slide 24

Sigma Factor and Bacterial Adaptation

  • Sigma factors play a crucial role in bacterial adaptation
  • Different Sigma factors respond to specific environmental cues
  • Changes in Sigma factor expression enable bacteria to survive and thrive in different conditions
  • Examples of Sigma factor involvement in stress response and nutrient utilization
  • Understanding Sigma factor regulation aids in developing strategies to combat bacterial infections

Slide 25

Sigma Factor Evolution and Genetic Variation

  • Sigma factors exhibit significant sequence and functional diversity among bacteria
  • Gene duplication events and horizontal gene transfer contribute to Sigma factor evolution
  • Natural selection acts on Sigma factors to optimize gene expression and adaptability
  • Genetic variation in Sigma factors leads to phenotypic diversity and evolutionary success
  • Comparative genomics help in studying the evolution of Sigma factors across species

Slide 26

Example: Sigma 32 Factor and Heat Shock Response

  • Sigma 32 factor is involved in regulating heat shock response in bacteria
  • Heat shock induces the synthesis of Sigma 32 factor
  • Sigma 32 factor directs RNA polymerase to transcribe genes involved in heat shock response
  • Heat shock proteins are produced, aiding in protein folding and stress adaptation
  • Understanding Sigma 32 factor function provides insights into cellular response to heat stress

Slide 27

Example: Sigma 54 Factor and Nitrogen Metabolism

  • Sigma 54 factor is involved in nitrogen metabolism regulation
  • Sigma 54 recognizes specific promoters involved in nitrogen assimilation
  • Gene expression program controlled by Sigma 54 factor enables efficient nitrogen usage
  • Mutations in Sigma 54 factor or its regulatory proteins can disrupt nitrogen metabolism
  • Studying Sigma 54 factor helps in improving nitrogen utilization in agriculture

Slide 28

Equation: Transcription Initiation plaintext Promoter DNA + RNA polymerase-holoenzyme + NTPs → Open complex + Initiation of RNA synthesis

  • Promoter DNA contains -35 and -10 regions recognized by the Sigma factor
  • RNA polymerase-holoenzyme consists of RNA polymerase and associated Sigma factor
  • NTPs (ribonucleotide triphosphates) serve as substrates for RNA synthesis
  • Open complex formation involves the separation of DNA strands at the transcription start site
  • Initiation of RNA synthesis occurs with the addition of the first nucleotide to the growing RNA molecule

Slide 29

Equation: Transcription Elongation plaintext RNA polymerase complex + Elongation NTPs → RNA synthesis + Template DNA strand movement

  • RNA polymerase complex includes the elongating RNA polymerase without the Sigma factor
  • Elongation NTPs (ribonucleotide triphosphates) provide the building blocks for RNA synthesis
  • RNA synthesis involves the addition of complementary nucleotides to the growing RNA molecule
  • Template DNA strand movement occurs as RNA polymerase advances along the DNA template
  • Template DNA strand rewinds after the passage of RNA polymerase

Slide 30

Equation: Transcription Termination plaintext Transcripts + Termination signal → RNA polymerase release + Termination of RNA synthesis

  • Transcripts refer to the completed RNA molecules synthesized during elongation
  • Termination signal can be intrinsic or factor-dependent
  • Intrinsic termination involves the formation of an RNA hairpin structure and a termination sequence
  • Factor-dependent termination requires additional factors, such as rho factor
  • RNA polymerase release occurs upon termination, leading to the termination of RNA synthesis