pp13 Responding pt 1

Microbial Response to Environmental Changes

  • Overview of Microbial Regulation

    • Microbes sense environmental changes and respond accordingly.

    • Responses occur at multiple regulatory levels:

    • Transcriptional level

    • Translational level

    • Post-translational level

    • Regulation involves both proteins and RNAs.

  • Regulation of Enzyme Activities

    • Example: Arginine operon

    • ArjA: first enzyme in arginine synthesis pathway.

    • Inhibited by the end product (arginine).

    • Microbial systems often evolve multiple levels of control due to competition for resources in the environment.

Molecular Regulation Mechanisms

  • Transcription Process Overview

    • DNA is transcribed into RNA as the first regulatory step.

    • mRNA is translated into protein, providing a second regulatory point.

    • Possible controls post-protein synthesis include:

    • Feedback inhibition

    • Protein-protein interactions

    • Covalent modifications

    • Degradation of proteins

Bacterial Transcription

  • Distinction between Bacteria and Archaea

    • Bacteria and archaea have different transcriptional apparatuses.

    • Archaeal RNA polymerase bears resemblance to eukaryotic RNA polymerase.

  • Key Stages in Bacterial Transcription

    • Initiation

    • Elongation

    • Termination

    • Fancy regulation of transcription is common in bacteria.

Initiation of Transcription

  • Major player: RNA polymerase (core enzyme)

    • Composed of:

      • Beta subunit

      • Beta prime subunit

      • Two alpha subunits for DNA tethering.

  • Sigma Factor: directs the RNA polymerase to a specific promoter.

    • Role of Sigma Factor:

      • Notifies core enzyme of where to bind.

      • Recognizes specific regions of DNA (e.g., -10 region called Pribnow box, -35 region).

  • Diversity of Sigma Factors:

    • Specialized sigma factors control different gene expressions:

      • Sigma 70: housekeeping sigma factor for general conditions.

      • Sigma 28: activates flagella synthesis.

      • Sigma 32: heat shock response sigma factor.

      • Sigma 38 (RPOS): starvation or stationary phase sigma factor for cell survival.

Transcription Process in Bacteria

  • Sigma subunit guides RNA polymerase to the promoter (holoenzyme formation).

  • Open Complex Formation: DNA strands separated to allow RNA synthesis.

  • Scrunch Complex Formation: RNA polymerase, tethered by sigma factor, experiences difficulty moving until sigma factor dissociates.

  • Following sigma factor dissociation, elongation proceeds until termination signal is reached.

Termination of Transcription

  • Importance of proper termination:

    • Prevents transcription of adjacent genes.

    • Recovers RNA polymerases for subsequent use.

    • Prevents transcription beyond damaged DNA.

  • Intrinsic Termination (80% of cases):

    • Characterized by formation of a hairpin structure in the RNA transcript.

    • Hairpin followed by a uracin-rich track: weak interaction leading to RNA release from the polymerase.

    • Requires GC pairs (strong) and U pairs (weak) for efficient release.

  • Rho-Dependent Termination (20% of cases):

    • Involves a hexameric Rho protein that latches onto mRNA at Rho Utilization Element (RUT).

    • Rho uses ATP to translocate along the mRNA until it encounters RNA polymerase, promoting termination.

Mechanisms and Implications

  • Challenges in regulating Rho protein action during termination (presence of weak interactions).

  • The choice between intrinsic and Rho-dependent termination is environment and sequence-dependent.

Post-Transcriptional Control

  • Various strategies exist beyond sigma factors:

    • Transcription Factors:

      • Regulate transcription in a more refined manner compared to sigma factors.

      • Can act as either repressors or activators.

      • Examples include the arginine operon:

      • Promoter, operator where repressors bind.

      • Active when arginine is absent; prevents unnecessary enzyme production.

      • Lac Operon: encodes genes for lactose uptake and degradation; activated in presence of allolactose (isomer of lactose) instead of lactose itself to regulate expression.

    • Conclusion

  • The lecture discusses complex regulatory mechanisms to control microbial gene expression in response to environmental factors. Will continue next class.