Gene Expression Control in Prokaryotes Part II-D (Exam 2)

Unpopular Opinion on the Greatest Threat to Humanity

• Humanity's greatest threat is a lack of emotional maturity, ineffective communication, and a lack of empathy when navigating conflict.
• This leads to internal and interpersonal conflict.
• Healing is needed to address these issues.

Control of Gene Expression (Prokaryotes)

• Gene expression control in bacteria occurs at multiple levels, including:
  • Genome/chromatin structure
  • Epigenetic profile (DNA methylation)
  • Transcriptional regulation
  • Post-transcriptional regulation
  • Regulation of translation
  • Regulation via non-coding RNAs

Chromatin Structure

• Nucleoid shape changes due to NAPs (nucleoid-associated proteins) and IncRNAs (long non-coding RNAs).
• NAPs:
  • Modify chromosome architecture.
  • Mediate interactions with ncRNAs (non-coding RNAs).
  • Regulate transcription by methods such as blocking promoters, facilitating RNAP (RNA polymerase) movement, and altering supercoiling.
  • Regulate virulence and xenogenic silencing.
• Transcription affects nucleoid structure, requiring available templates and positive supercoils in dsDNA.

Epigenetic Profile - DNA Methylation

• Involves adenine methylation, a key component of restriction-modification (R-M) systems.
• R-M systems protect bacterial chromosomes from their own endonucleases, and also cleave phage DNA.
• Orphan methylases (GATC sites):
  • Regulate gene expression by allowing the binding of activators or repressors.
  • Enable DNA repair through methyl-directed mismatch repair (MMR) mechanisms.
  • Initiate DNA replication by hemimethylation at the dnaA promoter and oriC, preventing unwanted reinitiation.

Transcriptional Regulation

• Bacterial genes are often organized into operons, grouping proteins of the same pathway.
• Operons facilitate swift responses to environmental changes, enabling bacteria to adapt quickly.
• Inducible operons: Transcription only occurs in the presence of a substrate.
• Repressible operons: Transcription is inhibited by a product.

Post-Transcriptional Regulation

• RNA editing: rNTPs (ribonucleoside triphosphates) are modified after transcription altering their properties, amino acid sequences, and codon recognition.
• RNA turnover: Balance between RNA synthesis and degradation, influencing RNA quantity and availability. This is modulated by RNase abundance and location, as well as binding to ncRNAs.

Regulation of Translation

• Numerous translational regulation mechanisms overlap with transcriptional regulation.
• Features of mRNA such as ribosome binding site presence and strength, as well as codon usage bias, are significant.
• Post-translational editing is also a part of the regulation process.

Regulation via Non-Coding RNAs

• Small non-coding RNAs (sncRNAs) are involved in most studied mechanisms.
• Gene expression regulation involves transcription, translation, and mRNA stability.
• This includes stress response, virulence, and xenogenic silencing regulation.

Examples of Regulation via sRNAs

• Cis-encoded ncRNA elements:
  • Structural motifs in the 5' untranslated region (UTR) respond to cellular or environmental changes.
  • Examples include attenuation, leader peptides, thermosensors, and riboswitches.
• Cis-encoded antisense RNAs: Target mRNAs for degradation or by forming a duplex with them.
• Trans-encoded antisense ncRNAs: Affect transcription and translation by targeting mRNAs, located outside the controlling gene's region.

Riboswitches

• Transcriptional switches regulated by a molecule's presence or absence.
• They directly affect the translation process.

Cis or Trans Encoded Antisense RNAs

• Cis-encoded: Target mRNA for degradation, in or close to the gene region, produced from an antisense promoter.
• Trans-encoded: Target mRNA to affect transcription and translation, located in a different genomic locus from the target gene.

Modes of Transcriptional Regulation

• Regulatory elements impact the transcription levels.
• Availability of sigma factor and RNA polymerase.
• Activator proteins facilitate transcription initiation.
• Repressor proteins block transcription.
• Attenuation and Antitermination modify mRNA production.

Role of Activator and Repressor in Transcription Regulation

• Activator proteins stimulate transcription.
• Repressor proteins inhibit transcription.

Mutation Studies and Merozygotes

• Study of mutations by observing how these change the expression patterns of genes.
• Merozygotes (partial diploids): Cells with partial copies of genes on different genetic elements, offering insight into gene function by studying changes in expression patterns.

Additional Information & Extra Slides

• Includes specific details about the arginine and maltose operons.

Application Exercise

• Determining the function of the different lac operon components based on their genotype and the presence or absence of lactose in the environment.

Levels of Gene Regulation

• Regulation occurs at several levels for both prokaryotic and eukaryotic cells, including chromatin, transcription, mRNA processing and stability, translation level, and post-translational modifications.

Inducible Operon Under Positive Control

• Substrate and activator work together to activate transcription.
• Activator aids RNA polymerase binding to the promoter.

Repressible Operon Under Positive Control

• Product and activator have opposite effects.
• Activator aids binding of RNA polymerase to the promoter.

lac Operon

• Detailed model of the lac operon, its controlling elements (like CAP sites) and its relation to the expression of lactose-related cellular functions.

Lactose Absent/Present

• The lac operon's regulatory genes (lacl, lacP, and laco) are affected by the presence or absence of lactose, affecting the production of various enzymes.

Carbon Catabolite Repression

• High glucose levels can repress the lac operon, impacting the expression levels of its components.

trp Operon

• Operon controlling tryptophan synthesis, involving attenuation as a mechanism to control gene expression.

Other Questions (trp operon)

• Analysis of mutations in the trp operon's regulatory regions.

Worksheet - Conclusions

• Summary table of various operon types and their underlying regulatory mechanisms.

Modes of Transcriptional Regulation (diagram)

• Diagram summarizing the different modes of transcriptional regulation, indicating the mechanisms and effect.

Attenuation in trp Operon

• Details of the attenuation process in the trp operon, showing the role of the ribosome and transcription and its various sequence regions, depending on the tryptophan levels in the environment.

Low and High Tryptophan Concentration (trp operon)

• Detailed scenarios explaining the trp operon's regulation mechanisms in response to low and high tryptophan concentrations.

Other (trp operon) - additional questions

• Analyzing the effects of deleting regions from the operon.

Other Questions (general)

• Understanding when and how a regulator protein binds, and what the consequence of such binding is.

Additional details about operons and regulatory mechanisms

• Discusses different types of operons, and the concept of cis and trans regulatory factors.

Other information

• Additional information on the operon systems and how operons function in various scenarios.