GC

Transcriptional Regulation in Prokaryotes Flashcards

Transcriptional Regulation in Prokaryotes

Session Overview

Topics Covered:

  • Transcription

  • Environmental Adaptation

  • General Principles of Transcriptional Regulation

  • Lac Operon as a significant example of transcriptional regulation.


Gene Expression: RNA Transcription

Process of Transcription

Transcription is the biological mechanism by which genetic information encoded in DNA is converted into RNA. This process is crucial for gene expression. The key enzyme responsible for this process is RNA Polymerase (RNAP), which carries out several essential steps:

  1. Initiation: RNAP binds to the promoter region of the gene, causing the DNA strands to unwind and expose the coding sequence.

  2. Elongation: RNAP synthesizes the RNA strand by pairing complementary RNA nucleotides with one of the DNA strands (template strand).

  3. Termination: Upon reaching a specific termination signal on the DNA, RNAP detaches from the RNA product, which then undergoes various modifications before it is used in protein synthesis.

The final product of this process is an RNA transcript, which may serve various functions - as mRNA, rRNA, or tRNA.


Understanding Promoter Sequences

Role of Promoters

Promoter sequences are specific DNA regions that mark the site at which transcription begins. They are typically located upstream (5' end) of the transcription initiation site. While promoter sequences lack extensive conservation across different genes, certain critical short motifs are conserved, which are integral to RNAP binding and transcription initiation.

Initiation of Transcription

The initiation of transcription involves the binding of RNAP, along with additional transcription factors, to the promoter. The characteristics of promoter sequences influence the direction of transcription and the efficiency of gene expression.

Coding vs Template Strands

  • Template Strand: The DNA strand that RNAP reads to produce the complementary RNA. Known as the antisense strand, it serves as a template for mRNA synthesis.

  • Coding Strand: This strand of DNA has the same sequence as the mRNA (with the exception that thymine (T) in DNA is replaced by uracil (U) in RNA).


Gene Organization in Prokaryotes

Key Requirements for Transcription

Transcription in prokaryotic cells requires:

  • Cis-acting DNA elements: Such as promoters, which are essential for providing a binding site for RNAP and determining transcription start sites.

  • Trans-acting factors (TFs): These include RNA polymerase and various transcription factors necessary for regulating transcription levels.

Prokaryotic Promoters

Key features of prokaryotic promoters include:

  • -35 motif: TTGACA

  • -10 motif: TAATGG

  • Discriminator: A sequence element that helps in determining the specificity of transcription initiation by RNAP.


The Transcriptional Machinery

RNA Polymerase Holoenzyme

The RNA polymerase holoenzyme is composed of a core enzyme and a sigma factor:

  • Sigma Factor: It is critical for the initiation stage of transcription by recognizing the promoter sequences.

  • Core Enzyme: This is the catalytic component responsible for the polymerization of the RNA strand.

Basic Stages of Transcription

  1. Initiation: RNAP binds to the promoter; transcription begins.

  2. Elongation: RNA synthesis progresses as nucleotides are added to the growing RNA chain.

  3. Termination: Transcription concludes when RNAP releases the newly synthesized RNA and detaches from the DNA template.


Comparison between Prokaryotic and Eukaryotic Transcription

Prokaryotic vs Eukaryotic Gene Expression

  • Prokaryotic Cells: Transcription and translation occur simultaneously in the cytoplasm, leading to rapid gene expression.

  • Eukaryotic Cells: Transcription occurs in the nucleus, followed by extensive mRNA processing, and finally, translation takes place in the cytoplasm.

Eukaryotic Transcriptional Control

This involves:

  • Core Promoter Elements: For instance, the TATA box, located near the transcription start site.

  • Upstream Regulatory Elements: These elements, both proximal and distal, significantly affect the transcriptional dynamics and regulation.

RNA Polymerases in Eukaryotes

Different eukaryotic RNA polymerases have distinct roles:

  • RNA Polymerase I: Transcribes ribosomal RNA (rRNA) genes except 5S rRNA.

  • RNA Polymerase II: Responsible for mRNA synthesis and small nuclear RNA (snRNA).

  • RNA Polymerase III: Engages in transcribing transfer RNA (tRNA) and other small rRNA.


Regulation of Gene Expression

Summary of Genomic Structures

  • Bacterial Genomes: Characterized by a single circular chromosome, with genes often organized into operons, allowing coordinated gene expression.

  • Eukaryotic Genomes: Comprised of multiple linear chromosomes and intricate regulatory elements, where DNA is associated with histones to form chromatin.

Transcriptional Regulation in Bacteria

Bacteria respond to environmental changes through transcriptional regulation, adjusting gene expression in the following ways:

  • Frequent and Random Changes: As seen under nutrient loading or exposure to drugs.

  • Fluctuating Changes: Such as adjustments in response to daily or seasonal variations.

Constitutive and Regulated Genes

  • Constitutive Genes: Expressed continuously, maintaining vital cellular functions.

  • Regulated Genes: Their expression varies based on specific environmental cues or conditions, allowing for adaptability.


Regulatory Proteins in Transcription Initiation

Activators: These proteins facilitate RNAP binding at promoters, enhancing transcription rates.Repressors: These proteins hinder RNAP binding, thus inhibiting transcription.

Ligands in Environmental Sensing

These are low-molecular-weight compounds whose concentration changes in response to environmental conditions. They modulate the activity of regulatory proteins by altering their conformational states, affecting transcriptional outcomes.

Mechanisms of Regulation

  • Negative Regulation: Involves bound repressor proteins that inhibit transcription by blocking RNAP access to the promoter.

  • Positive Regulation: Initiated by bound activator proteins that promote transcription by enhancing RNAP binding.

The presence or absence of ligands can effectively switch gene expression on or off by altering regulatory proteins' activities.


Lac Operon as a Model for Transcription Regulation

Overview of the Lac Operon

The lac operon comprises genes essential for lactose metabolism in E. coli, showcasing a sophisticated example of transcriptional regulation. Its transcription is induced in the presence of lactose while being suppressed when glucose is available.

Role of Lac Repressor

The lac I gene encodes a repressor protein that binds to the operator region, preventing transcription when lactose is absent. Conversely, in the presence of lactose, it undergoes a conformational change to a low-affinity state that allows transcription to proceed.

Effects of Glucose on Lac Operon Regulation

Glucose levels significantly affect lac operon transcription through catabolite repression. When glucose is abundant, the synthesis of cyclic AMP (cAMP) is hindered, resulting in decreased transcription of the lac operon, thereby prioritizing glucose metabolism over lactose utilization.

Final Summary of the Lac Operon

The lac operon exemplifies an intricate transcription initiation control mechanism that integrates signals from the environment, involving distinct regulatory proteins that respond to nutrient availability, thus illustrating the principles of transcriptional regulation in prokaryotes.