Organization of Genes in the Bacterial Genome

Before diving into the detailed mechanism of transcription in prokaryotes, it's essential to understand the structural organization of genes within the bacterial genome. Bacterial genes are often arranged in a continuous manner, forming polycistronic units that are regulated by a single promoter.

Gene Organization in Bacteria

Operons: An operon is a cluster of genes that are transcribed together from a single promoter. These genes typically encode proteins that function in the same biochemical pathway. Example: The lac operon in E. coli includes three genes: lacZ, lacY, and lacA, which are involved in lactose metabolism.
Promoter: The promoter is a DNA sequence located upstream of the genes it regulates. It serves as the binding site for RNA polymerase and transcription factors. The promoter initiates transcription of the downstream genes. Promoters often contain specific consensus sequences, such as the -10 (Pribnow box) and -35 regions, which are recognized by RNA polymerase and associated sigma factors.
Operator: The operator is a regulatory DNA sequence usually found near the promoter. It acts as a binding site for repressor proteins. When a repressor binds to the operator, it can inhibit the binding of RNA polymerase to the promoter, thus preventing transcription.
Regulatory Sequences: CAP Binding Site: In some operons, such as the lac operon, there are additional regulatory sequences where activator proteins (e.g., CAP-cAMP complex) can bind to enhance transcription.

Transcription Initiation in Prokaryotes

Transcription Elongation in Prokaryotes

Transcription Termination in Prokaryotes

Transcription Initiation

Transcription in prokaryotes is the process by which genetic information from DNA is copied into RNA

1. Initiation

Promoter Recognition and Binding:

Promoter Regions: Transcription initiation begins with the recognition of the promoter regions by RNA polymerase. The promoter is a specific DNA sequence located upstream of the gene to be transcribed. Key features of the prokaryotic promoter include:
- -35 Region: Located approximately 35 bases upstream of the transcription start site, often has the consensus sequence TTGACA.
- -10 Region (Pribnow Box): Located about 10 bases upstream of the start site, usually has the consensus sequence TATAAT.
RNA Polymerase Holoenzyme: In prokaryotes, the RNA polymerase holoenzyme, consisting of the core enzyme (α2ββ'ω) and the sigma factor (σ), binds to the promoter. The sigma factor is crucial for recognizing the promoter sequences.

Formation of the Transcription Bubble:

DNA Unwinding: The RNA polymerase unwinds a short segment of the DNA, creating a transcription bubble. This exposes the template strand of DNA.

Synthesis of the First Phosphodiester Bond:

Initial RNA Synthesis: RNA polymerase begins synthesizing RNA by adding ribonucleotides complementary to the DNA template. The first few nucleotides are synthesized without the need for a primer.

Transcription Elongation in Prokaryotes

2. Elongation

RNA Synthesis:

Elongation Complex: After the synthesis of the initial RNA nucleotides, the sigma factor dissociates from the RNA polymerase, allowing the core enzyme to proceed with elongation.
Directional Synthesis: RNA polymerase moves along the template strand of DNA in the 3' to 5' direction, synthesizing RNA in the 5' to 3' direction.
RNA Polymerase Activity: RNA polymerase catalyzes the formation of phosphodiester bonds between ribonucleotides, incorporating nucleotides complementary to the DNA template.

Transcription Bubble Maintenance:

Continuous Unwinding and Rewinding: As RNA polymerase moves along the DNA, it maintains a transcription bubble by unwinding the DNA ahead and rewinding it behind the enzyme. This allows the DNA to be read accurately while protecting the nascent RNA strand.

Transcription Termination in Prokaryotes

Termination

Termination Signals:

Transcription is terminated when RNA polymerase encounters specific termination signals in the DNA sequence. There are two main types of termination mechanisms in prokaryotes:

Rho-Independent Termination:

Hairpin Structure Formation: The RNA transcript forms a stable hairpin structure (stem-loop) followed by a series of uracil residues. The hairpin structure causes the RNA polymerase to pause.
Dissociation: The weak interaction between the RNA transcript and the DNA template in the U-rich region leads to the dissociation of the RNA transcript from the DNA.

Rho-Dependent Termination:

Rho Protein Binding: The rho protein, a helicase, binds to the nascent RNA at a rho utilization (rut) site, which is a specific RNA sequence.
Translocation and Termination: The rho protein moves along the RNA towards the RNA polymerase using ATP hydrolysis. When rho catches up to the RNA polymerase, it unwinds the RNA-DNA hybrid and releases the RNA transcript from the DNA.