Questions: Prokaryotic Promoters and Sigma Factors

Question 1

A bacterium encounters heat shock. A researcher observes that hundreds of heat shock genes are rapidly activated while most housekeeping genes are simultaneously downregulated. What single mechanism best explains this global shift?

• A. The cell mutates the promoters of all heat shock genes to make them stronger
• B. Ribosomes preferentially translate heat shock mRNAs due to special sequence elements
• C. The heat shock sigma factor (σ³²) accumulates, competes with σ⁷⁰ for core polymerase, and redirects transcription to promoters with σ³²-specific -10 and -35 sequences
• D. The cell degrades core RNA polymerase and synthesizes a new polymerase specialized for heat shock genes

Answer: (C)

The sigma factor swap is the elegance of prokaryotic transcriptional regulation. Under normal conditions, σ⁷⁰ is dominant and drives housekeeping gene expression. Under heat shock, σ³² is synthesized and stabilized. Because sigma factors compete for a limited pool of core polymerase, more σ³²-holoenzyme forms at the expense of σ⁷⁰-holoenzyme. The result: hundreds of genes regulated by σ³² promoters are upregulated while σ⁷⁰-dependent genes get fewer holoenzymes — a global reprogramming achieved by changing one protein.

Question 2

What is the significance of sigma factor dissociating from core polymerase after transcription initiation?

• A. It means core polymerase must be re-synthesized before initiating transcription at another gene
• B. It means sigma factor can be recycled — freed sigma associates with new core polymerases to initiate transcription at other promoters, making initiation rate sensitive to sigma abundance
• C. It means elongation is more error-prone than initiation because sigma factor normally ensures fidelity
• D. It prevents the sigma factor sequence from being transcribed into the mRNA

Answer: (B)

Sigma factor is a catalytic component for initiation: it helps core polymerase find and melt the promoter, then dissociates and is free to function again. This recycling mechanism means that the relative abundance of different sigma factors in the cell directly controls which promoters are active. A small pool of σ³² can initiate transcription at many heat shock promoters in sequence. The recycling also means that sigma factor stoichiometry is not 1:1 with active transcription units.

Question 3

Core RNA polymerase (without sigma factor) can initiate transcription at specific gene promoters, but does so less efficiently than the holoenzyme.

• T. True
• F. False

Answer: False

Core polymerase alone cannot initiate transcription at specific promoters at all — it binds DNA non-specifically and cannot recognize or melt the promoter in a directed way. Promoter specificity is entirely provided by the sigma factor. Without sigma, core polymerase would transcribe random genomic sequences. The holoenzyme (core + sigma) is the functional unit for specific, regulated transcription initiation.

Question 4

The spacing between the -10 and -35 promoter elements affects promoter strength because sigma factor must contact both elements simultaneously on the same face of the DNA helix.

• T. True
• F. False

Answer: True

Sigma factor makes direct protein-DNA contacts at both the -10 (TATAAT) and -35 (TTGACA) elements. Because the sigma factor is a rigid structure, the optimal spacing between these elements (approximately 17 bp, corresponding to about 1.6 helical turns) ensures they are presented on the same face of the double helix so sigma can bridge them simultaneously. Promoters with suboptimal spacing have reduced sigma binding affinity and are therefore weaker — fewer holoenzyme binding events per unit time.

Question 5

Explain how a single bacterium can rapidly reprogram the expression of hundreds of genes in response to environmental stress, using only the sigma factor mechanism.

Model answer: By changing which sigma factor is most abundant. The cell synthesizes or stabilizes an alternative sigma factor (e.g., σ³² for heat shock), which competes with the housekeeping σ⁷⁰ for binding to core polymerase. The dominant sigma factor determines which promoter sequences are recognized, effectively redirecting the entire transcriptional machinery to a new set of genes — without altering the polymerase itself or the DNA.

This is one of biology's most elegant regulatory solutions: a single regulatory variable (sigma factor identity) controls global gene expression. The mechanism is analogous to software: the core polymerase is the hardware, and the sigma factor is the program loaded into it. Swapping programs changes which genes are transcribed. The recycling of sigma after initiation, and competition between sigma factors for core polymerase, ensures that the regulatory response is graded: the more alternative sigma, the more of the stress-response genes are expressed.