Is sigma factor a transcription factor?

Question

After I googled 'sigma TF' I stumbled upon two papers(only).

From a paper:

Sigma factors (sigmas) are bacterial transcription factors that bind core RNA polymerase (RNAP) and direct transcription initiation at cognate promoter sites.

and another paper had the title -

Specific binding of the transcription factor sigma-54 to promoter DNA.

However this contradicts with my book- Principle of Genetics Snustard and Simmons:

Unlike their prokaryotic counterparts, eukaryotic RNAPs cannot initiate transcription by themselves .... require the assistance of protein transcription factors to start synthesis.

Is it a TF?

Note: From what TFs are, sigma factor seems to be a TF to me.

Answer 1

Having read @loolipop’s answer, you should realize that this is a semantic question, with no right or wrong answer. If you define it in terms of the known characteristics of eukaryotic transcription factors, prokaryotic sigma factors clearly do not conform. However, if you define transcription factor as a protein that is required for transcription (by analogy to the terminology for translation factors), or even as a protein that confers specificity on the initiation of transcription, then the sigma factors can be called transcription factors.

Because of the differences between the prokaryotic and eukaryotic systems, I think it more useful to maintain the historic terminology* (check Berg et al., for example) for prokaryotic transcription and, unlike the authors you quote, just refer to the sigma proteins as ‘sigma factors’. This allows you to discuss the similarities and differences between prokaryotic sigma factors and eukaryotic transcription factors without confusion.

*Historic Terminology. The prokaryotic transcription system was worked out in detail at a time that almost the only thing that was known about eukaryotic transcription was the existence of different RNA polymerases for mRNA and rRNA. The term transcription factor was never used for the sigma factors. The index of the 5th edition of Berg et al. (2001) contains no entry for transcription factor, and focuses on prokaryotic transcription. The index of the 11th edition of The Biochemistry of the Nucleic Acids (Adams et al.), about ten years earlier, does have entries, but almost exclusively for eukaryotes. The only entries that refer to prokaryotes actually relate to termination of transcription, and the term is used to distinguish between (rho) factor-dependent and factor-independent termination.

Answer 2

Prokaryotic sigma factors confer specific promoter recognition to RNAP via Sigma subunit σ1.1, which acts as a DNA 'mimic' - occupying the downstream DNA binding site. This interaction is displaced only when the promoter region is bound, hence conferring the specificity. Note that Sigma factor on its own cannot bind DNA, as σ1.1 binds σ4 in the unbound form, preventing binding to any sequence. Source: Section 2. Structural Organisation of σ70 and Other Group 1 σ Factors in this paper

This is in contrast to eukaryotic transcription factors, which can bind to the DNA on their own - indeed the assembly of the general transcriptional machinery in eukaryotes (read: In Yeast) is stepwise and involves first the binding of TFIID to the DNA, then TFIIA, then TFIIB, before finally the Polymerase is incorporated into the growing complex. Source: Molecular Biology of the Gene - James D. Watson, p.g.449-454

In prokaryotes, the sigma factor needs to be bound to the core enzyme (forming the holoenzyme) in order for this promoter specificity to be achieved. Your book 'Principle of Genetics - Snustard and Simmons' is referring to the core RNAP, not the holoenzyme with the Sigma factor bound.

This is why sigma factors are often not included under the umbrella term of 'transcription factor' - they achieve the same functionality as eukaryotic TFs, but are fundamentally different in terms of their binding to the polymerase.

Often authors note that eukaryotes need TFs whereas prokaryotes don't because the point they want to convey is that eukaryotes use huge multiprotein complexes bound to the Polymerase, whereas prokaryotes just use the RNAP holoenzyme, giving Sigma factors a somewhat 'special' place among the transcription factors.