Plant Sigma Factors


Photosynthesis within chloroplasts is crucial for ecosystem function and all agricultural productivity. Chloroplasts are a type of plastid and contain a small circular genome of prokaryotic origin. This genome encodes proteins crucial for chloroplast function and requires correct regulation of gene expression. One cellular mechanism regulating plastid gene transcription involves sigma factors, which in plants are nuclear‐encoded proteins forming part of the chloroplast transcriptional system. These are required for chloroplast gene promoter recognition and transcription initiation, with specific sigma factors thought to recognise specific chloroplast promoters. Plant sigma factors participate in the adjustment of chloroplast transcription in response to environmental fluctuations and during development. They appear to be ancient, originating from photosynthetic bacteria that were chloroplast ancestors, with an increase in sigma factor copy number during plant evolution providing an example of the evolution of cell signalling. We examine the origins, structure, function and environmental signalling by plant sigma factors.

Key Concepts

  • Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and machinery for plastid transcription/translation.
  • Some higher plant sigma factors participate in the integration of environmental signals that regulate chloroplast gene transcription.
  • Sigma factors are found in bacteria to higher plants. In plants, they are important regulators of chloroplast transcription.
  • Higher plant sigma factors allow the nuclear control of chloroplast transcription, forming a signalling pathway from the nucleus to chloroplasts.
  • Higher plant sigma factors are thought to have evolved from sigma factors of photosynthetic bacteria that were engulfed by eukaryotic cells during the evolution of chloroplasts. During plant evolution, they transferred to the nuclear genome.

Keywords: chloroplasts; transcription; sigma factors; signal transduction; photosynthesis; plant biology

Figure 1. Comparison of the structures of bacterial and plant sigma factors. (a) Domain structure within σ54 sigma factors; (b) generalised domain structure of bacterial σ70 sigma factor; (c) generalised structure of plastid sigma factors that have similarity with bacterial σ70 sigma factors. Abbreviations: A, acidic region; B, basic region; CR, conserved region; HTH, helix‐turn‐helix domain; TP, transit peptide; UCR, unconserved region.
Figure 2. Possible evolutionary history of sigma factors in the higher plants. SIG1, SIG5 and SIGX appear to have emerged within the Charophyta. SIG2 is present in Charophyta, although it might alternatively be related to sigma factors in other groups of green algae (Chlorophyta). SIG4 and SIG6 are present in the Gymnospermae, and SIG3 in the Angiospermae. Coloured spheres represent sigma factors, with arrows indicating the stages of higher plant evolution within which each sigma factor homolog might have emerged. Abbreviation: SIGn, sigma factor n. Figure combines work of Carter et al. , Lysenko , Lerbs‐Mache , Fu et al. .
Figure 3. Roles of plant sigma factors in anterograde and retrograde signalling. Sigma factors including SIG1, SIG2, SIG3, SIG4, SIG5, and SIG6 communicate information from the nucleus to chloroplasts. Within chloroplasts, the sigma factors regulate the transcription of PEP‐transcribed genes. Each sigma factor is thought to recruit PEP to a subset of chloroplast gene promoters. This includes photosynthesis‐related genes, and chloroplast genes encoding regulators of retrograde signalling such as tRNAGlu. This is likely to be why SIG2 and SIG6 appear to participate in retrograde signalling events that control expression of photosynthesis‐associated nuclear genes. Specific roles for each photoreceptor in the regulation of each sigma factor are described in the main text of this article. Abbreviations: PEP, plastid‐encoded plastid RNA polymerase; SIGn, sigma factor n; cry, cryptochrome photoreceptor; phy, phytochrome photoreceptor; UVR8, UVB‐RESISTANCE8, UV‐B photoreceptor.


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Further Reading

Kanamaru K, Fujiwara M, Seki M, et al. (1999) Plastidic RNA polymerase σ factors in Arabidopsis. Plant and Cell Physiology 40: 832–842.

Nott A, Jung H‐S, Koussevitzky S and Chory J (2006) Plastid‐to‐nucleus retrograde signalling in plants. Annual Review of Plant Biology 57: 739–759.

Water MT and Langdale JA (2009) The making of a chloroplast. EMBO Journal 28: 2861–2873.

Williams ME (2016) Carbon‐fixing reactions of photosynthesis. Teaching tools in plant biology: lecture notes. The Plant Cell 28: tpc.116.tt0716. DOI: 10.1105/tpc.116.tt0716.

Zhang R, Roose J and Williams ME (2015) Light‐dependent reactions of photosynthesis. Teaching tools in plant biology: lecture notes. The Plant Cell 27: tpc.115.tt0515. DOI: 10.1105/tpc.115.tt0515.

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Cuitun‐Coronado, David, and Dodd, Antony N(Jun 2020) Plant Sigma Factors. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0027974]