The integration of environmental and circadian signals to regulate transcription from the chloroplast genome

In plants, circadian oscillations in gene expression and physiology occur with a period of approximately 24 hrs. The coordination of these oscillations with environmental signals ensures appropriate biological responses depending on the time of day and season, presenting a fitness advantage. There are extensive roles for the transcription factors HY5 and HYH in the regulation of gene transcription in response to environmental and circadian signals. SIG5 is multiple stress-responsive and coordinates nuclear and chloroplast gene expression; ATHB17 regulates SIG5 transcription in response to salt stress. The work described in this thesis aimed to investigate roles for HY5/HYH in the signalling pathway to SIG5 and its chloroplast gene target psbD BLRP, and to identify whether ATHB17 regulates SIG5 in response to cold stress. qRT-PCR was used to monitor SIG5 and psbD BLRP transcript accumulation under circadian and diel conditions in mutants of HY5 and HYH. Roles for these transcription factors in the circadian and environmental regulation of chloroplast transcription were confirmed, suggesting redundancy between the two. Analysis of CCA1 relative expression over a circadian timeseries suggested that HY5/HYH act on the amplitude of SIG5 expression downstream of CCA1. Bioluminescence imaging was also used to assess SIG5 promoter activity in mutants of these transcription factors, suggesting regulation of SIG5 promoter activity by HY5/HYH. Furthermore, measurement of SIG5 transcript abundance following cold stress suggested it is unlikely that ATHB17 regulates SIG5 in response to cold. This research highlights the existence of both distinct and overlapping roles for HY5/HYH in regulating SIG5 in response to environmental and circadian cues. However, other factors contribute to the maintenance of SIG5 and psbD BLRP circadian rhythmicity. Therefore, future work should aim to identify these factors, as well as to further understand the distinct and intersecting roles for HY5/HYH in the regulation of SIG5 and psbD BLRP

Low-temperature and circadian signals are integrated by the sigma factor SIG5

Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions

Low-temperature and circadian signals are integrated by the sigma factor SIG5.

Acknowledgements: This research was funded by Biotechnology & Biological Sciences Research Council (UK) (BB/I005811/2, BB/J014400/1, BB/T003030/1, Institute Strategic Programme GEN BB/P013511/1 to A.N.D.; studentship 1518540 awarded to P.E.P.), Norwich Research Park Doctoral Training Partnership (BB/T008717/1, to R.D. and A.B.), The Leverhulme Trust (RPG-2018-216, to A.N.D.), the Bristol Centre for Agricultural Innovation (to A.N.D.), the Wolfson Foundation (to A.N.D.), NAGASE Science Technology Foundation (Japan), the Ministry of Education, Culture, Sports, Science and Technology (Japan) (Grants-in-Aid 17K07438, to K.T. and S.I.) and Tokyo Institute of Technology World Research Hub Initiative Program of Institute of Innovative Research (to K.T.). D.L.C.-R. is grateful to the Consejo Nacional de Ciencia y Tecnología (Mexico) for granting a PhD scholarship. We thank the University of Bristol Genomics Facility and Z. Song for experimental support; G. Jenkins for seed donation; S. Samwald, E. Tee, J. Sallmen and N. Holmes for help with protein analysis; C. Faulkner, T. Oyama and T. Muranaka for advice about transient expression; and M. Knight, Y. Yoshitake and M. Shimojima for technical advice. Figure 5 created with BioRender.com.Funder: Bristol Centre for Agricultural Innovation Consejo Nacional de Ciencia y Tecnología (Mexico)Funder: BBSRC (Durham) Studentship 1518540 The Leverhulme Trust RPG-2018-216Funder: NAGASE Science Technology Foundation Tokyo Institute of Technology World Research Hub InitiativeFunder: The Leverhulme Trust RPG-2018-216 Bristol Centre for Agricultural InnovationChloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions