RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae

Tardu, Mehmet; Dikbas, Ugur Meric; Barış, İbrahim; Kavaklı, İbrahim Halil

doi:10.1007/s10142-016-0521-0

Cited by 23 publications

(19 citation statements)

References 62 publications

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“…Although CmPHR6 might represent a transitional form between ssDNA repair and CRYs, its cellular function has not yet been determined . A recent RNA‐seq study indicated that 13 % of the total genes in C. merolae were regulated by blue light . Consistent with their role in global gene regulation, cryptochrome genes ( CmPHR2 , CmPHR3 and CmPHR7 ) were differentially regulated, suggesting that they have a potential role in light‐dependent transcriptional regulation in C. merolae .…”

Section: A Single‐strand Dna Repair Enzyme: Cryptochrome Dash (Cry‐dash)mentioning

confidence: 99%

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

Kavaklı

Barış

Tardu

et al. 2017

Photochem & Photobiology

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Light is a very important environmental factor that governs many cellular responses in organisms. As a consequence, organisms possess different kinds of light-sensing photoreceptors to regulate their physiological variables and adapt to a given habitat. The cryptochrome/photolyase family (CPF) includes photoreceptors that perform different functions in different organisms. Photolyases repair ultraviolet-induced DNA damage by a process known as photoreactivation using photons absorbed from the blue end of the light spectrum. On the other hand, cryptochromes act as blue light circadian photoreceptors in plants and Drosophila to regulate growth and development. In mammals, cryptochromes have lightindependent functions and are very important transcriptional regulators that act at the molecular level as negative transcriptional regulators of the circadian clock. In this review, we highlight current knowledge concerning the structural and functional relationships of CPF members.

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Section: A Single‐strand Dna Repair Enzyme: Cryptochrome Dash (Cry‐dash)mentioning

confidence: 99%

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

Kavaklı

Barış

Tardu

et al. 2017

Photochem & Photobiology

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“…The cDNA library preparation method was carried out as previously described57 and summarized in Supplementary Fig. S6.…”

Section: Methodsmentioning

confidence: 99%

MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae

Tardu

Bulut

Kavaklı

2017

Sci Rep

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Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. Genome-wide analysis revealed that transcription of 6.3% of V. cholerae genes were regulated by BL. We further showed that BL enhances ROS production, which is generated through the oxidative phosphorylation. To understand signaling mechanisms, we generated several knockouts and analyzed their transcriptome under BL exposure. Studies with a double-knockout confirm an anti-sigma factor (ChrR) and putative metalloregulatory-like protein (MerR) are responsible for the genome-wide regulation to BL response in V. cholerae. Collectively, these results demonstrate that MerR-like proteins, in addition to ChrR, are required for V. cholerae to mount an appropriate response against photo-oxidative stress induced by BL. Outside its natural host, V. cholerae can survive for extended periods in natural aquatic environments. Therefore, the regulation of light response for V. cholerae may be a critical cellular process for its survival in these environments.

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“…Nonetheless, C. merolae grown in red and blue light showed increased respiration (by about 25 and 30%, respectively) even after a long-term period of darkness (18-20 h) compared with those grown in white light (Table 4), which could be related to increased synthesis of pigments (Table 5). It was shown that both blue and red light are crucial to orchestrate the transcription of gens involved in carbon metabolism and pigment biosynthesis, as blue and red light regulate 35% of the total gens in C. merolae (Tardu et al 2016).…”

Section: Photosynthesis In White Lightmentioning

confidence: 99%

Photosynthesis of the Cyanidioschyzon merolae cells in blue, red, and white light

et al. 2020

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Photosynthesis and respiration rates, pigment contents, CO2 compensation point, and carbonic anhydrase activity in Cyanidioschizon merolae cultivated in blue, red, and white light were measured. At the same light quality as during the growth, the photosynthesis of cells in blue light was significantly lowered, while under red light only slightly decreased as compared with white control. In white light, the quality of light during growth had no effect on the rate of photosynthesis at low O2 and high CO2 concentration, whereas their atmospheric level caused only slight decrease. Blue light reduced markedly photosynthesis rate of cells grown in white and red light, whereas the effect of red light was not so great. Only cells grown in the blue light showed increased respiration rate following the period of both the darkness and illumination. Cells grown in red light had the greatest amount of chlorophyll a, zeaxanthin, and β-carotene, while those in blue light had more phycocyanin. The dependence on O2 concentration of the CO2 compensation point and the rate of photosynthesis indicate that this alga possessed photorespiration. Differences in the rate of photosynthesis at different light qualities are discussed in relation to the content of pigments and transferred light energy together with the possible influence of related processes. Our data showed that blue and red light regulate photosynthesis in C. merolae for adjusting its metabolism to unfavorable for photosynthesis light conditions.

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RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae

Cited by 23 publications

References 62 publications

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae

Photosynthesis of the Cyanidioschyzon merolae cells in blue, red, and white light

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