Cryptochrome 2 extensively regulates transcription of the chloroplast genome in tomato.

Paolo Facella,Fabrizio Carbone,Gaetano Perrotta,Antonio Placido

doi:10.1002/2211-5463.12082

Abstract

Light plays a key role in the regulation of many physiological processes required for plant and chloroplast development. Plant cryptochromes (crys) play an important role in monitoring, capturing, and transmitting the light stimuli. In this study, we analyzed the effects of CRY2 overexpression on transcription of tomato chloroplast genome by a tiling array, containing about 90 000 overlapping probes (5‐nucleotide resolution). We profiled transcription in leaves of wild‐type and CRY2‐overexpressing plants grown in a diurnal cycle, to generate a comprehensive map of chloroplast transcription and to monitor potential specific modulations of the chloroplast transcriptome induced by the overexpression of CRY2. Our results demonstrate that CRY2 is a master gene of transcriptional regulation in the tomato chloroplast. In fact, it modulates the day/night mRNA abundance of about 58% of the 114 ORFs. The effect of CRY2 includes a differential extension of some transcripts at their 5′‐end, according to the period of the day. We observed that the influence of CRY2 on chloroplast transcription is not limited to coding RNA; a great number of putative noncoding micro RNA also showed differential accumulation pattern. To our knowledge, this is the first study that highlights how a photoreceptor affects the day/night transcription of the chloroplast genome.

Highlights

Light plays a key role in the regulation of many physiological processes required for plant and chloroplast development
Our results demonstrate that CRY2 is a master gene of transcriptional regulation in the tomato chloroplast
To classify the time points at which the sampling was carried out, we used zeitgeber time (ZT) that is defined as the time in hours from the start of a normal day–light cycle [57]

Summary

Introduction

Light plays a key role in the regulation of many physiological processes required for plant and chloroplast development. We observed that the influence of CRY2 on chloroplast transcription is not limited to coding RNA; a great number of putative noncoding micro RNA showed differential accumulation pattern To our knowledge, this is the first study that highlights how a photoreceptor affects the day/ night transcription of the chloroplast genome. Abbreviations cp, chloroplast; CRY2-OX, CRY2-overexpressing plants; CRYs, cryptochromes; CV, coefficient of variance; FKF1, flavin-binding kelch repeat F-box; LD, long-day; LKP2, lov kelch protein 2; LRR, F-box/leucine-rich repeat protein; miRNA, noncoding micro RNA; NC, negative controls; ncRNA, noncoding RNA transcripts; NEP, nucleus-encoded RNA polymerase; ORFs, open reading frames; PEP, plastid-encoded RNA polymerase; PHOTs, phototropins; PHYs, phytochromes; rbcL, rubisco; RP, ribosomal protein; SIGs, sigma factors; TPR/PPR, tetra/ pentatricopeptide repeat protein; UVR8, UV resistance locus 8; WGAs, whole-genome tiling arrays; WT, wild-type plants; ZTL, Zeitlupe; ZT, zeitgeber time. Cry regulates chloroplast genome transcription [13,14,15,16]; CRY2 controls photoperiodic promotion of floral initiation [17,18] and mediates the hypocotyls and internode shortening under both low- and highfluence blue light [19,20]; CRY3 is a CRY-DASH protein that localizes to mitochondria and chloroplast [21] and is able to repair UV-induced lesions in singlestranded DNA [22] as well as in loop structures of double-stranded DNA [23]

Methods

Results

Conclusion