Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors

BACKGROUND: Circadian clocks are internal molecular time-keeping mechanisms that provide living organisms with the ability to adjust their growth and physiology and to anticipate diurnal environmental changes. Circadian clocks, without exception, respond to light and, in plants, light is the most potent and best characterized entraining stimulus. The capacity of plants to respond to light is achieved through a number of photo-perceptive proteins including cryptochromes and phytochromes. There is considerable experimental evidence demonstrating the roles of photoreceptors in providing light input to the clock. METHODOLOGY: In order to identify genes regulated by diurnal and circadian rhythms, and to establish possible functional relations between photoreceptors and the circadian clock in tomato, we monitored the temporal transcription pattern in plants entrained to long-day conditions, either by large scale comparative profiling, or using a focused approach over a number of photosensory and clock-related genes by QRT-PCR. In parallel, focused transcription analyses were performed in cry1a- and in CRY2-OX tomato genotypes. CONCLUSIONS: We report a large series of transcript oscillations that shed light on the complex network of interactions among tomato photoreceptors and clock-related genes. Alteration of cryptochrome gene expression induced major changes in the rhythmic oscillations of several other gene transcripts. In particular, over-expression of CRY2 had an impact not only on day/night fluctuations but also on rhythmicity under constant light conditions. Evidence was found for widespread diurnal oscillations of transcripts encoding specific enzyme classes (e.g. carotenoid biosynthesis enzymes) as well as for post-transcriptional diurnal and circadian regulation of the CRY2 transcript

Ligh-regulated and circadian expression of tomato photoreceptors

Doctorate Research in: Plant Biology,a.a. 2003-2006Università della Calabri

Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants

Abstract Background Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and accumulation of this natural polymer and could help to develop Tks into a rubber crop. Results We measured rubber content in the latex of 90 individual Tks plants from 9 accessions, observing a high degree of variability. We carried out de novo root transcriptome sequencing, assembly, annotation and comparison of gene expression of plants with the lower (LR plants) and the higher rubber content (HR plants). The transcriptome analysis also included one plant that did not expel latex, in principle depleted of latex transcripts. Moreover, the transcription of some genes well known to play a major role in rubber biosynthesis, was probed by qRT-PCR. Our analysis showed a high modulation of genes involved in the synthesis of NR between LR and HR plants, and evidenced that genes involved in sesquiterpenoids, monoterpenoids and phenylpropanoid biosynthesis are upregulated in LR plants. Conclusions Our results show that a higher amount of rubber in the latex in HR plants is positively correlated with high expression levels of a number of genes directly involved in rubber synthesis showing that NR production is highly controlled at transcriptional level. On the other hand, lower amounts of rubber in LR plants is related with higher expression of genes involved in the synthesis of other secondary metabolites that, we hypothesize, may compete towards NR biosynthesis. This dataset represents a fundamental genomic resource for the study of Tks and the comprehension of the synthesis of NR and other biochemically and pharmacologically relevant compounds in the Taraxacum genus

Diurnal expression pattern of Cryptochrome (A) and Phytochrome (B) transcripts analyzed by QRT-PCR in <i>wt</i>, <i>cry1a</i>- and <i>CRY2OX</i> IAA-treated tomato plants.

<p>Results are presented as a ratio after normalization with β-actin. Yellow and dark bars along the horizontal axis represent light and dark periods, respectively. Time points are measured in hours from dawn (zeitgeber Time [ZT]); data at ZT24 constitute a replotting of those at ZT0. The control data, of gene expression in the absence of hormone applications, are reproduced, for clarity, from those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030121#pone.0030121.s001" target="_blank">Figure S1</a>. Data shown are the average of two biological replicates, with error bars representing SEM. Hormone-treated plant transcripts significantly different from the corresponding ones of control plants are marked with a * (Student's t test, P≤0.05), two ** (Student's t test, P≤0.01) and three *** (Student's t test, P≤0.001). Data from control plants are replotted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030121#pone-0030121-g002" target="_blank">Figure 2</a>.</p

Number of transcription patterns altered in at least three points per cycle, by ZEA, GIB, AUX and ABA phyto-hormones in <i>wt</i>, <i>cry1a-</i> and <i>CRY2OX</i> genotypes.

<p>We considered four cryptochrome (CRYs (4)) and five phytochrome (PHYs (5)) gene transcripts. In the squares is indicated the number of altered patterns for each hormone.</p

Diurnal expression pattern of <i>CAB4</i> (A) and <i>GIGANTEA</i> (B) transcripts analyzed by QRT-PCR in <i>wt</i>, <i>cry1a</i>- and <i>CRY2OX</i> hormone-treated tomato plants.

<p>Results are presented as a ratio after normalization with β-actin. Yellow and dark bars along the horizontal axis represent light and dark periods, respectively. Time points are measured in hours from dawn (zeitgeber Time [ZT]); data at ZT24 constitute a replotting of those at ZT0. The control data, of gene expression in the absence of hormone applications, are reproduced, for clarity, from those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030121#pone.0030121.s001" target="_blank">Figure S1</a>. Data shown are the average of two biological replicates, with error bars representing SEM. Hormone-treated plant transcripts significantly different from the corresponding ones of control plants are marked with a * (Student's t test, P≤0.05), two ** (Student's t test, P≤0.01) and three *** (Student's t test, P≤0.001).</p

Diurnal expression pattern of Cryptochrome (A) and Phytochrome (B) transcripts analyzed by QRT-PCR in <i>wt</i>, <i>cry1a</i>- and <i>CRY2OX</i> GA₃-treated tomato plants.

<p>Results are presented as a ratio after normalization with β-actin. Yellow and dark bars along the horizontal axis represent light and dark periods, respectively. Time points are measured in hours from dawn (zeitgeber Time [ZT]); data at ZT24 constitute a replotting of those at ZT0. The control data, of gene expression in the absence of hormone applications, are reproduced, for clarity, from those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030121#pone.0030121.s001" target="_blank">Figure S1</a>. Data shown are the average of two biological replicates, with error bars representing SEM. Hormone-treated plant transcripts significantly different from the corresponding ones of control plants are marked with a * (Student's t test, P≤0.05), two ** (Student's t test, P≤0.01) and three *** (Student's t test, P≤0.001).</p

Diurnal expression pattern of Cryptochrome (A) and Phytochrome (B) transcripts analyzed by QRT-PCR in <i>wt</i>, <i>cry1a</i>- and <i>CRY2OX</i> ABA-treated tomato plants.

<p>Results are presented as a ratio after normalization with β-actin. Yellow and dark bars along the horizontal axis represent light and dark periods, respectively. Time points are measured in hours from dawn (zeitgeber Time [ZT]); data at ZT24 constitute a replotting of those at ZT0. The control data, of gene expression in the absence of hormone applications, are reproduced, for clarity, from those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030121#pone.0030121.s001" target="_blank">Figure S1</a>. Data shown are the average of two biological replicates, with error bars representing SEM. Hormone-treated plant transcripts significantly different from the corresponding ones of control plants are marked with a * (Student's t test, P≤0.05), two ** (Student's t test, P≤0.01) and three *** (Student's t test, P≤0.001). Data from control plants are replotted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030121#pone-0030121-g002" target="_blank">Figure 2</a>.</p