Circadian Control of Chloroplast Transcription by a Nuclear-Encoded Timing Signal

Noordally, Zeenat; Ishii, Katsue; Atkins, Kelly A.; Wetherill, Sarah J.; Kusakina, Jelena; Walton, Eleanor J.; Kato, Maiko; Azuma, Miyuki; Tanaka, Kan; Hanaoka, Mitsumasa; Dodd, Antony N.

doi:10.1126/science.1230397

Cited by 131 publications

(179 citation statements)

References 36 publications

Supporting

Mentioning

170

Contrasting

Unclassified

Order By: Relevance

“…As a result, matching internal clock lengths with external light cycles increases CO 2 fixation, growth, and fitness (Dodd et al, 2005). This is consistent with the recent finding of the circadian regulation of gene expression and photosynthetic activities in chloroplasts (Noordally et al, 2013). Indeed, altering the expression of circadian regulators increases chlorophyll biosynthesis and sugar and starch metabolism in Arabidopsis hybrids and allopolyploids (Ni et al, 2009).…”

Section: Introductionsupporting

confidence: 87%

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

Miller

et al. 2014

The Plant Cell

View full text Add to dashboard Cite

Hybrid plants and animals often show increased levels of growth and fitness, a phenomenon known as hybrid vigor or heterosis. Circadian rhythms optimize physiology and metabolism in plants and animals. In plant hybrids and polyploids, expression changes of the genes within the circadian regulatory network, such as CIRCADIAN CLOCK ASSOCIATED1 (CCA1), lead to heterosis. However, the relationship between allelic CCA1 expression and heterosis has remained elusive. Here, we show a parent-of-origin effect on altered circadian rhythms and heterosis in Arabidopsis thaliana F1 hybrids. This parent-of-origin effect on biomass heterosis correlates with altered CCA1 expression amplitudes, which are associated with methylation levels of CHH (where H = A, T, or C) sites in the promoter region. The direction of rhythmic expression and hybrid vigor is reversed in reciprocal F1 crosses involving mutants that are defective in the RNA-directed DNA methylation pathway (argonaute4 and nuclear RNA polymerase D1a) but not in the maintenance methylation pathway (methyltransferase1 and decrease in DNA methylation1). This parent-of-origin effect on circadian regulation and heterosis is established during early embryogenesis and maintained throughout growth and development.

show abstract

Section: Introductionsupporting

confidence: 87%

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

Miller

et al. 2014

The Plant Cell

View full text Add to dashboard Cite

show abstract

“…Nucleusencoded sigma factors control chloroplast-encoded genes, including components of the photosystems (Tsunoyama et al, 2004;Noordally et al, 2013;Puthiyaveetil et al, 2013). SIG2 is thought to regulate PsbA in C 3 Arabidopsis (Woodson et al, 2013), and since both transcripts derived from the SIG2 and PsbA genes are enriched in the M of S. viridis and maize, we infer that SIG2 drives the enrichment of PsbA in both species.…”

Section: Regulators Underlying Patterns Of Convergence In C 4 M and Bmentioning

confidence: 82%

Evolutionary Convergence of Cell-Specific Gene Expression in Independent Lineages of C4 Grasses

et al. 2014

View full text Add to dashboard Cite

Leaves of almost all C 4 lineages separate the reactions of photosynthesis into the mesophyll (M) and bundle sheath (BS). The extent to which messenger RNA profiles of M and BS cells from independent C 4 lineages resemble each other is not known. To address this, we conducted deep sequencing of RNA isolated from the M and BS of Setaria viridis and compared these data with publicly available information from maize (Zea mays). This revealed a high correlation (r = 0.89) between the relative abundance of transcripts encoding proteins of the core C 4 pathway in M and BS cells in these species, indicating significant convergence in transcript accumulation in these evolutionarily independent C 4 lineages. We also found that the vast majority of genes encoding proteins of the C 4 cycle in S. viridis are syntenic to homologs used by maize. In both lineages, 122 and 212 homologous transcription factors were preferentially expressed in the M and BS, respectively. Sixteen shared regulators of chloroplast biogenesis were identified, 14 of which were syntenic homologs in maize and S. viridis. In sorghum (Sorghum bicolor), a third C 4 grass, we found that 82% of these trans-factors were also differentially expressed in either M or BS cells. Taken together, these data provide, to our knowledge, the first quantification of convergence in transcript abundance in the M and BS cells from independent lineages of C 4 grasses. Furthermore, the repeated recruitment of syntenic homologs from large gene families strongly implies that parallel evolution of both structural genes and trans-factors underpins the polyphyletic evolution of this highly complex trait in the monocotyledons.

show abstract

“…seeds were surface-sterilized and sown on half-strength Murashige & Skoog (MS) basal salt mixture (0.5 MS; Duchefa) with 0.8% (w/v) agar (Noordally et al, 2013). Seeds were then stratified (3 d at 4°C) and germinated and grown for 7 d under 100 mmol m 22 s 21 of white light at 19°C, except Figure 2, B to E, where PAR was reduced.…”

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

“…RNA was extracted according to Noordally et al (2013), using the Machery-Nagel Nucleospin II plant RNA extraction kit incorporating DNase I treatment (Thermo Fisher Scientific), except approximately 60 seedlings were used per RNA sample. cDNA was synthesized using the High Capacity cDNA Reverse Transcription Kit with RNase Inhibitor (Applied Biosystems), according to manufacturer's instructions.…”

Section: Rna Extraction and Qrt-pcrmentioning

confidence: 99%

The Energy-Signaling Hub SnRK1 Is Important for Sucrose-Induced Hypocotyl Elongation

et al. 2017

Self Cite

View full text Add to dashboard Cite

Emerging seedlings respond to environmental conditions such as light and temperature to optimize their establishment. Seedlings grow initially through elongation of the hypocotyl, which is regulated by signaling pathways that integrate environmental information to regulate seedling development. The hypocotyls of Arabidopsis (Arabidopsis thaliana) also elongate in response to sucrose. Here, we investigated the role of cellular sugar-sensing mechanisms in the elongation of hypocotyls in response to Suc. We focused upon the role of SnRK1, which is a sugar-signaling hub that regulates metabolism and transcription in response to cellular energy status. We also investigated the role of TPS1, which synthesizes the signaling sugar trehalose-6-P that is proposed to regulate SnRK1 activity. Under light/dark cycles, we found that Suc-induced hypocotyl elongation did not occur in tps1 mutants and overexpressors of KIN10 (AKIN10/SnRK1.1), a catalytic subunit of SnRK1. We demonstrate that the magnitude of Suc-induced hypocotyl elongation depends on the day length and light intensity. We identified roles for auxin and gibberellin signaling in Suc-induced hypocotyl elongation under short photoperiods. We found that Suc-induced hypocotyl elongation under light/dark cycles does not involve another proposed sugar sensor, HEXOKINASE1, or the circadian oscillator. Our study identifies novel roles for KIN10 and TPS1 in mediating a signal that underlies Suc-induced hypocotyl elongation in light/dark cycles.

show abstract

Circadian Control of Chloroplast Transcription by a Nuclear-Encoded Timing Signal

Cited by 131 publications

References 36 publications

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

Evolutionary Convergence of Cell-Specific Gene Expression in Independent Lineages of C4 Grasses

The Energy-Signaling Hub SnRK1 Is Important for Sucrose-Induced Hypocotyl Elongation

Contact Info

Product

Resources

About