Phytochrome-regulated expression of genes encoding light-harvesting chlorophyll a/b-protein in two long hypocotyl mutants and wild type plants of Arabidopsis thaliana

Calmodulin7: recent insights into emerging roles in plant development and stress

Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca²⁺-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca²⁺ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.

Draft genome of Puya raimondii (Bromeliaceae), the Queen of the Andes

Puya raimondii, the Queen of the Andes, is an endangered high Andean species in the Bromeliaceae family. Here, we report its first genome to promote its conservation and evolutionary study. Comparative genomics showed P. raimondii diverged from Ananas comosus about 14.8 million years ago, and the long terminal repeats were likely to contribute to the genus diversification in last 3.5 million years. The gene families related to plant reproductive development and stress responses significantly expanded in the genome. At the same time, gene families involved in disease defense, photosynthesis and carbohydrate metabolism significantly contracted, which may be an evolutionary strategy to adapt to the harsh conditions in high Andes. The demographic history analysis revealed the P. raimondii population size sharply declined in the Pleistocene and then increased in the Holocene. We also designed and tested 46 pairs of universal primers for amplifying orthologous single-copy nuclear genes in Puya species.

Comparative transcriptome profiling of low light tolerant and sensitive rice varieties induced by low light stress at active tillering stage

Low light intensity is a great limitation for grain yield and quality in rice. However, yield is not significantly reduced in low light tolerant rice varieties. The work therefore planned for comparative transcriptome profiling under low light stress to decipher the genes involved and molecular mechanism of low light tolerance in rice. At active tillering stage, 50% low light exposure for 1 day, 3 days and 5 days were given to Swarnaprabha (low light tolerant) and IR8 (low light sensitive) rice varieties. Illumina (HiSeq) platform was used for transcriptome sequencing. A total of 6,652 and 12,042 genes were differentially expressed due to low light intensity in Swarnaprabha and IR8, respectively as compared to control. CAB, LRP, SBPase, MT15, TF PCL1 and Photosystem I & II complex related gene expressions were mostly increased in Swarnaprabha upon longer duration of low light exposure which was not found in IR8 as compared to control. Their expressions were validated by qRT-PCR. Overall study suggested that the maintenance of grain yield in the tolerant variety under low light might be results of accelerated expression of the genes which enable the plant to keep the photosynthetic processes moving at the same pace even under low light.

Light-harvesting chlorophyll a/b-binding proteins, positively involved in abscisic acid signalling, require a transcription repressor, WRKY40, to balance their function

The light-harvesting chlorophyll a/b-binding (LHCB) proteins are the apoproteins of the light-harvesting complex of photosystem II. In the present study, we observed that downregulation of any of the six LHCB genes resulted in abscisic acid (ABA)-insensitive phenotypes in seed germination and post-germination growth, demonstrating that LHCB proteins are positively involved in these developmental processes in response to ABA. ABA was required for full expression of different LHCB members and physiologically high levels of ABA enhanced LHCB expression. The LHCB members were shown to be targets of an ABA-responsive WRKY-domain transcription factor, WRKY40, which represses LHCB expression to balance the positive function of the LHCBs in ABA signalling. These findings revealed that ABA is an inducer that fine-tunes LHCB expression at least partly through repressing the WRKY40 transcription repressor in stressful conditions in co-operation with light, which allows plants to adapt to environmental challenges.

Light-harvesting chlorophyll a/b-binding proteins are required for stomatal response to abscisic acid in Arabidopsis

The light-harvesting chlorophyll a/b binding proteins (LHCB) are perhaps the most abundant membrane proteins in nature. It is reported here that the down-regulation or disruption of any member of the LHCB family, LHCB1, LHCB2, LHCB3, LHCB4, LHCB5, or LHCB6, reduces responsiveness of stomatal movement to ABA, and therefore results in a decrease in plant tolerance to drought stress in Arabidopsis thaliana. By contrast, over-expression of a LHCB member, LHCB6, enhances stomatal sensitivity to ABA. In addition, the reactive oxygen species (ROS) homeostasis and a set of ABA-responsive genes are altered in the lhcb mutants. These data demonstrate that LHCBs play a positive role in guard cell signalling in response to ABA and suggest that they may be involved in ABA signalling partly by modulating ROS homeostasis.

The tricks plants use to reach appropriate light

The perception of ambient light signals that produce a relevant response to ensure exposure to appropriate levels of light energy is vital for plants. In response to this, intricate molecular mechanisms to mediate light signaling have evolved in plants. Among the responses induced by light, seedling extension is a determining event for plant survival in darkness, especially in the initial stage of plant growth. Here we review previous studies and recent progress towards an understanding of light signaling that regulates seedling elongation. We focus on the three regions of the sunlight spectrum that primarily control seedling elongation, namely red/far-red light, blue/UV-A light and UV-B light, and summarize the four signaling pathways that correspond to the three effective spectra.

A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA

BMAA is a cycad-derived glutamate receptor agonist that causes a two- to three-fold increase in hypocotyl elongation on Arabidopsis seedlings grown in the light. To probe the role of plant glutamate receptors and their downstream mediators, we utilized a previously described genetic screen to identify a novel, BMAA insensitive morphology (bim) mutant, bim409. The normal BMAA-induced hypocotyl elongation response observed on wild-type seedlings grown in the light is impaired in the bim409 mutant. This BMAA-induced phenotype is light-specific, as the bim409 mutant exhibits normal hypocotyl elongation in etiolated (dark grown) plants (+ or - BMAA). The mutation in bim409 was identified to be in a gene encoding the Proteosomal Regulatory Particle AAA-ATPase-3 (RPT3). Possible roles of the proteosome in Glu-mediated signaling in plants is discussed.

Light-mediated regulation defines a minimal promoter region of TOP2

Light signaling has been demonstrated to be an important factor for plant growth and development; however, its role in the regulation of DNA replication and cell cycle has just started to be unraveled. In this work, we have demonstrated that the TOP2 promoter of Pisum sativum (pea) is activated by a broad spectrum of light including far-red light (FR), red light (RL) and blue light (BL). Deletion analyses of the TOP2 promoter in transformed plants, Arabidopsis thaliana and Nicotiana tobaccum (tobacco), define a minimal promoter region that is induced by RL, FR and BL, and is essential and sufficient for light-mediated activation. The minimal promoter of TOP2 follows the phytochrome- mediated low-fluence response similar to complex light regulated promoters. DNA-protein interaction studies reveal the presence of a DNA binding activity specific to a 106 bp region of the minimal promoter that is crucial for light-mediated activation. These results altogether indicate a direct involvement of light signaling in the regulation of expression of TOP2, one of the components of the DNA replication/cell cycle machinery.

FIN5 positively regulates far-red light responses in Arabidopsis thaliana

We report the characterization of a semi-dominant mutation fin5-1 (far-red insensitive 5-1) of Arabidopsis, which was isolated from genetic screening of phytochrome A (phyA) signaling components. Plants with the fin5-1 mutation exhibited a long hypocotyl phenotype when grown under far-red (FR) light, but not under red light. Physiological analyses implied that FIN5 might be differentially involved in diverse responses that are regulated by phyA under continuous FR light. Anthocyanin accumulation, gravitropic response of hypocotyl growth, and FR light-preconditioned blocking of greening were also impaired in the fin5-1 mutant, whereas photoperiodic floral induction was not, if at all, significantly affected. Moreover, light-regulated expression of the CHS, PORA and PsbS genes was attenuated in fin5-1 mutant plants, while the light-induced expression of CAB was normal. The mutation exhibited semi-dominance regarding control of hypocotyl growth in FR light. We suggest that FIN5 defines a novel branch in the network of phyA signaling in Arabidopsis.

Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis

The Z-box is one of the light-responsive elements (LREs) found in the promoters of light inducible genes. We have studied the light responsive characteristics of Z-box containing synthetic as well as native promoters. We show that promoters with Z-box as a single LRE or paired with another LRE can respond to a broad spectrum of light. The response is primarily mediated by phyA, phyB and CRY1 photoreceptors at their respective wavelengths of light. We have demonstrated that CAB1 and Z-GATA containing promoters are down-regulated in hy5 mutants in the light. On the other hand, a promoter with Z-box alone is down-regulated in hy5 mutants both in dark and in light conditions, suggesting involvement of a similar regulatory system in the regulation of the promoter in two distinct developmental pathways: skotomorphogenesis and photomorphogenesis. Furthermore, similar to the CAB1 promoter, a Z-GATA containing promoter is derepressed in cop1 mutants in the dark. DNA-protein interaction studies reveal the presence of a DNA-binding activity that is specific to Z-box. These results provide insights into the regulation of the Z-box LRE mediated by various light signaling components.

HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana

HFR1, a basic helix-loop-helix protein, is known to be required for a subset of phytochrome A (phyA)-dependent photoresponses. To investigate the role of HFR1 in light signalling, we have examined the genetic interaction between HFR1 and HY5, a positive regulator of light signalling, and COP1, a repressor of photomorphogenesis. Double mutant analysis suggests that HFR1 mediates phyA-dependent inhibition of hypocotyl elongation independently of HY5. HFR1 was shown to be necessary for a subset of cop1-triggered photomorphogenic phenotypes in the dark, including inhibition of hypocotyl elongation, gravitropic hypocotyl growth, and expression of the light-inducible genes CAB and RBCS. Phenotypic analysis of the triple mutant cop1hy5hfr1 indicated that both HFR1 and HY5 are required for cop1-mediated photomorphogenic seedling development in darkness, consistent with their additive roles in phyA-dependent signalling. Taken together, these results suggest that HFR1 might act downstream of COP1, in a separate pathway from HY5, to mediate photomorphogenesis in Arabidopsis.

shygrl1 is a mutant affected in multiple aspects of photomorphogenesis

We have used a counter-selection strategy based on aberrant phytochrome regulation of an Lhcb gene to isolate an Arabidopsis mutant designated shygrl1 (shg1). shg1 seedlings have reduced phytochrome-mediated induction of the Lhcb gene family, but normal phytochrome-mediated induction of several other genes, including the rbcS1a gene. Additional phenotypes observed in shg1 plants include reduced chlorophyll in leaves and additional photomorphogenic abnormalities when the seedlings are grown on medium containing sucrose. Mutations in the TATA-proximal region of the Lhcb1*3 promoter that are known to be important for phytochrome regulation affected reporter gene expression in a manner similar to the shg1 mutation. Our results are consistent with the possibility that the mutation either leads to defective chloroplast development or to aberrant phytochrome regulation. They also add to the evidence of complex interactions between light- and sucrose-regulated pathways.

Regions of the pea Lhcb1*4 promoter necessary for blue-light regulation in transgenic Arabidopsis

Pea (Pisum sativum) and Arabidopsis contain similar, if not identical, blue-light (BL)-responsive systems that alter expression of specific members of the Lhcb (light-harvesting chlorophyll-binding) gene family. In both plants a single, short pulse of low-fluence BL (threshold = 10(-1) micromol m-2) causes an increase in the rate of transcription from specific members of the Lhcb gene family in etiolated seedlings. Constructs of the BL-regulated pea Lhcb1*4 promoter (PsLhcb1*4) were created, which altered sequences previously implicated in light responses, deleted the 5'-promoter sequence, or removed the 5'-untranslated region. These constructs were tested for BL induction in transgenic Arabidopsis. The PsLhcb1*4 promoter deletions to -150 bp maintained normal fluence response, time course, and reciprocity characteristics. The 5'- untranslated region contained enhancer elements, but was not necessary for BL induction. The -95 to +2 promoter was capable of responding to BL, whereas sequences from -50 were not. Promoters that lack conserved light-regulatory elements or sequences directly implicated in phytochrome and circadian responses retained BL activity, suggesting that the low-fluence BL response utilizes regions of the promoter independent of those that modulate the phytochrome and circadian responses.

Antisense expression of the CK2 alpha-subunit gene in Arabidopsis. Effects on light-regulated gene expression and plant growth

The protein kinase CK2 (formerly casein kinase II) is thought to be involved in light-regulated gene expression in plants because of its ability to phosphorylate transcription factors that bind to the promoter regions of light-regulated genes in vitro. To address this possibility in vivo and to learn more about the potential physiological roles of CK2 in plants, we transformed Arabidopsis with an antisense construct of the CK2 alpha-subunit gene and investigated both morphological and molecular phenotypes. Antisense transformants had a smaller adult leaf size and showed increased expression of chs in darkness and of cab and rbcS after red-light treatment. The latter molecular phenotype implied that CK2 might serve as one of several negative and quantitative effectors in light-regulated gene expression. The possible mechanism of CK2 action and its involvement in the phytochrome signal transduction pathway are discussed.

Low temperature regulates Arabidopsis Lhcb gene expression in a light-independent manner

Low temperature treatment of dark-grown seedlings of Arabidopsis thaliana results in a rapid increase in the amount of mRNAs encoding for the major polypeptides of the light-harvesting complex of photosystem II (Lhcb1 genes). This increase is transient and seems to be due mainly to the accumulation of Lhcb1*3 transcripts, indicating that low temperature differentially regulates the expression of the Arabidopsis Lhcb1 gene family in the dark. A 1.34 kb fragment of the Lhcb1*3 promoter is sufficient to confer low temperature regulation to a reporter gene in transgenic Arabidopsis etiolated seedlings, suggesting that the regulation is occurring at the transcriptional level. The cold-induced accumulation of Lhcb1*3 mRNA is not part of a general response to stressful conditions since no accumulation is detected in response to water stress, anaerobiosis or salt stress. The amount of Lhcb1*3 mRNA decrease in response to exogenous abscisic acid (ABA) suggesting that this phytohormone acts as a negative regulator. Moreover, the accumulation of Lhcb1*3 mRNAs in cold-treated ABA deficient etiolated seedlings is higher than that of wild-type and ABA insensitive etiolated seedlings, indicating that low temperature regulation of Lhcb1*3 is not mediated by ABA.

A negative regulatory factor for the dark repression of Arabidopsis thaliana cab1 gene

A protein factor and its binding site involved in light-responsive gene expression of Arabidopsis thaliana cab1 were investigated. Mobility shift assays were performed to identify a nuclear protein factor and its binding sites on the cab1 promoter. For the binding assay, the Arabidopsis cab1 promoter was cleaved with endonucleases into small fragments (65-200 bp) and end-labeled with Klenow fragments. Nuclei were prepared from the light-grown plants and nuclear proteins were prepared by extracting the purified nuclei with 0.5 M ammonium sulfate. The binding site of the nuclear protein factor was scattered throughout the whole promoter region from the transcription start site to the far upstream region of the promoter. To identify the binding sites that are involved in the light responsiveness, mobility shift assays were performed between the cab1 promoter fragments and the nuclear extracts prepared from the 2 day dark-adapted sample. The mobility shift assay of the 65 bp (-318/ -254) fragment with nuclear extract from the dark-adapted sample showed an additional band, not seen with the light-grown sample. Because the new band was present only in the dark-adapted sample that repressed cab1 expression, it may represent a negative regulatory factor (NRF). The NRF was separable on a heparin-Sepharose column from the other factor present in both the light-grown and dark-adapted samples. The implications of the presence of the NRF have been discussed with respect to gene products of the photosignal transduction Arabidopsis mutants.

Arabidopsis mutants define downstream branches in the phototransduction pathway

Light regulates the development of Arabidopsis seedlings in a variety of ways, including inhibition of hypocotyl growth and promotion of leaf development, chloroplast differentiation, and light-responsive gene expression. Mutations that uncouple most or all of these responses from light control have been described, for example, det1, det2, and cop1. To identify regulatory components that define downstream branches in the light-regulated signal transduction pathway, mutants specifically affected in only one light-regulated response were isolated. A screen was designed to isolate mutants that overexpressed the CAB (photosystem II type I chlorophyll a/b-binding proteins) genes in the dark, by use of transgenic line containing a T-DNA construct with two CAB3 promoter-reporter fusions. Eight mutants that showed aberrant expression of both CAB3 promoters were isolated and were designated doc mutants (for dark overepression of CAB). All of the mutants have normal etiolated morphology in the dark. Genetic and phenotypic analyses indicate that most of the mutations are recessive and define at least three loci (doc1, doc2, doc3). Unlike det1 and det2 mutants, which affect the expression of CAB and RBCS (the small subunit of RuBP carboxylase) to approximately the same extent, all three doc mutations are much more specific in derepressing the expression of CAB. The phenotypes of doc mutants suggest that morphological changes can be genetically separated from changes in CAB gene expression. Moreover, the regulation of CAB gene expression can be separated further from the regulation of RBCS gene expression. Epistasis studies suggest that DOC1 and DET3 act downstream from DET1 on two separate branches in the phototransduction pathway. In contrast, DOC2 appears to act on a distinct pathway from DET1. Mutations in doc1, doc2, or doc3 also impair plant growth under short-day conditions.

Promoter and leader regions involved in the expression of the Arabidopsis ferredoxin A gene

Ferredoxin is a nuclear-encoded protein that is involved in a variety of electron transfer reactions in both photosynthetic and non-photosynthetic plastids. We show here that the expression of the ferredoxin A gene (FedA) in Arabidopsis thaliana is light-regulated, with its mRNA level increased 4.5-fold by transfer of dark-grown seedlings to white light for 3 h. A portion of this light regulation is mediated by phytochrome through a very low fluence type of response. In addition, it is likely that another photoreceptor(s) is also involved. The FedA promoter confers a light- and tissue-regulated expression pattern when fused to the beta-glucuronidase (GUS) and luciferase reporter genes, indicating that the gene is transcriptionally regulated. No evidence of cis-acting light-regulatory elements within the 5' untranslated leader region of the gene was detected. Nevertheless, elements within this leader are required for full activity since its deletion reduces expression both in the light and dark by 25-fold. This region includes a sequence, ACAAAA, which is also present in the 5' untranslated leader of the other three ferredoxin leaders that have been sequenced and in the leaders of 31 other plant genes or about 8% of all plant genes in the GenBank database. In addition to mediating light regulation, the FedA promoter also directs GUS expression in aerial tissues at 70-fold higher levels than in roots. GUS activity staining in aerial tissues is observed in both photosynthetic and non-photosynthetic cells. These data indicate that the FedA promoter also carries the information for expression of this gene in a highly tissue- and cell-specific manner.

Expression of the chlorophyll-a/b-protein multigene family in pea (Pisum sativum L.) : Evidence for distinct developmental responses

To measure transcript levels for individual members of the Cab (chlorophyll a/b protein) multigene family in pea under a range of developmental situations, we developed a system using cDNA synthesis, the polymerase chain reaction (PCR), and chemiluminescence detection. In order to design gene-specific PCR primers for all genes, a partial genomic clone for a fifth, Type I LHCII (light-harvesting complex of photosystem II) gene, Cab-9 The Cab-9 sequence appears in the Genbank/EMBL databases under the accession number M86906 , was isolated and sequenced. All seven known Cab genes in pea are expressed in light-grown buds and leaves, including several genes previously known only from genomic clones. There appear to be at least two groups of Cab genes in pea which differ in their response to light and development. The first group (consisting of Cab-8, AB96, Cab-215 and Cab-315) includes Type I, Type II and Type III genes, shows a relatively strong response to red light, and has bud transcript levels similar to or slightly higher than leaves. The second group, consisting of the Type I genes Cab-9, AB80 and AB66, shows little or no transcript accumulation 24 h after a red light pulse, and has higher transcript levels in leaves than in buds. Transcript levels for genes in this second group appear to be lower than those of the first group in all developmental situations examined. These data indicate that there has been an evolutionary divergence of the responses to light and development among the Type I LHCII genes.

Antagonistic blue- and red-light regulation of cab-gene expression during photosynthetic adaptation in Scenedesmus obliquus

During adaptation of the photosynthetic apparatus of the green alga Scenedesmus obliquus to various light qualities, the accumulation of chlorophylls and pigment-protein complexes (with specific consideration of chlorophyll a/b-binding (Cab) proteins) and cab-gene expression were determined. The fluence rate dependences for chlorophyll accumulation and cab-gene expression were very different. Very low fluence rates of violet (404 nm), blue (461 nm) and red (650 nm) light below the photosynthetic threshold, i.e. between 10(-3) and 10(-1) mumol m-2 s-1, inhibited all of these reactions in cells grown under heterotrophic conditions. At elevated fluence rates (above 1 mumol m-2 s-1), red light retained its negative regulation, whereas blue light stimulated pigment accumulation. Under autotrophic conditions the pattern was more complex, because chlorophyll accumulation was unaffected by light below the photosynthetic threshold. However, the expression of cab-genes was inhibited by red light but stimulated by blue light. Cells adapted to fluence rates, which ensured photosynthetic energy supply (above 1 mumol m-2 s-1), showed an increase in chlorophyll accumulation, blue light being more effective than red light. The results confirm and extend our previous discovery of two antagonistically acting photoreceptors in Scenedesmus which mediate and coordinate the complex functional and structural changes associated with photosynthetic adaptation. One of these receptor pigments is a blue-light receptor with positive action; the other is a violet-red-light receptor which can operate far below the photosynthetic threshold and exerts a negative regulation.