The pea light-independent photomorphogenesis1 mutant results from partial duplication of COP1 generating an internal promoter and producing two distinct transcripts

Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities

The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

The GmSTF1/2-GmBBX4 negative feedback loop acts downstream of blue-light photoreceptors to regulate isoflavonoid biosynthesis in soybean

Isoflavonoids, secondary metabolites derived from the phenylalanine pathway, are predominantly biosynthesized in legumes, especially soybean (Glycine max). They are not only essential for plant responses to biotic and abiotic stresses but also beneficial to human health. In this study, we report that light signaling controls isoflavonoid biosynthesis in soybean. Blue-light photoreceptors (GmCRY1s, GmCRY2s, GmPHOT1s, and GmPHOT2s) and the transcription factors GmSTF1 and GmSTF2 promote isoflavonoid accumulation, whereas the E3 ubiquitin ligase GmCOP1b negatively regulates isoflavonoid biosynthesis. GmPHOT1s and GmPHOT2s stabilize GmSTF1/2, whereas GmCOP1b promotes the degradation of these two proteins in soybean. GmSTF1/2 regulate the expression of approximately 27.9% of the genes involved in soybean isoflavonoid biosynthesis, including GmPAL2.1, GmPAL2.3, and GmUGT2. They also repress the expression of GmBBX4, a negative regulator of isoflavonoid biosynthesis in soybean. In addition, GmBBX4 physically interacts with GmSTF1 and GmSTF2 to inhibit their transcriptional activation activity toward target genes related to isoflavonoid biosynthesis. Thus, GmSTF1/2 and GmBBX4 form a negative feedback loop that acts downstream of photoreceptors in the regulation of isoflavonoid biosynthesis. Our study provides novel insights into the control of isoflavonoid biosynthesis by light signaling in soybean and will contribute to the breeding of soybean cultivars with high isoflavonoid content through genetic and metabolic engineering.

Induced Mutation in GmCOP1b Enhances the Performance of Soybean under Dense Planting Conditions

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is the key photomorphogenic inhibitor that has been extensively studied in higher plants. Nevertheless, its role has not been documented in the economically important soybean. Here we investigated the functions of two COP1 homologous genes, GmCOP1a and GmCOP1b, by analyzing Gmcop1a and Gmcop1b mutants with indels using CRISPR in soybean. We revealed that, although both genes are required for skotomorphogenesis in the dark, the GmCOP1b gene seems to play a more prominent role than GmCOP1a in promoting stem elongation under normal light conditions. Consistently, the bZIP transcriptional factors STF1/2, which repress stem elongation in soybean, accumulated to the highest level in the Gmcop1a1b double mutant, followed by the Gmcop1b and Gmcop1a mutants. Furthermore, the Gmcop1b mutants showed reduced shade response and enhanced performance under high-density conditions in field trials. Taken together, this study provides essential genetic resources for elucidating functional mechanisms of GmCOP1 and breeding of high yield soybean cultivars for future sustainable agriculture.

Beyond Light: Insights Into the Role of Constitutively Photomorphogenic1 in Plant Hormonal Signaling

Light is an important environmental factor with profound effects in plant growth and development. Constitutively photomorphogenic1 (COP1) is a vital component of the light signaling pathway as a negative regulator of photomorphogenesis. Although the role of COP1 in light signaling has been firmly established for some time, recent studies have proven that COP1 is also a crucial part of multiple plant hormonal regulatory pathways. In this article, we review the available evidence involving COP1 in hormone signaling, its molecular mechanisms, and its contribution to the complicated regulatory network linking light and plant hormone signaling.

Ethylene-independent promotion of photomorphogenesis in the dark by cytokinin requires COP1 and the CDD complex

The transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light, and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin inhibits hypocotyl elongation in dark-grown Arabidopsis plants when applied in high concentrations, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethylene production. Here, we show that cytokinin-induced inhibition of hypocotyl elongation is largely independent of ethylene and suggest a close connection between the cytokinin two-component system and the light-signaling networks. We show that this cytokinin signal is mainly mediated through the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE3 and the ARABIDOPSIS RESPONSE REGULATOR1 in combination with ARR12. Interestingly, mutation of CONSTITUTIVELY PHOTOMORPOGENIC1 (COP1), DE-ETIOLATED1, and CYTOKININ INSENSITIVE4/COP10 renders plants insensitive to cytokinin, and these factors are indispensable for the transcriptional response during cytokinin-induced de-etiolation, indicating that a functional light-signaling pathway is essential for this cytokinin response. In addition, the effect of cytokinin on hypocotyl elongation is strongly dependent on the light conditions, with higher light intensities causing a switch in the response to cytokinin from an inhibitor to a promoter of hypocotyl elongation.

COP1 plays a prominent role in drought stress tolerance in Arabidopsis and Pea

Constitutively photomorphogenic 1 (COP1) is an E3 ubiquitin ligase that has been studied extensively in the photomorphogenesis- and light-related processes in Arabidopsis. However, the possible role of COP1 in plant drought stress response remains unknown. Hence, in the present study, the stomatal behavior as one of the key elements in plant dehydration response was investigated in Arabidopsis cop1-4 and pea light-independent photomorphogenesis (lip1) mutants. We observed that water loss rate in the cop1-4 and lip1 detached leaves was significantly much faster than wild-type, resulting from failing to reduce the stomatal aperture by the mutants. But, interestingly, the cop1-4 and lip1 isolated leaves treated with abscisic acid (ABA) as well as cop1-4 and lip1 soil-grown under drought stress could close their stomata as wild-type. Hence, COP1 plays a fundamental role in the regulation of stomatal movements in response to dehydration and its function was conserved during evolution in both Arabidopsis and pea. Further evaluations showed the cop1-4 mutant was not significantly damaged from the oxidative stress derived from soil water limiting conditions when compared to wild-type. Similarly, the up-regulation level of several key stress-responsive genes was relatively lower in cop1-4 than wild-type. Therefore, COP1 might be considered as a potential key regulator of both short-and long-term dehydration response. Multiple stress-related cis-elements were also detected in the COP1 promoter region, which supported its up-regulation in response to drought, salt, and cold stresses. Besides, we figured out the constitutively open stomata of cop1-4 in darkness can be as a result of the reduced AtMYB61 expression.

Ethylene Signaling Influences Light-Regulated Development in Pea

Plant responses to light involve a complex network of interactions among multiple plant hormones. In a screen for mutants showing altered photomorphogenesis under red light, we identified a mutant with dramatically enhanced leaf expansion and delayed petal senescence. We show that this mutant exhibits reduced sensitivity to ethylene and carries a nonsense mutation in the single pea (Pisum sativum) ortholog of the ethylene signaling gene ETHYLENE INSENSITIVE2 (EIN2). Consistent with this observation, the ein2 mutation rescues the previously described effects of ethylene overproduction in mature phytochrome-deficient plants. In seedlings, ein2 confers a marked increase in leaf expansion under monochromatic red, far-red, or blue light, and interaction with phytochromeA, phytochromeB, and long1 mutants confirms that ein2 enhances both phytochrome- and cryptochrome-dependent responses in a LONG1-dependent manner. In contrast, minimal effects of ein2 on seedling development in darkness or high-irradiance white light show that ethylene is not limiting for development under these conditions. These results indicate that ethylene signaling constrains leaf expansion during deetiolation in pea and provide further evidence that down-regulation of ethylene production may be an important component mechanism in the broader control of photomorphogenic development by phytochrome and cryptochrome.

The role of strigolactones in photomorphogenesis of pea is limited to adventitious rooting

The recently discovered group of plant hormones, the strigolactones, have been implicated in regulating photomorphogenesis. We examined this extensively in our strigolactone synthesis and response mutants and could find no evidence to support a major role for strigolactone signaling in classic seedling photomorphogenesis (e.g. elongation and leaf expansion) in pea (Pisum sativum), consistent with two recent independent reports in Arabidopsis. However, we did find a novel effect of strigolactones on adventitious rooting in darkness. Strigolactone-deficient mutants, Psccd8 and Psccd7, produced significantly fewer adventitious roots than comparable wild-type seedlings when grown in the dark, but not when grown in the light. This observation in dark-grown plants did not appear to be due to indirect effects of other factors (e.g. humidity) as the constitutively de-etiolated mutant, lip1, also displayed reduced rooting in the dark. This role for strigolactones did not involve the MAX2 F-Box strigolactone response pathway as Psmax2 f-box mutants did not show a reduction in adventitious rooting in the dark compared with wild-type plants. The auxin-deficient mutant bushy also reduced adventitious rooting in the dark, as did decapitation of wild-type plants. Rooting was restored by the application of indole-3-acetic acid (IAA) to decapitated plants, suggesting a role for auxin in the rooting response. However, auxin measurements showed no accumulation of IAA in the epicotyls of wild-type plants compared with the strigolactone synthesis mutant Psccd8, suggesting that changes in the gross auxin level in the epicotyl are not mediating this response to strigolactone deficiency.

Genetic control of flowering time in legumes

The timing of flowering, and in particular the degree to which it is responsive to the environment, is a key factor in the adaptation of a given species to various eco-geographic locations and agricultural practices. Flowering time variation has been documented in many crop legumes, and selection for specific variants has permitted significant expansion and improvement in cultivation, from prehistoric times to the present day. Recent advances in legume genomics have accelerated the process of gene identification and functional analysis, and opened up new prospects for a molecular understanding of flowering time adaptation in this important crop group. Within the legumes, two species have been prominent in flowering time studies; the vernalization-responsive long-day species pea (Pisum sativum) and the warm-season short-day plant soybean (Glycine max). Analysis of flowering in these species is now being complemented by reverse genetics capabilities in the model legumes Medicago truncatula and Lotus japonicus, and the emergence of genome-scale resources in a range of other legumes. This review will outline the insights gained from detailed forward genetic analysis of flowering time in pea and soybean, highlighting the importance of light perception, the circadian clock and the FT family of flowering integrators. It discusses the current state of knowledge on genetic mechanisms for photoperiod and vernalization response, and concludes with a broader discussion of flowering time adaptation across legumes generally.

Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation

BACKGROUND

Plants have evolved light sensing mechanisms to optimally adapt their growth and development to the ambient light environment. The COP1/SPA complex is a key negative regulator of light signaling in the well-studied dicot Arabidopsis thaliana. COP1 and members of the four SPA proteins are part of an E3 ubiquitin ligase that acts in darkness to ubiquitinate several transcription factors involved in light responses, thereby targeting them for degradation by the proteasome. While COP1 is also found in humans, SPA proteins appear specific to plants. Here, we have functionally addressed evolutionary conservation of COP1 and SPA orthologs from the moss Physcomitrella, the monocot rice and the dicot Arabidopsis.

RESULTS

To this end, we analyzed the activities of COP1- and SPA-like proteins from Physcomitrella patens and rice when expressed in Arabidopsis. Expression of rice COP1 and Physcomitrella COP1 protein sequences predominantly complemented all phenotypic aspects of the viable, hypomorphic cop1-4 mutant and the null, seedling-lethal cop1-5 mutant of Arabidopsis: rice COP1 fully rescued the constitutive-photomorphogenesis phenotype in darkness and the leaf expansion defect of cop1 mutants, while it partially restored normal photoperiodic flowering in cop1. Physcomitrella COP1 partially restored normal seedling growth and flowering time, while it fully restored normal leaf expansion in the cop1 mutants. In contrast, expression of a SPA ortholog from Physcomitrella (PpSPAb) in Arabidopsis spa mutants did not rescue any facet of the spa mutant phenotype, suggesting that the PpSPAb protein is not functionally conserved or that the Arabidopsis function evolved after the split of mosses and seed plants. The SPA1 ortholog from rice (OsSPA1) rescued the spa mutant phenotype in dark-grown seedlings, but did not complement any spa mutant phenotype in light-grown seedlings or in adult plants.

CONCLUSION

Our results show that COP1 protein sequences from Physcomitrella, rice and Arabidopsis have been functionally conserved during evolution, while the SPA proteins showed considerable functional divergence. This may - at least in part - reflect the fact that COP1 is a single copy gene in seed plants, while SPA proteins are encoded by a small gene family of two to four members with possibly sub- or neofunctionalized tasks.

PAPP5 is involved in the tetrapyrrole mediated plastid signalling during chloroplast development

The initiation of chloroplast development in the light is dependent on nuclear encoded components. The nuclear genes encoding key components in the photosynthetic machinery are regulated by signals originating in the plastids. These plastid signals play an essential role in the regulation of photosynthesis associated nuclear genes (PhANGs) when proplastids develop into chloroplasts. One of the plastid signals is linked to the tetrapyrrole biosynthesis and accumulation of the intermediates the Mg-ProtoIX and its methyl ester Mg-ProtoIX-ME. Phytochrome-Associated Protein Phosphatase 5 (PAPP5) was isolated in a previous study as a putative Mg-ProtoIX interacting protein. In order to elucidate if there is a biological link between PAPP5 and the tetrapyrrole mediated signal we generated double mutants between the Arabidopsis papp5 and the crd mutants. The crd mutant over-accumulates Mg-ProtoIX and Mg-ProtoIX-ME and the tetrapyrrole accumulation triggers retrograde signalling. The crd mutant exhibits repression of PhANG expression, altered chloroplast morphology and a pale phenotype. However, in the papp5crd double mutant, the crd phenotype is restored and papp5crd accumulated wild type levels of chlorophyll, developed proper chloroplasts and showed normal induction of PhANG expression in response to light. Tetrapyrrole feeding experiments showed that PAPP5 is required to respond correctly to accumulation of tetrapyrroles in the cell and that PAPP5 is most likely a component in the plastid signalling pathway down stream of the tetrapyrrole Mg-ProtoIX/Mg-ProtoIX-ME. Inhibition of phosphatase activity phenocopied the papp5crd phenotype in the crd single mutant demonstrating that PAPP5 phosphatase activity is essential to mediate the retrograde signal and to suppress PhANG expression in the crd mutant. Thus, our results suggest that PAPP5 receives an inbalance in the tetrapyrrole biosynthesis through the accumulation of Mg-ProtoIX and acts as a negative regulator of PhANG expression during chloroplast biogenesis and development.

Plastid-to-nucleus communication, signals controlling the running of the plant cell

The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Ubiquitination in the control of photoperiodic flowering

Triggering flowering at the appropriate time is a key factor for the successful reproduction of plants. Daylength perception allows plants to synchronize flowering with seasonal changes, a process systematically analyzed in the model species Arabidopsis thaliana. Characterization of molecular components that participate in the photoperiodic control of floral induction has revealed that photoreceptors and the circadian oscillator interact in a complex manner to modulate the floral transition in response to daylength and in fact, photoperiodic flowering can be regarded as an output pathway of the circadian oscillator. Recent observations indicate that besides transcriptional regulation, the promotion of flowering in response to photoperiod appears to be also regulated by modulation of protein stability and degradation. Therefore, the ubiquitin/26S proteasome system for targeted protein degradation has emerged as a key element in photoperiodic flowering regulation. Different E3 ubiquitin ligases are involved in the proteolysis of a variety of photoperiod-regulated pathway components including photoreceptors, clock elements and flowering time proteins, all of which participate in the control of this developmental process. Given the large variety of plant ubiquitin ligase complexes, it is likely that new factors involved in mechanisms of protein-targeted degradation will soon be ascribed to various aspects of flowering time control.

PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variation in perennial flowering

Higher plants exhibit a variety of different life histories. Annual plants live for less than a year and after flowering produce seeds and senesce. By contrast perennials live for many years, dividing their life cycle into episodes of vegetative growth and flowering. Environmental cues control key check points in both life histories. Genes controlling responses to these cues exhibit natural genetic variation that has been studied most in short-lived annuals. We characterize natural genetic variation conferring differences in the perennial life cycle of Arabis alpina. Previously the accession Pajares was shown to flower after prolonged exposure to cold (vernalization) and only for a limited period before returning to vegetative growth. We describe five accessions of A. alpina that do not require vernalization to flower and flower continuously. Genetic complementation showed that these accessions carry mutant alleles at PERPETUAL FLOWERING 1 (PEP1), which encodes a MADS box transcription factor orthologous to FLOWERING LOCUS C in the annual Arabidopsis thaliana. Each accession carries a different mutation at PEP1, suggesting that such variation has arisen independently many times. Characterization of these alleles demonstrated that in most accessions, including Pajares, the PEP1 locus contains a tandem arrangement of a full length and a partial PEP1 copy, which give rise to two full-length transcripts that are differentially expressed. This complexity contrasts with the single gene present in A. thaliana and might contribute to the more complex expression pattern of PEP1 that is associated with the perennial life-cycle. Our work demonstrates that natural accessions of A. alpina exhibit distinct life histories conferred by differences in PEP1 activity, and that continuous flowering forms have arisen multiple times by inactivation of the floral repressor PEP1. Similar phenotypic variation is found in other herbaceous perennial species, and our results provide a paradigm for how characteristic perennial phenotypes might arise.

Perennial plants live for many years and cycle between flowering and vegetative growth. These stages of the life cycle are often initiated by environmental conditions and occur seasonally. However, many herbaceous perennial species such as strawberry, rose, or Arabis alpina contain varieties that flower continuously irrespective of the seasons. Here we characterize this genetic variation in A. alpina and show that five continuously flowering accessions carry independent mutations in the PERPETUAL FLOWERING 1 (PEP1) gene. These mutations impair the activity of the PEP1 floral repressor causing the plants to flower without requirement for winter cold and to flower continuously. This result has interesting parallels with strawberry and rose, where inactivation of a different floral repressor controlling response to day length gives rise to naturally occurring perpetual flowering forms. We also show that PEP1 in A. alpina has a complex duplicated structure that gives rise to two overlapping transcripts. This arrangement differs from the simple structure of PEP1 orthologues in related annual species, such as FLC of Arabidopsis thaliana, suggesting that duplication of PEP1 might contribute to the complex transcriptional patterns associated with PEP1 function in perennials. Our work provides insight into genetic variation contributing to the perennial life history of plants.

Plastid-to-nucleus communication, signals controlling the running of the plant cell

The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Myosin XI is required for actin-associated movement of plastid stromules

Stromules are highly dynamic stroma-filled tubules extending from the surface of plastids and occasionally interconnecting individual plastids, allowing the movement of complex biological molecules between the interconnected plastids. Experiments with inhibitors of cytoskeleton assembly have indicated the involvement of an actin-based system in stromule movement. However, the motor protein associated with the system had not been identified. Here, we present direct evidence that myosin XI is involved in the formation and movement of stromules in tobacco leaves. Application of 2,3-butanedione 2-monoxime, an inhibitor of myosin ATPase activity, resulted in the loss of stromules from tobacco leaf epidermal cells. Transient RNA interference of myosin XI in leaves of Nicotiana benthamiana also resulted in the loss of stromules from epidermal cells, without any effect on transcripts for actin or myosin VIII. Transient expression of a GFP-tagged myosin XI tail domain in tobacco leaf epidermal cells showed that the fusion protein localized to the chloroplast envelope, as well as to mitochondria and other organelles. Our findings identify myosin XI as a key protein involved in the formation and movement of stromules.

Update on the genetic control of flowering in garden pea

The garden pea has been a model for the genetics of flowering for several decades and numerous flowering loci have been identified, but until recently little was known about the molecular nature of these loci. This paper presents an update on recent work on the molecular genetics of flowering in pea, outlining progress in gene and mutant isolation, expression analyses, grafting and other physiological studies, and candidate gene assessment. Work so far has led to the identification of the LATE1 and DNE loci as orthologues of Arabidopsis GIGANTEA and ELF4, respectively, and candidate genes for several other loci are being evaluated. Expression analysis of an expanded FT-like gene family suggests a more complex role for this group of genes. These results provide the first insight into the circadian clock, photoperiod response mechanism, and mobile signals in pea, and identify both conserved and divergent features in comparison with Arabidopsis.

Light regulation of gibberellin biosynthesis in pea is mediated through the COP1/HY5 pathway

Light regulation of gibberellin (GA) biosynthesis occurs in several species, but the signaling pathway through which this occurs has not been clearly established. We have isolated a new pea (Pisum sativum) mutant, long1, with a light-dependent elongated phenotype that is particularly pronounced in the epicotyl and first internode. The long1 mutation impairs signaling from phytochrome and cryptochrome photoreceptors and interacts genetically with a mutation in LIP1, the pea ortholog of Arabidopsis thaliana COP1. Mutant long1 seedlings show a dramatic impairment in the light regulation of active GA levels and the expression of several GA biosynthetic genes, most notably the GA catabolism gene GA2ox2. The long1 mutant carries a nonsense mutation in a gene orthologous to the ASTRAY gene from Lotus japonicus, a divergent ortholog of the Arabidopsis bZIP transcription factor gene HY5. Our results show that LONG1 has a central role in mediating the effects of light on GA biosynthesis in pea and demonstrate the importance of this regulation for appropriate photomorphogenic development. By contrast, LONG1 has no effect on GA responsiveness, implying that interactions between LONG1 and GA signaling are not a significant component of the molecular framework for light-GA interactions in pea.

Plastid signals remodel light signaling networks and are essential for efficient chloroplast biogenesis in Arabidopsis

Plastid signals are among the most potent regulators of genes that encode proteins active in photosynthesis. Plastid signals help coordinate the expression of the nuclear and chloroplast genomes and the expression of genes with the functional state of the chloroplast. Here, we report the isolation of new cryptochrome1 (cry1) alleles from a screen for Arabidopsis thaliana genomes uncoupled mutants, which have defects in plastid-to-nucleus signaling. We also report genetic experiments showing that a previously unidentified plastid signal converts multiple light signaling pathways that perceive distinct qualities of light from positive to negative regulators of some but not all photosynthesis-associated nuclear genes (PhANGs) and change the fluence rate response of PhANGs. At least part of this remodeling of light signaling networks involves converting HY5, a positive regulator of PhANGs, into a negative regulator of PhANGs. We also observed that mutants with defects in both plastid-to-nucleus and cry1 signaling exhibited severe chlorophyll deficiencies. These data show that the remodeling of light signaling networks by plastid signals is a mechanism that plants use to integrate signals describing the functional and developmental state of plastids with signals describing particular light environments when regulating PhANG expression and performing chloroplast biogenesis.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome

Background

Human eosinophil-derived neurotoxin (edn) and eosinophil cationic protein (ecp) are members of a subfamily of primate ribonuclease (rnase) genes. Although they are generated by gene duplication event, distinct edn and ecp expression profile in various tissues have been reported.

Results

In this study, we obtained the upstream promoter sequences of several representative primate eosinophil rnases. Bioinformatic analysis revealed the presence of a shared 34-nucleotide (nt) sequence stretch located at -81 to -48 in all edn promoters and macaque ecp promoter. Such a unique sequence motif constituted a region essential for transactivation of human edn in hepatocellular carcinoma cells. Gel electrophoretic mobility shift assay, transient transfection and scanning mutagenesis experiments allowed us to identify binding sites for two transcription factors, Myc-associated zinc finger protein (MAZ) and SV-40 protein-1 (Sp1), within the 34-nt segment. Subsequent in vitro and in vivo binding assays demonstrated a direct molecular interaction between this 34-nt region and MAZ and Sp1. Interestingly, overexpression of MAZ and Sp1 respectively repressed and enhanced edn promoter activity. The regulatory transactivation motif was mapped to the evolutionarily conserved -74/-65 region of the edn promoter, which was guanidine-rich and critical for recognition by both transcription factors.

Conclusion

Our results provide the first direct evidence that MAZ and Sp1 play important roles on the transcriptional activation of the human edn promoter through specific binding to a 34-nt segment present in representative primate eosinophil rnase promoters.

The bromodomain protein GTE6 controls leaf development in Arabidopsis by histone acetylation at ASYMMETRIC LEAVES1

The transition from the juvenile to the mature phase during vegetative development in plants is characterized by changes in leaf shape. We show that GENERAL TRANSCRIPTION FACTOR GROUP E6 (GTE6) regulates differences in leaf patterning between juvenile and mature leaves in Arabidopsis. GTE6 encodes a novel small bromodomain-containing protein unique to plants. Mutations in GTE6 disrupt the formation of elliptical leaf laminae in mature leaves, whereas overexpression of GTE6 resulted in elongated juvenile leaves. GTE6 positively regulates the expression of ASYMMETRIC LEAVES1 (AS1), which encodes a myb-domain protein that controls proximodistal patterning of leaves. Using chromatin immunoprecipitation (ChIP) assays, we show that GTE6 is associated with the promoter and the start of the transcribed region of AS1 and up-regulates expression of AS1 through acetylation of histones H3 and H4. Genetic studies demonstrated that AS1 is epistatic to GTE6, indicating that GTE6 regulates AS1 during leaf morphogenesis. Chromatin remodeling at AS1 is a key regulatory mechanism in leaf development, which ensures the continual production of mature leaves following juvenile-adult transition, thereby maintaining the identity of the mature vegetative phase.

A dominant mutation in the pea PHYA gene confers enhanced responses to light and impairs the light-dependent degradation of phytochrome A

Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.

A Dominant Mutation in the Pea PHYA Gene Confers Enhanced Responses to Light and Impairs the Light-Dependent Degradation of Phytochrome A

Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.

Gibberellins repress photomorphogenesis in darkness

Plants undergo two different developmental programs depending on whether they are growing in darkness (skotomorphogenesis) or in the presence of light (photomorphogenesis). It has been proposed that the latter is the default pathway followed by many plants after germination and before the seedling emerges from soil. The transition between the two pathways is tightly regulated. The conserved COP1-based complex is central in the light-dependent repression of photomorphogenesis in darkness. Besides this control, hormones such as brassinosteroids (BRs), cytokinins, auxins, or ethylene also have been shown to regulate, to different extents, this developmental switch. In the present work, we show that the hormone gibberellin (GA) widely participates in this regulation. Studies from Arabidopsis show that both chemical and genetic reductions of endogenous GA levels partially derepress photomorphogenesis in darkness. This is based both on morphological phenotypes, such as hypocotyl elongation and hook and cotyledon opening, and on molecular phenotypes, such as misregulation of the light-controlled genes CAB2 and RbcS. Genetic studies indicate that the GA signaling elements GAI and RGA participate in these responses. Our results also suggest that GA regulation of this response partially depends on BRs. This regulation seems to be conserved across species because lowering endogenous GA levels in pea (Pisum sativum) induces full de-etiolation in darkness, which is not reverted by BR application. Our results, therefore, attribute an important role for GAs in the establishment of etiolated growth and in repression of photomorphogenesis.

Fluorescence lifetimes of protochlorophyllide in plants with different proportions of short-wavelength and long-wavelength protochlorophyllide spectral forms

Dark-grown leaves of maize (Zea mays), wheat (Triticum aestivum), wild-type pea (Pisum sativum) and its light-independent photomorphogenesis mutant (lip1) have different proportions of protochlorophyllide (Pchlide) forms as revealed by low-temperature fluorescence emission spectra. Four discrete spectral forms of Pchlide, with emission peaks around 633, 640, 656 and 670 nm, could be distinguished after Gaussian deconvolution. In maize and wheat the 656 nm component was the most prominent, whereas for wild-type pea and its lip1 mutant, the 633 and 640 nm components contributed mostly to the fluorescence emission spectra. For the fluorescence lifetimes measured at 77 K a double exponential model was the most adequate to describe the Pchlide fluorescence decay not only for the Pchlide(650-656) form but also for the short-wavelength Pchlide forms. A fast component in the range 0.3-0.8 ns and a slow component in the range 5.1-7.1 ns were present in all samples, but the values varied, depending on species. The long-wavelength Pchlide(650-656) form had a slow component with a lifetime between 5.1 and 6.7 ns, probably reflecting the fluorescence from aggregated Pchlide. The short-wavelength Pchlide(628-633) form had values of the slow component varying between 6.2 and 7.1 ns. This represents a monomeric but probably protein-bound Pchlide form because the free Pchlide in solution has a much longer lifetime around 10 ns at 77 K. The contribution of different Pchlide forms to the measured lifetime values is discussed.

Repressors of photomorphogenesis

The internal programs of plant development are informed in a profound way by environmental light conditions. This review summarizes the contribution of repressor proteins to the light-signaling machinery during seedling development, and discusses the integration of repressors with other, positively acting, light-signaling pathways and auxin and brassinosteroid hormone-signaling pathways. The main focus is placed on the mode of action of the COP/DET/FUS proteins, which were first identified in Arabidopsis but are now emerging in other plants. Their role in regulating protein turnover through ubiquitination is reviewed in light of parallel ongoing investigations of COP/DET/FUS homologues in metazoans and fungi.

A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation

The developmental program of nodulation is regulated systemically in leguminous host species. A mutant astray (Ljsym77) in Lotus japonicus has lost some sort of its ability to regulate this symtem, and shows enhanced and early nodulation. In the absence of rhizobia, this mutant exhibits characteristics associated with defects in light and gravity responses. These nonsymbiotic phenotypes of astray are very similar to those observed in photomorphogenic Arabidopsis mutant hy5. Based on this evidence, we predicted that astray might contain a mutation in the HY5 homologue of L. japonicus. The homologue, named LjBzf, encodes a basic leucine zipper protein in the C-terminal half that shows the highest level of identity with HY5 of all Arabidopsis proteins. It also encodes legume-characteristic combination of motifs, including a RING-finger motif and an acidic region in the N-terminal half. The astray phenotypes were cosegregated with LjBzf, and the failure to splice the intron was detected. Nonsymbiotic and symbiotic phenotypes of astray were complemented by introduction of CaMV35SLjBzf. It is noteworthy that although Arabidopsis hy5 showed an enhancement of lateral root initiation, Lotus astray showed an enhancement of nodule initiation but not of lateral root initiation. Legume-characteristic combination of motifs of ASTRAY may play specific roles in the regulation of nodule development.

Uncoupling brassinosteroid levels and de-etiolation in pea

The suggestion that brassinosteroids (BRs) have a negative regulatory role in de-etiolation is based largely on correlative evidence, which includes the de-etiolated phenotypes of, and increased expression of light-regulated genes in, dark-grown mutants defective in BR biosynthesis or response. However, we have obtained the first direct evidence which shows that endogenous BR levels in light-grown pea seedlings are increased, not decreased, in comparison with those grown in the dark. Similarly, we found no evidence of a decrease in castasterone (CS) levels in seedlings that were transferred from the dark to the light for 24 h. Furthermore, CS levels in the constitutively de-etiolated lip1 mutant are similar to those in wild-type plants, and are not reduced as is the case in the BR-deficient lkb plants. Unlike lip1, the pea BR-deficient mutants lk and lkb are not de-etiolated at the morphological or molecular level, as they exhibit neither a de-etiolated phenotype or altered expression of light-regulated genes when grown in the dark. Similarly, dark-grown WT plants treated with the BR biosynthesis inhibitor, Brz, do not exhibit a de-etiolated phenotype. In addition, analysis of the lip1lkb double mutant revealed an additive phenotype indicative of the two genes acting in independent pathways. Together these results strongly suggest that BR levels do not play a negative-regulatory role in de-etiolation in pea.

The distribution of protochlorophyllide and chlorophyll within seedlings of the lip1 mutant of Pea

The distribution of protochlorophyllide (Pchlide) and NADPH-Pchlide oxidoreductase (POR) was characterized in the epicotyls and roots of wild-type pea (Pisum sativum L. cv. Alaska) and lip1, a mutant with light-independent photomorphogenesis caused by a mutation in the COP1 locus. The upper part of the dark-grown lip1 mutant epicotyls had a high Pchlide content that decreased downward the organ. The elevated Pchlide level in lip1 seedlings was a result of the differentiation of more proplastids into Pchlide-containing plastids. The cortex cells in the lip1 epicotyl were filled with such plastids in contrast to the cortex cells of wild-type seedlings. The mutant also developed Pchlide-containing plastids in the roots, indicating the suppressing effect of the COP1 locus on development of plastids in the corresponding tissues in dark-grown wild-type plants. The distribution of Pchlide-containing plastids in dark-grown lip1 mutant stem and root was similar to the distribution of chloroplasts in irradiated wild-type plants. Both wild-type and lip1 epicotyls contained mostly short wavelength Pchlide fluorescing at 631 nm with only a small shoulder at 654 nm, which was transformed to a minute amount of chlorophyllide (Chlide) by flash irradiation. In contrast, with continuous irradiation a considerable amount of Chlide was formed especially in the lip1 epicotyls. Immunoblots indicated the presence of POR, as a 36 kDa band, in epicotyls of both dark-grown wild-type and lip1 mutant seedlings. However, lip1 stem tissue had a higher content of POR than the wild-type pea. The high content of POR was unexpected as lip1 lacked both the 654 nm fluorescing Pchlide form and the regular PLBs. In light, a significant amount of chlorophyll was formed also in the roots of the lip1 seedlings.