DDB2, DDB1A and DET1 exhibit complex interactions during Arabidopsis development

Genome-wide detection of genotype environment interactions for flowering time in Brassica napus

Flowering time is strongly related to the environment, while the genotype-by-environment interaction study for flowering time is lacking in Brassica napus. Here, a total of 11,700,689 single nucleotide polymorphisms in 490 B. napus accessions were used to associate with the flowering time and related climatic index in eight environments using a compressed variance-component mixed model, 3VmrMLM. As a result, 19 stable main-effect quantitative trait nucleotides (QTNs) and 32 QTN-by-environment interactions (QEIs) for flowering time were detected. Four windows of daily average temperature and precipitation were found to be climatic factors highly correlated with flowering time. Ten main-effect QTNs were found to be associated with these flowering-time-related climatic indexes. Using differentially expressed gene (DEG) analysis in semi-winter and spring oilseed rapes, 5,850 and 5,511 DEGs were found to be significantly expressed before and after vernalization. Twelve and 14 DEGs, including 7 and 9 known homologs in Arabidopsis, were found to be candidate genes for stable QTNs and QEIs for flowering time, respectively. Five DEGs were found to be candidate genes for main-effect QTNs for flowering-time-related climatic index. These candidate genes, such as BnaFLCs, BnaFTs, BnaA02.VIN3, and BnaC09.PRR7, were further validated by the haplotype, selective sweep, and co-expression networks analysis. The candidate genes identified in this study will be helpful to breed B. napus varieties adapted to particular environments with optimized flowering time.

Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean

The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.

Protecting DNA from errors and damage: an overview of DNA repair mechanisms in plants compared to mammals

The genome integrity of all organisms is constantly threatened by replication errors and DNA damage arising from endogenous and exogenous sources. Such base pair anomalies must be accurately repaired to prevent mutagenesis and/or lethality. Thus, it is not surprising that cells have evolved multiple and partially overlapping DNA repair pathways to correct specific types of DNA errors and lesions. Great progress in unraveling these repair mechanisms at the molecular level has been made by several talented researchers, among them Tomas Lindahl, Aziz Sancar, and Paul Modrich, all three Nobel laureates in Chemistry for 2015. Much of this knowledge comes from studies performed in bacteria, yeast, and mammals and has impacted research in plant systems. Two plant features should be mentioned. Plants differ from higher eukaryotes in that they lack a reserve germline and cannot avoid environmental stresses. Therefore, plants have evolved different strategies to sustain genome fidelity through generations and continuous exposure to genotoxic stresses. These strategies include the presence of unique or multiple paralogous genes with partially overlapping DNA repair activities. Yet, in spite (or because) of these differences, plants, especially Arabidopsis thaliana, can be used as a model organism for functional studies. Some advantages of this model system are worth mentioning: short life cycle, availability of both homozygous and heterozygous lines for many genes, plant transformation techniques, tissue culture methods and reporter systems for gene expression and function studies. Here, I provide a current understanding of DNA repair genes in plants, with a special focus on A. thaliana. It is expected that this review will be a valuable resource for future functional studies in the DNA repair field, both in plants and animals.

Arabidopsis DDB1-CUL4 E3 ligase complexes in det1 salt/osmotic stress resistant germination

A key regulatory mechanism in plant growth, development, and stress signaling utilizes E3 ubiquitin ligases, which target a variety of substrates for degradation. DE-ETIOLATED 1 (DET1) forms a complex with DDB1 (DAMAGED DNA BINDING protein 1) and CUL4 (CULLIN 4), and negatively regulates light signaling. Another DDB1-CUL4 complex containing DWA1 and DWA2 (DWD hypersensitive to ABA 1 and 2) has been shown to negatively regulate abscisic acid (ABA) signaling. Since distinct DDB1-CUL4 complexes have been shown to influence each other, we analyzed genetic interactions between DET1 and components of DDB1-CUL4 complexes during seed germination under salt and osmotic stress conditions. det1 germination was resistant to salt and osmotic stress and dwa1 and dwa2 enhanced this phenotype. In contrast, ddb1a partially suppressed the det1 germination phenotype on both salt and mannitol, while ddb1b had no effect. Mutations in DDB2, a DDB1-CUL4 complex component involved in DNA repair, also partially suppressed the det1 germination phenotype while mutants in COP1, another light signaling component, completely suppressed the det1 resistant germination phenotypes. Taken together these data suggest that components of E3 ubiquitin ligase complexes have variable but significant effects on det1 salt/osmotic stress responses.

Genetic interactions between DET1 and intermediate genes in Arabidopsis ABA signalling

Seed germination is regulated positively by light and negatively by the dormancy-promoting phytohormone abscisic acid (ABA). DE-ETIOLATED 1 (DET1) is a negative regulator of light signalling in Arabidopsis thaliana. In contrast, the bZIP transcription factor LONG HYPOCOTYL 5 (HY5) is a positive regulator of light signalling. HY5 also positively regulates ABA signalling by promoting the expression of ABA INSENSITIVE 5 (ABI5), a dormancy promoting transcription factor. Here we show that germination in det1 mutants is sensitive to ABA. Double mutant analysis indicates that det1 ABA sensitive germination requires HY5 and ABI5. DET1 forms a complex with DAMAGED DNA BINDING protein 1A/B (DDB1A/B). Another DDB1 complex containing DWA1 and 2 (DWD hypersensitive to ABA 1/2) has also been shown to negatively regulate ABA response. Double mutant analysis indicates that DWA1, DWA2, DDB1A, and DDB1B are also required for the det1 ABA sensitive germination phenotype. We also examined water loss in adult plants and found that the det1 rapid water loss phenotype is independent of HY5, ABI5, DWA1, DWA2, and DDB1B. These findings provide insight into interactions between ABA and light signalling in Arabidopsis.

Light and COP1 regulate level of overexpressed DET1 protein

de-etiolated 1 (det1) and constitutive photomorphogenic 1 (cop1) were initially identified as constitutively photomorphogenic Arabidopsis mutants, exhibiting light-grown phenotypes in the dark. Subsequently, both were shown to be components of Damaged DNA Binding protein 1 (DDB1)/CULLIN4-type complexes. Arabidopsis has two DDB1 homologues, DDB1A and DDB1B, and DDB1A mutants enhance det1 phenotypes. Here we examine ddb1a cop1 double mutants and find that ddb1a weakly enhances some cop1 phenotypes but not others, suggesting developmental regulation of COP1-DDB1A interaction. DET1 loss of function strongly enhances cop1 phenotypes. Here we show that MycDET1 overexpression also enhances cop1 phenotypes, thus MycDET1 overexpression in cop1 mutants also generates loss of function effects. Finally, the effect of the cop1 mutant background on the biochemical properties of MycDET1 was examined. MycDET1 levels were found to be lower in the dark than in the light and this difference required COP1. In summary, both DDB1A loss of function and MycDET1 overexpression enhance cop1 phenotypes, while cop1 mutants fail to exhibit light regulation of MycDET1 levels.

Interactions between Arabidopsis DNA repair genes UVH6, DDB1A, and DDB2 during abiotic stress tolerance and floral development

Plants must protect themselves from a spectrum of abiotic stresses. For example, the sun is a source of heat, intense light, and DNA-damaging ultraviolet (UV) rays. Damaged DNA binding protein 1A (DDB1A), DDB2, and UV hypersensitive 6 (UVH6)/XPD are all involved in the repair of UV-damaged DNA - DDB1A and DDB2 in the initial damage recognition stage, while the UVH6/XPD helicase unwinds the damaged strand. We find that, as predicted, Arabidopsis ddb1a and ddb2 mutants do not affect uvh6/xpd UV tolerance. In addition, uvh6 is heat sensitive, and ddb1a and ddb2 weakly enhance this trait. The uvh6 ddb1a and uvh6 ddb2 double mutants also exhibit sensitivity to oxidative stress, suggesting a role for DDB1 complexes in heat and oxidative stress tolerance. Finally, we describe a new uvh6 phenotype, the low penetrance production of flowers with five petals and five sepals. ddb1a and ddb2 suppress this phenotype in uvh6 mutants. Interestingly, heat treatment also induces five-petalled flowers in the ddb1a and ddb2 single mutants. Thus UVH6, DDB1A, and DDB2 all contribute to UV tolerance, heat tolerance and floral patterning.

Genetic interactions of Arabidopsis thaliana damaged DNA binding protein 1B (DDB1B) with DDB1A, DET1, and COP1

Damaged DNA Binding protein 1 (DDB1)–CULLIN4 E3 ubiquitin ligase complexes have been implicated in diverse biological processes in a range of organisms. Arabidopsis thaliana encodes two homologs of DDB1, DDB1A, and DDB1B. In this study we use a viable partial loss of function allele of DDB1B, ddb1b-2, to examine genetic interactions with DDB1A, DET1 and COP1. Although the ddb1b-2 ddb1a double mutant is lethal, ddb1a ddb1b-2/+ and ddb1b-2 ddb1a/+ heterozygotes exhibit few developmental phenotypes but do exhibit decreased tolerance of ultraviolet light. In addition, germination in ddb1a and ddb1a ddb1b-2/+ was found to be sensitive to salt and mannitol, and both DDB1 single mutants as well as the heterozygotes exhibited heat sensitivity. DE-ETIOLATED1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) are negative regulators of light development which interact with DDB1-CUL4 complexes. Although ddb1a strongly enhances det1 phenotypes in both dark- and light-grown seedlings, ddb1b-2 weakly enhanced the det1 short hypocotyl phenotype in the dark, as well as enhancing anthocyanin levels and suppressing the det1 low chlorophyll phenotype in light-grown seedlings. In adults, ddb1a suppresses det1 early flowering and enhances the det1 dwarf phenotype. A similar trend was observed in ddb1b-2 det1 double mutants, although the effects were smaller in magnitude. In cop1 mutants, ddb1b-2 enhanced the cop1-4 short hypocotyl phenotype in dark and light, enhanced anthocyanin levels in cop1-1 in the light, but had no effect in adults. Thus the requirement for DDB1B varies in the course of development, from COP1-specific effects in hypocotyls to DET1-specific in adults.

The Arabidopsis cell cycle checkpoint regulators TANMEI/ALT2 and ATR mediate the active process of aluminum-dependent root growth inhibition

Aluminum (Al) toxicity is a global issue that severely limits root growth in acidic soils. Isolation of suppressors of the Arabidopsis thaliana Al-hypersensitive mutant, als3-1, resulted in identification of a cell cycle checkpoint factor, ALUMINUM TOLERANT2 (ALT2), which monitors and responds to DNA damage. ALT2 is required for active stoppage of root growth after Al exposure, because alt2 loss-of-function mutants fail to halt root growth after Al exposure, do not accumulate CyclinB1;1 in the root tip, and fail to force differentiation of the quiescent center. Thus, alt2-1 mutants are highly tolerant of Al levels that are severely inhibitory to the wild type. The alt2-1 allele is a loss-of-function mutation in a protein containing a putative DDB1-binding WD40 motif, previously identified as TANMEI, which is required for assessment of DNA integrity, including monitoring of DNA crosslinks. alt2-1 and atr loss-of-function mutants, the latter of which affects the cell cycle checkpoint ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED, are severely sensitive to DNA crosslinking agents and have increased Al tolerance. These results suggest that Al likely acts as a DNA-damaging agent in vivo and that Al-dependent root growth inhibition, in part, arises from detection of and response to this damage by TANMEI/ALT2 and ATR, both of which actively halt cell cycle progression and force differentiation of the quiescent center.

det1-1-induced UV-C hyposensitivity through UVR3 and PHR1 photolyase gene over-expression

Obligate photoautotrophs such as plants must capture energy from sunlight and are therefore exposed to the damaging collateral effects of ultraviolet (UV) irradiation, especially on DNA. Here we investigated the interconnection between light signaling and DNA repair, two concomitant pathways during photomorphogenesis, the developmental transition associated with the first light exposure. It is shown that combination of an enhanced sunscreen effect and photoreactivation confers a greater level of tolerance to damaging UV-C doses in the constitutive photomorphogenic de-etiolated1-1 (det1--1) Arabidopsis mutant. In darkness, expression of the PHR1 and UVR3 photolyase genes, responsible for photoreactivation, is maintained at a basal level through the positive action of HY5 and HYH photomorphogenesis-promoting transcription factors and the repressive effects of DET1 and COP1. Upon light exposure, HY5 and HYH activate PHR1 gene expression while the constitutively expressed nuclear-localized DET1 protein exerts a strong inhibitory effect. Altogether, the data presented indicate a dual role for DET1 in controlling expression of light-responsive and DNA repair genes, and describe more precisely the contribution of photomorphogenic regulators in the control of light-dependent DNA repair.

Arabidopsis DDB1a and DDB1b are critical for embryo development

DNA Damaged binding protein 1 (DDB1) is a highly conserved protein of around 125 kDa. It serves as a substrate adaptor subunit to a CUL4-based E3 ubiquitin ligase within the ubiquitin proteasome pathway. However, based on a set of three beta-propellers, the protein is able to mediate various protein-protein interactions, suggesting that it participates in many developmental and physiological processes in the plant. Arabidopsis encodes for two closely related DDB1 proteins, named DDB1a and DDB1b. While loss-of DDB1a does not severely affect development, loss-of DDB1b has been reported to result in an embryo lethal phenotype. Here we describe two novel ddb1b T-DNA insertion mutants that are not embryo lethal, which we utilized as genetic tools to dissect DDB1b from DDB1a function. Information generated by these studies showed that the C-terminal part of the DDB1 proteins is critical for specific protein-protein interactions. In addition, we demonstrated that DDB1a, like DDB1b, is critical for embryo development, and that both proteins have distinct functions in whole plant development.

The DDB1a interacting proteins ATCSA-1 and DDB2 are critical factors for UV-B tolerance and genomic integrity in Arabidopsis thaliana

The integrity of the genome is a fundamental prerequisite for the well-being of all living organisms. Critical for the genomic integrity are effective DNA damage detection mechanisms that enable the cell to rapidly activate the necessary repair machinery. Here, we describe Arabidopsis thaliana ATCSA-1, which is an ortholog of the mammalian Cockayne Syndrome type-A protein involved in transcription-coupled DNA repair processes. ATCSA-1 is a critical component for initiating the repair of UV-B-induced DNA lesions, and, together with the damage-specific DNA binding protein 2 (DDB2), is necessary for light-independent repair processes in Arabidopsis. The transcriptional profile of both genes revealed that ATCSA-1 is strongly expressed in most tissues, whereas DDB2 is only weakly expressed, predominantly in the root tips and anthers of flowers. In contrast to ATCSA-1, DDB2 expression is rapidly inducible by UV treatment. Like DDB2, ATCSA-1 is localized to the nucleus, and assembles with DDB1 and CUL4 proteins into a complex. ATCSA-1 is an unstable protein that is degraded in a 26S proteasome-dependent manner. Overall, the results presented here form a functional description of a plant Cockayne syndrome factor A (CSA) ortholog, and demonstrate the importance of ATCSA-1 for UV-B tolerance.

Effect of overexpression of Arabidopsis damaged DNA-binding protein 1A on de-etiolated 1

In Arabidopsis thaliana, de-etiolated 1 mutants (det1) grown in the dark resemble light-grown wild-type seedlings. Arabidopsis DET1 encodes a 62 kD protein, which is a negative regulator of light signaling. UV-damaged DNA-binding protein 1 (DDB1) was initially identified due to its role in human DNA damage repair. Arabidopsis has two DDB1 homologs: DDB1A and DDB1B. DDB1A mutation enhances det1 mutant phenotypes. In this study, we generated Arabidopsis lines that overexpress DDB1A-3HA in wild-type, det1, as well as Myc-DET1 or GFP-DET1 rescued genetic backgrounds. DDB1A-3HA overexpression resulted in decreased apical hook formation in wild-type dark-grown seedlings, and enhanced det1 small rosette and early flowering time phenotypes. In the Myc-DET1 background, DDB1A-3HA overexpression resulted in decreased rescue of dark- and light-grown hypocotyl length, light-grown anthocyanin and chlorophyll levels, adult height and stem number phenotypes. This result is consistent with the decreased levels of Myc-DET1 protein detected in the DDB1A-3HA overexpression line. The GFP-DET1 DDB1A-3HA double overexpression line exhibited increased rescue of dark and light-grown hypocotyl length and light-grown chlorophyll level phenotypes relative to GFP-DET1 alone, despite the fact that GFP-DET1 protein also decreased in the double overexpression line. In addition, increased DET1 resulted in decreased DDB1A-3HA levels due to proteasomal degradation. Overall, DDB1A-3HA overexpression affected phenotypes in a variety of DET1 backgrounds, reduced epitope-tagged DET1 levels, and, correlatively, in general dampened the rescue of det1 mutants by the DET1-DDB1A complex.

CRL4s: the CUL4-RING E3 ubiquitin ligases

The evolutionarily conserved cullin family proteins can assemble as many as 400 distinct E3 ubiquitin ligase complexes that regulate diverse cellular pathways. CUL4, one of three founding cullins conserved from yeast to humans, uses a large beta-propeller protein, DDB1, as a linker to interact with a subset of WD40 proteins that serve as substrate receptors, forming as many as 90 E3 complexes in mammals. Many CRL4 complexes are involved in chromatin regulation and are frequently hijacked by different viruses.

Overexpression of Arabidopsis damaged DNA binding protein 1A (DDB1A) enhances UV tolerance

Damaged DNA Binding protein 1 (DDB1) is a conserved protein and a component of multiple cellular complexes. Arabidopsis has two homologues of DDB1: DDB1A and DDB1B. In this study we examine the role of DDB1A in Arabidopsis UV tolerance and DNA repair using a DDB1A null mutant (ddb1a) and overexpression lines. DDB1A overexpression lines showed higher levels of UV-resistance than wild-type in a range of assays as well as faster DNA repair. However a significant difference between wild-type plants and ddb1a mutants was only observed immediately following UV treatment in root length and photoproduct repair assays. DDB1A and DDB1B mRNA levels increased 3 h after UV exposure and DDB1A is required for UV regulation of DDB1B and DDB2 mRNA levels. In conclusion, while DDB1A is sufficient to increase Arabidopsis UV tolerance, it is only necessary for immediate response to UV damage.

Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4

Fruits are a major source of nutrition in human diets, providing carbohydrates, fiber, vitamins and phytonutrients. Carotenoids are a principal class of compounds found in many fruits, providing nutritional benefits both as precursors to essential vitamins and as antioxidants. Molecular characterization revealed that the tomato high pigment mutant genes (hp1 and hp2) encode UV-DAMAGED DNA BINDING PROTEIN-1 (DDB1) and DE-ETIOLATED-1 (DET1) homologs, respectively, and both are essential components of the recently identified CUL4-based E3 ligase complex. Here we have isolated a tomato CUL4 homolog and performed yeast two-hybrid assays to suggest possible association of tomato DDB1 with CUL4 and DET1. Real-time RT-PCR analysis indicated that both HP1 and CUL4 are expressed constitutively. Abscisic acid is implicated in plastid division control and its application substantially enhances HP1/DDB1 mRNA accumulation. Transformation of constructs expressing CUL4-YFP and DDB1-YFP fusion proteins driven by the CaMV 35S promoter reveals that both CUL4 and DDB1 are targeted to tomato plastids and nuclei simultaneously. Using fruit-specific promoters combined with RNAi technology, we show that downregulated DDB1 expression in transgenic fruits results in a significant increase in the number of plastids and corresponding enhanced pigment accumulation. CUL4-RNAi repression lines provide insight regarding CUL4 function during tomato development, and reveal that this tomato cullin is important in the regulation of plastid number and pigmentation, which in turn have a direct impact on fruit nutrient quality.