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 deubiquitinating protein USP24 interacts with DDB2 and regulates DDB2 stability

Damage-specific DNA-binding protein 2 (DDB2) was first isolated as a subunit of the UV-DDB heterodimeric complex that is involved in DNA damage recognition in the nucleotide excision repair pathway (NER). DDB2 is required for efficient repair of CPDs in chromatin and is a component of the CRL4^DDB2 E3 ligase that targets XPC, histones and DDB2 itself for ubiquitination. In this study, a yeast two-hybrid screening of a human cDNA library was performed to identify potential DDB2 cellular partners. We identified a deubiquitinating enzyme, USP24, as a likely DDB2-interacting partner. Interaction between DDB2 and USP24 was confirmed by co-precipitation. Importantly, knockdown of USP24 in two human cell lines decreased the steady-state levels of DDB2, indicating that USP24-mediated DDB2 deubiquitination prevents DDB2 degradation. In addition, we demonstrated that USP24 can cleave an ubiquitinated form of DDB2 in vitro. Taken together, our results suggest that the ubiquitin-specific protease USP24 is a novel regulator of DDB2 stability.     

The deubiquitinating protein USP24 interacts with DDB2 and regulates DDB2 stability

Damage-specific DNA-binding protein 2 (DDB2) was first isolated as a subunit of the UV-DDB heterodimeric complex that is involved in DNA damage recognition in the nucleotide excision repair pathway (NER). DDB2 is required for efficient repair of CPDs in chromatin and is a component of the CRL4^DDB2 E3 ligase that targets XPC, histones and DDB2 itself for ubiquitination. In this study, a yeast two-hybrid screening of a human cDNA library was performed to identify potential DDB2 cellular partners. We identified a deubiquitinating enzyme, USP24, as a likely DDB2-interacting partner. Interaction between DDB2 and USP24 was confirmed by co-precipitation. Importantly, knockdown of USP24 in two human cell lines decreased the steady-state levels of DDB2, indicating that USP24-mediated DDB2 deubiquitination prevents DDB2 degradation. In addition, we demonstrated that USP24 can cleave an ubiquitinated form of DDB2 in vitro. Taken together, our results suggest that the ubiquitin-specific protease USP24 is a novel regulator of DDB2 stability.     

DDB2, DDB1A and DET1 exhibit complex interactions during Arabidopsis development

Damaged DNA-binding proteins 1 and 2 (DDB1 and DDB2) are subunits of the damaged DNA-binding protein complex (DDB). DDB1 is also found in the same complex as DE-ETIOLATED 1 (DET1), a negative regulator of light-mediated responses in plants. Arabidopsis has two DDB1 homologs, DDB1A and DDB1B. ddb1a single mutants have no visible phenotype while ddb1b mutants are lethal. We have identified a partial loss-of-function allele of DDB2. To understand the genetic interaction among DDB2, DDB1A, and DET1 during Arabidopsis light signaling, we generated single, double, and triple mutants. det1 ddb2 partially enhances the short hypocotyl and suppresses the high anthocyanin content of dark-grown det1 and suppresses the low chlorophyll content, early flowering time (days), and small rosette diameter of light-grown det1. No significant differences were observed between det1 ddb1a and det1 ddb1a ddb2 in rosette diameter, dark hypocotyl length, and anthocyanin content, suggesting that these are DDB1A-dependent phenotypes. In contrast, det1 ddb1a ddb2 showed higher chlorophyll content and later flowering time than det1 ddb1a, indicating that these are DDB1A-independent phenotypes. We propose that the DDB1A-dependent phenotypes indicate a competition between DDB2- and DET1-containing complexes for available DDB1A, while, for DDB1A-independent phenotypes, DDB1B is able to fulfill this role.     

Cellular concentrations of DDB2 regulate dynamic binding of DDB1 at UV-induced DNA damage

Nucleotide excision repair (NER) is the principal pathway for counteracting cytotoxic and mutagenic effects of UV irradiation. To provide insight into the in vivo regulation of the DNA damage recognition step of global genome NER (GG-NER), we constructed cell lines expressing fluorescently tagged damaged DNA binding protein 1 (DDB1). DDB1 is a core subunit of a number of cullin 4-RING ubiquitin ligase complexes. UV-activated DDB1-DDB2-CUL4A-ROC1 ubiquitin ligase participates in the initiation of GG-NER and triggers the UV-dependent degradation of its subunit DDB2. We found that DDB1 rapidly accumulates on DNA damage sites. However, its binding to damaged DNA is not static, since DDB1 constantly dissociates from and binds to DNA lesions. DDB2, but not CUL4A, was indispensable for binding of DDB1 to DNA damage sites. The residence time of DDB1 on the damage site is independent of the main damage-recognizing protein of GG-NER, XPC, as well as of UV-induced proteolysis of DDB2. The amount of DDB1 that is temporally immobilized on damaged DNA critically depends on DDB2 levels in the cell. We propose a model in which UV-dependent degradation of DDB2 is important for the release of DDB1 from continuous association to unrepaired DNA and makes DDB1 available for its other DNA damage response functions.     

The complexities of dystroglycan

The notion of dystroglycan as a simple laminin-binding receptor is increasingly being challenged. New roles and new binding partners are continually emerging. Recent structural advances have provided exciting new insights into the precise molecular interactions between dystroglycan and other key components of the dystroglycan complex. Coupled with an increasing understanding of dystroglycan function at the molecular level, we are finally beginning to probe the complexities of dystroglycan, not only in disease, but in development, adhesion and signalling.     

SUMOylation of damaged DNA-binding protein DDB2

Damaged DNA-binding protein (DDB) is a heterodimer composed of two subunits, p127 and p48, which have been designated DDB1 and DDB2, respectively. DDB2 recognizes and binds to UV-damaged DNA during nucleotide excision repair. Here, we demonstrated that DDB2 was SUMOylated in a UV-dependent manner, and its major SUMO E3 ligase was PIASy as determined by RNA interference-mediated knockdown. The UV-induced physical interaction between DDB2 and PIASy supported this notion. PIASy knockdown reduced the removal of cyclobutane pyrimidine dimers (CPDs) from total genomic DNA, but did not affect that of 6-4 pyrimidine pyrimidone photoproducts (6-4PPs). Thus, DDB2 plays an indispensable role in CPD repair, but not in 6-4PP repair, which is consistent with the observation that DDB2 was SUMOylated by PIASy. These results suggest that the SUMOylation of DDB2 facilitates CPD repair.     

DDB2 induces nuclear accumulation of the hepatitis B virus X protein independently of binding to DDB1

The hepatitis B virus (HBV) X protein (HBx) is critical for the life cycle of the virus. HBx associates with several host cell proteins including the DDB1 subunit of the damaged-DNA binding protein DDB. Recent studies on the X protein encoded by the woodchuck hepadnavirus have provided correlative evidence indicating that the interaction with DDB1 is important for establishment of infection by the virus. In addition, the interaction with DDB1 has been implicated in the nuclear localization of HBx. Because the DDB2 subunit of DDB is required for the nuclear accumulation of DDB1, we investigated the role of DDB2 in the nuclear accumulation of HBx. Here we show that expression of DDB2 increases the nuclear levels of HBx. Several C-terminal deletion mutants of DDB2 that fail to bind DDB1 are able to associate with HBx, suggesting that DDB2 may associate with HBx independently of binding to DDB1. We also show that DDB2 enhances the nuclear accumulation of HBx independently of binding to DDB1, since a mutant that does not bind DDB1 is able to enhance the nuclear accumulation of HBx. HBV infection is associated with liver pathogenesis. We show that the nuclear levels of DDB1 and DDB2 are tightly regulated in hepatocytes. Studies with regenerating mouse liver indicate that during late G1 phase the nuclear levels of both subunits of DDB are transiently increased, followed by a sharp decrease in S phase. Taken together, these results suggest that DDB1 and DDB2 would participate in the nuclear functions of HBx effectively only during the late-G1 phase of the cell cycle.     

Developmental complexities of simple leaves

Recent papers have explored early events in the development of simple leaves. Functional compartmentalization of the shoot apical meristem correlates with distinct fields of cells connected by plasmodesmata. Molecules important in the initiation of phyllotactic pattern are described and the relationship between dorsoventral patterning and lateral leaf expansion is investigated.     

Dynamic complexities in host-parasitoid interaction

In the 1970s ecological research detected chaos and other forms of complex dynamics in simple population dynamics models, initiating a new research tradition in ecology. However, the investigations of complex population dynamics have mainly concentrated on single populations and not on higher dimensional ecological systems. Here we report a detailed study of the complicated dynamics occurring in a basic discrete-time model of host-parasitoid interaction. The complexities include (a) non-unique dynamics, meaning that several attractors coexist, (b) basins of attraction (defined as the set of the initial conditions leading to a certain type of an attractor) with fractal properties (pattern of self-similarity and fractal basin boundaries), (c) intermittency, (d) supertransients, (e) chaotic attractors, and (f) "transient chaos". Because of these complexities minor changes in parameter or initial values may strikingly change the dynamic behavior of the system. All the phenomena presented in this paper should be kept in mind when examining and interpreting the dynamics of ecological systems. Copyright 1999 Academic Press.     

The complexities of DNA computation

Over the past few years, a handful of insightful researchers have bridged the gap between biological computing theory and actual DNA-based computation. By using ingenious encoding techniques and clever molecular-biological manipulations, simple versions of computationally complex problems have been experimentally approached or resolved. However, the technical problems revealed during the execution of these scientific set pieces make it unlikely that DNA will ever rival silicon for the solution of any real-world problem.     

The fascinating complexities of steroid-binding enzymes

Enzymes that modulate the level of circulating steroid hormone can be used to combat steroid-dependent disorders. Members of the NADPH-dependent short chain dehydrogenase/reductase (SDR) family control blood pressure, fertility, and natural and neoplastic growth. Despite the fact that only one amino acid residue is strictly conserved in the 60 known members of the family, all appear to have the dinucleotide-binding Rossmann fold and homologous catalytic residues containing the conserved tyrosine. Variation in the amino acid composition of the substrate binding pocket creates specificity of binding for steroids, prostaglandins, sugars and alcohols. Licorice induces high blood pressure by inhibiting an SDR in the kidney, and appears to combat ulcers by inhibiting another in the stomach. Detailed X-ray analyses of various members of the family should allow the design of potent, tissue-specific, highly selective inhibitors.     

Time-dependent kinetic complexities in cholinesterase-catalyzed reactions

Cholinesterases (ChEs) display a hysteretic behavior with certain substrates and inhibitors. Kinetic cooperativity in hysteresis of ChE-catalyzed reactions is characterized by a lag or burst phase in the approach to steady state. With some substrates damped oscillations are shown to superimpose on hysteretic lags. These time dependent peculiarities are observed for both butyrylcholinesterase and acetylcholinesterase from different sources. Hysteresis in ChE-catalyzed reactions can be interpreted in terms of slow transitions between two enzyme conformers E and E′. Substrate can bind to E and/or E′, both Michaelian complexes ES and E’s can be catalytically competent, or only one of them can make products. The formal reaction pathway depends on both the chemical structure of the substrate and the type of enzyme. In particular, damped oscillations develop when substrate exists in different, slowly interconvertible, conformational, and/or micellar forms, of which only the minor form is capable of binding and reacting with the enzyme. Biphasic pseudo-first-order progressive inhibition of ChEs by certain carbamates and organophosphates also fits with a slow equilibrium between two reactive enzyme forms. Hysteresis can be modulated by medium parameters (pH, chaotropic and kosmotropic salts, organic solvents, temperature, osmotic pressure, and hydrostatic pressure). These studies showed that water structure plays a role in hysteretic behavior of ChEs. Attempts to provide a molecular mechanism for ChE hysteresis from mutagenesis studies or crystallographic studies failed so far. In fact, several lines of evidence suggest that hysteresis is controlled by the conformation of His438, a key residue in the catalytic triad of cholinesterases. Induction time may depend on the probability of His438 to adopt the operative conformation in the catalytic triad. The functional significance of ChE hysteresis is puzzling. However, the accepted view that proteins are in equilibrium between preexisting functional and non-functional conformers, and that binding of a ligand to the functional form shifts equilibrium towards the functional conformation, suggests that slow equilibrium between two conformational states of these enzymes may have a regulatory function in damping out the response to certain ligands and irreversible inhibitors. This is particularly true for immobilized (membrane bound) enzymes where the local substrate and/or inhibitor concentrations depend on influx in crowded organellar systems, e.g. cholinergic synaptic clefts. Therefore, physiological or toxicological relevance of the hysteretic behavior and damped oscillations in ChE-catalyzed reactions and inhibition cannot be ruled out.