InteractiveFly: GeneBrief

courtless: Biological Overview | Developmental Biology | Effects of Mutation | Evolutionary Homologs | References

BIOLOGICAL OVERVIEW

The courtless (crl) mutation disrupts early steps of courtship behavior in Drosophila males, as well as the development of their sperm. Most of the homozygous crl mutant males (78%) do not court at all. Only 5% perform the entire ritual and copulate, yet these matings produce no progeny. The crl gene encodes two proteins that differ in their carboxy termini and are the Drosophila homologs of the yeast ubiquitin-conjugating enzyme UBC7. The crl mutation is caused by an insertion of a P element into the 3' UTR of the gene, which probably disrupts translational regulatory elements. As a consequence, the homozygous mutants exhibit a six- to seven-fold increase in the level of the Crl protein. The crl product is essential, and deletions that remove the crl gene are lethal. During embryonic development crl is expressed primarily in the CNS. These results implicate the ubiquitin-mediated system in the development and function of the nervous system and in meiosis during spermatogenesis (Orgad, 2000).

When wild-type mature males are presented with virgin females, they initiate the courtship ritual almost instantaneously, spending most of their time performing the different courtship steps, culminating in a copulation rate of >90%. However, in homozygous crl males, 78% of the males tested did not court at all, and only 17% performed some of the courtship steps. Of these courting mutant males (13%) most performed only the early steps of courtship (orienting, following, and wing extension). Only 5% of the crl/crl males eventually copulated, but none of these matings produced progeny. The courtship index (C.I.) representing the fraction of the observation time that each male actually spent courting was 72% for wild-type (Canton-S) males and only 12% for crl homozygous males (breaking down this value for the noncourting and courting mutant males gives a C.I. value of 0 for noncourting and 23% for courting mutant males). In contrast, crl/crl females are fertile when mated to wild-type males, behave normally, and are as receptive to males as are wild-type females (Orgad, 2000).

Genes at the top of the sex determination hierarchy are involved in the control of courtship. Besides these, known mutants that act earliest in the ritual are those that affect the courtship song -- as in cacophony, dissonance, and croaker. The crl mutation blocks courtship at the very beginning of the sequence. Most homozygous crl males do not court at all and those few that do generally fail to progress beyond the early steps of following and wing extension. These early steps in courtship have been associated with male-specific development in the dorsal posterior brain (Orgad, 2000).

Mutants that are generally defective in locomotor behavior are also often defective in courtship. This sometimes manifests itself as a sluggish phenotype with a low probability of initiating courtship. However, the behavioral defect in crl homozygous males is not due to general sluggishness since their locomotor activity is as high as that of their crl/CyO sibling or wild-type males (Orgad, 2000).

Visual, rhythm, as well as learning and memory mutants have been found to court less rigorously than wild-type males and to have prolonged latency of the initiation of this behavior. However, the visual and olfactory systems in crl homozygous flies appear to be normal and cannot account for the mutant phenotype of crl. Therefore, the abnormal courtship behavior of the crl mutant may be attributed to defects in those parts of the central nervous system (CNS) that are responsible for this behavior. A general feature of courtship mutants is their pleiotropic nature. However, the abnormalities they engender are usually not global but rather are restricted to a small number of particular behaviors. For example, two mutants, cacophony and dissonance, isolated in a screen for mutants affecting the male courtship song were later, and rather surprisingly, found to be allelic to previously identified visual mutations. The former, although not visually defective, is an allele of the nbA gene, which, when mutated, causes poor performance in optomotor and phototactic tests, and the latter is allelic to the nonA mutation, which leads to absence of the light-on and light-off transient spikes, but does not affect the courtship song. Two additional examples for pleiotropy among courtship-defective mutants are fruitless and period, both of which display at least two distinct behavioral abnormalities: one is a defect in courtship song, which is common to both mutants, and the other is abnormal circadian rhythm (in the case of per) or display of homosexual behavior (in fru). Given that courtship behavior is complex, utilizing most of the sensory modalities, it is not surprising that mutations affecting vision, olfaction, and audition lead to aberrant courtship behavior (Orgad, 2000).

The courtless mutation is pleiotropic too, affecting distinct systems such as the nervous system and spermatogenesis. While homozygous crl females behave normally, are as receptive to males as wild-type females, and are fertile, homozygous crl males hardly court virgin females and produce abnormal sperm. The defect in spermatogenesis in crl homozygous males appears to be very similar to the phenotype reported for the ms(1)413, ms(1)RD11, and ms(1)682 mutants. In all three, mitochondrial aggregation occurs prematurely, meiotic spindles are not formed, and the primary spermatocytes are transformed directly into tetraploid spermatids. These mutants and crl fall into a distinct phenotypic class of spermatogenic mutants, which includes mutants in the genes for the cell cycle regulatory phosphatase twine, and the cell cycle kinase cdc2. In both mutants certain meiotic events are skipped, yet spermatid differentiation proceeds. As a result, testes of twine or cdc2 males contain bundles of 16 4N-cells that grow flagellar axonemes and undergo DNA condensation and nuclear shaping, as has been observed in crl males. A similar pleiotropy affecting both the nervous system and the reproductive tract has been reported for the dunce mutation. Several male sterile mutations affecting mitochondrial aggregation during spermatogenesis display, in addition, a common behavioral defect: they shake their appendages abnormally. Another example of a gene that encodes a component of the ubiquitin pathway is UbcD1 (effete: Cenci, 1997). effete mutants affect meiosis in males (Orgad, 2000 and references therein).

For normal courtship to occur, certain changes must take place in the CNS during its pupal-adult metamorphosis, and the subsequent reproductive maturation of the newly eclosed fly may entail specifically the dorsal posterior brain and the thoracic ganglion, known to be involved in normal sexual behavior. The molecular details of these processes are largely unknown (Orgad, 2000).

The courtless gene encodes the Drosophila homolog of the ubiquitin-conjugating enzyme UBC7. A distinctive property of the ubiquitin-mediated system is its remarkable functional diversity. It is implicated in various cellular functions including DNA repair (Jentsch, 1987), cell cycle control (Goebl, 1988), and transcription (Hochstrasser, 1991). The individual components of this system display remarkable functional specialization, suggesting narrow substrate specificities (Orgad, 2000).

The courtless gene potentially encodes two proteins that share a conserved UBC domain, but have different carboxy extensions. The C-terminal extensions of UBCs are believed to contribute to the substrate specificity of these enzymes and to their intracellular localization (Sung, 1988). The crl gene products are involved, at least, in two different processes, CNS development/function and spermatogenesis. The results suggest that the level of the Crl protein is critical for courtship. crl/+ males have approximately three times as much Crl protein as have wild-type males, and their courtship is normal. However, crl/crl males have at least seven times the Crl protein that the wild-type males have and are highly defective in courtship. One speculation may be that excess Crl protein may be compatible with normal courtship, as long as its level does not reach a certain threshold (Orgad, 2000).

The ben product was the first to exemplify the involvement of the ubiquitin-mediated system in the development and function of the CNS of Drosophila (Muralidhar, 1993). Recently this system was implicated in the regulation of the circadian feedback loop of the fly (Naidoo, 1999). The results with respect to courtless suggest that the ubiquitin-mediated system is involved in additional aspects of CNS function, in those parts of the brain important for courtship behavior (mushroom bodies, antennal lobes, etc.). This system, via the role of crl, is implicated in spermatogenesis as well. These data strengthen the finding that a mouse gene A1s9, which has been implicated in spermatogenesis, is homologous to the ubiquitin-activating enzyme E1 from yeast (Kay, 1991) and that the phenotype of mice knocked out for the mHR6B gene, the homolog of the yeast RAD6 ubiquitin-conjugating enzyme, is male infertility (Orgad, 2000).

In Drosophila a single regulatory hierarchy controls all aspects of somatic sexual differentiation, including those parts of the CNS involved in sexual behavior. Differentiation of those aspects of the CNS responsible for male-specific courtship occurs during the middle of the pupal period, when the CNS undergoes extensive reorganization, concomitant with the accumulation of crl transcripts. This set of genes, which determines the innate property of sexual behavior, has to be active continuously in the adult to maintain normal courtship behavior (Orgad, 2000).

In adults, sexual differences were found in crl expression, as determined by Northern blots, and the transcripts that retain the fourth intron are male specific. In embryos the crl transcripts are found throughout the CNS with no obvious sex-specific expression. In situ hybridization to sectioned CNS from pupae and adults should allow further studies to determine whether crl is expressed in those parts of the brain known to be involved in sexual behavior (Orgad, 2000).

The P element in the original crl mutant has inserted into the 3' UTR of the crl gene 200 bp upstream of the end of the transcription unit. The 3' UTR of various genes is involved in regulation of the stability of the transcript as well as its translation. In mammals, as well as in Drosophila, AU-rich sequences residing in the 3' UTR act as negative regulatory elements to facilitate degradation of the transcript. In Drosophila, several additional motifs that negatively regulate transcript stability and its translation efficiency were identified in the 3' UTR of various proneural genes of the acaete-scute complex, including Brd-box (CAGTTTAA), GY-box (GTCTTCC), and K-box (TGTGAT). The crl transcript contains in its 3' UTR two Brd-like boxes, one K-box, and several AU-rich motifs, suggesting regulation of its stability and translation efficiency. Indeed, the insertion of the P element in the crl mutant into the 3' UTR causes both reduction in the level of the crl transcript and elevation in the level of its translation. Although there is as yet no explanation for this phenomenon, such a situation has been reported for the 3' UTR of the growth factor TGF-ß1 gene. This UTR contains a CG-rich region that has been identified as being responsible for decrease in transcription, rather than instability of the mRNA, as well as stimulation of translation (Orgad, 2000 and references therein).

The primary role of ubiquitination is to target proteins for degradation. However, existence of stable ubiquitinated proteins has been documented, as well as of proteins that are reversibly ubiquitinated. This suggests that the ubiquitin-mediated system plays a role also in modification of protein function. Thus, the function of the crl-encoded UBC, in ensuring proper development and function of specific parts of the fly's CNS that are important for male sexual behavior, could conceivably be accomplished as follows. It may stably ubiquitinate a substrate protein(s) that is directly involved in patterning of the relevant connections in the CNS as was shown for arthrin, which is a stable actin-ubiquitin conjugate involved in the assembly or function of thin filaments in the Drosophila flight muscles. Alternatively, crl may mark specific substrate proteins for degradation, affording the means for close regulation of the function of proteins by modulating their half-life. This may enable these proteins to act as on/off switches of CNS functions. Overexpression of the Crl protein in the crl mutant may shift the delicate balance between Crl and its specific substrate required for normal development and proper activity of the CNS, culminating in the manifested phenotype of the crl mutant. Yet loss of function of the crl gene is fatal and causes lethality at the larval stage. Identification and characterization of genes that genetically interact with crl, and therefore could serve as a target substrate for Crl, may help in understanding the molecular mechanisms that underlie this complex behavior. It should also lead to better understanding of the increasingly sophisticated role the ubiquitin-mediated system is turning out to play in normal development and function of the CNS and of the neural diseases brought about by its malfunction (Orgad, 2000 and references therein).

DEVELOPMENTAL BIOLOGY

Embryonic

The courtless gene is expressed throughout Drosophila development, and its expression is developmentally regulated. Two transcripts, 1.1 and 1.3 kb, are present in equimolar amounts in embryos. The smaller (1.1 kb) transcript is probably composed of a mixture of the two classes of crl transcripts, which are similar in size (classes 1b and 2). Expression of these transcripts declines in larvae but increases at the pupal stage, and even more at the adult stage. The level of expression of the crl transcripts was compared in males and females of crl/crl, crl/CyO, and wild-type flies by Northern blot. When the entire class 1a cDNA was used as a probe (potentially capable of detecting all three transcripts), the same two bands were visible in both sexes, although higher levels were found in males than in females in all three genotypes. Densitometry indicates that in homozygous crl males the level of expression is four times lower than in wild-type males. When the membrane is stripped and reprobed with the fourth intron, it becomes evident that classes 1a and 1b transcripts that retain this intron are male specific. The only 1.3-kb cDNA isolated corresponds to the transcript that retains the fourth intron. Such a transcript is not present in females, yet females do have a 1.3-kb transcript. This indicates that at least one additional 1.3-kb crl transcript has yet to be identified (Orgad, 2000).

The spatial distribution of crl transcripts was determined by in situ hybridization of digoxigenin-labeled RNA probes corresponding to class 1a cDNA. Early in the blastoderm stage (~ 2 hr of development), crl transcripts are present both in the egg yolk, suggesting a maternal origin, and in the peripheral blastoderm cells, reflecting either maternal contribution or zygotic expression. Subsequently (3 hr of development), they are found in the mesoderm and in the cephalic furrow, and later (5 hr of development) in the extending germ band, in the neuroblasts, and in the stomodial invagination. As development proceeds, in 15-hr-old embryos, expression is confined to the central nervous system (Orgad, 2000).

Class 1a transcript was modified to include a His-tag, and was expressed in Escherichia coli. The tagged protein was used to immunize rabbits. Western blot analysis using the polyclonal antibodies and extracts from male flies of the crl/crl, crl/CyO, and wild-type genotypes reveals elevated amounts of the Crl protein in the mutant flies. Homozygous and heterozygous crl males express at least seven and three times, respectively, more of the Crl protein than the wild type. When this experiment was repeated using extracts from embryos and larvae of one of the homozygous lethal excision lines of crl, no difference was observed in the expression of the Crl protein between the homozygous mutant and heterozygotes at the embryonic stage, as expected of a transcript that is maternally deposited. However, when extracts of first and second instar larvae were used, the Crl protein was detected in the heterozygous larvae, but almost no protein was present in the homozygous mutant larvae. The lack of the Crl protein may account for the lethal phase of the excision line and provides a genetic control for the specificity of the antibodies (Orgad, 2000).

The spatial distribution of the Crl protein was determined using antibodies that were raised against the two different putative carboxy termini of the Crl proteins. In general, the two antibodies revealed a similar pattern of Crl expression, which was comparable to the distribution of the crl transcript, as determined by in situ hybridization. However, at the blastoderm stage the Crl protein is localized to the poles, while the transcripts are present in the egg yolk and in all the peripheral blastoderm cells (Orgad, 2000).

EVOLUTIONARY HOMOLOGS

Other ubiquitin conjugating enzymes of Drosophila

The identification and functional characterization of ariadne-1 (ari-1), a novel and vital Drosophila gene required for the correct differentiation of most cell types in the adult organism is reported. A sequence-related gene, ari-2, and the corresponding mouse and human homologs of both genes, are described. All these sequences define a new protein family by the Acid-rich, RING finger, B-box, RING finger, coiled-coil (ARBRCC) motif string. In Drosophila, ari-1 is expressed throughout development in all tissues. The mutant phenotypes are most noticeable in cells that undergo a large and rapid membrane deposition, such as rewiring neurons during metamorphosis, large tubular muscles during adult myogenesis, and photoreceptors. Occasional survivors of null alleles exhibit reduced life span, motor impairments, and short and thin bristles. Single substitutions at key cysteines in each RING finger cause lethality with no survivors and a drastic reduction of rough endoplasmic reticulum that can be observed in the photoreceptors of mosaic eyes. In yeast two-hybrid assays, the protein ARI-1 interacts with a novel ubiquitin-conjugating enzyme, UbcD10, whose sequence is also reported in this study. The N-terminal RING-finger motif is necessary and sufficient to mediate this interaction. Mouse and fly homologs of both ARI proteins and the Ubc can substitute for each other in the yeast two-hybrid assay, indicating that ARI represents a conserved novel mechanism in development. In addition to ARI homologs, the RBR signature is also found in the Parkinson-disease-related protein Parkin, adjacent to an ubiquitin-like domain, suggesting that the study of this mechanism could be relevant for human pathology (Aguilera, 2000).

This study reports on ARIADNE-1, the first member of a conserved new family of proteins whose multiple structural domains include a RING finger that interacts with an E2 enzyme of the ubiquitin system. In Drosophila, ari-1 is expressed in all tissues throughout development although the mutant phenotypes indicate differential requirements in tissues and developmental stages (Aguilera, 2000).

A new protein family: The primary sequence of ARI-1 serves to define a novel protein family characterized by the string of motifs ARBRCC. Drosophila ARI-1 and ARI-2 are the first two members of this family and conserved homologs in yeast, worms, mice, and humans have been identified as well. On the basis of structural criteria, ARI proteins are related to the RBCC family that is composed mostly by signal transducers and transcription factors. In these proteins, the RBCC signature appears in conjuction with other motifs like bromodomain, RFP, and PHD fingers. Within the string of motifs that the ARI family defines, RBR is proposed as a new signature. As in the case of RBCC proteins, RBR is also found associated to other domains, i.e., an ubiquitin-like domain in Parkin or an ill-defined N-terminal domain in ARA54. In addition, the RBR signature is found in many other functionally uncharacterized proteins across eukaryotic species. Most of these sequences are derived from genome projects and their number is increasing rapidly, suggesting that RBR is an ancient and widespread modular element of protein structure (Aguilera, 2000).

Functional role: ARI-1 becomes an additional case lending credence to the role that the ubiquitin system seems to play in neural connectivity. The first precedent was illustrated by the bendless mutant. This gene encodes a ubiquitin-conjugating enzyme whose depletion leads to neural defects. The UbcD10 identified as interacting with ARI belongs to the same subfamily as UbcD3 encoded in ben. Mutations in ben have the most extreme effects in neural connectivity, particularly in the optic ganglia. Defective medulla rotation, the abnormal course of axon bundles, and reduced rhabdomeres, mostly R7, are reported as consistent features of ben eyes along with the original phenotype of incomplete bending of the cervical giant fiber axon. Adult muscles are also affected, albeit the tubular TDT to a greater extent than the indirect flight muscles. Finally, ben null mutants are pupal lethals with a few short-lived and motor-impaired adult escapers. Mutant ari-1 traits reported in this study coincide with those of ben; however, ari-1 phenotypes are more extreme in every tissue analyzed. Preliminary tests (double heterozygotes and gene dosage) were performed, searching for genetic evidence of interactions between ari-1 and the nine Ubc encoding genes including ben, but no positive indication has been found so far. Thus, it seems that UbcD3 on the one hand and UbcD10 and ARI-1 on the other are components of two mechanisms within the ubiquitin system (Aguilera, 2000).

Considering the general expression of ari-1, it is likely that all cell types require its activity. However, at the light microscope level and under the procedures used, the mutant phenotypes become most evident in adult tissues. The failure to detect larval phenotypes cannot be justified, at least solely, on the basis of a large maternal deposit of the normal product. The germline mosaics of null mutations yield regular escapers identical in frequency and phenotype to those produced from heterozygous ovaries. It is more probable that the phenotypes in the larval tissues are subtler than in the adult, requiring a level of observation beyond that used in this study. It is worth noting that the cell types in which the mutant phenotypes are most apparent are those that require a massive and rapid membrane deposition, namely, macrobristles, photoreceptors, large tubular muscles, and rewiring neurons at metamorphosis. These processes represent a high demand on the physiology of the cell. In particular, proteins and membranous cisternae must be supplied efficiently (Aguilera, 2000).

A substantial reduction of rough endoplasmic reticulum was detected in mutant photoreceptors. This trait is more difficult to evaluate in other cell types because their ultrastructure is not as well characterized as that of the photoreceptors. However, this membrane system plays such a central role in the biology of the cell that it is plausible that it could account for the variety of phenotypes observed. The endoplasmic reticulum is the port of entry of most compartmentalized, membrane-anchored, and secretory proteins. It is also the site of folding and modification of nascent protein chains and assembly of multisubunit complexes. The ubiquitin pathway plays a central role in the 'quality control' machinery to remove those proteins that fail to fold properly or to oligomerize, as has been demonstrated for the cystic fibrosis transmembrane conductance regulator and the T-cell receptor. Interestingly, a RING-finger protein, Der3p/Hrd1p, is an integral component of a retrograde transport system in yeast endoplasmic reticulum. The system interacts with the 26S proteasome and includes a Ubc enzyme, Ubc7p. Also, mutations in the Drosophila ninaA cyclophilin homologue, involved in the protein folding and secretory pathway of rhodopsin 1, lead to an accumulation of endoplasmic reticulum in photoreceptors. The reduction of endoplasmic reticulum in ari-1 mutant photoreceptors could indicate a role of ARI proteins in ubiquitin-mediated mechanisms. In turn, a reduced endoplasmic reticulum is a likely origin for the small rhabdomeres and short bristles that all alleles show (Aguilera, 2000).

Regarding the cellular compartment in which ARI-1 performs its function, the protein appears to localize mainly in the cytoplasm according to Western blots of cytoplasm vs. nuclear enriched fractions. Nevertheless, a transient nuclear localization cannot be formally excluded since a putative nuclear localization signal, KKWIKK, can be found between amino acids 268 and 273. In conyrast, the N-terminal acid cluster shows the requirements for transcription activation domains and, in a yeast reporter assay, it was found that this domain is necessary for the autonomous transcription activity of the ARI-1-GAL4BD fusion. Thus, considering the multiple domains present in ARI-1, it is plausible that the protein might perform distinct interactions in several cellular compartments (Aguilera, 2000).

Interaction mechanisms: Cysteines 150 and 309 are key residues for the activity of each RING finger of ARI-1 since alleles ari-1² and ari-1³ are full lethals. In addition, the C150Y version of the protein fails to sustain one of the identified interactions of ARI-1, that with UbcD10. These in vivo and in vitro observations coincide with findings in the breast/ovarian cancer susceptibility gene product BRCA-1 where the RING motif of this human protein also mediates an interaction with a ubiquitin enzyme, the ubiquitin hydrolase BAP1. The implication of a RING-finger protein in the ubiquitin pathway raises the possibility that ARI-1 might be a substrate for UbcD10-mediated ubiquitination and targeted for degradation. ARI-1 Western blots show a single 59-kD band throughout development without any smear or ladder-like signals that could result from ubiquitin-mediated degradation. Although ARI-1 ubiquitination cannot be excluded at this point, a more likely role for ARI proteins might be the modulation of Ubc activity upon other substrates. Recent studies have shown common structural features among ubiquitination complexes such as SCF (Skp1-Cdc53/CUL1-F-box), APC (anaphase promoting complex), or VCB (Von Hippel-Landau-ElonginC-ElonginB). Apart from proteins with E2 and E3 activities, SCF, APC, and VCB also contain adaptor proteins with a variety of protein-protein interaction modules and a conserved domain (F-box or SOCS-box). None of these domains are present in ARI proteins; thus, ARI might represent a new class of adaptor proteins in ubiquitination complexes. In fact, the recent identification of Rbx1 as a common component of SCF and VCB complexes already has introduced the RING-finger motif as a keystone in the combinatorial control of ubiquitination. Rbx1 is a RING-finger protein that interacts with E2 and E3 enzymes as well as with some adaptor proteins. These interactions are necessary to stimulate the catalytic activity of the fully assembled complex, thereby limiting its substrate specificity. This speculative proposal of ARI-1 as an adaptor in a multimeric complex need not be restricted to a ubiquitin tagging system. For example, the SUMO-1 or Rub-1 tagging systems share components with the ubiquitination complexes. In this context, PML, a RBCC protein involved in acute promyelocytic leukemia, is covalently modified by SUMO-1. This modification requires the interaction between Ubc9, a nuclear E2 enzyme, and the R motif in PML (Duprez et al. 1999) (Aguilera, 2000).

Relevance to human pathologies: The interaction between ARI-1 and UbcD10 detected in the yeast two hybrid assay is a conserved mechanism since mouse and fly homologues substitute for each other. Although a genetic test that could validate this interaction in vivo cannot be carried out at this point, the interspecific functional substitution is a strong argument to support its biological relevance. This functional substitution has a potential clinical interest. The sequence of human UbcH7 is 100% identical to UbcM4. In turn, UbcH7 is known to interact with E6-AP, a ubiquitin ligase that uses the tumor suppressor p53 as a substrate. In addition, a defective E6-AP is implicated in Angelman's syndrome. As a logical derivative from the data in Drosophila, the possible interaction between human ARI-1 and the doublet UbcH7/E6-AP should be considered (Aguilera, 2000).

Several human pathologies are caused by functional deficits in RING-finger proteins. Aside from PML and SIAH-1 discussed above, mutations that delete the RING motif of PEX10 cause defects in peroxisome biogenesis leading to Zellweger's syndrome. However, the most direct link with ARI proteins is found in parkin, a gene associated with juvenile parkinsonism. During the search for sequence homologies, the Parkin protein was identified because of a RING-finger motif. Upon closer inspection, however, an RBR signature was evident. In addition, this motif seems to be directly linked to the pathology as the disease can be caused by a point mutation, T240R, which corresponds to the R1 motif in ARI-1. Since this protein also exhibits a ubiquitin-like domain, it has been proposed that Parkin might cause alterations in the ubiquitin system or defects in its own functional maturation eventually leading to selective neurodegeneration. Although defective ubiquitination is a common feature of cellular inclusions such as the Lewy bodies, a hallmark of Parkinson disease, the juvenile form of parkinsonism does not exhibit Lewy's bodies. Also, the early onset of the disease points toward a developmental etiology. As an alternative mechanism to ubiquitination, Parkin could be involved in protein tagging of the SUMO-1 or Rub-1 type. In any event, two important questions arise from the results reported in this study: (1) Are human ARI proteins involved in the biology of Parkin? and (2) Does Parkin interact with a Ubc enzyme? (Aguilera, 2000).

UBC7 structure and interactions with ubiquitin protein ligases

Ubiquitin-conjugating enzymes are a family of related proteins that participate in the ubiquitination of proteins. Studies on the crystal structures of Saccharomyces cerevisiae Ubc4 and Arabidopsis thaliana Ubc1 have indicated that the smallest enzymes (class I), which consist entirely of the conserved core domain, share a common tertiary fold. The three-dimensional structure of the S. cerevisiae class I enzyme encoded by the UBC7 gene is reported. The crystal structure has been solved using molecular replacement techniques and refined by simulated annealing to an R-factor of 0.183 at 2.93 Å resolution. Bond lengths and angles in the molecule have root-mean-square deviations from ideal values of 0.016 Å and 2.3 degrees, respectively. Ubc7 is an alpha/beta protein with four alpha-helices and a four-stranded antiparallel beta-sheet. With the exception of two regions where extra residues are present, the tertiary folding of Ubc7 is similar to those of the other two enzymes. The ubiquitin-accepting cysteine is located in a cleft between two loops. One of these loops is nonconserved, since this region of the Ubc7 molecule differs from the other two enzymes by having 13 extra residues. There is also a second single amino acid insertion that alters the orientation of the turn between the first two beta-strands. Analysis of the 13 ubiquitin-conjugating enzyme sequences in S. cerevisiae indicates that there may be two other regions where extra residues could be inserted into the common tertiary fold. Both of these other regions exhibit significant deviations in the superposition of the three structures and, like the two insertion regions in Ubc7, may represent hypervariable regions within a common tertiary fold. As ubiquitin-conjugating enzymes interact with different substrates or other accessory proteins in the ubiquitination pathway, these variable surface regions may confer distinct specificity to individual enzymes (Cook, 1997).

Substrate discrimination in the ubiquitin-proteasome system is believed to be dictated by specific combinations of ubiquitin-protein ligases (E3s) and ubiquitin-conjugating enzymes (E2s). Doa10/Ssm4 has been identified as a yeast E3 that is embedded in the endoplasmic reticulum (ER)/nuclear envelope yet can target the soluble transcription factor Matalpha2. Doa10 contains an unusual RING finger, which has ubiquitin-ligase activity in vitro and is essential in vivo for degradation of alpha2 via its Deg1 degradation signal. Doa10 functions with two E2s, Ubc6 and Ubc7, to ubiquitinate Deg1-bearing substrates, and it is also required for the degradation of at least one ER membrane protein. Interestingly, different short-lived ER proteins show distinct requirements for Doa10 and another ER-localized E3, Hrd1. Nevertheless, the two E3s overlap in function: A doa10Delta hrd1Delta mutant is far more sensitive to cadmium relative to either single mutant and displays strong constitutive induction of the unfolded protein response; this suggests a role for both E3s in eliminating aberrant ER proteins. The likely human ortholog of DOA10 is in the cri-du-chat syndrome critical region on chromosome 5p, suggesting that defective ubiquitin ligation might contribute to this common genetic disorder (Swanson, 2001).

The Deg1 degradation signal of the transcriptional repressor Matalpha2 confers compartment-specific turnover to a reporter protein. Rapid degradation of a Deg1-containing fusion protein is observed only when the reporter is efficiently imported into the nucleus. In contrast, a reporter that is constantly exported from the nucleus exhibits an extended half-life. Furthermore, nuclear import functions are crucial for both Deg1-induced degradation as well as for the turnover of the endogenous yeast transcription factor Matalpha2. The conjugation of ubiquitin to a Deg1-containing reporter protein is abrogated in mutants affected in nuclear import. Obviously, the Deg1 signal initiates rapid proteolysis within the nucleoplasm, whereas in the cytosol it mediates turnover via a slower pathway. In both pathways the ubiquitin-conjugating enzymes Ubc6p/Ubc7p play a pivotal role. These observations imply that both the cellular targeting of a substrate and the compartment-specific activity of components of the ubiquitin-proteasome system define the half-life of naturally short-lived proteins (Lenk, 2001).

Ubiquitin conjugating enzymes: interactions with ubiquitin protein ligases

The hect domain protein family was originally identified by sequence similarity of its members to the C-terminal region of E6-AP, an E3 ubiquitin-protein ligase. Since the C terminus of E6-AP mediates thioester complex formation with ubiquitin, a necessary intermediate step in E6-AP-dependent ubiquitination, it has been proposed that members of the hect domain family in general have E3 activity. The hect domain is approximately 350 amino acids in length, and the hect domain of E6-AP is necessary and sufficient for ubiquitin thioester adduct formation. Furthermore, the human genome encodes at least 20 different hect domain proteins, and in further support of the hypothesis that hect domain proteins represent a family of E3s, several of these have been shown to form thioester complexes with ubiquitin. In addition, some hect domain proteins interact preferentially with UbcH5 (Drosophila homolog: UbcD10), whereas others interact with UbcH7, indicating that human hect domain proteins can be grouped into at least two classes based on their E2 specificity. Since E3s are thought to play a major role in substrate recognition, the presence of a large family of E3s should contribute to ensure the specificity and selectivity of ubiquitin-dependent proteolytic pathways (Schwarz, 1998).

The structural basis by which ubiquitin (Ub)-conjugating enzymes (E2s) determine substrate specificity remains unclear. Rabbit reticulocyte E217K has been cloned because unlike the similarly sized class I E2s, E214K and UBC4, it is unable to support ubiquitin-protein ligase (E3)-dependent conjugation to endogenous proteins. RNA analysis reveals that this E2 is expressed in all tissues tested, with higher levels in the testis. Analysis of testis RNA from rats of different ages shows that E217K mRNA is induced from days 15 to 30. The predicted amino acid sequence indicates that E217K is a 19. 5-kDa class I E2 but differs from other class I enzymes in possessing an insertion of 13 amino acids distal to the active site cysteine. E217K shows 74% amino acid identity with Saccharomyces cerevisiae UBC7, and therefore, it has been renamed mammalian UBC7. Yeast UBC7 crystal structure indicates that this insertion forms a loop out of the otherwise conserved folding structure. Sequence analysis of E2s had previously suggested that this loop is a hypervariable region and may play a role in substrate specificity. Mutant UBC7 lacking the loop (ubc7Deltaloop) and a mutant E214k with an inserted loop (E214k+loop) have been created and their biochemical functions have been characterized. Ubc7Deltaloop has higher affinity for the E1-Ub thiol ester than native UBC7 and permits conjugation of Ub to selected proteins in the testis but does not permit the broad spectrum E3-dependent conjugation to endogenous reticulocyte proteins. Surprisingly, E214k+loop is unable to accept Ub from ubiquitin-activating enzyme (E1) but is able to accept NEDD8 from E1. E214k+loop is able to support conjugation of NEDD8 to endogenous reticulocyte proteins but with much lower efficiency than E214k. Thus, the loop can influence interactions of the E2 with charged E1 as well as with E3s or substrates, but the exact nature of these interactions depends on divergent sequences in the remaining conserved core domain (Lin, 1999).

The E6AP ubiquitin-protein ligase (E3) mediates the human papillomavirus-induced degradation of the p53 tumor suppressor in cervical cancer and is mutated in Angelman syndrome, a neurological disorder. The crystal structure of the catalytic hect domain of E6AP reveals a bi-lobal structure with a broad catalytic cleft at the junction of the two lobes. The cleft consists of conserved residues whose mutation interferes with ubiquitin-thioester bond formation and is the site of Angelman syndrome mutations. The crystal structure of the E6AP hect domain bound to the UbcH7 ubiquitin-conjugating enzyme (E2) reveals the determinants of E2-E3 specificity and provides insights into the transfer of ubiquitin from the E2 to the E3 (Huang, 1999).

c-Cbl plays a negative regulatory role in tyrosine kinase signaling by an as yet undefined mechanism. Using the yeast two-hybrid system and an in vitro binding assay, it has been demonstrated that the c-Cbl RING finger domain interacts with UbcH7, a ubiquitin-conjugating enzyme (E2). UbcH7 interacts with the wild-type c-Cbl RING finger domain but not with a RING finger domain that lacks the amino acids that are deleted in 70Z-Cbl, an oncogenic mutant of c-Cbl. The in vitro interaction is enhanced by sequences on both the N- and C-terminal sides of the RING finger. In vivo and in vitro experiments reveal that c-Cbl and UbcH7 synergistically promote the ligand-induced ubiquitination of the epidermal growth factor receptor (EGFR). In contrast, 70Z-Cbl markedly reduces the ligand-induced, UbcH7-mediated ubiquitination of the EGFR. MG132, a proteasome inhibitor, significantly prolongs the ligand-induced phosphorylation of both the EGFR and c-Cbl. Thus, c-Cbl plays an essential role in the ligand-induced ubiquitination of the EGFR by a mechanism that involves an interaction of the RING finger domain with UbcH7. This mechanism participates in the down-regulation of tyrosine kinase receptors and loss of this function, as occurs in the naturally occurring 70Z-Cbl isoform, probably contributes to oncogenic transformation (Yokouchi, 1999).

Ubiquitin-protein ligases (E3s) regulate diverse cellular processes by mediating protein ubiquitination. The c-Cbl proto-oncogene is a RING family E3 that recognizes activated receptor tyrosine kinases, promotes their ubiquitination by a ubiquitin-conjugating enzyme (E2) and terminates signaling. The crystal structure of c-Cbl bound to a cognate E2 (UbcH7) and a kinase peptide shows how the RING domain recruits the E2. A comparison with a HECT family E3-E2 complex indicates that a common E2 motif is recognized by the two E3 families. The structure reveals a rigid coupling between the peptide binding and the E2 binding domains and a conserved surface channel leading from the peptide to the E2 active site, suggesting that RING E3s may function as scaffolds that position the substrate and the E2 optimally for ubiquitin transfer (Zheng, 2000).

Ubiquitinylation of proteins appears to be mediated by the specific interplay between ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s). However, cognate E3s and/or substrate proteins have been identified for only a few E2s. To identify proteins that can interact with the human E2 UbcH7, a yeast two-hybrid screen was performed. Two proteins were identified and termed human homolog of Drosophila ariadne (HHARI) and UbcH7-associated protein (H7-AP1). Both proteins, which are widely expressed, are characterized by the presence of RING finger and in-between-RING-finger (IBR) domains. No other overt structural similarity was observed between the two proteins. In vitro binding studies reveal that an N-terminal RING finger motif (HHARI) and the IBR domain (HHARI and H7-AP1) are involved in the interaction of these proteins with UbcH7. Furthermore, binding of these two proteins to UbcH7 is specific insofar as both HHARI and H7-AP1 can bind to the closely related E2, UbcH8, but not to the unrelated E2s UbcH5 and UbcH1. Although it is not clear at present whether HHARI and H7-AP1 serve, for instance, as substrates for UbcH7 or represent proteins with E3 activity, these data suggest that a subset of RING finger/IBR proteins are functionally linked to the ubiquitin/proteasome pathway (Moynihan, 1999).

gp78, also known as the tumor autocrine motility factor receptor, is a transmembrane protein whose expression is correlated with tumor metastasis. gp78 is a RING finger-dependent ubiquitin protein ligase (E3) of the endoplasmic reticulum (ER). Consistent with this, gp78 specifically recruits MmUBC7, a ubiquitin-conjugating enzyme (E2) implicated in ER-associated degradation (ERAD), through a region distinct from the RING finger. gp78 can target itself for proteasomal degradation in a RING finger- and MmUBC7-dependent manner. Importantly, gp78 can also mediate degradation of CD3-delta, a well-characterized ERAD substrate. In contrast, gp78 lacking an intact RING finger or its multiple membrane-spanning domains stabilizes CD3-delta. gp78 has thus been found to be an example of a mammalian cellular E3 intrinsic to the ER, suggesting a potential link between ubiquitylation, ERAD, and metastasis (Fang, 2001).

HHARI (human homologue of Drosophila ariadne) binds to the human ubiquitin-conjugating enzyme UbcH7 in vitro. HHARI interacts and co-localizes with UbcH7 in mammalian cells, particularly in the perinuclear region. A minimal interaction region of HHARI has been defined comprising residues 186-254. Individual amino acid residues essential for the interaction have been identified, and the distance between the RING1 finger and IBR domains has been shown to be critical to maintaining binding. The RING1 finger of HHARI cannot be substituted for by the highly homologous RING finger domains of either of the ubiquitin-protein ligase components c-CBL or Parkin, despite their similarity in structure and their independent capabilities to bind UbcH7. Furthermore, mutation of the RING1 finger domain of HHARI from a RING-HC to a RING-H2 type abolishes interaction with UbcH7. These studies demonstrate that very subtle changes to the domains that regulate recognition between highly conserved components of the ubiquitin pathway can dramatically affect their ability to interact (Ardley, 2001).

Autosomal recessive juvenile parkinsonism (AR-JP), one of the most common familial forms of Parkinson disease, is characterized by selective dopaminergic neural cell death and the absence of the Lewy body, a cytoplasmic inclusion body consisting of aggregates of abnormally accumulated proteins. PARK2, whose mutations cause AR-JP, has been cloned, but the function of the gene product, parkin, remains unknown. Parkin is reported here to be involved in protein degradation as a ubiquitin-protein ligase collaborating with the ubiquitin-conjugating enzyme UbcH7, and mutant parkins from AR-JP patients show loss of the ubiquitin-protein ligase activity. These findings indicate that accumulation of proteins that have yet to be identified causes a selective neural cell death without formation of Lewy bodies. These findings should enhance the exploration of the molecular mechanisms of neurodegeneration in Parkinson's disease as well as in other neurodegenerative diseases that are characterized by involvement of abnormal protein ubiquitination, including Alzheimer's disease, other tauopathies, CAG triplet repeat disorders and amyotrophic lateral sclerosis (Shimura, 2000).

Parkinson's disease (PD) is a common neurodegenerative disorder characterized by the progressive accumulation in selected neurons of protein inclusions containing alpha-synuclein and ubiquitin. Rare inherited forms of PD are caused by autosomal dominant mutations in alpha-synuclein or by autosomal recessive mutations in parkin, an E3 ubiquitin ligase. It is hypothesized that these two gene products interact functionally, namely, that parkin ubiquitinates alpha-synuclein normally and that this process is altered in autosomal recessive PD. A protein complex has been identified in normal human brain that includes parkin as the E3 ubiquitin ligase; UbcH7 is its associated E2 ubiquitin conjugating enzyme, and a new 22-kilodalton glycosylated form of alpha-synuclein (alphaSp22) is its substrate. In contrast to normal parkin, mutant parkin associated with autosomal recessive PD fails to bind alphaSp22. In an in vitro ubiquitination assay, alphaSp22 was modified by normal but not mutant parkin into a polyubiquitinated, high molecular weight species. Accordingly, alphaSp22 accumulated in a non-ubiquitinated form in parkin-deficient PD brains. It is concluded that alphaSp22 is a substrate for parkin's ubiquitin ligase activity in normal human brain and that loss of parkin function causes pathological alphaSp22 accumulation. These findings demonstrate a critical biochemical reaction between the two PD-linked gene products and suggest that this reaction underlies the accumulation of ubiquitinated alpha-synuclein in conventional PD (Shimura, 2001).

Parkin is a product of the Park2 gene, whose mutation causes autosomal recessive juvenile parkinsonism (AR-JP) characterized by selective dopaminergic neuronal death and absence of Lewy bodies. Parkin is directly linked to the ubiquitin (Ub)-proteasome pathway as a Ub-protein ligase (E3) collaborating with a Ub-conjugating enzyme (E2) UbcH7. The expression of mRNAs for parkin and UbcR7 (rat ortholog of human UbcH7) in the developing rat brain has been examined. Parkin mRNA increases in parallel with neuronal maturation, but is unevenly distributed in various brain regions after four postnatal days. The expression pattern of the UbcR7 mRNA is almost identical to that of the parkin mRNA in all cases examined. Both parkin and UbcR7 mRNAs are distributed in neurons but not glial cells. These findings indicate that parkin is expressed not only in the substantia nigra, but also uniformly in various brain regions in a development-dependent manner. Co-expression of UbcR7 with parkin suggests that UbcR7 may interact with parkin in vivo for ubiquitination of yet unidentified target protein(s) (Wang, 2001).

Ubiquitin conjugating enzymes and the degradation of ER membrane proteins

The degradation of subunits of the trimeric Sec61p complex, a key component of the protein translocation apparatus of the ER membrane, has been investigated. A mutant form of Sec6lp and one of the two associated proteins (Sss1p) are selectively degraded, while the third constituent of the complex (Sbh1p) is stable. These results demonstrate that the proteolysis of the multispanning membrane protein Sec61p is mediated by the ubiquitin-proteasome pathway, since it requires polyubiquitination, the presence of a membrane-bound (Ubc6) and a soluble (Ubc7) ubiquitin-conjugating enzyme and a functional proteasome. The process is proposed to be specific for unassembled Sec61p and Sss1p. Thus, these results suggest that one pathway of ER degradation of abnormal or unassembled membrane proteins is initiated at the cytoplasmic side of the ER (Biederer, 1996).

Ubiquitin conjugation during endoplasmic-reticulum-associated degradation (ERAD) depends on the activity of Ubc7. Ubc1 acts as a further ubiquitin-conjugating enzyme in this pathway. Absence of both enzymes results in marked stabilization of an ERAD substrate and induction of the unfolded-protein response (UPR). Furthermore, basic ERAD activity is sufficient to eliminate unfolded proteins under normal conditions. However, when stress is applied, the UPR is required to increase ERAD activity. This study thus demonstrates a regulatory loop between ERAD and the UPR, which is essential for normal growth of yeast cells (Friedlander, 2000).

Proteolysis by the ubiquitin-proteasome system is highly selective. Specificity is achieved by the cooperation of diverse ubiquitin-conjugating enzymes (Ubcs or E2s) with a variety of ubiquitin ligases (E3s) and other ancillary factors. These recognize degradation signals characteristic of their target proteins. Signals have been identified that direct the degradation of beta-galactosidase and Ura3p fusion proteins via a subsidiary pathway of the ubiquitin-proteasome system involving Ubc6p and Ubc7p. This pathway is essential for the degradation of misfolded and regulated proteins in the endoplasmic reticulum (ER) lumen and membrane: such proteins are transported to the cytoplasm via the Sec61p translocon. Mutant backgrounds which prevent retrograde transport of ER proteins (hrd1/der3Delta and sec61-2) do not inhibit the degradation of the beta-galactosidase and Ura3p fusions carrying Ubc6p/Ubc7p pathway signals. It is therefore concluded that the ubiquitination of these fusion proteins takes place on the cytosolic face of the ER without prior transfer to the ER lumen. The contributions of different sequence elements to a 16-amino-acid-residue Ubc6p-Ubc7p-specific signal were analyzed by mutation. A patch of bulky hydrophobic residues is an essential element. In addition, positively charged residues are essential. Unexpectedly, certain substitutions of bulky hydrophobic or positively charged residues with alanine create novel degradation signals, channeling the degradation of fusion proteins to an unidentified proteasomal pathway not involving Ubc6p and Ubc7p (Gilon, 2000).

In eukaryotes, endoplasmic reticulum-associated degradation (ERAD) functions in cellular quality control and regulation of normal ER-resident proteins. ERAD proceeds by the ubiquitin-proteasome pathway, in which the covalent attachment of ubiquitin to proteins targets them for proteasomal degradation. Ubiquitin-protein ligases (E3s) play a crucial role in this process by recognizing target proteins and initiating their ubiquitination. Hrd1p, which is identical to Der3p, is an E3 for ERAD. Hrd1p is required for the degradation and ubiquitination of several ERAD substrates and physically associates with relevant ubiquitin-conjugating enzymes (E2s). A soluble Hrd1 fusion protein shows E3 activity in vitro, catalysing the ubiquitination of itself and test proteins. In this capacity, Hrd1p has an apparent preference for misfolded proteins. Hrd1p functions as an E3 in vivo, using only Ubc7p or Ubc1p to specifically program the ubiquitination of ERAD substrates (Bays, 2001).

Function of UBC7 homologs in kinetochore function

A new conditional-lethal mutation, ndc10-2, has been isolated in the NDC10/CBF2/CTF14 gene that encodes the 110-kD subunit of the Saccharomyces cerevisiae CBF3 kinetochore complex. At the restrictive temperature of 37 degrees, ndc10-2 cells are able to assemble anaphase spindles, but fail to segregate their DNA, consistent with a defect in kinetochore function. To identify other factors that play a role in kinetochore assembly or function, both dosage and second site suppressors of the ndc10-2 mutation have been isolated. These screens identified UBC6 as a dosage suppressor, and mutations in UBC6 and UBC7 as second-site suppressors of ndc10-2 heat sensitivity. Both UBC6 and UBC7 encode ubiquitin-conjugating enzymes that function in ubiquitin-mediated protein degradation. Furthermore, overexpression of a mutant ubiquitin suppresses the ndc10-2 mutation. These results implicate the ubiquitin system in the regulation of ndc10-2 function and suggest a role for the ubiquitin system in kinetochore function (Kopski, 1997).

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date revised: 3 March 2002

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