All-trans retinoic acid induces cell-cycle arrest in human cutaneous squamous carcinoma cells by inhibiting the mitogen-activated protein kinase-activated protein 1 pathway.

BACKGROUND: All-trans retinoic acid (ATRA) has been tried for the treatment and prevention of a number of epithelial cancers. However, the precise mechanism by which ATRA inhibits the growth of cutaneous squamous cell carcinoma (cSCC) remains elusive. AIMS: To determine the suppressive effects of ATRA on the human cSCC cell line SCL-1, and explore the possible mechanisms involved. METHODS: SCL-1 cells were treated with ATRA, then cell proliferation was measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, while apoptosis and cell cycle progression were analysed by flow cytometry. Protein levels of cell-cycle regulatory proteins and the activation of extracellular signal-regulated kinase (ERK) and Jun kinase (JNK) were detected by western blotting analysis. Transcriptional activity of activator protein (AP)-1 was examined by luciferase reporter assay. RESULTS: ATRA inhibited the proliferation of SCL-1 cells and had modest proapoptotic effects. ATRA also induced G1 cell-cycle arrest, inhibited the expression of cyclin D1/cyclin-dependent kinase (CDK)4 and cyclinE/CDK2, and increased the expression of the cyclin-dependent kinase inhibitors p21 and p27. In addition, ATRA significantly decreased the phosphorylation of ERK1/2 and JNK1/2, and inhibited AP-1 transcriptional activity. CONCLUSIONS: ATRA induces cell-cycle arrest in human cSCC cells by inhibiting the mitogen-activated protein kinase (MAPK)-AP1 pathway, and could be effective in the prevention and chemotherapy of human cSCC.

Effect of a c-Met-specific, ATP-competitive small-molecule inhibitor SU11274 on human ovarian carcinoma cell growth, motility, and invasion.

Increased expression of the receptor tyrosine kinase c-Met has been shown to correlate with enhanced cell proliferation, motility, and invasion. The objectives of this study were to characterize total and activated c-Met expression in both normal and malignant human ovarian epithelial cells and to determine the effects of inhibiting the activation of c-Met on ovarian epithelial cell growth, motility, and invasion. Total c-Met was overexpressed in 82 (68%) of 119 ovarian carcinomas, as shown by immunohistochemistry. Quantitative reverse transcription-polymerase chain reaction and Western blot analyses revealed that ovarian carcinoma cell lines had higher levels of c-Met messenger RNA, total protein, and activated protein expression compared to normal ovarian epithelial cell cultures. Using a specific adenosine triphosphate-competitive small-molecule inhibitor, SU11274, activated c-Met was decreased in normal and ovarian carcinoma cell lines. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays showed that cell growth inhibition directly correlated to the level of activated c-Met detected in each cell line (r =-0.87, P = 0.012). Using modified Boyden chamber assays, ovarian carcinoma cells treated with SU11274 demonstrated significantly decreased cell motility and invasion compared to untreated cells (P = 0.003 and P < 0.001, respectively). These data indicate that c-Met is overexpressed in the majority of malignant ovarian epithelial cells both in vivo and in vitro and that decreasing activated c-Met in vitro can significantly decrease ovarian carcinoma cell growth, motility, and invasion. Developing therapies that specifically inhibit the activation of c-Met may represent a novel therapeutic modality for patients with ovarian carcinomas expressing high levels of c-Met.

A pharmacologically distinct cyclic AMP receptor is responsible for the regulation of gp80 expression in Dictyostelium discoideum.

The EDTA-resistant cell-cell adhesion expressed at the aggregation stage of Dictyostelium discoideum is mediated by a cell surface glycoprotein of Mr 80,000 (gp80). The expression of gp80 is developmentally regulated by cyclic AMP (cAMP). In vitro nuclear run-on experiments show that transcription of the gp80 gene is initiated soon after the onset of development. The basal level of gp80 transcription is significantly augmented by exogenous cAMP pulses. Interestingly, in analog studies, 2'-deoxy-cAMP, 8-bromo-cAMP, and N6-monobutyryl-cAMP are all capable of inducing a rapid accumulation of gp80 mRNA, suggesting the presence of a unique cAMP receptor that responds equally well to these analogs. To determine whether intracellular cAMP plays a role in the regulation of gp80 expression, caffeine was used to block cAMP-induced receptor-mediated adenylate cyclase activation. Expression of gp80 mRNA was blocked in caffeine-treated cells but could be substantially restored by treatment with exogenous cAMP pulses, suggesting that adenylate cyclase activation is not required. gp80 expression was also examined in the signal transduction mutants synag 7 and frigid A. In both mutants, gp80 was expressed at the basal level. Pulses of cAMP as well as 2'-deoxy-cAMP and N6-monobutyryl-cAMP were capable of restoring the normal level of gp80 expression in synag 7 cells. These results, taken together, indicate bimodal regulation of gp80 expression during development and the involvement of a novel cAMP receptor in the transmembrane signalling pathway that regulates gp80 gene expression.

Activation of ephrinB-EphB receptor signalling in rat spinal cord contributes to maintenance of diabetic neuropathic pain.

BACKGROUND: Diabetic neuropathic pain (DNP) is severe and intractable in clinic. The specific cellular and molecular mechanisms underlying DNP remain elusive and its treatment are limited. We investigated roles of EphB1 receptor in the development of DNP. METHODS: Diabetic neuropathic pain was produced in male, adult, Sprague-Dawley rats by a single i.p. streptozotocin (STZ) or alloxan. Western blot analysis and immunohistochemistry were used to analyse expression of EphB1 receptor as well as the activation of the glial cells and the pro-inflammatory cytokines in the spinal cord. DNP manifested as mechanical allodynia, which was determined by measuring incidence of foot withdrawal in response to mechanical indentation of the hind paw by an electro von Frey filament. RESULTS: Diabetic neuropathic pain and high blood glucose were exhibited simultaneously in around 70% of animals that received i.p. STZ or alloxan. Phosphorylation of EphB1, activation of the astrocytes and microglial cells, and level of tumour necrosis factor (TNF)-α and interleukin (IL)-1ß in the spinal cord were significantly increased in rats with DNP. Spinal blocking EphB1 receptor activation in the late phase after STZ injection significantly suppressed the established mechanical allodynia as well as activation of the astrocytes and microglial cells and activity of TNF-α and IL-1ß. However, spinal treatment of EphB1-Fc in the early phase after STZ injection did not prevent the induction of DNP. CONCLUSIONS: EphB1 receptor activation in the spinal cord is critical to the maintenance, but not induction of diabetic pain. EphB1 receptor may be a potential target for relieving the established diabetic pain. SIGNIFICANCE: Activation of EphB1 receptor in the spinal cord is critical to maintaining the established diabetic neuropathic pain, but not to diabetic pain induction. Spinal blocking EphB1 receptor activation suppresses ongoing diabetic neuropathic pain.

Tracking MET de-addiction in lung cancer: A road towards the oncogenic target.

The discovery of druggable oncogenic drivers (i.e. EGFR and ALK), along with the introduction of comprehensive tumor genotyping techniques into the daily clinical practice define non-small-cell lung cancer (NSCLC) asa group of heterogeneous diseases, requiring a context-personalized clinico-therapeutical approach. Among the most investigated biomarkers, the MET proto-oncogene has been extensively demonstrated to play a crucial role throughout the lung oncogenesis, unbalancing the proliferation/apoptosis signaling and influencing the epithelial-mesenchymal transition and the invasive phenotype. Nevertheless, although different mechanisms eliciting the aberrant MET-associated oncogenic stimulus have been detected in lung cancer (such as gene amplification, increased gene copy number, mutations and MET/HGF overexpression), to date no clinically impactful results have been achieved with anti-MET tyrosine kinase inhibitors and monoclonal antibodies in the context of an unselected or MET enriched population. Recently, MET exon 14 splicing abnormalities have been identified asa potential oncogenic target in lung cancer, able to drive the activity of MET inhibitors in molecularly selected patients. In this paper, the major advancement and drawbacks of MET history in lung cancer are reviewed, underlying the renewed scientific euphoria related to the recent identification of MET exon 14 splicing variants asan actionable oncogenic target.

Simpson's paradox - aggregating and partitioning populations in health disparities of lung cancer patients.

It is well known that non-small cell lung cancer (NSCLC) is a heterogeneous group of diseases. Previous studies have demonstrated genetic variation among different ethnic groups in the epidermal growth factor receptor (EGFR) in NSCLC. Research by our group and others has recently shown a lower frequency of EGFR mutations in African Americans with NSCLC, as compared to their White counterparts. In this study, we use our original study data of EGFR pathway genetics in African American NSCLC as an example to illustrate that univariate analyses based on aggregation versus partition of data leads to contradictory results, in order to emphasize the importance of controlling statistical confounding. We further investigate analytic approaches in logistic regression for data with separation, as is the case in our example data set, and apply appropriate methods to identify predictors of EGFR mutation. Our simulation shows that with separated or nearly separated data, penalized maximum likelihood (PML) produces estimates with smallest bias and approximately maintains the nominal value with statistical power equal to or better than that from maximum likelihood and exact conditional likelihood methods. Application of the PML method in our example data set shows that race and EGFR-FISH are independently significant predictors of EGFR mutation.

Ultrasonic image analysis of the arterial wall in atherosclerosis.

BACKGROUND: Atherosclerotic carotid artery plaques can be classified on the basis of their ultrasound appearance according to the pattern of echolucency and echogenicity. The most commonly used classification is the one described by Gray-Weale who defined 4 plaque types. METHODS: The images of the carotid and femoral arteries of 9 healthy volunteers and 21 non-insulin dependent diabetic patients were analysed. In this study 16 atherosclerotic carotid artery plaques were imaged by B-mode high resolution ultrasonography and then subjected to analysis of the digitised images. RESULTS: The results show that the plaques could be separated into 3 groups according to their echogenic properties. Gray-Weale plaques types 2 and 3 could not be distinguished and it is proposed that these should be classified as a single group. CONCLUSIONS: An increased echogenicity in the intima-media complex of non-insulin dependent diabetics as well as a relationship with risk factors for the development of cardiovascular disease and with the ultrasound score could not be determined in this study.

Zinc deficiency: its role in gastric secretion and stress-induced gastric ulceration in rats.

The effects of zinc deficiency on gastric secretion and on cold-restraint stress-induced ulceration in rat stomachs have been studied. Administration of graded zinc deficient diets for 5 weeks significantly depressed the serum zinc concentration and decreased body weight gain in the rats. These diets significantly increased the gastric secretory volume, acid and pepsin. Zinc deficiency produced or aggravated the formation of glandular ulceration in the absence or presence of stress, respectively; it also decreased the mast cell count in the gastric glandular mucosa. It is concluded that zinc deficiency adversely affects the rats by reducing the body weight gain and producing ulceration which is probably mast cell-mediated. On the other hand, it increases gastric secretory functions.

[16-Hydroxytriptolide, a new active diterpene isolated from Tripterygium wilford II].

A new diterpene triepoxide, 16-hydroxytriptolide was isolated from the root and leaves of Tripterygium wilfordii Hook.f. 16-Hydroxytriptolide was obtained as white cluster crystal, mp 232-233.5 degrees C. Its molecular formula is C20H24O7. The structure and stereochemistry of 16-hydroxytriptolide was established as L2 on the basis of spectral data (IR, MS, UV, 1H-NMR, 13C-NMR, 2d-NMR, NOE) and X-ray crystallographic analysis. In the pharmacologic screening, 16-hydroxytriptolide showed definite antiinflammatory actions and strong immunosuppressive and antifertile activities. In antiinflammatory action, its half effective dose (ED50) was 0.12 mg/kg with the model of croton oil induced ear swelling of mice. In immunosuppressive action, its ED50 was 0.05 mg/kg with the model of the formation of haemolysinantibody of mice. Its lowest effective dose (po) was 0.027mg/kg x 33d in antifertile action.

[Studies on diterpenoids from leaves of Tripterygium wilfordii].

Tripterygium wilfordii Hook f. has been used as a medicinal herb in traditional Chinese medicine and as an insecticide by the Chinese for hundreds of years. Recently, this plant has been used to treat cancer, rheumatic arthritis and various skin diseases in some Chinese clinics. It is of interest to note that Tripterygium also showed significant antifertility activities. The active principles of the anti-inflammatory, immunosuppressive and antifertile actions in Tripterygium are diterpenoid containing triepoxides, but information on its chemistry is limited to the woody part of the root and the root bark. Recently, we have studies the leaves of Tripterygium (collected at Zhejiang province, China), and isolated two novel diterpenoids by chromatography named tripdioltonide (8) and 13,14-epoxide 9,11,12-trihydroxytriptolide (9), besides triptonide (1), triptolide (2), tripdiolide (3), triptolidenol (4), 16-hydroxyl-triptolide (5), tripchlorolide (6) and triptriolide (7). Their structures were established by chemical reactions, TLC, UV, MS, IR, 1H-1H COSY, 1H-13C COSY, DEPT spectrometric investigation. The structure of tripdioltonide was further confirmed by X-ray analysis.

Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

Targeted therapy against epidermal growth factor receptor (EGFR) represents a major therapeutic advance in lung cancer treatment. Somatic mutations of the EGFR gene, most commonly L858R (exon 21) and short in-frame exon 19 deletions, have been found to confer enhanced sensitivity toward the inhibitors gefitinib and erlotinib. We have recently identified an EGFR mutation E884K, in combination with L858R, in a patient with advanced lung cancer who progressed on erlotinib maintenance therapy, and subsequently had leptomeningeal metastases that responded to gefitinib. The somatic E884K substitution appears to be relatively infrequent and resulted in a mutant lysine residue that disrupts an ion pair with residue R958 in the EGFR kinase domain C-lobe, an interaction that is highly conserved within the human kinome as demonstrated by our sequence analysis and structure analysis. Our studies here, using COS-7 transfection model system, show that E884K works in concert with L858R in-cis, in a dominant manner, to change downstream signaling, differentially induce Mitogen-activated protein kinase (extracellular signaling-regulated kinase 1/2) signaling and associated cell proliferation and differentially alter sensitivity of EGFR phosphorylation inhibition by ERBB family inhibitors in an inhibitor-specific manner. Mutations of the conserved ion pair E884-R958 may result in conformational changes that alter kinase substrate recognition. The analogous E1271K-MET mutation conferred differential sensitivity toward preclinical MET inhibitors SU11274 (unchanged) and PHA665752 (more sensitive). Systematic bioinformatics analysis of the mutation catalog in the human kinome revealed the presence of cancer-associated mutations involving the conserved E884 homologous residue, and adjacent residues at the ion pair, in known proto-oncogenes (KIT, RET, MET and FAK) and tumor-suppressor gene (LKB1). Targeted therapy using small-molecule inhibitors should take into account potential cooperative effects of multiple kinase mutations, and their specific effects on downstream signaling and inhibitor sensitivity. Improved efficacy of targeted kinase inhibitors may be achieved by targeting the dominant activating mutations present.

Dual MET-EGFR combinatorial inhibition against T790M-EGFR-mediated erlotinib-resistant lung cancer.

Despite clinical approval of erlotinib, most advanced lung cancer patients are primary non-responders. Initial responders invariably develop secondary resistance, which can be accounted for by T790M-EGFR mutation in half of the relapses. We show that MET is highly expressed in lung cancer, often concomitantly with epidermal growth factor receptor (EGFR), including H1975 cell line. The erlotinib-resistant lung cancer cell line H1975, which expresses L858R/T790M-EGFR in-cis, was used to test for the effect of MET inhibition using the small molecule inhibitor SU11274. H1975 cells express wild-type MET, without genomic amplification (CNV = 1.1). At 2 microM, SU 11274 had significant in vitro pro-apoptotic effect in H1975 cells, 3.9-fold (P = 0.0015) higher than erlotinib, but had no effect on the MET and EGFR-negative H520 cells. In vivo, SU11274 also induced significant tumour cytoreduction in H1975 murine xenografts in our bioluminescence molecular imaging assay. Using small-animal microPET/MRI, SU11274 treatment was found to induce an early tumour metabolic response in H1975 tumour xenografts. MET and EGFR pathways were found to exhibit collaborative signalling with receptor cross-activation, which had different patterns between wild type (A549) and L858R/T790M-EGFR (H1975). SU11274 plus erlotinib/CL-387,785 potentiated MET inhibition of downstream cell proliferative survival signalling. Knockdown studies in H1975 cells using siRNA against MET alone, EGFR alone, or both, confirmed the enhanced downstream inhibition with dual MET-EGFR signal path inhibition. Finally, in our time-lapse video-microscopy and in vivo multimodal molecular imaging studies, dual SU11274-erlotinib concurrent treatment effectively inhibited H1975 cells with enhanced abrogation of cytoskeletal functions and complete regression of the xenograft growth. Together, our results suggest that MET-based targeted inhibition using small-molecule MET inhibitor can be a potential treatment strategy for T790M-EGFR-mediated erlotinib-resistant non-small-cell lung cancer. Furthermore, optimised inhibition may be further achieved with MET inhibition in combination with erlotinib or an irreversible EGFR-TKI.

Downstream signalling and specific inhibition of c-MET/HGF pathway in small cell lung cancer: implications for tumour invasion.

The c-MET receptor can be overexpressed, amplified, or mutated in solid tumours including small cell lung cancer (SCLC). In c-MET-overexpressing SCLC cell line NCI-H69, hepatocyte growth factor (HGF) dramatically induced c-MET phosphorylation at phosphoepitopes pY1230/1234/1235 (catalytic tyrosine kinase), pY1003 (juxtamembrane), and also of paxillin at pY31 (CRKL-binding site). We utilised a global proteomics phosphoantibody array approach to identify further c-MET/HGF signal transduction intermediates in SCLC. Strong HGF induction of specific phosphorylation sites in phosphoproteins involved in c-MET/HGF signal transduction was detected, namely adducin-alpha [S724], adducin-gamma [S662], CREB [S133], ERK1 [T185/Y187], ERK1/2 [T202/Y204], ERK2 [T185/Y187], MAPKK (MEK) 1/2 [S221/S225], MAPKK (MEK) 3/6 [S189/S207], RB [S612], RB1 [S780], JNK [T183/Y185], STAT3 [S727], focal adhesion kinase (FAK) [Y576/S722/S910], p38alpha-MAPK [T180/Y182], and AKT1[S473] and [T308]. Conversely, inhibition of phosphorylation by HGF in protein kinase C (PKC), protein kinase R (PKR), and also CDK1 was identified. Phosphoantibody-based immunohistochemical analysis of SCLC tumour tissue and microarray established the role of c-MET in SCLC biology. This supports a role of c-MET activation in tumour invasive front in the tumour progression and invasion involving FAK and AKT downstream. The c-MET serves as an attractive therapeutic target in SCLC, as shown through small interfering RNA (siRNA) and selective prototype c-MET inhibitor SU11274, inhibiting the phosphorylation of c-MET itself and its downstream molecules such as AKT, S6 kinase, and ERK1/2. Investigation of mechanisms of invasion and, ultimately, metastasis in SCLC would be very useful with these signal transduction molecules.

Home care for the mentally ill in Taiwan: a public health model.

In 1985 the nursing staff at the Provincial Institute of Health, Taipei, Taiwan, began to make follow-up visits to patients discharged from three psychiatric hospitals, brought about by the Institute's concern about the psychological (and sometimes physical) abuse of these patients. Previously, chronically ill psychiatric patients received little community follow-up by public health nurses. The result was a model follow-up programme developed by the nursing staff that could be used in other public health stations throughout the country; a manual providing intervention examples and an evaluation programme. Below, how the model works and a survey of mental illness in Taiwan.

Enteric parasites and antibodies to human immunodeficiency virus in homosexual men with diarrhea.

A total of 260 homosexual men with gastrointestinal illness, 77 of them with AIDS, were selected for a study of the prevalence of enteric parasites and its association with antibodies against human immuno-deficiency virus (HIV). HIV antibodies were demonstrated in the sera of all the AIDS patients and in 111 (60.7%) of the non-AIDS patients. In the AIDS patients, 39 (50.6%) of them had enteric parasites and 33 had a single parasite recorded. By contrast, 49 (26.8%) of the non-AIDS patients had enteric protozoa detected and 25 of them had a single parasite. The protozoa most frequently recovered from the non-AIDS and the AIDS patients were Endolimax nana and Cryptosporidium, respectively. These findings indicate that immune dysfunction in AIDS patients can enhance the colonization of parasites and alter the spectrum of the intestinal flora.

Intention to relocate to the United States.

OBJECTIVES: To gain insight into family medicine residents' attitudes toward relocating to the United States and to examine factors influencing their decisions. DESIGN: Cross-sectional mailed survey. SETTING: University of Toronto family medicine program. PARTICIPANTS: First- and second-year residents in the academic year 1995 to 1996. A 74.6% response rate (144 of 193 residents) was achieved. MAIN OUTCOME MEASURES: Intention to relocate to the United States. Degree of importance of 11 motivational factors in residents' decisions to relocate. RESULTS: In this survey, 48% of residents reported they intended to relocate to the United States, but only 17% recalled expecting to relocate before Ontario's introduction of geographic billing restriction legislation. Geographic billing restriction was the motivational factor most residents (86.8%) considered very important in their decision-making process. The two factors potentially predicting US relocation were finance and climate. CONCLUSIONS: Many factors influence family medicine residents' intention to relocate to the United States. Geographic billing restriction was the most significant motivational factor, and its introduction has likely precipitated a marked shift in residents' attitudes favouring US relocation.

Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation.

The crystal structure of a MyoD basic-helix-loop-helix (bHLH) domain-DNA complex has been solved and refined at 2.8 A resolution. This structure proves that bHLH and bHLH-leucine zipper (bHLH-ZIP) proteins are remarkably similar; it helps us understand subtle differences in binding preferences for these proteins; and it has surprising implications for our understanding of transcription. Specifically, Ala-114 and Thr-115, which are required for positive control in the myogenic proteins, are buried at the protein-DNA interface. These residues are not available for direct protein-protein contacts, but they may determine the conformation of Arg-111. Comparisons with Max suggest that the conformation of this arginine, which is different in the two structures, may play an important role in myogenic transcription.

Fibronectin enhances viability and alters cytoskeletal functions (with effects on the phosphatidylinositol 3-kinase pathway) in small cell lung cancer.

Small cell lung cancer (SCLC) is a rapidly progressive disease with ultimate poor outcome. SCLC has been shown to interact closely with the stromal and extracellular matrix (ECM) components of the diseased host. ECM consists of type I/IV collagen, laminin, vitronectin, and fibronectin (FN) among others. Herein, we investigated the behavior of a SCLC cell line (NCI-H446) on FN-coated surface. Over a course of 72 h, FN (10 micro g/ml) caused both increased survival and proliferation of NCI-H446 cells. Survival under serum-starved conditions increased 1.44-fold and proliferation in the presence of fetal calf serum increased by 1.30-fold. The phosphatidylinositol 3-kinase (PI3-K) inhibitor LY294002 reduced both survival and proliferation of NCI-H446 cells (0.48- and 0.27-fold, respectively), even on FN-coated surface. We next determined the effects of FN on cytoskeletal function such as cell motility/morphology and adhesion. Over a course of 24 h, FN reduced aggregation of NCI-H446 cells and induced flattened cellular morphology with neurite-like projections after 1 h, however, in the presence of LY294002, the cells rounded up. Adhesion of NCI-H446 cells also increased with FN (4.47-fold) which was abrogated with LY294002 treatment. This correlated with phosphorylation of the cytoskeletal protein p125FAK, on Tyr397, Tyr861 and Ser843 residues with FN. Even in the presence of LY294002, these serine/tyrosine residues were still phosphorylated on FN-coated surface. In contrast, the focal adhesion protein paxillin was not phosphorylated at Tyr31 with FN. In summary, FN stimulation of SCLC cells leads to enhancement of viability and changes in cytoskeletal function that are partially mediated through the PI3-K pathway.

A proteolytic pathway that recognizes ubiquitin as a degradation signal.

Previous work has shown that a fusion protein bearing a "nonremovable" N-terminal ubiquitin (Ub) moiety is short-lived in vivo, the fusion's Ub functioning as a degradation signal. The proteolytic system involved, termed the UFD pathway (Ub fusion degradation), was dissected in the yeast Saccharomyces cerevisiae by analyzing mutations that perturb the pathway. Two of the five genes thus identified, UFD1 and UFD5, function at post-ubiquitination steps in the UFD pathway. UFD3 plays a role in controlling the concentration of Ub in a cell: ufd3 mutants have greatly reduced levels of free Ub, and the degradation of Ub fusions in these mutants can be restored by overexpressing Ub. UFD2 and UFD4 appear to influence the formation and topology of a multi-Ub chain linked to the fusion's Ub moiety. UFD1, UFD2, and UFD4 encode previously undescribed proteins of 40, 110, and 170 kDa, respectively. The sequence of the last approximately 280 residues of Ufd4p is similar to that of E6AP, a human protein that binds to both the E6 protein of oncogenic papilloma viruses and the tumor suppressor protein p53, whose Ub-dependent degradation involves E6AP. UFD5 is identical to the previously identified SON1, isolated as an extragenic suppressor of sec63 alleles that impair the transport of proteins into the nucleus. UFD5 is essential for activity of both the UFD and N-end rule pathways (the latter system degrades proteins that bear certain N-terminal residues). We also show that a Lys --> Arg conversion at either position 29 or position 48 in the fusion's Ub moiety greatly reduces ubiquitination and degradation of Ub fusions to beta-galactosidase. By contrast, the ubiquitination and degradation of Ub fusions to dihydrofolate reductase are inhibited by the UbR29 but not by the UbR48 moiety. ufd4 mutants are unable to ubiquitinate the fusion's Ub moiety at Lys29, whereas ufd2 mutants are impaired in the ubiquitination at Lys48. These and related findings suggest that Ub-Ub isopeptide bonds in substrate-linked multi-Ub chains involve not only the previously identified Lys48 but also Lys29 of Ub, and that structurally different multi-Ub chains have distinct functions in Ub-dependent protein degradation.