LRRC59 serves as a novel biomarker for predicting the progression and prognosis of bladder cancer

BACKGROUND

Leucine-rich repeat-containing protein 59 (LRRC59) is an endoplasmic reticulum membrane protein involved in various cancers, but its role in bladder cancer (BC) has not been reported. The aim of the present study was to investigate the role of LRRC59 protein in BC progression and prognosis.

METHODS

The expression profile and clinical significance were retrieved from BC patients in the Cancer Genome Atlas database. The methylation status of LRRC59 was analyzed by UALCAN and MethSurv databases. Potential signaling pathways and biological functions were explored by functional enrichment analysis. Immunocyte infiltration was evaluated by CIBERSORT analysis. The prognostic value of LRRC59 was evaluated by Kaplan-Meier and Cox regression analyses. Overall survival (OS) was predicted by the nomogram plot established in this study. LRRC59 expression in 10 pairs BC and adjacent noncancerous tissues were analyzed by immunohistochemistry (IHC). Cell proliferation, migration, and invasion were detected by CCK8, colony formation assay, transwell assay, and cell scratch assay, respectively. Proteins related to epithelial-mesenchymal transition and apoptosis were detected by western blot.

RESULTS

LRRC59 overexpression significantly decreased OS, disease-specific survival, and progress-free interval of BC patients. LRRC59 was a prognostic marker for OS and its hypomethylation status signified a poor prognosis. LRRC59 overexpression was correlated with infiltration of resting memory CD4 T cells, memory activated CD4 T cells, resting NK cells, macrophages M0, M1, M2, and neutrophils. IHC showed that the LRRC59 expression in BC tissue was significantly higher than that in adjacent noncancerous tissue. Knockdown of LRRC59 expression inhibited the proliferation of BC cells and reduced their migratory ability. Western blot showed that Snail and vimentin protein expressions decreased, while E-cadherin expressions increased.

CONCLUSIONS

LRRC59 expression can predict the outcome of BC independently and serve as a new biomarker for diagnosis.

Bibliometric analysis of scientific publications on cryptorchidism: Research hotspots and trends between 2000 and 2022

Background

Cryptorchidism is defined as failure of unilateral or bilateral testicular descent, which increases the risk of infertility and testicular carcinoma. Although there is much research on cryptorchidism, few studies have used the bibliometric analysis method. The purpose of this study was to conduct a comprehensive analysis of cryptorchidism from muti-dimensional perspectives to summarize the research hotspots and trends in cryptorchidism research.

Methods

Relevant studies on cryptorchidism were retrieved from the Web of Science Core Collection (WoSCC) database from 2000 to 2022. A comprehensive bibliometric analysis of cryptorchidism was performed by using the CiteSpace, Tableau Public, and VOSviewer software, including the annual distributions of publications, countries, authors, institutions, journals, references, and keywords.

Results

From January 1st, 2000 to May 17th, 2022, a total of 5023 papers concerning cryptorchidism were identified for analysis. The USA contributed the most publications (n = 1193) in this field, and the annual number of publications rose rapidly in China. The University of Melbourne published the largest number of papers (n = 131). "Hutson, John M." was the most core author ranked by publications (n = 51), and "Skakkebaek, Niels E." enjoyed the largest number of citations (4441). The JOURNAL OF UROLOGY published the largest number of papers (n = 225), while the average citations per publication of the 75 papers in HUMAN REPRODUCTION reached 62.38. Additionally, burstness analysis of references and keywords showed that cryptorchidism research was mainly focused on the exploration of the optimal mode of treatment for cryptorchidism, including hypogonadism such as Kallmann syndrome and Klinefelter syndrome.

Conclusion

Cryptorchidism has attracted continuous attention from the scientific community concerned. International collaboration in the field has witnessed significant growth in recent years and remains essential to further enhance collaborative efforts between scholars from different countries. In addition, the exploration of the optimal treatment modality for cryptorchidism, especially in the prevention of adult infertility, remains a major focus of future research. High-quality follow-up studies are also needed in the future. The pathogenesis (especially at the genetic level) and treatment of hypogonadism such as Kallmann syndrome and Klinefelter syndrome have attracted increasing attention recently, which may usher in some breakthroughs in coming years.

Global research status and hotspots of radiotherapy for prostate cancer: a bibliometric analysis based on Web of Science from 2010-2022

Background

Radiotherapy (RT) is one of the important treatments for various cancer types and its application to prostate cancer (PCa) has also gradually gained increasing attention. However, there is a lack of comprehensive and objective studies on the overall status of research on RT for PCa. This article aims to summarize and quantify the dynamic trends of RT in PCa by using bibliometrics.

Methods

Studies on RT for PCa were screened from the Web of Science Core Collection (WoSCC) database between 1 January 2010 and 21 November 2022 to collate and quantify information characteristics by analyzing parameters including annual publications, countries/regions, institutions and authors with the aid of the bibliometric software CiteSpace and VOSviewer. In addition, research trends and hotspots were explored by analyzing keywords and co-cited references.

Results

A total of 21338 documents were retrieved. The United States of America (USA) ranked first and maintained the leading position among all countries in the number of publications (8489) and total citations (266342). The University of Toronto was the most active institution in total publications (n=587). Paul L Nguyen enjoyed the most publications (n=179), and Michael J Zelefsky enjoyed the most co-citations (n=3376). INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS published the most papers (n=1026), and was the most frequently co-cited journal (n=78550). The largest and closest cluster in the reference cluster analysis was "oligorecurrent prostate cancer". The timeline view of keywords reveals that cluster "biochemical recurrence(BCR)" is ongoing. Moreover, keywords burstness analysis showed that "radiation dosimetry", "dose rate brachytherapy(BT)", "salvage radiotherapy", "stereotactic body radiotherapy(SBRT)", "guideline", and "multicenter" were the terms with great bursts in the past a few years.

Conclusion

The application of RT targeting oligometastatic prostate cancer(OMPC) has garnered considerable attention among researchers. SBRT and BT have become hot topics in the field. Additionally, the BCR of PCa has long been a critical issue requiring extensive research and resolution, and salvage radiotherapy has currently emerged as a closely related research focus. Related large-scale multicenter studies have been conducted over the past few years, providing valuable insights. More high-quality research is expected to be employed to guide clinical decision-making.

The prognostic value and immunological role of SULF2 in adrenocortical carcinoma

Background

Adrenocortical carcinoma (ACC) represents the rare urological epithelial cancer of urinary tract, which has a large mass and is usually diagnosed at the advanced stage, thus inducing the poor prognosis. As a result, early detection and diagnosis are more important for the prognosis rather than the treatment of ACC. There is evidence supporting the association of Sulfatase2 (SULF2) with bladder cancer. However, the relationships of SULF2 with the clinical features and immune infiltration of ACC remain unclear.

Methods

This work comprehensively investigated the different expression levels of SULF2 within ACC and its prognostic significance through various databases including Gene Expression Profiling Interaction Analysis (GEPIA), Tumor Immune Estimation Resource (TIMER), The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Kaplan-Meier (KM) plotter and UALCAN. Besides, SULF2 levels within different tumor and paraneoplastic tissues were examined based on Human Protein Atlas (HPA) and TIMER. Afterwards, this study identified differentially expressed genes (DEGs) in high-compared with low-SULF2-expression groups. To predict the possible interaction between SULF2 and its targets, a protein-protein interaction (PPI) network was constructed based on relevant data collected in STRING database. Besides, the SULF2 functional annotation was carried out, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and GSEA. In addition, gene mutation analysis was also performed based on the cBioPortal database. The relation of SULF2 with immune infiltration was analyzed from various aspects by using the resources of various databases including TIMER, TISIDB, and GEPIA, which was first reported in this work. Finally, R package was utilized to plot the receiver operating characteristic (ROC) curves of diagnosis, time-dependent survival, and the association of SULF2 with cancer stage and the nomogram model. Finally, CellMiner dataset was adopted for SULF2 correlation as well as drug sensitivity analysis.

Results

Relative to healthy people, SULF2 level markedly elevated within ACC tissues. Besides, SULF2 up-regulation significantly predicted the dismal prognostic outcome, which may be an important prognostic factor. Afterwards, the PPI network was constructed, and the possible link of SULF2 with the corresponding targets was predicted. Besides, up-regulated SULF2 expression was tightly related to immune regulation and tumor-infiltration immune cell (TIICs), including CD8⁺, CD4⁺ and mast cells. Finally, SULF2 expression was speculated to help determine the sensitivity of certain drugs.

Conclusions

SULF2 may offer a new therapeutic target for ACC patients and become an important potential prognostic biomarker.

Research trends and hotspots of COVID-19 impact on sexual function: A bibliometric analysis based on Web of Science

Background

The outbreak of coronavirus disease 2019 (COVID-19) has brought indelible harms to the world and aroused great concern worldwide. This paper aims to analyze the impact of COVID-19 on sexual function using bibliometrics, and summarize research hotspots in this field.

Methods

Relevant publications concerning the impact of COVID-19 on sexual function in the Web of Science collection database (WoSCC) between January 1, 2020 and March 12, 2022 were screened and analyzed by bibliometric analysis using the visualization software CiteSpace and VOSviewer.

Results

Of the 1,054 publications screened, the United States (US) contributed the most (398/37.8%), followed by the United Kingdom (UK) (119/11.3%). Among all institutions, the University of Toronto in Canada enjoyed the largest number of publications (30), and Johns Hopkins University in the US enjoyed the highest frequency of citation (235). The journal INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH published the largest number of studies in this field (31), and the most-cited journal was LANCET. "Chow, Eric," "Ong, Jason J," and "Stephenson, Rob" tied for first place in publications (8), and "Fish, Jessica N." enjoyed the highest number of citations (99). Burstness analysis of references and keywords showed that the developing research trends in this field mainly focused on "sexual transmission" and "angiotensin converting-enzyme 2 (ACE2)" during the COVID-19 pandemic.

Conclusion

The impact of COVID-19 on sexual function remains an urgent concern at present, and the management of sexual health during the pandemic needs to be further improved. More frequent and deeper cooperation between countries and institutions is required in future. Meanwhile, searching for more evidence on whether COVID-19 can achieve sexual transmission and the pathophysiological mechanisms underlying the impact of COVID-19 on sexual function remains a focus of research in the coming years.

Poly (ADP-ribose) polymerase inhibitors (PARPi) for advanced malignancies with multiple DNA-repair genetic aberrations

INTRODUCTION

Poly (ADP-ribose) polymerase inhibitors (PARPi) have been approved for the treatment of advanced tumors with defects in genes involved in homologous recombination repair (HRR), including cancers of the prostate, pancreas, breast, and ovary. In these advanced tumors, PARPi afford 'synthetic lethality' by blocking the PARP-associated repair pathway in cancer cells with HRR genetic mutations, resulting in chromosome instability and cellular apoptosis. According to the synthetic lethality theory, patients with a greater burden of genetic alterations, in proportion (relative quantity) or category, would have more satisfactory outcomes after PARPi administration. However, this issue remains obscure based on the existing sporadic evidence.

AREAS COVERED

We summarize the therapeutic effects of PARPi in advanced tumors with multiple HRR genetic mutations, and attempted to compare these results with those obtained for cancers with a single mutation.

EXPERT OPINION

Limited evidence has provided a possibly encouraging response to PARPi among patients carrying multiple HRR genetic mutations compared with those with a single mutation (although the treatment effect was negative in some patients). Further research is needed to understand the role of PARPi in tumor cells with multiple HRR genetic mutations.

A Novel Pyroptosis-Related Gene Signature for Predicting Prognosis in Kidney Renal Papillary Cell Carcinoma

Pyroptosis is defined as an inflammatory form of programmed cell death. Increasing studies have demonstrated that pyroptosis is closely related to tumor development and antitumor process. However, the role of pyroptosis in kidney renal papillary cell carcinoma (KIRP) remains obscure. In this study, we analyzed the expression of 52 pyroptosis-related genes (PRGs) in KIRP, of which 20 differentially expressed PRGs were identified between tumor and normal tissues. Consensus clustering analysis based on these PRGs was used to divided patients into two clusters, from which a significant difference in survival was found (p = 0.0041). The prognostic risk model based on six PRGs (CASP8, CASP9, CHMP2A, GPX4, IL6, and IRF1) was built using univariate Cox regression and LASSO–Cox regression analysis, with good performance in predicting one-, three-, and five-year overall survival. Kaplan–Meier survival analysis showed that the high-risk group had a poor survival outcome (p < 0.001) and risk score was an independent prognostic factor (HR: 2.655, 95% CI 1.192–5.911, p = 0.016). Immune profiling revealed differences in immune cell infiltration between the two groups, and the infiltration of M2 macrophages was significantly upregulated in the tumor immune microenvironment, implying that tumor immunity participated in the KIRP progression. Finally, we identified two hub genes in tumor tissues (IL6 and CASP9), which were validated in vitro. In conclusion, we conducted a comprehensive analysis of PRGs in KIRP and tried to provide a pyroptosis-related signature for predicting the prognosis.

Effect of Brachytherapy vs. External Beam Radiotherapy on Sexual Function in Patients With Clinically Localized Prostate Cancer: A Meta-Analysis

Purpose: The aim of this study was to compare the effect of brachytherapy (BT) versus external beam radiotherapy (EBRT) on sexual function in patients with localized prostate cancer (PCa).

Methods: Data were retrieved from the PubMed, Cochrane Library, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang Database until March 4, 2021. Analysis was performed by using RevMan 5.4.1. The main clinical outcomes were the Prostate Cancer Symptom Indices (PCSI) scale and the Expanded Prostate Cancer Index Composite (EPIC) scale scores for sexual function. A meta-analysis was performed to calculate standardized mean differences (SMDs) and their 95% CI. This study has undergone PROSPERO registration (No. CDR42021245438).

Results: Among the 962 studies retrieved, eight prospective cohort studies met the inclusion criteria, covering a total of 2,340 patients, including 1,138 treated with BT alone and 1,202 treated with EBRT alone. The results demonstrated that BT was to some extent advantageous over EBRT in overall sexual function scores in patients with localized PCa during the immediate post-treatment period (SMD = −0.09, 95% CI: −0.18 to −0.01, p = 0.03), but this difference was not detectable at 3 months (SMD = −0.07, 95% CI: −0.18–0.05, and p = 0.25), 12 months (SMD = −0.01, 95% CI: −0.21–0.20, and p = 0.96), and 24 months (SMD = −0.09, 95% CI: −0.20–0.01, and p = 0.09) after treatment.

Conclusion: Our analysis showed that BT showed a short-term advantage over EBRT in terms of sexual function in patients with localized PCa, but this difference diminished over time, though the conclusion needs to be further verified by a longer-term follow-up study.

The relationships of acute kidney injury duration and severity with long-term functional deterioration following partial nephrectomy

PURPOSE

To evaluate the effect of acute kidney injury (AKI) duration and severity on long-term renal functional outcomes in patients undergoing partial nephrectomy (PN).

METHODS

Altogether 292 consecutive patients undergoing laparoscopic PN from 2010 to 2018 were identified in two medical centers. In addition, the AKI duration {transient AK [≤ 3d] or persistent AKI [> 3d]} was combined with AKI severity (stages) to elucidate their relationships with long-term functional results. Kaplan-Meier (KM) analysis was also used to compare among patients with no AKI, transient AKI, and persistent AKI. Moreover, the Cox-proportional hazards regression model was utilized to assess the risk factors for renal function deterioration.

RESULTS

Altogether 67 patients (22.9%) experienced postoperative AKI. 75% eGFR preserve rate during the follow-up was compared among patients with no AKI, transient AKI and persistent AKI using KM analysis and log-rank test, which revealed significant difference. After adjusting for age and warm ischemia time by multivariate model proportional hazards analysis, AKI duration and severity were identified as the risk factors (Stage 1-transient AKI vs. non-AKI: adjusted hazard ratio (HR) 4.361, 95% confidential interval (CI) [2.062-9.233], p < 0.001; stage 1-persistent AKI vs. non-AKI: adjusted HR 6.706, 95% CI [2.405-18.699], p < 0.001; stage 2/3-transient AKI vs. non-AKI: adjusted HR 8.949, 95% CI [1.571-50.963], p = 0.014; stage 2/3-persistent AKI vs. non-AKI: adjusted HR 13.453, 95% CI [11.353-133.798], p = 0.027).

CONCLUSIONS

The AKI duration after PN is an important risk factor for long-term renal functional deterioration. Besides, AKI duration combined with AKI severity can be more comprehensive to understand the role of AKI on ultimately renal function.

TRIAL REGISTRATION

Chinese ClinicalTrials: ChiCTR2000034080.

Laparoscopic and Robotic-Assisted Partial Nephrectomy: An Overview of Hot Issues

Laparoscopic partial nephrectomy and robot-assisted partial nephrectomy are attracting increased attention from urologists. They can achieve the same effect of oncology control as radical nephrectomy; moreover, they can offer better preservation of renal function, thus obtaining long-term living benefits. The indications are also expanding, making it possible for larger and more difficult tumors. Laparoscopic partial nephrectomy and robot-assisted partial nephrectomy can be performed by transperitoneal and retroperitoneal approaches, with their individual advantages and limitations. In addition, the renal tumor scoring systems have been widely used and studied in laparoscopic partial nephrectomy and robot-assisted partial nephrectomy. In -order to better preserve renal function, the zero-ischemia technique is widely used. The application of intraoperative imaging technology provides convenience and greater benefits. Besides, whether minimal invasive partial nephrectomy can be performed without stop antiplatelet treatment is still disputed. Clinicians perform substantial exploration and practice to achieve the "trifecta" of surgery: complete resection of the tumor, maximum protection of renal function, and no complications.

Squamous cell carcinoma of the renal parenchyma presenting as hydronephrosis: a case report and review of the recent literature

BACKGROUND

Primary squamous cell carcinoma of the renal parenchyma is extremely rare, only 5 cases were reported.

CASE PRESENTATION

We probably report the fifth case of primary Squamous cell carcinoma (SCC) of the renal parenchyma in a 61-year-old female presenting with intermittent distending pain for 2 months. Contrast-enhanced computed tomography (CECT) revealed hydronephrosis of the right kidney, but a tumor cannot be excluded completely. Finally, nephrectomy was performed, and histological analysis determined that the diagnosis was kidney parenchyma squamous cell carcinoma involving perinephric adipose tissue.

CONCLUSIONS

The present case emphasizes that it is difficult to make an accurate preoperative diagnosis with the presentation of hidden malignancy, such as hydronephrosis.

Prevention of Prostate Tumor Development by Stimulation of Antitumor Immunity Using a Standardized Herbal Extract (Deep Immune®) in TRAMP Mice

Low-risk prostate cancer (PCa) does not require immediate treatment, but PCa progression after years of active surveillance will need the treatment. This study was to test the efficacy of immunostimulant Deep Immune (DI) in controlling PCa progression. DI is an extract of eight different medicinal herbs. In vitro activity of DI was determined by phagocytosis activation using flow cytometric analysis of fluorescence-labeled latex bead uptake, expression of immune-modulating 84 genes using PCRarray, and tumor killing using coculturing with immune cells. Anti-PCa activity of DI in vivo was examined in male TRAMP mice. In vitro DI stimulated phagocytosis and expression of a panel of inflammatory mediators (C4b, CXCL3, lymphotoxin, NOS2, TLR1, TNF, and TNFSF14) in cultured macrophages and increased tumor killing of both macrophages and TRAMP mouse splenocytes. Daily intake of this herbal product significantly suppressed the tumor size (P = 0.0368) with lower histopathologic scores (P = 0.0364) in TRAMP mice, which were associated with an increase in both splenocyte cytotoxicity against tumor cells and numbers of CD8 T cells, macrophages, and dendritic cells in the spleens in vivo. In conclusion, daily intake of DI prevents PCa progression in TRAMP mice, suggesting the possible effectiveness of the immunostimulant herbal products on prevention of PCa progression after diagnosis of low-risk PCa.

Expression and clinical implications of homeobox gene Six1 in cervical cancer cell lines and cervical epithelial tissues

INTRODUCTION

The homeobox gene Six1 is overexpressed in multiple human tumors, playing a role in promoting tumorigenesis and metastasis. The present study was aimed to investigate the clinical implications of Six1 expression in cervical cancer.

METHODS

Six1 messenger RNA (mRNA) and protein expression was detected by reverse transcription (RT) polymerase chain reaction and Western blotting, respectively, in human cervical cancer cell lines CaSki, HeLa, C33A and 20 normal cervical specimens, 21 specimens of cervical intraepithelial neoplasias (CINs), and 54 specimens of cervical cancer tissue, and the clinical implications of Six1 gene expression was analyzed.

RESULTS

There was Six1 mRNA and protein overexpression in cervical cancer cell lines CaSki, HeLa, and C33A. The Six1 expression level was higher in CaSki and HeLa cells than in C33A cells (P < 0.05). Six1 mRNA and protein expression increased from normal cervical epithelial tissues, to CINs, and then to cervical cancer tissue (normal cervical epithelial tissue vs CIN, P < 0.05; normal cervical epithelial tissue vs cervical cancer, and CIN vs cervical cancer, P < 0.01). The status of Six1 overexpression was correlated to clinical staging and lymph node metastasis of cervical cancer (P < 0.01) but not to pathological grading, tumor size, and age of the patient (P > 0.05).

CONCLUSION

Six1 was overexpressed in cervical cancer cell lines and in cervical cancer tissues. Alteration of Six1 expression might contribute to the occurrence and development of cervical cancer.

Construction of a DNA vaccine encoding Flk-1 extracellular domain and C3d fusion gene and investigation of its suppressing effect on tumor growth

Although the critical role of complement component C3d as a molecular adjuvant in preventing virus infection is well established, its role in cancer prophylaxis and treatment is unclear. In this study, we constructed a recombinant plasmid encoding Flk-1 and C3d3 fusion proteins and investigated its transient expression in vitro in transfected eukaryotic cells and its antibody response in immunized mice. Subsequently, we investigated the vaccine's ability to elicit an immune response leading to suppression of angiogenesis and tumor growth in mice bearing bladder transitional cell carcinoma. Using Western blotting, immunocytochemistry, and flow cytometry, we detected the expression of Flk-1 and C3d3 fusion proteins in COS-7 cells transfected with these recombinant plasmids. Further binding experiment using CR2 (C3d receptor) positive Raji cells that were incubated with transfected COS-7 supernatant indicated that C3d was successfully fused to Flk-1. Although both vaccines elicited peak antibody levels at 5 weeks, Flk-1-specific antibody titer in pSG.SS.Flk-1(ECD).C3d3.YL-immunized mice was significantly higher when compared to pSG.SS.Flk-1(ECD).YL-immunized mice. The results of experiments with bladder tumor-bearing mice showed that the vaccine inhibited tumor growth significantly. These results suggest that C3d plays a critical role in tumor immunotherapy by promoting antibody response in Flk-1-based DNA vaccines. This approach may provide a new strategy for the rational design of anti-angiogenic therapies for the treatment of solid tumors and provide a basis for the further exploitation and application of the anti-angiogenesis DNA vaccines.

Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis

The Escherichia coli undecaprayl-pyrophosphate synthase (UPPs) structure has been solved using the single wavelength anomalous diffraction method. The putative substrate-binding site is located near the end of the betaA-strand with Asp-26 playing a critical catalytic role. In both subunits, an elongated hydrophobic tunnel is found, surrounded by four beta-strands (betaA-betaB-betaD-betaC) and two helices (alpha2 and alpha3) and lined at the bottom with large residues Ile-62, Leu-137, Val-105, and His-103. The product distributions formed by the use of the I62A, V105A, and H103A mutants are similar to those observed for wild-type UPPs. Catalysis by the L137A UPPs, on the other hand, results in predominantly the formation of the C(70) polymer rather than the C(55) polymer. Ala-69 and Ala-143 are located near the top of the tunnel. In contrast to the A143V reaction, the C(30) intermediate is formed to a greater extent and is longer lived in the process catalyzed by the A69L mutant. These findings suggest that the small side chain of Ala-69 is required for rapid elongation to the C(55) product, whereas the large hydrophobic side chain of Leu-137 is required to limit the elongation to the C(55) product. The roles of residues located on a flexible loop were investigated. The S71A, N74A, or R77A mutants displayed 25-200-fold decrease in k(cat) values. W75A showed an 8-fold increase of the FPP K(m) value, and 22-33-fold increases in the IPP K(m) values were observed for E81A and S71A. The loop may function to bridge the interaction of IPP with FPP, needed to initiate the condensation reaction and serve as a hinge to control the substrate binding and product release.

Refolding and characterization of a yeast dehydrodolichyl diphosphate synthase overexpressed in Escherichia coli

Dehydrodolichyl diphosphate synthase (DDPPs) catalyzes the sequential condensation of isopentenyl diphosphate with farnesyl diphosphate to synthesize long-chain dehydrodolichyl diphosphate, which serves as a precursor of glycosyl carrier in glycoprotein biosynthesis in eukaryotes. To perform kinetic and structural studies of DDPPs, we have expressed yeast DDPPs using Escherichia coli as the host cell. Thioredoxin and His tag were utilized to increase the solubility of the recombinant protein and facilitate its purification using Ni-nitrilotriacetic acid (NTA) column. The protein was overexpressed in E. coli but mostly existed in pellet in the absence of detergent. The low quantity of soluble DDPPs was purified using Ni-NTA, Mono Q anion-exchange, and size-column chromatographies. The protein in the pellet was solubilized with 7 M urea and purified using Ni-NTA under denaturing condition. The protein refolding was achieved via the stepwise dialysis to remove the denaturant in the presence of 6 mM beta-mercaptoethanol. Detergent n-octyl-beta-d-glucopyranoside and Triton X-100 increased the solubility of the DDPPs so that refolding can be performed at higher protein concentration. Alternatively, on-column refolding was carried out in a single step to obtain the active protein in large quantities. beta-Mercaptoethanol and Triton were both required in this quick refolding process. The kinetic studies indicated that the soluble and refolded DDPPs have comparable activities (k(cat) = 2 x 10(-4) s(-1)). Unlike its bacterial homologue, undecaprenyl diphosphate synthase, yeast DDPPs activity was not enhanced by Triton.

Steady-state kinetic characterization of substrates and metal-ion specificities of the full-length and N-terminally truncated recombinant human methionine aminopeptidases (type 2)

The steady-state kinetics of a full-length and truncated form of the type 2 human methionine aminopeptidase (hMetAP2) were analyzed by continuous monitoring of the amide bond cleavage of various peptide substrates and methionyl analogues of 7-amido-4-methylcoumarin (AMC) and p-nitroaniline (pNA), utilizing new fluorescence-based and absorbance-based assay substrates and a novel coupled-enzyme assay method. The most efficient substrates for hMetAP2 appeared to be peptides of three or more amino acids for which the values of k(cat)/K(m) were approximately 5 x 10(5) M(-1) min(-1). It was found that while the nature of the P1' residue of peptide substrates dictates the substrate specificity in the active site of hMetAP2, the P2' residue appears to play a key role in the kinetics of peptidolysis. The catalytic efficiency of dipeptide substrates was found to be at least 250-fold lower than those of the tripeptides. This substantially diminished catalytic efficiency of hMetAP2 observed with the alternative substrates MetAMC and MetpNA is almost entirely due to the reduction in the turnover rate (k(cat)), suggesting that cleavage of the amide bond is at least partially rate-limiting. The 107 N-terminal residues of hMetAP2 were not required for either the peptidolytic activity of the enzyme or its stability. Steady-state kinetic comparison and thermodynamic analyses of an N-terminally truncated form and full-length enzyme yielded essentially identical kinetic behavior and physical properties. Addition of exogenous Co(II) cation was found to significantly activate the full-length hMetAP2, while Zn(II) cation, on the other hand, was unable to activate hMetAP2 under any concentration that was tested.

Effect of site-directed mutagenesis of the conserved aspartate and glutamate on E. coli undecaprenyl pyrophosphate synthase catalysis

Undecaprenyl pyrophosphate synthase (UPPs) catalyzes condensation of eight molecules of isopentenyl pyrophosphate with farnesyl pyrophosphate to yield C(55)-undecaprenyl pyrophosphate. We have mutated the aspartates and glutamates in the five conserved regions (I to V) of UPPs protein sequence to evaluate their effects on substrate binding and catalysis. The mutant enzymes including D26A, E73A, D150A, D190A, E198A, E213A, D218A, and D223A were expressed and purified to great homogeneity. Kinetic analyses of these mutant enzymes indicated that the substitution of D26 in region I with alanine resulted in a 10(3)-fold decrease of k(cat) value compared to wild-type UPPs. Its IPP K(m) value has only minor change. The mutagenesis of D150A has caused a much lower IPP affinity with IPP K(m) value 50-fold larger than that of wild-type UPPs but did not affect the FPP K(m) and the k(cat). The E213A mutant UPPs has a 70-fold increased IPP K(m) value and has a 100-fold decreased k(cat) value compared to wild-type. These results suggest that D26 of region I is critical for catalysis and D150 in region IV plays a significant role of IPP binding. The E213 residue in region V is also important in IPP binding as well as catalysis. Other mutant UPPs enzymes in this study have shown no significant change (<5-fold) of k(cat) with exception of E73A and D218A. Both enzymes have 10-fold lower k(cat) value relative to wild-type UPPs.

Product distribution and pre-steady-state kinetic analysis of Escherichia coli undecaprenyl pyrophosphate synthase reaction

Undecaprenyl pyrophosphate synthase (UPPs) catalyzes the condensation of eight molecules of isopentenyl pyrophosphate (IPP) with farnesyl pyrophosphate (FPP) to generate C(55) undecaprenyl pyrophosphate. We investigated the kinetics and mechanism of this reaction pathway using Escherichia coli UPPs. With a variety of different ratios of enzyme to substrate and FPP to IPP in the presence or absence of Triton, different product distributions were found. In the presence of excess FPP, the intermediates (C(25)-C(50)) accumulated. Under a condition with enzyme and FPP in excess of IPP, instead of C(20)-geranylgeranyl pyrophosphate, C(20), C(25), and C(30) were the major products. The UPPs steady-state k(cat) value (2.5 s(-1)) in the presence of 0.1% Triton was 190-fold larger than in the absence of Triton (0.013 s(-1)). The k(cat) value matched the rate constant of each IPP condensation obtained from the enzyme single-turnover experiments. This suggested that the IPP condensation rather than product release was the rate-limiting step in the presence of Triton. In the absence of Triton, the intermediates formed and disappeared in a similar manner under enzyme single turnover in contrast to the slow steady-state rate, which indicated a step after product generation was rate limiting. This was further supported by a burst product formation. Judging from the accumulation level of C(55), C(60), and C(65), their dissociation from the enzyme cannot be too slow and an even slower enzyme conformational change with a rate of 0.001 s(-1) might govern the UPPs reaction rate under the steady-state condition in the absence of Triton.

Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality

Caspases have been strongly implicated to play an essential role in apoptosis. A critical question regarding the role(s) of these proteases is whether selective inhibition of an effector caspase(s) will prevent cell death. We have identified potent and selective non-peptide inhibitors of the effector caspases 3 and 7. The inhibition of apoptosis and maintenance of cell functionality with a caspase 3/7-selective inhibitor is demonstrated for the first time, and suggests that targeting these two caspases alone is sufficient for blocking apoptosis. Furthermore, an x-ray co-crystal structure of the complex between recombinant human caspase 3 and an isatin sulfonamide inhibitor has been solved to 2.8-A resolution. In contrast to previously reported peptide-based caspase inhibitors, the isatin sulfonamides derive their selectivity for caspases 3 and 7 by interacting primarily with the S(2) subsite, and do not bind in the caspase primary aspartic acid binding pocket (S(1)). These inhibitors blocked apoptosis in murine bone marrow neutrophils and human chondrocytes. Furthermore, in camptothecin-induced chondrocyte apoptosis, cell functionality as measured by type II collagen promoter activity is maintained, an activity considered essential for cartilage homeostasis. These data suggest that inhibiting chondrocyte cell death with a caspase 3/7-selective inhibitor may provide a novel therapeutic approach for the prevention and treatment of osteoarthritis, or other disease states characterized by excessive apoptosis.

Crystallographic studies of phosphonate-based alpha-reaction transition-state analogues complexed to tryptophan synthase

In an effort to use a structure-based approach for the design of new herbicides, the crystal structures of complexes of tryptophan synthase with a series of phosphonate enzyme inhibitors were determined at 2.3 A or higher resolution. These inhibitors were designed to mimic the transition state formed during the alpha-reaction of the enzyme and, as expected, have affinities much greater than that of the natural substrate indole-3-glycerol phosphate or its nonhydrolyzable analogue indole propanol phosphate (IPP). These inhibitors are ortho-substituted arylthioalkylphosphonate derivatives that have an sp(3)-hybridized sulfur atom, designed to mimic the putative tetrahedral transition state at the C3 atom of the indole, and lack the C2 atom to allow for higher conformational flexibility. Overall, the inhibitors bind in a fashion similar to that of IPP. Glu-49 and Phe-212 are the two active site residues whose conformation changes upon inhibitor binding. A very short hydrogen bond between a phosphonate oxygen and the Ser-235 hydroxyl oxygen may be responsible for stabilization of the enzyme-inhibitor complexes. Implications for the mechanism of catalysis as well as directions for more potent inhibitors are discussed.

Catalytic mechanism of Kdo8P synthase: transient kinetic studies and evaluation of a putative reaction intermediate

The mechanistic pathway for the reaction catalyzed by Kdo8P synthase has been investigated, and the cyclic bisphosphate 2 has been examined as a putative reaction intermediate. Two parallel approaches were used: (1) chemical synthesis of 2 and evaluation as an alternate substrate for the enzyme and (2) transient kinetic studies using rapid chemical quench methodology to provide direct observation and characterization of putative intermediate(s) during enzyme catalysis. The putative cyclic bisphosphate intermediate 2, possessing the stereochemistry of the beta-pyranose form, was synthesized and evaluated as a substrate and as an inhibitor of Kdo8P synthase. The substrate activity was examined by monitoring the release of anomeric phosphate over time using proton-decoupled 31P NMR spectroscopy. A very similar time course for the formation of inorganic phosphate was found in each experiment and the corresponding control experiment; i.e., no enzyme-catalyzed acceleration in the anomeric phosphate hydrolysis was detected. It was found however that 2 binds to the enzyme and is a competitive inhibitor with respect to phosphoenolpyruvate binding, having a Ki value of 35 microM. In a parallel study, we have performed single-turnover rapid chemical quench experiments to examine both the forward and reverse directions to identify a putative enzyme intermediate(s). Our results clearly demonstrate that the cyclic bisphosphate intermediate 2 does not accumulate under single-enzyme turnover conditions. This observation, coupled with the results obtained through the evaluation of synthetic 2 as a substrate, strongly suggests that the Kdo8P synthase catalytic pathway does not involve the formation of 2 as a reaction intermediate. Taken together, these combined results support the original hypothesis [Hedstrom, L., and Abeles, R. H. (1988) Biochem. Biophys. Res. Commun. 157, 816-820], which suggests a reaction pathway involving an acyclic bisphosphate intermediate 1.

Substrate channeling and domain-domain interactions in bifunctional thymidylate synthase-dihydrofolate reductase

The thymidylate synthase (TS) and dihydrofolate reductase (DHFR) enzymes are found on a single polypeptide chain in several species of protozoa such as the parasitic Leishmania major. Earlier studies with the bifunctional TS-DHFR enzyme from L. major have suggested that this enzyme exhibits a phenomenon known as substrate channeling [Meek, T. D., et al. (1985) Biochemistry 24, 678-686]. This is a process by which a metabolite or intermediate is directly transferred from one enzyme active site to the next without being released free into solution. The crystal structure for the bifunctional TS-DHFR enzyme from L. major was recently solved, and it was shown that the TS active site was located 40 A from the DHFR active site [Knighton, D. R., et al. (1994) Nat. Struct. Biol. 1, 186-194]. On the basis of the crystal structure, a novel mechanism has been proposed for the channeling of the intermediate, dihydrofolate, from the TS active site to the DHFR active site [Knighton, D. R., et al. (1994) Nat. Struct. Biol. 1, 186-194]. They suggest that the dihydrofolate is transferred via an "electrostatic" channel on the protein surface which connects the two active sites. In this report, we describe the use of a rapid transient kinetic analysis in examining the kinetics of substrate channeling as well as domain-domain interactions in the bifunctional TS-DHFR from L. major.

Kinetic reaction scheme for the dihydrofolate reductase domain of the bifunctional thymidylate synthase-dihydrofolate reductase from Leishmania major

In several species of protozoa, the catalytic activities for the enzymes dihydrofolate reductase (DHFR) and thymidylate synthase (TS) reside on a single polypeptide chain constituting a bifunctional thymidylate synthase-dihydrofolate reductase enzyme. In most other species, however, these enzymes occur as monofunctional catalytic activities on separate enzymes. In this study, the kinetic reaction scheme for the dihydrofolate reductase activity from the bifunctional thymidylate synthase-dihydrofolate reductase (TS-DHFR) isolated from the parasite Leishmania major is compared to that of the monofunctional DHFR purified from Escherichia coli. Examination using pre-steady-state kinetic methods reveals interesting differences between the bifunctional and monofunctional forms of the dihydrofolate reductase enzymes. The rate-limiting step in the kinetic pathway for the monofunctional E. coli enzyme is the release of product, tetrahydrofolate. In contrast, for the L. major bifunctional enzyme, the kinetic step which limits the steady-state turnover is a conformational change associated with the release of NADP+. A complete kinetic description for the dihydrofolate reductase reaction pathway for the bifunctional enzyme is presented.

Site-directed mutagenesis probing the catalytic role of arginines 165 and 166 of human cytomegalovirus protease

Human cytomegalovirus (CMV) is a member of the Herpesviridae family of viruses that also includes herpes simplex viruses (HSV-1 and HSV-2), varicella-zoster virus (VZV), human herpes virus-6, 7, and 8 (HHV-6, HHV-7, and HHV-8), and Epstein-Barr virus (EBV). Each member of this family encodes a serine protease that is a potential target for antiviral therapeutic intervention. We recently reported the crystal structure of CMV proteases [Qiu, X., Culp, J. S., DiLella, A. G., Hellmig, B., Hoog, S. S., Janson, C. A., Smith, W. W., and Abdel-Meguid, S. S. (1996) Nature 383, 275-279] and proposed that the highly conserved Arg165 and Arg166 residues are involved in stabilizing the oxyanion intermediate in human herpes protease catalyzed reactions through the backbone NH and side chain, respectively. In the current study, site-directed mutagenesis was carried out to probe the catalytic function of these two amino acid residues. Substitution of Arg166 with an alanine has led to ablation of enzymatic activity without detectable change in CMV protease conformation, supporting suggestions from the crystal structure that Arg166 side chain plays a major role in catalysis. The wild-type has a Km = 138 +/- 17 microM and kcat = 19.9 +/- 1.1 min-1, while R166A has only residual activity, with a kcat = 0.012 +/- 0.001 min-1 and an unaltered Km = 145 +/- 18 microM. In the crystal structure, the side chain of Arg166 was shown previously to hold a water molecule that can act as a hydrogen-bond donor to the oxyanion and was thus proposed to stabilize the oxyanion intermediate. However, kinetic characterization of the mutant R165A only reveals a 2.7-fold lower activity than wild-type, with a Km = 166 +/- 19 microM and a kcat = 7.4 +/- 0.4 min-1. These results confirm that Arg165 side chain is not involved in the stabilization of the oxyanion. It is likely that Arg165 only utilizes the backbone NH for catalysis as suggested by the crystal structure.

Loop closure and intersubunit communication in tryptophan synthase

Crystal structures of wild-type tryptophan synthase alpha2beta2 complexes from Salmonella typhimurium were determined to investigate the mechanism of allosteric activation of the alpha-reaction by the aminoacrylate intermediate formed at the beta-active site. Using a flow cell, the aminoacrylate (A-A) intermediate of the beta-reaction () was generated in the crystal under steady state conditions in the presence of serine and the alpha-site inhibitor 5-fluoroindole propanol phosphate (F-IPP). A model for the conformation of the Schiff base between the aminoacrylate and the beta-subunit cofactor pyridoxal phosphate (PLP) is presented. The structure is compared with structures of the enzyme determined in the absence (TRPS) and presence (TRPSF-IPP) of F-IPP. A detailed model for binding of F-IPP to the alpha-subunit is presented. In contrast to findings by Hyde et al. [(1988) J. Biol. Chem. 263,17857-17871] and Rhee et al. [(1997) Biochemistry 36, 7664-7680], we find that the presence of an alpha-site alone ligand is sufficient for loop alphaL6 closure atop the alpha-active site. Part of this loop, alphaThr183, is important not only for positioning the catalytic alphaAsp60 but also for coordinating the concomitant ordering of loop alphaL2 upon F-IPP binding. On the basis of the three structures, a pathway for communication between the alpha- and beta-active sites has been established. The central element of this pathway is a newly defined rigid, but movable, domain that on one side interacts with the alpha-subunit via loop alphaL2 and on the other side with the beta-active site. These findings provide a structural basis for understanding the allosteric properties of tryptophan synthase.

Leishmania major pteridine reductase 1 belongs to the short chain dehydrogenase family: stereochemical and kinetic evidence

Pteridine reductase 1 (PTR1) is a novel broad spectrum enzyme of pterin and folate metabolism in the protozoan parasite Leishmania. Overexpression of PTR1 confers methotrexate resistance to these protozoa, arising from the enzyme's ability to reduce dihydrofolate and its relative insensitivity to methotrexate. The kinetic mechanism and stereochemical course for the catalyzed reaction confirm PTR1's membership within the short chain dehydrogenase/reductase (SDR) family. With folate as a substrate, PTR1 catalyzes two rounds of reduction, yielding 5,6,7, 8-tetrahydrofolate and oxidizing 2 equiv of NADPH. Dihydrofolate accumulates transiently during folate reduction and is both a substrate and an inhibitor of PTR1. PTR1 transfers the pro-S hydride of NADPH to carbon 6 on the si face of dihydrofolate, producing the same stereoisomer of THF as does dihydrofolate reductase. Product inhibition and isotope partitioning studies support an ordered ternary complex mechanism, with NADPH binding first and NADP+ dissociating after the reduced pteridine. Identical kinetic mechanisms and NAD(P)H hydride chirality preferences are seen with other SDRs. An observed tritium effect upon V/K for reduction of dihydrofolate arising from isotopic substitution of the transferred hydride was suppressed at a high concentration of dihydrofolate, consistent with a steady-state ordered kinetic mechanism. Interestingly, half of the binary enzyme-NADPH complex appears to be incapable of rapid turnover. Fluorescence quenching results also indicate the existence of a nonproductive binary enzyme-dihydrofolate complex. The nonproductive complexes observed between PTR1 and its substrates are unique among members of the SDR family and may provide leads for developing antileishmanial therapeutics.

Pre-steady-state kinetic analysis of the trichodiene synthase reaction pathway

The pre-steady-state kinetics of the trichodiene synthase reaction were investigated by rapid chemical quench methods. The single-turnover rate was found to be 3.5-3.8 s-1, a rate 40 times faster than the steady-state catalytic rate (kcat = 0.09 s-1) for trichodiene synthase-catalyzed conversion of farnesyl diphosphate (FPP) to trichodiene at 15 degrees C. In a multiturnover experiment, a burst phase (kb = 4.2 s-1) corresponding to the accumulation of trichodiene on the surface of the enzyme was followed by a slower, steady-state release of products (klin = 0.086 s-1) which corresponds to kcat. These results strongly suggest that the release of trichodiene from the enzyme active site is the rate-limiting step in the overall reaction, while the consumption of FPP is the step which limits chemical catalysis at the active site. Single-turnover experiments with trichodiene synthase mutant D101E, for which the steady-state rate constant kcat is 1/3 of that of wild type, revealed that the mutation actually depresses the rate of FPP consumption by a factor of 100. The deuterium isotope effect on the consumption of [1-2H,1,2-14C]FPP was found to be 1.11 +/- 0.06. Single turnover reactions of [1,2-14C]FPP catalyzed by trichodiene synthase were carried out at 4, 15, or 30 degrees C in an effort to provide direct observation of the proposed intermediate nerolidyl diphosphate (NPP). However, no NPP was detected, indicating that the conversion of NPP must be too fast to be observed within the detection limits of the assay. Taken together, these observations suggest that the isomerization of FPP to NPP is the step which limits the rate of chemical catalysis in the trichodiene synthase reaction pathway.

Evidence for electrophilic catalysis in the 4-chlorobenzoyl-CoA dehalogenase reaction: UV, Raman, and 13C-NMR spectral studies of dehalogenase complexes of benzoyl-CoA adducts

This paper reports on the mechanism of substrate activation by the enzyme 4-chlorobenzoyl coenzyme A dehalogenase. This enzyme catalyzes the hydrolytic dehalogenation of 4-chlorobenzoyl coenzyme A (4-CBA-CoA) to form 4-hydroxybenzoyl coenzyme A (4-HBA-CoA). The mechanism of this reaction is known to involve attack of an active site carboxylate (Asp or Glu side chain) at C(4) of the substrate benzoyl ring to form a Meisenheimer complex. Loss of chloride ion from this intermediate results in the formation of an arylated enzyme intermediate. The arylated enzyme is hydrolyzed to free enzyme plus 4-HBA-CoA by the addition of water at the acyl carbon [Yang, G., Liang, P.-H., & Dunaway-Mariano, D. (1994) Biochemistry 33, 8527]. The present studies have focused on the activation of the 4-CBA-CoA for nucleophilic attack by the active site carboxylate group. UV-visible, 13C-NMR, and Raman spectroscopic techniques were used to monitor changes in the distribution of the pi electrons of the benzoyl moiety of benzoyl-CoA adducts [substituted at C(4) with methyl (4-MeBA-CoA), methoxy (4-MeOBA-CoA), or hydroxyl (4-HBA-CoA) groups or at C(2) or C(3) with a hydroxyl group (2-HBA-CoA and 3-HBA-CoA)] resulting from the binding of these ligands to the dehalogenase active site. The UV-visible spectra measured for 4-HBA-CoA in aqueous buffer at pH 7.5 and in the dehalogenase active site revealed that a large red shift (from 292 to 373 nm) in the lambda max of the benzoyl moiety occurs upon binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Evidence for nucleophilic catalysis in the aromatic substitution reaction catalyzed by (4-chlorobenzoyl)coenzyme A dehalogenase

(4-Chlorobenzoyl)coenzyme A dehalogenase catalyzes the hydrolytic dehalogenation of (4-chlorobenzoyl)coenzyme A (4-CBA-CoA) to (4-hydroxybenzoyl)coenzyme A (4-HBA-CoA). Rapid-quench techniques were used in conjunction with [14C]-4-CBA-CoA to test for the formation of a covalent enzyme intermediate during catalysis. The rate of [14C]-4-CBA-CoA (37 microM) consumption in the presence of a 2-fold excess of dehalogenase (75 microM) was determined to proceed at k = 6.5 s-1, coincident with the formation of an enzyme intermediate containing covalently bound radiolabel. The radiolabeled enzyme reached a maximum level at 100 ms, corresponding to 27% of the starting [14C]-4-CBA-CoA, before declining. The kinetics of formation and consumption of the radiolabeled enzyme observed during turnover are consistent with its intermediacy in the overall reaction. A single turnover reaction carried out in 98% 18O-enriched water produced 4-HBA-CoA with 73-75% 16O and 27-25% 18O at the benzoyl ring C(4)-OH. In contrast, a multiple turnover reaction carried out in 93% H2(18)O produced 4-HBA-CoA labeled at the C(4)-OH with 89% 18O and 11% 16O. These results were interpreted as evidence for formation of an aryl enzyme intermediate during 4-CBA-CoA hydrolytic dechlorination in the dehalogenase active site.

Specificity of 4-chlorobenzoyl coenzyme A dehalogenase catalyzed dehalogenation of halogenated aromatics

Steady-state and transient kinetic techniques were used to evaluate the efficiency of 4-chlorobenzoyl coenzyme A (4-CBA-CoA) turnover catalyzed by 4-CBA-CoA dehalogenase from Pseudomonas sp. CBS-3. The kcat for a single turnover on the enzyme was found to be 2 s-1, while that for multiple turnovers was found to be 0.6 s-1. Catalysis rather than product release was judged to be rate limiting. Comparison of the rates of turnover of 4-bromobenzoyl-CoA (1.4 s-1), 4-iodobenzoyl-CoA (1.1 s-1), and 4-fluorobenzoyl-CoA (8 x 10(-6) s-1) indicated that cleavage of the carbon-halogen bond occurs in the rate-limiting transition state of the reaction. Structure-activity measurements made with 4-CBA-CoA analogs bearing electron-donating or -withdrawing substituents at C(2) or C(3) suggested the importance of steric/solvation effects on the enzymatic reaction and failed to provide insight into the nature of the reaction intermediate. The inhibition constants measured for benzoyl-CoA (72 microM), CoA (140 microM), and 4-chlorobenzoate (21 mM) compared to the Km measured for 4-CBA-CoA (4 microM) suggest the dominant role played by the CoA moiety in substrate anchoring.

Isolation and characterization of the three polypeptide components of 4-chlorobenzoate dehalogenase from Pseudomonas sp. strain CBS-3

The three genes encoding the 4-chlorobenzene dehalogenase polypeptides were excised from a Pseudomonas sp. CBS-3 DNA fragment and separately cloned and expressed in Escherichia coli. The three enzymes were purified from the respective subclones by using an ammonium sulfate precipitation step followed by one or two column chromatographic steps. The 4-chlorobenzoate:coenzyme A ligase was found to be a homodimer (57-kDa subunit size), to require Mg2+ (Co2+ and Mn2+ are also activators) for activity, and to turn over MgATP (Km = 100 microM), coenzyme A (Km = 80 microM), and 4-chlorobenzoate (Km = 9 microM) at a rate of 30 s-1 at pH 7.5 and 25 degrees C. Benzoate, 4-bromobenzoate, 4-iodobenzoate, and 4-methylbenzoate were shown to be alternate substrates while 4-hydroxybenzoate, 4-aminobenzoate, 2-aminobenzoate, 2,3-dihydroxybenzoate, 4-coumarate, palmate, laurate, caproate, butyrate, and phenylacetate were not substrate active. The 4-chlorobenzoate-coenzyme A dehalogenase was found to be a homotetramer (30 kDa subunit size) to have a Km = 15 microM and kcat = 0.3 s-1 at pH 7.5 and 25 degrees C and to be catalytically inactive toward hydration of crotonyl-CoA, alpha-methylcrotonyl-CoA, and beta-methylcrotonyl-CoA. The 4-hydroxybenzoate-coenzyme A thioesterase was shown to be a homotetramer (16 kDa subunit size), to have a Km = 5 microM and kcat = 7 s-1 at pH 7.5 and 25 degrees C, and to also catalyze the hydrolyses of benzoyl-coenzyme A and 4-chlorobenzoate-coenzyme A. Acetyl-coenzyme A, hexanoyl-coenzyme A, and palmitoyl-coenzyme A were not hydrolyzed by the thioesterase.

Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases

We have deduced the nucleotide sequence of the genes encoding the three components of 4-chlorobenzoate (4-CBA) dehalogenase from Pseudomonas sp. CBS-3 and examined the origin of these proteins by homology analysis. Open reading frame 1 (ORF1) encodes a 30-kDa 4-CBA-coenzyme A dehalogenase related to enoyl-coenzyme A hydratases functioning in fatty acid beta-oxidation. ORF2 encodes a 57-kDa protein which activates 4-CBA by acyl adenylation/thioesterification. This 4-CBA:coenzyme A ligase shares significant sequence similarity with a large group of proteins, many of which catalyze similar chemistry in beta-oxidation pathways or in siderophore and antibiotic synthetic pathways. These proteins have in common a short stretch of sequence, (T,S)(S,G)G(T,S)(T,E)G(L,X)PK(G,-), which is particularly highly conserved and which may represent an important new class of "signature" sequence. We were unable to find any proteins homologous in sequence to the 16-kDa 4-hydroxybenzoate-coenzyme A thioesterase encoded by ORF3. Analysis of the chemistry and function of the proteins found to be structurally related to the 4-CBA:coenzyme A ligase and the 4-CBA-coenzyme A dehalogenase supports the proposal that they evolved from a beta-oxidation pathway.