Figure 8 - uploaded by Shahienaz Emma Hampton
Content may be subject to copyright.
Source publication
Ras converting enzyme 1 (Rce1) is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins, whose members play important roles in cell signaling processes. Examples include the Ras family of small GTPases, the γ-subunit of heterotrimeric GTPases...
Contexts in source publication
Context 1
... number of inhibitors can be justifiably classified as substrate mimetics based on structural elements that mimic the natural substrate features. The first specific, non-reversible inhibitor of Rce1 was created by modify- ing TPCK and TLCK with a farnesyl group and replacing the sulfonamide with a tert-butylcarbamate to create BFCCMK (K i ¼ 30 lM) (Figure 8) (Chen et al. 1996). Replacement of the thiofarnesyl unit with a tridecyl group gave a more stable and cell-permeable analog, UM96001 (Chen 1998). ...
Context 2
... acyloxymethyl ketones (AOMKs) inhibit Rce1 ( Porter et al. 2007). The peptidyl portion modulates the inhibitory properties of these compounds, but signifi- cant improvement of inhibitory properties is not likely achievable through alteration of the peptidyl portion alone (Dechert et al. 2010) (Figure 8). Because AOMKs are known to be irreversible cysteine protease inhibi- tors, the reactivity of these derivatives can also be modulated by altering the acyloxy leaving group. ...
Context 3
... derivatives with differing benzyloxy groups have been evaluated, but AOMKs surveyed had weak inhibitory properties against ScRce1 (>40% ScRce1 activity remaining after 100-lM treatment). A substi- tuted analog that did not contain a leaving group suit- able for an irreversible binding mechanism ("warhead- free" AOMK, Figure 8) proved to be the best inhibitory compound ($25% ScRce1 activity remaining after 100-lM treatment). These results suggest that AOMKs do not likely work as mechanism-based inhibitors and are most likely non-covalent, reversible inhibitors of Rce1. ...
Similar publications
Lu Lu Huimin He Jindi Feng- [...]
Tao Wang
Vitiligo is a chronic dermatological condition marked by the loss of skin pigmentation. Its complex etiology involves multiple factors and has not been completely elucidated. Protein post-translational modification pathways have been proven to play a significant role in inflammatory skin diseases, yet research in the context of vitiligo remains lim...
Cancer stem cells (CSCs) are a small subset of stem-like cells inside tumors, which possess abilities of unlimited self-renewal, differentiation and proliferation. Extensive studies have suggested that CSCs are one of the major drivers of tumor initiation, metastasis, relapse and therapeutic resistance. Several regulatory networks including transcr...
Motivation:
Protein phosphorylation is a ubiquitous mechanism of post-translational modification that plays a central role in cellular signaling. Phosphorylation is particularly important in the context of cancer, as down-regulation of tumor suppressors and up-regulation of oncogenes by the dysregulation of associated kinase and phosphatase networ...
The plasma membrane is a dynamic lipid bilayer that engages with the extracellular microenvironment and intracellular cytoskeleton. Caveolae are distinct plasma membrane invaginations lined by integral membrane proteins Caveolin1, 2, and 3. Caveolae formation and stability is further supported by additional proteins including Cavin1, EHD2, Pacsin2...
Calmodulin (CaM) is a highly-expressed Ca2+ binding protein known to bind hundreds of protein targets. Its binding selectivity to many of these targets is partially attributed to the protein’s flexible alpha helical linker that connects its N- and C-domains. It is not well established how its linker mediates CaM’s binding to regulatory targets yet....
Citations
... ZMPSTE24/Ste24p is a zinc metalloprotease with a distinct role in processing prelamin A in all eukaryotes and the a-factor specifically in yeast. Conversely, Rce1 demonstrates broader specificity, catalyzing the processing of all farnesylated and geranylgeranylated CAAX proteins, encompassing the a-factor in yeast and members of the Ras superfamily of small GTPases [14]. ...
... Rce1 is a member of the ABI (Abortive Infection) family of putative integral membrane proteases, which lacks paralogs in eukaryotes [14]. Although prenylation modifications are not observed in prokaryotic cells and archaebacteria, numerous Rce1p orthologs have been identified across all three domains of life [18,19]. ...
... The pair-wise identity among RCE1 orthologs varies between 14 and 27%. Despite this relatively low level of primary sequence conservation, all examined Rce1p orthologs have been found to be capable of substituting for yeast Rce1p in the maturation of the yeast a-factor mating pheromone [14,19,20]. These findings imply that the RCE family may possess conserved substrate specificity. ...
Lawsonia intracellularis , a Gram-negative obligate intracellular bacterium causing porcine proliferative enteropathy, possesses a type III secretion system (T3SS), yet only a handful of its substrates have been experimentally characterized. In this study, we identify that LI0758 can be secreted by the Yersinia T3SS, which suppresses yeast growth and activates mitogen-activated protein kinase (MAPK) and nuclear factor-kappa B (NF-κB) signaling pathway in mammalian cells. Bioinformatics analyses indicate that LI0758 is an ortholog of Rce1, a eukaryotic CAAX protein endoprotease, sharing a similar subcellular localization on the endoplasmic reticulum (ER). While displaying unique activity in the yeast a-factor reporter system, LI0758 restores Ras2 localization in Rce1Δ mutant strains, implying functional similarity. Our findings underscore LI0758’s pivotal role in activating MAPK pathways and suggest its potential to modulate the localization and function of host CAAX proteins. Further investigation holds promise for elucidating novel bacteria-host interaction mechanisms and fostering the development of innovative therapies against proliferative enteritis.
... This motif is located at the C-terminus of RAS proteins. In the ER, further processing involves cleavage of the AAX sequence from the prenylated cysteine by RAS-converting enzyme 1 (RCE1) [95], after which isoprenylcysteine is methylated by carboxyl methyltransferase (ICMT) at the liberated COOH group of cysteine [96]. Processed NRAS and HRAS then migrate to the Golgi apparatus, where they attach to the cytosolic side of the Golgi membrane. ...
The epidermal growth factor receptor (EGFR) regulates gene expression through two primary mechanisms: as a growth factor in the nucleus, where it translocates upon binding its ligand, or via its intrinsic tyrosine kinase activity in the cytosol, where it modulates key signaling pathways such as RAS/MYC, PI3K, PLCγ, and STAT3. During tumorigenesis, these pathways become deregulated, leading to uncontrolled proliferation, enhanced migratory and metastatic capabilities, evasion of programmed cell death, and resistance to chemotherapy or radiotherapy. The RAS and MYC oncogenes are pivotal in tumorigenesis, driving processes such as resistance to apoptosis, replicative immortality, cellular invasion and metastasis, and metabolic reprogramming. These oncogenes are subject to regulation by a range of epigenetic and post-transcriptional modifications. This review focuses on the deregulation of EGFR, RAS, and MYC expression caused by (epi)genetic alterations and post-translational modifications. It also explores the therapeutic potential of targeting these regulatory proteins, emphasizing the importance of phenotyping neoplastic tissues to inform the treatment of cancer.
... Rce1 plays an essential role in cancer and many infectious diseases. Therefore, it is a potential therapeutic target [15]. In contrast, MlrA is the first enzyme involved in the biodegradation of microsystins (MCs), one of the most abundant toxins associated with freshwater algal blooms [16]. ...
Glutamic proteases (GPs) represent one of the seven peptidase families described in the MEROPS database of peptidases (also known as proteases, proteinases, and proteolytic enzymes). Currently, the GP family is divided into six sub-families (G1–G6) distributed across three clans (GA, GB, and GC). A glutamic acid and another variable amino acid are the catalytic residues in this family. Members of the GP family are involved in a wide variety of biological functions. For example, they act as bacterial and plant pathogens, and are involved in cancer and celiac disease. These enzymes are considered potential drug targets given their crucial roles in numerous biological processes. Characterizing GPs provides insights into their structure–function relationships, enabling the design of specific inhibitors or modulators. Such advancements directly contribute to drug discovery by identifying novel therapeutic targets and guiding the development of potent and selective drugs for various diseases, including cancers and autoimmune disorders. To address the challenges associated with labor-intensive experimental methods, we developed GPpred, an innovative support vector machine (SVM)-based predictor to identify GPs from their primary sequences. The workflow involves systematically extracting six distinct feature sets from primary sequences, and optimization using a recursive feature elimination (RFE) algorithm to identify the most informative hybrid encodings. These optimized encodings were then used to evaluate multiple machine learning classifiers, including K-Nearest Neighbors (KNNs), Random Forest (RF), Naïve Bayes (NB), and SVM. Among these, the SVM demonstrated a consistent performance, with an accuracy of 97% during the cross-validation and independent validation. Computational methods like GPpred accelerate this process by analyzing large datasets, predicting potential enzyme targets, and prioritizing candidates for experimental validation, thereby significantly reducing time and costs. GPpred will be a valuable tool for discovering GPs from large datasets, and facilitating drug discovery efforts by narrowing down viable therapeutic candidates.
... In addition, MlrA contains ABI conserved structural domains and belongs to the CPBP family. CPBP is involved in the membrane anchoring process of CAAX in eukaryotes (Hampton et al., 2018). The hydrophobic peptides of MlrA can affect ribosome translation and destroy the cellular structure of the recombinant bacteria, affecting their growth negatively (Dziga et al., 2012;Dexter et al., 2018). ...
Microcystinase (MlrA) is a key endopeptidase that catalyzes microcystin degradation without generating harmful byproduct. However, the application of MlrA in the field is primarily impeded by its limited productivity and short lifespan. Therefore, the MlrA's function was studied by modelling its structure, which subsequently increased its heterologous expression and high-temperature stability. Results demonstrate that after the irregular sequence at the C-terminus of MlrA was removed, enzyme solubility was significantly decreased. In addition, three fusion tags, namely maltose-binding protein, glutathione S-transferase (GST), and N-utilization substance A (NusA) were used to enhance the overexpression of soluble recombinant MlrA, among which NusA-MlrA exhibited the highest solubility. Moreover, NusA-MlrA was active in pH 4-10 at 20-80 °C; even at 80 °C, approximately 35.8% of fusion protein remained active. NusA-MlrA retained 89% of MlrA's activity even after 7 d of storage at 50 °C; and on day 7, the protein retained >90% of its activity at pH 7. Finally, a stable, soluble, and long-lasting heterologous MlrA was successfully constructed that could eliminate microcystins in Escherichia coli C43 (DE3). This study enriched the comprehension of MlrA's structure and enzymatic properties, by particularly addressing the endopeptidase's low expression and short lifespan, which improved its suitability for future applications.
... MmRce1 was chosen as a model protein meant to represent eukaryotic Rce1, which localizes to the membrane of the endoplasmic reticulum (ER). Target proteins of Rce1, such as the Ras family GTPases H-Ras and K-Ras (39,40), after processing, are anchored by C-terminal lipid into the ER membrane from the cytosolic side. A conical cavity, for substrate access to the active site region of Rce1, faces the cytosolic, not the luminal side, of the ER membrane. ...
The LPXTG protein-sorting signal, found in surface proteins of various Gram-positive pathogens, was the founding member of a growing panel of prokaryotic small C-terminal sorting domains. Sortase A cleaves LPXTG, exosortases (XrtA and XrtB) cleave the PEP-CTERM sorting signal, archaeosortase A cleaves PGF-CTERM, and rhombosortase cleaves GlyGly-CTERM domains. Four sorting signal domains without previously known processing proteases are the MYXO-CTERM, JDVT-CTERM, Synerg-CTERM, and CGP-CTERM domains. These exhibit the standard tripartite architecture of a short signature motif, a hydrophobic transmembrane segment, and an Arg-rich cluster. Each has an invariant cysteine in its signature motif. Computational evidence strongly suggests that each of these four Cys-containing sorting signals is processed, at least in part, by a cognate family of glutamic-type intramembrane endopeptidases related to the eukaryotic type II CAAX-processing protease Rce1. For the MYXO-CTERM sorting signals of different lineages, their sorting enzymes, called myxosortases, include MrtX (MXAN_2755 in Myxococcus xanthus ), MrtC, and MrtP, all with radically different N-terminal domains but with a conserved core. Related predicted sorting enzymes were also identified for JDVT-CTERM (MrtJ), Synerg-CTERM (MrtS), and CGP-CTERM (MrtA). This work establishes a major new family of protein-sorting housekeeping endopeptidases contributing to the surface attachment of proteins in prokaryotes.
IMPORTANCE
Homologs of the eukaryotic type II CAAX-box protease Rce1, a membrane-embedded endopeptidase found in yeast and human ER and involved in sorting proteins to their proper cellular locations, are abundant in prokaryotes but not well understood there. This bioinformatics paper identifies several subgroups of the family as cognate endopeptidases for four protein-sorting signals processed by previously unknown machinery. Sorting signals with newly identified processing enzymes include three novel ones, but also MYXO-CTERM, which had been the focus of previous experimental work in the model fruiting and gliding bacterium Myxococcus xanthus . The new findings will substantially improve our understanding of Cys-containing C-terminal protein-sorting signals and of protein trafficking generally in bacteria and archaea.
... Such compounds are expected to have better cell permeability and be easier to synthesize compared to peptide and natural compoundbased inhibitors. However, no effective and specific Rce1 inhibitors have been identified yet (Mohammed et al., 2016;Hampton et al., 2018). ...
The term “undruggable” is to describe molecules that are not targetable or at least hard to target pharmacologically. Unfortunately, some targets with potent oncogenic activity fall into this category, and currently little is known about how to solve this problem, which largely hampered drug research on human cancers. Ras, as one of the most common oncogenes, was previously considered “undruggable”, but in recent years, a few small molecules like Sotorasib (AMG-510) have emerged and proved their targeted anti-cancer effects. Further, myc, as one of the most studied oncogenes, and tp53, being the most common tumor suppressor genes, are both considered “undruggable”. Many attempts have been made to target these “undruggable” targets, but little progress has been made yet. This article summarizes the current progress of direct and indirect targeting approaches for ras, myc, two oncogenes, and tp53, a tumor suppressor gene. These are potential therapeutic targets but are considered “undruggable”. We conclude with some emerging research approaches like proteolysis targeting chimeras (PROTACs), cancer vaccines, and artificial intelligence (AI)-based drug discovery, which might provide new cues for cancer intervention. Therefore, this review sets out to clarify the current status of targeted anti-cancer drug research, and the insights gained from this review may be of assistance to learn from experience and find new ideas in developing new chemicals that directly target such “undruggable” molecules.
... Another potential host off-target of the HIV PIs is the Ras converting CaaX endopeptidase 1 (RCE1), which is a glutamyl protease that can be classified as a member of the zinc metalloproteinase family [141,142]. RCE1 was initially identified through the total RNAsequencing of RNA from HepG2 cells treated with RTV and LPV [125]. The levels of the RCE1 protein were inhibited not only in cultured HepG2 but also in primary hepatocytes and in the liver of mice treated with the anti-HIV drugs. ...
Antiviral protease inhibitors are peptidomimetic molecules that block the active catalytic center of viral proteases and, thereby, prevent the cleavage of viral polyprotein precursors into maturation. They continue to be a key class of antiviral drugs that can be used either as boosters for other classes of antivirals or as major components of current regimens in therapies for the treatment of infections with human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, sustained/lifelong treatment with the drugs or drugs combined with other substance(s) often leads to severe hepatic side effects such as lipid abnormalities, insulin resistance, and hepatotoxicity. The underlying pathogenic mechanisms are not fully known and are under continuous investigation. This review focuses on the general as well as specific molecular mechanisms of the protease inhibitor-induced hepatotoxicity involving transporter proteins, apolipoprotein B, cytochrome P450 isozymes, insulin-receptor substrate 1, Akt/PKB signaling, lipogenic factors, UDP-glucuronosyltransferase, pregnane X receptor, hepatocyte nuclear factor 4α, reactive oxygen species, inflammatory cytokines, off-target proteases, and small GTPase Rab proteins related to ER-Golgi trafficking, organelle stress, and liver injury. Potential pharmaceutical/therapeutic solutions to antiviral drug-induced hepatic side effects are also discussed.
... Despite an objective response rate that compares favorably with historical data, efficacy of farnesyl transferase inhibitors is always transient and limited by hematological toxicities in this setting leading to dose reduction. farnesylation, HRAS undergoes a penultimate modification in the endoplasmic reticulum by the elimination of the C-terminal AAX group by RCE1 (RAS-converting Enzyme 1) [16] and the methylation of the cysteine by isoprenylcysteine carboxymethyltranseferase [17]. The HRAS protein is finally shifted to the Golgi apparatus to be palmitoylated on cysteines 181 and 184 [18]. ...
Purpose of review:
Despite recent advances, treatment personalization remains an issue for recurrent metastatic head and neck squamous cell carcinoma (RM HNSCC) patients. After human papilloma virus (HPV) and programmed death ligand 1 (PDL1) expression, Harvey rat sarcoma viral oncogene homolog (HRAS) appears as an emerging target in this field. In this review, we summarize the features of HRAS-mutated HNSCC and its targeting by farnesyl transferase inhibitors.
Recent findings:
HRAS mutations define a small subgroup of RM HNSCC patients with a poor prognosis and often refractory to the standard treatments. Posttranslational processing of HRAS being dependent on farnesylation, farnesyl transferase inhibitors have been evaluated in HRAS-mutated tumors. Tipifarnib, a first in class farnesyl transferase inhibitor, has shown efficacy in phase 2 trials with HRAS-mutated tumors. Despite reported high response rates in selected population, the efficacy of Tipifarnib is inconsistent and always transient, probably because of limiting hematological toxicities leading to dose reduction and occurrence of secondary resistance mutations.
Summary:
Tipifarnib is the first in the class of farnesyl transferase inhibitors to show efficacy in HRAS-mutated RM HNSCC. The understanding of mechanisms of resistance will pave the way for the design of second-generation farnesyl transferases inhibitors.
... Plant hormones are involved in the growth, development, ripening, and senescence of fruits. As an important regulator, hormones play a very critical role in the regulation of physiological disorders, defense, and stress responses, among other processes [17,18] . Herein, using cDNA-AFLP technology, four hormone-related genes were found to be involved in the incidence of granulation in pummelo. ...
Citrus fruits produced in China are often affected by granulation. Granulation is an altered physiological state of citrus fruits occurring usually before harvest but whose underlying mechanisms remain elusive. In this study, cDNA-AFLP technology enabled the identification of 116 granulation-associated genes in pummelo (C. grandis) juice sacs. Differentially expressed transcript-derived fragments (TDFs) were shown to be mainly involved in biological regulation and signal transduction, carbohydrate and energy metabolism, nucleic acid, protein metabolism, stress responses, and cell metabolism. Therefore, granulation in pummelo juice sacs seems to involve the following alterations: (1) changes in hormone levels; (2) activation of metabolic pathways related to ATP and sugar synthesis to produce more energy; (3) nucleic acid accumulation and increased protein degradation; (4) activation of stress-responsive metabolic pathways; (5) accelerated juice sac senescence. Our findings provide an overview of differential responses occurring at the transcriptional level in granulated juice sacs, thus revealing new insights into the adaptive mechanisms underlying this altered physiological state in 'Guanximiyou' pummelo (C. grandis) juice sacs.
... Farnesyltransferase (FTase) and geranylgeranyltransferase-I (GGTase-I) facilitate the isoprenoid addition to the CaaX cysteine thiol, with GGTase-I targeting the subset of CaaX sequences having Leu, Phe or Met at the X position [2][3][4]. For many CaaX proteins, initial isoprenylation is followed by proteolysis that removes the aaX tripeptide, mediated by Rce1p or Ste24p, and carboxymethylation of the isoprenylated cysteine, mediated by isoprenylcysteine carboxyl methyltransferase (ICMT; Ste14p in yeast) [5]. These modifications increase the overall COOH-terminal hydrophobicity of modified proteins and often occur to CaaX proteins well-known to be membrane associated (e.g., Ras GTPases) ( Fig 1A). ...
Protein prenylation by farnesyltransferase (FTase) is often described as the targeting of a cysteine-containing motif (CaaX) that is enriched for aliphatic amino acids at the a1 and a2 positions, while quite flexible at the X position. Prenylation prediction methods often rely on these features despite emerging evidence that FTase has broader target specificity than previously considered. Using a machine learning approach and training sets based on canonical (prenylated, proteolyzed, and carboxymethylated) and recently identified shunted motifs (prenylation only), this study aims to improve prenylation predictions with the goal of determining the full scope of prenylation potential among the 8000 possible Cxxx sequence combinations. Further, this study aims to subdivide the prenylated sequences as either shunted (i.e., uncleaved) or cleaved (i.e., canonical). Predictions were determined for Saccharomyces cerevisiae FTase and compared to results derived using currently available prenylation prediction methods. In silico predictions were further evaluated using in vivo methods coupled to two yeast reporters, the yeast mating pheromone a-factor and Hsp40 Ydj1p, that represent proteins with canonical and shunted CaaX motifs, respectively. Our machine learning-based approach expands the repertoire of predicted FTase targets and provides a framework for functional classification.