Changes in Proteolysis in Fermented Milk Produced by Streptococcus Thermophilus in Co-Culture with Lactobacillus Plantarum Or Bifidobacterium Animalis Subsp
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Characterisation of Aspergillus Niger Prolyl Aminopeptidase
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Wageningen University & Research Publications Mol Gen Genomics (2005) 272: 673–679 DOI 10.1007/s00438-004-1094-5 ORIGINAL PAPER Danie¨lle E. J. W. Basten Æ Antoine P. H. A. Moers Albert J. J. van. Ooyen Æ Peter J. Schaap Characterisation of Aspergillus niger prolyl aminopeptidase Received: 29 April 2004 / Accepted: 16 November 2004 / Published online: 15 January 2005 Ó Springer-Verlag 2005 Abstract We have cloned a gene (papA) that encodes a ases and tripeptidases and finally by carboxypeptidases prolyl aminopeptidase from Aspergillus niger. Homolo- and aminopeptidases. The turnover of proteins by pro- gous genes are present in the genomes of the Eurotiales teases provides a ready pool of amino acids as precur- A. nidulans, A. fumigatus and Talaromyces emersonii, sors for the synthesis of new proteins (Bennet and Klich but the gene is not present in the genome of the yeast 1992). Saccharomyces cerevisiae. Cell extracts of strains over- Proteases normally do not hydrolyse bonds adjacent expressing the gene under the control of its own pro- to proline residues. Instead a specialised group of en- moter showed a fourfold to sixfold increase in prolyl zymes has evolved that hydrolyses these bonds. Their aminopeptidase activity, but no change in phenylalanine activity depends on both the isomeric state of the proline or leucine aminopeptidase activity. The overexpressed residue and its position in the peptide chain (Vanhoof enzyme was subsequently purified and characterised. et al. 1995; Cunningham and O’Connor 1997). Proline The enzyme specifically removes N-terminal proline and aminopeptidases (Pap, prolyl iminopeptidase, EC hydroxyproline residues from peptides. -
Ubiquitin-Mediated Proteolysis the Nobel Prize in Chemistry for 2004 Is
Advanced information on the Nobel Prize in Chemistry, 6 October 2004 Information Department, P.O. Box 50005, SE-104 05 Stockholm, Sweden Phone: +46 8 673 95 00, Fax: +46 8 15 56 70, E-mail: [email protected], Website: www.kva.se Ubiquitin-mediated proteolysis The Nobel Prize in Chemistry for 2004 is shared between three scientists who have made fundamental discoveries concerning how cells regulate the breakdown of intracellular proteins with extreme specificity as to target, time and space. Aaron Ciechanover, Avram Hershko and Irwin Rose together discovered ubiquitin- mediated proteolysis, a process where an enzyme system tags unwanted proteins with many molecules of the 76-amino acid residue protein ubiquitin. The tagged proteins are then transported to the proteasome, a large multisubunit protease complex, where they are degraded. Numerous cellular processes regulated by ubiquitin-mediated proteolysis include the cell cycle, DNA repair and transcription, protein quality control and the immune response. Defects in this proteolysis have a causal role in many human diseases, including a variety of cancers. Fig. 1 Ubiquitin-mediated proteolysis and its many biological functions 2 Introduction Eukaryotic cells, from yeast to human, contain some 6000 to 30000 protein-encoding genes and at least as many proteins. While much attention and research had been devoted to how proteins are synthesized, the reverse process, i.e. how proteins are degraded, long received little attention. A pioneer in this field was Schoenheimer, who in 1942 published results from isotope tracer techniques indicating that proteins in animals are continuously synthesized and degraded and therefore are in a dynamic state (Schoenheimer, 1942). -
Methionine Aminopeptidase Emerging Role in Angiogenesis
Chapter 2 Methionine Aminopeptidase Emerging role in angiogenesis Joseph A. Vetro1, Benjamin Dummitt2, and Yie-Hwa Chang2 1Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Ave., Lawrence, KS 66047, USA. 2Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Health Sciences Center, 1402 S. Grand Blvd., St. Louis, MO 63104, USA. Abstract: Angiogenesis, the formation of new blood vessels from existing vasculature, is a key factor in a number of vascular-related pathologies such as the metastasis and growth of solid tumors. Thus, the inhibition of angiogenesis has great potential as a therapeutic modality in the treatment of cancer and other vascular-related diseases. Recent evidence suggests that the inhibition of mammalian methionine aminopeptidase type 2 (MetAP2) catalytic activity in vascular endothelial cells plays an essential role in the pharmacological activity of the most potent small molecule angiogenesis inhibitors discovered to date, the fumagillin class. Methionine aminopeptidase (MetAP, EC 3.4.11.18) catalyzes the non-processive, co-translational hydrolysis of initiator N-terminal methionine when the second residue of the nascent polypeptide is small and uncharged. Initiator Met removal is a ubiquitous and essential modification. Indirect evidence suggests that removal of initiator Met by MetAP is important for the normal function of many proteins involved in DNA repair, signal transduction, cell transformation, secretory vesicle trafficking, and viral capsid assembly and infection. Currently, much effort is focused on understanding the essential nature of methionine aminopeptidase activity and elucidating the role of methionine aminopeptidase type 2 catalytic activity in angiogenesis. In this chapter, we give an overview of the MetAP proteins, outline the importance of initiator Met hydrolysis, and discuss the possible mechanism(s) through which MetAP2 inhibition by the fumagillin class of angiogenesis inhibitors leads to cytostatic growth arrest in vascular endothelial cells. -
Insights Into Clpxp Proteolysis: Heterooligomerization and Partial Deactivation Cite This: Chem
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Insights into ClpXP proteolysis: heterooligomerization and partial deactivation Cite this: Chem. Sci.,2017,8,1592 enhance chaperone affinity and substrate turnover in Listeria monocytogenes† a a a b a Dora´ Balogh,‡ Maria Dahmen,‡ Matthias Stahl, Marcin Poreba, Malte Gersch,§ Marcin Dragb and Stephan A. Sieber*a Caseinolytic proteases (ClpP) are important for recognition and controlled degradation of damaged proteins. While the majority of bacterial organisms utilize only a single ClpP, Listeria monocytogenes expresses two isoforms (LmClpP1 and LmClpP2). LmClpPs assemble into either a LmClpP2 homocomplex or a LmClpP1/2 heterooligomeric complex. The heterocomplex in association with the chaperone ClpX, exhibits a boost in proteolytic activity for unknown reasons. Here, we use a combined chemical and biochemical strategy to unravel two activation principles of LmClpPs. First, determination Creative Commons Attribution 3.0 Unported Licence. of apparent affinity constants revealed a 7-fold elevated binding affinity between the LmClpP1/2 heterocomplex and ClpX, compared to homooligomeric LmClpP2. This tighter interaction favors the formation of the proteolytically active complex between LmClpX and LmClpP1/2 and thereby accelerating the overall turnover. Second, screening a diverse library of fluorescent labeled peptides and proteins with various ClpP mutants allowed the individual analysis of substrate preferences for both isoforms within the heterocomplex. In addition to Leu and Met, LmClpP2 preferred a long aliphatic chain (2-Aoc) in the P1 position for cleavage. Strikingly, design and synthesis of a corresponding 2-Aoc chloromethyl ketone inhibitor resulted in stimulation of proteolysis by 160% when LmClpP2 was partially Received 2nd August 2016 This article is licensed under a alkylated on 20% of the active sites. -
Regulated Proteolysis of a Cross-Link–Specific Peptidoglycan Hydrolase Contributes to Bacterial Morphogenesis
Regulated proteolysis of a cross-link–specific peptidoglycan hydrolase contributes to bacterial morphogenesis Santosh Kumar Singh1, Sadiya Parveen, L SaiSree, and Manjula Reddy2 Centre for Cellular and Molecular Biology, Hyderabad, India 500007 Edited by Joe Lutkenhaus, University of Kansas Medical Center, Kansas City, KS, and approved July 27, 2015 (received for review April 21, 2015) Bacterial growth and morphogenesis are intimately coupled to ex- (4, 5). The TP activity of PBP1a and PBP1b is activated, respec- pansion of peptidoglycan (PG), an extensively cross-linked macro- tively, by their cognate lipoprotein cofactors LpoA and LpoB, molecule that forms a protective mesh-like sacculus around the located in the outer membrane (6, 7). cytoplasmic membrane. Growth of the PG sacculus is a dynamic Given that the interconnecting peptide bridges in the PG sac- event requiring the concerted action of hydrolases that cleave the culus need to be cleaved for the insertion of new murein material, cross-links for insertion of new material and synthases that catalyze hydrolytic enzymes with such activity are expected to be critical for cross-link formation; however, the factors that regulate PG expan- PG expansion and thus for bacterial viability (2, 3, 8). Essential sion during bacterial growth are poorly understood. Here, we show cross-link–specific hydrolases have recently been identified in both that the PG hydrolase MepS (formerly Spr), which is specific to cleav- Gram-positive and -negative bacteria (9–13). E. coli possesses age of cross-links during PG expansion in Escherichia coli, is modulated several hydrolytic enzymes specific for D-ala−mDAP cross-links by proteolysis. -
1 No. Affymetrix ID Gene Symbol Genedescription Gotermsbp Q Value 1. 209351 at KRT14 Keratin 14 Structural Constituent of Cyto
1 Affymetrix Gene Q No. GeneDescription GOTermsBP ID Symbol value structural constituent of cytoskeleton, intermediate 1. 209351_at KRT14 keratin 14 filament, epidermis development <0.01 biological process unknown, S100 calcium binding calcium ion binding, cellular 2. 204268_at S100A2 protein A2 component unknown <0.01 regulation of progression through cell cycle, extracellular space, cytoplasm, cell proliferation, protein kinase C inhibitor activity, protein domain specific 3. 33323_r_at SFN stratifin/14-3-3σ binding <0.01 regulation of progression through cell cycle, extracellular space, cytoplasm, cell proliferation, protein kinase C inhibitor activity, protein domain specific 4. 33322_i_at SFN stratifin/14-3-3σ binding <0.01 structural constituent of cytoskeleton, intermediate 5. 201820_at KRT5 keratin 5 filament, epidermis development <0.01 structural constituent of cytoskeleton, intermediate 6. 209125_at KRT6A keratin 6A filament, ectoderm development <0.01 regulation of progression through cell cycle, extracellular space, cytoplasm, cell proliferation, protein kinase C inhibitor activity, protein domain specific 7. 209260_at SFN stratifin/14-3-3σ binding <0.01 structural constituent of cytoskeleton, intermediate 8. 213680_at KRT6B keratin 6B filament, ectoderm development <0.01 receptor activity, cytosol, integral to plasma membrane, cell surface receptor linked signal transduction, sensory perception, tumor-associated calcium visual perception, cell 9. 202286_s_at TACSTD2 signal transducer 2 proliferation, membrane <0.01 structural constituent of cytoskeleton, cytoskeleton, intermediate filament, cell-cell adherens junction, epidermis 10. 200606_at DSP desmoplakin development <0.01 lectin, galactoside- sugar binding, extracellular binding, soluble, 7 space, nucleus, apoptosis, 11. 206400_at LGALS7 (galectin 7) heterophilic cell adhesion <0.01 2 S100 calcium binding calcium ion binding, epidermis 12. 205916_at S100A7 protein A7 (psoriasin 1) development <0.01 S100 calcium binding protein A8 (calgranulin calcium ion binding, extracellular 13. -
Amidoligases with ATP-Grasp, Glutamine Synthetase-Like and Acetyltransferase-Like Domains: Synthesis of Novel Metabolites and Peptide Modifications of Proteinswz
View Article Online / Journal Homepage / Table of Contents for this issue Molecular BioSystems This article was published as part of the Computational and Systems Biology themed issue Please take a look at the full table of contents to access the other papers in this issue. Open Access Article. Published on 13 October 2009. Downloaded 9/27/2021 9:23:51 AM. View Article Online PAPER www.rsc.org/molecularbiosystems | Molecular BioSystems Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteinswz Lakshminarayan M. Iyer,a Saraswathi Abhiman,a A. Maxwell Burroughsb and L. Aravind*a Received 28th August 2009, Accepted 28th August 2009 First published as an Advance Article on the web 13th October 2009 DOI: 10.1039/b917682a Recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. Preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. Following up on these observations, we systematically investigated the non-ribosomal amidoligases of the ATP-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the known members and identifying novel versions. We then established their contextual connections using information from domain architectures and conserved gene neighborhoods. This showed remarkable, previously uncharacterized functional links between diverse peptide ligases, several peptidases of unrelated folds and enzymes involved in synthesis of modified amino acids. Using the network of contextual connections we were able to predict numerous novel pathways for peptide synthesis and modification, amine-utilization, secondary metabolite synthesis and potential peptide-tagging systems. -
Table S3. Bootstrapped Frequency of COG Occurrences for Specific Metabolic Processes Encoded in the Antarctic Bacterioplankton Environmental Genomes
Table S3. Bootstrapped frequency of COG occurrences for specific metabolic processes encoded in the Antarctic bacterioplankton environmental genomes. Category COG Predicted Protein WEG SEG Inorganic carbon COG1850 Ribulose 1,5-bisphosphate carboxylase, large subunit 4.34 0.85 COG4451 Ribulose bisphosphate carboxylase small subunit 1.19 0.83 COG0574 Phosphoenolpyruvate synthase/pyruvate phosphate dikinase 13.7 6.63 COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit 7.91 4.85 Sulfur Metabolism (inorganic) COG2897 Rhodanese-related sulfurtransferase 5.64 3.25 COG0607 Rhodanese-related sulfurtransferase 6.02 5.68 COG2895 GTPases - Sulfate adenylate transferase subunit 1 2.28 4.88 COG1054 Predicted sulfurtransferase 2.53 4.17 COG0306 Phosphate/sulphate permeases 7.56 3.27 COG0659 Sulfate permease and related transporters (MFS superfamily) 15.72 15.22 COG0529 Adenylylsulfate kinase and related kinases 1.98 4.16 COG0225 Peptide methionine sulfoxide reductase 7.03 3.22 COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase 3.77 2.47 COG0641 Arylsulfatase regulator (Fe-S oxidoreductase) 0.67 0 COG0526 Thiol-disulfide isomerase and thioredoxins 6.99 4.12 COG1651 Protein-disulfide isomerase 10.75 1.65 COG2041 Sulfite oxidase and related enzymes 5.51 3.05 COG2046 ATP sulfurylase (sulfate adenylyltransferase) 4.34 3.46 COG2221 Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits 1.21 0 COG2920 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit 1.9 0 COG0155 Sulfite reductase, -
Protacs: Chimeric Molecules That Target Proteins to the Skp1–Cullin–F Box Complex for Ubiquitination and Degradation
Protacs: Chimeric molecules that target proteins to the Skp1–Cullin–F box complex for ubiquitination and degradation Kathleen M. Sakamoto*†‡, Kyung B. Kim§, Akiko Kumagai†, Frank Mercurio¶, Craig M. Crews§, and Raymond J. Deshaies†‡ʈ *Department of Pediatrics and Pathology, Mattel Children’s Hospital at University of California Los Angeles, University of California Los Angeles School of Medicine, Gwynn Hazen Cherry Memorial Laboratories, and Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095-1752; †Division of Biology, and ʈHoward Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125; §Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520; and ¶Signal Division, Celgene Pharmaceuticals, La Jolla, CA 92121 Communicated by Alexander Varshavsky, California Institute of Technology, Pasadena, CA, May 10, 2001 (received for review March 29, 2001) The intracellular levels of many proteins are regulated by ubiq- to be the primary target of the potent angiogenesis inhibitors uitin-dependent proteolysis. One of the best-characterized en- fumagillin and ovalicin (OVA; refs. 7 and 8). Both of these zymes that catalyzes the attachment of ubiquitin to proteins is a compounds inhibit MetAP-2 by covalently binding His-231 in the ubiquitin ligase complex, Skp1-Cullin-F box complex containing active site. The consequent reduction in MetAP-2 activity is Hrt1 (SCF). We sought to artificially target a protein to the SCF thought to block endothelial cell proliferation by causing p53- complex for ubiquitination and degradation. To this end, we tested dependent arrest in the G1 phase of the cell cycle (9). Impor- methionine aminopeptidase-2 (MetAP-2), which covalently binds tantly, MetAP-2 is not known to be ubiquitinated or a substrate the angiogenesis inhibitor ovalicin. -
Proteolytic Cleavage—Mechanisms, Function
Review Cite This: Chem. Rev. 2018, 118, 1137−1168 pubs.acs.org/CR Proteolytic CleavageMechanisms, Function, and “Omic” Approaches for a Near-Ubiquitous Posttranslational Modification Theo Klein,†,⊥ Ulrich Eckhard,†,§ Antoine Dufour,†,¶ Nestor Solis,† and Christopher M. Overall*,†,‡ † ‡ Life Sciences Institute, Department of Oral Biological and Medical Sciences, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada ABSTRACT: Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein’s structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissuefrom 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C- termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms -
The Amyloid-β Pathway in Alzheimer’S Disease
Molecular Psychiatry www.nature.com/mp REVIEW ARTICLE OPEN The Amyloid-β Pathway in Alzheimer’s Disease ✉ Harald Hampel 1 , John Hardy2, Kaj Blennow3,4, Christopher Chen 5, George Perry 6, Seung Hyun Kim7, 8,9 10 11 12 13 1 14,15 Victor L. Villemagne , Paul Aisen , Michele✉ Vendruscolo , Takeshi Iwatsubo , Colin L. Masters , Min Cho , Lars Lannfelt , Jeffrey L. Cummings16 and Andrea Vergallo 1 © The Author(s) 2021 Breakthroughs in molecular medicine have positioned the amyloid-β (Aβ) pathway at the center of Alzheimer’s disease (AD) pathophysiology. While the detailed molecular mechanisms of the pathway and the spatial-temporal dynamics leading to synaptic failure, neurodegeneration, and clinical onset are still under intense investigation, the established biochemical alterations of the Aβ cycle remain the core biological hallmark of AD and are promising targets for the development of disease-modifying therapies. Here, we systematically review and update the vast state-of-the-art literature of Aβ science with evidence from basic research studies to human genetic and multi-modal biomarker investigations, which supports a crucial role of Aβ pathway dyshomeostasis in AD pathophysiological dynamics. We discuss the evidence highlighting a differentiated interaction of distinct Aβ species with other AD-related biological mechanisms, such as tau-mediated, neuroimmune and inflammatory changes, as well as a neurochemical imbalance. Through the lens of the latest development of multimodal in vivo biomarkers of AD, this cross- disciplinary review examines the compelling hypothesis- and data-driven rationale for Aβ-targeting therapeutic strategies in development for the early treatment of AD. Molecular Psychiatry; https://doi.org/10.1038/s41380-021-01249-0 INTRODUCTION neuronal loss and ultimately clinical manifestations by up to 20–30 Alzheimer’s disease (AD) is the primary cause of dementia, years [6]. -
Intrinsic Evolutionary Constraints on Protease Structure, Enzyme
Intrinsic evolutionary constraints on protease PNAS PLUS structure, enzyme acylation, and the identity of the catalytic triad Andrew R. Buller and Craig A. Townsend1 Departments of Biophysics and Chemistry, The Johns Hopkins University, Baltimore MD 21218 Edited by David Baker, University of Washington, Seattle, WA, and approved January 11, 2013 (received for review December 6, 2012) The study of proteolysis lies at the heart of our understanding of enzyme evolution remain unanswered. Because evolution oper- biocatalysis, enzyme evolution, and drug development. To un- ates through random forces, rationalizing why a particular out- derstand the degree of natural variation in protease active sites, come occurs is a difficult challenge. For example, the hydroxyl we systematically evaluated simple active site features from all nucleophile of a Ser protease was swapped for the thiol of Cys at serine, cysteine and threonine proteases of independent lineage. least twice in evolutionary history (9). However, there is not This convergent evolutionary analysis revealed several interre- a single example of Thr naturally substituting for Ser in the lated and previously unrecognized relationships. The reactive protease catalytic triad, despite its greater chemical similarity rotamer of the nucleophile determines which neighboring amide (9). Instead, the Thr proteases generate their N-terminal nu- can be used in the local oxyanion hole. Each rotamer–oxyanion cleophile through a posttranslational modification: cis-autopro- hole combination limits the location of the moiety facilitating pro- teolysis (10, 11). These facts constitute clear evidence that there ton transfer and, combined together, fixes the stereochemistry of is a strong selective pressure against Thr in the catalytic triad that catalysis.