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Lyons PJ. Inactive metallopeptidase homologs: the secret lives of pseudopeptidases. Front Mol Biosci 2024; 11:1436917. [PMID: 39050735 PMCID: PMC11266112 DOI: 10.3389/fmolb.2024.1436917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Inactive enzyme homologs, or pseudoenzymes, are proteins, found within most enzyme families, that are incapable of performing catalysis. Rather than catalysis, they are involved in protein-protein interactions, sometimes regulating the activity of their active enzyme cousins, or scaffolding protein complexes. Pseudoenzymes found within metallopeptidase families likewise perform these functions. Pseudoenzymes within the M14 carboxypeptidase family interact with collagens within the extracellular space, while pseudopeptidase members of the M12 "a disintegrin and metalloprotease" (ADAM) family either discard their pseudopeptidase domains as unnecessary for their roles in sperm maturation or utilize surface loops to enable assembly of key complexes at neuronal synapses. Other metallopeptidase families contain pseudopeptidases involved in protein synthesis at the ribosome and protein import into organelles, sometimes using their pseudo-active sites for these interactions. Although the functions of these pseudopeptidases have been challenging to study, ongoing work is teasing out the secret lives of these proteins.
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Affiliation(s)
- Peter J. Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, United States
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2
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Verma RK, Roman-Reyna V, Raanan H, Coaker G, Jacobs JM, Teper D. Allelic variations in the chpG effector gene within Clavibacter michiganensis populations determine pathogen host range. PLoS Pathog 2024; 20:e1012380. [PMID: 39028765 PMCID: PMC11290698 DOI: 10.1371/journal.ppat.1012380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 07/31/2024] [Accepted: 06/27/2024] [Indexed: 07/21/2024] Open
Abstract
Plant pathogenic bacteria often have a narrow host range, which can vary among different isolates within a population. Here, we investigated the host range of the tomato pathogen Clavibacter michiganensis (Cm). We determined the genome sequences of 40 tomato Cm isolates and screened them for pathogenicity on tomato and eggplant. Our screen revealed that out of the tested isolates, five were unable to cause disease on any of the hosts, 33 were exclusively pathogenic on tomato, and two were capable of infecting both tomato and eggplant. Through comparative genomic analyses, we identified that the five non-pathogenic isolates lacked the chp/tomA pathogenicity island, which has previously been associated with virulence in tomato. In addition, we found that the two eggplant-pathogenic isolates encode a unique allelic variant of the putative serine hydrolase chpG (chpGC), an effector that is recognized in eggplant. Introduction of chpGC into a chpG inactivation mutant in the eggplant-non-pathogenic strain Cm101, failed to complement the mutant, which retained its ability to cause disease in eggplant and failed to elicit hypersensitive response (HR). Conversely, introduction of the chpG variant from Cm101 into an eggplant pathogenic Cm isolate (C48), eliminated its pathogenicity on eggplant, and enabled C48 to elicit HR. Our study demonstrates that allelic variation in the chpG effector gene is a key determinant of host range plasticity within Cm populations.
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Affiliation(s)
- Raj Kumar Verma
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Volcani Institute, Rishon LeZion, Israel
| | - Veronica Roman-Reyna
- Dept. Of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Hagai Raanan
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Gilat Research Center, Negev, Israel
| | - Gitta Coaker
- Dept. of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Jonathan M. Jacobs
- Dept. of Plant Pathology, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Doron Teper
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Volcani Institute, Rishon LeZion, Israel
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3
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Zhiganov NI, Vinokurov KS, Salimgareev RS, Tereshchenkova VF, Dunaevsky YE, Belozersky MA, Elpidina EN. The Set of Serine Peptidases of the Tenebrio molitor Beetle: Transcriptomic Analysis on Different Developmental Stages. Int J Mol Sci 2024; 25:5743. [PMID: 38891931 PMCID: PMC11172050 DOI: 10.3390/ijms25115743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Serine peptidases (SPs) of the chymotrypsin S1A subfamily are an extensive group of enzymes found in all animal organisms, including insects. Here, we provide analysis of SPs in the yellow mealworm Tenebrio molitor transcriptomes and genomes datasets and profile their expression patterns at various stages of ontogeny. A total of 269 SPs were identified, including 137 with conserved catalytic triad residues, while 125 others lacking conservation were proposed as non-active serine peptidase homologs (SPHs). Seven deduced sequences exhibit a complex domain organization with two or three peptidase units (domains), predicted both as active or non-active. The largest group of 84 SPs and 102 SPHs had no regulatory domains in the propeptide, and the majority of them were expressed only in the feeding life stages, larvae and adults, presumably playing an important role in digestion. The remaining 53 SPs and 23 SPHs had different regulatory domains, showed constitutive or upregulated expression at eggs or/and pupae stages, participating in regulation of various physiological processes. The majority of polypeptidases were mainly expressed at the pupal and adult stages. The data obtained expand our knowledge on SPs/SPHs and provide the basis for further studies of the functions of proteins from the S1A subfamily in T. molitor.
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Affiliation(s)
- Nikita I. Zhiganov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
| | - Konstantin S. Vinokurov
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budejovice, Czech Republic;
| | - Ruslan S. Salimgareev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia;
| | | | - Yakov E. Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
| | - Mikhail A. Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
| | - Elena N. Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (N.I.Z.); (Y.E.D.); (M.A.B.)
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4
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Claushuis B, Cordfunke RA, de Ru AH, van Angeren J, Baumann U, van Veelen PA, Wuhrer M, Corver J, Drijfhout JW, Hensbergen PJ. Non-prime- and prime-side profiling of Pro-Pro endopeptidase specificity using synthetic combinatorial peptide libraries and mass spectrometry. FEBS J 2024. [PMID: 38767318 DOI: 10.1111/febs.17160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
A group of bacterial proteases, the Pro-Pro endopeptidases (PPEPs), possess the unique ability to hydrolyze proline-proline bonds in proteins. Since a protease's function is largely determined by its substrate specificity, methods that can extensively characterize substrate specificity are valuable tools for protease research. Previously, we achieved an in-depth characterization of PPEP prime-side specificity. However, PPEP specificity is also determined by the non-prime-side residues in the substrate. To gain a more complete insight into the determinants of PPEP specificity, we characterized the non-prime- and prime-side specificity of various PPEPs using a combination of synthetic combinatorial peptide libraries and mass spectrometry. With this approach, we deepened our understanding of the P3-P3' specificities of PPEP-1 and PPEP-2, while identifying the endogenous substrate of PPEP-2 as the most optimal substrate in our library data. Furthermore, by employing the library approach, we investigated the altered specificity of mutants of PPEP-1 and PPEP-2. Additionally, we characterized a novel PPEP from Anoxybacillus tepidamans, which we termed PPEP-4. Based on structural comparisons, we hypothesized that PPEP-4 displays a PPEP-1-like prime-side specificity, which was substantiated by the experimental data. Intriguingly, another putative PPEP from Clostridioides difficile, CD1597, did not display Pro-Pro endoproteolytic activity. Collectively, we characterized PPEP specificity in detail using our robust peptide library method and, together with additional structural information, provide more insight into the intricate mechanisms that govern protease specificity.
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Affiliation(s)
- Bart Claushuis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Robert A Cordfunke
- Department of Immunology, Leiden University Medical Center, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Jordy van Angeren
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Germany
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Jeroen Corver
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, The Netherlands
| | - Jan W Drijfhout
- Department of Immunology, Leiden University Medical Center, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
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5
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Duran Ş, Üstüntanir Dede AF, Dündar Orhan Y, Arslanyolu M. Genome-wide identification and in-silico analysis of papain-family cysteine protease encoding genes in Tetrahymena thermophila. Eur J Protistol 2024; 92:126033. [PMID: 38088016 DOI: 10.1016/j.ejop.2023.126033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/06/2023] [Accepted: 11/02/2023] [Indexed: 02/06/2024]
Abstract
Tetrahymena thermophila is a promising host for recombinant protein production, but its utilization in biotechnology is mostly limited due to the presence of intracellular and extracellular papain-family cysteine proteases (PFCPs). In this study, we employed bioinformatics approaches to investigate the T. thermophila PFCP genes and their encoded proteases (TtPFCPs), the most prominent protease family in the genome. Results from the multiple sequence alignment, protein modeling, and conserved motif analyses revealed that all TtPFCPs showed considerably high homology with mammalian cysteine cathepsins and contained conserved amino acid motifs. The total of 121 TtPFCP-encoding genes, 14 of which were classified as non-peptidase homologs, were found. Remaining 107 true TtPFCPs were divided into four distinct subgroups depending on their homology with mammalian lysosomal cathepsins: cathepsin L-like (TtCATLs), cathepsin B-like (TtCATBs), cathepsin C-like (TtCATCs), and cathepsin X-like (TtCATXs) PFCPs. The majority of true TtPFCPs (96 out of the total) were in TtCATL-like peptidase subgroup. Both phylogenetic and chromosomal localization analyses of TtPFCPs supported the hypothesis that TtPFCPs likely evolved through tandem gene duplication events and predominantly accumulated on micronuclear chromosome 5. Additionally, more than half of the identified TtPFCP genes are expressed in considerably low quantities compared to the rest of the TtPFCP genes, which are expressed at a higher level. However, their expression patterns fluctuate based on the stage of the life cycle. In conclusion, this study provides the first comprehensive in-silico analysis of TtPFCP genes and encoded proteases. The results would help designing an effective strategy for protease knockout mutant cell lines to discover biological function and to improve the recombinant protein production in T. thermophila.
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Affiliation(s)
- Şeyma Duran
- Department of Molecular Biology, Graduate School of Sciences, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Türkiye.
| | - Ayça Fulya Üstüntanir Dede
- Department of Molecular Biology, Graduate School of Sciences, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Türkiye.
| | - Yeliz Dündar Orhan
- Department of Advanced Technologies, Graduate School of Sciences, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Türkiye.
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskişehir 26470, Türkiye.
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6
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Chua W, Marsh CO, Poh SE, Koh WL, Lee MLY, Koh LF, Tang XZE, See P, Ser Z, Wang SM, Sobota RM, Dawson TL, Yew YW, Thng S, O'Donoghue AJ, Oon HH, Common JE, Li H. A Malassezia pseudoprotease dominates the secreted hydrolase landscape and is a potential allergen on skin. Biochimie 2024; 216:181-193. [PMID: 37748748 DOI: 10.1016/j.biochi.2023.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Malassezia globosa is abundant and prevalent on sebaceous areas of the human skin. Genome annotation reveals that M. globosa possesses a repertoire of secreted hydrolytic enzymes relevant for lipid and protein metabolism. However, the functional significance of these enzymes is uncertain and presence of these genes in the genome does not always translate to expression at the cutaneous surface. In this study we utilized targeted RNA sequencing from samples isolated directly from the skin to quantify gene expression of M. globosa secreted proteases, lipases, phospholipases and sphingomyelinases. Our findings indicate that the expression of these enzymes is dynamically regulated by the environment in which the fungus resides, as different growth phases of the planktonic culture of M. globosa show distinct expression levels. Furthermore, we observed significant differences in the expression of these enzymes in culture compared to healthy sebaceous skin sites. By examining the in situ gene expression of M. globosa's secreted hydrolases, we identified a predicted aspartyl protease, MGL_3331, which is highly expressed on both healthy and disease-affected dermatological sites. However, molecular modeling and biochemical studies revealed that this protein has a non-canonical active site motif and lacks measurable proteolytic activity. This pseudoprotease MGL_3331 elicits a heightened IgE-reactivity in blood plasma isolated from patients with atopic dermatitis compared to healthy individuals and invokes a pro-inflammatory response in peripheral blood mononuclear cells. Overall, our study highlights the importance of studying fungal proteins expressed in physiologically relevant environments and underscores the notion that secreted inactive enzymes may have important functions in influencing host immunity.
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Affiliation(s)
- Wisely Chua
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Carl O Marsh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Si En Poh
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Winston Lc Koh
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Melody Li Ying Lee
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Li Fang Koh
- A∗STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, 138648, Singapore
| | - Xin-Zi Emily Tang
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Peter See
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Shi Mei Wang
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Thomas L Dawson
- A∗STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, 138648, Singapore; College of Pharmacy, Department of Drug Discovery, Medical University of South Carolina, USA
| | - Yik Weng Yew
- National Skin Centre, National Healthcare Group, 1 Mandalay Rd, 308205, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - Steven Thng
- National Skin Centre, National Healthcare Group, 1 Mandalay Rd, 308205, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - Hazel H Oon
- National Skin Centre, National Healthcare Group, 1 Mandalay Rd, 308205, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - John E Common
- A∗STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, 138648, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - Hao Li
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
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Florin-Christensen M, Sojka D, Ganzinelli S, Šnebergerová P, Suarez CE, Schnittger L. Degrade to survive: the intricate world of piroplasmid proteases. Trends Parasitol 2023; 39:532-546. [PMID: 37271664 DOI: 10.1016/j.pt.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 06/06/2023]
Abstract
Piroplasmids of the genera Babesia, Theileria, and Cytauxzoon are tick-transmitted parasites with a high impact on animals and humans. They have complex life cycles in their definitive arthropod and intermediate vertebrate hosts involving numerous processes, including invasion of, and egress from, host cells, parasite growth, transformation, and migration. Like other parasitic protozoa, piroplasmids are equipped with different types of protease to fulfill many of such essential processes. Blockade of some key proteases, using inhibitors or antibodies, hinders piroplasmid growth, highlighting their potential usefulness in drug therapies and vaccine development. A better understanding of the functional significance of these enzymes will contribute to the development of improved control measures for the devastating animal and human diseases caused by these pathogens.
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Affiliation(s)
- Monica Florin-Christensen
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham 1686, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina.
| | - Daniel Sojka
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Branišovská 1160/31, CZ-37005 České Budějovice, Czech Republic
| | - Sabrina Ganzinelli
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham 1686, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Pavla Šnebergerová
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Branišovská 1160/31, CZ-37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, CZ-370 05 České Budějovice, Czech Republic
| | - Carlos E Suarez
- Washington State University/Animal Disease Research Unit USDA, Pullman, WA, USA
| | - Leonhard Schnittger
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham 1686, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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Comparative Degradome Analysis of the Bovine Piroplasmid Pathogens Babesia bovis and Theileria annulata. Pathogens 2023; 12:pathogens12020237. [PMID: 36839509 PMCID: PMC9965338 DOI: 10.3390/pathogens12020237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Babesia bovis and Theileria annulata are tick-borne hemoprotozoans that impact bovine health and are responsible for considerable fatalities in tropical and subtropical regions around the world. Both pathogens infect the same vertebrate host, are closely related, and contain similar-sized genomes; however, they differ in invertebrate host specificity, absence vs. presence of a schizont stage, erythrocyte invasion mechanism, and transovarial vs. transstadial transmission. Phylogenetic analysis and bidirectional best hit (BBH) identified a similar number of aspartic, metallo, and threonine proteinases and nonproteinase homologs. In contrast, a considerably increased number of S54 serine rhomboid proteinases and S9 nonproteinase homologs were identified in B. bovis, whereas C1A cysteine proteinases and A1 aspartic nonproteinase homologs were found to be expanded in T. annulata. Furthermore, a single proteinase of families S8 (subtilisin-like protein) and C12 (ubiquitin carboxyl-terminal hydrolase), as well as four nonproteinase homologs, one with dual domains M23-M23 and three with S9-S9, were exclusively present in B. bovis. Finally, a pronounced difference in species-specific ancillary domains was observed between both species. We hypothesize that the observed degradome differences represent functional correlates of the dissimilar life history features of B. bovis and T. annulata. The presented improved classification of piroplasmid proteinases will facilitate an informed choice for future in-depth functional studies.
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9
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Zupanič N, Počič J, Leonardi A, Šribar J, Kordiš D, Križaj I. Serine pseudoproteases in physiology and disease. FEBS J 2022; 290:2263-2278. [PMID: 35032346 DOI: 10.1111/febs.16355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/20/2021] [Accepted: 01/12/2022] [Indexed: 01/01/2023]
Abstract
Serine proteases (SPs) constitute a very important family of enzymes, both physiologically and pathologically. The effects produced by these proteins have been explained by their proteolytic activity. However, the discovery of pharmacologically active SP molecules that show no enzymatic activity, as the so-called pseudo SPs or SP homologs (SPHs), has exposed a profoundly neglected possibility of nonenzymatic functions of these SP molecules. In this review, the most thoroughly described SPHs are presented. The main physiological domains in which SPHs operate appear to be in reproduction, embryonic development, immune response, host defense, and hemostasis. Hitherto unexplained actions of SPs should therefore be considered also as the result of the ligand-like attributes of SPs. The gain of a novel function by an SPH is a consequence of specific amino acid replacements that have resulted in a novel interaction interface or a 'catalytic trap'. Unraveling the SP/SPH interactome will provide a description of previously unknown physiological functions of SPs/SPHs, aiding the creation of innovative medical approaches.
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Affiliation(s)
- Nina Zupanič
- Department of Molecular and Biomedical Sciences Jožef Stefan Institute Ljubljana Slovenia
| | - Jernej Počič
- Department of Molecular and Biomedical Sciences Jožef Stefan Institute Ljubljana Slovenia
- Biotechnical Faculty University of Ljubljana Slovenia
| | - Adrijana Leonardi
- Department of Molecular and Biomedical Sciences Jožef Stefan Institute Ljubljana Slovenia
| | - Jernej Šribar
- Department of Molecular and Biomedical Sciences Jožef Stefan Institute Ljubljana Slovenia
| | - Dušan Kordiš
- Department of Molecular and Biomedical Sciences Jožef Stefan Institute Ljubljana Slovenia
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences Jožef Stefan Institute Ljubljana Slovenia
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10
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Florin-Christensen M, Wieser SN, Suarez CE, Schnittger L. In Silico Survey and Characterization of Babesia microti Functional and Non-Functional Proteases. Pathogens 2021; 10:1457. [PMID: 34832610 PMCID: PMC8621943 DOI: 10.3390/pathogens10111457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/29/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022] Open
Abstract
Human babesiosis caused by the intraerythrocytic apicomplexan Babesia microti is an expanding tick-borne zoonotic disease that may cause severe symptoms and death in elderly or immunocompromised individuals. In light of an increasing resistance of B. microti to drugs, there is a lack of therapeutic alternatives. Species-specific proteases are essential for parasite survival and possible chemotherapeutic targets. However, the repertoire of proteases in B. microti remains poorly investigated. Herein, we employed several combined bioinformatics tools and strategies to organize and identify genes encoding for the full repertoire of proteases in the B. microti genome. We identified 64 active proteases and 25 nonactive protease homologs. These proteases can be classified into cysteine (n = 28), serine (n = 21), threonine (n = 14), asparagine (n = 7), and metallopeptidases (n = 19), which, in turn, are assigned to a total of 38 peptidase families. Comparative studies between the repertoire of B. bovis and B. microti proteases revealed differences among sensu stricto and sensu lato Babesia parasites that reflect their distinct evolutionary history. Overall, this data may help direct future research towards our understanding of the biology and pathogenicity of Babesia parasites and to explore proteases as targets for developing novel therapeutic interventions.
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Affiliation(s)
- Monica Florin-Christensen
- Instituto de Patobiologia Veterinaria (IPVET), Centro de Investigaciones en Ciencias Veterinarias y Agronomicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham C1033AAE, Argentina; (S.N.W.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Sarah N. Wieser
- Instituto de Patobiologia Veterinaria (IPVET), Centro de Investigaciones en Ciencias Veterinarias y Agronomicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham C1033AAE, Argentina; (S.N.W.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Carlos E. Suarez
- Animal Disease Research Unit, USDA-ARS, Pullman, WA 99163, USA;
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99163, USA
| | - Leonhard Schnittger
- Instituto de Patobiologia Veterinaria (IPVET), Centro de Investigaciones en Ciencias Veterinarias y Agronomicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham C1033AAE, Argentina; (S.N.W.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
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11
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Tereshchenkova VF, Zhiganov NI, Akentyev PI, Gubaidullin II, Kozlov DG, Belyaeva NV, Filippova IY, Elpidina EN. Preparation and Properties of the Recombinant Tenebrio molitor SerPH122—Proteolytically Active Homolog of Serine Peptidase. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821050161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Mishra LS, Funk C. The FtsHi Enzymes of Arabidopsis thaliana: Pseudo-Proteases with an Important Function. Int J Mol Sci 2021; 22:5917. [PMID: 34072887 PMCID: PMC8197885 DOI: 10.3390/ijms22115917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/01/2023] Open
Abstract
FtsH metalloproteases found in eubacteria, animals, and plants are well-known for their vital role in the maintenance and proteolysis of membrane proteins. Their location is restricted to organelles of endosymbiotic origin, the chloroplasts, and mitochondria. In the model organism Arabidopsis thaliana, there are 17 membrane-bound FtsH proteases containing an AAA+ (ATPase associated with various cellular activities) and a Zn2+ metalloprotease domain. However, in five of those, the zinc-binding motif HEXXH is either mutated (FtsHi1, 2, 4, 5) or completely missing (FtsHi3), rendering these enzymes presumably inactive in proteolysis. Still, homozygous null mutants of the pseudo-proteases FtsHi1, 2, 4, 5 are embryo-lethal. Homozygous ftshi3 or a weak point mutant in FTSHi1 are affected in overall plant growth and development. This review will focus on the findings concerning the FtsHi pseudo-proteases and their involvement in protein import, leading to consequences in embryogenesis, seed growth, chloroplast, and leaf development and oxidative stress management.
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Affiliation(s)
| | - Christiane Funk
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden;
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13
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Nixon CF, Lim SA, Sailer ZR, Zheludev IN, Gee CL, Kelch BA, Harms MJ, Marqusee S. Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family. Biochemistry 2021; 60:170-181. [PMID: 33433210 DOI: 10.1021/acs.biochem.0c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In addition to encoding the tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determine the speed of folding. How these kinetic barriers are encoded is not well understood. Here, we use evolutionary sequence variation in the α-lytic protease (αLP) protein family to probe the relationship between sequence and energy landscape. αLP has an unusual energy landscape: the native state of αLP is not the most thermodynamically favored conformation and, instead, remains folded due to a large kinetic barrier preventing unfolding. To fold, αLP utilizes an N-terminal pro region similar in size to the protease itself that functions as a folding catalyst. Once folded, the pro region is removed, and the native state does not unfold on a biologically relevant time scale. Without the pro region, αLP folds on the order of millennia. A phylogenetic search uncovers αLP homologs with a wide range of pro region sizes, including some with no pro region at all. In the resulting phylogenetic tree, these homologs cluster by pro region size. By studying homologs naturally lacking a pro region, we demonstrate they can be thermodynamically stable, fold much faster than αLP, yet retain the same fold as αLP. Key amino acids thought to contribute to αLP's extreme kinetic stability are lost in these homologs, supporting their role in kinetic stability. This study highlights how the entire energy landscape plays an important role in determining the evolutionary pressures on the protein sequence.
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Affiliation(s)
- Charlotte F Nixon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Shion A Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Zachary R Sailer
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry & Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Ivan N Zheludev
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, United States
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, United States
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Michael J Harms
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry & Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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14
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Fernando DD, Fischer K. Proteases and pseudoproteases in parasitic arthropods of clinical importance. FEBS J 2020; 287:4284-4299. [PMID: 32893448 DOI: 10.1111/febs.15546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/18/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022]
Abstract
Parasitic arthropods feed on blood or skin tissue and share comparable repertoires of proteases involved in haematophagy, digestion, egg development and immunity. While proteolytically active proteases of multiple classes dominate, an increasing number of pseudoproteases have been discovered that have no proteolytic function but are pharmacologically active biomolecules, evolved to carry out alternative functions as regulatory, antihaemostatic, anti-inflammatory or immunomodulatory compounds. In this review, we provide an overview of proteases and pseudoproteases from clinically important arthropod parasites. Many of these act in central biological pathways of parasite survival and host-parasite interaction and may be potential targets for therapeutic interventions.
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Affiliation(s)
- Deepani Darshika Fernando
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - Katja Fischer
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
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15
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Smyth P, Sessler T, Scott CJ, Longley DB. FLIP(L): the pseudo-caspase. FEBS J 2020; 287:4246-4260. [PMID: 32096279 PMCID: PMC7586951 DOI: 10.1111/febs.15260] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/10/2020] [Accepted: 02/24/2020] [Indexed: 12/27/2022]
Abstract
Possessing structural homology with their active enzyme counterparts but lacking catalytic activity, pseudoenzymes have been identified for all major enzyme groups. Caspases are a family of cysteine‐dependent aspartate‐directed proteases that play essential roles in regulating cell death and inflammation. Here, we discuss the only human pseudo‐caspase, FLIP(L), a paralog of the apoptosis‐initiating caspases, caspase‐8 and caspase‐10. FLIP(L) has been shown to play a key role in regulating the processing and activity of caspase‐8, thereby modulating apoptotic signaling mediated by death receptors (such as TRAIL‐R1/R2), TNF receptor‐1 (TNFR1), and Toll‐like receptors. In this review, these canonical roles of FLIP(L) are discussed. Additionally, a range of nonclassical pseudoenzyme roles are described, in which FLIP(L) functions independently of caspase‐8. These nonclassical pseudoenzyme functions enable FLIP(L) to play key roles in the regulation of a wide range of biological processes beyond its canonical roles as a modulator of cell death.
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Affiliation(s)
- Peter Smyth
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Tamas Sessler
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Christopher J Scott
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Daniel B Longley
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
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16
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Zaru R, Magrane M, Orchard S. Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. FEBS J 2019; 287:4114-4127. [PMID: 31618524 DOI: 10.1111/febs.15100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022]
Abstract
The universal protein knowledgebase (UniProtKB) collects and centralises functional information on proteins across a wide range of species. In addition to the functional information added to all protein entries, for enzymes, which represent 20-40% of most proteomes, UniProtKB provides additional information about Enzyme Commission classification, catalytic activity, cofactors, enzyme regulation, kinetics and pathways, all based on critical assessment of published experimental data. Computer-based analysis and structural data are used to enrich the annotation of the sequence through the identification of active sites and binding sites. While the annotation of enzymes is well-defined, the curation of pseudoenzymes in UniProtKB has highlighted some challenges: how to identify them, how to assess their lack of catalytic activity, how to annotate their lack of catalytic activity in a consistent way and how much can be inferred and propagated from experimental data obtained from other species. Through various examples, we illustrate some of these issues and discuss some of the changes we propose to enhance the annotation and discovery of pseudoenzymes. Ultimately, improving the curation of pseudoenzymes will provide the scientific community with a comprehensive resource for pseudoenzymes, which in turn will lead to a better understanding of the evolution of these molecules, the aetiology of related diseases and the development of drugs.
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Affiliation(s)
- Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
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- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.,SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.,Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA.,Protein Information Resource, University of Delaware, Newark, DE, USA
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17
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Van Opdenbosch N, Lamkanfi M. Caspases in Cell Death, Inflammation, and Disease. Immunity 2019; 50:1352-1364. [PMID: 31216460 DOI: 10.1016/j.immuni.2019.05.020] [Citation(s) in RCA: 683] [Impact Index Per Article: 136.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 01/01/2023]
Abstract
Caspases are an evolutionary conserved family of cysteine proteases that are centrally involved in cell death and inflammation responses. A wealth of foundational insight into the molecular mechanisms that control caspase activation has emerged in recent years. Important advancements include the identification of additional inflammasome platforms and pathways that regulate activation of inflammatory caspases; the discovery of gasdermin D as the effector of pyroptosis and interleukin (IL)-1 and IL-18 secretion; and the existence of substantial crosstalk between inflammatory and apoptotic initiator caspases. A better understanding of the mechanisms regulating caspase activation has supported initial efforts to modulate dysfunctional cell death and inflammation pathways in a suite of communicable, inflammatory, malignant, metabolic, and neurodegenerative diseases. Here, we review current understanding of caspase biology with a prime focus on the inflammatory caspases and outline important topics for future experimentation.
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Affiliation(s)
- Nina Van Opdenbosch
- Janssen Immunosciences, World Without Disease Accelerator, Pharmaceutical Companies of Johnson & Johnson, Beerse, 2340, Belgium
| | - Mohamed Lamkanfi
- Janssen Immunosciences, World Without Disease Accelerator, Pharmaceutical Companies of Johnson & Johnson, Beerse, 2340, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, 9000, Belgium.
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18
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Sharir-Ivry A, Xia Y. Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures. Mol Biol Evol 2019; 35:2597-2606. [PMID: 30202983 DOI: 10.1093/molbev/msy177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Enzymes are known to fine-tune their sequences to optimize catalytic function, yet quantitative evolutionary design principles of enzymes remain elusive on the proteomic scale. Recently, it was found that the catalytic site in enzymes induces long-range evolutionary constraint, where even sites distant to the catalytic site are more conserved than expected. Given that protein-fold usage is generally different between enzymes and nonenzymes, it remains an open question to what extent this long-range evolutionary constraint in enzymes is dictated, either directly or indirectly, by the special three-dimensional structure of the enzyme. To investigate this question, we have compared evolutionary properties of enzymes with those of counterpart pseudoenzymes that share the same protein fold but are catalytically inactive. We found that the long-range evolutionary constraint observed in enzymes is significantly reduced in pseudoenzyme counterparts, despite very high structural similarity (∼1.5 Å RMSD on average). Furthermore, this significant reduction in long-range evolutionary constraint is observed even in pseudoenzyme counterparts which retain the ligand-binding ability of enzymes. Finally, the distance between the site that induces the highest gradient of sequence conservation and the pseudocatalytic site in pseudoenzymes is significantly larger than the corresponding distance in enzymes. Taken together, our results suggest that the long-range evolutionary constraint in enzymes is induced mainly by the presence of the catalytic site rather than by the special three-dimensional structure of the enzyme, and that such long-range evolutionary constraint in enzymes depends mainly on the catalytic function of the active site rather than on the ligand-binding ability of the enzyme.
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Affiliation(s)
| | - Yu Xia
- Department of Bioengineering, McGill University, Montreal, QC, Canada
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19
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Klemenčič M, Asplund-Samuelsson J, Dolinar M, Funk C. Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:293. [PMID: 30923531 PMCID: PMC6426788 DOI: 10.3389/fpls.2019.00293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Orthocaspases are prokaryotic caspase homologs - proteases, which cleave their substrates after positively charged residues using a conserved histidine - cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.
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Affiliation(s)
- Marina Klemenčič
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Marko Dolinar
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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20
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Lu S, Parizi LF, Torquato RJS, Vaz Junior IS, Tanaka AS. Novel pseudo-aspartic peptidase from the midgut of the tick Rhipicephalus microplus. Sci Rep 2019; 9:435. [PMID: 30679545 PMCID: PMC6345952 DOI: 10.1038/s41598-018-36849-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/29/2018] [Indexed: 11/23/2022] Open
Abstract
The characterization of Rhipicephalus microplus tick physiology can support efforts to develop and improve the efficiency of control methods. A sequence containing a domain with similarity to one derived from the aspartic peptidase family was isolated from the midgut of engorged female R. microplus. The lack of the second catalytic aspartic acid residue suggest that it may be a pseudo-aspartic peptidase, and it was named RmPAP. In this work we confirm the lack of proteolytic activity of RmPAP and investigate it’s non-proteolytic interaction with bovine hemoglobin by Surface Plasmon Resonance and phage display. Moreover we carried out RNAi interference and artificial feeding of ticks with anti-RmPAP antibodies to assess it’s possible biological role, although no changes were observed in the biological parameters evaluated. Overall, we hypothesize that RmPAP may act as a carrier of hemoglobin/heme between the tick midgut and the ovaries.
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Affiliation(s)
- S Lu
- Department of Biochemistry, Federal University of Sao Paulo (UNIFESP), SP, Brazil
| | - L F Parizi
- Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), RS, Brazil
| | - R J S Torquato
- Department of Biochemistry, Federal University of Sao Paulo (UNIFESP), SP, Brazil
| | - I S Vaz Junior
- Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), RS, Brazil.,School of Veterinary, Federal University of Rio Grande do Sul (UFRGS), RS, Brazil.,National Institute of Science and Technology in Molecular Entomology (INTC-EM), RJ, Brazil
| | - A S Tanaka
- Department of Biochemistry, Federal University of Sao Paulo (UNIFESP), SP, Brazil. .,National Institute of Science and Technology in Molecular Entomology (INTC-EM), RJ, Brazil.
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21
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Armistead JS, Jennison C, O'Neill MT, Lopaticki S, Liehl P, Hanson KK, Annoura T, Rajasekaran P, Erickson SM, Tonkin CJ, Khan SM, Mota MM, Boddey JA. Plasmodium falciparum
subtilisin-like ookinete protein SOPT plays an important and conserved role during ookinete infection of the Anopheles stephensi
midgut. Mol Microbiol 2018; 109:458-473. [DOI: 10.1111/mmi.13993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Jennifer S. Armistead
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Charlie Jennison
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Matthew T. O'Neill
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
| | - Sash Lopaticki
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
| | - Peter Liehl
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; 1649-028 Lisbon Portugal
| | - Kirsten K. Hanson
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; 1649-028 Lisbon Portugal
| | - Takeshi Annoura
- Leiden Malaria Research Group, Parasitology; Leiden University Medical Centre; 2333ZA Leiden the Netherlands
| | - Pravin Rajasekaran
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Sara M. Erickson
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Christopher J. Tonkin
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Shahid M. Khan
- Leiden Malaria Research Group, Parasitology; Leiden University Medical Centre; 2333ZA Leiden the Netherlands
| | - Maria M. Mota
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; 1649-028 Lisbon Portugal
| | - Justin A. Boddey
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
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22
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Afanador GA, Tomchick DR, Phillips MA. Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation between Pseudoenzyme Paralogs. Structure 2018; 26:1499-1512.e5. [PMID: 30197036 DOI: 10.1016/j.str.2018.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
Trypanosoma brucei is a neglected tropical disease endemic to Africa. The polyamine spermidine is essential for post-translational hypusine modification of eukaryotic initiation factor 5A (eIF5A), which is catalyzed by deoxyhypusine synthase (TbDHS). In trypanosomatids, deoxyhypusine synthase (DHS) activity is dependent on heterotetramer formation between two paralogs, DHSc and DHSp, both with minimal activity on their own due to missing catalytic residues. We determined the X-ray structure of TbDHS showing a single functional shared active site is formed at the DHSc/DHSp heterodimer interface, with deficiencies in one subunit complemented by the other. Each heterodimer contains two NAD+ binding sites, one housed in the functional catalytic site and the second bound in a remnant dead site that lacks key catalytic residues. Functional analysis of these sites by site-directed mutagenesis identified long-range contributions to the catalytic site from the dead site. Differences between trypanosomatid and human DHS that could be exploited for drug discovery were identified.
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Affiliation(s)
- Gustavo A Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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23
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Fernando DD, Reynolds SL, Zakrzewski M, Mofiz E, Papenfuss AT, Holt D, Fischer K. Phylogenetic relationships, stage-specific expression and localisation of a unique family of inactive cysteine proteases in Sarcoptes scabiei. Parasit Vectors 2018; 11:301. [PMID: 29769145 PMCID: PMC5956821 DOI: 10.1186/s13071-018-2862-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/23/2018] [Indexed: 11/17/2022] Open
Abstract
Background Scabies is worldwide one of the most common, yet neglected, parasitic skin infections, affecting a wide range of mammals including humans. Limited treatment options and evidence of emerging mite resistance against the currently used drugs drive our research to explore new therapeutic candidates. Previously, we discovered a multicopy family of genes encoding cysteine proteases with their catalytic sites inactivated by mutation (SMIPP-Cs). This protein family is unique in parasitic scabies mites and is absent in related non-burrowing mites. We postulated that the SMIPP-Cs have evolved as an adaptation to the parasitic lifestyle of the scabies mite. To formulate testable hypotheses for their functions and to propose possible strategies for translational research we investigated whether the SMIPP-Cs are common to all scabies mite varieties and where within the mite body as well as when throughout the parasitic life-cycle they are expressed. Results SMIPP-C sequences from human, pig and dog mites were analysed bioinformatically and the phylogenetic relationships between the SMIPP-C multi-copy gene families of human, pig and dog mites were established. Results suggest that amplification of the SMIPP-C genes occurred in a common ancestor and individual genes evolved independently in the different mite varieties. Recombinant human mite SMIPP-C proteins were produced and used for murine polyclonal antibody production. Immunohistology on skin sections from human patients localised the SMIPP-Cs in the mite gut and in mite faeces within in the epidermal skin burrows. SMIPP-C transcription into mRNA in different life stages was assessed in human and pig mites by reverse transcription followed by droplet digital PCR (ddPCR). High transcription levels of SMIPP-C genes were detected in the adult female life stage in comparison to all other life stages. Conclusions The fact that the SMIPP-Cs are unique to three Sarcoptes varieties, present in all burrowing life stages and highly expressed in the digestive system of the infective adult female life stage may highlight an essential role in parasitism. As they are excreted from the gut in scybala they presumably are able to interact or interfere with host proteins present in the epidermis. Electronic supplementary material The online version of this article (10.1186/s13071-018-2862-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepani D Fernando
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.,School of Veterinary Sciences, University of Queensland, Gatton, QLD, 4343, Australia.,Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Simone L Reynolds
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Martha Zakrzewski
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Ehtesham Mofiz
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, 3000, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Deborah Holt
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Katja Fischer
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
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Craft TR, Forrester WC. The Caenorhabditis elegans matrix non-peptidase MNP-1 is required for neuronal cell migration and interacts with the Ror receptor tyrosine kinase CAM-1. Dev Biol 2017; 424:18-27. [PMID: 28238735 DOI: 10.1016/j.ydbio.2017.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 10/20/2022]
Abstract
Directed cell migration is critical for metazoan development. During Caenorhabditis elegans development many neuronal, muscle and other cell types migrate. Multiple classes of proteins have been implicated in cell migration including secreted guidance cues, receptors for guidance cues and intracellular proteins that respond to cues to polarize cells and produce the forces that move them. In addition, cell surface and secreted proteases have been identified that may clear the migratory route and process guidance cues. We report here that mnp-1 is required for neuronal cell and growth cone migrations. MNP-1 is expressed by migrating cells and functions cell autonomously for cell migrations. We also find a genetic interaction between mnp-1 and cam-1, which encodes a Ror receptor tyrosine kinase required for some of the same cell migrations.
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Affiliation(s)
- Teresa R Craft
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, United States
| | - Wayne C Forrester
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, United States.
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25
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Perkin LC, Elpidina EN, Oppert B. RNA interference and dietary inhibitors induce a similar compensation response in Tribolium castaneum larvae. INSECT MOLECULAR BIOLOGY 2017; 26:35-45. [PMID: 27770578 DOI: 10.1111/imb.12269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tribolium castaneum is a major agriculture pest damaging stored grains and cereal products. The T. castaneum genome contains 26 cysteine peptidase genes, mostly cathepsins L and B, and seven have a major role in digestion. We targeted the expression of the most highly expressed cathepsin L gene on chromosome 10, TC011001, by RNA interference (RNAi), using double-stranded RNA (dsRNA) constructs of different regions of the gene (3', middle, 5' and entire coding regions). RNA sequencing and quantitation (RNA-seq) was used to evaluate knockdown and specificity amongst the treatments. Overall, target gene expression decreased in all treatment groups, but was more severe and specific in dsRNA targeting the 3' and entire coding regions, encoding the proteolytic active site in the enzyme. Additional cysteine cathepsin genes also were down-regulated (off-target effects), but some were up-regulated in response to RNAi treatment. Notably, some serine peptidase genes were increased in expression, especially in dsRNA targeting 5' and middle regions, and the response was similar to the effects of dietary cysteine protease inhibitors. We manually annotated these serine peptidase genes to gain insight into function and relevance to the RNAi study. The data indicate that T. castaneum larvae compensate for the loss of digestive peptidase activity in the larval gut, regardless of the mechanism of disruption.
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Affiliation(s)
- L C Perkin
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS, USA
| | - E N Elpidina
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - B Oppert
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS, USA
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26
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Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. eLife 2016; 5. [PMID: 27977001 PMCID: PMC5201418 DOI: 10.7554/elife.20198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 12/11/2016] [Indexed: 02/06/2023] Open
Abstract
Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures of Trypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomeric TbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving a cis-to-trans proline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved. DOI:http://dx.doi.org/10.7554/eLife.20198.001
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Affiliation(s)
- Oleg A Volkov
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisa Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carson Ariagno
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shihua Zhong
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute,University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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27
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Abstract
Pseudoenzymes are catalytically deficient variants of enzymes that are represented in all major enzyme families. Their regulatory functions in signalling pathways are shedding new light on the non-catalytic functions of active enzymes, and are suggesting new ways to target cellular signalling mechanisms with drugs.
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Affiliation(s)
- Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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28
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Exported Epoxide Hydrolases Modulate Erythrocyte Vasoactive Lipids during Plasmodium falciparum Infection. mBio 2016; 7:mBio.01538-16. [PMID: 27795395 PMCID: PMC5082902 DOI: 10.1128/mbio.01538-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Erythrocytes are reservoirs of important epoxide-containing lipid signaling molecules, including epoxyeicosatrienoic acids (EETs). EETs function as vasodilators and anti-inflammatory modulators in the bloodstream. Bioactive EETs are hydrolyzed to less active diols (dihydroxyeicosatrienoic acids) by epoxide hydrolases (EHs). The malaria parasite Plasmodium falciparum infects host red blood cells (RBCs) and exports hundreds of proteins into the RBC compartment. In this study, we show that two parasite epoxide hydrolases, P. falciparum epoxide hydrolases 1 (PfEH1) and 2 (PfEH2), both with noncanonical serine nucleophiles, are exported to the periphery of infected RBCs. PfEH1 and PfEH2 were successfully expressed in Escherichia coli, and they hydrolyzed physiologically relevant erythrocyte EETs. Mutations in active site residues of PfEH1 ablated the ability of the enzyme to hydrolyze an epoxide substrate. Overexpression of PfEH1 or PfEH2 in parasite-infected RBCs resulted in a significant alteration in the epoxide fatty acids stored in RBC phospholipids. We hypothesize that the parasite disruption of epoxide-containing signaling lipids leads to perturbed vascular function, creating favorable conditions for binding and sequestration of infected RBCs to the microvascular endothelium. The malaria parasite exports hundreds of proteins into the erythrocyte compartment. However, for most of these proteins, their physiological function is unknown. In this study, we investigate two “hypothetical” proteins of the α/β-hydrolase fold family that share sequence similarity with epoxide hydrolases (EHs)—enzymes that destroy bioactive epoxides. Altering EH expression in parasite-infected erythrocytes resulted in a significant change in the epoxide fatty acids stored in the host cell. We propose that these EH enzymes may help the parasite to manipulate host blood vessel opening and inflame the vessel walls as they pass through the circulation system. Understanding how the malaria parasite interacts with its host RBCs will aid in our ability to combat this deadly disease.
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29
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Mellado L, Arst HN, Espeso EA. Proteolytic activation of both components of the cation stress-responsive Slt pathway in Aspergillus nidulans. Mol Biol Cell 2016; 27:2598-612. [PMID: 27307585 PMCID: PMC4985261 DOI: 10.1091/mbc.e16-01-0049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/10/2016] [Indexed: 12/14/2022] Open
Abstract
Tolerance of Aspergillus nidulans to alkalinity and elevated cation concentrations requires both SltA and SltB. Transcription factor SltA and the putative pseudokinase/protease signaling protein SltB comprise a regulatory pathway specific to filamentous fungi. In vivo, SltB is proteolytically cleaved into its two principal domains. Mutational analysis defines a chymotrypsin-like serine protease domain that mediates SltB autoproteolysis and proteolytic cleavage of SltA. The pseudokinase domain might modulate the protease activity of SltB. Three forms of the SltA transcription factor coexist in cells: a full-length, 78-kDa version and a processed, 32-kDa form, which is found in phosphorylated and unphosphorylated states. The SltA32kDa version mediates transcriptional regulation of sltB and, putatively, genes required for tolerance to cation stress and alkalinity. The full-length form, SltA78kDa, apparently has no transcriptional function. In the absence of SltB, only the primary product of SltA is detectable, and its level equals that of SltA78kDa. Mutations in sltB selected as suppressors of null vps alleles and resulting in cation/alkalinity sensitivity either reduced or eliminated SltA proteolysis. There is no evidence for cation or alkalinity regulation of SltB cleavage, but activation of sltB expression requires SltA. This work identifies the molecular mechanisms governing the Slt pathway.
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Affiliation(s)
- Laura Mellado
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Herbert N Arst
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain Section of Microbiology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
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