1
|
Nemoto TK, Nishimata H, Shirakura K, Ohara-Nemoto Y. Potential elevation of exopeptidase activity of Glu-specific endopeptidase I/GluV8 mediated by hydrophobic P1'-position amino acid residue. Biochimie 2023; 220:99-106. [PMID: 38159715 DOI: 10.1016/j.biochi.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
We recently reported that the activities of dipeptidyl-peptidase (DPP)7 and DPP11, S46-family exopeptidases were significantly elevated by the presence of prime-side amino acid residues of substrates caused by an increase in kcat [Ohara-Nemoto Y. et al., J Biol Chem 298(3):101585. doi: 10.1016/j.jbc.2022]. In the present study, the effects of prime-side residues on Glu-specific endopeptidase I/GluV8 from Staphylococcus aureus were investigated using a two-step cleavage method with tetrapeptidyl-methycoumaryl-7-amide (MCA) carrying P2- to P2'-position residues coupled with DPP11 as the second enzyme. GluV8 showed maximal activity toward benzyloxycarbonyl (Z)-LLE-MCA, while the effects of hydrolysis of substrates one residue shorter, such as acetyl (Ac)-Val-Glu- and Leu-Glu-MCA, were negligible. Nevertheless, activity towards Ac-VE-|-ID-MCA, a substrate carrying P1' and P2' residues, emerged and reached a level 44 % of that for Z-LLE-MCA. Among 11 Ac-HAXD-MCA (X is a varied amino acid), the highest level of activity enhancement was achieved with P1'-Leu and Ile, followed by Phe, Val, Ser, Tyr, and Ala, while Gly and Lys showed scant effects. This activation order was in parallel with the hydrophobicity indexes of these amino acids. The prime-side residues increased kcat/KM primarily through a maximum 500-fold elevation of kcat as well as S46-family exopeptidases. The MEROPS substrate database also indicates a close relationship between activity and hydrophobicity of the P1' residues in 93 N-terminal-truncated substrates, though no correlation was observed among all 4328 GluV8 entities examined. Taken together, these results are the first to demonstrate N-terminal exopeptidase activity of GluV8, considered to be prompted by hydrophobic P1' amino acid residues.
Collapse
Affiliation(s)
- Takayuki K Nemoto
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan; Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, 1-1-1 Idai-dori, Yahaba-cho, Iwate, 028-3694, Japan.
| | - Haruka Nishimata
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan.
| | - Kana Shirakura
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan.
| | - Yuko Ohara-Nemoto
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan; Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, 1-1-1 Idai-dori, Yahaba-cho, Iwate, 028-3694, Japan.
| |
Collapse
|
2
|
Dickerson F, Vaidya D, Liu Y, Yolken R. Levels of Matrix Metalloproteinase 9 Are Elevated in Persons With Schizophrenia or Bipolar Disorder: The Role of Modifiable Factors. Biol Psychiatry Glob Open Sci 2023; 3:766-772. [PMID: 37881562 PMCID: PMC10593883 DOI: 10.1016/j.bpsgos.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
Background Matrix metalloproteinases (MMPs) are a diverse set of enzymes associated with inflammation. MMP-9 is of particular interest because it has been associated with autoimmune and cardiopulmonary disorders, tobacco smoking, and obesity, prevalent in psychiatric populations. Methods Sensitive enzyme immunoassays measured MMP-9 in blood samples from 1121 individuals (mean age = 35.6 [SD = 13.0] years; 47.7% male; 440 with schizophrenia, 399 with bipolar disorder, and 282 without a psychiatric disorder). We estimated the odds of diagnosis associated with MMP-9, demographic variables, tobacco smoking, and obesity, and also the partial explained variance using regression methods. We also determined the association between psychiatric medications and MMP-9 levels. Results Individuals with elevated MMP-9 levels had higher odds of schizophrenia or bipolar disorder compared with the nonpsychiatric group adjusted for demographic variables. Partial correlation analyses indicated the demographic-adjusted variance associated with MMP-9, smoking, obesity, and their interaction explained 59.6% for schizophrenia and 39.9% for bipolar disorder. Levels of MMP-9 were substantially lower in individuals receiving valproate, particularly relatively high doses. Conclusions Individuals with higher levels of MMP-9 have significantly higher odds of schizophrenia or bipolar disorder. Individuals receiving valproate had substantially lower levels of MMP-9, possibly related to its ability to inhibit histone deacetylation. A substantial portion of the variance in clinical disorders associated with MMP-9 can be attributed to smoking or obesity. Interventions to reduce smoking and obesity might reduce the morbidity and mortality associated with elevated MMP-9 levels and improve the health outcomes of individuals with these disorders.
Collapse
Affiliation(s)
- Faith Dickerson
- Stanley Research Program, Sheppard Pratt, Baltimore, Maryland
| | - Dhananjay Vaidya
- Department of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yisi Liu
- Department of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert Yolken
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
3
|
Phillips TA, Robia SL. Regulation of the regulator: Endopeptidase cleavage controls the expression of a micropeptide that regulates SERCA. Cell Calcium 2022; 107:102655. [PMID: 36179466 DOI: 10.1016/j.ceca.2022.102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
Micropeptides regulate cellular calcium handling by modulating the function of the calcium transporter SERCA. In a recent Nature Communications paper [4] authors Schiemann et al. describe regulation of an invertebrate SERCA-active micropeptide, sarcolamban, by an endopeptidase called neprilysin 4 (NEP4). NEP4 activity limits sarcolamban expression by cleavage of luminal residues near the micropeptide's c-terminus. This cleavage event liberates sarcolamban from the membrane, reduces its oligomerization, and prevents it from inhibiting SERCA. The study reveals a novel mechanism for "regulation of the regulator" that may be a general feature of micropeptide/SERCA physiology.
Collapse
Affiliation(s)
- Taylor A Phillips
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood 60153, IL, United States of America
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood 60153, IL, United States of America.
| |
Collapse
|
4
|
Tüten N, Malik E, Gök K, Hamzaoglu K, Makul M, Öner YÖ, Bulut H, Tüten A, Güralp O. Serum neprilysin levels are elevated in preeclampsia. Taiwan J Obstet Gynecol 2021; 60:869-873. [PMID: 34507663 DOI: 10.1016/j.tjog.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To evaluate the possible associations between serum Neprilysin (NEP) levels and preeclampsia and mild and severe preeclampsia subgroups. MATERIALS AND METHODS Fifty-five consecutive women with mild preeclampsia and fifty-five consecutive women with severe preeclampsia were compared with 110 approximately gestational age-matched (±1 week) women with an uncomplicated pregnancy. RESULTS Mean serum NEP was significantly higher in women with preeclampsia compared to that of the gestational age-matched-controls (231.62 ± 65.30 pg/mL vs. 187.75 ± 84.38 pg/mL, p < 0.001). Mean serum NEP was significantly higher in the mild preeclampsia group compared to its gestational age-matched control group (228.84 ± 67.26 pg/mL vs. 186.14 ± 85.09 pg/mL, p = 0.008); and in the severe preeclampsia group compared to its gestational age-matched control group (234.45 ± 63.85 pg/mL vs. 189.29 ± 84.59 pg/mL, p = 0.004). Serum NEP was positively correlated with systolic and diastolic blood pressure, BUN, uric acid, and creatinine. CONCLUSION Mean serum NEP was significantly higher in women with preeclampsia than women with an uncomplicated pregnancy. Further studies are needed to elucidate the possible therapeutic role of NEP inhibitors to treat preeclampsia.
Collapse
Affiliation(s)
- Nevin Tüten
- Kanuni Sultan Suleyman Education and Research Hospital, Obstetrics and Gynecology Istanbul, Turkey
| | - Eduard Malik
- Carl von Ossietzky Oldenburg University, University Hospital for Gynecology and Obstetrics, Klinikum Oldenburg AöR, Oldenburg, Germany
| | - Koray Gök
- Sakarya University, Education and Research Hospital, Obstetrics and Gynecology, Sakarya, Turkey
| | - Kübra Hamzaoglu
- Istanbul Cerrahpasa University, Department of Obstetrics and Gynecology, Istanbul, Turkey
| | - Melike Makul
- Istanbul Cerrahpasa University, Department of Obstetrics and Gynecology, Istanbul, Turkey
| | - Yahya Özgün Öner
- Istanbul Cerrahpasa University, Department of Obstetrics and Gynecology, Istanbul, Turkey
| | - Huri Bulut
- Istinye University, Faculty of Medicine, Medical Biochemistry Department, Istanbul, Turkey
| | - Abdullah Tüten
- Istanbul Cerrahpasa University, Department of Obstetrics and Gynecology, Istanbul, Turkey.
| | - Onur Güralp
- Carl von Ossietzky Oldenburg University, University Hospital for Gynecology and Obstetrics, Klinikum Oldenburg AöR, Oldenburg, Germany
| |
Collapse
|
5
|
Han G, Ma H, Ren S, Gao X, He X, Zhu S, Deng R, Zhang S. Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor. Microbiologyopen 2020; 9:e1042. [PMID: 32529805 PMCID: PMC7424253 DOI: 10.1002/mbo3.1042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/19/2020] [Accepted: 03/28/2020] [Indexed: 01/14/2023] Open
Abstract
Fungal mycelia can eliminate almost all cocultured cyanobacterial cells within a short time. However, molecular mechanisms of algicidal fungi are poorly understood. In this study, a time‐course transcriptomic analysis of algicidal fungus Bjerkandera adusta T1 was applied to investigate gene expression and regulation. A total of 132, 300, 422, and 823 differentially expressed genes (DEGs) were identified at 6, 12, 24, and 48 hr, respectively. Most DEGs exhibited high endopeptidase activity, cellulose catabolic process, and transmembrane transporter activity by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Many decomposition genes encoding endopeptidases were induced a little later in B. adusta T1 when compared with previously investigated algicidal fungus Trametes versicolor F21a. Besides, the accumulated expression of Polysaccharide lyases8 (PL8) gene with peptidoglycan and alginate decomposition abilities was greatly delayed in B. adusta T1 relative to T. versicolor F21a. It was implied that endopeptidases and enzymes of PL8 might be responsible for the strong algicidal ability of B. adusta T1 as well as T. versicolor F21a.
Collapse
Affiliation(s)
- Guomin Han
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Hui Ma
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shenrong Ren
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xueyan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaolong He
- Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Suwen Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Ruining Deng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shihua Zhang
- Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| |
Collapse
|
6
|
Sah SK, Shefali S, Yadav A, Som P, Komath SS. The caspase-like Gpi8 subunit of Candida albicans GPI transamidase is a metal-dependent endopeptidase. Biochem Biophys Res Commun 2020; 525:S0006-291X(20)30268-0. [PMID: 32081427 DOI: 10.1016/j.bbrc.2020.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
Abstract
GPI anchored proteins (GPI-APs) act at the frontiers of cells, decoding environmental cues and determining host-pathogen interactions in several lower eukaryotes. They are also essential for viability in lower eukaryotes. The GPI biosynthetic pathway begins at the ER and follows a roughly linear pathway to generate the complete precursor (CP) glycolipid. The GPI transamidase (GPIT) transfers this glycolipid to the C-terminal end of newly translated proteins after removing their GPI attachment signal sequence (SS). The GPIT subunit that cleaves SS is Gpi8, a protein with a conserved Cys/His catalytic dyad typical of cysteine proteases. A CaGPI8 heterozygous mutant accumulates CPs and has reduced cell surface GPI-APs. Using a simple cell-free assay, we demonstrate that the heterozygous CaGPI8 strain has low endopeptidase activity as well. The revertant strain is restored in all these phenotypes. CaGpi8 is also shown to be a metalloenzyme, whose protease activity is sensitive to agents that modify Cys/His residues.
Collapse
Affiliation(s)
- Sudisht Kumar Sah
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Shailja Shefali
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anshuman Yadav
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Punnag Som
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneha Sudha Komath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
7
|
Rezaei-Mojaz S, Nazmara Z, Najafi M, Movahedin M, Zandieh Z, Shirinbayan P, Roshanpajouh M, Asgari HR, Abbasi M, Koruji M. Evaluation of Enkephalin-Degrading Enzymes in Sperm from Heroin-Addicted Men. Int J Fertil Steril 2019; 13:301-306. [PMID: 31710191 PMCID: PMC6875862 DOI: 10.22074/ijfs.2020.5817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 06/09/2019] [Indexed: 12/13/2022]
Abstract
Background The aim of this study was to investigate two enkephalin-degrading enzymes, aminopeptidase N (APN/
CD13) and endopeptidase (NEP/CD10), gene and protein expression levels in sperm samples of fertile and heroin-
addicted men, and the correlation between their expressions and semen quality. Materials and Methods In this case-controlled study, semen was collected from 24 normozoospermic healthy
(as a control group) and 24 heroin-addicted men donors (as case or addiction group). Sperm cells isolated by Cook
Medical gradient (40-80%) and followed up by swim-up techniques were used for real-time quantitative polymer-
ase chain reaction (qPCR) and flow cytometry techniques to assess APN/CD13 and NEP/CD10 genes and proteins
subsequently. Semen parameters were analyzed by computer-assisted sperm analysis. Results The findings revealed that there were significant differences in sperm total motility (41.07 ± 3.63 vs. 63.03
± 3.31 %, P=0.0001), progressive motility (35.21 ± 2.64 vs. 20.93 ± 3.22%, P=0.001) and viability (69.9 ± 4.69 vs.
86.81 ± 1.26 %, P=0.002) in the addicted group vs. control ones. APN and NEP gene expression levels in the addicted
group decreased compared with the control ones (1.00 ± 0.67 vs. 0.36 ± 0.13, P= 0.008 and 1.07 ± 0.11 vs. 0.52 ± 0.12
0.002, respectively). Flow cytometry analysis showed that the average percent of APN/CD13 in heroin consumers
significantly decreased compared with the healthy ones, while NEP/CD10 rate between two groups was similar. We
also observed that duration of drug dependence is correlated with sperm viability (r=-0.627, P=0.016) and motility
(r=-0.410, P=0.05), NEP (r=-0.434, P= 0.049), and APN (r=-0.641, P=0.002) gene expression levels. Conclusion We conclude that semen quality and enkephalin-degrading enzymes were altered in heroin-addicted men.
other confirming the internal validity of our estimates.
Collapse
Affiliation(s)
- Samira Rezaei-Mojaz
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zohreh Nazmara
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Najafi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mansoureh Movahedin
- Anatomical Sciences Department, School of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Zahra Zandieh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.,Shahid Akbarabadi Clinical Research Development Unit (ShACRDU), Iran University of Medical Sciences, Tehran, Iran
| | - Peymaneh Shirinbayan
- Pediatric Neuro-Rehabilitation Research Center, The University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohsen Roshanpajouh
- School of Behavioral Sciences and mental Health, Tehran Psychiatry Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Asgari
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Abbasi
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Morteza Koruji
- Department of Anatomical Sciences, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran. Electronic Address:
| |
Collapse
|
8
|
Mallick S, Das J, Verma J, Mathew S, Maiti TK, Ghosh AS. Role of Escherichia coli endopeptidases and dd-carboxypeptidases in infection and regulation of innate immune response. Microbes Infect 2019; 21:464-474. [PMID: 31085336 DOI: 10.1016/j.micinf.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 01/13/2023]
Abstract
The low-molecular-mass penicillin-binding proteins, involved in peptidoglycan recycling can also produce peptidoglycan fragments capable of activating an innate immune response in host. To investigate how these proteins in Enterobacteriaceae play a role to elicit/evade innate immune responses during infections, we deleted certain endopeptidases and dd-carboxypeptidases from Escherichia coli CS109 and studied the viability of these mutants in macrophages. The ability of infected macrophages to exert oxidative killing, express surface activation markers TLR2, MHC class II and release TNFα, were assessed. Immune responses were elevated in macrophages infected with dd-carboxypeptidase mutants but reduced for endopeptidase mutants. However, the NFκB, iNOS, and TLR2 transcripts remained elevated in macrophages infected with both mutant types. Overall, we have shown, under normal conditions endopeptidases have a tendency to elicit the immune response but their effect is suppressed by the presence of dd-carboxypeptidases. Conversely, DD-carboxypeptidases, normally, tend to reduce immune responses, as their deletions enhanced the same in macrophages. Therefore, we conclude that the roles of endopeptidases and dd-carboxypeptidases are possibly counter-active in wild-type cells where either class of enzymes suppresses each other's immunogenic properties rendering overall maintenance of low immunogenicity that helps E. coli in evading the host immune responses.
Collapse
Affiliation(s)
- Sathi Mallick
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Joyjyoti Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Samatha Mathew
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Tapas K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India.
| |
Collapse
|
9
|
Kohler V, Probst I, Aufschnaiter A, Büttner S, Schaden L, Rechberger GN, Koraimann G, Grohmann E, Keller W. Conjugative type IV secretion in Gram-positive pathogens: TraG, a lytic transglycosylase and endopeptidase, interacts with translocation channel protein TraM. Plasmid 2017; 91:9-18. [PMID: 28219792 DOI: 10.1016/j.plasmid.2017.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/30/2017] [Accepted: 02/02/2017] [Indexed: 11/24/2022]
Abstract
Conjugative transfer plays a major role in the transmission of antibiotic resistance in bacteria. pIP501 is a Gram-positive conjugative model plasmid with the broadest transfer host-range known so far and is frequently found in Enterococcus faecalis and Enterococcus faecium clinical isolates. The pIP501 type IV secretion system is encoded by 15 transfer genes. In this work, we focus on the VirB1-like protein TraG, a modular peptidoglycan metabolizing enzyme, and the VirB8-homolog TraM, a potential member of the translocation channel. By providing full-length traG in trans, but not with a truncated variant, we achieved full recovery of wild type transfer efficiency in the traG-knockout mutant E. faecalis pIP501ΔtraG. With peptidoglycan digestion experiments and tandem mass spectrometry we could assign lytic transglycosylase and endopeptidase activity to TraG, with the CHAP domain alone displaying endopeptidase activity. We identified a novel interaction between TraG and TraM in a bacterial-2-hybrid assay. In addition we found that both proteins localize in focal spots at the E. faecalis cell membrane using immunostaining and fluorescence microscopy. Extracellular protease digestion to evaluate protein cell surface exposure revealed that correct membrane localization of TraM requires the transmembrane helix of TraG. Thus, we suggest an essential role for TraG in the assembly of the pIP501 type IV secretion system.
Collapse
|
10
|
Sharma AK, Kumar S, K H, Dhakan DB, Sharma VK. Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins. BMC Genomics 2016; 17:411. [PMID: 27229861 PMCID: PMC4882796 DOI: 10.1186/s12864-016-2753-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/19/2016] [Indexed: 12/21/2022] Open
Abstract
Background The efficacy of antibiotics against bacterial infections is decreasing due to the development of resistance in bacteria, and thus, there is a need to search for potential alternatives to antibiotics. In this scenario, peptidoglycan hydrolases can be used as alternate antibacterial agents due to their unique property of cleaving peptidoglycan cell wall present in both gram-positive and gram-negative bacteria. Along with a role in maintaining overall peptidoglycan turnover in a cell and in daughter cell separation, peptidoglycan hydrolases also play crucial role in bacterial pathophysiology requiring development of a computational tool for the identification and classification of novel peptidoglycan hydrolases from genomic and metagenomic data. Results In this study, the known peptidoglycan hydrolases were divided into multiple classes based on their site of action and were used for the development of a computational tool ‘HyPe’ for identification and classification of novel peptidoglycan hydrolases from genomic and metagenomic data. Various classification models were developed using amino acid and dipeptide composition features by training and optimization of Random Forest and Support Vector Machines. Random Forest multiclass model was selected for the development of HyPe tool as it showed up to 71.12 % sensitivity, 99.98 % specificity, 99.55 % accuracy and 0.80 MCC in four different classes of peptidoglycan hydrolases. The tool was validated on 24 independent genomic datasets and showed up to 100 % sensitivity and 0.94 MCC. The ability of HyPe to identify novel peptidoglycan hydrolases was also demonstrated on 24 metagenomic datasets. Conclusions The present tool helps in the identification and classification of novel peptidoglycan hydrolases from complete genomic or metagenomic ORFs. To our knowledge, this is the only tool available for the prediction of peptidoglycan hydrolases from genomic and metagenomic data. Availability: http://metagenomics.iiserb.ac.in/hype/ and http://metabiosys.iiserb.ac.in/hype/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2753-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ashok K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India
| | - Sanjiv Kumar
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India.,Department of Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Harish K
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India
| | - Darshan B Dhakan
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, India.
| |
Collapse
|
11
|
Chang TW, Janardhanan P, Mello CM, Singh BR, Cai S. Selection of RNA Aptamers Against Botulinum Neurotoxin Type A Light Chain Through a Non-Radioactive Approach. Appl Biochem Biotechnol 2016; 180:10-25. [PMID: 27085355 DOI: 10.1007/s12010-016-2081-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/07/2016] [Indexed: 12/15/2022]
Abstract
Botulinum neurotoxin (BoNT), a category A agent, is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. Currently, antidotes are not available to reverse the flaccid paralysis caused by BoNT. In the present study, a non-radioactive-based systematic evolution of ligands by exponential enrichment (SELEX) process is developed by utilizing surface plasmon resonance to monitor the binding enrichment. Two RNA aptamers have been identified as strong binders against light chain of botulinum neurotoxin type A. These two aptamers showed strong inhibition activity on LCA, with IC50 in nanomolar range. Inhibition kinetic studies reveal mid nanomolar KI and non-competitive nature of their inhibition, suggesting that they have strong potential as antidotes that can reverse the symptom caused by BoNT/A. More importantly, we observed that the 2'-fluorine-pyrimidine-modified RNA aptamers identified here do not change their binding and biological activities. This observation could lead to a cost-effective way for SELEX, by using regular nucleotide during SELEX, and 2'-fluorine-pyrimidine-modified nucleotide for final application to enhance their RNase-resistance.
Collapse
|
12
|
Kondo MY, Gouvea IE, Okamoto DN, Santos JAN, Souccar C, Oda K, Juliano L, Juliano MA. Analysis of catalytic properties of tripeptidyl peptidase I (TTP-I), a serine carboxyl lysosomal protease, and its detection in tissue extracts using selective FRET peptide substrate. Peptides 2016; 76:80-6. [PMID: 26775801 DOI: 10.1016/j.peptides.2016.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/01/2016] [Accepted: 01/10/2016] [Indexed: 11/30/2022]
Abstract
Tripeptidyl peptidase I (TPP-I), also named ceroid lipofuscinosis 2 protease (CLN2p), is a serine carboxyl lysosomal protease involved in neurodegenerative diseases, and has both tripeptidyl amino- and endo- peptidase activities under different pH conditions. We developed fluorescence resonance energy transfer (FRET) peptides using tryptophan (W) as the fluorophore to study TPP-I hydrolytic properties based on previous detailed substrate specificity study (Tian Y. et al., J. Biol. Chem. 2006, 281:6559-72). Tripeptidyl amino peptidase activity is enhanced by the presence of amino acids in the prime side and the peptide NH2-RWFFIQ-EDDnp is so far the best substrate described for TPP-I. The hydrolytic parameters of this peptide and its analogues indicated that the S4 subsite of TPP-I is occluded and there is an electrostatic interaction of the positively charged substrate N-terminus amino group and a negative locus in the region of the enzyme active site. KCl activated TPP-I in contrast to the inhibition by Ca(2+) and NaCl. Solvent kinetic isotope effects (SKIEs) show the importance of the free N-terminus amino group of the substrates, whose absence results in a more complex solvent-dependent enzyme: substrate interaction and catalytic process. Like pure TPP-I, rat spleen and kidney homogenates cleaved NH2-RWFFIQ-EDDnp only at F-F bond and is not inhibited by pepstatin, E-64, EDTA or PMSF. The selectivity of NH2-RWFFIQ-EDDnp to TPP-I was also demonstrated by the 400 times higher k(cat)/K(M) compared to generally used substrate, NH2-AAF-MCA and by its resistance to hydrolysis by cathepsin D that is present in high levels in kidneys.
Collapse
Affiliation(s)
- Marcia Y Kondo
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Iuri E Gouvea
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Débora N Okamoto
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Jorge A N Santos
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Caden Souccar
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil.
| |
Collapse
|
13
|
Abstract
Zymography of cell wall hydrolases is a simple technique to specifically detect cell wall or peptidoglycan hydrolytic activity. The zymographic method can be used for assessing the hydrolytic activities of purified target proteins, cell surface proteins, and proteins secreted to culture. Here, methods of cell wall and peptidoglycan purification, extraction of cell surface proteins containing cell wall hydrolases, and zymographic analysis are described. The purified or extracted proteins are separated by electrophoresis using an SDS gel containing cell wall or peptidoglycan material and then the proteins are renatured in the gel. The renatured cell wall hydrolases in the gel hydrolyze the material around the proteins. The cell wall or peptidoglycan in the gel is stained by methylene blue and the hydrolyzed material cannot be stained, resulting in the detection of cell wall hydrolytic activities of the enzymes on the gel.
Collapse
Affiliation(s)
- Tatsuya Fukushima
- Division of Gene Research, Department of Life Sciences, Research Center for Human and Environmental Sciences, Shinshu University, 3-15-1 Tokida, Ueda, Nagano, 386-8567, Japan.
| | - Junichi Sekiguchi
- Department of Applied Biology, Graduate School of Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda-shi, Nagano, 386-8567, Japan.
| |
Collapse
|
14
|
Schwechheimer C, Rodriguez DL, Kuehn MJ. NlpI-mediated modulation of outer membrane vesicle production through peptidoglycan dynamics in Escherichia coli. Microbiologyopen 2015; 4:375-89. [PMID: 25755088 PMCID: PMC4475382 DOI: 10.1002/mbo3.244] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/10/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Outer membrane vesicles (OMVs) are ubiquitously secreted from the outer membrane (OM) of Gram-negative bacteria. These heterogeneous structures are composed of OM filled with periplasmic content from the site of budding. By analyzing mutants that have vesicle production phenotypes, we can gain insight into the mechanism of OMV budding in wild-type cells, which has thus far remained elusive. In this study, we present data demonstrating that the hypervesiculation phenotype of the nlpI deletion mutant of Escherichia coli correlates with changes in peptidoglycan (PG) dynamics. Our data indicate that in stationary phase cultures the nlpI mutant exhibits increased PG synthesis that is dependent on spr, consistent with a model in which NlpI controls the activity of the PG endopeptidase Spr. In log phase, the nlpI mutation was suppressed by a dacB mutation, suggesting that NlpI regulates penicillin-binding protein 4 (PBP4) during exponential growth. The data support a model in which NlpI negatively regulates PBP4 activity during log phase, and Spr activity during stationary phase, and that in the absence of NlpI, the cell survives by increasing PG synthesis. Further, the nlpI mutant exhibited a significant decrease in covalent outer membrane (OM-PG) envelope stabilizing cross-links, consistent with its high level of OMV production. Based on these results, we propose that one mechanism wild-type Gram-negative bacteria can use to modulate vesiculation is by altering PG-OM cross-linking via localized modulation of PG degradation and synthesis.
Collapse
Affiliation(s)
- Carmen Schwechheimer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710
| | - Daniel L Rodriguez
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710
| | - Meta J Kuehn
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710
| |
Collapse
|
15
|
Castro LM, Cavalcanti DM, Araujo CB, Rioli V, Icimoto MY, Gozzo FC, Juliano M, Juliano L, Oliveira V, Ferro ES. Peptidomic analysis of the neurolysin-knockout mouse brain. J Proteomics 2014; 111:238-48. [PMID: 24727097 DOI: 10.1016/j.jprot.2014.03.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 03/20/2014] [Accepted: 03/31/2014] [Indexed: 12/12/2022]
Abstract
UNLABELLED A large number of intracellular peptides are constantly produced following protein degradation by the proteasome. A few of these peptides function in cell signaling and regulate protein-protein interactions. Neurolysin (Nln) is a structurally defined and biochemically well-characterized endooligopeptidase, and its subcellular distribution and biological activity in the vertebrate brain have been previously investigated. However, the contribution of Nln to peptide metabolism in vivo is poorly understood. In this study, we used quantitative mass spectrometry to investigate the brain peptidome of Nln-knockout mice. An additional in vitro digestion assay with recombinant Nln was also performed to confirm the identification of the substrates and/or products of Nln. Altogether, the data presented suggest that Nln is a key enzyme in the in vivo degradation of only a few peptides derived from proenkephalin, such as Met-enkephalin and octapeptide. Nln was found to have only a minor contribution to the intracellular peptide metabolism in the entire mouse brain. However, further studies appear necessary to investigate the contribution of Nln to the peptide metabolism in specific areas of the murine brain. BIOLOGICAL SIGNIFICANCE Neurolysin was first identified in the synaptic membranes of the rat brain in the middle 80's by Frederic Checler and colleagues. Neurolysin was well characterized biochemically, and its brain distribution has been confirmed by immunohistochemical methods. The neurolysin contribution to the central and peripheral neurotensin-mediated functions in vivo has been delineated through inhibitor-based pharmacological approaches, but its genuine contribution to the physiological inactivation of neuropeptides remains to be firmly established. As a result, the main significance of this work is the first characterization of the brain peptidome of the neurolysin-knockout mouse. This article is part of a Special Issue entitled: Proteomics, mass spectrometry and peptidomics, Cancun 2013. Guest Editors: César López-Camarillo, Victoria Pando-Robles and Bronwyn Jane Barkla.
Collapse
|
16
|
Federico C. Natriuretic Peptide system and cardiovascular disease. Heart Views 2010; 11:10-5. [PMID: 21042458 PMCID: PMC2964706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The mammalian Natriuretic Peptide (NP) system consists of neuro-hormones, such as atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), c-type natriuretic peptide (CNP), and the N-Terminal fragment of BNP (NT-pro-BNP). In response to some cardiovascular derangement the heart (acting as an endocrine organ), brain and other structures secretes natriuretic peptides in an attempt to restore normal circulatory conditions. Their actions are modulated through membrane-bound guanylyl cyclased (GC) receptors. They induce diuresis, natriuresis and vasodilation in the presence of congestive heart failure. These neuro-hormones also play a role in the suppression of neointimal formation after vascular injury. In addition, they act as antifibrotic and antihypertrophic agents preventing cardiac remodeling after myocardial infarction. Further, NP have diagnostic and prognostic role in heart failure, vasoconstriction, left ventricular late remodeling after MI and others. At present, some drugs such as Nesiritide, NEP inhibitors and vasopeptidase inhibitors were synthetized from NP, to antagonize these cardiovascular derengements. In future, it will be possibile to elaborate some drugs similar to petidase inhibitors and some CNP-like drugs able to reduce many symptoms of cardiovascular derangements without significant side effects.
Collapse
Affiliation(s)
- Cacciapuoti Federico
- Associate Professor of Internal Medicine, Second University of Naples, Italy,Correspondence to: prof. Federico Cacciapuoti, Cattedra di Medicina Interna, Facoltà di Medicina e Chirurgia, Seconda, Università di Napoli, Piazza L. Miraglia 2,Napoli-80138 Phone: +081/5665022
| |
Collapse
|