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Reder A, Hentschker C, Steil L, Gesell Salazar M, Hammer E, Dhople VM, Sura T, Lissner U, Wolfgramm H, Dittmar D, Harms M, Surmann K, Völker U, Michalik S. MassSpecPreppy-An end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications. Proteomics 2024; 24:e2300294. [PMID: 37772677 DOI: 10.1002/pmic.202300294] [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] [Received: 07/31/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Abstract
In proteomics, fast, efficient, and highly reproducible sample preparation is of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open science OT-2 liquid handling robot from Opentrons. This platform can prepare up to 96 samples at once, performing tasks like BCA protein concentration determination, sample digestion with normalization, reduction/alkylation and peptide elution into vials or loading specified peptide amounts onto Evotips in an automated and flexible manner. The performance of the developed workflows using MassSpecPreppy was compared with standard manual sample preparation workflows. The BCA assay experiments revealed an average recovery of 101.3% (SD: ± 7.82%) for the MassSpecPreppy workflow, while the manual workflow had a recovery of 96.3% (SD: ± 9.73%). The species mix used in the evaluation experiments showed that 94.5% of protein groups for OT-2 digestion and 95% for manual digestion passed the significance thresholds with comparable peptide level coefficient of variations. These results demonstrate that MassSpecPreppy is a versatile and scalable platform for automated sample preparation, producing injection-ready samples for proteomics research.
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Affiliation(s)
- Alexander Reder
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M Dhople
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Sura
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Lissner
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Hannes Wolfgramm
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Denise Dittmar
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Marco Harms
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kristin Surmann
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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Yeak KYC, Tempelaars M, Wu JL, Westerveld W, Reder A, Michalik S, Dhople VM, Völker U, Pané-Farré J, Wells-Bennik MHJ, Abee T. SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus. BMC Microbiol 2023; 23:37. [PMID: 36759782 PMCID: PMC9912610 DOI: 10.1186/s12866-023-02783-3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND The Bacillus cereus Sigma B (SigB) dependent general stress response is activated via the two-component RsbKY system, which involves a phosphate transfer from RsbK to RsbY. It has been hypothesized that the Hpr-like phosphocarrier protein (Bc1009) encoded by bc1009 in the SigB gene cluster may play a role in this transfer, thereby acting as a regulator of SigB activation. Alternatively, Bc1009 may be involved in the activation of a subset of SigB regulon members. RESULTS We first investigated the potential role of bc1009 to act as a SigB regulator but ruled out this possibility as the deletion of bc1009 did not affect the expression of sigB and other SigB gene cluster members. The SigB-dependent functions of Bc1009 were further examined in B. cereus ATCC14579 via comparative proteome profiling (backed up by transcriptomics) of wt, Δbc1009 and ΔsigB deletion mutants under heat stress at 42 °C. This revealed 284 proteins displaying SigB-dependent alterations in protein expression levels in heat-stressed cells, including a subgroup of 138 proteins for which alterations were also Bc1009-dependent. Next to proteins with roles in stress defense, newly identified SigB and Bc1009-dependent proteins have roles in cell motility, signal transduction, transcription, cell wall biogenesis, and amino acid transport and metabolism. Analysis of lethal stress survival at 50 °C after pre-adaptation at 42 °C showed intermediate survival efficacy of Δbc1009 cells, highest survival of wt, and lowest survival of ΔsigB cells, respectively. Additional comparative proteome analysis of non-stressed wt and mutant cells at 30 °C revealed 96 proteins with SigB and Bc1009-dependent differences in levels: 51 were also identified under heat stress, and 45 showed significant differential expression at 30 °C. This includes proteins with roles in carbohydrate/ion transport and metabolism. Overlapping functions at 30 °C and 42 °C included proteins involved in motility, and ΔsigB and Δbc1009 cells showed reduced motility compared to wt cells in swimming assays at both temperatures. CONCLUSION Our results extend the B. cereus SigB regulon to > 300 members, with a novel role of SigB-dependent Bc1009 in the activation of a subregulon of > 180 members, conceivably via interactions with other transcriptional regulatory networks.
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Affiliation(s)
- Kah Yen Claire Yeak
- grid.419921.60000 0004 0588 7915NIZO, Kernhemseweg 2, PO Box 20, 6718 ZB Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Marcel Tempelaars
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Jia Lun Wu
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Wouter Westerveld
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Alexander Reder
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M. Dhople
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- grid.10253.350000 0004 1936 9756Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Karl-Von-Frisch-Strasse 14, 35043 Marburg, Germany
| | | | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV, Wageningen, The Netherlands.
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Benkner A, Rüdebusch J, Nath N, Hammer E, Grube K, Gross S, Dhople VM, Eckstein G, Meitinger T, Kaderali L, Völker U, Fielitz J, Felix SB. Riociguat attenuates left ventricular proteome and microRNA profile changes after experimental aortic stenosis in mice. Br J Pharmacol 2022; 179:4575-4592. [PMID: 35751875 DOI: 10.1111/bph.15910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/08/2021] [Revised: 04/15/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Development and progression of heart failure (HF) involve endothelial and myocardial dysfunction as well as a dysregulation of the nitric oxide - soluble guanylyl cyclase - cyclic guanosine monophosphate (NO-sGC-cGMP) signalling pathway. Recently, we reported that the sGC stimulator riociguat (RIO) has beneficial effects on cardiac remodelling and progression of HF in response to chronic pressure overload. Here, we examined if these favourable RIO effects are also reflected in alterations of the myocardial proteome and microRNA profiles. EXPERIMENTAL APPROACH Male C57BL/6N mice underwent transverse aortic constriction (TAC) and sham operated mice served as controls. TAC and sham animals were randomised and treated with either RIO or vehicle for five weeks, starting three weeks post-surgery when cardiac hypertrophy was established. Afterwards we performed mass spectrometric proteome analyses and microRNA sequencing of proteins and RNAs, respectively, isolated from left ventricles (LV). KEY RESULTS TAC-induced changes of the LV proteome were significantly reduced by RIO treatment. Bioinformatics analyses revealed that RIO improved TAC-induced cardiovascular disease related pathways, metabolism and energy production, e.g. reversed alterations in the levels of myosin heavy chain 7 (MYH7), cardiac phospholamban (PLN), and ankyrin repeat domain-containing protein 1 (ANKRD1). RIO also attenuated TAC-induced changes of microRNA levels in the LV. CONCLUSION AND IMPLICATIONS The sGC stimulator RIO has beneficial effects on cardiac structure and function during pressure overload, which is accompanied by a reversal of TAC-induced changes of the cardiac proteome and microRNA profile. Our data support the potential of RIO as a novel HF therapeutic.
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Affiliation(s)
- Alexander Benkner
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Julia Rüdebusch
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Karina Grube
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Gross
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M Dhople
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, Helmholtz Centre Munich, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Centre Munich, Neuherberg, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Lars Kaderali
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jens Fielitz
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B Felix
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
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Reddy HM, Bhattacharya R, Tiwari S, Mishra K, Annapurna P, Jehan Z, Praveena NM, Alex JL, Dhople VM, Singh L, Sivaramakrishnan M, Chaturvedi A, Rangaraj N, Shiju TM, Sreedevi B, Kumar S, Dereddi RR, Rayabandla SM, Jesudasan RA. Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis. BMC Biol 2021; 19:198. [PMID: 34503492 PMCID: PMC8428117 DOI: 10.1186/s12915-021-01125-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/06/2021] [Accepted: 08/17/2021] [Indexed: 12/03/2022] Open
Abstract
Background Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Functions of the noncoding transcripts from Y chromosomal repeats however, remain unclear. While a majority of the genes expressed during spermatogenesis are autosomal, mice with different deletions of the long arm of the Y chromosome (Yq) were previously also shown to be characterized by subfertility, sterility and sperm abnormalities, suggesting the presence of effectors of spermatogenesis at this location. Here we report a set of novel noncoding RNAs from mouse Yq and explore their connection to some of the autosomal genes expressed in testis. Results We describe a set of novel mouse male-specific Y long arm (MSYq)-derived long noncoding (lnc) transcripts, named Pirmy and Pirmy-like RNAs. Pirmy shows a large number of splice variants in testis. We also identified Pirmy-like RNAs present in multiple copies at different loci on mouse Y chromosome. Further, we identified eight differentially expressed autosome-encoded sperm proteins in a mutant mouse strain, XYRIIIqdel (2/3 Yq-deleted). Pirmy and Pirmy-like RNAs have homology to 5′/3′UTRs of these deregulated autosomal genes. Several lines of experiments show that these short homologous stretches correspond to piRNAs. Thus, Pirmy and Pirmy-like RNAs act as templates for several piRNAs. In vitro functional assays reveal putative roles for these piRNAs in regulating autosomal genes. Conclusions Our study elucidates a set of autosomal genes that are potentially regulated by MSYq-derived piRNAs in mouse testis. Sperm phenotypes from the Yq-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of MSYq-derived ncRNAs in male sterility and speciation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01125-x.
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Affiliation(s)
- Hemakumar M Reddy
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Present address: Brown University BioMed Division, Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street room 257, Sidney Frank Life Sciences Building, Providence, RI, 02912, USA
| | - Rupa Bhattacharya
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,, Pennington, NJ, 08534, USA
| | - Shrish Tiwari
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Kankadeb Mishra
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Department of Cell Biology, Memorial Sloan Kettering Cancer Centre, Rockefeller Research Laboratory, 430 East 67th Street, RRL 445, New York, NY, 10065, USA
| | - Pranatharthi Annapurna
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Departments of Orthopaedic Surgery & Bioengineering, University of Pennsylvania, 376A Stemmler Hall, 36th Street & Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Zeenath Jehan
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Department of Genetics and Molecular Medicines, Vasavi Medical and Research Centre, 6-1-91 Khairatabad, Hyderabad, 500 004, India
| | | | - Jomini Liza Alex
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Vishnu M Dhople
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Department of Functional Genomics, Ernst-Moritz-Arndt-University of Greifswald Interfaculty Institute for Genetics and Functional Genomics, Friedrich-Ludwig-Jahn-Straße 15 a, 17487, Greifswald, Germany
| | - Lalji Singh
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Mahadevan Sivaramakrishnan
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Jubilant Biosystems Ltd., #96, Industrial Suburb, 2nd Stage, Yeshwantpur, Bangalore, Karnataka, 560022, India
| | - Anurag Chaturvedi
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Nandini Rangaraj
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Thomas Michael Shiju
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, 44120, USA
| | - Badanapuram Sreedevi
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Sachin Kumar
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Ram Reddy Dereddi
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Institute for Anatomy and Cell Biology, building-307, Heidelberg, Germany
| | - Sunayana M Rayabandla
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Telangana Social Welfare Residential Degree College for Women, Suryapet, Telangana, 508213, India
| | - Rachel A Jesudasan
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India. .,Department of Genetics, Osmania University, Hyderabad, Telangana, 500007, India. .,Inter University Centre for Genomics & Gene Technology, Karyavattom Campus, University of Kerala, Trivandrum, Kerala, India.
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Natani S, Dhople VM, Parveen A, Sruthi KK, Khilar P, Bhukya S, Ummanni R. AMPK/SIRT1 signaling through p38MAPK mediates Interleukin-6 induced neuroendocrine differentiation of LNCaP prostate cancer cells. Biochim Biophys Acta Mol Cell Res 2021; 1868:119085. [PMID: 34171447 DOI: 10.1016/j.bbamcr.2021.119085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/29/2022]
Abstract
Neuroendocrine Prostate Cancer (NEPC) is an aggressive form of androgen independent prostate cancer (AIPC), correlated with therapeutic resistance. Interleukin (IL)-6 promotes proliferation and neuroendocrine differentiation (NED) of androgen dependent LNCaP cells. We treated LNCaP cells with IL-6 and observed for in vitro NED of cells and also expression of NE markers βIII tubulin, neuron-specific enolase (NSE) and chromogranin A (ChA). Here we investigated the proteins and/or pathways involved in NED of LNCaP cells induced by IL-6 and characterized their role in NED of PCa cells. We found that the altered proteins modulated AMPK signaling pathway in NE cells. Remarkably, IL-6 induces NED of LNCaP cells through activation of AMPK and SIRT1 and also both of these are co-regulated while playing a predominant role in NED of LNCaP cells. Of the few requirements of AMPK-SIRT1 activation, increased eNOS is essential for NED by elevating Nitric oxide (NO) levels. Pleiotropic effects of NO ultimately regulate p38MAPK in IL-6 induced NED. Hence, IL-6 induced AMPK-SIRT1 activation eventually transfers its activation signals through p38MAPK for advancing NED of LNCaP cells. Moreover, inactivation of p38MAPK with specific inhibitor (SB203580) attenuated IL-6 induced NED of LNCaP cells. Therefore, IL-6 promotes NED of PCa cells via AMPK/SIRT1/p38MAPK signaling. Finally, targeting AMPK-SIRT1 or p38MAPK in androgen independent PC3 cells with neuroendocrine features reversed their neuroendocrine characteristics. Taken together these novel findings reveal that targeting p38MAPK mitigated NED of PCa cells, and thus it can be a favorable target to overcome progression of NEPC.
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Affiliation(s)
- Sirisha Natani
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishnu M Dhople
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Asha Parveen
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - K K Sruthi
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priyanka Khilar
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Supriya Bhukya
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
| | - Ramesh Ummanni
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Howland V, Klaedtke M, Ruhnau J, Dhople VM, Grabe HJ, Völker U, Heckmann M, Hammer E. Impact of Storage Conditions on the Breast Milk Peptidome. Nutrients 2020; 12:nu12092733. [PMID: 32911625 PMCID: PMC7551425 DOI: 10.3390/nu12092733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 12/17/2022] Open
Abstract
Human donor milk (HDM) provides appropriate nutrition and offers protective functions in preterm infants. The aim of the study is to examine the impact of different storage conditions on the stability of the human breast milk peptidome. HDM was directly frozen at −80 °C or stored at −20 °C (120 h), 4 °C (6 h), or room temperature (RT for 6 or 24 h). The milk peptidome was profiled by mass spectrometry after peptide collection by ultrafiltration. Profiling of the peptidome covered 3587 peptides corresponding to 212 proteins. The variance of the peptidome increased with storage temperature and time and varied for different peptides. The highest impact was observed when samples were stored at RT. Smaller but significant effects were still observed in samples stored at 4 °C, while samples showed highest similarity to those immediately frozen at −80 °C when stored at −20 °C. Peptide structures after storage at RT for 24 h point to the increased activity of thrombin and other proteases cleaving proteins at lysine/arginine. The results point to an ongoing protein degradation/peptide production by milk-derived proteases. They underline the need for immediate freezing of HDM at −20 °C or −80 °C to prevent degradation of peptides and enable reproducible investigation of prospectively collected samples.
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Affiliation(s)
- Vanessa Howland
- Department of Neonatology and Paediatric Intensive Care, University Medicine Greifswald, D-17475 Greifswald, Germany;
| | - Maik Klaedtke
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, D-17475 Greifswald, Germany; (M.K.); (V.M.D.); (U.V.)
| | - Johanna Ruhnau
- Department of Neurology, University Medicine Greifswald, D-17475 Greifswald, Germany;
| | - Vishnu M. Dhople
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, D-17475 Greifswald, Germany; (M.K.); (V.M.D.); (U.V.)
| | - Hans J. Grabe
- Department of Psychiatry & Psychotherapy, University Medicine Greifswald, D-17475 Greifswald, Germany;
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, D-17475 Greifswald, Germany; (M.K.); (V.M.D.); (U.V.)
| | - Matthias Heckmann
- Department of Neonatology and Paediatric Intensive Care, University Medicine Greifswald, D-17475 Greifswald, Germany;
- Correspondence: (M.H.); (E.H.); Tel.: +49-3834-86-6421 (M.H.); +49-3834-420-5811 (E.H.)
| | - Elke Hammer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, D-17475 Greifswald, Germany; (M.K.); (V.M.D.); (U.V.)
- Correspondence: (M.H.); (E.H.); Tel.: +49-3834-86-6421 (M.H.); +49-3834-420-5811 (E.H.)
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7
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Oviedo JM, Surmann K, Gorgojo JP, Valdez H, Dhople VM, Lamberti Y, Völker U, Rodriguez ME. Shotgun proteomic analysis of Bordetella parapertussis provides insights into the physiological response to iron starvation and potential new virulence determinants absent in Bordetella pertussis. J Proteomics 2019; 206:103448. [PMID: 31325608 DOI: 10.1016/j.jprot.2019.103448] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/19/2019] [Accepted: 07/11/2019] [Indexed: 01/05/2023]
Abstract
Bordetella parapertussis is one of the pathogens that cause whooping cough. Even though its incidence has been rising in the last decades, this species remained poorly investigated. This study reports the first extensive proteome analysis of this bacterium. In an attempt to gain some insight into the infective phenotype, we evaluated the response of B. parapertussis to iron starvation, a critical stress the bacteria face during infection. Among other relevant findings, we observed that the adaptation to this condition involves significant changes in the abundance of two important virulence factors of this pathogen, namely, adenylate cyclase and the O-antigen. We further used the proteomic data to search for B. parapertussis proteins that are absent or classified as pseudogenes in the genome of Bordetella pertussis to unravel differences between both whooping cough causative agents. Among them, we identified proteins involved in stress resistance and virulence determinants that might help to explain the differences in the pathogenesis of these species and the lack of cross-protection of current acellular vaccines. Altogether, these results contribute to a better understanding of B. parapertussis biology and pathogenesis. SIGNIFICANCE: Whooping cough is a reemerging disease caused by both Bordetella pertussis and Bordetella parapertussis. Current vaccines fail to induce protection against B parapertussis and the incidence of this species has been rising over the years. The proteomic analysis of this study provided relevant insights into potential virulence determinants of this poorly-studied pathogen. It further identified proteins produced by B. parapertussis not present in B. pertussis, which might help to explain both the differences on their respective infectious process and the current vaccine failure. Altogether, the results of this study contribute to the better understanding of B. parapertussis pathogenesis and the eventual design of improved preventive strategies against whooping cough.
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Affiliation(s)
- Juan Marcos Oviedo
- CINDEFI (UNLP CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Juan Pablo Gorgojo
- CINDEFI (UNLP CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Hugo Valdez
- CINDEFI (UNLP CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Vishnu M Dhople
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Yanina Lamberti
- CINDEFI (UNLP CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - María Eugenia Rodriguez
- CINDEFI (UNLP CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
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8
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Strakova K, Kowalski-Jahn M, Gybel T, Valnohova J, Dhople VM, Harnos J, Bernatik O, Ganji RS, Zdrahal Z, Mulder J, Lindskog C, Bryja V, Schulte G. Dishevelled enables casein kinase 1-mediated phosphorylation of Frizzled 6 required for cell membrane localization. J Biol Chem 2018; 293:18477-18493. [PMID: 30309985 DOI: 10.1074/jbc.ra118.004656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 07/02/2018] [Revised: 10/05/2018] [Indexed: 11/06/2022] Open
Abstract
Frizzleds (FZDs) are receptors for secreted lipoglycoproteins of the Wingless/Int-1 (WNT) family, initiating an important signal transduction network in multicellular organisms. FZDs are G protein-coupled receptors (GPCRs), which are well known to be regulated by phosphorylation, leading to specific downstream signaling or receptor desensitization. The role and underlying mechanisms of FZD phosphorylation remain largely unexplored. Here, we investigated the phosphorylation of human FZD6 Using MS analysis and a phospho-state- and -site-specific antibody, we found that Ser-648, located in the FZD6 C terminus, is efficiently phosphorylated by casein kinase 1 ϵ (CK1ϵ) and that this phosphorylation requires the scaffolding protein Dishevelled (DVL). In an overexpression system, DVL1, -2, and -3 promoted CK1ϵ-mediated FZD6 phosphorylation on Ser-648. This DVL activity required an intact DEP domain and FZD-mediated recruitment of this domain to the cell membrane. Substitution of the CK1ϵ-targeted phosphomotif reduced FZD6 surface expression, suggesting that Ser-648 phosphorylation controls membrane trafficking of FZD6 Phospho-Ser-648 FZD6 immunoreactivity in human fallopian tube epithelium was predominantly apical, associated with cilia in a subset of epithelial cells, compared with the total FZD6 protein expression, suggesting that FZD6 phosphorylation contributes to asymmetric localization of receptor function within the cell and to epithelial polarity. Given the key role of FZD6 in planar cell polarity, our results raise the possibility that asymmetric phosphorylation of FZD6 rather than asymmetric protein distribution accounts for polarized receptor signaling.
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Affiliation(s)
- Katerina Strakova
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic.,Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum (6D), Tomtebodavägen 16, SE-17165 Stockholm, Sweden
| | - Maria Kowalski-Jahn
- Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum (6D), Tomtebodavägen 16, SE-17165 Stockholm, Sweden
| | - Tomas Gybel
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - Jana Valnohova
- Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum (6D), Tomtebodavägen 16, SE-17165 Stockholm, Sweden
| | - Vishnu M Dhople
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, 17487 Greifswald, Germany
| | - Jakub Harnos
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - Ondrej Bernatik
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
| | - Ranjani Sri Ganji
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic.,Central European Institute for Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Zbynek Zdrahal
- Central European Institute for Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Tomtebodavägen 16 17165 Stockholm, Sweden, and
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
| | - Vitezslav Bryja
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic,
| | - Gunnar Schulte
- From the Laboratory of WNT Signaling, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic, .,Section for Receptor Biology and Signaling, Department of Physiology and Pharmacology, Karolinska Institutet, Biomedicum (6D), Tomtebodavägen 16, SE-17165 Stockholm, Sweden
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9
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Kuchibhotla B, Kola SR, Medicherla JV, Cherukuvada SV, Dhople VM, Nalam MR. Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:1216-1226. [PMID: 28349438 DOI: 10.1007/s13361-017-1606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/30/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. Graphical Abstract ᅟ.
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Affiliation(s)
- Bhanuramanand Kuchibhotla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sankara Rao Kola
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Jagannadham V Medicherla
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Swamy V Cherukuvada
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Vishnu M Dhople
- Department of Functional Genomics, University Medicine Greifswald, Interface Institute Genetics & Functional Genomics, D-17475, Greifswald, Germany
| | - Madhusudhana Rao Nalam
- Center for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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10
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Murr A, Pink C, Hammer E, Michalik S, Dhople VM, Holtfreter B, Völker U, Kocher T, Gesell Salazar M. Cross-Sectional Association of Salivary Proteins with Age, Sex, Body Mass Index, Smoking, and Education. J Proteome Res 2017; 16:2273-2281. [DOI: 10.1021/acs.jproteome.7b00133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Annette Murr
- Department
of Functional Genomics, Interfaculty Institute for Genetics and Functional
Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Christiane Pink
- Unit
of Periodontology, Department of Restorative Dentistry, Periodontology,
Endodontology, Preventive and Pediatric Dentistry, University Medicine Greifswald, Rotgerberstr. 8, 17475 Greifswald, Germany
| | - Elke Hammer
- Department
of Functional Genomics, Interfaculty Institute for Genetics and Functional
Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Stephan Michalik
- Department
of Functional Genomics, Interfaculty Institute for Genetics and Functional
Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Vishnu M. Dhople
- Department
of Functional Genomics, Interfaculty Institute for Genetics and Functional
Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Birte Holtfreter
- Unit
of Periodontology, Department of Restorative Dentistry, Periodontology,
Endodontology, Preventive and Pediatric Dentistry, University Medicine Greifswald, Rotgerberstr. 8, 17475 Greifswald, Germany
| | - Uwe Völker
- Department
of Functional Genomics, Interfaculty Institute for Genetics and Functional
Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Thomas Kocher
- Unit
of Periodontology, Department of Restorative Dentistry, Periodontology,
Endodontology, Preventive and Pediatric Dentistry, University Medicine Greifswald, Rotgerberstr. 8, 17475 Greifswald, Germany
| | - Manuela Gesell Salazar
- Department
of Functional Genomics, Interfaculty Institute for Genetics and Functional
Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
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11
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Wenzel K, Samal R, Hammer E, Dhople VM, Gross S, Völker U, Felix SB, Könemann S. Pathophysiological aldosterone levels modify the secretory activity of cardiac progenitor cells. Mol Cell Endocrinol 2017; 439:16-25. [PMID: 27742487 DOI: 10.1016/j.mce.2016.10.009] [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: 06/02/2016] [Revised: 09/13/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022]
Abstract
Cardiac progenitor cells (CPCs) trigger regenerative processes via paracrine mechanisms in response to changes in their environment. In the present study we explored alterations in the secretory activity of CPCs induced by raised aldosterone levels symptomatic for heart failure. The cytokine profile of the supernatant of CPCs that were treated with the mineralocorticoid showed an induction of interleukin-6 secretion. Mass spectrometric analyses revealed an increase in the abundance of secreted proteins associated with regeneration and cell migration like gelsolin and galectin-1. Differential regulation of proteins associated with the extracellular matrix further points to an activation of cell migration. In response to supernatant, migration and proliferation were induced in CPCs, indicating a potential role of paracrine factors in the activation of CPCs from other regions of the heart or extra-cardiac sources. Changes in the secretory activity of CPCs might aim to compensate for the detrimental actions of aldosterone in heart failure.
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Affiliation(s)
- Kristin Wenzel
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
| | - Rasmita Samal
- Interfaculty Institute for Genetic and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
| | - Elke Hammer
- Interfaculty Institute for Genetic and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
| | - Vishnu M Dhople
- Interfaculty Institute for Genetic and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
| | - Stefan Gross
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
| | - Uwe Völker
- Interfaculty Institute for Genetic and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
| | - Stephan B Felix
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
| | - Stephanie Könemann
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Germany.
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12
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Surmann K, Simon M, Hildebrandt P, Pförtner H, Michalik S, Dhople VM, Bröker BM, Schmidt F, Völker U. Proteome data from a host-pathogen interaction study with Staphylococcus aureus and human lung epithelial cells. Data Brief 2016; 7:1031-1037. [PMID: 27761493 PMCID: PMC5063755 DOI: 10.1016/j.dib.2016.03.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 12/23/2015] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 10/24/2022] Open
Abstract
To simultaneously obtain proteome data of host and pathogen from an internalization experiment, human alveolar epithelial A549 cells were infected with Staphylococcus aureus HG001 which carried a plasmid (pMV158GFP) encoding a continuously expressed green fluorescent protein (GFP). Samples were taken hourly between 1.5 h and 6.5 h post infection. By fluorescence activated cell sorting GFP-expressing bacteria could be enriched from host cell debris, but also infected host cells could be separated from those which did not carry bacteria after contact (exposed). Additionally, proteome data of A549 cells which were not exposed to S. aureus but underwent the same sample processing steps are provided as a control. Time-resolved changes in bacterial protein abundance were quantified in a label-free approach. Proteome adaptations of host cells were monitored by comparative analysis to a stable isotope labeled cell culture (SILAC) standard. Proteins were extracted from the cells, digested proteolytically, measured by nanoLC-MS/MS, and subsequently identified by database search and then quantified. The data presented here are related to a previously published research article describing the interplay of S. aureus HG001 and human epithelial cells (Surmann et al., 2015 [1]). They have been deposited to the ProteomeXchange platform with the identifiers PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002384 for the S. aureus HG001 proteome dataset and PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002388 for the A549 proteome dataset.
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Affiliation(s)
- Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Marjolaine Simon
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Henrike Pförtner
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Vishnu M Dhople
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Barbara M Bröker
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Sauerbruchstr. DZ7, 17475 Greifswald, Germany
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
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13
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Surmann K, Simon M, Hildebrandt P, Pförtner H, Michalik S, Stentzel S, Steil L, Dhople VM, Bernhardt J, Schlüter R, Depke M, Gierok P, Lalk M, Bröker BM, Schmidt F, Völker U. A proteomic perspective of the interplay of Staphylococcus aureus and human alveolar epithelial cells during infection. J Proteomics 2015; 128:203-17. [PMID: 26244908 DOI: 10.1016/j.jprot.2015.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 07/06/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022]
Abstract
Infectious diseases caused by pathogens such as Staphylococcus aureus are still a major threat for human health. Proteome analyses allow detailed monitoring of the molecular interplay between pathogen and host upon internalization. However, the investigation of the responses of both partners is complicated by the large excess of host cell proteins compared to bacterial proteins as well as by the fact that only a fraction of host cells are infected. In the present study we infected human alveolar epithelial A549 cells with S. aureus HG001 pMV158GFP and separated intact bacteria from host cell debris or infected from non-infected A549 cells by cell sorting to enable detailed proteome analysis. During the first 6.5h in the intracellular milieu S. aureus displayed reduced growth rate, induction of the stringent response, adaptation to microaerobic conditions as well as cell wall stress. Interestingly, both truly infected host cells and those not infected but exposed to secreted S. aureus proteins and host cell factors showed differences in the proteome pattern compared to A549 cells which had never been in contact with S. aureus. However, adaptation reactions were more pronounced in infected compared to non-infected A549 bystander cells.
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Affiliation(s)
- Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Marjolaine Simon
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Henrike Pförtner
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Sebastian Stentzel
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Sauerbruchstr. DZ7, 17475 Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Vishnu M Dhople
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Maren Depke
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Philipp Gierok
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Barbara M Bröker
- Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Sauerbruchstr. DZ7, 17475 Greifswald, Germany
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany; ZIK-FunGene Junior Research Group Applied Proteomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17475 Greifswald, Germany.
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14
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Menck K, Scharf C, Bleckmann A, Dyck L, Rost U, Wenzel D, Dhople VM, Siam L, Pukrop T, Binder C, Klemm F. Tumor-derived microvesicles mediate human breast cancer invasion through differentially glycosylated EMMPRIN. J Mol Cell Biol 2014; 7:143-53. [PMID: 25503107 PMCID: PMC4401212 DOI: 10.1093/jmcb/mju047] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [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: 08/18/2014] [Accepted: 10/11/2014] [Indexed: 12/13/2022] Open
Abstract
Tumor cells secrete not only a variety of soluble factors, but also extracellular vesicles that are known to support the establishment of a favorable tumor niche by influencing the surrounding stroma cells. Here we show that tumor-derived microvesicles (T-MV) also directly influence the tumor cells by enhancing their invasion in a both autologous and heterologous manner. Neither the respective vesicle-free supernatant nor MV from benign mammary cells mediate invasion. Uptake of T-MV is essential for the proinvasive effect. We further identify the highly glycosylated form of the extracellular matrix metalloproteinase inducer (EMMPRIN) as a marker for proinvasive MV. EMMPRIN is also present at high levels on MV from metastatic breast cancer patients in vivo. Anti-EMMPRIN strategies, such as MV deglycosylation, gene knockdown, and specific blocking peptides, inhibit MV-induced invasion. Interestingly, the effect of EMMPRIN-bearing MV is not mediated by matrix metalloproteinases but by activation of the p38/MAPK signaling pathway in the tumor cells. In conclusion, T-MV stimulate cancer cell invasion via a direct feedback mechanism dependent on highly glycosylated EMMPRIN.
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Affiliation(s)
- Kerstin Menck
- Department of Hematology/Oncology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Christian Scharf
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medicine Greifswald, Walther-Rathenau-Str. 43-45, 17475 Greifswald, Germany Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Annalen Bleckmann
- Department of Hematology/Oncology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Lydia Dyck
- Department of Hematology/Oncology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Ulrike Rost
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Dirk Wenzel
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Vishnu M Dhople
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487 Greifswald, Germany
| | - Laila Siam
- Department of Neurosurgery, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Tobias Pukrop
- Department of Hematology/Oncology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Claudia Binder
- Department of Hematology/Oncology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Florian Klemm
- Department of Hematology/Oncology, University Medical Center Göttingen, 37099 Göttingen, Germany Present address: Sloan Kettering Institute, Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, 417 E 68th St., Z-1306, New York, NY 10065, USA
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Kanugula AK, Dhople VM, Völker U, Ummanni R, Kotamraju S. Fluvastatin mediated breast cancer cell death: a proteomic approach to identify differentially regulated proteins in MDA-MB-231 cells. PLoS One 2014; 9:e108890. [PMID: 25268751 PMCID: PMC4182601 DOI: 10.1371/journal.pone.0108890] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/04/2014] [Indexed: 01/12/2023] Open
Abstract
Statins are increasingly being recognized as anti-cancer agents against various cancers including breast cancer. To understand the molecular pathways targeted by fluvastatin and its differential sensitivity against metastatic breast cancer cells, we analyzed protein alterations in MDA-MB-231 cells treated with fluvastatin using 2-DE in combination with LC-MS/MS. Results revealed dys-regulation of 39 protein spots corresponding to 35 different proteins. To determine the relevance of altered protein profiles with breast cancer cell death, we mapped these proteins to major pathways involved in the regulation of cell-to-cell signaling and interaction, cell cycle, Rho GDI and proteasomal pathways using IPA analysis. Highly interconnected sub networks showed that vimentin and ERK1/2 proteins play a central role in controlling the expression of altered proteins. Fluvastatin treatment caused proteolysis of vimentin, a marker of epithelial to mesenchymal transition. This effect of fluvastatin was reversed in the presence of mevalonate, a downstream product of HMG-CoA and caspase-3 inhibitor. Interestingly, fluvastatin neither caused an appreciable cell death nor did modulate vimentin expression in normal mammary epithelial cells. In conclusion, fluvastatin alters levels of cytoskeletal proteins, primarily targeting vimentin through increased caspase-3- mediated proteolysis, thereby suggesting a role for vimentin in statin-induced breast cancer cell death.
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Affiliation(s)
| | - Vishnu M. Dhople
- Interfacultary Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfacultary Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ramesh Ummanni
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- * E-mail: (SK); (RU)
| | - Srigiridhar Kotamraju
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- * E-mail: (SK); (RU)
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16
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de Groot REA, Ganji RS, Bernatik O, Lloyd-Lewis B, Seipel K, Šedová K, Zdráhal Z, Dhople VM, Dale TC, Korswagen HC, Bryja V. Huwe1-mediated ubiquitylation of dishevelled defines a negative feedback loop in the Wnt signaling pathway. Sci Signal 2014; 7:ra26. [PMID: 24643799 DOI: 10.1126/scisignal.2004985] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Wnt signaling plays a central role in development, adult tissue homeostasis, and cancer. Several steps in the canonical Wnt/β-catenin signaling cascade are regulated by ubiquitylation, a protein modification that influences the stability, subcellular localization, or interactions of target proteins. To identify regulators of the Wnt/β-catenin pathway, we performed an RNA interference screen in Caenorhabditis elegans and identified the HECT domain-containing ubiquitin ligase EEL-1 as an inhibitor of Wnt signaling. In human embryonic kidney 293T cells, knockdown of the EEL-1 homolog Huwe1 enhanced the activity of a Wnt reporter in cells stimulated with Wnt3a or in cells that overexpressed casein kinase 1 (CK1) or a constitutively active mutant of the Wnt co-receptor low-density lipoprotein receptor-related protein 6 (LRP6). However, knockdown of Huwe1 had no effect on reporter gene expression in cells expressing constitutively active β-catenin, suggesting that Huwe1 inhibited Wnt signaling upstream of β-catenin and downstream of CK1 and LRP6. Huwe1 bound to and ubiquitylated the cytoplasmic Wnt pathway component Dishevelled (Dvl) in a Wnt3a- and CK1ε-dependent manner. Mass spectrometric analysis showed that Huwe1 promoted K63-linked, but not K48-linked, polyubiquitination of Dvl. Instead of targeting Dvl for degradation, ubiquitylation of the DIX domain of Dvl by Huwe1 inhibited Dvl multimerization, which is necessary for its function. Our findings indicate that Huwe1 is part of an evolutionarily conserved negative feedback loop in the Wnt/β-catenin pathway.
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Affiliation(s)
- Reinoud E A de Groot
- 1Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
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17
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Pförtner H, Burian MS, Michalik S, Depke M, Hildebrandt P, Dhople VM, Pané-Farré J, Hecker M, Schmidt F, Völker U. Activation of the alternative sigma factor SigB of Staphylococcus aureus following internalization by epithelial cells – An in vivo proteomics perspective. Int J Med Microbiol 2014; 304:177-87. [DOI: 10.1016/j.ijmm.2013.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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18
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Kota V, Dhople VM, Fullbright G, Smythe NM, Szulc ZM, Bielawska A, Hama H. 2'-hydroxy C16-ceramide induces apoptosis-associated proteomic changes in C6 glioma cells. J Proteome Res 2013; 12:4366-75. [PMID: 23987666 DOI: 10.1021/pr4003432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ceramide is a bioactive sphingolipid involved in regulation of numerous cell signaling pathways. Evidence is accumulating that differences in ceramide structure, such as N-acyl chain length and desaturation of sphingoid base, determine the biological activities of ceramide. Using synthetic (R)-2'-hydroxy-C16-ceramide, which is the naturally occurring stereoisomer, we demonstrate that this ceramide has more potent pro-apoptotic activity compared to its (S) isomer or non-hydroxylated C16-ceramide. Upon exposure to (R)-2'-hydroxy-ceramide, C6 glioma cells rapidly underwent apoptosis as indicated by caspase-3 activation, PARP cleavage, chromatin condensation, and annexin V stain. A 2D gel proteomics analysis identified 28 proteins whose levels were altered during the initial 3 h of exposure. Using the list of 28 proteins, we performed a software-assisted pathway analysis to identify possible signaling events that would result in the observed changes. The result indicated that Akt and MAP kinase pathways are among the possible pathways regulated by (R)-2'-hydroxy-ceramide. Experimental validation confirmed that 2'-hydroxy-ceramide significantly altered phosphorylation status of Akt and its downstream effector GSK3β, as well as p38, ERK1/2, and JNK1/2 MAP kinases. Unexpectedly, robust phosphorylation of Akt was observed within 1 h of exposure to 2'-hydroxy-ceramide, followed by dephosphorylation. Phosphorylation status of MAPKs showed a complex pattern, in which rapid phosphorylation of ERK1/2 was followed by dephosphorylation of p38 and ERK1/2 and phosphorylation of the 46 kDa isoform of JNK1/2. These data indicate that (R)-2'-hydroxy-ceramide regulates multiple signaling pathways by affecting protein kinases and phosphatases with kinetics distinct from that of the extensively studied non-hydroxy-ceramide or its unnatural stereoisomer.
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Affiliation(s)
- Venkatesh Kota
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina , Charleston, South Carolina 29425, United States
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Salazar MG, Jehmlich N, Murr A, Dhople VM, Holtfreter B, Hammer E, Völker U, Kocher T. Identification of periodontitis associated changes in the proteome of whole human saliva by mass spectrometric analysis. J Clin Periodontol 2013; 40:825-32. [DOI: 10.1111/jcpe.12130] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Manuela Gesell Salazar
- Department of Functional Genomics; Interfaculty Institute for Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Nico Jehmlich
- Department of Functional Genomics; Interfaculty Institute for Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Annette Murr
- Department of Functional Genomics; Interfaculty Institute for Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Vishnu M. Dhople
- Department of Functional Genomics; Interfaculty Institute for Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Birte Holtfreter
- Unit of Periodontology; Department of Restorative Dentistry, Periodontology and Endodontology; University Medicine Greifswald; Greifswald Germany
| | - Elke Hammer
- Department of Functional Genomics; Interfaculty Institute for Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Uwe Völker
- Department of Functional Genomics; Interfaculty Institute for Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Thomas Kocher
- Unit of Periodontology; Department of Restorative Dentistry, Periodontology and Endodontology; University Medicine Greifswald; Greifswald Germany
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20
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Jehmlich N, Dinh KHD, Gesell-Salazar M, Hammer E, Steil L, Dhople VM, Schurmann C, Holtfreter B, Kocher T, Völker U. Quantitative analysis of the intra- and inter-subject variability of the whole salivary proteome. J Periodontal Res 2012; 48:392-403. [PMID: 23164135 DOI: 10.1111/jre.12025] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVE Interest in human saliva is increasing for disease-specific biomarker discovery studies. However, protein composition of whole saliva can grossly vary with physiological and environmental factors over time and it comprises human as well as bacterial proteins. MATERIAL AND METHODS We compared intra- and inter-subject variabilities using complementary gel-based (two-dimensional difference gel electrophoresis, 2-D DIGE) and gel-free (liquid chromatography tandem mass spectrometry, LC-MS/MS) proteomics profiling of saliva. Unstimulated whole saliva of four subjects was examined at three different time-points (08.00 h, 12.00 h and 17.00 h) and variability of the saliva proteome was analyzed on two successive days by LC-MS/MS. RESULTS In the 2-D DIGE experiment, the median coefficient of variation (CV) for intra-subject variability was significantly lower (CV of 0.39) than that for inter-subject variability (CV of 0.57; CV of technical replicates 0.17). LC-MS/MS data confirmed the significantly lower variation within subjects over time (CV of 0.37) than the inter-subject variability (CV of 0.53; CV of technical replicates 0.11), and that the inter-subject variability was not time-dependent. CONCLUSION Both techniques revealed similar trends of variations on technical, intra- and inter-subject level but provided peptide and protein focused information and should thus be used as complementary approaches. The data presented indicate that 2-D DIGE as well as LC-MS/MS approaches are suitable for biomarker screening in saliva.
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Affiliation(s)
- N Jehmlich
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
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21
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Sievert H, Venz S, Platas-Barradas O, Dhople VM, Schaletzky M, Nagel CH, Braig M, Preukschas M, Pällmann N, Bokemeyer C, Brümmendorf TH, Pörtner R, Walther R, Duncan KE, Hauber J, Balabanov S. Protein-protein-interaction network organization of the hypusine modification system. Mol Cell Proteomics 2012; 11:1289-305. [PMID: 22888148 PMCID: PMC3494187 DOI: 10.1074/mcp.m112.019059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/27/2012] [Indexed: 12/12/2022] Open
Abstract
Hypusine modification of eukaryotic initiation factor 5A (eIF-5A) represents a unique and highly specific post-translational modification with regulatory functions in cancer, diabetes, and infectious diseases. However, the specific cellular pathways that are influenced by the hypusine modification remain largely unknown. To globally characterize eIF-5A and hypusine-dependent pathways, we used an approach that combines large-scale bioreactor cell culture with tandem affinity purification and mass spectrometry: "bioreactor-TAP-MS/MS." By applying this approach systematically to all four components of the hypusine modification system (eIF-5A1, eIF-5A2, DHS, and DOHH), we identified 248 interacting proteins as components of the cellular hypusine network, with diverse functions including regulation of translation, mRNA processing, DNA replication, and cell cycle regulation. Network analysis of this data set enabled us to provide a comprehensive overview of the protein-protein interaction landscape of the hypusine modification system. In addition, we validated the interaction of eIF-5A with some of the newly identified associated proteins in more detail. Our analysis has revealed numerous novel interactions, and thus provides a valuable resource for understanding how this crucial homeostatic signaling pathway affects different cellular functions.
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Affiliation(s)
- Henning Sievert
- From the ‡Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumor Zentrum, University Hospital Eppendorf, Hamburg, Germany
| | - Simone Venz
- §Department of Medical Biochemistry and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Oscar Platas-Barradas
- ¶Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Vishnu M. Dhople
- ‖Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - Martin Schaletzky
- ¶Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Claus-Henning Nagel
- **Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Melanie Braig
- From the ‡Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumor Zentrum, University Hospital Eppendorf, Hamburg, Germany
| | - Michael Preukschas
- From the ‡Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumor Zentrum, University Hospital Eppendorf, Hamburg, Germany
| | - Nora Pällmann
- From the ‡Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumor Zentrum, University Hospital Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- From the ‡Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumor Zentrum, University Hospital Eppendorf, Hamburg, Germany
| | - Tim H. Brümmendorf
- ‡‡Clinic for Internal Medicine IV, Hematology and Oncology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Ralf Pörtner
- ¶Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Reinhard Walther
- §Department of Medical Biochemistry and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Kent E. Duncan
- §§Neuronal Translational Control Group, Center for Molecular Neurobiology, ZMNH, University of Hamburg Medical School, Hamburg, Germany
| | - Joachim Hauber
- **Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Stefan Balabanov
- From the ‡Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumor Zentrum, University Hospital Eppendorf, Hamburg, Germany
- ¶¶Division of Hematology, University Hospital Zurich, Zurich, Switzerland
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Kota V, Dhople VM, Shivaji S. Tyrosine phosphoproteome of hamster spermatozoa: Role of glycerol-3-phosphate dehydrogenase 2 in sperm capacitation. Proteomics 2009; 9:1809-26. [DOI: 10.1002/pmic.200800519] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Krishnan K, Kathiresan T, Raman R, Rajini B, Dhople VM, Aggrawal RK, Sharma Y. Ubiquitous lens alpha-, beta-, and gamma-crystallins accumulate in anuran cornea as corneal crystallins. J Biol Chem 2007; 282:18953-9. [PMID: 17452334 DOI: 10.1074/jbc.m609275200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Corneal epithelium is known to have high levels of some metabolic enzymes such as aldehyde dehydrogenase in mammals, gelsolin in zebrafish, and alpha-enolase in several species. Analogous to lens crystallins, these enzymes and proteins are referred to as corneal crystallins, although their precise function is not established in any species. Although it is known that after lentectomy, the outer cornea undergoes transdifferentiation to regenerate a lens only in anuran amphibians, major proteins expressed in an anuran cornea have not been identified. This study therefore aimed to identify the major corneal proteins in the Indian toad (Bufo melanostictus) and the Indian frog (Rana tigrina). Soluble proteins of toad and frog corneas were resolved on two-dimensional gels and identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight and electrospray ionization quadrupole time-of-flight. We report that anuran cornea is made up of the full complement of ubiquitous lens alpha-, beta-, and gamma-crystallins, mainly localized in the corneal epithelium. In addition, some taxon-specific lens crystallins and novel proteins, such as alpha- or beta-enolase/tau-crystallin, were also identified. Our data present a unique case of the anuran cornea where the same crystallins are used in the lens and in the cornea, thus supporting the earlier idea that crystallins are essential for the visual functions of the cornea as they perform for the lens. High levels of lens alpha-, beta-, and gamma-crystallins have not been reported in the cornea of any species studied so far and may offer a possible explanation for their inability to regenerate a lens after lentectomy. Our data that anuran cornea has an abundant quantity of almost all the lens crystallins are consistent with its ability to form a lens, and this connection is worthy of further studies.
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Affiliation(s)
- Kannan Krishnan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India
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24
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Kathiresan T, Krishnan K, Krishnakumar V, Agrawal R, Anand A, Muralidhar D, Mishra AK, Dhople VM, Aggrawal RK, Sharma Y. Triose phosphate isomerase, a novel enzyme-crystallin, and tau-crystallin in crocodile cornea. FEBS J 2006; 273:3370-80. [PMID: 16857018 DOI: 10.1111/j.1742-4658.2006.05344.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several enzymes are known to accumulate in the cornea in unusually high concentrations. Based on the analogy with lens crystallins, these enzymes are called corneal crystallins, which are diverse and species-specific. Examining crystallins in lens and cornea in multiple species provides great insight into their evolution. We report data on major proteins present in the crocodile cornea, an evolutionarily distant taxon. We demonstrate that tau-crystallin/alpha-enolase and triose phosphate isomerase (TIM) are among the major proteins expressed in the crocodile cornea as resolved by 2D gel electrophoresis and identified by MALDI-TOF. These proteins might be classified as putative corneal crystallins. tau-Crystallin, known to be present in turtle and crocodile lens, has earlier been identified in chicken and bovine cornea, whereas TIM has not been identified in the cornea of any species. Immunostaining showed that tau-crystallin and TIM are concentrated largely in the corneal epithelium. Using western blot, immunofluorescence and enzymatic activity, we demonstrate that high accumulation of tau-crystallin and TIM starts in the late embryonic development (after the 24th stage of embryonic development) with maximum expression in a two-week posthatched animal. The crocodile corneal extract exhibits significant alpha-enolase and TIM activities, which increases in the corneal extract with development. Our results establishing the presence of tau-crystallin in crocodile, in conjunction with similar reports for other species, suggest that it is a widely prevalent corneal crystallin. Identification of TIM in the crocodile cornea reported here adds to the growing list of corneal crystallins.
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25
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Chumbalkar VC, Subhashini C, Dhople VM, Sundaram CS, Jagannadham MV, Kumar KN, Srinivas PNBS, Mythili R, Rao MK, Kulkarni MJ, Hegde S, Hegde AS, Samual C, Santosh V, Singh L, Sirdeshmukh R. Differential protein expression in human gliomas and molecular insights. Proteomics 2005; 5:1167-77. [PMID: 15759318 DOI: 10.1002/pmic.200401202] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gliomas are the most common of the primary intracranial tumors with astrocytomas constituting about 40%. Using clinically and histologically assessed astrocytomas, we have studied their protein profiles using a two-dimensional gel electrophoresis-mass spectrometry approach and identified differentially expressed proteins which may be useful molecular indicators to understand these tumors. Examination of the protein profiles of 27 astrocytoma samples of different grades revealed 72 distinct, differentially expressed proteins belonging to various functional groups such as cytoskeleton and intermediate filament proteins, heat shock proteins (HSPs), enzymes and regulatory proteins. Based on the consistency of their differential expression, 29 distinct proteins could be short-listed and may have a role in the pathology of astrocytomas. Some were found to be differentially expressed in both Grade III and IV astrocytomas while others were associated with a particular grade. A notable observation was underexpression of Prohibitin, a potential tumor suppressor protein, Rho-GDP dissociation inhibitor, Rho-GDI, a regulator of Rho GTPases and HSPs as well as destabilization of glial fibrillary acidic protein, GFAP, major protein of the glial filaments, in Grade III malignant tumors. We attempt to explain glioma malignancy and progression in terms of their combined role.
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26
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Chumbalkar VC, Subhashini C, Dhople VM, Sundaram CS, Jagannadham MV, Kumar KN, Srinivas PNBS, Mythili R, Rao MK, Kulkarni MJ, Hegde S, Hegde AS, Samual C, Santosh V, Singh L, Sirdeshmukh R. Differential protein expression in human gliomas and molecular insights. Proteomics 2005. [DOI: 10.1002/pmic.200590038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Delta-Lysin is a 26-residue hemolytic peptide secreted by Staphylococcus aureus. Unlike the bee venom peptide melittin, delta-lysin does not exhibit antibacterial activity. We have synthesized delta-lysin and several analogs wherein the N-terminal residues of the toxin were sequentially deleted. The toxin has three aspartic acids, four lysines and no prolines. Analogs were also generated in which all the aspartic acids were replaced with lysines. A proline residue was introduced in the native sequences as well as in the analogs where aspartic acids were replaced with lysines. We observed that 20- and 22-residue peptides corresponding to residues 7-26 and 5-26 of delta-lysin, respectively, had greater hemolytic activity than the parent peptide. These shorter peptides, unlike delta-lysin, did not self-associate to adopt alpha-helical conformation in water, at lytic concentrations. Introduction of proline or substitution of aspartic acids by lysines resulted in loss in propensity to adopt helical conformation in water. When proline was introduced in the peptides corresponding to the native toxin sequence, loss of hemolytic activity was observed. Substitution of all the aspartic acids with lysines resulted in enhanced hemolytic activity in all the analogs. However, when both proline and aspartic acid to lysine changes were made, only antibacterial activity was observed in the shorter peptides. Our investigations on delta-lysin and its analogs provide insights into the positioning of anionic, cationic residues and proline in determining hemolytic and antibacterial activities.
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Affiliation(s)
- Vishnu M Dhople
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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Moudgal NR, Krishnamurthy HN, Surekha S, Krishnamurthy H, Dhople VM, Nagaraj R, Sairam MR. Immunobiology of a synthetic luteinizing hormone receptor peptide 21-41. J Androl 2001; 22:992-8. [PMID: 11700864 DOI: 10.1002/j.1939-4640.2001.tb03440.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Immunization of adult male rabbits with a synthetic luteinizing hormone-receptor peptide (LH-RP; representing amino-acids 21-41 of the extracellular domain of the rat LH receptor) resulted in production of high-titer antibodies capable of interacting with particulate and cell-based LH receptors. The antibody produced was able to inhibit binding of 125I-labeled human chorionic gonadotropin (hCG) to a particulate sheep luteal LH receptor preparation by 40%-50%. Maximal inhibitory activity was correlated with high antibody titer. Immunocytometry revealed that the antibody could directly bind to cells having LH receptors, such as rat granulosa and Leydig cells. The antibodies recognized a 77-kilodalton membrane protein in Western blots of mouse testicular extracts. Interaction of endogenous Leydig cell LH receptor with the LH-RP antibody resulted in both hormone agonist and antagonistic activities. The hormone-mimicking activity (increase in serum testosterone over control) was confined only to the early phase of immunization when the antibody titer was low. Blockade of LH receptor during the later part of immunization resulted in a significant reduction in serum testosterone over controls and inhibition of spermatogenesis. DNA flow cytometry showed that a specific and significant inhibition of meiosis (transformation of primary spermatocytes to round and elongated spermatids P < .01) and spermiogenesis (transformation of round spermatids to elongated spermatids P < .0001) occurred following blockade of LH function.
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Affiliation(s)
- N R Moudgal
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore
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Ranganathan S, Kundu D, Tamilarasu N, Nagaraj R, Dhople VM, Jaganadham MV. The gramicidin pore: Selective tryptophan replacement with aspartic acid. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)01050-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Dhople VM, Nagaraj R. Generation of analogs having potent antimicrobial and hemolytic activities with minimal changes from an inactive 16-residue peptide corresponding to the helical region of Staphylococcus aureus delta-toxin. Protein Eng 1995; 8:315-8. [PMID: 7479693 DOI: 10.1093/protein/8.3.315] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The delta-toxin is a 26-residue peptide from Staphylococcus aureus with the sequence formyl-MAQDIISTIGDLVKWIIDTVNKFTKK. NMR studies indicate that the segment IISTIGDLVKWIIDTV occurs in an alpha-helical conformation in the toxin. A synthetic peptide corresponding to this segment, although helical, did not exhibit hemolytic activity. Since charged residues like D and K are likely to modulate cytolytic activity, analogs of the 16-residue peptide were synthesized where D was systematically replaced by K. Analogs in which the first D and both Ds were replaced by K showed potent antimicrobial and hemolytic activities. The analog in which the second D was replaced by K was relatively less active. However, all the peptides showed an alpha-helical structure with similar helical content. The activities of the peptides were found to correlate directly with their ability to permeabilize model membranes. Thus, by minimal judicious replacement of charged amino acids, it should be possible to generate cytolytic peptides from short segments of peptide toxins.
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Affiliation(s)
- V M Dhople
- Centre for Cellular and Molecular Biology, Hyderabad, India
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Dhople VM, Nagaraj R. Delta-toxin, unlike melittin, has only hemolytic activity and no antimicrobial activity: rationalization of this specific biological activity. Biosci Rep 1993; 13:245-50. [PMID: 8305635 DOI: 10.1007/bf01123506] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The antimicrobial activity of a synthetic peptide corresponding to delta-hemolysin had been examined. The peptide did not exhibit antimicrobial activity against gram negative and gram positive micro-organisms unlike other hemolytic peptides like melittin. This lack of antibacterial activity arises due to the inability of delta-hemolysin to perturb the negatively charged bacterial cell surface and permeabilize the bacterial plasma membrane. However, the red blood cell surface has a structure considerably different from bacteria and does not act as a barrier to molecules reaching the lipid membrane. Hence delta-toxin can lyse erythrocytes. Thus, the specificity in biological activity has been rationalized in terms of differences in the interaction of the toxin with the bacterial and red blood cell surfaces.
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Affiliation(s)
- V M Dhople
- Centre for Cellular and Molecular Biology, Hyderabad, India
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