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Kawahara R, Rosa-Fernandes L, Dos Santos AF, Bandeira CL, Dombrowski JG, Souza RM, Da Fonseca MP, Festuccia WT, Labriola L, Larsen MR, Marinho CRF, Palmisano G. Integrated Proteomics Reveals Apoptosis-related Mechanisms Associated with Placental Malaria. Mol Cell Proteomics 2019; 18:182-199. [PMID: 30242111 PMCID: PMC6356084 DOI: 10.1074/mcp.ra118.000907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/15/2018] [Indexed: 12/27/2022] Open
Abstract
Malaria in pregnancy is a public health concern in malaria-endemic areas. Accumulation of maternal immune cells in the placenta and increased levels of inflammatory cytokines caused by sequestration of Plasmodium falciparum-infected erythrocytes have been associated to poor neonatal outcomes, including low birth weight because of fetal growth restriction. Little is known about the molecular changes occurring in a P. falciparum-infected placenta that has developed placental malaria during pregnancy but had the parasites cleared by pharmacological treatment (past infection). We conducted an integrated proteome, phosphoproteome and glycoproteome analysis in past P. falciparum-infected placentas aiming to find molecular changes associated with placental malaria. A total of 2946 proteins, 1733 N-linked glycosites and 4100 phosphosites were identified and quantified in this study, disclosing overrepresented processes related to oxidative stress, protein folding and regulation of apoptosis in past-infected placentas Moreover, AKT and ERK signaling pathways activation, together with clinical data, were further correlated to an increased apoptosis in past-infected placentas. This study showed apoptosis-related mechanisms associated with placental malaria that can be further explored as therapeutic target against adverse pregnancy outcomes.
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Affiliation(s)
- Rebeca Kawahara
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Biochemistry and Molecular biology, University of Southern Denmark, Odense, Denmark
| | | | - Carla Letícia Bandeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | - Rodrigo M Souza
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil
| | | | - William T Festuccia
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Leticia Labriola
- Department of Biochemistry, Chemistry Institute, University of São Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular biology, University of Southern Denmark, Odense, Denmark
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil;.
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo São Paulo, Brazil;.
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Hwang JR, Chou CL, Medvar B, Knepper MA, Jung HJ. Identification of β-catenin-interacting proteins in nuclear fractions of native rat collecting duct cells. Am J Physiol Renal Physiol 2017; 313:F30-F46. [PMID: 28298358 PMCID: PMC5538839 DOI: 10.1152/ajprenal.00054.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 02/06/2023] Open
Abstract
The gene encoding the aquaporin-2 water channel is regulated transcriptionally in response to vasopressin. In the renal collecting duct, vasopressin stimulates the nuclear translocation and phosphorylation (at Ser552) of β-catenin, a multifunctional protein that acts as a transcriptional coregulator in the nucleus. The purpose of this study was to identify β-catenin-interacting proteins that might be involved in transcriptional regulation in rat inner medullary collecting duct (IMCD) cells, using experimental and computational approaches. We used a standard chromatin immunoprecipitation procedure coupled to mass spectrometry (ChIP-MS) in a nuclear fraction isolated from rat IMCD suspensions. Over four biological replicates, we reproducibly identified 43 β-catenin-binding proteins, including several known β-catenin-binding partners as well as novel interacting proteins. Multiple proteins involved in transcriptional regulation were identified (Taf1, Jup, Tdrd3, Cdh1, Cenpj, and several histones). Many of the identified β-catenin-binding partners were found in prior studies to translocate to the nucleus in response to vasopressin. There was only one DNA-binding transcription factor (TF), specifically Taf1, part of the RNA-polymerase II preinitiation complex. To identify sequence-specific TFs that might interact with β-catenin, Bayes' theorem was used to integrate data from several information sources. The analysis identified several TFs with potential binding sites in the Aqp2 gene promoter that could interact with β-catenin in the regulation of Aqp2 gene transcription, specifically Jun, Junb, Jund, Atf1, Atf2, Mef2d, Usf1, Max, Pou2f1, and Rxra. The findings provide information necessary for modeling the transcriptional response to vasopressin.
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Affiliation(s)
- Jacqueline R Hwang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Barbara Medvar
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Hyun Jun Jung
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Ohkawa K, Miura Y, Nomura T, Arai R, Abe K, Tsukada M, Hirabayashi K. Long-range periodic sequence of the cement/silk protein of Stenopsyche marmorata: purification and biochemical characterisation. BIOFOULING 2013; 29:357-367. [PMID: 23574115 DOI: 10.1080/08927014.2013.774376] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The long-range periodic amino acid sequence of the bifunctional silk/cement protein from larvae of the caddisfly, Stenopsyche marmorata, is discussed in this study. The protein, named the S. marmorata silk protein (Smsp-1), was first purified to electrophoretic homogeneity. The results of Edman-based sequencing of Smsp-1 tryptic digests were consistent with the amino acid sequence deduced from a cDNA clone of the Smsp-1 gene. All undetected amino acids in the Edman-based sequencing were encoded as Ser, suggesting the presence of O-phospho-Ser. (31)P-NMR and an O-phospho-amino acid analysis successfully showed that the O-phospho-Ser residue occurred in a clustered manner, serving a cement function for Smsp-1. Two patterns of non-phosphorylated repeats, -SLGPYGDPRGDXLGPYGG- (X = V, G or D) and -GVGPYGDGLGPYGG-, were enriched in Smsp-1 compared with the O-phospho-Ser cluster, and have fibre-forming functions.
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Affiliation(s)
- Kousaku Ohkawa
- Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano Prefecture, Japan.
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4
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Silvestroni A, Jewell KA, Lin WJ, Connelly JE, Ivancic MM, Tao WA, Rajagopal L. Identification of serine/threonine kinase substrates in the human pathogen group B streptococcus. J Proteome Res 2009; 8:2563-74. [PMID: 19309132 PMCID: PMC2863997 DOI: 10.1021/pr900069n] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All living organisms respond to changes in their internal and external environment for their survival and existence. Signaling is primarily achieved through reversible phosphorylation of proteins in both prokaryotes and eukaryotes. A change in the phosphorylation state of a protein alters its function to enable the control of cellular responses. A number of serine/threonine kinases regulate the cellular responses of eukaryotes. Although common in eukaryotes, serine/threonine kinases have only recently been identified in prokaryotes. We have described that the human pathogen Group B Streptococcus (GBS, Streptococcus agalactiae) encodes a single membrane-associated, serine/threonine kinase (Stk1) that is important for virulence of this bacterium. In this study, we used a combination of phosphopeptide enrichment and mass spectrometry to enrich and identify serine (S) and threonine (T) phosphopeptides of GBS. A comparison of S/T phosphopeptides identified from the Stk1 expressing strains to the isogenic stk1 mutant indicates that 10 proteins are potential substrates of the GBS Stk1 enzyme. Some of these proteins are phosphorylated by Stk1 in vitro and a site-directed substitution of the phosphorylated threonine to an alanine abolished phosphorylation of an Stk1 substrate. Collectively, these studies provide a novel approach to identify serine/threonine kinase substrates for insight into their signaling in human pathogens like GBS.
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Affiliation(s)
| | | | | | | | | | | | - Lakshmi Rajagopal
- Corresponding author. Mailing address: Seattle Children’s Hospital Research Institute, 1900 Ninth Ave., Seattle, WA 98101-1304. Phone: (206) 884-7336. Fax: (206) 884-7311.
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Lin WJ, Walthers D, Connelly JE, Burnside K, Jewell KA, Kenney LJ, Rajagopal L. Threonine phosphorylation prevents promoter DNA binding of the Group B Streptococcus response regulator CovR. Mol Microbiol 2009; 71:1477-95. [PMID: 19170889 DOI: 10.1111/j.1365-2958.2009.06616.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
All living organisms communicate with the external environment for their survival and existence. In prokaryotes, communication is achieved by two-component systems (TCS) comprising histidine kinases and response regulators. In eukaryotes, signalling is accomplished by serine/threonine and tyrosine kinases. Although TCS and serine/threonine kinases coexist in prokaryotes, direct cross-talk between these families was first described in Group B Streptococcus (GBS). A serine/threonine kinase (Stk1) and a TCS (CovR/CovS) co-regulate toxin expression in GBS. Typically, promoter binding of regulators like CovR is controlled by phosphorylation of the conserved active site aspartate (D53). In this study, we show that Stk1 phosphorylates CovR at threonine 65. The functional consequence of threonine phosphorylation of CovR in GBS was evaluated using phosphomimetic and silencing substitutions. GBS encoding the phosphomimetic T65E allele are deficient for CovR regulation unlike strains encoding the non-phosphorylated T65A allele. Further, compared with wild-type or T65A CovR, the T65E CovR is unable to bind promoter DNA and is decreased for phosphorylation at D53, similar to Stk1-phosphorylated CovR. Collectively, we provide evidence for a novel mechanism of response regulator control that enables GBS (and possibly other prokaryotes) to fine-tune gene expression for environmental adaptation.
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Affiliation(s)
- Wan-Jung Lin
- Department of Pediatric Infectious Diseases, University of Washington School of Medicine and Seattle Children's Hospital Research Institute, Seattle, WA 98101, USA
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Illario M, Cavallo AL, Bayer KU, Di Matola T, Fenzi G, Rossi G, Vitale M. Calcium/calmodulin-dependent protein kinase II binds to Raf-1 and modulates integrin-stimulated ERK activation. J Biol Chem 2003; 278:45101-8. [PMID: 12954639 DOI: 10.1074/jbc.m305355200] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Integrin activation generates different signalings in a cell type-dependent manner and stimulates cell proliferation through the Ras/Raf-1/Mek/Erk pathway. In this study, we demonstrate that integrin stimulation by fibronectin (FN), besides activating the Ras/Erk pathway, generates an auxiliary calcium signal that activates calmodulin and the Ca2+/calmodulin-dependent protein kinase II (CaMKII). This signal regulates Raf-1 activation by Ras and modulates the FN-stimulated extracellular signal-regulated kinase (Erk-1/2). The binding of soluble FN to integrins induced increase of intracellular calcium concentration associated with phosphorylation and activation of CaMKII. In two different cell lines, inhibition of CaMKII activity by specific inhibitors inhibited Erk-1/2 phosphorylation. Whereas CaMK inhibition affected neither integrin-stimulated Akt phosphorylation nor p21Ras or Mek-1 activity, it was necessary for Raf-1 activity. FN-induced Raf-1 activity was abrogated by the CaMKII specific inhibitory peptide ant-CaNtide. Integrin activation by FN induced the formation of a Raf-1/CaMKII complex, abrogated by inhibition of CaMKII. Active CaMKII phosphorylated Raf-1 in vitro. This is the first demonstration that CaMKII interplays with Raf-1 and regulates Erk activation induced by Ras-stimulated Raf-1. These findings also provide evidence supporting the possible existence of cross-talk between other intracellular pathways involving CaMKII and Raf-1.
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Affiliation(s)
- Maddalena Illario
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II, Napoli, 80131 Italy
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Jakobi R, Huang Z, Walter BN, Tuazon PT, Traugh JA. Substrates enhance autophosphorylation and activation of p21-activated protein kinase gamma-PAK in the absence of activation loop phosphorylation. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:4414-21. [PMID: 10880965 DOI: 10.1046/j.1432-1327.2000.01488.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The p21-activated protein kinase gamma-PAK from rabbit, expressed in insect cells, is activated following binding of Cdc42(GTPgammaS). The rate of autophosphorylation is increased fivefold and the protein kinase activity 13-fold, as measured with the synthetic heptapeptide (AKRESAA). The mutant K278R, where the invariant lysine in the catalytic site is replaced by arginine, shows neither autophosphorylation nor activity. Replacement of the conserved threonine in the catalytic domain with alanine (T402A) reduces autophosphorylation and protein kinase activity to 1% that of the wild-type gamma-PAK, indicating autophosphorylation of Thr402 in the activation loop is essential for protein kinase activity. In contrast, certain protein substrates such as histone 2B, histone 4 and myelin basic protein, stimulate both autophosphorylation and protein kinase activity to levels similar to those observed with Cdc42(GTPgammaS). This substrate-level activation does not require autophosphorylation of Thr402 in the activation loop. As shown with T402A, the protein kinase activity with histone 4 is similar to that observed with recombinant wild-type gamma-PAK. Basic proteins or peptides which are not substrates of gamma-PAK, such as histone 1 and polylysine, do not stimulate autophosphorylation or activity. Other substrates such as the Rous sarcoma virus protein NC are phosphorylated by gamma-PAK following activation by Cdc42(GTPgammaS), but are not phosphorylated by T402A. The data suggest that some substrates can override the requirement for Cdc42(GTPgammaS), by activating gamma-PAK directly.
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Affiliation(s)
- R Jakobi
- Department of Biochemistry, University of California, Riverside 92521, USA
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8
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Hsu CC, Thomas C, Chen W, Davis KM, Foos T, Chen JL, Wu E, Floor E, Schloss JV, Wu JY. Role of synaptic vesicle proton gradient and protein phosphorylation on ATP-mediated activation of membrane-associated brain glutamate decarboxylase. J Biol Chem 1999; 274:24366-71. [PMID: 10446215 DOI: 10.1074/jbc.274.34.24366] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previously, we have shown that the soluble form of brain glutamic acid decarboxylase (GAD) is inhibited by ATP through protein phosphorylation and is activated by calcineurin-mediated protein dephosphorylation (Bao, J., Cheung, W. Y., and Wu, J. Y. (1995) J. Biol. Chem. 270, 6464-6467). Here we report that the membrane-associated form of GAD (MGAD) is greatly activated by ATP, whereas adenosine 5'-[beta,gamma-imido]triphosphate (AMP-PNP), a non-hydrolyzable ATP analog, has no effect on MGAD activity. ATP activation of MGAD is abolished by conditions that disrupt the proton gradient of synaptic vesicles, e.g. the presence of vesicular proton pump inhibitor, bafilomycin A1, the protonophore carbonyl cyanide m-chorophenylhydrazone or the ionophore gramicidin, indicating that the synaptic vesicle proton gradient is essential in ATP activation of MGAD. Furthermore, direct incorporation of (32)P from [gamma-(32)P]ATP into MGAD has been demonstrated. In addition, MGAD (presumably GAD65, since it is recognized by specific monoclonal antibody, GAD6, as well as specific anti-GAD65) has been reported to be associated with synaptic vesicles. Based on these results, a model linking gamma-aminobutyric acid (GABA) synthesis by MGAD to GABA packaging into synaptic vesicles by proton gradient-mediated GABA transport is presented. Activation of MGAD by phosphorylation appears to be mediated by a vesicular protein kinase that is controlled by the vesicular proton gradient.
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Affiliation(s)
- C C Hsu
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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9
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Wera S. An EXCEL-based method to search for potential Ser/Thr-phosphorylation sites in proteins. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 1999; 58:65-68. [PMID: 10195647 DOI: 10.1016/s0169-2607(98)00068-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A user-friendly, inexpensive EXCEL-based program to find potential phosphorylation sites in proteins is presented. The input of the program is a protein sequence in single letter code. The program searches for 93 different protein kinase recognition sites from 30 different protein kinases. The output is a list of these sites and their position in the sequence. The program can easily be updated in case new recognition sites are described. With a few adaptations, the tool can also be used to find other patterns in a protein sequence.
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Affiliation(s)
- S Wera
- Laboratorium voor Moleculaire Celbiologie, Katholieke Universiteit Leuven, Leuven-Heverlee, Belgium.
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Yan JX, Packer NH, Gooley AA, Williams KL. Protein phosphorylation: technologies for the identification of phosphoamino acids. J Chromatogr A 1998; 808:23-41. [PMID: 9652109 DOI: 10.1016/s0021-9673(98)00115-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein phosphorylation plays a central role in many biological and biomedical phenomena. In this review, while a brief overview of the occurrence and function of protein phosphorylation is given, the primary focus is on studies related to the detection and analysis of phosphorylation both in vivo and in vitro. We focus on phosphorylation of serine, threonine and tyrosine, the most commonly phosphorylated amino acids in eukaryotes. Technologies such as radiolabelling, antibody recognition, chromatographic methods (HPLC, TLC), electrophoresis, Edman sequencing and mass spectrometry are reviewed. We consider the speed, simplicity and sensitivity of tools for detection and identification of protein phosphorylation, as well as quantitation and site characterisation. The limitations of currently available methods are summarised.
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Affiliation(s)
- J X Yan
- Macquarie University Centre for Analytical Biotechnology, School of Biological Sciences, Macquarie University, Sydney NSW, Australia
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Rensing L, Mohsenzadeh S, Ruoff P, Meyer U. Temperature compensation of the circadian period length--a special case among general homeostatic mechanisms of gene expression? Chronobiol Int 1997; 14:481-98. [PMID: 9298284 DOI: 10.3109/07420529709001470] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In Neurospora crassa, as well as in other organisms, the expression of housekeeping genes is transiently suppressed after exposure to higher temperatures (30-45 degrees C); expression is then reactivated and adapts after a few-hours to values closer to the initial rates. Adaptive mechanisms apparently exist in the processes of transcription, RNA processing, and translation and render protein synthesis rates temperature compensated. Heat shock proteins (HSPs) play an important role within these mechanisms ("acquired thermotolerance of protein synthesis"), but their function is as yet not exactly known. Adaptive mechanisms seem also to involve intracellular ion changes after exposure to moderate temperature elevation. The expression of heat shock genes is transiently enhanced after exposure to higher temperatures and also adapts after a few hours. The adaptation mechanism includes inactivation of the heat shock transcription factor (HSF) by means of phosphorylation changes and possibly by binding of a gene product (HSP70)-a mechanism representing a negative feedback control. These examples demonstrate the existence of general adaptive mechanisms at different levels of gene expression that may also be at work in the temperature compensation of clock gene expression. Apart from such adaptation processes, antagonistic reactions within the processes of gene expression and protein modification might be equally enhanced or suppressed by temperature changes, leaving the equilibrium unaffected or balanced (antagonistic balance, see Ruoff et al., this issue of Chronobiology International). This principle is shown to apply to the effect of temperature elevation on total protein synthesis and degradation. It may also apply to other antagonistic processes such as phosphorylation-dephosphorylation or monomer-dimer formation. The circadian clock mechanism is assumed to consist of several processes that can either adapt or produce a balance. Single amino acid changes in a clock protein are assumed to partially upset this adaptation or balance.
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Affiliation(s)
- L Rensing
- Institute of Cell Biology, Biochemistry and Biotechnology, University of Bremen, Germany
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Pinna LA, Ruzzene M. How do protein kinases recognize their substrates? BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1314:191-225. [PMID: 8982275 DOI: 10.1016/s0167-4889(96)00083-3] [Citation(s) in RCA: 342] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- L A Pinna
- Dipartimento di Chimica Biologica, Università di Padova, Italy.
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