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Ribeiro Filho HV, Bernardi Videira N, Bridi AV, Tittanegro TH, Helena Batista FA, de Carvalho Pereira JG, de Oliveira PSL, Bajgelman MC, Le Maire A, Figueira ACM. Screening for PPAR Non-Agonist Ligands Followed by Characterization of a Hit, AM-879, with Additional No-Adipogenic and cdk5-Mediated Phosphorylation Inhibition Properties. Front Endocrinol (Lausanne) 2018; 9:11. [PMID: 29449830 PMCID: PMC5799700 DOI: 10.3389/fendo.2018.00011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a member of a nuclear receptor superfamily and acts as a ligand-dependent transcription factor, playing key roles in maintenance of adipose tissue and in regulation of glucose and lipid homeostasis. This receptor is the target of thiazolidinediones, a class of antidiabetic drugs, which improve insulin sensitization and regulate glycemia in type 2 diabetes. Despite the beneficial effects of drugs, such as rosiglitazone and pioglitazone, their use is associated with several side effects, including weight gain, heart failure, and liver disease, since these drugs induce full activation of the receptor. By contrast, a promising activation-independent mechanism that involves the inhibition of cyclin-dependent kinase 5 (CDK5)-mediated PPARγ phosphorylation has been related to the insulin-sensitizing effects induced by these drugs. Thus, we aimed to identify novel PPARγ ligands that do not possess agonist properties by conducting a mini-trial with 80 compounds using the sequential steps of thermal shift assay, 8-anilino-1-naphthalenesulfonic acid fluorescence quenching, and a cell-based transactivation assay. We identified two non-agonist PPARγ ligands, AM-879 and P11, and one partial-agonist, R32. Using fluorescence anisotropy, we show that AM-879 does not dissociate the NCOR corepressor in vitro, and it has only a small effect on TRAP coactivator recruitment. In cells, AM-879 could not induce adipocyte differentiation or positively regulate the expression of genes associated with adipogenesis. In addition, AM-879 inhibited CDK5-mediated phosphorylation of PPARγ in vitro. Taken together, these findings supported an interaction between AM-879 and PPARγ; this interaction was identified by the analysis of the crystal structure of the PPARγ:AM-879 complex and evidenced by AM-879's mechanism of action as a putative PPARγ non-agonist with antidiabetic properties. Moreover, we present an optimized assay pipeline capable of detecting ligands that physically bind to PPARγ but do not cause its activation as a new strategy to identify ligands for this nuclear receptor.
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Affiliation(s)
- Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Natália Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Aline Villanova Bridi
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thais Helena Tittanegro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - José Geraldo de Carvalho Pereira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcio Chaim Bajgelman
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Albane Le Maire
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Centre de Biochimie Structurale CNRS, Université de Montpellier, Montpellier, France
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Post Graduation Program in Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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Soprano AS, Giuseppe POD, Shimo HM, Lima TB, Batista FAH, Righetto GL, Pereira JGDC, Granato DC, Nascimento AFZ, Gozzo FC, de Oliveira PSL, Figueira ACM, Smetana JHC, Paes Leme AF, Murakami MT, Benedetti CE. Crystal Structure and Regulation of the Citrus Pol III Repressor MAF1 by Auxin and Phosphorylation. Structure 2017; 25:1360-1370.e4. [PMID: 28781084 DOI: 10.1016/j.str.2017.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 03/06/2017] [Revised: 05/16/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022]
Abstract
MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate. Additionally, mTOR phosphorylated recombinant CsMAF1 and the mTOR inhibitor AZD8055 blocked canker formation in normal but not CsMAF1-silenced plants. These results indicate that the role of TOR on cell growth induced by Xanthomonas citri depends on CsMAF1 and that auxin controls CsMAF1 interaction with Pol III in citrus.
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Affiliation(s)
- Adriana Santos Soprano
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Hugo Massayoshi Shimo
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Tatiani Brenelli Lima
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil; Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Germanna Lima Righetto
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - José Geraldo de Carvalho Pereira
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Daniela Campos Granato
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Andrey Fabricio Ziem Nascimento
- XALOC Beamline, Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain; Structural Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Carrer Baldiri Reixac 15, 3 A17, 08028 Barcelona, Spain
| | - Fabio Cesar Gozzo
- Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Juliana Helena Costa Smetana
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil.
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Xavier-Neto J, Carvalho M, Pascoalino BDS, Cardoso AC, Costa ÂMS, Pereira AHM, Santos LN, Saito Â, Marques RE, Smetana JHC, Consonni SR, Bandeira C, Costa VV, Bajgelman MC, de Oliveira PSL, Cordeiro MT, Gonzales Gil LHV, Pauletti BA, Granato DC, Paes Leme AF, Freitas-Junior L, Holanda de Freitas CBM, Teixeira MM, Bevilacqua E, Franchini K. Hydrocephalus and arthrogryposis in an immunocompetent mouse model of ZIKA teratogeny: A developmental study. PLoS Negl Trop Dis 2017; 11:e0005363. [PMID: 28231241 PMCID: PMC5322881 DOI: 10.1371/journal.pntd.0005363] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/27/2017] [Indexed: 11/18/2022] Open
Abstract
The teratogenic mechanisms triggered by ZIKV are still obscure due to the lack of a suitable animal model. Here we present a mouse model of developmental disruption induced by ZIKV hematogenic infection. The model utilizes immunocompetent animals from wild-type FVB/NJ and C57BL/6J strains, providing a better analogy to the human condition than approaches involving immunodeficient, genetically modified animals, or direct ZIKV injection into the brain. When injected via the jugular vein into the blood of pregnant females harboring conceptuses from early gastrulation to organogenesis stages, akin to the human second and fifth week of pregnancy, ZIKV infects maternal tissues, placentas and embryos/fetuses. Early exposure to ZIKV at developmental day 5 (second week in humans) produced complex manifestations of anterior and posterior dysraphia and hydrocephalus, as well as severe malformations and delayed development in 10.5 days post-coitum (dpc) embryos. Exposure to the virus at 7.5-9.5 dpc induces intra-amniotic hemorrhage, widespread edema, and vascular rarefaction, often prominent in the cephalic region. At these stages, most affected embryos/fetuses displayed gross malformations and/or intrauterine growth restriction (IUGR), rather than isolated microcephaly. Disrupted conceptuses failed to achieve normal developmental landmarks and died in utero. Importantly, this is the only model so far to display dysraphia and hydrocephalus, the harbinger of microcephaly in humans, as well as arthrogryposis, a set of abnormal joint postures observed in the human setting. Late exposure to ZIKV at 12.5 dpc failed to produce noticeable malformations. We have thus characterized a developmental window of opportunity for ZIKV-induced teratogenesis encompassing early gastrulation, neurulation and early organogenesis stages. This should not, however, be interpreted as evidence for any safe developmental windows for ZIKV exposure. Late developmental abnormalities correlated with damage to the placenta, particularly to the labyrinthine layer, suggesting that circulatory changes are integral to the altered phenotypes.
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Affiliation(s)
- Jose Xavier-Neto
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
- * E-mail: (JXN); (KF)
| | - Murilo Carvalho
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Bruno dos Santos Pascoalino
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Alisson Campos Cardoso
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Ângela Maria Sousa Costa
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Ana Helena Macedo Pereira
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Luana Nunes Santos
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ângela Saito
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Juliana Helena Costa Smetana
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Silvio Roberto Consonni
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Carla Bandeira
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Vivian Vasconcelos Costa
- Laboratório de Imunofarmacologia, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG, Brazil
| | - Marcio Chaim Bajgelman
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Marli Tenorio Cordeiro
- CPqAM-Fiocruz. Federal University of Pernambuco, Av. Professor Moraes Rego s/n, Cidade Universitária, Recife, PE, Brazil
| | - Laura Helena Vega Gonzales Gil
- CPqAM-Fiocruz. Federal University of Pernambuco, Av. Professor Moraes Rego s/n, Cidade Universitária, Recife, PE, Brazil
| | - Bianca Alves Pauletti
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Daniela Campos Granato
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Lucio Freitas-Junior
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | | | - Mauro Martins Teixeira
- Laboratório de Imunofarmacologia, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG, Brazil
| | - Estela Bevilacqua
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Kleber Franchini
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
- * E-mail: (JXN); (KF)
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Beppler J, Mkaddem SB, Michaloski J, Honorato RV, Velasco IT, de Oliveira PSL, Giordano RJ, Monteiro RC, Pinheiro da Silva F. Negative regulation of bacterial killing and inflammation by two novel CD16 ligands. Eur J Immunol 2016; 46:1926-35. [PMID: 27226142 DOI: 10.1002/eji.201546118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 04/14/2016] [Accepted: 05/23/2016] [Indexed: 12/14/2022]
Abstract
Sepsis, a leading cause of death worldwide, involves exacerbated proinflammatory responses and inefficient bacterial clearance. Phagocytic cells play a crucial part in the prevention of sepsis by clearing bacteria through host innate receptors. Here, we used a phage display library to identify two peptides in Escherichia coli that interact with host innate receptors. One of these peptides, encoded by the wzxE gene of E. coli K-12, was involved in the transbilayer movement of a trisaccharide-lipid intermediate in the assembly of enterobacterial common antigen. Peptide-receptor interactions induced CD16-mediated inhibitory immunoreceptor tyrosine-based activating motif signaling, blocking the production of ROS and bacterial killing. This CD16-mediated inhibitory signaling was abrogated in a WzxE(-/-) mutant of E. coli K-12, restoring the production of ROS and bacterial killing. Taken together, the two novel CD16 ligands identified negatively regulate bacterial killing and inflammation. Our findings may contribute toward the development of new immunotherapies for E. coli-mediated infectious diseases and inflammation.
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Affiliation(s)
- Jaqueline Beppler
- Emergency Medicine Department, University of Sao Paulo, Sao Paulo, Brazil
| | - Sanae Ben Mkaddem
- Inserm Unit 1149 and ERL CNRS 8252, Center for Research on Inflammation, University Paris Diderot, Paris, France
| | - Jussara Michaloski
- Vascular Biology Laboratory, Chemistry Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | | | | | - Ricardo José Giordano
- Vascular Biology Laboratory, Chemistry Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Renato C Monteiro
- Inserm Unit 1149 and ERL CNRS 8252, Center for Research on Inflammation, University Paris Diderot, Paris, France
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Santos CR, Hoffmam ZB, de Matos Martins VP, Zanphorlin LM, de Paula Assis LH, Honorato RV, Lopes de Oliveira PS, Ruller R, Murakami MT. Molecular mechanisms associated with xylan degradation by Xanthomonas plant pathogens. J Biol Chem 2014; 289:32186-32200. [PMID: 25266726 PMCID: PMC4231694 DOI: 10.1074/jbc.m114.605105] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 08/18/2014] [Revised: 09/22/2014] [Indexed: 11/06/2022] Open
Abstract
Xanthomonas pathogens attack a variety of economically relevant plants, and their xylan CUT system (carbohydrate utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, xynA and xynB, which influence biofilm formation and virulence by molecular mechanisms that are still elusive. Herein, we demonstrated that XynA is a rare reducing end xylose-releasing exo-oligoxylanase and not an endo-β-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the β7-α7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan, and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-β-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB proved to be a classical endo-β-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell wall barrier, providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses.
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Affiliation(s)
- Camila Ramos Santos
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Zaira Bruna Hoffmam
- Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Vanesa Peixoto de Matos Martins
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Leticia Maria Zanphorlin
- Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Leandro Henrique de Paula Assis
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Rodrigo Vargas Honorato
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Roberto Ruller
- Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil
| | - Mario Tyago Murakami
- Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil.
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Duarte ML, Pena DA, Nunes Ferraz FA, Berti DA, Paschoal Sobreira TJ, Costa-Junior HM, Abdel Baqui MM, Disatnik MH, Xavier-Neto J, Lopes de Oliveira PS, Schechtman D. Protein folding creates structure-based, noncontiguous consensus phosphorylation motifs recognized by kinases. Sci Signal 2014; 7:ra105. [PMID: 25372052 DOI: 10.1126/scisignal.2005412] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Linear consensus motifs are short contiguous sequences of residues within a protein that can form recognition modules for protein interaction or catalytic modification. Protein kinase specificity and the matching of kinases to substrates have been mostly defined by phosphorylation sites that occur in linear consensus motifs. However, phosphorylation can also occur within sequences that do not match known linear consensus motifs recognized by kinases and within flexible loops. We report the identification of Thr(253) in α-tubulin as a site that is phosphorylated by protein kinase C βI (PKCβI). Thr(253) is not part of a linear PKC consensus motif. Instead, Thr(253) occurs within a region on the surface of α-tubulin that resembles a PKC phosphorylation site consensus motif formed by basic residues in different parts of the protein, which come together in the folded protein to form the recognition motif for PKCβI. Mutations of these basic residues decreased substrate phosphorylation, confirming the presence of this "structurally formed" consensus motif and its importance for the protein kinase-substrate interaction. Analysis of previously reported protein kinase A (PKA) and PKC substrates identified sites within structurally formed consensus motifs in many substrates of these two kinase families. Thus, the concept of consensus phosphorylation site motif needs to be expanded to include sites within these structurally formed consensus motifs.
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Affiliation(s)
- Mariana Lemos Duarte
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Darlene Aparecida Pena
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Felipe Augusto Nunes Ferraz
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Denise Aparecida Berti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Tiago José Paschoal Sobreira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | | | - Munira Muhammad Abdel Baqui
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Marie-Hélène Disatnik
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - José Xavier-Neto
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | | | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil.
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Alfonso de Almeida MA, Vançan Russo Horimoto AR, Lopes de Oliveira PS, Krieger JE, da Costa Pereira A. Different approaches for dealing with rare variants in family-based genetic studies: application of a Genetic Analysis Workshop 17 problem. BMC Proc 2011; 5 Suppl 9:S78. [PMID: 22373261 PMCID: PMC3287918 DOI: 10.1186/1753-6561-5-s9-s78] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Rare variants are becoming the new candidates in the search for genetic variants that predispose individuals to a phenotype of interest. Their low prevalence in a population requires the development of dedicated detection and analytical methods. A family-based approach could greatly enhance their detection and interpretation because rare variants are nearly family specific. In this report, we test several distinct approaches for analyzing the information provided by rare and common variants and how they can be effectively used to pinpoint putative candidate genes for follow-up studies. The analyses were performed on the mini-exome data set provided by Genetic Analysis Workshop 17. Eight approaches were tested, four using the trait’s heritability estimates and four using QTDT models. These methods had their sensitivity, specificity, and positive and negative predictive values compared in light of the simulation parameters. Our results highlight important limitations of current methods to deal with rare and common variants, all methods presented a reduced specificity and, consequently, prone to false positive associations. Methods analyzing common variants information showed an enhanced sensibility when compared to rare variants methods. Furthermore, our limited knowledge of the use of biological databases for gene annotations, possibly for use as covariates in regression models, imposes a barrier to further research.
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Affiliation(s)
- Marcio Augusto Alfonso de Almeida
- Laboratory of Genetic and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Av, Dr, Eneas C Aguiar, 44-10 andar, São Paulo 05403-000, Brazil.
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