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Araujo TT, Dionizio A, Carvalho TS, Boas Feitosa CMV, Vertuan M, Câmara JVF, Henrique-Silva F, Marchetto R, Chiaratti MR, Santos AC, Alves LO, Ferro M, Buzalaf MAR. Acquired enamel pellicle and biofilm engineering with a combination of acid-resistant proteins (CaneCPI-5, StN15, and Hemoglobin) for enhanced protection against dental caries - in vivo and in vitro investigations. Clin Oral Investig 2024; 28:261. [PMID: 38642171 DOI: 10.1007/s00784-024-05651-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/02/2024] [Indexed: 04/22/2024]
Abstract
OBJECTIVE This study was designed in two-legs. In the in vivo, we explored the potential of a rinse solution containing a combination (Comb) of 0.1 mg/mL CaneCPI-5 (sugarcane-derive cystatin), 1.88 × 10- 5M StN15 (statherin-derived peptide) and 1.0 mg/mL hemoglobin (Hb) to change the protein profile of the acquired enamel pellicle(AEP) and the microbiome of the enamel biofilm. The in vitro, was designed to reveal the effects of Comb on the viability and bacterial composition of the microcosm biofilm, as well as on enamel demineralization. MATERIALS AND METHODS In vivo study, 10 participants rinsed (10mL,1 min) with either deionized water (H2O-control) or Comb. AEP and biofilm were collected after 2 and 3 h, respectively, after rinsing. AEP samples underwent proteomics analysis, while biofilm microbiome was assessed via 16 S-rRNA Next Generation Sequencing(NGS). In vitro study, a microcosm biofilm protocol was employed. Ninety-six enamel specimens were treated with: 1)Phosphate-Buffered Solution-PBS(negative-control), 2)0.12%Chlorhexidine, 3)500ppmNaF and 4)Comb. Resazurin, colony-forming-units(CFU) and Transversal Microradiography(TMR) were performed. RESULTS The proteomic results revealed higher quantity of proteins in the Comb compared to control associated with immune system response and oral microbial adhesion. Microbiome showed a significant increase in bacteria linked to a healthy microbiota, in the Comb group. In the in vitro study, Comb group was only efficient in reducing mineral-loss and lesion-depth compared to the PBS. CONCLUSIONS The AEP modification altered the subsequent layers, affecting the initial process of bacterial adhesion of pathogenic and commensal bacteria, as well as enamel demineralization. CLINICAL RELEVANCE Comb group shows promise in shaping oral health by potentially introducing innovative approaches to prevent enamel demineralization and deter tooth decay.
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Affiliation(s)
- Tamara Teodoro Araujo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, São Paulo, Bauru, 17012- 901, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, São Paulo, Bauru, 17012- 901, Brazil
| | - Thamyris Souza Carvalho
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, São Paulo, Bauru, 17012- 901, Brazil
| | - Chelsea Maria Vilas Boas Feitosa
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, São Paulo, Bauru, 17012- 901, Brazil
| | - Mariele Vertuan
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, São Paulo, Bauru, 17012- 901, Brazil
| | - João Victor Frazão Câmara
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, University Hospital, Saarland University, Building 73, 66421, Homburg, Saarland, Germany
| | - Flavio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Reinaldo Marchetto
- Department of Biochemistry and Organic Chemistry, Paulista State University (UNESP), Araraquara, 14800-900, Brazil
| | - Marcos Roberto Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Angélica Camargo Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Lindomar Oliveira Alves
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Milene Ferro
- Department of General and Applied Biology, Paulista State University (UNESP), Rio Claro, 13500230, Brazil
| | - Marília Afonso Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, São Paulo, Bauru, 17012- 901, Brazil.
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Araujo TT, Carvalho TS, Dionizio A, Rodrigues CMVBF, Henrique-Silva F, Chiaratti M, Santos A, Alves L, Ferro M, Buzalaf MAR. Acquired Pellicle and Biofilm engineering by rinsing with hemoglobin solution. Caries Res 2024:000537976. [PMID: 38432208 DOI: 10.1159/000537976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/04/2024] [Indexed: 03/05/2024] Open
Abstract
INTRODUCTION The identification of acid-resistant proteins, including hemoglobin (Hb), within the acquired enamel pellicle (AEP) led to the proposition of the "acquired pellicle engineering" concept, which involves the modification of the AEP by incorporating specific proteins, presenting a novel strategy to prevent dental demineralization. OBJECTIVE Combining in vivo and in vitro proof-of-concept protocols we sought to reveal the impact of AEP engineering with Hb protein on the biofilm microbiome and enamel demineralization. METHODS In the in vivo studies, 10-volunteers, in 2 independent experiments, rinsed (10mL,1min) with: deionized water-negative control or 1.0mg/mL Hb. The AEP and biofilm formed along 2 or 3h, respectively, were collected. AEP was analyzed by quantitative shotgun-label-free proteomics and biofilm by 16S-rRNA Next-Generation-Sequencing (NGS). In vitro study, a microcosm biofilm protocol was employed. Seventy-two bovine enamel specimens were treated with: 1)Phosphate-Buffered Solution-PBS, 2)0.12% Chlorhexidine, 3)500ppm NaF; 4)1.0mg/mL Hb; 5)2.0mg/mL Hb, and 6)4.0mg/mL Hb. The biofilm was cultivated for 5-days. Resazurin, colony-forming-units(CFU) and Transversal Microradiography(TMR) were performed. RESULTS Proteomics and NGS analysis revealed that Hb increased proteins with antioxidant, antimicrobial, acid-resistance, hydroxyapatite-affinity, calcium-binding properties and showed a reduction in oral pathogenic bacteria. In vitro experiments demonstrated that the lowest Hb concentration was the most effective in reducing bacterial activity, CFU and enamel demineralization compared to PBS. CONCLUSION These findings suggest that Hb could be incorporated into anticaries dental products to modify the oral microbiome and control caries, highlighting its potential for AEP and biofilm microbiome engineering.
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Carvalho TS, Araújo TT, Ventura TMO, Dionizio A, Câmara JVF, Moraes SM, Leme JC, Grizzo LT, Crusca E, Shibao PYT, Marchetto R, Henrique-Silva F, Pessan JP, Buzalaf MAR. Hemoglobin Protects Enamel against Intrinsic Enamel Erosive Demineralization. Caries Res 2024; 58:90-107. [PMID: 38198757 DOI: 10.1159/000536200] [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: 09/11/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION This study investigated the changes in the acquired enamel pellicle (AEP) proteome when this integument is formed in vivo after treatment with sugarcane-derived cystatin (CaneCPI-5), hemoglobin (HB), and a statherin-derived peptide (StN15), or their combination and then exposed to an intrinsic acid challenge. The effectiveness of these treatments in preventing intrinsic erosion was also evaluated. METHODS Ten volunteers, after prophylaxis, in 5 crossover phases, rinsed with the following solutions (10 mL, 1 min): control (deionized water-H2O) - group 1, 0.1 mg/mL CaneCPI-5 - group 2, 1.0 mg/mL HB - group 3, 1.88 × 10-5M StN15 - group 4, or a blend of these - group 5. Following this, AEP formation occurred (2 h) and an enamel biopsy (10 µL, 0.01 m HCl, pH 2.0, 10 s) was conducted on one incisor. The biopsy acid was then analyzed for calcium (Arsenazo method). The vestibular surfaces of the other teeth were treated with the same acid. Acid-resistant proteins in the residual AEP were then collected and analyzed quantitatively via proteomics. RESULTS Compared to control, treatment with the proteins/peptide, mixed or isolated, markedly enhanced acid-resistant proteins in the AEP. Notable increases occurred in pyruvate kinase PKM (11-fold, CaneCPI-5), immunoglobulins and submaxillary gland androgen-regulated protein 3B (4-fold, StN15), Hb, and lysozyme C (2-fold, StN15). Additionally, a range of proteins not commonly identified in the AEP but known to bind calcium or other proteins were identified in groups treated with the tested proteins/peptide either in isolation or as a mixture. The mean (SD, mM) calcium concentrations released from enamel were 3.67 ± 1.48a, 3.11 ± 0.72a, 1.94 ± 0.57b, 2.37 ± 0.90a, and 2.38 ± 0.45a for groups 1-5, respectively (RM-ANOVA/Tukey, p < 0.05). CONCLUSIONS Our findings demonstrate that all treatments, whether using a combination of proteins/peptides or in isolation, enhanced acid-resistant proteins in the AEP. However, only HB showed effectiveness in protecting against intrinsic erosive demineralization. These results pave the way for innovative preventive methods against intrinsic erosion, using "acquired pellicle engineering" techniques.
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Affiliation(s)
- Thamyris Souza Carvalho
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | - Tamara Teodoro Araújo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | | | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | - João Victor Frazão Câmara
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | - Samanta Mascarenhas Moraes
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | - Júlia Chaparro Leme
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | - Larissa Tercilia Grizzo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Sao Paulo, Brazil
| | - Edson Crusca
- Department of Biochemistry and Technology, Institute of Chemistry, São Paulo State University (UNESP), Sao Paulo, Brazil
| | | | - Reinaldo Marchetto
- Department of Biochemistry and Technology, Institute of Chemistry, São Paulo State University (UNESP), Sao Paulo, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, São Carlos Federal University, Sao Carlos, Brazil
| | - Juliano Pelim Pessan
- Department of Preventive and Restorative Dentistry, School of Dentistry, Araçatuba, São Paulo State University (UNESP), Aracatuba, Brazil
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Pelá VT, Gironda CC, Taira EA, Brito L, Pieretti JC, Seabra AB, Cardoso CDAB, Rodrigues MC, Henrique-Silva F, Buzalaf MAR. Different vehicles containing CaneCPI-5 reduce erosive dentin wear in situ. Clin Oral Investig 2023; 27:5559-5568. [PMID: 37481640 DOI: 10.1007/s00784-023-05175-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
OBJECTIVE This study evaluated the protective capacity of a sugarcane-derived cystatin (CaneCPI-5) in different vehicles (1-solution and 2-chitosan gel) against erosive dentin wear in situ. METHODS In part-1, 15 volunteers participated in a crossover protocol (solutions): Water; Elmex™ and CaneCPI-5. The volunteers wore an appliance with 4 dentin samples for 5 days. These samples were treated with a drop of the solutions for 1 min (4X/d), then the acquired pellicle (AP) was formed and the samples were subjected to erosive challenges (EROSION: citric acid, for 90 s, 4X/day). 2X/day, half of the samples were also abraded for 15 s (ABRASION). In part-2, 16 volunteers participated in a crossover protocol (gel): No gel, Chitosan gel, Chitosan gel + NaF and Chitosan gel + CaneCPI-5. The volunteers also wore an appliance. The samples were treated once/day with the gel or not for 4 min, then the AP was formed and the samples were subjected to erosive and abrasive challenges, as reported in part-1. Dentin wear was measured by profilometry. Data were analyzed by two-way RM-ANOVA and Sidak's tests (p < 0.05). RESULTS Part-1: Elmex™ and CaneCPI-5 significantly reduced dentin loss in comparison with Water for the EROSION/ABRASION conditions (p < 0.05). Part-2, all the treated groups significantly reduced the dentin loss in comparison to the No gel. The greatest reduction was found for the gel + CaneCPI-5 group for the EROSION/ABRASION (p < 0.05). CONCLUSION The solution and chitosan gel containing CaneCPI-5 protected against erosive dentin wear in situ. CLINICAL RELEVANCE These different vehicles are probably sufficient for protecting people with high risk of developing erosive dentin wear.
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Affiliation(s)
- Vinicius Taioqui Pelá
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, Bauru, SP, 17012-901, Brazil
| | - Carlos Condarco Gironda
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, Bauru, SP, 17012-901, Brazil
| | - Even Akemi Taira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, Bauru, SP, 17012-901, Brazil
| | - Leonardo Brito
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, Bauru, SP, 17012-901, Brazil
| | - Joana Claudio Pieretti
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, 09210-580, Brazil
| | - Amedea Barozzi Seabra
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, 09210-580, Brazil
| | | | | | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, 13565-905, Brazil
| | - Marília Afonso Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, Bauru, SP, 17012-901, Brazil.
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Fernandes CJDC, Cassiano AFB, Henrique-Silva F, Cirelli JA, de Souza EP, Coaguila-Llerena H, Zambuzzi WF, Faria G. Recombinant sugarcane cystatin CaneCPI-5 promotes osteogenic differentiation. Tissue Cell 2023; 83:102157. [PMID: 37451011 DOI: 10.1016/j.tice.2023.102157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Cysteine proteases orchestrate bone remodeling, and are inhibited by cystatins. In reinforcing our hypothesis that exogenous and naturally obtained inhibitors of cysteine proteases (cystatins) act on bone remodeling, we decided to challenge osteoblasts with sugarcane-derived cystatin (CaneCPI-5) for up to 7 days. To this end, we investigated molecular issues related to the decisive, preliminary stages of osteoblast biology, such as adhesion, migration, proliferation, and differentiation. Our data showed that CaneCPI-5 negatively modulates both cofilin phosphorylation at Ser03, and the increase in cytoskeleton remodeling during the adhesion mechanism, possibly as a prerequisite to controlling cell proliferation and migration. This is mainly because CaneCPI-5 also caused the overexpression of the CDK2 gene, and greater migration of osteoblasts. Extracellular matrix remodeling was also evaluated in this study by investigating matrix metalloproteinase (MMP) activities. Our data showed that CaneCPI-5 overstimulates both MMP-2 and MMP-9 activities, and suggested that this cellular event could be related to osteoblast differentiation. Additionally, differentiation mechanisms were better evaluated by investigating Osterix and alkaline phosphatase (ALP) genes, and bone morphogenetic protein (BMP) signaling members. Altogether, our data showed that CaneCPI-5 can trigger biological mechanisms related to osteoblast differentiation, and broaden the perspectives for better exploring biotechnological approaches for bone disorders.
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Affiliation(s)
- Célio Junior da Costa Fernandes
- Bioassays and Cell Dynamics Lab, Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Botucatu, São Paulo, Brazil; Exercise Cell Biology Lab, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil; Department of Biophysics and Pharmacology, Institute of Biosciences, Sao Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Ana Flávia Balestrero Cassiano
- Department of Restorative Dentistry, School of Dentistry at Araraquara, Sao Paulo State University - UNESP, Araraquara, São Paulo, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, São Paulo, Brazil
| | - Joni Augusto Cirelli
- Department of Diagnosis and Surgery, School of Dentistry at Araraquara, Sao Paulo State University -UNESP, Araraquara, São Paulo, Brazil
| | - Eduardo Pereira de Souza
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, São Paulo, Brazil
| | - Hernán Coaguila-Llerena
- Department of Restorative Dentistry, School of Dentistry at Araraquara, Sao Paulo State University - UNESP, Araraquara, São Paulo, Brazil
| | - Willian Fernando Zambuzzi
- Bioassays and Cell Dynamics Lab, Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Botucatu, São Paulo, Brazil.
| | - Gisele Faria
- Department of Restorative Dentistry, School of Dentistry at Araraquara, Sao Paulo State University - UNESP, Araraquara, São Paulo, Brazil.
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Araújo TT, Carvalho TS, Dionizio A, Debortolli ALB, Ventura TMO, Souza BM, Feitosa CMVB, Barbosa HAP, Ribeiro CFDS, Martini T, Taira E, Shibao PYT, Henrique-Silva F, Marchetto R, Buzalaf MAR. Protein-based engineering of the initial acquired enamel pellicle in vivo: Proteomic evaluation. J Dent 2021; 116:103874. [PMID: 34798481 DOI: 10.1016/j.jdent.2021.103874] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE To study the proteomic alterations in the initial AEP after rinsing with CaneCPI-5, StN15 or Hb or their combination. MATERIALS AND METHODS In five crossover phases, after prophylaxis, 10 volunteers in 5 consecutive days, rinsed (10 mL, 1 min) with the following solutions: deionized water (H2O- negative control- 1), 0.1 mg/mL CaneCPI-5 (2), 1.88×10-5 M StN15 (3), 1.0 mg/mL Hb (4) or their combination (5). The AEP formed after 3 min was collected with electrode filter papers soaked in 3% citric acid. After protein extraction, samples were analyzed by quantitative shotgun label-free proteomics. RESULTS Rinsing with the proteins/peptide increased the amounts of proteins in the AEP. The total numbers of proteins identified after rinsing with CaneCPI-5, StN15, Hb or their combination versus water, were 131, 167, 148 and 142, respectively. The treatment with the proteins/peptide or their combination increased proteins that bind calcium, phosphate and interact with distinct proteins, as well as proteins with antimicrobial and acid-resistant properties, such as, Cornifin-B (7.7, 12.6, and 4.3-fold for CaneCPI-5, StN15 and Hb, respectively), isoforms of Cystatin (2.2-2.4-fold for CaneCPI-5 and StN15), Proline-rich-protein 4 (4.3-fold; StN15), Histatin-1 (2.8-fold; StN15) and Hemoglobin (7.7-25-fold for Hb and Combination). Immunoglobulin, Keratin and Histone were exclusively identified upon treatment with the proteins/peptide, alone or combined. CONCLUSION Rinsing with proteins/peptide, alone or combined, increased protective proteins in the initial AEP. CLINICAL RELEVANCE Our results suggest that rinsing with the proteins/peptide or their combination increases the proteins capable of enhancing the protective function of the basal layer of AEP.
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Affiliation(s)
- Tamara Teodoro Araújo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thamyris Souza Carvalho
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Ana Luiza Bogaz Debortolli
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | - Beatriz Martines Souza
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | | | | | - Tatiana Martini
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Even Taira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | - Flavio Henrique-Silva
- Department of Genetics and Evolution, São Carlos Federal University, São Carlos, Brazil
| | - Reinaldo Marchetto
- Department of Biochemistry and Technology, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
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Santos LA, Martini T, Câmara JVF, Reis FN, Ortiz ADC, Camiloti GD, Levy FM, Shibao PYT, Honorio HM, Henrique-Silva F, Pieretti JC, Seabra AB, Cardoso CDAB, Buzalaf MAR. Solutions and Gels Containing a Sugarcane-Derived Cystatin (CaneCPI-5) Reduce Enamel and Dentin Erosion in vitro. Caries Res 2021; 55:594-602. [PMID: 34670214 DOI: 10.1159/000520261] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/14/2021] [Indexed: 11/19/2022] Open
Abstract
The effect of solutions and gels containing a sugarcane-derived cystatin (CaneCPI-5) on the protection against enamel and dentin erosion in vitro was evaluated. Bovine enamel and dentin specimens were divided into 2 groups (n = 135 and 153/group for enamel and dentin, respectively) that were treated with solutions or chitosan gels containing 0.1 or 0.25 mg/mL CaneCPI-5. The positive controls for solutions and gels were Elmex Erosion Protection™ solution and NaF gel (12,300 ppm F), respectively. Deionized water and chitosan gel served as controls, respectively. The solutions were first applied on the specimens for 1 min and the gels for 4 min. Stimulated saliva was collected from 3 donors and used to form a 2-h acquired pellicle on the specimens. Then, the specimens were submitted to an erosive pH cycling protocol 4 times/day for 7 days (0.1% citric acid pH 2.5/90 s, artificial saliva/2 h, and artificial saliva overnight). The solutions and gels were applied again during pH cycling, 2 times/day for 1 min and 4 min, respectively, after the first and last erosive challenges. Enamel and dentin losses (µm) were assessed by contact profilometry. Data were analyzed by 2-way ANOVA and Tukey's test (p < 0.05). All the treatments significantly reduced enamel and dentin loss in comparison with controls. Both CaneCPI-5 concentrations had a similar protective effect against enamel erosion, but only the higher concentration was as effective against dentin erosion as the positive control. Regarding the vehicles, only the 0.1 mg/mL gel performed worse than the positive control for dentin. CaneCPI-5 reduced enamel and dentin erosion to a similar extent as the fluoride-containing vehicles. However, dentin requires higher CaneCPI-5 concentrations, in the case of gels. Solutions or gels containing CaneCPI-5 might be a new approach to protect against dental erosion.
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Affiliation(s)
| | - Tatiana Martini
- Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | | | | | | | | | | | | | | | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Amedea Barozzi Seabra
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, Brazil
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Maia LBL, Pereira HD, Garratt RC, Brandão-Neto J, Henrique-Silva F, Toyama D, Dias RO, Bachega JFR, Peixoto JV, Silva-Filho MC. Structural and Evolutionary Analyses of PR-4 SUGARWINs Points to a Different Pattern of Protein Function. Front Plant Sci 2021; 12:734248. [PMID: 34567046 PMCID: PMC8458871 DOI: 10.3389/fpls.2021.734248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
SUGARWINs are PR-4 proteins associated with sugarcane defense against phytopathogens. Their expression is induced in response to damage by Diatraea saccharalis larvae. These proteins play an important role in plant defense, in particular against fungal pathogens, such as Colletothricum falcatum (Went) and Fusarium verticillioides. The pathogenesis-related protein-4 (PR-4) family is a group of proteins equipped with a BARWIN domain, which may be associated with a chitin-binding domain also known as the hevein-like domain. Several PR-4 proteins exhibit both chitinase and RNase activity, with the latter being associated with the presence of two histidine residues H11 and H113 (BARWIN) [H44 and H146, SUGARWINs] in the BARWIN-like domain. In sugarcane, similar to other PR-4 proteins, SUGARWIN1 exhibits ribonuclease, chitosanase and chitinase activities, whereas SUGARWIN2 only exhibits chitosanase activity. In order to decipher the structural determinants involved in this diverse range of enzyme specificities, we determined the 3-D structure of SUGARWIN2, at 1.55Å by X-ray diffraction. This is the first structure of a PR-4 protein where the first histidine has been replaced by asparagine and was subsequently used to build a homology model for SUGARWIN1. Molecular dynamics simulations of both proteins revealed the presence of a flexible loop only in SUGARWIN1 and we postulate that this, together with the presence of the catalytic histidine at position 42, renders it competent as a ribonuclease. The more electropositive surface potential of SUGARWIN1 would also be expected to favor complex formation with RNA. A phylogenetic analysis of PR-4 proteins obtained from 106 Embryophyta genomes showed that both catalytic histidines are widespread among them with few replacements in these amino acid positions during the gene family evolutionary history. We observe that the H11 replacement by N11 is also present in two other sugarcane PR-4 proteins: SUGARWIN3 and SUGARWIN4. We propose that RNase activity was present in the first Embryophyta PR-4 proteins but was recently lost in members of this family during the course of evolution.
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Affiliation(s)
| | | | | | - José Brandão-Neto
- Diamond Light Source, Harwell Science and Innovation Campus Didcot, Harwell, United Kingdom
| | - Flavio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazi
| | - Danyelle Toyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazi
| | - Renata O. Dias
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - José Fernando Ruggiero Bachega
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
- Programa de Pós-Graduação de Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Julia Vasconcellos Peixoto
- Programa de Pós-Graduação de Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcio C. Silva-Filho
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
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9
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Oliveira MDS, Rocha SV, Schneider VK, Henrique-Silva F, Soares MR, Soares-Costa A. Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum. PeerJ 2021; 9:e11461. [PMID: 34249482 PMCID: PMC8247702 DOI: 10.7717/peerj.11461] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/26/2021] [Indexed: 11/20/2022] Open
Abstract
Background Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils. Methods Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress. Results Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.
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Affiliation(s)
| | - Sâmara Vieira Rocha
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marcio Roberto Soares
- Department of Natural Resources and Environmental Protection/Agrarian Sciences Center, Federal University of São Carlos, Araras, SP, Brazil
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
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10
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Frazão Câmara JV, Araujo TT, Mendez DAC, da Silva NDG, de Medeiros FF, Santos LA, de Souza Carvalho T, Reis FN, Martini T, Moraes SM, Shibao PYT, Groisman S, Magalhães AC, Henrique-Silva F, Buzalaf MAR. Effect of a sugarcane cystatin on the profile and viability of microcosm biofilm and on dentin demineralization. Arch Microbiol 2021; 203:4133-4139. [PMID: 34059945 DOI: 10.1007/s00203-021-02403-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022]
Abstract
To analyze the effect of a sugarcane cystatin (CaneCPI-5) on the microbial profile and viability, as well as on the prevention of dentin demineralization using a microcosm biofilm model. Ninety bovine dentine specimens were divided into five experimental groups according with the solution they were treated for 60 s: (1) PBS (negative control), (2) 0.12% chlorhexidine (positive control), (3) Fluoride (500 ppm F, as NaF), (4) 0.025 mg/ml CaneCPI-5, and (5) 0.05 mg/ml CaneCPI-5. Specimens were incubated with inoculum (McBain's saliva plus human saliva) in the first 8 h, and from then on, they were exposed to McBain saliva containing sucrose and daily treated (60 s) with the solutions for 5 days. Resazurin and colony-forming unit counting assays were performed. Dentin demineralization was measured by transverse micro-radiography (TMR). 0.12% chlorhexidine significantly reduced the metabolic activity of the microcosm biofilm in relation to the negative control and treated groups (p < 0.01). CHX and F significantly reduced the counts of total microorganisms, mutans group streptococci, and lactobacilli when compared with the negative control. None of the treatments was able to significantly reduce dentin demineralization in comparison with the negative control. In the model evaluated, CaneCPI-5 neither altered the microcosm biofilm profile and viability nor protected dentin against demineralization.
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Affiliation(s)
- João Victor Frazão Câmara
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil.
| | - Tamara Teodoro Araujo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Daniela Alejandra Cusicanqui Mendez
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Natara Dias Gomes da Silva
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Felipe Fávaro de Medeiros
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Lethycia Almeida Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Thamyris de Souza Carvalho
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Fabiana Navas Reis
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Tatiana Martini
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Samanta Mascarenhas Moraes
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | | | - Sonia Groisman
- School of Dentistry, Federal University of Rio de Janeiro, Cidade Universitária da Universidade Federal Do Rio de Janeiro, R. Prof. Rodolpho Paulo Rocco, 325, Rio de Janeiro, RJ, 21941-617, Brazil
| | - Ana Carolina Magalhães
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
| | - Flavio Henrique-Silva
- Federal University of São Carlos, Rod. Washington Luiz, s/n, São Carlos, SP, 13565-905, Brazil
| | - Marília Afonso Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Dr. Octávio Pinheiro Brisolla, 9-75-Vila Regina, Bauru, SP, 17011-220, Brazil
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11
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Pelá VT, Lunardelli JGQ, Tokuhara CK, Gironda CC, Silva NDG, Carvalho TS, Santiago AC, Souza BM, Moraes SM, Henrique-Silva F, Magalhães AC, Oliveira RC, Buzalaf MAR. Safety and In Situ Antierosive Effect of CaneCPI-5 on Dental Enamel. J Dent Res 2021; 100:1344-1350. [PMID: 33970042 DOI: 10.1177/00220345211011590] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The sugarcane cystatin (CaneCPI-5) was recently cloned and showed strong binding force to dental enamel and protection against initial erosion. However, evaluations on its safety and efficacy in a situation closer to the clinical condition are necessary. In the present study we analyzed 1) the cytotoxicity of CaneCPI-5 on human gingival fibroblasts (HGFs); 2) the ability of CaneCPI-5 to reduce enamel erosion and erosion+abrasion in situ. In part 1, HGFs were treated with CaneCPI-5 (0.025, 0.05, 0.1, 0.5 or 1.0 mg/mL) or no treatment (control). The cytotoxicity was assessed after 60 s and 24 h by mitochondrial activity (MTT), confocal microscopy, and hematoxylin/eosin staining. In part 2, 15 volunteers participated in a double-blind crossover protocol consisting of 3 phases, according to the following treatments: 1) 0.1 mg/mL CaneCPI-5; 2) SnCl2/NaF/AmF (Elmex; positive control); 3) water (negative control). The volunteers wore an appliance containing 4 bovine enamel specimens for 5 d. Each day, the specimens were individually treated with 50 µL of the tested solutions per 60 s and then subjected to erosive challenges (0.1% citric acid, pH 2.5, for 90 s, 4 times per day). After the first and last erosive challenge each day, 2 samples were abraded (toothbrushing, 15 s). Enamel wear was measured by contact profilometry. One or two-way analysis of variance (ANOVA)/Tukey's or Sidak's tests (P < 0.05) were applied. Regardless of the concentration and the experimental time, CaneCPI-5 did not decrease the cell viability compared to the negative control (P < 0.05). Erosion+abrasion led to significantly greater wear compared to erosion only. For both conditions, the lowest wear was found for SnCl2 and CaneCPI-5, which did not differ significantly from each other, but showed significant protection when compared to the negative control. In conclusion, CaneCPI-5 is safe on HGFs and reduces enamel erosive wear to the same extent as a commercial solution used to control erosive tooth wear (ETW).
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Affiliation(s)
- V T Pelá
- Department of Genetics and Evolution, São Carlos Federal University, São Carlos, São Paulo, Brazil
| | - J G Q Lunardelli
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - C K Tokuhara
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - C C Gironda
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - N D G Silva
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - T S Carvalho
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - A C Santiago
- Department of Genetics and Evolution, São Carlos Federal University, São Carlos, São Paulo, Brazil
| | - B M Souza
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - S M Moraes
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - F Henrique-Silva
- Department of Genetics and Evolution, São Carlos Federal University, São Carlos, São Paulo, Brazil
| | - A C Magalhães
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - R C Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - M A R Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
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12
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Mohan C, Shibao PYT, de Paula FFP, Toyama D, Vieira MAS, Figueira A, Scotton D, Soares-Costa A, Henrique-Silva F. hRNAi-mediated knock-down of Sphenophorus levis V-ATPase E in transgenic sugarcane (Saccharum spp interspecific hybrid) affects the insect growth and survival. Plant Cell Rep 2021; 40:507-516. [PMID: 33389048 DOI: 10.1007/s00299-020-02646-5] [Citation(s) in RCA: 3] [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: 09/03/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Transgenic sugarcane expressing V-ATPase subunit E dsRNA affects growth and survival of Sphenophorus levis. Plants being sessile organisms are constantly confronted with several biotic and abiotic stresses. Sugarcane (Saccharum spp) is a major tropical crop widely cultivated for its sugar and other by-products. In Brazil, sugarcane plantations account for significant production losses due to Sphenophorus levis (sugarcane weevil) infestations. With the existing control measures being less effective, there arises a necessity for advanced strategies. Our bioassay injection experiments with V-ATPase E dsRNA in S. levis larvae showed significant mortality and reduction in transcription levels. Furthermore, we down-regulated the V-ATPase E gene of S. levis in transgenic sugarcane using an RNAi approach. The resultant RNAi transgenic lines exhibited reduction in larval growth and survival, without compromising plant performance under controlled environment. Our results illustrate that RNAi-mediated down-regulation of key genes is a promising approach in imparting resistance to sugarcane weevil.
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Affiliation(s)
- Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Danyelle Toyama
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | - Antonio Figueira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Danielle Scotton
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil.
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13
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Araujo TT, Camiloti GD, Valle AD, Silva NDG, Souza BM, Carvalho TDS, Câmara JVF, Shibao PYT, Henrique-Silva F, Cruvinel T, Magalhães AC, Buzalaf MAR. A sugarcane cystatin (CaneCPI-5) alters microcosm biofilm formation and reduces dental caries. Biofouling 2021; 37:109-116. [PMID: 33588651 DOI: 10.1080/08927014.2021.1881065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/03/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
The antimicrobial and anticaries effects of CaneCPI-5 were evaluated. Ninety bovine enamel samples were treated for 60 s with either phosphate-buffered-saline (PBS), 0.12% chlorhexidine (CHX), 0.05 mg ml-1 CaneCPI-5, 0.1 mg ml-1 CaneCPI-5 or 0.5 mg ml-1 CaneCPI-5. They were incubated with inoculum (human saliva + McBain's saliva) for the first 8 h. From then until the end of the experiment, the enamel was exposed to McBain saliva with sucrose and, once a day, for 5 days, they were treated with the solutions. At the end of the experimental period, resazurin and viable plate count assays were performed. Enamel demineralization was also measured. All concentrations of CaneCPI-5 and CHX significantly reduced the activity of biofilms compared with PBS. For viable plate counts, all treatments similarly reduced the lactobacilli and total streptococci; for the mutans streptococci, 0.05 mg ml-1 CaneCPI-5 performed better than CHX. All CaneCPI-5 concentrations significantly reduced the integrated mineral loss. This study represents the first step regarding the use of CaneCPI-5 within the concept of acquired enamel pellicle and biofilm engineering to prevent dental caries.
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Affiliation(s)
- Tamara Teodoro Araujo
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Gabriel Domingues Camiloti
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Aline Dionizio Valle
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Natara Dias Gomes Silva
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Beatriz Martines Souza
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Thamyris de Souza Carvalho
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - João Victor Frazão Câmara
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Priscila Yumi Tanaka Shibao
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Flavio Henrique-Silva
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Thiago Cruvinel
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
| | - Ana Carolina Magalhães
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
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14
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Shibao PYT, Santos-Júnior CD, Santiago AC, Mohan C, Miguel MC, Toyama D, Vieira MAS, Narayanan S, Figueira A, Carmona AK, Schiermeyer A, Soares-Costa A, Henrique-Silva F. Sugarcane cystatins: From discovery to biotechnological applications. Int J Biol Macromol 2020; 167:676-686. [PMID: 33285201 DOI: 10.1016/j.ijbiomac.2020.11.185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022]
Abstract
Phytocystatins are tight-binding cysteine protease inhibitors produced by plants. The first phytocystatin described was isolated from Oryza sativa and, since then, cystatins from several plant species were reported, including from sugarcane. Sugarcane cystatins were unraveled in Sugarcane EST project database, after sequencing of cDNA libraries from various sugarcane tissues at different developmental stages and six sugarcane cystatins were cloned, expressed and characterized (CaneCPI-1 to CaneCPI-6). These recombinant proteins were produced in different expression systems and inhibited several cysteine proteases, including human cathepsins B and L, which can be involved in pathologies, such as cancer. In this review, we summarize a comprehensive history of all sugarcane cystatins, presenting an updated phylogenetic analysis; chromosomal localization, and genomic organization. We also present protein docking of CaneCPI-5 in the active site of human cathepsin B, insights about canecystatins structures; recombinant expression in different systems, comparison of their inhibitory activities against human cysteine cathepsins B, K, L, S, V, falcipains from Plasmodium falciparum and a cathepsin L-like from the sugarcane weevil Sphenophorus levis; and enlighten their potential and current applications in agriculture and health.
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Affiliation(s)
- Priscila Yumi Tanaka Shibao
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Célio Dias Santos-Júnior
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | | | - Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mariana Cardoso Miguel
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Danyelle Toyama
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Subramonian Narayanan
- Genetic Transformation Laboratory, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Antonio Figueira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Adriana K Carmona
- Department of Biophysics, Federal University of São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
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15
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Carriero MM, Henrique-Silva F, Meira CM, Gato IMQ, Caetano AR, Lobo FP, Alves AL, Varela ES, Maia AAM. Molecular characterization and gene expression analysis of the pro-inflammatory cytokines IL-1β and IL-8 in the South American fish Piaractus mesopotamicus challenged with Aeromonas dhakensis. Genet Mol Biol 2020; 43:e20200006. [PMID: 33174977 PMCID: PMC7687281 DOI: 10.1590/1678-4685-gmb-2020-0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/06/2020] [Indexed: 11/24/2022] Open
Abstract
In the present study, the complete characterization of cDNA and genomic sequences of IL-1β and IL-8, as well as the expression profile of these genes in the South American fish pacu (Piaractus mesopotamicus) is provided. The full-length pmIL-1β cDNA was composed of 1208 nucleotides that would produce a precursor peptide with 273 amino acid residues. A putative caspase-1 cleavage site, similar to what is found in mammalian IL-1β, was identified producing a mature peptide with a theoretical molecular weight of 17.21 kDa. The pmIL-8 cDNA sequence consisted of 1019 nucleotides which encoded a 95-amino acid protein with a theoretical molecular weight of 10.43 kDa that showed all typical CXC chemokine features, including a 20-residue signal peptide and four conserved cysteine residues. Constitutive mRNA expression was detected for both genes in the liver, head kidney, gill, intestine, skin and spleen. After a bacterial challenge, up-regulation was detected for both pmIL-1β and pmIL-8 in the spleen and head kidney at 12 h post-infection. At 24 h post-infection there was a decrease in the expression of both genes, with pmIL-8 showing a significant down-regulation in the liver and head kidney when compared to the control groups.
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Affiliation(s)
- Mateus Maldonado Carriero
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Flavio Henrique-Silva
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Caroline Munhoz Meira
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Igor Mateus Queiroz Gato
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Alexandre Rodrigues Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Empresa Brasileira de Pesquisa Agropecuária, Brasília, DF, Brazil
| | - Francisco Pereira Lobo
- Embrapa Informática na Agricultura, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
| | - Anderson Luis Alves
- Embrapa Pesca e Aquicultura, Empresa Brasileira de Pesquisa Agropecuária, Palmas, TO, Brazil
| | - Eduardo Sousa Varela
- Embrapa Pesca e Aquicultura, Empresa Brasileira de Pesquisa Agropecuária, Palmas, TO, Brazil
| | - Antonio Augusto Mendes Maia
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
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16
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Carvalho TS, Araújo TT, Ventura TMO, Dionizio A, Câmara JVF, Moraes SM, Pelá VT, Martini T, Leme JC, Derbotolli ALB, Grizzo LT, Crusca E, Shibao PYT, Marchetto R, Henrique-Silva F, Pessan JP, Buzalaf MAR. Acquired pellicle protein-based engineering protects against erosive demineralization. J Dent 2020; 102:103478. [DOI: 10.1016/j.jdent.2020.103478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/24/2022] Open
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17
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Ferrara TFS, Schneider VK, Lima PS, Bronze FS, Machado MFM, Henrique-Silva F, Soares-Costa A, Carmona AK. Gene expression studies and molecular characterization of a cathepsin L-like from the Asian citrus psyllid Diaphorina citri, vector of Huanglongbing. Int J Biol Macromol 2020; 158:375-383. [PMID: 32360970 DOI: 10.1016/j.ijbiomac.2020.04.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/30/2022]
Abstract
Huanglongbing (HLB) is a devastating citrus disease associated with Candidatus Liberibacter asiaticus (CLas) and is transmitted by the psyllid Diaphorina citri Kuwayama. Diaphorina citri belongs to Hemiptera order, which has cysteine peptidases as the most abundant proteolytic enzymes present in digestive tract. As cysteine peptidases are involved in different insect development processes, this class of enzymes has acquired biotechnological importance. In this context, we identified a cathepsin L-like (DCcathL1) from the Diaphorina citri transcriptome database and expressed the enzyme in E. coli. Quantitative real-time RT-PCR was conducted to determine DCcathL1 gene expression in different parts and developmental phases of the insect. We observed that DCcathL1 expression in the gut was 2.59 and 2.87-fold higher than in the head and carcass, respectively. Furthermore, DCcathL1 expression was greater in eggs than in nymphs and adults, suggesting a putative role of the enzyme in the embryonic development. In addition, enzymatic inhibitory activity using four recombinant Citrus cystatins were performed. Among them, CsinCPI-2 was the strongest DCcathL1 inhibitor with a Ki value of 0.005 nM. Our results may contribute in the development of strategies for D. citri control, such as silencing the DCcathL1 gene and the use of transgenic plants that overexpress peptidase inhibitors.
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Affiliation(s)
- Taise F S Ferrara
- Departamento de Biofísica, Universidade Federal de São Paulo, 04039-032 São Paulo, Brazil
| | - Vanessa K Schneider
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905 São Paulo, Brazil
| | - Patricia Silva Lima
- Departamento de Biofísica, Universidade Federal de São Paulo, 04039-032 São Paulo, Brazil
| | - Fellipe S Bronze
- Departamento de Biofísica, Universidade Federal de São Paulo, 04039-032 São Paulo, Brazil
| | - Marcelo F M Machado
- Departamento de Biofísica, Universidade Federal de São Paulo, 04039-032 São Paulo, Brazil
| | - Flavio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905 São Paulo, Brazil
| | - Andrea Soares-Costa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905 São Paulo, Brazil.
| | - Adriana K Carmona
- Departamento de Biofísica, Universidade Federal de São Paulo, 04039-032 São Paulo, Brazil.
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Leguizamón NDP, Rodrigues EM, de Campos ML, Nogueira AVB, Viola KS, Schneider VK, Neo-Justino DM, Tanomaru-Filho M, Zambuzzi WF, Henrique-Silva F, Soares-Costa A, Faria G, Cirelli JA. In vivo and in vitro anti-inflammatory and pro-osteogenic effects of citrus cystatin CsinCPI-2. Cytokine 2019; 123:154760. [DOI: 10.1016/j.cyto.2019.154760] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
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Santiago A, Khan Z, Miguel M, Gironda C, Soares-Costa A, Pelá V, Leite A, Edwardson J, Buzalaf M, Henrique-Silva F. A New Sugarcane Cystatin Strongly Binds to Dental Enamel and Reduces Erosion. J Dent Res 2017; 96:1051-1057. [DOI: 10.1177/0022034517712981] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cystatin B was recently identified as an acid-resistant protein in acquired enamel pellicle; it could therefore be included in oral products to protect against caries and erosion. However, human recombinant cystatin is very expensive, and alternatives to its use are necessary. Phytocystatins are reversible inhibitors of cysteine peptidases that are found naturally in plants. In plants, they have several biological and physiological functions, such as the regulation of endogenous processes, defense against pathogens, and response to abiotic stress. Previous studies performed by our research group have reported high inhibitory activity and potential agricultural and medical applications of several sugarcane cystatins, including CaneCPI-1, CaneCPI-2, CaneCPI-3, and CaneCPI-4. In the present study, we report the characterization of a novel sugarcane cystatin, named CaneCPI-5. This cystatin was efficiently expressed in Escherichia coli, and inhibitory assays demonstrated that it was a potent inhibitor of human cathepsins B, K, and L ( Ki = 6.87, 0.49, and 0.34 nM, respectively). The ability of CaneCPI-5 to bind to dental enamel was evaluated using atomic force microscopy. Its capacity to protect against initial enamel erosion was also tested in vitro via changes in surface hardness. CaneCPI-5 showed a very large force of interaction with enamel (e.g., compared with mucin and casein) and significantly reduced initial enamel erosion. These results suggest that the inclusion of CaneCPIs in dental products might confer protection against enamel erosion.
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Affiliation(s)
- A.C. Santiago
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Z.N. Khan
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - M.C. Miguel
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - C.C. Gironda
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - A. Soares-Costa
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - V.T. Pelá
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - A.L. Leite
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - J.M. Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - M.A.R. Buzalaf
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - F. Henrique-Silva
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
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20
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Toyama D, Santos-Júnior CD, Kishi LT, Oliveira TCS, Garcia JW, Sarmento H, Miranda FP, Henrique-Silva F. A snapshot on prokaryotic diversity of the Solimões River basin (Amazon, Brazil). Genet Mol Res 2017; 16:gmr-16-02-gmr.16029567. [PMID: 28525656 DOI: 10.4238/gmr16029567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Amazon region has the largest hydrographic basin on the planet and
is well known for its huge biodiversity of plants and animals. However,
there is a lack of studies on aquatic microbial biodiversity in the
Solimões River, one of its main water courses. To investigate the
microbial biodiversity of this region, we performed 16S rRNA gene clone
libraries from Solimões River and adjacent rivers and lakes. Our question was which microorganisms inhabit the different types of aquatic
environments in this part of the basin, and how diversity varies among
these environments (rivers and lakes). The microbial
diversity generating 13 clone libraries of the bacterial 16S rRNA gene
and 5 libraries of the archaeal 16S rRNA gene was assessed. Diversity measured by several alpha diversity indices (ACE, Chao, Shannon and Simpson) revealed significant differences in diversity indices between lake and river samples. The site with higher microbial diversity was in the Solimões River (4S), downstream the confluence with Purus River. The most common bacterial taxon was the cosmopolitan Polynucleobacter genus, widely observed in all samples. The phylum Thaumarchaeota was the prevailing archaeal taxon. Our results provide the first insight into the microbial diversity of the world's largest river basin.
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Affiliation(s)
- D Toyama
- Laboratório de Biologia Molecular, Departamento de Genética e Evolução, , , Brasil
| | - C D Santos-Júnior
- Laboratório de Biologia Molecular, Departamento de Genética e Evolução, , , Brasil
| | - L T Kishi
- Laboratório de Biologia Molecular, Departamento de Genética e Evolução, , , Brasil
| | | | - J W Garcia
- Noosfera Projetos Especiais Ltda., , Brasil
| | - H Sarmento
- Laboratório de Biodiversidade e Processos Microbianos, Departamento de Hidrobiologia, , , Brasil
| | | | - F Henrique-Silva
- Laboratório de Biologia Molecular, Departamento de Genética e Evolução, , , Brasil
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21
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Schneider VK, Soares-Costa A, Chakravarthi M, Ribeiro C, Chabregas SM, Falco MC, Henrique-Silva F. Transgenic sugarcane overexpressing CaneCPI-1 negatively affects the growth and development of the sugarcane weevil Sphenophorus levis. Plant Cell Rep 2017; 36:193-201. [PMID: 27837261 DOI: 10.1007/s00299-016-2071-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 08/05/2016] [Accepted: 11/03/2016] [Indexed: 05/26/2023]
Abstract
Transgenic sugarcane expressing CaneCPI-1 exhibits resistance to Sphenophorus levis larvae. Transgenic plants have widely been used to improve resistance against insect attack. Sugarcane is an economically important crop; however, great losses are caused by insect attack. Sphenophorus levis is a sugarcane weevil that digs tunnels in the stem base, leading to the destruction of the crop. This insect is controlled inefficiently by chemical insecticides. Transgenic plants expressing peptidase inhibitors represent an important strategy for impairing insect growth and development. Knowledge of the major peptidase group present in the insect gut is critical when choosing the most effective inhibitor. S. levis larvae use cysteine peptidases as their major digestive enzymes, primarily cathepsin L-like activity. In this study, we developed transgenic sugarcane plants that overexpress sugarcane cysteine peptidase inhibitor 1 (CaneCPI-1) and assessed their potential through feeding bioassays with S. levis larvae. Cystatin overexpression in the transgenic plants was evaluated using semi-quantitative RT-PCR, RT-qPCR, and immunoblot assays. A 50% reduction of the average weight was observed in larvae that fed on transgenic plants in comparison to larvae that fed on non-transgenic plants. In addition, transgenic sugarcane exhibited less damage caused by larval attack than the controls. Our results suggest that the overexpression of CaneCPI-1 in sugarcane is a promising strategy for improving resistance against this insect.
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Affiliation(s)
- Vanessa Karine Schneider
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washigton Luis, Km 235, São Carlos, SP, 13565-905, Brazil
| | - Andrea Soares-Costa
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washigton Luis, Km 235, São Carlos, SP, 13565-905, Brazil
| | - Mohan Chakravarthi
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washigton Luis, Km 235, São Carlos, SP, 13565-905, Brazil
| | - Carolina Ribeiro
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washigton Luis, Km 235, São Carlos, SP, 13565-905, Brazil
| | - Sabrina Moutinho Chabregas
- Centro de Tecnologia Canavieira, Fazenda Santo Antônio, s/n, cp. 162, Piracicaba, SP, CEP 13400-970, Brazil
| | - Maria Cristina Falco
- Centro de Tecnologia Canavieira, Fazenda Santo Antônio, s/n, cp. 162, Piracicaba, SP, CEP 13400-970, Brazil
| | - Flavio Henrique-Silva
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washigton Luis, Km 235, São Carlos, SP, 13565-905, Brazil.
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22
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Carriero MM, Mendes Maia AA, Moro Sousa RL, Henrique-Silva F. Characterization of a new strain of Aeromonas dhakensis isolated from diseased pacu fish (Piaractus mesopotamicus) in Brazil. J Fish Dis 2016; 39:1285-1295. [PMID: 26850370 DOI: 10.1111/jfd.12457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 11/17/2015] [Revised: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
This study provides a detailed description and characterization of a strain of Aeromonas dhakensis isolated from a diseased juvenile Piaractus mesopotamicus obtained from the fish farm of the National Center for Continental Fish Research and Conservation (CEPTA/ICMBio), in the state of São Paul, Brazil. Biochemical tests using the VITEK 2 automated bacterial identification system identified the isolate to genus level; however, further molecular analysis of the 16S rRNA, gyrB and rpoD genes showed that the strain belonged to the species A. dhakensis. As expected, the isolated A. dhakensis strain was resistant to ampicillin and ampicillin/sulbactam, as resistance to ampicillin is a typical characteristic of the genus Aeromonas. Resistance to cefoxitin and meropenem was also observed, but the strain was susceptible to most of the tested antibiotics. The isolated strain of A. dhakensis caused acute haemorrhagic septicaemia in experimentally infected P. mesopotamicus, with a fifty per cent lethal dose of 1.14 × 105 CFU/fish. This is the first report of the occurrence of an A. dhakensis strain causing an infection in a fish species of South America, providing important epidemiologic data relating to this important pathogenic species.
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Affiliation(s)
- M M Carriero
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
| | - A A Mendes Maia
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - R L Moro Sousa
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - F Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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23
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Piubeli F, de Lourdes Moreno M, Kishi LT, Henrique-Silva F, García MT, Mellado E. Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert. Indian J Microbiol 2015; 55:392-9. [PMID: 26543264 PMCID: PMC4627947 DOI: 10.1007/s12088-015-0539-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 02/19/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022] Open
Abstract
The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations .
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Affiliation(s)
- Francine Piubeli
- />Department of Genetics and Evolution (DGE), UFSCar, Via Washington Luis, Km. 235, São Carlos, SP Brazil
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
| | - María de Lourdes Moreno
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
| | - Luciano Takeshi Kishi
- />Department of Genetics and Evolution (DGE), UFSCar, Via Washington Luis, Km. 235, São Carlos, SP Brazil
| | - Flavio Henrique-Silva
- />Department of Genetics and Evolution (DGE), UFSCar, Via Washington Luis, Km. 235, São Carlos, SP Brazil
| | - María Teresa García
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
| | - Encarnación Mellado
- />Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, C/Profesor García González, 2, 41012 Seville, Spain
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24
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Evangelista DE, Schutzer de Godoy A, Fonseca Pereira de Paula F, Henrique-Silva F, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the pectin methylesterase from the sugar cane weevil Sphenophorus levis. Acta Crystallogr F Struct Biol Commun 2014; 70:331-4. [PMID: 24598920 PMCID: PMC3944695 DOI: 10.1107/s2053230x14001630] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 01/22/2014] [Indexed: 11/11/2022] Open
Abstract
Pectin methylesterase removes the methyl groups from the main chain of pectin, the major component of the middle lamella of the plant cell wall. The enzyme is involved in plant cell-wall development, is part of the enzymatic arsenal used by microorganisms to attack plants and also has a wide range of applications in the industrial sector. Therefore, there is a considerable interest in studies of the structure and function of this enzyme. In this work, the pectin methylesterase from Sphenophorus levis was produced in Pichia pastoris and purified. Crystals belonging to the monoclinic space group C2, with unit-cell parameters a = 122.181, b = 82.213, c = 41.176 Å, β = 97.48°, were obtained by the sitting-drop vapour-diffusion method and an X-ray diffraction data set was collected to 2.1 Å resolution. Structure refinement and model building are in progress.
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Affiliation(s)
- Danilo Elton Evangelista
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Andre Schutzer de Godoy
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Fernando Fonseca Pereira de Paula
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos-SP, Brazil
| | - Flavio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos-SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
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25
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Soares-Costa A, Nakayama DG, Andrade LDF, Catelli LF, Bassi APG, Ceccato-Antonini SR, Henrique-Silva F. Industrial PE-2 strain of Saccharomyces cerevisiae: from alcoholic fermentation to the production of recombinant proteins. N Biotechnol 2014; 31:90-7. [DOI: 10.1016/j.nbt.2013.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 08/13/2013] [Accepted: 08/15/2013] [Indexed: 10/26/2022]
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26
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Gonçalves VR, Sobrinho IS, Malagó W, Henrique-Silva F, de Brito RA. Transcriptome analysis of female reproductive tissues of Anastrepha obliqua and molecular evolution of eggshell proteins in the fraterculus group. Insect Mol Biol 2013; 22:551-561. [PMID: 24137793 DOI: 10.1111/imb.12045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The investigation of cDNA libraries has been an important tool for the identification of new genes in nonmodel species such as the fruit flies from the Anastrepha fraterculus group. In the present study, we constructed a cDNA library from the female reproductive tissues of Anastrepha obliqua aiming to identify genes with high evolutionary rates. We sequenced 2304 clones obtained from the female reproductive tissues of A. obliqua flies. The expressed sequence tags generated a total of 816 unigenes which were classified into different protein classes. Among these,we identified chorionic and vitelline protein genes as being among the most highly expressed. We used unigene sequences to amplify a set of chorionic and vitelline genes, involved in the formation of the eggshell,in species of the fraterculus group. Four chorionic genes and two vitelline genes showed evidence of positive selection along the Anastrepha and/or Tephritidae lineage. The signal of selection detected for Vm26Aa was possibly generated by a gene duplication event. The rapid evolutionary rates indicate that these genes could serve as important markers in population and evolutionary studies, not only for species of this group, but possibly also for other Diptera.
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Affiliation(s)
- V R Gonçalves
- Departamento de Genética e Evolução, UniversidadeFederal de São Carlos, São Carlos, Brazil
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27
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Koroiva R, Souza CWO, Toyama D, Henrique-Silva F, Fonseca-Gessner AA. Lignocellulolytic enzymes and bacteria associated with the digestive tracts of Stenochironomus (Diptera: Chironomidae) larvae. Genet Mol Res 2013; 12:3421-34. [PMID: 23613276 DOI: 10.4238/2013.april.2.2] [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: 11/03/2022]
Abstract
We analyzed the digestive activity of the enzymes that digest cellulose and hemicellulose and the bacterial community that is capable of hydrolyzing wood compounds in the digestive tracts of Stenochironomus (Diptera: Chironomidae) larvae, which are miners of decomposing submerged tree and bush branches. Based on quantification of reducing sugars, these larvae have a limited capacity for cellulose degradation but a good capacity for xylan hydrolysis. We isolated 31 types of colonies from two larval morphotypes, of which 19 tested positive for the capacity to hydrolyze at least one of the four substrates that were used as the main carbon source in the culture media. Their woody compound degradation capacity was assessed using colorimetric tests. The bacteria were identified by the analysis of the 16S rRNA gene. None of the bacteria were capable of degrading lignin. The genus Pseudomonas had the greatest species richness; Bacillus spp exhibited the greatest capacity for degrading the different substrates, and Sphingobium was found in both morphotypes. Microorganisms participate in the degradation of wood consumed by Stenochironomus larvae. This is the first report of lignocellulolytic bacteria and enzymes in the digestive tracts of mining chironomids.
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Affiliation(s)
- R Koroiva
- Laboratório de Ecologia de Insetos Aquáticos, Departamento de Hidrobiologia, Centro de Ciências Biológicas da Saúde, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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28
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Soares-Costa A, Silveira RS, Novo MTM, Alves MFM, Carmona AK, Belasque J, Henrique-Silva F. Recombinant expression and characterization of a cysteine peptidase from Xanthomonas citri subsp citri. Genet Mol Res 2012; 11:4043-57. [PMID: 23212341 DOI: 10.4238/2012.november.28.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Xanthomonas citri subsp citri (Xac) is the bacterium responsible for citrus canker disease in citrus plants. The aim of this study was to describe the recombinant expression, purification, and characterization of a cysteine peptidase from Xac strain 306, which is a candidate for involvement in the pathogenicity of this bacterium. The gene was cloned and expressed in Pichia pastoris, and the cysteine peptidase was successfully expressed, secreted, and purified using affinity chromatography with a yield of approximately 10 mg/L. A polyclonal antibody produced against cysteine peptidase from X. citri subsp citri fused with HIS tag ((HIS)CPXAC) recognized the purified recombinant cysteine peptidase (HIS)CPXAC, confirming the correct production of this protein in P. pastoris. The same antibody detected the protein in the culture supernatant of Xac grown in pathogenicity-inducing medium. Kinetic analysis revealed that (HIS)CPXAC hydrolyzed the carbobenzoxy-Leu-Arg-7-amido-4-methylcoumarin substrate with a catalytic efficiency (k(cat)/K(m)) of 47 μM(-1)∙s(-1). The purified ((HIS))CPXAC displayed maximal catalytic activity at pH 5.5 and 30°C. The recombinant enzyme was inhibited by the specific cysteine peptidase inhibitor E-64, as well as by the recombinant cysteine peptidase inhibitors CaneCPI-1, CaneCPI-2, CaneCPI-3, and CaneCPI-4, with K(i) values of 1.214, 84.64, 0.09, 0.09, and 0.012 nM, respectively. Finally, the N-terminal sequencing of the purified protein enabled the identification of the first 5 amino acid residues (AVHGM) immediately after the putative signal peptide, thereby enabling the identification of the cleavage point and corroborating previous studies that have identified this sequence in a secreted protein from Xanthomonas spp.
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Affiliation(s)
- A Soares-Costa
- Laboratório de Biologia Molecular, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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29
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Santos-Silva LK, Soares-Costa A, Gerald LTS, Meneghin SP, Henrique-Silva F. Recombinant expression and biochemical characterization of sugarcane legumain. Plant Physiol Biochem 2012; 57:181-92. [PMID: 22721948 DOI: 10.1016/j.plaphy.2012.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 05/17/2012] [Indexed: 05/01/2023]
Abstract
Plant legumains, also termed vacuolar processing enzymes (VPEs), are cysteine peptidases that play key roles in plant development, senescence, programmed cell death and defense against pathogens. Despite the increasing number of reports on plant cysteine peptidases, including VPEs, the characterization of sugarcane VPEs and their inhibition by endogenous cystatins have not yet been described. This is the first report of the biochemical characterization of a sugarcane cysteine peptidase. In this work, a recombinant sugarcane legumain was expressed in Pichia pastoris and characterized. Kinetic studies of the recombinant CaneLEG revealed that this enzyme has the main characteristics of VPEs, such as self-activation and activity under acidic pH. CaneLEG activity was strongly inhibited when incubated with sugarcane cystatin 3 (CaneCPI-3). Quantitative analysis of CaneLEG and CaneCPI-3 gene expression indicated a tissue-specific expression pattern for both genes throughout sugarcane growth, with the strong accumulation of CaneLEG transcripts throughout the internode development. Furthermore, the CaneLEG and CaneCPI-3 genes exhibited up-regulation in plantlets treated with abscisic acid (ABA). These results suggest that CaneCPI-3 may be a potential endogenous inhibitor of CaneLEG and these genes may be involved in plant stress response mediated by ABA. Also, the expression analysis provides clues for the putative involvement of CaneLEG and CaneCPI-3 in sugarcane development and phytohormone response.
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Affiliation(s)
- Ludier K Santos-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luís, São Carlos SP, Brazil
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Generoso WC, Malagó W, Pereira N, Henrique-Silva F. Recombinant expression and characterization of an endoglucanase III (cel12a) from Trichoderma harzianum (Hypocreaceae) in the yeast Pichia pastoris. Genet Mol Res 2012; 11:1544-57. [PMID: 22653604 DOI: 10.4238/2012.may.21.11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Filamentous fungi from the genus Trichoderma have been widely investigated due to their considerable production of important biotechnological enzymes. Previous studies have demonstrated that the T. harzianum strain IOC-3844 has a high degree of cellulolytic activity. After excluding the native signal peptide, the open reading frame of the T. harzianum endoglucanase III enzyme was cloned in the expression vector pPICZαA, enabling protein secretion to the culture medium. The recombinant plasmid was used to transform Pichia pastoris. Recombinant expression in the selected clone yielded 300 mg pure enzyme per liter of induced medium. The recombinant enzyme proved to be active in a qualitative analysis using Congo red. A quantitative assay, using dinitrosalicylic acid, revealed a high degree of activity at pH 5.5 and around 48°C. This information contributes to our understanding of the cellulolytic repertory of T. harzianum and the determination of a set of enzymes that can be incorporated into mixes for second-generation ethanol production.
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Affiliation(s)
- W C Generoso
- Laboratório de Biologia Molecular, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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31
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Abstract
Transgenic plants have been widely used as expression systems of recombinant proteins in recent years because it can be an efficient alternative for the large-scale production of proteins. This is an area with great potential but is still not much explored. Indeed, this system can bring a breakthrough in the expression of any protein. The model used here as a protein factory was sugarcane, a crop of great global importance. This chapter describes the system that has been adopted in the routine production of transgenic sugarcane coupled with protein purification protocol. In this chapter, we describe production of transgenic sugarcane expressing a His-tagged cystatin under the control of the maize ubiquitin promoter. A transformed sugarcane plant presented high levels of protein expression and was selected for the purification of this protein through affinity chromatography in a nickel column. These studies demonstrate that sugarcane can be a viable expression system for recombinant protein production and that the His-tag purification strategy used to isolate the purified protein was effective.
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Affiliation(s)
- Flavio Henrique-Silva
- Laboratory of Molecular Biology, Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
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Rinke R, Costa AS, Fonseca FPP, Almeida LC, Delalibera Júnior I, Henrique-Silva F. Microbial diversity in the larval gut of field and laboratory populations of the sugarcane weevil Sphenophorus levis (Coleoptera, Curculionidae). Genet Mol Res 2011; 10:2679-91. [PMID: 22057964 DOI: 10.4238/2011.november.1.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The sugarcane weevil, Sphenophorus levis, is a wide-spread sugarcane pest in Brazil. Sphenophorus levis may depend on microorganisms that inhabit its intestinal tract. We examined the diversity of the gut microbiota of S. levis, which was characterized using culture-dependent and culture-independent methods. Analysis of 16S rRNA amplified directly from the gut community revealed the presence of 14 genera, one group from the Candidatus category, one uncultured group assigned to the family Flavobacteriaceae, and one uncultured group assigned to the family Enterobacteriaceae; all of them are members of the Alpha-Proteobacteria, Beta-Proteobacteria, Gamma-Proteobacteria, Firmicutes, and Bacteroidetes phyla. Microorganisms isolated through culture-dependent methods were classified according to morphological parameters and by 16S rRNA gene sequences. In addition to bacteria, four filamentous fungi were isolated. A higher bacterial diversity was observed in field populations of larvae than in laboratory populations, according to the Shannon index (Field H' = 3.36; Laboratory H' = 3.26). Five genera of bacteria and two filamentous fungi were found to have cellulolytic activity. This is the first report of S. levis gut microbiota; it may contribute to development of strategies for controlling this sugarcane pest.
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Affiliation(s)
- R Rinke
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F. Metagenomics of the water column in the pristine upper course of the Amazon river. PLoS One 2011; 6:e23785. [PMID: 21915244 PMCID: PMC3158796 DOI: 10.1371/journal.pone.0023785] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [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: 04/15/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022] Open
Abstract
River water is a small percentage of the total freshwater on Earth but represents an essential resource for mankind. Microbes in rivers perform essential ecosystem roles including the mineralization of significant quantities of organic matter originating from terrestrial habitats. The Amazon river in particular is famous for its size and importance in the mobilization of both water and carbon out of its enormous basin. Here we present the first metagenomic study on the microbiota of this river. It presents many features in common with the other freshwater metagenome available (Lake Gatun in Panama) and much less similarity with marine samples. Among the microbial taxa found, the cosmopolitan freshwater acI lineage of the actinobacteria was clearly dominant. Group I Crenarchaea and the freshwater sister group of the marine SAR11 clade, LD12, were found alongside more exclusive and well known freshwater taxa such as Polynucleobacter. A metabolism-centric analysis revealed a disproportionate representation of pathways involved in heterotrophic carbon processing, as compared to those found in marine samples. In particular, these river microbes appear to be specialized in taking up and mineralizing allochthonous carbon derived from plant material.
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Affiliation(s)
- Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- * E-mail: (FRV); (FHS)
| | - Katherine D. McMahon
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Danyelle Toyama
- Laboratory of Molecular Biology, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - Raquel Rinke
- Laboratory of Molecular Biology, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | | | | | - Fernando Pellon de Miranda
- Petróleo Brasileiro S.A. – Petrobras, Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Melo, Rio de Janeiro, RJ, Brasil
| | - Flavio Henrique-Silva
- Laboratory of Molecular Biology, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
- * E-mail: (FRV); (FHS)
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Adriano E, Arana S, Alves A, Silva M, Ceccarelli P, Henrique-Silva F, Maia A. Myxobolus cordeiroi n. sp., a parasite of Zungaro jahu (Siluriformes: Pimelodiade) from Brazilian Pantanal: Morphology, phylogeny and histopathology. Vet Parasitol 2009; 162:221-9. [DOI: 10.1016/j.vetpar.2009.03.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 03/05/2009] [Accepted: 03/14/2009] [Indexed: 10/21/2022]
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Ribeiro CW, Soares-Costa A, Falco MC, Chabregas SM, Ulian EC, Cotrin SS, Carmona AK, Santana LA, Oliva MLV, Henrique-Silva F. Production of a His-tagged canecystatin in transgenic sugarcane and subsequent purification. Biotechnol Prog 2008; 24:1060-1066. [PMID: 19194914 DOI: 10.1007/s12355-008-0048-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 05/27/2023]
Abstract
Transgenic plants have been used widely as expression systems of recombinant proteins in recent years. This process can be an efficient alternative for the large-scale production of proteins. In this work, we present the establishment of transgenic sugarcane expressing a His-tagged canecystatin under the control of the maize ubiquitin promoter. A number of studies have demonstrated that cystatins, which are natural inhibitors of cysteine proteinases, can be used for protection against insect attacks. A transformed sugarcane plant that presented high levels of (HIS)CaneCPI-1 expression, was selected for the purification of this protein through affinity chromatography in a nickel column. This purified (HIS)CaneCPI-1 was immunodetected using a polyclonal antibody, which was also able to detect the (HIS)CaneCPI-1 in a crude extract from transgenic plant leaves. Assays of inhibitory activity performed with the purified (HIS)CaneCPI-1 revealed its ability to inhibit the catalytic activity of midgut cysteine proteinase partially purified from the sugarcane weevil Sphenophorus levis and human cathepsin L in nanomolar order. These studies demonstrate that sugarcane is a viable expression system for recombinant protein production.
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Affiliation(s)
- Carolina W Ribeiro
- Dept of Genetic and Evolution, Laboratory of Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
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Ribeiro CW, Soares-Costa A, Falco MC, Chabregas SM, Ulian EC, Cotrin SS, Carmona AK, Santana LA, Oliva MLV, Henrique-Silva F. Production of a His-tagged canecystatin in transgenic sugarcane and subsequent purification. Biotechnol Prog 2008; 24:1060-6. [DOI: 10.1002/btpr.45] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Even though the molecular mechanisms underlying the Down syndrome (DS) phenotypes remain obscure, the characterization of the genes and conserved non-genic sequences of HSA21 together with large-scale gene expression studies in DS tissues are enhancing our understanding of this complex disorder. Also, mouse models of DS provide invaluable tools to correlate genes or chromosome segments to specific phenotypes. Here we discuss the possible contribution of HSA21 genes to DS and data from global gene expression studies of trisomic samples.
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Affiliation(s)
- CA. Sommer
- Universidade Federal de São Carlos, Brazil
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Tagliavini SA, Mikawa AY, Yamanaka H, Henrique-Silva F, Costa PI. Polysiloxane-poly(propylene oxide) hybrid discs as solid phase in anti-HCV detection using a recombinant core protein. Talanta 2008; 75:461-5. [PMID: 18371907 DOI: 10.1016/j.talanta.2007.11.036] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 11/13/2007] [Accepted: 11/13/2007] [Indexed: 11/18/2022]
Abstract
In this work, siloxane-poly(propylene oxide) discs (PPO disc) prepared using the sol-gel process were used as solid phase in enzyme-linked immunosorbent assays (ELISA) for the detection of anti-hepatitis C virus (HCV) antibodies. The HCV RNA from serum (genotype 1b) was submitted to the RT-PCR technique and subsequent amplification of the HCV core 408 pb. This fragment was cloned into expression vector pET42a and expressed in Escherichia coli as recombinant protein with glutathione S-transferase (GST). Cell cultures were grown and induced having a final concentration of 0.4 x 10(-3) mol L(-1) of IPTG. After induction, the cells were harvested and the soluble fraction was analyzed using polyacrilamide gel 15% showing a band with an approximate molecular weight of 44 kDa, the expected size for this GST-fused recombinant protein. The recombinant protein was purified and confirmed by immunological detection using HCV-positive serum and showed no cross-reactivity with positive samples for other infectious diseases. An ELISA was established using 1.25 ng of recombinant protein per PPO disc, a dilution of 1:10,000 and 1:40 for a peroxidase conjugate and serum, respectively, and solutions of hydrogen peroxide and 3,3',5,5'-tetra-methylbenzidine in a ratio of 1:1. The proposed methodology was compared with the ELISA conventional polystyrene-plate procedure and the performance of the PPO discs as a matrix for immunodetection gave an easy synthesis, good performance and reproducibility for commercial application.
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Affiliation(s)
- S A Tagliavini
- Unesp-Universidade Estadual Paulista, Instituto de Química, R. Prof. Francisco Degni s/n, 14800-900 Araraquara, Brazil.
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Sommer CA, Pavarino-Bertelli EC, Goloni-Bertollo EM, Henrique-Silva F. Identification of dysregulated genes in lymphocytes from children with Down syndrome. Genome 2008; 51:19-29. [PMID: 18356936 DOI: 10.1139/g07-100] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The molecular mechanisms by which trisomy of human chromosome 21 disrupts normal development are not well understood. Global transcriptome studies attempting to analyze the consequences of trisomy in Down syndrome (DS) tissues have reported conflicting results, which have led to the suggestion that the analysis of specific tissues or cell types may be more productive. In the present study, we set out to analyze global changes of gene expression in lymphocytes from children with trisomy 21 by means of the serial analysis of gene expression (SAGE) methodology. Two SAGE libraries were constructed using pooled RNA of normal and Down syndrome children. Comparison between DS and normal profiles revealed that most of the transcripts were expressed at similar levels and functional classes of abundant genes were equally represented. Among the 242 significantly differentially expressed SAGE tags, several transcripts downregulated in DS code for proteins involved in T-cell and B-cell receptor signaling (e.g., PI3Kdelta, RGS2, LY6E, FOS, TAGAP, CD46). The SAGE data and interindividual variability were validated by real-time quantitative PCR. Our results indicate that trisomy 21 induces a modest dysregulation of disomic genes that may be related to the immunological perturbations seen in DS.
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Affiliation(s)
- Cesar A Sommer
- Department of Genetics and Evolution, Federal University of Sao Carlos, Rodovia Washington Luis km 235, 13565-905, Sao Carlos, Sao Paulo, Brazil
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Souza ADL, Rodrigues-Filho E, Souza AQL, Henrique-Silva F, Pereira JO. A new guaiane mannoside from a Eutypa-like fungus isolated from Murraya paniculata in Brazil. J BRAZIL CHEM SOC 2008. [DOI: 10.1590/s0103-50532008000700014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Henrique-Silva F, Cervini M, Rios WM, Lusa AL, Lopes A, Gonçalves D, Fonseca D, Franzin F, Damalio J, Scaramuzzi K, Camilo R, Ferrarezi T, Liberato M, Mortari N, Matheucci E. Rapid identification of capybara (Hydrochaeris hydrochaeris) using allele-specific PCR. BRAZ J BIOL 2007; 67:189-90. [PMID: 17505769 DOI: 10.1590/s1519-69842007000100027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- F Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos - UFSCar, São Carlos, SP, Brazil.
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Davies KJA, Ermak G, Rothermel BA, Pritchard M, Heitman J, Ahnn J, Henrique-Silva F, Crawford D, Canaider S, Strippoli P, Carinci P, Min KT, Fox DS, Cunningham KW, Bassel-Duby R, Olson EN, Zhang Z, Williams RS, Gerber HP, Pérez-Riba M, Seo H, Cao X, Klee CB, Redondo JM, Maltais LJ, Bruford EA, Povey S, Molkentin JD, McKeon FD, Duh EJ, Crabtree GR, Cyert MS, de la Luna S, Estivill X. Renaming the DSCR1/Adapt78 gene family as RCAN: regulators of calcineurin. FASEB J 2007; 21:3023-8. [PMID: 17595344 DOI: 10.1096/fj.06-7246com] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kelvin J A Davies
- Ethel Percy Andrus Gerontology Center, and Division of Molecular & Computational Biology, The University of Southern California, Los Angeles, CA 90089-0191, USA.
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Affiliation(s)
- W Malagó-Júnior
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luis, Km 235, CEP 13565-905, São Carlos, SP, Brazil
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Malagó W, Sommer CA, Del Cistia Andrade C, Soares-Costa A, Abrao Possik P, Cassago A, Santejo Silveira HC, Henrique-Silva F. Gene expression profile of human Down syndrome leukocytes. Croat Med J 2005; 46:647-56. [PMID: 16100769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
AIM Identification of differences in the gene expression patterns of Down syndrome and normal leukocytes. METHODS We constructed the first Down syndrome leukocyte serial analysis of gene expression (SAGE) library from a 28 year-old patient. This library was analyzed and compared with a normal leukocyte SAGE library using the eSAGE software. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to validate the results. RESULTS We found that a large number of unidentified transcripts were overexpressed in Down syndrome leukocytes and some transcripts coding for growth factors (e.g. interleukin 8, IL-8), ribosomaproteins (e.g. L13a, L29, and L37), and transcription factors (e.g., Jun B, Jun D, and C/EBP beta) were underexpressed. The SAGE data were successfully validated for the genes IL-8, CXCR4, BCL2A1, L13a, L29, L37, and GTF3A using RT-PCR. CONCLUSION Our analysis identified significant changes in the expression pattern of Down syndrome leukocytes compared with normal ones, including key regulators of growth and proliferation, ribosomal proteins, and a large number of overexpressed transcripts that were not matched in UniGene clusters and that may represent novel genes related to Down syndrome. This study offers a new insight into transcriptional changes in Down syndrome leukocytes and indicates candidate genes for further investigations into the molecular mechanism of Down syndrome pathology.
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Affiliation(s)
- Wilson Malagó
- Department of Genetics and Evolution, Federal University of Sao Carlos, Rodovia Washington Luis, Km 235, CEP 13565-905, Sao Carlos, SP, Brazil
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Novo MTM, Soares-Costa A, de Souza AQL, Figueira ACM, Molina GC, Palacios CA, Kull CR, Monteiro IF, Baldan-Pineda PH, Henrique-Silva F. A complete approach for recombinant protein expression training: From gene cloning to assessment of protein functionality*. Biochem Mol Biol Educ 2005; 33:34-40. [PMID: 21638537 DOI: 10.1002/bmb.2005.494033010418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A practical course was given to undergraduate biology students enrolled in the elective course "Introduction to Genetic Engineering" at the Federal University of São Carlos (UFSCar), São Paulo, Brazil. The goal of the course was to teach current molecular biology tools applied to a real research situation that could be reported by the students themselves. The purpose was to produce a plant recombinant protein and demonstrate a heretofore unreported biological activity. Cystatins, natural inhibitors of cysteine proteases, were proposed for these studies. Initially, the students searched for plant cystatin cDNA sequences in the NCBI databases and selected the Oryzacystatin I gene (ocI) from rice, Oriza sativa, as the target gene for this study. Total RNA was extracted from rice-germinating seeds and primers containing restriction sites for NdeI and EcoRI were designed based on the ocI cDNA sequence and then used to amplify the open reading frame (ORF). RT-PCR amplification provided a band of the expected size for ocI ORF (309 bp). The PCR product was cut with NdeI and EcoRI restriction enzymes and cloned directly in the pET28a expression vector digested with the same enzymes. A pET28-ocI recombinant clone was selected, checked by sequencing, and used to transform Escherichia coli BL21 (DE3) expression strain. After induction of the bacteria with isopropylthiogalactoside and cellular disruption, the His-tagged OCI protein, present mainly in the soluble fraction, was purified by affinity chromatography in a nickel column. The purified protein was successfully used to inhibit fungal growth (Trichoderma reesei). The results were discussed extensively and the students contributed to the writing of this article, of which they are co-authors.
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Affiliation(s)
- M Teresa Marques Novo
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos-SP, Brazil
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Oliva MLV, Carmona AK, Andrade SS, Cotrin SS, Soares-Costa A, Henrique-Silva F. Inhibitory selectivity of canecystatin: a recombinant cysteine peptidase inhibitor from sugarcane. Biochem Biophys Res Commun 2004; 320:1082-6. [PMID: 15249200 DOI: 10.1016/j.bbrc.2004.06.053] [Citation(s) in RCA: 22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Indexed: 11/29/2022]
Abstract
The cDNA of a cystein peptidase inhibitor was isolated from sugarcane and expressed in Escherichia coli. The protein, named canecystatin, has previously been shown to exert antifungal activity on the filamentous fungus Trichoderma reesei. Herein, the inhibitory specificity of canecystatin was further characterized. It inhibits the cysteine peptidases from plant source papain (Ki =3.3nM) and baupain (Ki=2.1x10(-8)M), but no inhibitory effect was observed on ficin or bromelain. Canecystatin also inhibits lysosomal cysteine peptidases such as human cathepsin B (Ki=125nM), cathepsin K (Ki=0.76nM), cathepsin L (Ki=0.6nM), and cathepsin V (Ki=1.0nM), but not the aspartyl peptidase cathepsin D. The activity of serine peptidases such as trypsin, chymotrypsin, pancreatic, and neutrophil elastases, and human plasma kallikrein is not affected by the inhibitor, nor is the activity of the metallopeptidases angiotensin converting enzyme and neutral endopeptidase. This is the first report of inhibitory activity of a sugarcane cystatin on cysteine peptidases.
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Affiliation(s)
- Maria Luiza Vilela Oliva
- Department of Biochemistry, Universidade Federal de São Paulo-Escola Paulista de Medicina, Rua Três de Maio, 100, 04044-020 São Paulo, SP, Brazil.
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Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJG, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MAV, De Souza SJ, Faria M, Giuliatti S, Kopp L, de Oliveira PSL, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LEC, Baia GS, Briones MRS, Cavaleiro-Luna AMS, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MAHZ, Furchi JRF, Giannella-Neto D, Goldman GH, Goldman MHS, Gruber A, Guimarães GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SKN, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paço-Larson ML, Paixão BMC, Pandolfi JRC, Pardini MIMC, Passos Bueno MR, Passos GAS, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sá RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA, Silva IDCG, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, Zanette DL. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res 2004; 14:1413-23. [PMID: 15197164 PMCID: PMC442158 DOI: 10.1101/gr.2111304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/12/2004] [Indexed: 11/24/2022]
Abstract
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.
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Possik PA, Sommer CA, Issa Hori J, Machado-Santelli GM, Jamur MC, Henrique-Silva F. DSCR2, a Down syndrome critical region protein, is localized to the endoplasmic reticulum of mammalian cells. Eur J Histochem 2004; 48:267-72. [PMID: 15590417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
We used immunocytochemical and fluorescence assays to investigate the subcellular location of the protein encoded by Down syndrome critical region gene 2 (DSCR2) in transfected cells. It was previously suggested that DSCR2 is located in the plasma membrane as an integral membrane protein. Interestingly, we observed this protein in the endoplasmic reticulum (ER) of cells. We also studied whether the truncated forms of DSCR2 showed different subcellular distributions. Our observations indicate that DSCR2 probably is not inserted into the membrane of the endoplasmic reticulum since the fragments lacking the predicted transmembrane (TM) helices remained associated with the ER. Our analyses suggest that, although DSCR2 is associated with the endoplasmic reticulum, it is not an integral membrane protein and it is maintained on the cytoplasmic side of the ER by indirect interaction with the ER membrane or with another protein.
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Affiliation(s)
- P A Possik
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
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Silveira HCS, Sommer CA, Soares-Costa A, Henrique-Silva F. A calcineurin inhibitory protein overexpressed in Down's syndrome interacts with the product of a ubiquitously expressed transcript. Braz J Med Biol Res 2004; 37:785-9. [PMID: 15264020 DOI: 10.1590/s0100-879x2004000600002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [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: 11/22/2022] Open
Abstract
The Down's syndrome candidate region 1 (DSCR1) protein, encoded by a gene located in the human chromosome 21, interacts with calcineurin and is overexpressed in Down's syndrome patients. As an approach to clarifying a putative function for this protein, in the present study we used the yeast two-hybrid system to identify DSCR1 partners. The two-hybrid system is a method that allows the identification of protein-protein interactions through reconstitution of the activity of the yeast GAL 4 transcriptional activator. The gene DSCR1 fused to the GAL 4 binding domain (BD) was used to screen a human fetal brain cDNA library cloned in fusion with the GAL 4 activation domain (AD). Three positive clones were found and sequence analysis revealed that all the plasmids coded for the ubiquitously expressed transcript (UXT). UXT, which is encoded in human Xp11, is a 157-amino acid protein present in both cytosol and nucleus of the cells. This positive interaction of DSCR1 and UXT was confirmed in vivo by mating the yeast strain AH109 (MATa) expressing AD-UXT with the strain Y187 (MATalpha) expressing BD-DSCR1, and in vitro by co-immunoprecipitation experiments. These results may help elucidate a new function for DSCR1 and its participation in Down's syndrome pathogenesis.
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Affiliation(s)
- H C S Silveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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50
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Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MIT, Henrique-Silva F, Giglioti EA, Lemos MVF, Coutinho LL, Nobrega MP, Carrer H, França SC, Bacci Júnior M, Goldman MHS, Gomes SL, Nunes LR, Camargo LEA, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon MLPN, Ferro JA, Silveira HCS, Marini DC, Lemos EGM, Monteiro-Vitorello CB, Tambor JHM, Carraro DM, Roberto PG, Martins VG, Goldman GH, de Oliveira RC, Truffi D, Colombo CA, Rossi M, de Araujo PG, Sculaccio SA, Angella A, Lima MMA, de Rosa Júnior VE, Siviero F, Coscrato VE, Machado MA, Grivet L, Di Mauro SMZ, Nobrega FG, Menck CFM, Braga MDV, Telles GP, Cara FAA, Pedrosa G, Meidanis J, Arruda P. Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 2003; 13:2725-35. [PMID: 14613979 PMCID: PMC403815 DOI: 10.1101/gr.1532103] [Citation(s) in RCA: 216] [Impact Index Per Article: 10.3] [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: 11/24/2022]
Abstract
To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.
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MESH Headings
- Computational Biology/methods
- Computational Biology/statistics & numerical data
- DNA, Complementary/analysis
- DNA, Complementary/classification
- DNA, Complementary/physiology
- DNA, Plant/analysis
- DNA, Plant/classification
- DNA, Plant/physiology
- Expressed Sequence Tags
- Gene Expression Regulation, Plant
- Gene Library
- Molecular Sequence Data
- Organ Specificity/genetics
- Peptides/classification
- Peptides/genetics
- Peptides/physiology
- Plant Proteins/classification
- Plant Proteins/genetics
- Plant Proteins/physiology
- Polymorphism, Genetic/genetics
- Protein Structure, Tertiary/genetics
- Saccharum/genetics
- Saccharum/growth & development
- Saccharum/physiology
- Sequence Analysis, DNA/methods
- Signal Transduction/genetics
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Affiliation(s)
- André L Vettore
- Centro de Biologia Molecular e Engenharia Genética, Instituto da Computação, Universidade Estadual de Campinas, 13083-970 Campinas-SP, Brazil
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