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Almeida-Silva F, Pedrosa-Silva F, Venancio TM. The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1041-1051. [PMID: 37681739 DOI: 10.1111/tpj.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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Barbosa JAS, da Silva LLS, João JMLG, de Campos EC, Fukuzaki S, Camargo LDN, dos Santos TM, dos Santos HT, Bezerra SKM, Saraiva-Romanholo BM, Lopes FDTQDS, Bonturi CR, Oliva MLV, Leick EA, Righetti RF, Tibério IDFLC. Investigating the Effects of a New Peptide, Derived from the Enterolobium contortisiliquum Proteinase Inhibitor (EcTI), on Inflammation, Remodeling, and Oxidative Stress in an Experimental Mouse Model of Asthma-Chronic Obstructive Pulmonary Disease Overlap (ACO). Int J Mol Sci 2023; 24:14710. [PMID: 37834157 PMCID: PMC10573003 DOI: 10.3390/ijms241914710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The synthesized peptide derived from Enterolobium contortisiliquum (pep3-EcTI) has been associated with potent anti-inflammatory and antioxidant effects, and it may be a potential new treatment for asthma-COPD overlap-ACO). Purpose: To investigate the primary sequence effects of pep3-EcTI in an experimental ACO. BALB/c mice were divided into eight groups: SAL (saline), OVA (ovalbumin), ELA (elastase), ACO (ovalbumin + elastase), ACO-pep3-EcTI (treated with inhibitor), ACO-DX (treated with dexamethasone), ACO-DX-pep3-EcTI (treated with dexamethasone and inhibitor), and SAL-pep3-EcTI (saline group treated with inhibitor). We evaluated the hyperresponsiveness to methacholine, exhaled nitric oxide, bronchoalveolar lavage fluid (BALF), mean linear intercept (Lm), inflammatory markers, tumor necrosis factor (TNF-α), interferon (IFN)), matrix metalloproteinases (MMPs), growth factor (TGF-β), collagen fibers, the oxidative stress marker inducible nitric oxide synthase (iNOS), transcription factors, and the signaling pathway NF-κB in the airways (AW) and alveolar septa (AS). Statistical analysis was conducted using one-way ANOVA and t-tests, significant when p < 0.05. ACO caused alterations in the airways and alveolar septa. Compared with SAL, ACO-pep3-EcTI reversed the changes in the percentage of resistance of the respiratory system (%Rrs), the elastance of the respiratory system (%Ers), tissue resistance (%Gtis), tissue elastance (%Htis), airway resistance (%Raw), Lm, exhaled nitric oxide (ENO), lymphocytes, IL-4, IL-5, IL-6, IL-10, IL-13, IL-17, TNF-α, INF-γ, MMP-12, transforming growth factor (TGF)-β, collagen fibers, and iNOS. ACO-DX reversed the changes in %Rrs, %Ers, %Gtis, %Htis, %Raw, total cells, eosinophils, neutrophils, lymphocytes, macrophages, IL-1β, IL-6, IL-10, IL-13, IL-17, TNF-α, INF-γ, MMP-12, TGF-β, collagen fibers, and iNOS. ACO-DX-pep3-EcTI reversed the changes, as was also observed for the pep3-EcTI and the ACO-DX-pep3-EcTI. Significance: The pep3-EcTI was revealed to be a promising strategy for the treatment of ACO, asthma, and COPD.
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Affiliation(s)
- Jéssica Anastácia Silva Barbosa
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Hospital Sírio Libanês, São Paulo 01308-050, Brazil
| | - Luana Laura Sales da Silva
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
| | - Juliana Morelli Lopes Gonçalves João
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Hospital Sírio Libanês, São Paulo 01308-050, Brazil
| | - Elaine Cristina de Campos
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Hospital Sírio Libanês, São Paulo 01308-050, Brazil
| | - Silvia Fukuzaki
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
| | - Leandro do Nascimento Camargo
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Hospital Sírio Libanês, São Paulo 01308-050, Brazil
| | - Tabata Maruyama dos Santos
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Hospital Sírio Libanês, São Paulo 01308-050, Brazil
| | - Henrique Tibucheski dos Santos
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
| | - Suellen Karoline Moreira Bezerra
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
| | - Beatriz Mangueira Saraiva-Romanholo
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Department of Medicine, University City of São Paulo, São Paulo 03071-000, Brazil
| | - Fernanda Degobbi Tenório Quirino dos Santos Lopes
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
| | - Camila Ramalho Bonturi
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), São Paulo 04039-002, Brazil; (C.R.B.); (M.L.V.O.)
| | - Maria Luiza Vilela Oliva
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), São Paulo 04039-002, Brazil; (C.R.B.); (M.L.V.O.)
| | - Edna Aparecida Leick
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
| | - Renato Fraga Righetti
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
- Hospital Sírio Libanês, São Paulo 01308-050, Brazil
| | - Iolanda de Fátima Lopes Calvo Tibério
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil; (J.A.S.B.); (L.L.S.d.S.); (J.M.L.G.J.); (E.C.d.C.); (S.F.); (L.d.N.C.); (T.M.d.S.); (H.T.d.S.); (S.K.M.B.); (B.M.S.-R.); (F.D.T.Q.d.S.L.); (E.A.L.); (R.F.R.)
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Escandón M, Bigatton ED, Guerrero-Sánchez VM, Hernández-Lao T, Rey MD, Jorrín-Novo JV, Castillejo MA. Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species Quercus ilex. FRONTIERS IN PLANT SCIENCE 2022; 13:907042. [PMID: 35832232 PMCID: PMC9271950 DOI: 10.3389/fpls.2022.907042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 05/09/2023]
Abstract
Proteases and protease inhibitors have been identified in the recalcitrant species Quercus ilex using in silico and wet methods, with focus on those present in seeds during germination. In silico analyses showed that the Q. ilex transcriptome database contained 2,240 and 97 transcripts annotated as proteases and protease inhibitors, respectively. They belonged to the different families according to MEROPS, being the serine and metallo ones the most represented. The data were compared with those previously reported for other Quercus species, including Q. suber, Q. lobata, and Q. robur. Changes in proteases and protease inhibitors alongside seed germination in cotyledon and embryo axis tissues were assessed using proteomics and in vitro and in gel activity assays. Shotgun (LC-MSMS) analysis of embryo axes and cotyledons in nonviable (NV), mature (T1) and germinated (T3) seeds allowed the identification of 177 proteases and 12 protease inhibitors, mostly represented by serine and metallo types. Total protease activity, as determined by in vitro assays using azocasein as substrate, was higher in cotyledons than in embryo axes. There were not differences in activity among cotyledon samples, while embryo axis peaked at germinated T4 stage. Gel assays revealed the presence of protease activities in at least 10 resolved bands, in the Mr range of 60-260 kDa, being some of them common to cotyledons and embryo axes in either nonviable, mature, and germinated seeds. Bands showing quantitative or qualitative changes upon germination were observed in embryo axes but not in cotyledons at Mr values of 60-140 kDa. Proteomics shotgun analysis of the 10 bands with protease activity supported the results obtained in the overall proteome analysis, with 227 proteases and 3 protease inhibitors identified mostly represented by the serine, cysteine, and metallo families. The combined use of shotgun proteomics and protease activity measurements allowed the identification of tissue-specific (e.g., cysteine protease inhibitors in embryo axes of mature acorns) and stage-specific proteins (e.g., those associated with mobilization of storage proteins accumulated in T3 stage). Those proteins showing differences between nonviable and viable seeds could be related to viability, and those variables between mature and germinated could be associated with the germination process. These differences are observed mostly in embryo axes but not in cotyledons. Among them, those implicated in mobilization of reserve proteins, such as the cathepsin H cysteine protease and Clp proteases, and also the large number of subunits of the CNS and 26S proteasome complex differentially identified in embryos of the several stages suggests that protein degradation via CNS/26S plays a major role early in germination. Conversely, aspartic proteases such as nepenthesins were exclusively identified in NV seeds, so their presence could be used as indicator of nonviability.
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Affiliation(s)
- Monica Escandón
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Ezequiel D. Bigatton
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
- Agricultural Microbiology, Faculty of Agricultural Science, National University of Córdoba, CONICET, Córdoba, Argentina
| | - Victor M. Guerrero-Sánchez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Tamara Hernández-Lao
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Maria-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Jesus V. Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
- Jesus V. Jorrín-Novo,
| | - Maria Angeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
- *Correspondence: Maria Angeles Castillejo,
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