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Comparison of the root, leaf and internode transcriptomes in Sugarcane (Saccharum spp. hybrids). CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Xavier LR, Almeida FA, Pinto VB, Passamani LZ, Santa-Catarina C, de Souza Filho GA, Mooney BP, Thelen JJ, Silveira V. Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153587. [PMID: 34906795 DOI: 10.1016/j.jplph.2021.153587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/14/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Plant embryogenic cell culture allows mass propagation and genetic manipulation, but the mechanisms that determine the fate of these totipotent cells in somatic embryos have not yet been elucidated. Here, we performed label-free quantitative proteomics and phosphoproteomics analyses to determine signaling events related to sugarcane somatic embryo differentiation, especially those related to protein phosphorylation. Embryogenic calli were compared at multiplication (EC0, dedifferentiated cells) and after 14 days of maturation (EC14, onset of embryo differentiation). Metabolic pathway analysis showed enriched lysine degradation and starch/sucrose metabolism proteins during multiplication, whereas the differentiation of somatic embryos was found to involve the enrichment of energy metabolism, including the TCA cycle and oxidative phosphorylation. Multiplication-related phosphoproteins were associated with transcriptional regulation, including SNF1 kinase homolog 10 (KIN10), SEUSS (SEU), and LEUNIG_HOMOLOG (LUH). The regulation of multiple light harvesting complex photosystem II proteins and phytochrome interacting factor 3-LIKE 5 were predicted to promote bioenergetic metabolism and carbon fixation during the maturation stage. A motif analysis revealed 15 phosphorylation motifs. The [D-pS/T-x-D] motif was overrepresented during somatic embryo differentiation. A protein-protein network analysis predicted interactions among SNF1-related protein kinase 2 (SnRK2), abscisic acid-responsive element-binding factor 2 (ABF2), and KIN10, which indicated the role of these proteins in embryogenic competence. The predicted interactions between TOPLESS (TPL) and histone deacetylase 19 (HD19) may be involved in posttranslational protein regulation during somatic embryo differentiation. These results reveal the protein regulation dynamics of somatic embryogenesis and new players in somatic embryo differentiation, including their predicted phosphorylation motifs and phosphosites.
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Affiliation(s)
- Lucas R Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Felipe A Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Vitor B Pinto
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | - Lucas Z Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | | | - Gonçalo A de Souza Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Brian P Mooney
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211, Columbia, MO, USA
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211, Columbia, MO, USA
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Campos dos Goytacazes, RJ, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
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Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane. Funct Integr Genomics 2021; 21:73-99. [PMID: 33404914 DOI: 10.1007/s10142-020-00762-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3'H1, C3'H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.
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Figueroa-Rodríguez KA, Hernández-Rosas F, Figueroa-Sandoval B, Velasco-Velasco J, Aguilar Rivera N. What Has Been the Focus of Sugarcane Research? A Bibliometric Overview. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16183326. [PMID: 31509963 PMCID: PMC6765814 DOI: 10.3390/ijerph16183326] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022]
Abstract
Sugarcane is one of the main crops worldwide, and it has an important impact on environmental issues. A bibliometric mapping analysis of the research on sugarcane was carried out, using data on the titles, abstracts, and keywords of articles published in leading journals and other peer-reviewed documents available in the SCOPUS database from 1858 to 2019 (27 August), and this was subsequently analyzed with the software VOSviewer. The three most important countries that publish research and were most-cited regarding sugarcane were Brazil, the USA, and India. The analysis of the co-occurrence of terms shows that the main research areas were sugarcane bagasse and terms related to bioenergy, and on a second level of relevance agronomy topics related to increasing crop yields. This first attempt to visualize the abundance of publications regarding sugarcane in their totality is in itself a good starting point for further scientific discussion.
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Affiliation(s)
- Katia A Figueroa-Rodríguez
- Colegio de Postgraduados-Campus Córdoba, Programa de Innovación Agroalimentaria Sustentable, Km. 348 Carretera Córdoba-Veracruz, Congregación Manuel León, Amatlán de los Reyes, Veracruz, CP 94953, Mexico.
| | - Francisco Hernández-Rosas
- Colegio de Postgraduados-Campus Córdoba, Programa de Innovación Agroalimentaria Sustentable, Km. 348 Carretera Córdoba-Veracruz, Congregación Manuel León, Amatlán de los Reyes, Veracruz, CP 94953, Mexico.
| | - Benjamín Figueroa-Sandoval
- Colegio de Postgraduados-Campus San Luis, Programa de Innovación en el Manejo de Recursos Naturales, Calle de Iturbide 73, Salinas de Hidalgo, San Luis Potosí, CP 78622, Mexico.
| | - Joel Velasco-Velasco
- Colegio de Postgraduados-Campus Córdoba, Programa de Innovación Agroalimentaria Sustentable, Km. 348 Carretera Córdoba-Veracruz, Congregación Manuel León, Amatlán de los Reyes, Veracruz, CP 94953, Mexico.
| | - Noé Aguilar Rivera
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Peñuela, Amatlán de los Reyes, Veracruz, CP 94945 Mexico.
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Zhou D, Liu X, Gao S, Guo J, Su Y, Ling H, Wang C, Li Z, Xu L, Que Y. Foreign cry1Ac gene integration and endogenous borer stress-related genes synergistically improve insect resistance in sugarcane. BMC PLANT BIOLOGY 2018; 18:342. [PMID: 30526526 PMCID: PMC6288918 DOI: 10.1186/s12870-018-1536-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/19/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Sugarcane (Saccharum spp. hybrids) is considered the most globally important sugar-producing crop and raw material for biofuel. Insect attack is a major issue in sugarcane cultivation, resulting in yield losses and sucrose content reductions. Stem borer (Diatraea saccharalis F.) causes serious yield losses in sugarcane worldwide. However, insect-resistant germplasms for sugarcane are not available in any collections all over the world, and the molecular mechanism of insect resistance has not been elucidated. In this study, cry1Ac transgenic sugarcane lines were obtained and the biological characteristics and transgene dosage effect were investigated and a global exploration of gene expression by transcriptome analysis was performed. RESULTS The transgene copies of foreign cry1Ac were variable and random. The correlation between the cry1Ac protein and cry1Ac gene copies differed between the transgenic lines from FN15 and ROC22. The medium copy lines from FN15 showed a significant linear relationship, while ROC22 showed no definite dosage effect. The transgenic lines with medium copies of cry1Ac showed an elite phenotype. Transcriptome analysis by RNA sequencing indicated that up/down regulated differentially expressed genes were abundant among the cry1Ac sugarcane lines and the receptor variety. Foreign cry1Ac gene and endogenous borer stress-related genes may have a synergistic effect. Three lines, namely, A1, A5, and A6, were selected for their excellent stem borer resistance and phenotypic traits and are expected to be used directly as cultivars or crossing parents for sugarcane borer resistance breeding. CONCLUSIONS Cry1Ac gene integration dramatically improved sugarcane insect resistance. The elite transgenic offspring contained medium transgene copies. Foreign cry1Ac gene integration and endogenous borer stress-related genes may have a synergistic effect on sugarcane insect resistance improvement.
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Affiliation(s)
- Dinggang Zhou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, Hunan University of Science and Technology, School of Life Science, Xiangtan, 411201 Hunan China
| | - Xiaolan Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, Hunan University of Science and Technology, School of Life Science, Xiangtan, 411201 Hunan China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Chunfeng Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Zhu Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
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Silva P, Silva CL, Perestrelo R, Nunes FM, Câmara JS. Fingerprint targeted compounds in authenticity of sugarcane honey - An approach based on chromatographic and statistical data. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.04.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Passamani LZ, Bertolazi AA, Ramos AC, Santa-Catarina C, Thelen JJ, Silveira V. Embryogenic Competence Acquisition in Sugar Cane Callus Is Associated with Differential H+-Pump Abundance and Activity. J Proteome Res 2018; 17:2767-2779. [DOI: 10.1021/acs.jproteome.8b00213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lucas Z. Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Amanda A. Bertolazi
- Laboratório de Fisiologia e Bioquímica de Microrganismos, CBB-UENF, Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Alessandro C. Ramos
- Laboratório de Fisiologia e Bioquímica de Microrganismos, CBB-UENF, Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, CBB-UENF, Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | | | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Avenue Alberto Lamego 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
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Alessio VM, Cavaçana N, Dantas LLDB, Lee N, Hotta CT, Imaizumi T, Menossi M. The FBH family of bHLH transcription factors controls ACC synthase expression in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2511-2525. [PMID: 29514290 PMCID: PMC5920332 DOI: 10.1093/jxb/ery083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/27/2018] [Indexed: 05/21/2023]
Abstract
Ethylene is a phytohormone involved in the regulation of several aspects of plant development and in responses to biotic and abiotic stress. The effects of exogenous application of ethylene to sugarcane plants are well characterized as growth inhibition of immature internodes and stimulation of sucrose accumulation. However, the molecular network underlying the control of ethylene biosynthesis in sugarcane remains largely unknown. The chemical reaction catalyzed by 1-aminocyclopropane-1-carboxylic acid synthase (ACS) is an important rate-limiting step that regulates ethylene production in plants. In this work, using a yeast one-hybrid approach, we identified three basic helix-loop-helix (bHLH) transcription factors, homologs of Arabidopsis FBH (FLOWERING BHLH), that bind to the promoter of ScACS2 (Sugarcane ACS2), a sugarcane type 3 ACS isozyme gene. Protein-protein interaction assays showed that sugarcane FBH1 (ScFBH1), ScFBH2, and ScFBH3 form homo- and heterodimers in the nucleus. Gene expression analysis revealed that ScFBHs and ScACS2 transcripts are more abundant in maturing internodes during afternoon and night. In addition, Arabidopsis functional analysis demonstrated that FBH controls ethylene production by regulating transcript levels of ACS7, a homolog of ScACS2. These results indicate that ScFBHs transcriptionally regulate ethylene biosynthesis in maturing internodes of sugarcane.
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Affiliation(s)
- Valter Miotto Alessio
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, CP, Campinas, SP, Brazil
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Natale Cavaçana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Marcelo Menossi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, CP, Campinas, SP, Brazil
- Correspondence:
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Heringer AS, Santa-Catarina C, Silveira V. Insights from Proteomic Studies into Plant Somatic Embryogenesis. Proteomics 2018; 18:e1700265. [DOI: 10.1002/pmic.201700265] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/08/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Angelo Schuabb Heringer
- Laboratório de Biotecnologia; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
- Unidade de Biologia Integrativa; Setor de Genômica e Proteômica; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
- Unidade de Biologia Integrativa; Setor de Genômica e Proteômica; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
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Salvato F, Wilson R, Portilla Llerena JP, Kiyota E, Lima Reis K, Boaretto LF, Balbuena TS, Azevedo RA, Thelen JJ, Mazzafera P. Luxurious Nitrogen Fertilization of Two Sugar Cane Genotypes Contrasting for Lignin Composition Causes Changes in the Stem Proteome Related to Carbon, Nitrogen, and Oxidant Metabolism but Does Not Alter Lignin Content. J Proteome Res 2017; 16:3688-3703. [PMID: 28836437 DOI: 10.1021/acs.jproteome.7b00397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sugar cane is an important crop for sugar and biofuel production. Its lignocellulosic biomass represents a promising option as feedstock for second-generation ethanol production. Nitrogen fertilization can affect differently tissues and its biopolymers, including the cell-wall polysaccharides and lignin. Lignin content and composition are the most important factors associated with biomass recalcitrance to convert cell-wall polysaccharides into fermentable sugars. Thus it is important to understand the metabolic relationship between nitrogen fertilization and lignin in this feedstock. In this study, a large-scale proteomics approach based on GeLC-MS/MS was employed to identify and relatively quantify proteins differently accumulated in two contrasting genotypes for lignin composition after excessive nitrogen fertilization. From the ∼1000 nonredundant proteins identified, 28 and 177 were differentially accumulated in response to nitrogen from IACSP04-065 and IACSP04-627 lines, respectively. These proteins were associated with several functional categories, including carbon metabolism, amino acid metabolism, protein turnover, and oxidative stress. Although nitrogen fertilization has not changed lignin content, phenolic acids and lignin composition were changed in both species but not in the same way. Sucrose and reducing sugars increased in plants of the genotype IACSP04-065 receiving nitrogen.
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Affiliation(s)
- Fernanda Salvato
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, São Paulo 13083-862, Brazil.,Universidade de São Paulo , Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, São Paulo 13418-900, Brazil
| | - Rashaun Wilson
- Department of Biochemistry, University of Missouri Columbia, Missouri 65201, United States
| | - Juan Pablo Portilla Llerena
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, São Paulo 13083-862, Brazil
| | - Eduardo Kiyota
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, São Paulo 13083-862, Brazil
| | - Karina Lima Reis
- Universidade de São Paulo , Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, São Paulo 13418-900, Brazil
| | - Luis Felipe Boaretto
- Universidade de São Paulo , Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, São Paulo 13418-900, Brazil
| | - Tiago S Balbuena
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho" , Jaboticabal, São Paulo 14884-900, Brazil
| | - Ricardo A Azevedo
- Universidade de São Paulo , Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, São Paulo 13418-900, Brazil
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri Columbia, Missouri 65201, United States
| | - Paulo Mazzafera
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, São Paulo 13083-862, Brazil.,Universidade de São Paulo , Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, São Paulo 13418-900, Brazil
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Proteomic approaches in microalgae: perspectives and applications. 3 Biotech 2017; 7:197. [PMID: 28667637 DOI: 10.1007/s13205-017-0831-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
Biofuels are the promising sources which are produced by various microalgae or in the form of metabolic by-products from organic or food waste products. Microalgae have been widely reported for the production of biofuels since these have a high storage of lipids as triacylglycerides, which can mainly be converted into biofuels. Recently, products such as biodiesel, bioethanol and biogas have renewed the interest toward the microalgae. The proteomics alone will not pave the way toward finding an ideal alga which will fulfill the current energy demands, but a combined approach of proteomics, genomics and bioinformatics can be pivotal for a sustainable solution. The present review emphasizes various technologies currently involved in algal proteomics for the efficient production of biofuels.
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de Souza RSC, Okura VK, Armanhi JSL, Jorrín B, Lozano N, da Silva MJ, González-Guerrero M, de Araújo LM, Verza NC, Bagheri HC, Imperial J, Arruda P. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci Rep 2016; 6:28774. [PMID: 27358031 PMCID: PMC4928081 DOI: 10.1038/srep28774] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/10/2016] [Indexed: 12/13/2022] Open
Abstract
Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes.
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Affiliation(s)
- Rafael Soares Correa de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Vagner Katsumi Okura
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Jaderson Silveira Leite Armanhi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Beatriz Jorrín
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA Campus Montegancedo UPM, 28223 -Pozuelo de Alarcón (Madrid), Spain
| | - Núria Lozano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA Campus Montegancedo UPM, 28223 -Pozuelo de Alarcón (Madrid), Spain
| | - Márcio José da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA Campus Montegancedo UPM, 28223 -Pozuelo de Alarcón (Madrid), Spain
| | - Laura Migliorini de Araújo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Natália Cristina Verza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | | | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA Campus Montegancedo UPM, 28223 -Pozuelo de Alarcón (Madrid), Spain
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-970, Campinas, SP, Brazil
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Reis RS, Vale EDM, Heringer AS, Santa-Catarina C, Silveira V. Putrescine induces somatic embryo development and proteomic changes in embryogenic callus of sugarcane. J Proteomics 2016; 130:170-9. [DOI: 10.1016/j.jprot.2015.09.029] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/27/2015] [Accepted: 09/21/2015] [Indexed: 01/29/2023]
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Mattiello L, Riaño-Pachón DM, Martins MCM, da Cruz LP, Bassi D, Marchiori PER, Ribeiro RV, Labate MTV, Labate CA, Menossi M. Physiological and transcriptional analyses of developmental stages along sugarcane leaf. BMC PLANT BIOLOGY 2015; 15:300. [PMID: 26714767 PMCID: PMC4696237 DOI: 10.1186/s12870-015-0694-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane. RESULTS Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize. CONCLUSION This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.
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Affiliation(s)
- Lucia Mattiello
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Marina Camara Mattos Martins
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Larissa Prado da Cruz
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Denis Bassi
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Paulo Eduardo Ribeiro Marchiori
- Laboratório de Fisiologia de Plantas "Coaracy M. Franco", Centro de Pesquisa e Desenvolvimento em Ecofisiologia e Biofísica, Instituto Agronômico, Caixa Postal 28, Campinas, 13020-902, SP, Brazil.
| | - Rafael Vasconcelos Ribeiro
- Departamento de Biologia de Plantas, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, 13083-970, SP, Brazil.
| | - Mônica T Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Marcelo Menossi
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
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Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol 2015; 3:182. [PMID: 26636072 PMCID: PMC4646955 DOI: 10.3389/fbioe.2015.00182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.
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Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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Vicentini R, Bottcher A, Brito MDS, dos Santos AB, Creste S, Landell MGDA, Cesarino I, Mazzafera P. Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content. PLoS One 2015; 10:e0134909. [PMID: 26241317 PMCID: PMC4524650 DOI: 10.1371/journal.pone.0134909] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/15/2015] [Indexed: 12/16/2022] Open
Abstract
Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.
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Affiliation(s)
- Renato Vicentini
- Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, SP, Brazil
- * E-mail:
| | - Alexandra Bottcher
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Michael dos Santos Brito
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
- Sugarcane Center, Agronomic Institute of Campinas, Ribeirão Preto, SP, Brazil
| | | | - Silvana Creste
- Sugarcane Center, Agronomic Institute of Campinas, Ribeirão Preto, SP, Brazil
| | | | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
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18
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Heringer AS, Barroso T, Macedo AF, Santa-Catarina C, Souza GHMF, Floh EIS, de Souza-Filho GA, Silveira V. Label-Free Quantitative Proteomics of Embryogenic and Non-Embryogenic Callus during Sugarcane Somatic Embryogenesis. PLoS One 2015; 10:e0127803. [PMID: 26035435 PMCID: PMC4452777 DOI: 10.1371/journal.pone.0127803] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/18/2015] [Indexed: 02/05/2023] Open
Abstract
The development of somatic cells in to embryogenic cells occurs in several stages and ends in somatic embryo formation, though most of these biochemical and molecular changes have yet to be elucidated. Somatic embryogenesis coupled with genetic transformation could be a biotechnological tool to improve potential crop yields potential in sugarcane cultivars. The objective of this study was to observe somatic embryo development and to identify differentially expressed proteins in embryogenic (E) and non-embryogenic (NE) callus during maturation treatment. E and NE callus were cultured on maturation culture medium supplemented with different concentrations (0.0, 0.75, 1.5 and 2.0 g L(-1)) of activated charcoal (AC). Somatic embryo formation and differential protein expression were evaluated at days 0 and 21 using shotgun proteomic analyses. Treatment with 1.5 g L(-1) AC resulted in higher somatic embryo maturation rates (158 somatic embryos in 14 days) in E callus but has no effect in NE callus. A total of 752 co-expressed proteins were identified through the SUCEST (The Sugarcane EST Project), including many housekeeping proteins. E callus showed 65 exclusive proteins on day 0, including dehydrogenase, desiccation-related protein, callose synthase 1 and nitric oxide synthase. After 21 days on maturation treatment, 14 exclusive proteins were identified in E callus, including catalase and secreted protein. NE callus showed 23 exclusive proteins on day 0 and 10 exclusive proteins after 21 days on maturation treatment, including many proteins related to protein degradation. The induction of maturation leads to somatic embryo development, which likely depends on the expression of specific proteins throughout the process, as seen in E callus under maturation treatment. On the other hand, some exclusive proteins can also specifically prevent of somatic embryos development, as seen in the NE callus.
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Affiliation(s)
- Angelo Schuabb Heringer
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
| | - Tatiana Barroso
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
| | - Amanda Ferreira Macedo
- Laboratório de Biologia Celular de Plantas, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | | | | | - Eny Iochevet Segal Floh
- Laboratório de Biologia Celular de Plantas, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Gonçalo Apolinário de Souza-Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
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19
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Furtado A, Lupoi JS, Hoang NV, Healey A, Singh S, Simmons BA, Henry RJ. Modifying plants for biofuel and biomaterial production. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1246-58. [PMID: 25431201 DOI: 10.1111/pbi.12300] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/28/2014] [Accepted: 10/23/2014] [Indexed: 05/08/2023]
Abstract
The productivity of plants as biofuel or biomaterial crops is established by both the yield of plant biomass per unit area of land and the efficiency of conversion of the biomass to biofuel. Higher yielding biofuel crops with increased conversion efficiencies allow production on a smaller land footprint minimizing competition with agriculture for food production and biodiversity conservation. Plants have traditionally been domesticated for food, fibre and feed applications. However, utilization for biofuels may require the breeding of novel phenotypes, or new species entirely. Genomics approaches support genetic selection strategies to deliver significant genetic improvement of plants as sources of biomass for biofuel manufacture. Genetic modification of plants provides a further range of options for improving the composition of biomass and for plant modifications to assist the fabrication of biofuels. The relative carbohydrate and lignin content influences the deconstruction of plant cell walls to biofuels. Key options for facilitating the deconstruction leading to higher monomeric sugar release from plants include increasing cellulose content, reducing cellulose crystallinity, and/or altering the amount or composition of noncellulosic polysaccharides or lignin. Modification of chemical linkages within and between these biomass components may improve the ease of deconstruction. Expression of enzymes in the plant may provide a cost-effective option for biochemical conversion to biofuel.
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Affiliation(s)
- Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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20
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Soares JSM, Gentile A, Scorsato V, Lima ADC, Kiyota E, Dos Santos ML, Piattoni CV, Huber SC, Aparicio R, Menossi M. Oligomerization, membrane association, and in vivo phosphorylation of sugarcane UDP-glucose pyrophosphorylase. J Biol Chem 2014; 289:33364-77. [PMID: 25320091 DOI: 10.1074/jbc.m114.590125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Sugarcane is a monocot plant that accumulates sucrose to levels of up to 50% of dry weight in the stalk. The mechanisms that are involved in sucrose accumulation in sugarcane are not well understood, and little is known with regard to factors that control the extent of sucrose storage in the stalks. UDP-glucose pyrophosphorylase (UGPase; EC 2.7.7.9) is an enzyme that produces UDP-glucose, a key precursor for sucrose metabolism and cell wall biosynthesis. The objective of this work was to gain insights into the ScUGPase-1 expression pattern and regulatory mechanisms that control protein activity. ScUGPase-1 expression was negatively correlated with the sucrose content in the internodes during development, and only slight differences in the expression patterns were observed between two cultivars that differ in sucrose content. The intracellular localization of ScUGPase-1 indicated partial membrane association of this soluble protein in both the leaves and internodes. Using a phospho-specific antibody, we observed that ScUGPase-1 was phosphorylated in vivo at the Ser-419 site in the soluble and membrane fractions from the leaves but not from the internodes. The purified recombinant enzyme was kinetically characterized in the direction of UDP-glucose formation, and the enzyme activity was affected by redox modification. Preincubation with H2O2 strongly inhibited this activity, which could be reversed by DTT. Small angle x-ray scattering analysis indicated that the dimer interface is located at the C terminus and provided the first structural model of the dimer of sugarcane UGPase in solution.
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Affiliation(s)
- Jose Sergio M Soares
- From the Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, C.P. 6109, Campinas, SP, Brazil
| | - Agustina Gentile
- From the Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, C.P. 6109, Campinas, SP, Brazil
| | - Valeria Scorsato
- the Laboratório de Biologia Estrutural e Cristalografia, Instituto de Química, Universidade Estadual de Campinas, C.P. 6154, Campinas, SP, Brazil
| | - Aline da C Lima
- the Laboratório de Biologia Estrutural e Cristalografia, Instituto de Química, Universidade Estadual de Campinas, C.P. 6154, Campinas, SP, Brazil
| | - Eduardo Kiyota
- the Laboratório de Biologia Estrutural e Cristalografia, Instituto de Química, Universidade Estadual de Campinas, C.P. 6154, Campinas, SP, Brazil
| | - Marcelo Leite Dos Santos
- the Centro de Ciências Exatas e Tecnologia, Núcleo de Química, Universidade Federal do Sergipe, C.P. 49500000, Itabaiana, SE, Brazil
| | - Claudia V Piattoni
- the Instituto de Agrobiotecnologia del Litoral (UNL-CONICET), Universidad Nacional del Litoral, Ciudad Universitaria-Paraje El Pozo, CC242, S3000ZAA Santa Fe, Argentina
| | - Steven C Huber
- the Department of Agriculture Agricultural Research Service, and Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Ricardo Aparicio
- the Laboratório de Biologia Estrutural e Cristalografia, Instituto de Química, Universidade Estadual de Campinas, C.P. 6154, Campinas, SP, Brazil
| | - Marcelo Menossi
- From the Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, C.P. 6109, Campinas, SP, Brazil,
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21
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Affiliation(s)
- Khaled Moustafa
- Institut Mondor de la Recherche Biomédicale - Institut National de la Santé et de la Recherche Médicale Créteil, France
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22
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Moyle RL, Birch RG. Diversity of sequences and expression patterns among alleles of a sugarcane loading stem gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1775-82. [PMID: 23546592 DOI: 10.1007/s00122-013-2091-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/21/2013] [Indexed: 05/13/2023]
Abstract
Modern sugarcane cultivars are highly polyploid and aneuploid hybrids, which are propagated as clones. Their complex genome structure comprises 100-130 chromosomes and 10-13 hom(e)ologous copies of most loci. There is preliminary evidence of very high heterozygosity, with implications for genetic improvement approaches ranging from marker-assisted selection to transgenics. Here, we report that sugarcane cultivar Q200 has at least nine alleles at the Loading Stem Gene (ScLSG) locus. Exon-intron structure is identical and the predicted protein products show at least 92 % identity, across sugarcane alleles and the Sorghum homologue Sb07g027880. There is substantial variation in the 5' UTR and promoter regions including numerous allele-specific nucleotide polymorphisms, insertions and deletions. We developed an allele-specific qRT-PCR method to undertake the first compelling test of allele-specific expression in polyploid sugarcane. Seven alleles distinguished by this method all showed peak expression in the sucrose-loading zone of the stem, but there was apparent variability in expression patterns across other tissues. The ScLSG2 and ScLSG5 alleles appear promising for specificity of expression in stems, relative to leaf, meristem, emerging shoot and root tissues. Within the stem, there was activity in parenchyma, vascular and rind tissues. This expression pattern is of interest in basic research and biotechnology aimed at enhanced sucrose content, engineering value-added products, and manipulation of stem biomass composition.
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Affiliation(s)
- Richard L Moyle
- Hines Plant Science Building, University of Queensland, Brisbane 4072, Australia
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23
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Ndimba BK, Ndimba RJ, Johnson TS, Waditee-Sirisattha R, Baba M, Sirisattha S, Shiraiwa Y, Agrawal GK, Rakwal R. Biofuels as a sustainable energy source: an update of the applications of proteomics in bioenergy crops and algae. J Proteomics 2013; 93:234-44. [PMID: 23792822 DOI: 10.1016/j.jprot.2013.05.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/28/2013] [Accepted: 05/30/2013] [Indexed: 11/29/2022]
Abstract
Sustainable energy is the need of the 21st century, not because of the numerous environmental and political reasons but because it is necessary to human civilization's energy future. Sustainable energy is loosely grouped into renewable energy, energy conservation, and sustainable transport disciplines. In this review, we deal with the renewable energy aspect focusing on the biomass from bioenergy crops to microalgae to produce biofuels to the utilization of high-throughput omics technologies, in particular proteomics in advancing our understanding and increasing biofuel production. We look at biofuel production by plant- and algal-based sources, and the role proteomics has played therein. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Bongani Kaiser Ndimba
- Proteomics Research and Services Unit, Biotechnology Platform, Agricultural Research Council, Infruitec-Nietvoorbij Campus, Stellenbosch, South Africa; Proteomics Research Group, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
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Fladung M, Hoenicka H, Raj Ahuja M. Genomic stability and long-term transgene expression in poplar. Transgenic Res 2013; 22:1167-78. [DOI: 10.1007/s11248-013-9719-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
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Cesarino I, Araújo P, Sampaio Mayer JL, Vicentini R, Berthet S, Demedts B, Vanholme B, Boerjan W, Mazzafera P. Expression of SofLAC, a new laccase in sugarcane, restores lignin content but not S:G ratio of Arabidopsis lac17 mutant. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1769-81. [PMID: 23418623 DOI: 10.1093/jxb/ert045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lignin is a complex phenolic heteropolymer deposited in the secondarily thickened walls of specialized plant cells to provide strength for plants to stand upright and hydrophobicity to conducting cells for long-distance water transport. Although essential for plant growth and development, lignin is the major plant cell-wall component responsible for biomass recalcitrance to industrial processing. Peroxidases and laccases are generally thought to be responsible for lignin polymerization, but, given their broad substrate specificities and large gene families, specific isoforms involved in lignification are difficult to identify. This study used a combination of co-expression analysis, tissue/cell-type-specific expression analysis, and genetic complementation to correlate a sugarcane laccase gene, SofLAC, to the lignification process. A co-expression network constructed from 37 cDNA libraries showed that SofLAC was coordinately expressed with several phenylpropanoid biosynthesis genes. Tissue-specific expression analysis by quantitative RT-PCR showed that SofLAC was expressed preferentially in young internodes and that expression levels decrease with stem maturity. Cell-type-specific expression analysis by in situ hybridization demonstrated the localization of SofLAC mRNA in lignifying cell types, mainly in inner and outer portions of sclerenchymatic bundle sheaths. To investigate whether SofLAC is able to oxidize monolignols during lignification, the Arabidopsis lac17 mutant, which has reduced lignin levels, was complemented by expressing SofLAC under the control of the Arabidopsis AtLAC17 promoter. The expression of SofLAC restored the lignin content but not the lignin composition in complemented lac17 mutant lines. Taken together, these results suggest that SofLAC participates in lignification in sugarcane.
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Affiliation(s)
- Igor Cesarino
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970 Campinas, SP, Brazil.
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Calviño M, Messing J. Sweet sorghum as a model system for bioenergy crops. Curr Opin Biotechnol 2011; 23:323-9. [PMID: 22204822 DOI: 10.1016/j.copbio.2011.12.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 12/07/2011] [Accepted: 12/07/2011] [Indexed: 01/20/2023]
Abstract
Bioenergy is the reduction of carbon via photosynthesis. Currently, this energy is harvested as liquid fuel through fermentation. A major concern, however, is input cost, in particular use of excess water and nitrogen, derived from an energy-negative process, the Haber-Bosch method. Furthermore, the shortage of arable land creates competition between uses for food and fuel, resulting in increased living expenses. This review seeks to summarize recent knowledge in genetics, genomics, and gene expression of a rising model species for bioenergy applications, sorghum. Its diploid genome has been sequenced, it has favorable low-input cost traits, and genetic crosses between different cultivars can be used to study allelic variations of genes involved in stem sugar metabolism and incremental biomass.
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Affiliation(s)
- Martín Calviño
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, United States
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