1
|
Estevam BR, Riaño-Pachón DM. CoCoView - A Codon Conservation Viewer via Sequence Logos. MethodsX 2022; 9:101803. [PMID: 35990812 PMCID: PMC9382315 DOI: 10.1016/j.mex.2022.101803] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022] Open
Abstract
Sequence logos are a simple way to display a set of aligned sequences, and they are useful to identify conserved patterns. Since their introduction, several tools have been developed for generating these representations at the single residue level (amino acids or nucleotides). We have developed a tool to build sequence logos of protein-coding sequences at the codon level, allowing more accurate analysis of coding-sequences as they represent synonymous and non-synonymous changes instead of showing only changes that imply on amino acid substitutions. We built CoCoView on top of the Logomaker Python API. It creates codon sequence logos from a multiple sequence alignment of protein-coding sequences. Some properties of the data and the generated logos can be controlled by the end-users, such as data redundancy, plot type and alphabet color. • Split aligned sequences into codon positions; • For each position compute codon frequency and information content; • Use the computed information to plot the graphic.
Collapse
|
2
|
de Oliveira LP, Navarro BV, de Jesus Pereira JP, Lopes AR, Martins MCM, Riaño-Pachón DM, Buckeridge MS. Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane. Sci Rep 2022; 12:7516. [PMID: 35525890 PMCID: PMC9079074 DOI: 10.1038/s41598-022-11508-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.
Collapse
Affiliation(s)
- Lauana Pereira de Oliveira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Bruno Viana Navarro
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - João Pedro de Jesus Pereira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | | | - Marina C M Martins
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia Computacional, Centro de Energia Nuclear na Agricultura, Evolutiva e de Sistemas, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
| |
Collapse
|
3
|
Zuvanov L, Basso Garcia AL, Correr FH, Bizarria R, Filho APDC, da Costa AH, Thomaz AT, Pinheiro ALM, Riaño-Pachón DM, Winck FV, Esteves FG, Margarido GRA, Casagrande GMS, Frajacomo HC, Martins L, Cavalheiro MF, Grachet NG, da Silva RGC, Cerri R, Ramos RTJ, de Medeiros SDS, Tavares TV, Corrêa dos Santos RA. The experience of teaching introductory programming skills to bioscientists in Brazil. PLoS Comput Biol 2021; 17:e1009534. [PMID: 34762646 PMCID: PMC8584955 DOI: 10.1371/journal.pcbi.1009534] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners. Here, we describe the conception, organization, and implementation of the Brazilian Python Workshop for Biological Data. This workshop has been organized by graduate and undergraduate students and supported, mostly in administrative matters, by experienced faculty members since 2017. The workshop was conceived for teaching bioscientists, mainly students in Brazil, on how to program in a biological context. The goal of this article was to share our experience with the 2020 edition of the workshop in its virtual format due to the Coronavirus Disease 2019 (COVID-19) pandemic and to compare and contrast this year's experience with the previous in-person editions. We described a hands-on and live coding workshop model for teaching introductory Python programming. We also highlighted the adaptations made from in-person to online format in 2020, the participants' assessment of learning progression, and general workshop management. Lastly, we provided a summary and reflections from our personal experiences from the workshops of the last 4 years. Our takeaways included the benefits of the learning from learners' feedback (LLF) that allowed us to improve the workshop in real time, in the short, and likely in the long term. We concluded that the Brazilian Python Workshop for Biological Data is a highly effective workshop model for teaching a programming language that allows bioscientists to go beyond an initial exploration of programming skills for data analysis in the medium to long term.
Collapse
Affiliation(s)
- Luíza Zuvanov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University, Rio Claro, Brazil
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, Brazil
| | | | | | - Andréa T. Thomaz
- School of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Ana Lucia Mendes Pinheiro
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Flavia Vischi Winck
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Franciele Grego Esteves
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, Brazil
| | | | | | | | - Leonardo Martins
- Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Mariana Feitosa Cavalheiro
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Genomics for Climate Change Research Center, University of Campinas, Campinas, Brazil
| | | | - Raniere Gaia Costa da Silva
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, Special Administrative Region, People’s Republic of China
| | - Ricardo Cerri
- Department of Computer Science, Federal University of São Carlos, São Carlos, Brazil
| | | | | | - Thayana Vieira Tavares
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Renato Augusto Corrêa dos Santos
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
- Institute of Biology, State University of Campinas, Campinas, Brazil
- * E-mail:
| |
Collapse
|
4
|
Busso-Lopes AF, Carnielli CM, Winck FV, Patroni FMDS, Oliveira AK, Granato DC, E Costa RAP, Domingues RR, Pauletti BA, Riaño-Pachón DM, Aricetti J, Caldana C, Graner E, Coletta RD, Dryden K, Fox JW, Paes Leme AF. A Reductionist Approach Using Primary and Metastatic Cell-Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis. Mol Cell Proteomics 2021; 20:100118. [PMID: 34186243 PMCID: PMC8350068 DOI: 10.1016/j.mcpro.2021.100118] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/28/2021] [Accepted: 06/20/2021] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher their role in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of EVs derived from human primary tumor (SCC-9) cells and matched lymph node metastatic (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 63 lipids differentially abundant between LN1 cell– and SCC-9 cell–derived EVs. A multi-omics integration identified 11 ‘hub proteins’ significantly decreased at the metastatic site compared with primary tumor–derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases and found that low abundance of seven ‘hub proteins’ in EVs from metastatic lymph nodes (ALDH7A1, CAD, CANT1, GOT1, MTHFD1, PYGB, and SARS) is correlated with reduced survival and tumor aggressiveness in patients with cancer. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis and which may potentially serve as prognostic markers in OSCC. Proteomic, miRNA, metabolomic, and lipidomic profiles were mapped in oral cancer EVs. The molecular profile of EVs was associated with the lymph node metastatic phenotype. A multi-omics integrative analysis revealed 11 highly connected ‘hub proteins.’ ‘Hub proteins’ from EVs are candidates as prognostic markers in oral cancer.
Collapse
Affiliation(s)
- Ariane Fidelis Busso-Lopes
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Carolina Moretto Carnielli
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Flavia Vischi Winck
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fábio Malta de Sá Patroni
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Ana Karina Oliveira
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Rute Alves Pereira E Costa
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Romênia Ramos Domingues
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Bianca Alves Pauletti
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Juliana Aricetti
- Laboratório Nacional de Biorrenováveis - LNBR, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Edgard Graner
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, Piracicaba, SP, Brazil
| | - Ricardo Della Coletta
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, Piracicaba, SP, Brazil
| | - Kelly Dryden
- Molecular Electron Microscopy Core, University of Virginia, Charlottesville, Virginia, USA
| | - Jay William Fox
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil.
| |
Collapse
|
5
|
Fanelli A, Rancour DM, Sullivan M, Karlen SD, Ralph J, Riaño-Pachón DM, Vicentini R, Silva TDF, Ferraz A, Hatfield RD, Romanel E. Overexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell Wall. Front Plant Sci 2021; 12:626168. [PMID: 33995431 PMCID: PMC8117936 DOI: 10.3389/fpls.2021.626168] [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] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 05/11/2023]
Abstract
The purification of hydroxycinnamic acids [p-coumaric acid (pCA) and ferulic acid (FA)] from grass cell walls requires high-cost processes. Feedstocks with increased levels of one hydroxycinnamate in preference to the other are therefore highly desirable. We identified and conducted expression analysis for nine BAHD acyltransferase ScAts genes from sugarcane. The high conservation of AT10 proteins, together with their similar gene expression patterns, supported a similar role in distinct grasses. Overexpression of ScAT10 in maize resulted in up to 75% increase in total pCA content. Mild hydrolysis and derivatization followed by reductive cleavage (DFRC) analysis showed that pCA increase was restricted to the hemicellulosic portion of the cell wall. Furthermore, total FA content was reduced up to 88%, resulting in a 10-fold increase in the pCA/FA ratio. Thus, we functionally characterized a sugarcane gene involved in pCA content on hemicelluloses and generated a C4 plant that is promising for valorizing pCA production in biorefineries.
Collapse
Affiliation(s)
- Amanda Fanelli
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| | | | - Michael Sullivan
- U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, Madison, WI, United States
| | - Steven D. Karlen
- Department of Biochemistry, and The Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI, United States
| | - John Ralph
- Department of Biochemistry, and The Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI, United States
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Renato Vicentini
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Tatiane da Franca Silva
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| | - André Ferraz
- Laboratório de Ciências da Madeira, Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| | - Ronald D. Hatfield
- U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, Madison, WI, United States
| | - Elisson Romanel
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| |
Collapse
|
6
|
da Silva VCH, Martins MCM, Calderan-Rodrigues MJ, Artins A, Monte Bello CC, Gupta S, Sobreira TJP, Riaño-Pachón DM, Mafra V, Caldana C. Shedding Light on the Dynamic Role of the "Target of Rapamycin" Kinase in the Fast-Growing C 4 Species Setaria viridis, a Suitable Model for Biomass Crops. Front Plant Sci 2021; 12:637508. [PMID: 33927734 PMCID: PMC8078139 DOI: 10.3389/fpls.2021.637508] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C4 grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR complex (TORC) suppression in the model Setaria viridis. In addition to previously described responses to TORC inhibition (i.e., general growth arrest, translational repression, and primary metabolism reprogramming) in Arabidopsis thaliana (C3), the magnitude of changes was smaller in S. viridis, particularly regarding nutrient use efficiency and C allocation and partitioning that promote biosynthetic growth. Besides photosynthetic differences, S. viridis and A. thaliana present several specificities that classify them into distinct lineages, which also contribute to the observed alterations mediated by TOR. Indeed, cell wall metabolism seems to be distinctly regulated according to each cell wall type, as synthesis of non-pectic polysaccharides were affected in S. viridis, whilst assembly and structure in A. thaliana. Our results indicate that the metabolic network needed to achieve faster growth seems to be less stringently controlled by TORC in S. viridis.
Collapse
Affiliation(s)
| | | | | | - Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Saurabh Gupta
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | | | | | - Valéria Mafra
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Camila Caldana
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| |
Collapse
|
7
|
Matias Hurtado FM, Pinto MDS, de Oliveira PN, Riaño-Pachón DM, Inocente LB, Carrer H. Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition. Genes (Basel) 2019; 11:E20. [PMID: 31878092 PMCID: PMC7016782 DOI: 10.3390/genes11010020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.
Collapse
Affiliation(s)
- Fernando Manuel Matias Hurtado
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Maísa de Siqueira Pinto
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Perla Novais de Oliveira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo. Av. Centenário 303, Piracicaba, SP 13416-000, Brazil;
| | - Laura Beatriz Inocente
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| |
Collapse
|
8
|
Castro JC, Valdés I, Gonzalez-García LN, Danies G, Cañas S, Winck FV, Ñústez CE, Restrepo S, Riaño-Pachón DM. Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans. Theor Biol Med Model 2019; 16:7. [PMID: 30961611 PMCID: PMC6454757 DOI: 10.1186/s12976-019-0103-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 08/20/2018] [Accepted: 03/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN). We present a simple yet effective method to estimate transcription factors’ GRNs from transcriptional data. Method We defined interactions between pairs of genes (edges in the GRN) as the partial mutual information between these genes that takes into account time and possible lags in time from one gene in relation to another. We call this method Gene Regulatory Networks on Transfer Entropy (GRNTE) and it corresponds to Granger causality for Gaussian variables in an autoregressive model. To evaluate the reconstruction accuracy of our method, we generated several sub-networks from the GRN of the eukaryotic yeast model, Saccharomyces cerevisae. Then, we applied this method using experimental data of the plant pathogen Phytophthora infestans. We evaluated the transcriptional expression levels of 48 transcription factors of P. infestans during its interaction with one moderately resistant and one susceptible cultivar of yellow potato (Solanum tuberosum group Phureja), using RT-qPCR. With these data, we reconstructed the regulatory network of P. infestans during its interaction with these hosts. Results We first evaluated the performance of our method, based on the transfer entropy (GRNTE), on eukaryotic datasets from the GRNs of the yeast S. cerevisae. Results suggest that GRNTE is comparable with the state-of-the-art methods when the parameters for edge detection are properly tuned. In the case of P. infestans, most of the genes considered in this study, showed a significant change in expression from the onset of the interaction (0 h post inoculum - hpi) to the later time-points post inoculation. Hierarchical clustering of the expression data discriminated two distinct periods during the infection: from 12 to 36 hpi and from 48 to 72 hpi for both the moderately resistant and susceptible cultivars. These distinct periods could be associated with two phases of the life cycle of the pathogen when infecting the host plant: the biotrophic and necrotrophic phases. Conclusions Here we presented an algorithmic solution to the problem of network reconstruction in time series data. This analytical perspective makes use of the dynamic nature of time series data as it relates to intrinsically dynamic processes such as transcription regulation, were multiple elements of the cell (e.g., transcription factors) act simultaneously and change over time. We applied the algorithm to study the regulatory network of P. infestans during its interaction with two hosts which differ in their level of resistance to the pathogen. Although the gene expression analysis did not show differences between the two hosts, the results of the GRN analyses evidenced rewiring of the genes’ interactions according to the resistance level of the host. This suggests that different regulatory processes are activated in response to different environmental cues. Applications of our methodology showed that it could reliably predict where to place edges in the transcriptional networks and sub-networks. The experimental approach used here can help provide insights on the biological role of these interactions on complex processes such as pathogenicity. The code used is available at https://github.com/jccastrog/GRNTE under GNU general public license 3.0. Electronic supplementary material The online version of this article (10.1186/s12976-019-0103-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Juan Camilo Castro
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | - Ivan Valdés
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | | | - Giovanna Danies
- Department of Design, Universidad de los Andes, Bogotá D.C, Colombia
| | - Silvia Cañas
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | - Flavia Vischi Winck
- Regulatory Systems Biology Laboratory, Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carlos Eduardo Ñústez
- School of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá D.C, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture, Universidade de São Paulo, Piracicaba, SP, Brazil.
| |
Collapse
|
9
|
Fonseca BC, Riaño-Pachón DM, Guazzaroni ME, Reginatto V. Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant. Genet Mol Biol 2019; 42:139-144. [PMID: 30730526 PMCID: PMC6428130 DOI: 10.1590/1678-4685-gmb-2017-0315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/12/2018] [Indexed: 11/22/2022] Open
Abstract
We report on the nearly complete genome sequence of Clostridium
beijerinckii strain Br21, formerly isolated from a sugarcarne
vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in
length and resembles the size of previously published C.
beijerinckii genomes. We annotated the genome sequence and
predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows
it to exploit diverse sugars that are often found after lignocellulosic biomass
pretreatment to yield products of commercial interest. Besides the whole set of
genes encoding for enzymes underlying hydrogen production, the genome of the new
strain includes genes that enable carbon sources conversion into butanol,
ethanol, acetic acid, butyric acid, and the chemical block 1,3-propanediol,
which is used to obtain polymers. Moreover, the genome of strain Br21 has a
higher number of ORFs with predicted beta-glucosidase activity as compared to
other C. beijerinckii strains described in the KEGG database.
These characteristics make C. beijerinckii strain Br21 a
remarkable candidate for direct use in biotechnological processes and attest
that it is a potential biocatalyst supplier.
Collapse
Affiliation(s)
- Bruna Constante Fonseca
- Laboratório de Biotecnologia Ambiental e Energias Renováveis (LABIORE), Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - María-Eugenia Guazzaroni
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Valeria Reginatto
- Laboratório de Biotecnologia Ambiental e Energias Renováveis (LABIORE), Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
10
|
Borin GP, Carazzolle MF, Dos Santos RAC, Riaño-Pachón DM, Oliveira JVDC. Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30. Front Bioeng Biotechnol 2018; 6:151. [PMID: 30406095 PMCID: PMC6204389 DOI: 10.3389/fbioe.2018.00151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022] Open
Abstract
The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, ~70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, β-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol.
Collapse
Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, Brazil
| |
Collapse
|
11
|
de Gouvêa PF, Bernardi AV, Gerolamo LE, de Souza Santos E, Riaño-Pachón DM, Uyemura SA, Dinamarco TM. Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. BMC Genomics 2018; 19:232. [PMID: 29614953 PMCID: PMC5883313 DOI: 10.1186/s12864-018-4627-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS. RESULTS The maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome. CONCLUSIONS This is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.
Collapse
Affiliation(s)
- Paula Fagundes de Gouvêa
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Aline Vianna Bernardi
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luis Eduardo Gerolamo
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Emerson de Souza Santos
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory, Campinas, São Paulo, Brazil
- Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sergio Akira Uyemura
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Taisa Magnani Dinamarco
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
12
|
Augusto Corrêa Dos Santos R, Goldman GH, Riaño-Pachón DM. ploidyNGS: visually exploring ploidy with Next Generation Sequencing data. Bioinformatics 2018; 33:2575-2576. [PMID: 28383704 DOI: 10.1093/bioinformatics/btx204] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/04/2017] [Indexed: 11/12/2022] Open
Abstract
Summary ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way. Availability and Implementation ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R. Contact diriano@gmail.com.
Collapse
Affiliation(s)
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto
| | - Diego Mauricio Riaño-Pachón
- Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas.,Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
13
|
Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS, Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. Biochim Biophys Acta Proteins Proteom 2017; 1865:1758-1769. [PMID: 28890404 DOI: 10.1016/j.bbapap.2017.09.001] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 12/30/2022]
Abstract
Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62Awt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62Awt and the non-glycosylated enzyme from E. coli (AnAbf62Adeglyc) were highly similar. In addition, the designed glycomutant AnAbf62AN83Q presented similar patterns of secretion and activity to the AnAbf62Awt, indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62Adeglyc was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62AY312F and AnAbf62AY312S showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.
Collapse
Affiliation(s)
- Fabiano Jares Contesini
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil; Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil
| | - Marcelo Vizoná Liberato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil
| | - Marcelo Ventura Rubio
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil
| | - Felipe Calzado
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil
| | | | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil; Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, CEP: 05508-000, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, (UNISO), Sorocaba, SP, CEP 18023-000, Brazil
| | - Fabricio Bracht
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP CEP: 13084-862, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP CEP: 13084-862, Brazil
| | - André Ricardo Damasio
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil.
| |
Collapse
|
14
|
Borin GP, Sanchez CC, de Santana ES, Zanini GK, Dos Santos RAC, de Oliveira Pontes A, de Souza AT, Dal'Mas RMMTS, Riaño-Pachón DM, Goldman GH, Oliveira JVDC. Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei. BMC Genomics 2017; 18:501. [PMID: 28666414 PMCID: PMC5493111 DOI: 10.1186/s12864-017-3857-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [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: 12/22/2016] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Background Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. Results Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. Conclusions This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3857-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Camila Cristina Sanchez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Eliane Silva de Santana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Guilherme Keppe Zanini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Angélica de Oliveira Pontes
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Aline Tieppo de Souza
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Roberta Maria Menegaldo Tavares Soares Dal'Mas
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.,Current address: Laboratório de Biologia de Sistemas Regulatórios, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748 - Butantã - São Paulo - SP, São Paulo, CEP 05508-000, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, Ribeirão Preto, CEP, São Paulo, 14040-903, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.
| |
Collapse
|
15
|
Abstract
Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.
Collapse
Affiliation(s)
- Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Lucia Mattiello
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| |
Collapse
|
16
|
Abstract
Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.
Collapse
Affiliation(s)
- Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Lucia Mattiello
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| |
Collapse
|
17
|
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio ARDL, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JVDC, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 2017; 18:28. [PMID: 28196534 PMCID: PMC5307856 DOI: 10.1186/s13059-017-1151-0] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
Collapse
Affiliation(s)
- Ronald P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ad Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Guillermo Aguilar-Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National University of Mexico, Ciudad Universitaria, D.F. C.P. 04510 Mexico
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Present address: VTT Brasil, Alameda Inajá, 123, CEP 06460-055 Barueri, São Paulo Brazil
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Marion Askin
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: CSIRO Publishing, Unipark, Building 1 Level 1, 195 Wellington Road, Clayton, VIC 3168 Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Biology, Maynooth University, Maynooth, Co. Kildare Ireland
| | - Tiziano Benocci
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, Sao Paulo Brazil
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Vienna, Austria
| | | | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, CEP 13083-862 Campinas, SP Brazil
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Susanne Freyberg
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Provinciale Lecce-Monteroni, 73100 Lecce, Italy
| | - Christos Gournas
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
- Present address: Université Libre de Bruxelles Institute of Molecular Biology and Medicine (IBMM), Brussels, Belgium
| | - Rob Habgood
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | | | - María Laura Harispe
- Institut Pasteur de Montevideo, Unidad Mixta INIA-IPMont, Mataojo 2020, CP11400 Montevideo, Uruguay
- Present address: Instituto de Profesores Artigas, Consejo de Formación en Educación, ANEP, CP 11800, Av. del Libertador 2025, Montevideo, Uruguay
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ryan Hope
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Abeer Hossain
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Karabika
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
- Present Address: Department of Chemistry, University of Ioannina, Ioannina, 45110 Greece
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Nada Kraševec
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Medical Informatics, University Medical Centre, Robert-Koch-Str.40, 37075 Göttingen, Germany
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen, 37073 Germany
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ellen L. Lagendijk
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alla Lapidus
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Present address: Center for Algorithmic Biotechnology, St.Petersburg State University, St. Petersburg, Russia
| | - Anthony Levasseur
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Andrew MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Petter Melin
- Uppsala BioCenter, Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
- Present address: Swedish Chemicals Agency, Box 2, 172 13 Sundbyberg, Sweden
| | - Vera Meyer
- Institute of Biotechnology, Department Applied and Molecular Microbiology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Natalia Mielnichuk
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Present address: Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., 4032 Debrecen, Hungary
| | - Ákos P. Molnár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Giuseppina Mulé
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Margarita Orejas
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Erzsébet Orosz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Jean Paul Ouedraogo
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Karin M. Overkamp
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francois Piumi
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: INRA UMR1198 Biologie du Développement et de la Reproduction - Domaine de Vilvert, Jouy en Josas, 78352 Cedex France
| | - Peter J. Punt
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Stefan Rauscher
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Eric Record
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - 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 CEP 13083-970, Campinas, São Paulo Brasil
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Julian Röhrig
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Nadhira S. Salih
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Department of Biology, School of Science, University of Sulaimani, Al Sulaymaneyah, Iraq
| | - Rob A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Tabea Schütze
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Ekaterina Shelest
- Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA
| | - Vicky Sophianopoulou
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Hui Sun
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Richard B. Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Shiela E. Unkles
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
| | - Nathalie van de Wiele
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Tammi C. Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Jaap Visser
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 USA
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Scott E. Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, 99352 USA
| | - Isabelle Benoit
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present address: Centre of Functional and Structure Genomics Biology Department Concordia University, 7141 Sherbrooke St. W., Montreal, QC H4B 1R6 Canada
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI) and Institute for Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903 Ribeirão Preto, São Paulo Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Patricia A. vanKuyk
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jennifer Wortman
- Broad Institute, 415 Main St, Cambridge, MA 02142 USA
- Present address: Seres Therapeutics, 200 Sidney St, Cambridge, MA 02139 USA
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| |
Collapse
|
18
|
Riaño-Pachón DM, Mattiello L. Draft genome sequencing of the sugarcane hybrid SP80-3280. F1000Res 2017. [PMID: 28713559 DOI: 10.12688/f1000research10.12688/f1000research.11859.2] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.
Collapse
Affiliation(s)
- Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Lucia Mattiello
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| |
Collapse
|
19
|
Brown NA, Ries LNA, Reis TF, Rajendran R, Corrêa dos Santos RA, Ramage G, Riaño-Pachón DM, Goldman GH. RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose. Biotechnol Biofuels 2016; 9:145. [PMID: 27437031 PMCID: PMC4950808 DOI: 10.1186/s13068-016-0558-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/24/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sugarcane is one of the world's most profitable crops. Waste steam-exploded sugarcane bagasse (SEB) is a cheap, abundant, and renewable lignocellulosic feedstock for the next-generation biofuels. In nature, fungi seldom exist as planktonic cells, similar to those found in the nutrient-rich environment created within an industrial fermenter. Instead, fungi predominantly form biofilms that allow them to thrive in hostile environments. RESULTS In turn, we adopted an RNA-sequencing approach to interrogate how the model fungus, Aspergillus nidulans, adapts to SEB, revealing the induction of carbon starvation responses and the lignocellulolytic machinery, in addition to morphological adaptations. Genetic analyses showed the importance of hydrophobins for growth on SEB. The major hydrophobin, RodA, was retained within the fungal biofilm on SEB fibres. The StuA transcription factor that regulates fungal morphology was up-regulated during growth on SEB and controlled hydrophobin gene induction. The absence of the RodA or DewC hydrophobins reduced biofilm formation. The loss of a RodA or a functional StuA reduced the retention of the hydrolytic enzymes within the vicinity of the fungus. Hence, hydrophobins promote biofilm formation on SEB, and may enhance lignocellulose utilisation via promoting a compact substrate-enzyme-fungus structure. CONCLUSION This novel study highlights the importance of hydrophobins to the formation of biofilms and the efficient deconstruction of lignocellulose.
Collapse
Affiliation(s)
- Neil Andrew Brown
- />Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Laure N. A. Ries
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila F. Reis
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Ranjith Rajendran
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, The University of Glasgow, Glasgow, UK
| | - Renato Augusto Corrêa dos Santos
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, SP CEP 13083-970 Brazil
| | - Gordon Ramage
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, The University of Glasgow, Glasgow, UK
| | - 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, Campinas, SP CEP 13083-970 Brazil
| | - Gustavo H. Goldman
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
20
|
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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
21
|
Winck FV, Prado Ribeiro AC, Ramos Domingues R, Ling LY, Riaño-Pachón DM, Rivera C, Brandão TB, Gouvea AF, Santos-Silva AR, Coletta RD, Paes Leme AF. Insights into immune responses in oral cancer through proteomic analysis of saliva and salivary extracellular vesicles. Sci Rep 2015; 5:16305. [PMID: 26538482 PMCID: PMC4633731 DOI: 10.1038/srep16305] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [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: 03/04/2015] [Accepted: 10/09/2015] [Indexed: 01/08/2023] Open
Abstract
The development and progression of oral cavity squamous cell carcinoma (OSCC) involves complex cellular mechanisms that contribute to the low five-year survival rate of approximately 20% among diagnosed patients. However, the biological processes essential to tumor progression are not completely understood. Therefore, detecting alterations in the salivary proteome may assist in elucidating the cellular mechanisms modulated in OSCC and improve the clinical prognosis of the disease. The proteome of whole saliva and salivary extracellular vesicles (EVs) from patients with OSCC and healthy individuals were analyzed by LC-MS/MS and label-free protein quantification. Proteome data analysis was performed using statistical, machine learning and feature selection methods with additional functional annotation. Biological processes related to immune responses, peptidase inhibitor activity, iron coordination and protease binding were overrepresented in the group of differentially expressed proteins. Proteins related to the inflammatory system, transport of metals and cellular growth and proliferation were identified in the proteome of salivary EVs. The proteomics data were robust and could classify OSCC with 90% accuracy. The saliva proteome analysis revealed that immune processes are related to the presence of OSCC and indicate that proteomics data can contribute to determining OSCC prognosis.
Collapse
Affiliation(s)
- Flavia V. Winck
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, SP, Brazil
| | | | - Romênia Ramos Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, SP, Brazil
| | - Liu Yi Ling
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, CTBE, CNPEM, Campinas, SP, Brazil
| | | | - César Rivera
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, SP, Brazil
- Departamento de Ciencias Básicas Biomédicas, Universidad de Talca (UTALCA), Talca, Chile
| | - Thaís Bianca Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, ICESP, São Paulo, SP, Brazil
| | - Adriele Ferreira Gouvea
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, ICESP, São Paulo, SP, Brazil
| | - Alan Roger Santos-Silva
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, SP, Brazil
| | - Ricardo D. Coletta
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, SP, Brazil
| | - Adriana F. Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, SP, Brazil
| |
Collapse
|
22
|
Affiliation(s)
- Marçal Mariné
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Neil Andrew Brown
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol—CTBE, Campinas, São Paulo, Brazil
- * E-mail:
| |
Collapse
|
23
|
Buitrago-Flórez FJ, Restrepo S, Riaño-Pachón DM. Identification of transcription factor genes and their correlation with the high diversity of stramenopiles. PLoS One 2014; 9:e111841. [PMID: 25375671 PMCID: PMC4222949 DOI: 10.1371/journal.pone.0111841] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/01/2014] [Indexed: 11/19/2022] Open
Abstract
The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.
Collapse
Affiliation(s)
- Francisco Javier Buitrago-Flórez
- Group of Computational and Evolutionary Biology, Universidad de los Andes, Bogotá, Colombia
- Micology and Plant Pathology Laboratory, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Micology and Plant Pathology Laboratory, Universidad de los Andes, Bogotá, Colombia
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnología do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brasil
| |
Collapse
|
24
|
Oliveira JVDC, Borges TA, Corrêa Dos Santos RA, Freitas LFD, Rosa CA, Goldman GH, Riaño-Pachón DM. Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots. Int J Syst Evol Microbiol 2014; 64:2159-2168. [PMID: 24682702 DOI: 10.1099/ijs.0.060103-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001(T) ( = CBS 13268(T) = UFMG-CM-Y307(T)) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.
Collapse
Affiliation(s)
- Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Thuanny A Borges
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil
| | - Larissa F D Freitas
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Augusto Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, 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 6170, 13083-970 Campinas, São Paulo, Brazil
| |
Collapse
|
25
|
Cristancho MA, Botero-Rozo DO, Giraldo W, Tabima J, Riaño-Pachón DM, Escobar C, Rozo Y, Rivera LF, Durán A, Restrepo S, Eilam T, Anikster Y, Gaitán AL. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. Front Plant Sci 2014; 5:594. [PMID: 25400655 PMCID: PMC4215621 DOI: 10.3389/fpls.2014.00594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/11/2014] [Indexed: 05/20/2023]
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
Collapse
Affiliation(s)
- Marco A. Cristancho
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- *Correspondence: Marco A. Cristancho, Department of Plant Pathology, National Center for Coffee Research – CENICAFÉ, Km 4 vía a Manizales, Chinchiná 2427, Colombia e-mail:
| | - David Octavio Botero-Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - William Giraldo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Javier Tabima
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | | | - Carolina Escobar
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Yomara Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Luis F. Rivera
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Andrés Durán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - Tamar Eilam
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Yehoshua Anikster
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Alvaro L. Gaitán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| |
Collapse
|
26
|
Oliveira JVDC, dos Santos RAC, Borges TA, Riaño-Pachón DM, Goldman GH. Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane. Genome Announc 2013; 1:e00920-13. [PMID: 24356824 PMCID: PMC3868848 DOI: 10.1128/genomea.00920-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/18/2013] [Indexed: 11/20/2022]
Abstract
Here, we present the nuclear and mitochondrial genome sequences of Pseudozyma brasiliensis sp. nov. strain GHG001. P. brasiliensis sp. nov. is the closest relative of Pseudozyma vetiver. P. brasiliensis sp. nov. is capable of growing on xylose or xylan as a sole carbon source and has great biotechnological potential.
Collapse
Affiliation(s)
- Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Thuanny A. Borges
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | | |
Collapse
|
27
|
Vischi Winck F, Arvidsson S, Riaño-Pachón DM, Hempel S, Koseska A, Nikoloski Z, Urbina Gomez DA, Rupprecht J, Mueller-Roeber B. Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS One 2013; 8:e79909. [PMID: 24224019 PMCID: PMC3816576 DOI: 10.1371/journal.pone.0079909] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 11/03/2012] [Accepted: 10/01/2013] [Indexed: 11/18/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO 2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
Collapse
Affiliation(s)
- Flavia Vischi Winck
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Samuel Arvidsson
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Mauricio Riaño-Pachón
- Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | - Sabrina Hempel
- University of Potsdam, Institute of Physics, Potsdam-Golm, Germany
- Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Aneta Koseska
- University of Potsdam, Institute of Physics, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - David Alejandro Urbina Gomez
- Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | - Jens Rupprecht
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail:
| |
Collapse
|
28
|
Dreyer I, Gomez-Porras JL, Riaño-Pachón DM, Hedrich R, Geiger D. Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs). Front Plant Sci 2012; 3:263. [PMID: 23226151 PMCID: PMC3509319 DOI: 10.3389/fpls.2012.00263] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 11/12/2012] [Indexed: 05/02/2023]
Abstract
Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.
Collapse
Affiliation(s)
- Ingo Dreyer
- Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
- *Correspondence: Ingo Dreyer, Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, Pozuelo de Alarcón, Madrid E-28223, Spain. e-mail:
| | - Judith Lucia Gomez-Porras
- Molecular Biology of Winter Dormancy and Cold Acclimation in Woody Plants, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
| | - Diego Mauricio Riaño-Pachón
- Grupo de Biología Computacional y Evolutiva, Departamento de Ciencias Biológicas, Universidad de los AndesBogotá DC, Colombia
| | - Rainer Hedrich
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, Universität WürzburgWürzburg, Germany
| | - Dietmar Geiger
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, Universität WürzburgWürzburg, Germany
| |
Collapse
|
29
|
Gomez-Porras JL, Riaño-Pachón DM, Benito B, Haro R, Sklodowski K, Rodríguez-Navarro A, Dreyer I. Phylogenetic analysis of k(+) transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants. Front Plant Sci 2012; 3:167. [PMID: 22876252 PMCID: PMC3410407 DOI: 10.3389/fpls.2012.00167] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/05/2012] [Indexed: 05/18/2023]
Abstract
As heritage from early evolution, potassium (K(+)) is absolutely necessary for all living cells. It plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. Land plants even enlarged this spectrum of K(+) utilization after having gone ashore, despite the fact that K(+) is far less available in their new oligotrophic habitats than in sea water. Inevitably, plant cells had to improve and to develop unique transport systems for K(+) accumulation and distribution. In the past two decades a manifold of K(+) transporters from flowering plants has been identified at the molecular level. The recently published genome of the fern ally Selaginella moellendorffii now helps in providing a better understanding on the molecular changes involved in the colonization of land and the development of the vasculature and the seeds. In this article we present an inventory of K(+) transporters of this lycophyte and pigeonhole them together with their relatives from the moss Physcomitrella patens, the monocotyledon Oryza sativa, and two dicotyledonous species, the herbaceous plant Arabidopsis thaliana, and the tree Populus trichocarpa. Interestingly, the transition of green plants from an aqueous to a dry environment coincides with a dramatic reduction in the diversity of voltage-gated potassium channels followed by a diversification on the basis of one surviving K(+) channel class. The first appearance of K(+) release (K(out)) channels in S. moellendorffii that were shown in Arabidopsis to be involved in xylem loading and guard cell closure coincides with the specialization of vascular plants and may indicate an important adaptive step.
Collapse
Affiliation(s)
| | - Diego Mauricio Riaño-Pachón
- Grupo de Biología Computacional y Evolutiva, Departamento de Ciencias Biológicas, Universidad de los AndesBogotá D.C., Colombia
| | - Begoña Benito
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
| | - Rosario Haro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
| | - Kamil Sklodowski
- Institut für Biochemie und Biologie, Universität PotsdamPotsdam, Germany
- Max-Planck-Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | | | - Ingo Dreyer
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
- Institut für Biochemie und Biologie, Universität PotsdamPotsdam, Germany
- *Correspondence: Ingo Dreyer, Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 37.7, E-28223-Pozuelo de Alarcón (Madrid), Spain. e-mail:
| |
Collapse
|
30
|
Rohrmann J, Tohge T, Alba R, Osorio S, Caldana C, McQuinn R, Arvidsson S, van der Merwe MJ, Riaño-Pachón DM, Mueller-Roeber B, Fei Z, Nesi AN, Giovannoni JJ, Fernie AR. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 2011; 68:999-1013. [PMID: 21851430 DOI: 10.1111/j.1365-313x.2011.04750.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.
Collapse
Affiliation(s)
- Johannes Rohrmann
- Max-Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LGG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga SI, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WWGT, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011; 332:960-3. [PMID: 21551031 PMCID: PMC3166216 DOI: 10.1126/science.1203810] [Citation(s) in RCA: 582] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
Collapse
Affiliation(s)
- Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Riaño-Pachón DM, Kleessen S, Neigenfind J, Durek P, Weber E, Engelsberger WR, Walther D, Selbig J, Schulze WX, Kersten B. Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 2010; 11:411. [PMID: 20594336 PMCID: PMC2996939 DOI: 10.1186/1471-2164-11-411] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/01/2010] [Indexed: 12/26/2022] Open
Abstract
Background Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites. Results From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented. These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected. Conclusions We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future.
Collapse
|
33
|
Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LGG, Rensing SA, Kersten B, Mueller-Roeber B. PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 2009; 38:D822-7. [PMID: 19858103 PMCID: PMC2808933 DOI: 10.1093/nar/gkp805] [Citation(s) in RCA: 489] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.
Collapse
Affiliation(s)
- Paulino Pérez-Rodríguez
- Department of Molecular Biology, Institute of Biochemistry and Biology, GoFORSYS, University of Potsdam, Karl-Liebknecht-Str 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | | | | | | | | | | |
Collapse
|
34
|
Arvidsson S, Kwasniewski M, Riaño-Pachón DM, Mueller-Roeber B. QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics 2008; 9:465. [PMID: 18976492 PMCID: PMC2612009 DOI: 10.1186/1471-2105-9-465] [Citation(s) in RCA: 383] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 11/01/2008] [Indexed: 11/21/2022] Open
Abstract
Background Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%. Conclusion QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.
Collapse
Affiliation(s)
- Samuel Arvidsson
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| | | | | | | |
Collapse
|
35
|
Riaño-Pachón DM, Nagel A, Neigenfind J, Wagner R, Basekow R, Weber E, Mueller-Roeber B, Diehl S, Kersten B. GabiPD: the GABI primary database--a plant integrative 'omics' database. Nucleic Acids Res 2008; 37:D954-9. [PMID: 18812395 PMCID: PMC2686513 DOI: 10.1093/nar/gkn611] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.
Collapse
Affiliation(s)
- Diego Mauricio Riaño-Pachón
- GabiPD team, Bioinformatics group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Berlin, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Senescence is a highly regulated process, eventually leading to cell and tissue disintegration: a physiological process associated with nutrient (e.g. nitrogen) redistribution from leaves to reproductive organs. Senescence is not observed in young leaves, indicating that repressors efficiently act to suppress cell degradation during early leaf development and/or that senescence activators are switched on when a leaf ages. Thus, massive regulatory network re-wiring likely constitutes an important component of the pre-senescence process. Transcription factors (TFs) have been shown to be central elements of such regulatory networks. Here, we used quantitative real-time polymerase chain reaction (qRT-PCR) analysis to study the expression of 1880 TF genes during pre-senescence and early-senescence stages of leaf development, using Arabidopsis thaliana as a model. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. Our analysis identified 41 TF genes that were gradually up-regulated as leaves progressed through these developmental stages. We also identified 144 TF genes that were down-regulated during senescence. A considerable number of the senescence-regulated TF genes were found to respond to abiotic stress, and salt stress appeared to be the major factor controlling their expression. Our data indicate a peculiar fine-tuning of developmental shifts during late-leaf development that is controlled by TFs.
Collapse
Affiliation(s)
- S Balazadeh
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany
| | | | | |
Collapse
|
37
|
Corrêa LGG, Riaño-Pachón DM, Schrago CG, dos Santos RV, Mueller-Roeber B, Vincentz M. The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PLoS One 2008; 3:e2944. [PMID: 18698409 PMCID: PMC2492810 DOI: 10.1371/journal.pone.0002944] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.8] [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: 02/18/2008] [Accepted: 07/22/2008] [Indexed: 01/07/2023] Open
Abstract
Background Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. Methodology/Principal Findings We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. Conclusions/Significance Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments.
Collapse
Affiliation(s)
- Luiz Gustavo Guedes Corrêa
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- Department of Molecular Biology, University of Potsdam, Potsdam-Golm, Germany
- Cooperative Research Group, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Mauricio Riaño-Pachón
- Department of Molecular Biology, University of Potsdam, Potsdam-Golm, Germany
- GabiPD Team, Bioinformatics Group, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Carlos Guerra Schrago
- Laboratório de Biodiversidade Molecular, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renato Vicentini dos Santos
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, University of Potsdam, Potsdam-Golm, Germany
- Cooperative Research Group, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- * E-mail:
| |
Collapse
|
38
|
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Ferris P, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WCA, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007; 318:245-50. [PMID: 17932292 PMCID: PMC2875087 DOI: 10.1126/science.1143609] [Citation(s) in RCA: 1788] [Impact Index Per Article: 105.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
Collapse
Affiliation(s)
- Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Simon E. Prochnik
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Olivier Vallon
- CNRS, UMR 7141, CNRS/Université Paris 6, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | | | - Steven J. Karpowicz
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - George B. Witman
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Astrid Terry
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Asaf Salamov
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lillian K. Fritz-Laylin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
| | | | - Wallace F. Marshall
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Liang-Hu Qu
- Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
| | - David R. Nelson
- Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA
| | - Anton A. Sanderfoot
- Department of Plant Biology, University of Minnesota, St. Paul MN 55108, USA
| | - Martin H. Spalding
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Qinghu Ren
- The Institute for Genomic Research, Rockville, MD 20850, USA
| | - Patrick Ferris
- Plant Biology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Erika Lindquist
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Harris Shapiro
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Susan M. Lucas
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jane Grimwood
- Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Jeremy Schmutz
- Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Pierre Cardol
- CNRS, UMR 7141, CNRS/Université Paris 6, Institut de Biologie Physico-Chimique, 75005 Paris, France
- Plant Biology Institute, Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Heriberto Cerutti
- University of Nebraska-Lincoln, School of Biological Sciences–Plant Science Initiative, Lincoln, NE 68588, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chun-Long Chen
- Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, CNRS, 67084 Strasbourg Cedex, France
| | - Martin T. Croft
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Rachel Dent
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Susan Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
| | - Patrick Ferris
- Plant Biology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México 04510 DF, Mexico
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, D-33615 Bielefeld, Germany
| | - Marc Hanikenne
- Plant Biology Institute, Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Michael Hippler
- Department of Biology, Institute of Plant Biochemistry and Biotechnology, University of Münster, 48143 Münster, Germany
| | - William Inwood
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Kamel Jabbari
- CNRS UMR 8186, Département de Biologie, Ecole Normale Supérieure, 75230 Paris, France
| | - Ming Kalanon
- Plant Cell Biology Research Centre, The School of Botany, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Richard Kuras
- CNRS, UMR 7141, CNRS/Université Paris 6, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Paul A. Lefebvre
- Department of Plant Biology, University of Minnesota, St. Paul MN 55108, USA
| | - Stéphane D. Lemaire
- Institut de Biotechnologie des Plantes, UMR 8618, CNRS/Université Paris-Sud, Orsay, France
| | - Alexey V. Lobanov
- Department of Biochemistry, N151 Beadle Center, University of Nebraska, Lincoln, NE 68588–0664, USA
| | - Martin Lohr
- Institut für Allgemeine Botanik, Johannes Gutenberg-Universität, 55099 Mainz, Germany
| | - Andrea Manuell
- Department of Cell Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Iris Meier
- PCMB and Plant Biotechnology Center, Ohio State University, Columbus, OH 43210, USA
| | - Laurens Mets
- Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Maria Mittag
- Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Telsa Mittelmeier
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - James V. Moroney
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Moseley
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94306, USA
| | - Carolyn Napoli
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Aurora M. Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada E3B 6E1
| | - Krishna Niyogi
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Sergey V. Novoselov
- Department of Biochemistry, N151 Beadle Center, University of Nebraska, Lincoln, NE 68588–0664, USA
| | - Ian T. Paulsen
- The Institute for Genomic Research, Rockville, MD 20850, USA
| | - Greg Pazour
- Department of Physiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Saul Purton
- Department of Biology, University College London, London WC1E 6BT, UK
| | - Jean-Philippe Ral
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS/USTL, IFR 118, Université des Sciences et Technologies de Lille, Cedex, France
| | | | - Wayne Riekhof
- Department of Medicine, National Jewish Medical and Research Center, Denver, CO 80206, USA
| | - Linda Rymarquis
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Michael Schroda
- Institute of Biology II/Plant Biochemistry, 79104 Freiburg, Germany
| | - David Stern
- Boyce Thompson Institute for Plant Research at Cornell University, Ithaca, NY 14853, USA
| | - James Umen
- Plant Biology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Robert Willows
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Nedra Wilson
- Department of Anatomy and Cell Biology, Oklahoma State University, Center for Health Sciences, Tulsa, OK 74107, USA
| | - Sara Lana Zimmer
- Boyce Thompson Institute for Plant Research at Cornell University, Ithaca, NY 14853, USA
| | - Jens Allmer
- Izmir Ekonomi Universitesi, 35330 Balcova-Izmir Turkey
| | - Janneke Balk
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Katerina Bisova
- Institute of Microbiology, Czech Academy of Sciences, Czech Republic
| | - Chong-Jian Chen
- Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
| | - Marek Elias
- Department of Plant Physiology, Faculty of Sciences, Charles University, 128 44 Prague 2, Czech Republic
| | - Karla Gendler
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Charles Hauser
- Bioinformatics Program, St. Edward's University, Austin, TX 78704, USA
| | - Mary Rose Lamb
- Department of Biology, University of Puget Sound, Tacoma, WA 98407, USA
| | - Heidi Ledford
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Joanne C. Long
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jun Minagawa
- Institute of Low-Temperature Science, Hokkaido University, 060-0819, Japan
| | - M. Dudley Page
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Junmin Pan
- Department of Biology, Tsinghua University, Beijing, China 100084
| | - Wirulda Pootakham
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94306, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | | | - Eric Stahlberg
- PCMB and Plant Biotechnology Center, Ohio State University, Columbus, OH 43210, USA
| | - Aimee M. Terauchi
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pinfen Yang
- Department of Biology, Marquette University, Milwaukee, WI 53233, USA
| | - Steven Ball
- UMR8576 CNRS, Laboratory of Biological Chemistry, 59655 Villeneuve d'Ascq, France
| | - Chris Bowler
- CNRS UMR 8186, Département de Biologie, Ecole Normale Supérieure, 75230 Paris, France
- Cell Signaling Laboratory, Stazione Zoologica, I 80121 Naples, Italy
| | - Carol L. Dieckmann
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Vadim N. Gladyshev
- Department of Biochemistry, N151 Beadle Center, University of Nebraska, Lincoln, NE 68588–0664, USA
| | - Pamela Green
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Richard Jorgensen
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Stephen Mayfield
- Department of Cell Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Sathish Rajamani
- Graduate Program in Biophysics, Ohio State University, Columbus, OH 43210, USA
| | - Richard T. Sayre
- PCMB and Plant Biotechnology Center, Ohio State University, Columbus, OH 43210, USA
| | - Peter Brokstein
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Inna Dubchak
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - David Goodstein
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Leila Hornick
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Y. Wayne Huang
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jinal Jhaveri
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yigong Luo
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Diego Martínez
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wing Chi Abby Ngau
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Bobby Otillar
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alexander Poliakov
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Aaron Porter
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lukasz Szajkowski
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gregory Werner
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Kemin Zhou
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Igor V. Grigoriev
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Daniel S. Rokhsar
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
| | - Arthur R. Grossman
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94306, USA
| |
Collapse
|
39
|
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WCA, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007. [PMID: 17932292 DOI: 10.1126/science.1143609.the] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
Collapse
Affiliation(s)
- Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Gómez-Porras JL, Riaño-Pachón DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 2007; 8:260. [PMID: 17672917 PMCID: PMC2000901 DOI: 10.1186/1471-2164-8-260] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [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: 04/30/2007] [Accepted: 08/01/2007] [Indexed: 11/16/2022] Open
Abstract
Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.
Collapse
Affiliation(s)
- Judith L Gómez-Porras
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- University of Bielefeld, Institute of Molecular Cell Physiology, Department of Biology, Universitätsstr. 25, D-33501 Germany
| | - Diego Mauricio Riaño-Pachón
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ingo Dreyer
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Jorge E Mayer
- Center for Applied Biosciences, University of Freiburg, Stefan-Meier-Str. 8, D-79104 Freiburg, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| |
Collapse
|
41
|
Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B. PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 2007; 8:42. [PMID: 17286856 PMCID: PMC1802092 DOI: 10.1186/1471-2105-8-42] [Citation(s) in RCA: 264] [Impact Index Per Article: 15.5] [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: 12/22/2006] [Accepted: 02/07/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes. DESCRIPTION PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family. CONCLUSION We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de. Further data will be included in the future when the sequences of other plant genomes become available.
Collapse
Affiliation(s)
- Diego Mauricio Riaño-Pachón
- Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25 Haus 20, D-14476, Golm, Germany
- Cooperative Research Group, Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Golm, Germany
| | - Slobodan Ruzicic
- Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25 Haus 20, D-14476, Golm, Germany
- Cooperative Research Group, Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Golm, Germany
| | - Ingo Dreyer
- Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25 Haus 20, D-14476, Golm, Germany
- Cooperative Research Group, Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Golm, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25 Haus 20, D-14476, Golm, Germany
- Cooperative Research Group, Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Golm, Germany
| |
Collapse
|
42
|
Riaño-Pachón DM, Dreyer I, Mueller-Roeber B. Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant J 2005; 43:205-12. [PMID: 15998307 DOI: 10.1111/j.1365-313x.2005.02438.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome.
Collapse
Affiliation(s)
- Diego Mauricio Riaño-Pachón
- Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25, Haus 20, D-14476 Golm/Potsdam, Germany
| | | | | |
Collapse
|