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Behzadi P, Ranjbar R. DNA microarray technology and bioinformatic web services. Acta Microbiol Immunol Hung 2019; 66:19-30. [PMID: 30010394 DOI: 10.1556/030.65.2018.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pan-genomic microarray technique is used for environmental and/or clinical studies. Although microarray is an accurate and sharp diagnostic tool, the expertized bioinformaticians were able to minimize the outcome biases and maximize the flexibility and accuracy of the technique. The knowledge of bioinformatics plays a key role in association with probe designing and the utilization of correct probe sets and platforms. This technique is divided into two parts as dry lab (in silico studies) and wet lab (in vitro studies). Each part covers the other and are known as complementary divisions. In the case of microarray probe designing, a wide range of software, tools, and databases are necessary. Obviously, the application of right databases, software, and tools decreases the probable biases in the outcomes. Due to the importance of suitable probe designing, this article has focused its look onto a variety of online/offline databases, software, and tools.
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Affiliation(s)
- Payam Behzadi
- 1 Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ranjbar
- 2 Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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2
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Benchouaia M, Ripoche H, Sissoko M, Thiébaut A, Merhej J, Delaveau T, Fasseu L, Benaissa S, Lorieux G, Jourdren L, Le Crom S, Lelandais G, Corel E, Devaux F. Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida glabrata. Front Microbiol 2018; 9:2689. [PMID: 30505294 PMCID: PMC6250833 DOI: 10.3389/fmicb.2018.02689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/22/2018] [Indexed: 11/21/2022] Open
Abstract
In this work, we used comparative transcriptomics to identify regulatory outliers (ROs) in the human pathogen Candida glabrata. ROs are genes that have very different expression patterns compared to their orthologs in other species. From comparative transcriptome analyses of the response of eight yeast species to toxic doses of selenite, a pleiotropic stress inducer, we identified 38 ROs in C. glabrata. Using transcriptome analyses of C. glabrata response to five different stresses, we pointed out five ROs which were more particularly responsive to iron starvation, a process which is very important for C. glabrata virulence. Global chromatin Immunoprecipitation and gene profiling analyses showed that four of these genes are actually new targets of the iron starvation responsive Aft2 transcription factor in C. glabrata. Two of them (HBS1 and DOM34b) are required for C. glabrata optimal growth in iron limited conditions. In S. cerevisiae, the orthologs of these two genes are involved in ribosome rescue by the NO GO decay (NGD) pathway. Hence, our results suggest a specific contribution of NGD co-factors to the C. glabrata adaptation to iron starvation.
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Affiliation(s)
- Médine Benchouaia
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Hugues Ripoche
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Mariam Sissoko
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Antonin Thiébaut
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Jawad Merhej
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thierry Delaveau
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Laure Fasseu
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Sabrina Benaissa
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Geneviève Lorieux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Laurent Jourdren
- École Normale Supérieure, PSL Research University, CNRS, Inserm U1024, Institut de Biologie de l’École Normale Supérieure, Plateforme Génomique, Paris, France
| | - Stéphane Le Crom
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Évolution, Paris, France
| | - Gaëlle Lelandais
- UMR 9198, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, UPSay, Gif-sur-Yvette, France
| | - Eduardo Corel
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Évolution, Paris, France
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- *Correspondence: Frédéric Devaux,
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3
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Zahra S, Singh A, Kumar S. Synthetic Probes, Their Applications and Designing. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Li R, Fristensky B, Wang G. Sequence data analysis and preprocessing for oligo probe design in microbial genomes. AIMS BIOENGINEERING 2017. [DOI: 10.3934/bioeng.2017.1.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Parisot N, Peyretaillade E, Dugat-Bony E, Denonfoux J, Mahul A, Peyret P. Probe Design Strategies for Oligonucleotide Microarrays. Methods Mol Biol 2016; 1368:67-82. [PMID: 26614069 DOI: 10.1007/978-1-4939-3136-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters.
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Affiliation(s)
- Nicolas Parisot
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France
| | - Eric Peyretaillade
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France
| | - Eric Dugat-Bony
- Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, INRA, AgroParisTech, UMR 782, Thiverval-Grignon, France
| | - Jérémie Denonfoux
- Genomic Platform and R&D, Genoscreen, Campus de l'Institut Pasteur, Lille, France
| | | | - Pierre Peyret
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France.
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Merhej J, Delaveau T, Guitard J, Palancade B, Hennequin C, Garcia M, Lelandais G, Devaux F. Yap7 is a transcriptional repressor of nitric oxide oxidase in yeasts, which arose from neofunctionalization after whole genome duplication. Mol Microbiol 2015; 96:951-72. [DOI: 10.1111/mmi.12983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Jawad Merhej
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
| | - Thierry Delaveau
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
| | - Juliette Guitard
- Sorbonne Universités, UPMC Univ Paris 06, CR7; Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris); 91 Bd de l'hôpital F-75013 Paris France
- Inserm; U1135; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
- Assistance Publique-Hôpitaux de Paris, Hôpital St Antoine; Service de Parasitologie-Mycologie; F-75012 Paris France
- CNRS; ERL 8255; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot; Sorbonne Paris Cité; F-75205 Paris France
| | - Christophe Hennequin
- Sorbonne Universités, UPMC Univ Paris 06, CR7; Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris); 91 Bd de l'hôpital F-75013 Paris France
- Inserm; U1135; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
- Assistance Publique-Hôpitaux de Paris, Hôpital St Antoine; Service de Parasitologie-Mycologie; F-75012 Paris France
- CNRS; ERL 8255; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
| | - Mathilde Garcia
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
| | - Gaëlle Lelandais
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot; Sorbonne Paris Cité; F-75205 Paris France
| | - Frédéric Devaux
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
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Bretes H, Rouviere JO, Leger T, Oeffinger M, Devaux F, Doye V, Palancade B. Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs. Nucleic Acids Res 2014; 42:5043-58. [PMID: 24500206 PMCID: PMC4005672 DOI: 10.1093/nar/gku124] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Assembly of messenger ribonucleoparticles (mRNPs) is a pivotal step in gene expression, but only a few molecular mechanisms contributing to its regulation have been described. Here, through a comprehensive proteomic survey of mRNP assembly, we demonstrate that the SUMO pathway specifically controls the association of the THO complex with mRNPs. We further show that the THO complex, a key player in the interplay between gene expression, mRNA export and genetic stability, is sumoylated on its Hpr1 subunit and that this modification regulates its association with mRNPs. Altered recruitment of the THO complex onto mRNPs in sumoylation-defective mutants does not affect bulk mRNA export or genetic stability, but impairs the expression of acidic stress-induced genes and, consistently, compromises viability in acidic stress conditions. Importantly, inactivation of the nuclear exosome suppresses the phenotypes of the hpr1 non-sumoylatable mutant, showing that SUMO-dependent mRNP assembly is critical to allow a specific subset of mRNPs to escape degradation. This article thus provides the first example of a SUMO-dependent mRNP-assembly event allowing a refined tuning of gene expression, in particular under specific stress conditions.
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Affiliation(s)
- Hugo Bretes
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France, Ecole Doctorale Gènes Génomes Cellules, Université Paris Sud-11, Orsay, France, Proteomics facility, Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France, Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montreal, Québec, Canada H2W 1R7, Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada H3T 1J4, Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3, Université Pierre et Marie Curie, UMR7238, 15, rue de l'Ecole de Médecine, 75006 Paris, France and CNRS, UMR7238, Laboratoire de Génomique des Microorganismes, 75006 Paris, France
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Poggi-Parodi D, Bidard F, Pirayre A, Portnoy T, Blugeon C, Seiboth B, Kubicek CP, Le Crom S, Margeot A. Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:173. [PMID: 25550711 PMCID: PMC4279801 DOI: 10.1186/s13068-014-0173-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/18/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. RESULTS We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. CONCLUSIONS This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
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Affiliation(s)
- Dante Poggi-Parodi
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- />Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France
| | - Frédérique Bidard
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Aurélie Pirayre
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Thomas Portnoy
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Plateforme Génomique, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France
| | - Corinne Blugeon
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Plateforme Génomique, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France
| | - Bernhard Seiboth
- />Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Getreidemarkt 9/166, A- 1060 Vienna, Austria
| | | | - Stéphane Le Crom
- />Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Plateforme Génomique, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, Paris, F-75005 France
- />Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, CNRS, UMR 8197, Paris, F-75005 France
| | - Antoine Margeot
- />IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Tulpan D, Ghiggi A, Montemanni R. Computational Sequence Design Techniques for DNA Microarray Technologies. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In systems biology and biomedical research, microarray technology is a method of choice that enables the complete quantitative and qualitative ascertainment of gene expression patterns for whole genomes. The selection of high quality oligonucleotide sequences that behave consistently across multiple experiments is a key step in the design, fabrication and experimental performance of DNA microarrays. The aim of this chapter is to outline recent algorithmic developments in microarray probe design, evaluate existing probe sequences used in commercial arrays, and suggest methodologies that have the potential to improve on existing design techniques.
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Affiliation(s)
- Dan Tulpan
- National Research Council of Canada, Canada
| | | | - Roberto Montemanni
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale, Switzerland
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Atanasova L, Crom SL, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS. Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics 2013; 14:121. [PMID: 23432824 PMCID: PMC3599271 DOI: 10.1186/1471-2164-14-121] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 02/19/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Trichoderma is a genus of mycotrophic filamentous fungi (teleomorph Hypocrea) which possess a bright variety of biotrophic and saprotrophic lifestyles. The ability to parasitize and/or kill other fungi (mycoparasitism) is used in plant protection against soil-borne fungal diseases (biological control, or biocontrol). To investigate mechanisms of mycoparasitism, we compared the transcriptional responses of cosmopolitan opportunistic species and powerful biocontrol agents Trichoderma atroviride and T. virens with tropical ecologically restricted species T. reesei during confrontations with a plant pathogenic fungus Rhizoctonia solani. RESULTS The three Trichoderma spp. exhibited a strikingly different transcriptomic response already before physical contact with alien hyphae. T. atroviride expressed an array of genes involved in production of secondary metabolites, GH16 ß-glucanases, various proteases and small secreted cysteine rich proteins. T. virens, on the other hand, expressed mainly the genes for biosynthesis of gliotoxin, respective precursors and also glutathione, which is necessary for gliotoxin biosynthesis. In contrast, T. reesei increased the expression of genes encoding cellulases and hemicellulases, and of the genes involved in solute transport. The majority of differentially regulated genes were orthologues present in all three species or both in T. atroviride and T. virens, indicating that the regulation of expression of these genes is different in the three Trichoderma spp. The genes expressed in all three fungi exhibited a nonrandom genomic distribution, indicating a possibility for their regulation via chromatin modification. CONCLUSION This genome-wide expression study demonstrates that the initial Trichoderma mycotrophy has differentiated into several alternative ecological strategies ranging from parasitism to predation and saprotrophy. It provides first insights into the mechanisms of interactions between Trichoderma and other fungi that may be exploited for further development of biofungicides.
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Affiliation(s)
- Lea Atanasova
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Stephane Le Crom
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, F-75005, Paris, France
- Inserm, U1024, F-75005, Paris, France
- CNRS, UMR 8197, F-75005, Paris, France
- UPMC Univ Paris 06, UMR7622, Laboratoire de Biologie du Développement, 9 quai St. Bernard, F-75005, Paris, France
- CNRS, UMR7622, Laboratoire de Biologie du Développement, 9 quai St. Bernard, F-75005, Paris, France
| | - Sabine Gruber
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Fanny Coulpier
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, F-75005, Paris, France
- Inserm, U1024, F-75005, Paris, France
- CNRS, UMR 8197, F-75005, Paris, France
| | - Verena Seidl-Seiboth
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Christian P Kubicek
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
- Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Irina S Druzhinina
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
- Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
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In the fast lane: Large-scale bacterial genome engineering. J Biotechnol 2012; 160:72-9. [DOI: 10.1016/j.jbiotec.2012.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 11/15/2022]
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12
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Tulpan D, Ghiggi A, Montemanni R. Computational Sequence Design Techniques for DNA Microarray Technologies. SYSTEMIC APPROACHES IN BIOINFORMATICS AND COMPUTATIONAL SYSTEMS BIOLOGY 2011. [DOI: 10.4018/978-1-61350-435-2.ch003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In systems biology and biomedical research, microarray technology is a method of choice that enables the complete quantitative and qualitative ascertainment of gene expression patterns for whole genomes. The selection of high quality oligonucleotide sequences that behave consistently across multiple experiments is a key step in the design, fabrication and experimental performance of DNA microarrays. The aim of this chapter is to outline recent algorithmic developments in microarray probe design, evaluate existing probe sequences used in commercial arrays, and suggest methodologies that have the potential to improve on existing design techniques.
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Affiliation(s)
- Dan Tulpan
- National Research Council of Canada, Canada
| | | | - Roberto Montemanni
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Switzerland
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Portnoy T, Margeot A, Linke R, Atanasova L, Fekete E, Sándor E, Hartl L, Karaffa L, Druzhinina IS, Seiboth B, Le Crom S, Kubicek CP. The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation. BMC Genomics 2011; 12:269. [PMID: 21619626 PMCID: PMC3124439 DOI: 10.1186/1471-2164-12-269] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 05/27/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known. RESULTS Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes. CONCLUSIONS Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
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Affiliation(s)
- Thomas Portnoy
- IFP Energies nouvelles, Département Biotechnologie, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
- École normale supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France. Inserm, U1024, Paris, F-75005 France. CNRS, UMR 8197, Paris, F-75005 France
| | - Antoine Margeot
- IFP Energies nouvelles, Département Biotechnologie, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Rita Linke
- Austrian Center of Industrial Biotechnology, c/o Institute of Chemical Engineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Lea Atanasova
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4010, P.O.Box 56, Debrecen, Hungary
| | - Erzsébet Sándor
- Department of Plant Protection, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, H-4032 Böszörményi út 138., Debrecen, Hungary
| | - Lukas Hartl
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4010, P.O.Box 56, Debrecen, Hungary
| | - Irina S Druzhinina
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
| | - Stéphane Le Crom
- École normale supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France. Inserm, U1024, Paris, F-75005 France. CNRS, UMR 8197, Paris, F-75005 France
| | - Christian P Kubicek
- Research Area Gene Technology and Applied Biochemistry, Institute of ChemicalEngineering, Technische Universität Wien, Getreidemarkt 9/166, A-1060 Vienna, Austria
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Bidard F, Imbeaud S, Reymond N, Lespinet O, Silar P, Clavé C, Delacroix H, Berteaux-Lecellier V, Debuchy R. A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina. BMC Res Notes 2010; 3:171. [PMID: 20565839 PMCID: PMC2908635 DOI: 10.1186/1756-0500-3-171] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 06/18/2010] [Indexed: 01/16/2023] Open
Abstract
Background The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. Findings We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. Conclusions A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.
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Affiliation(s)
- Frédérique Bidard
- Univ Paris-Sud 11, Institut de Génétique et Microbiologie UMR8621, F- 91405 Orsay, France.
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