Gillian Colebatch

Max Planck Society

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Michael K. Udvardi

Noble Research Institute

Ben Trevaskis

Commonwealth Scientific and Industrial Research Organisation

Sebastian Kloska

Max Planck Society

Maren Wandrey

Max Planck Institute of Molecular Plant Physiology

Guilhem Desbrosses

Université de Montpellier

Thomas Altmann

Leibniz Institute of Plant Genetics and Crop Plant Research

Lene Krusell

Sejet Plant Breeding

Paul D. Cooper

Australian National University

Joachim Kopka

Max Planck Institute of Molecular Plant Physiology

Ombretta Montanari

Max Planck Institute of Molecular Plant Physiology

Cooperative Institutions

Max Planck Institute of Molecular Plant Physiology

Max Planck Society

John Innes Centre

Ludwig-Maximilians-Universität München

Kazusa DNA Research Institute

Norwich Research Park

Noble Research Institute

Commonwealth Scientific and Industrial Research Organisation

University of Potsdam

Max Planck Institute for Plant Breeding Research

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Functional genomics: tools of the trade

New Phytologist (2002)

Gillian Colebatch Ben Trevaskis Michael K. Udvardi

Summary Functional genomics is transforming the way biological research is done in the 21st century. Functional genomics brings together high‐throughput genetics with multiparallel analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome‐sequencing projects: what is the biological function of each and every gene? Functional genomics is driving a shift in the research paradigm away from vertical analysis of single genes, proteins, or metabolites, towards horizontal analysis of full suites of genes, proteins, and metabolites. By identifying and measuring many, if not all of the molecular players that participate in a given biological process, functional genomics offers the prospect of obtaining a truly holistic picture of life. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline is likely to have in the future.

Functional Genomics

Structural genomics

Genome Biology

Comparative Genomics

10.1046/j.0028-646x.2001.00303.x

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Citations (43)

Preliminary characterisation of digestive proteases of the green mirid, Creontiades dilutus (Hemiptera: Miridae)

Insect Biochemistry and Molecular Biology (2001)

Gillian Colebatch Peter D. East Paul D. Cooper

Protease inhibitor (pharmacology)

10.1016/s0965-1748(00)00136-3

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Citations (41)

The Soybean GmN6L Gene Encodes a Late Nodulin Expressed in the Infected Zone of Nitrogen-Fixing Nodules

Molecular Plant-Microbe Interactions (2002)

Ben Trevaskis Maren Wandrey Gillian Colebatch Michael K. Udvardi

Previously, we determined the N-terminal amino acid sequences of a number of putative peribacteroid membrane proteins from soybean. Here, we report the cloning of a gene, GmN6L, that encodes one of these proteins. The protein encoded by GmN6L is similar in sequence to MtN6, an early nodulin expressed in Medicago truncatula roots in response to infection by Sinorhizobium meliloti. The GmN6L gene was strongly expressed in mature nodules but not in other plant organs. GmN6L protein was first detected 2 weeks after inoculation with Bradyrhizobium japonicum and was limited to the infected zone of nodules. GmN6L protein was found in symbiosomes isolated from mature soybean nodules, both as a soluble protein and as a peripheral membrane protein bound to the peribacteroid membrane. These data indicate that GmN6L is a late nodulin, which is not involved in the infection process. Homology between GmN6L and FluG, a protein involved in signaling in Aspergillus nidulans, suggests that GmN6L may play a role in communication between the host and microsymbionts during symbiotic nitrogen fixation.

Medicago truncatula

Bradyrhizobium japonicum

Sinorhizobium

Sinorhizobium meliloti

Bradyrhizobium

Homology

Cloning (programming)

10.1094/mpmi.2002.15.7.630

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Citations (24)

Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus

The Plant Journal (2004)

Gillian Colebatch Guilhem Desbrosses Thomas Ott Lene Krusell Ombretta Montanari

Summary Research on legume nodule metabolism has contributed greatly to our knowledge of primary carbon and nitrogen metabolism in plants in general, and in symbiotic nitrogen fixation in particular. However, most previous studies focused on one or a few genes/enzymes involved in selected metabolic pathways in many different legume species. We utilized the tools of transcriptomics and metabolomics to obtain an unprecedented overview of the metabolic differentiation that results from nodule development in the model legume, Lotus japonicus . Using an array of more than 5000 nodule cDNA clones, representing 2500 different genes, we identified approximately 860 genes that were more highly expressed in nodules than in roots. One‐third of these are involved in metabolism and transport, and over 100 encode proteins that are likely to be involved in signalling, or regulation of gene expression at the transcriptional or post‐transcriptional level. Several metabolic pathways appeared to be co‐ordinately upregulated in nodules, including glycolysis, CO 2 fixation, amino acid biosynthesis, and purine, haem, and redox metabolism. Insight into the physiological conditions that prevail within nodules was obtained from specific sets of induced genes. In addition to the expected signs of hypoxia, numerous indications were obtained that nodule cells also experience P‐limitation and osmotic stress. Several potential regulators of these stress responses were identified. Metabolite profiling by gas chromatography coupled to mass spectrometry revealed a distinct metabolic phenotype for nodules that reflected the global changes in metabolism inferred from transcriptome analysis.

Lotus japonicus

Metabolic pathway

Secondary metabolism

Nitrogen Cycle

10.1111/j.1365-313x.2004.02150.x

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Citations (299)

Insights into nodule physiology and metabolism from transcriptomics, metabolomics, bioinformatics, and genetics

Michael K. Udvardi Troy Ott Lene Krusell Guilhem Desbrosses V. A. Voroshilova

Source

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cDNA cloning of a salivary chymotrypsin-like protease and the identification of six additional cDNAs encoding putative digestive proteases from the green mirid, Creontiades dilutus (Hemiptera: Miridae)

Insect Biochemistry and Molecular Biology (2002)

Gillian Colebatch Paul D. Cooper P. D. East

MASP1

TMPRSS6

Catalytic triad

10.1016/s0965-1748(02)00044-9

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Citations (27)

Symbiotic nitrogen fixation research in the postgenomics era

New Phytologist (2002)

Gillian Colebatch Ben Trevaskis Michael K. Udvardi

Summary Nitrogen‐fixing symbioses between legumes and rhizobia are important for sustainable agriculture and contribute significantly to the global nitrogen cycle. The genomes of two rhizobial species, Mesorhizobium loti and Sinorhizobium meliloti have now been completely sequenced. Hundreds of thousands of expressed sequence tags representing tens of thousands of different genes from three major legume species; soybean, Medicago truncatula and Lotus japonicus have also been deposited in the public domain. Lotus japonicus recently became the focus of a genome project that aims to sequence one third of the entire genome over the next 5 yr. With this as a backdrop, the stage is set for a renaissance in symbiosis research, which will provide new insight into the complex molecular interplay that underpins symbiotic nitrogen fixation. This review considers how functional genomics might contribute to this renaissance.

Lotus japonicus

Medicago truncatula

Sinorhizobium meliloti

10.1046/j.0028-646x.2001.00304.x

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Citations (48)

Lotus japonicus functional genomics: cDNA microarray analysis uncovers novel nodulins.

CABI Publishing eBooks (2002)

Michael K. Udvardi Thomas Altmann Bernd Essigmann Gillian Colebatch Sebastian Kloska

Lotus japonicus

Functional Genomics

10.1079/9780851995915.0109

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Novel Aspects of Symbiotic Nitrogen Fixation Uncovered by Transcript Profiling with cDNA Arrays

Molecular Plant-Microbe Interactions (2002)

Gillian Colebatch Sebastian Kloska Ben Trevaskis Susanne Freund Thomas Altmann

An array of 2,304 cDNA clones derived from nitrogen-fixing nodules of Lotus japonicus was produced and used to detect differences in relative gene transcript abundance between nodules and uninfected roots. Transcripts of 83 different genes were found to be more abundant in nodules than in roots. More than 50 of these have never before been identified as nodule-induced in any species. Expression of 36 genes was detected in nodules but not in roots. Several known nodulin genes were included among the nodule-induced genes. Also included were genes involved in sucrose breakdown and glycolysis, CO 2 recycling, and amino acid synthesis, processes that are known to be accelerated in nodules compared with roots. Genes involved in membrane transport, hormone metabolism, cell wall and protein synthesis, and signal transduction and regulation of transcription were also induced in nodules. Genes that may subvert normal plant defense responses, including two encoding enzymes involved in detoxification of active oxygen species and one that may prohibit phytoalexin synthesis, were also identified. The data represent a rich source of information for hypothesis building and future exploration of symbiotic nitrogen fixation.

Ribosome profiling

10.1094/mpmi.2002.15.5.411

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Citations (137)

Differentiation of Plant Cells During Symbiotic Nitrogen Fixation

Comparative and Functional Genomics (2002)

Ben Trevaskis Gillian Colebatch Guilhem Desbrosses Maren Wandrey Stefanie Wienkoop

Nitrogen-fixing symbioses between legumes and bacteria of the family Rhizobiaceae involve differentiation of both plant and bacterial cells. Differentiation of plant root cells is required to build an organ, the nodule, which can feed and accommodate a large population of bacteria under conditions conducive to nitrogen fixation. An efficient vascular system is built to connect the nodule to the root, which delivers sugars and other nutrients to the nodule and removes the products of nitrogen fixation for use in the rest of the plant. Cells in the outer cortex differentiate to form a barrier to oxygen diffusion into nodules, which helps to produce the micro-aerobic environment necessary for bacterial nitrogenase activity. Cells of the central, infected zone of nodules undergo multiple rounds of endoreduplication, which may be necessary for colonisation by rhizobia and may enable enlargement and greater metabolic activity of these cells. Infected cells of the nodule contain rhizobia within a unique plant membrane called the peribacteroid or symbiosome membrane, which separates the bacteria from the host cell cytoplasm and mediates nutrient and signal exchanges between the partners. Rhizobia also undergo differentiation during nodule development. Not surprisingly, perhaps, differentiation of each partner is dependent upon interactions with the other. High-throughput methods to assay gene transcripts, proteins, and metabolites are now being used to explore further the different aspects of plant and bacterial differentiation. In this review, we highlight recent advances in our understanding of plant cell differentiation during nodulation that have been made, at least in part, using high-throughput methods.

Plant cell

10.1002/cfg.155

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Citations (18)