1
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Nan X, Hardinge P, Hoehn S, Dighe SN, Ukeri J, Pease DF, Griffin J, Warrington JI, Saud Z, Hottinger E, Webster G, Jones D, Kille P, Weightman A, Stanton R, Castell OK, Murray JAH, Jurkowski TP. VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance. Sci Rep 2023; 13:20832. [PMID: 38012215 PMCID: PMC10681975 DOI: 10.1038/s41598-023-47289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 08/04/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023] Open
Abstract
The COVID-19 pandemic demonstrated the need for rapid molecular diagnostics. Vaccination programs can provide protection and facilitate the opening of society, but newly emergent and existing viral variants capable of evading the immune system endanger their efficacy. Effective surveillance for Variants of Concern (VOC) is therefore important. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. Here we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to provide rapid and sensitive discrimination of SARS-CoV-2 VOCs that can be used at point of care, implemented in the pipelines of small or large testing facilities, and even determine the proportion of VOCs in pooled population-level wastewater samples. This technology complements sequencing efforts to allow facile and rapid identification of individuals infected with VOCs to help break infection chains. We show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants and the rapid adaptability of the technique for new and emerging VOCs.
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Affiliation(s)
- Xinsheng Nan
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Patrick Hardinge
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Sven Hoehn
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Shrinivas Nivrutti Dighe
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - John Ukeri
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Darius F Pease
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Joshua Griffin
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Jessica I Warrington
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- Biodexa Pharmaceuticals (Wales) Ltd, 1 Caspian Point, Caspian Way, Cardiff, CF10 4DQ, UK
| | - Zack Saud
- Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Emma Hottinger
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Gordon Webster
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Davey Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Peter Kille
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew Weightman
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Richard Stanton
- Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Oliver K Castell
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Tomasz P Jurkowski
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
- COVID-19 Screening Service, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
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2
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Williamson D, Tasker-Brown W, Murray JAH, Jones AR, Band LR. Modelling how plant cell-cycle progression leads to cell size regulation. PLoS Comput Biol 2023; 19:e1011503. [PMID: 37862377 PMCID: PMC10653611 DOI: 10.1371/journal.pcbi.1011503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 03/06/2023] [Revised: 11/16/2023] [Accepted: 09/07/2023] [Indexed: 10/22/2023] Open
Abstract
Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present a mathematical model of the key interactions in the plant cell cycle. Model simulations reveal that the network of interactions exhibits limit-cycle solutions, with biological switches underpinning both the G1/S and G2/M cell-cycle transitions. Embedding this network model within growing cells, we test hypotheses as to how cell-cycle progression can depend on cell size. We investigate two different mechanisms at both the G1/S and G2/M transitions: (i) differential expression of cell-cycle activator and inhibitor proteins (with synthesis of inhibitor proteins being independent of cell size), and (ii) equal inheritance of inhibitor proteins after cell division. The model demonstrates that both these mechanisms can lead to larger daughter cells progressing through the cell cycle more rapidly, and can thus contribute to cell-size control. To test how these features enable size homeostasis over multiple generations, we then simulated these mechanisms in a cell-population model with multiple rounds of cell division. These simulations suggested that integration of size-control mechanisms at both G1/S and G2/M provides long-term cell-size homeostasis. We concluded that while both size independence and equal inheritance of inhibitor proteins can reduce variations in cell size across individual cell-cycle phases, combining size-control mechanisms at both G1/S and G2/M is essential to maintain size homeostasis over multiple generations. Thus, our study reveals how features of the cell-cycle network enable cell-cycle progression to depend on cell size, and provides a mechanistic understanding of how plant cell populations maintain consistent size over generations.
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Affiliation(s)
- Daniel Williamson
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - William Tasker-Brown
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Angharad R. Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Leah R. Band
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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3
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Jathoul AP, Branchini BR, Anderson JC, Murray JAH. A higher spectral range of beetle bioluminescence with infraluciferin. Front Bioeng Biotechnol 2022; 10:897272. [PMID: 36091447 PMCID: PMC9459109 DOI: 10.3389/fbioe.2022.897272] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Coleopteran bioluminescence is unique in that beetle luciferases emit colors ranging between green (ca.550 nm) and red (ca.600 nm), including intermediate colors such as yellow and orange, allowing up to 3 simultaneous parameters to be resolved in vitro with natural luciferin (D-LH2). Here, we report a more than doubling of the maximum bioluminescence wavelength range using a single synthetic substrate, infraluciferin (iLH2). We report that different luciferases can emit colors ranging from visible green to near-infrared (nIR) with iLH2, including in human cells. iLH2 was designed for dual color far-red to nIR bioluminescence imaging (BLI) in small animals and has been utilized in different mouse models of cancer (including a metastatic hepatic model showing detailed hepatic morphology) and for robust dual parameter imaging in vivo (including in systemic hematological models). Here, we report the properties of different enzymes with iLH2: Lampyrid wild-type (WT) Photinus pyralis (Ppy) firefly luciferase, Ppy-based derivatives previously engineered to be thermostable with D-LH2, and also color-shifted Elaterid-based enzymes: blue-shifted Pyrearinus termitilluminans derivative Eluc (reported D-LH2 λmax = 538 nm) and red-shifted Pyrophorus plagiopthalamus derivative click beetle red (CBR) luciferase (D-LH2 λmax = 618 nm). As purified enzyme, in bacteria or in human cells, Eluc emitted green light (λmax = 536 nm) with DL-iLH2 whereas Ppy Fluc (λmax = 689 nm), x2 Fluc (λmax = 704 nm), x5 Fluc (λmax = 694 nm), x11 Fluc (λmax = 694 nm) and CBR (λmax = 721 nm) produced far-red to nIR peak wavelengths. Therefore, with iLH2, enzyme λmaxes can be separated by ca.185nm, giving almost non-overlapping spectra. This is the first report of single-substrate bioluminescence color emission ranging from visible green to nIR in cells and may help shed light on the color tuning mechanism of beetle luciferases. We also report on the reason for the improvement in activity of x11 Fluc with iLH2 and engineer an improved infraluciferase (iluc) based on this mutant.
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Affiliation(s)
- Amit P Jathoul
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom.,Bioflares Ltd., Trowbridge, Wiltshire, United Kingdom
| | | | - James C Anderson
- Department of Chemistry, University College London, London, United Kingdom
| | - James A H Murray
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom
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4
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Hardinge P, Murray JAH. Full Dynamic Range Quantification using Loop-mediated Amplification (LAMP) by Combining Analysis of Amplification Timing and Variance between Replicates at Low Copy Number. Sci Rep 2020; 10:916. [PMID: 31969573 PMCID: PMC6976701 DOI: 10.1038/s41598-020-57473-1] [Citation(s) in RCA: 8] [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] [Received: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022] Open
Abstract
Quantification of nucleic acid targets at low copy number is problematic with the limit of detection at 95 percent confidence predicted to be 3 molecules or higher for quantitative PCR. Conversely the accuracy of digital PCR is diminished at higher concentrations of template approaching 100 percent positive partitions, with the Poisson distribution showing that an average of only 3 molecules per partition represents an amplification frequency of greater than 95 percent. Therefore a full range of template concentrations cannot be quantified accurately with these methods alone without dilution. Here we report the development of quantification metrics for use with loop-mediated amplification (LAMP) as a bridge between concentrated and dilute template concentrations. The basis for this is that real-time monitoring of LAMP reactions either by bioluminescent reporting (BART) or by fluorescent dye binding shows increasing variation in timings between replicates at low copy number due to the LAMP amplification mechanism. This effect increases with decreasing copy number, closely associated with the amplification frequency. The use of an artificial template showed that the increasing variation is not linked to the use of displacement primers during the initiation of amplification and is therefore a fundamental feature of the LAMP initiation event. Quantification between 1 and 10 copies of a template was successfully achieved with a number of methods with a low number of replicates with the strongest correlation to timing variance. These ultra-quantification methods for LAMP amplification either singularly or in combination have potential in a full dynamic range quantification strategy based on LAMP, in a closed tube, undiluted sample molecular diagnostic.
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Affiliation(s)
- Patrick Hardinge
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - James A H Murray
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff, CF10 3AX, UK
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5
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Jones AR, Band LR, Murray JAH. Double or Nothing? Cell Division and Cell Size Control. Trends Plant Sci 2019; 24:1083-1093. [PMID: 31630972 DOI: 10.1016/j.tplants.2019.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/08/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Size is a fundamental property that must be tightly regulated to ensure that cells and tissues function efficiently. Dynamic size control allows unicellular organisms to adapt to environmental changes, but cell size is also integral to multicellular development, affecting tissue size and structure. Despite clear evidence for homeostatic cell size maintenance, we are only now beginning to understand cell size regulation in the actively dividing meristematic tissues of higher plants. We discuss here how coupled advances in live cell imaging and modelling are uncovering dynamic mechanisms for size control mediated at the cellular level. We argue that integrated models of cell growth and division will be necessary to predict cell size and fully understand multicellular growth and development.
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Affiliation(s)
- Angharad R Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK.
| | - Leah R Band
- Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK; Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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6
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Hardinge P, Murray JAH. Lack of specificity associated with using molecular beacons in loop mediated amplification assays. BMC Biotechnol 2019; 19:55. [PMID: 31370820 PMCID: PMC6676609 DOI: 10.1186/s12896-019-0549-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background Loop mediated isothermal amplification of nucleic acid templates is a rapid, sensitive and specific method suitable for molecular diagnostics. However the complexity of primer design and the number of primers involved can lead to false positives from non-specific primer interactions. Standard methods of LAMP detection utilise the increasing concentrations of DNA or inorganic pyrophosphate and therefore lack specificity for identifying the desired LAMP amplification. Molecular beacons used in PCR reactions are target specific and may enhance specificity with LAMP. Results We present a potential molecular beacon approach to LAMP detection targeting the single stranded region between loops, and test this for LAMP molecular beacons targeting the 35S promoter and NOS terminator sequences commonly used in GM crops. From these studies we show that molecular beacons used in LAMP, despite providing a change in fluorescent intensity with amplification, appear not to anneal to specific target sequences and therefore target specificity is not a benefit of this method. However, molecular beacons demonstrate a change in fluorescence which is indicative of LAMP amplification products. We identify the LAMP loop structure as likely to be responsible for this change in signal. Conclusions Molecular beacons can be used to detect LAMP amplification but do not provide sequence specificity. The method can be used to determine effectively LAMP amplification from other primer-driven events, but does not discriminate between different LAMP amplicons. It is therefore unsuitable for multiplex LAMP reactions due to non-specific detection of LAMP amplification. Electronic supplementary material The online version of this article (10.1186/s12896-019-0549-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Hardinge
- Cardiff School of Biosciences, Cardiff, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff, Museum Avenue, Cardiff, CF10 3AX, UK
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7
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Mullins AJ, Murray JAH, Bull MJ, Jenner M, Jones C, Webster G, Green AE, Neill DR, Connor TR, Parkhill J, Challis GL, Mahenthiralingam E. Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria. Nat Microbiol 2019; 4:996-1005. [PMID: 30833726 PMCID: PMC6544543 DOI: 10.1038/s41564-019-0383-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 06/05/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022]
Abstract
Beneficial microorganisms are widely used in agriculture for control of plant pathogens but a lack of efficacy and safety information has limited the exploitation of multiple promising biopesticides. We applied phylogeny-led genome mining, metabolite analyses and biological control assays to define the efficacy of Burkholderia ambifaria, a naturally beneficial bacterium with proven biocontrol properties, but potential pathogenic risk. A panel of 64 B. ambifaria strains demonstrated significant antimicrobial activity against priority plant pathogens. Genome sequencing, specialized metabolite biosynthetic gene cluster mining and metabolite analysis revealed an armoury of known and unknown pathways within B. ambifaria. The biosynthetic gene cluster responsible for the production of the metabolite, cepacin, was identified and directly shown to mediate protection of germinating crops against Pythium damping-off disease. B. ambifaria maintained biopesticidal protection and overall fitness in soil after deletion of its third replicon, a non-essential plasmid associated with virulence in B. cepacia complex bacteria. Removal of the third replicon reduced B. ambifaria persistence in a murine respiratory infection model. Here we show that by using interdisciplinary phylogenomic, metabolomic and functional approaches, the mode of action of natural biological control agents related to pathogens can be systematically established to facilitate their future exploitation.
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Affiliation(s)
- Alex J Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK.
| | - James A H Murray
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Matthew J Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Matthew Jenner
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Cerith Jones
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK.,Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Angharad E Green
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Daniel R Neill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Thomas R Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Gregory L Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology,Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, UK.
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8
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Scofield S, Murison A, Jones A, Fozard J, Aida M, Band LR, Bennett M, Murray JAH. Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development 2018; 145:dev157081. [PMID: 29650590 PMCID: PMC5992597 DOI: 10.1242/dev.157081] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 03/21/2018] [Indexed: 01/29/2023]
Abstract
The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is crucial for shoot apical meristem (SAM) function, yet the components and structure of the STM gene regulatory network (GRN) are largely unknown. Here, we show that transcriptional regulators are overrepresented among STM-regulated genes and, using these as GRN components in Bayesian network analysis, we infer STM GRN associations and reveal regulatory relationships between STM and factors involved in multiple aspects of SAM function. These include hormone regulation, TCP-mediated control of cell differentiation, AIL/PLT-mediated regulation of pluripotency and phyllotaxis, and specification of meristem-organ boundary zones via CUC1. We demonstrate a direct positive transcriptional feedback loop between STM and CUC1, despite their distinct expression patterns in the meristem and organ boundary, respectively. Our further finding that STM activates expression of the CUC1-targeting microRNA miR164c combined with mathematical modelling provides a potential solution for this apparent contradiction, demonstrating that these proposed regulatory interactions coupled with STM mobility could be sufficient to provide a mechanism for CUC1 localisation at the meristem-organ boundary. Our findings highlight the central role for the STM GRN in coordinating SAM functions.
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Affiliation(s)
- Simon Scofield
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Alexander Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Angharad Jones
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - John Fozard
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Mitsuhiro Aida
- International Research Organization for Advanced Science and Technology (IROAST) Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Leah R Band
- Centre for Plant Integrative Biology, Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Malcolm Bennett
- Centre for Plant Integrative Biology, Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - James A H Murray
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
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9
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Weimer AK, Matos JL, Sharma N, Patell F, Murray JAH, Dewitte W, Bergmann DC. Lineage- and stage-specific expressed CYCD7;1 coordinates the single symmetric division that creates stomatal guard cells. Development 2018; 145:dev.160671. [PMID: 29467245 DOI: 10.1242/dev.160671] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/13/2018] [Indexed: 11/20/2022]
Abstract
Plants, with cells fixed in place by rigid walls, often utilize spatial and temporally distinct cell division programs to organize and maintain organs. This leads to the question of how developmental regulators interact with the cell cycle machinery to link cell division events with particular developmental trajectories. In Arabidopsis leaves, the development of stomata, two-celled epidermal valves that mediate plant-atmosphere gas exchange, relies on a series of oriented stem cell-like asymmetric divisions followed by a single symmetric division. The stomatal lineage is embedded in a tissue in which other cells transition from proliferation to postmitotic differentiation earlier, necessitating stomatal lineage-specific factors to prolong competence to divide. We show that the D-type cyclin, CYCD7;1, is specifically expressed just prior to the symmetric guard cell-forming division, and that it is limiting for this division. Further, we find that CYCD7;1 is capable of promoting divisions in multiple contexts, likely through RBR1-dependent promotion of the G1/S transition, but that CYCD7;1 is regulated at the transcriptional level by cell type-specific transcription factors that confine its expression to the appropriate developmental window.
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Affiliation(s)
- Annika K Weimer
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Juliana L Matos
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nidhi Sharma
- Howard Hughes Medical Institute (HHMI), Stanford University, Stanford, CA 94305, USA
| | - Farah Patell
- Cardiff School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.,Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK
| | - James A H Murray
- Cardiff School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.,Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK
| | - Walter Dewitte
- Cardiff School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.,Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, UK
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305, USA .,Howard Hughes Medical Institute (HHMI), Stanford University, Stanford, CA 94305, USA
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10
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Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol 2017; 175:1499-1509. [PMID: 29208732 PMCID: PMC5717721 DOI: 10.1104/pp.17.01490] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 05/20/2023]
Abstract
Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development.
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Affiliation(s)
- Joanna Friesner
- Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, University of California, Davis, California 95616
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802
| | - Ruth Bastow
- GARNet, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Volker Brendel
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana 47405
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Alexander Bucksch
- Department of Plant Biology, Warnell School of Forestry and Natural Resources, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Jose R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Pascal Falter-Braun
- Institute of Network Biology, Department of Environmental Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Rodrigo Gutierrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile 8331150
| | - Ute Kramer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, CNRS, INRA, Montpellier SupAgro, Université Montpellier, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier cedex, France
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, California 95616
| | - Molly Megraw
- Department of Botany and Plant Pathology, Department of Computer Science, and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132; Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A H Murray
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, United Kingdom
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Sue Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Roger Smith
- Syngenta Crop Protection, Research Triangle Park, North Carolina 27709
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, Maryland 20855
| | | | - Keiko U Torii
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, Washington 98195
| | - Chris Town
- J. Craig Venter Institute, Rockville, Maryland 20850
| | - Matthew Vaughn
- Life Sciences Computing, Texas Advanced Computing Center, Austin, Texas 78758
| | - Richard Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; U.S. Department of Agriculture Agricultural Research Service, Ithaca, New York 14853
| | - Olivia Wilkins
- Department of Plant Science, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Siobhan M Brady
- Department of Plant Biology, Genome Center, University of California, Davis, California 95616
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11
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Halliwell LM, Jathoul AP, Bate JP, Worthy HL, Anderson JC, Jones DD, Murray JAH. ΔFlucs: Brighter Photinus pyralis firefly luciferases identified by surveying consecutive single amino acid deletion mutations in a thermostable variant. Biotechnol Bioeng 2017; 115:50-59. [PMID: 28921549 DOI: 10.1002/bit.26451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/05/2022]
Abstract
The bright bioluminescence catalyzed by Photinus pyralis firefly luciferase (Fluc) enables a vast array of life science research such as bio imaging in live animals and sensitive in vitro diagnostics. The effectiveness of such applications is improved using engineered enzymes that to date have been constructed using amino acid substitutions. We describe ΔFlucs: consecutive single amino acid deletion mutants within six loop structures of the bright and thermostable ×11 Fluc. Deletion mutations are a promising avenue to explore new sequence and functional space and isolate novel mutant phenotypes. However, this method is often overlooked and to date there have been no surveys of the effects of consecutive single amino acid deletions in Fluc. We constructed a large semi-rational ΔFluc library and isolated significantly brighter enzymes after finding ×11 Fluc activity was largely tolerant to deletions. Targeting an "omega-loop" motif (T352-G360) significantly enhanced activity, altered kinetics, reduced Km for D-luciferin, altered emission colors, and altered substrate specificity for redshifted analog DL-infraluciferin. Experimental and in silico analyses suggested remodeling of the Ω-loop impacts on active site hydrophobicity to increase light yields. This work demonstrates the further potential of deletion mutations, which can generate useful Fluc mutants and broaden the palette of the biomedical and biotechnological bioluminescence enzyme toolbox.
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Affiliation(s)
| | - Amit P Jathoul
- School of Biosciences, University of Cardiff, Cardiff, UK
| | - Jack P Bate
- School of Biosciences, University of Cardiff, Cardiff, UK
| | | | | | - D Dafydd Jones
- School of Biosciences, University of Cardiff, Cardiff, UK
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12
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Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet 2017; 13:e1006988. [PMID: 28902852 PMCID: PMC5597176 DOI: 10.1371/journal.pgen.1006988] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more complete digestion of chromatin to nucleosomes. We conclude that wide-spectrum analysis of the Arabidopsis genome by differential MNase digestion allows detection of sensitive features hereto obscured, and the comparisons between genome-wide subNSP profiles reveals dynamic changes in their distribution, particularly at distinct genomic locations (i.e. 5'UTRs). The method here employed allows insight into the complex influence of genetic and extrinsic factors in modifying the sub-nucleosomal landscape in association with transcriptional changes.
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Affiliation(s)
- Daniel Antony Pass
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Emily Sornay
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Angela Marchbank
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Margaret R. Crawford
- Genome Centre, University of Sussex, Sussex House, Falmer, Brighton, United Kingdom
| | - Konrad Paszkiewicz
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Nicholas A. Kent
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
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13
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Anderson JC, Grounds H, Jathoul AP, Murray JAH, Pacman SJ, Tisi L. Convergent synthesis and optical properties of near-infrared emitting bioluminescent infra-luciferins. RSC Adv 2017; 7:3975-3982. [PMID: 28496975 PMCID: PMC5361108 DOI: 10.1039/c6ra19541e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/15/2016] [Indexed: 11/21/2022] Open
Abstract
Infra-luciferin, an alkene linked analogue of luciferin, gives bioluminescence emission >700 nm and has the potential to be used for multiparametric in vivo imaging. We report here a high yielding, scalable and convergent synthesis of infra-luciferin which will allow the synthesis of other conjugated luciferins for investigation in near-infrared bioluminescence imaging. We demonstrated this potential by using the new route to synthesise a diene linked analogue of luciferin, the fluorescent and bioluminescent properties of which were compared to those of d-luciferin and infra-luciferin. We found that extension of conjugation to a diene linker resulted in the specific bioluminescence activity being reduced by 3-4 orders of magnitude compared to d-luciferin. Analogous to its fluorescence emission spectrum, the diene linked analogue exhibited two peaks in its bioluminescence spectrum, the major one being slightly blue-shifted compared to natural d-luciferin, and a minor peak at ca. 800 nm. The fluorescence quantum yield and pH dependence of fluorescence were also determined.
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Affiliation(s)
- James C Anderson
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK .
| | - Helen Grounds
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK .
| | - Amit P Jathoul
- School of Biosciences , University of Cardiff , Sir Martin Evans Building, Museum Avenue , Cardiff , CF10 3AX , UK
| | - James A H Murray
- School of Biosciences , University of Cardiff , Sir Martin Evans Building, Museum Avenue , Cardiff , CF10 3AX , UK
| | - Steven J Pacman
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK .
| | - Laurence Tisi
- Erba Diagnostics Mannheim , Unit 4, Cambridgeshire Business Park, Bartholomew's Walk , Ely , CB7 4EA , UK
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14
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Nieuwland J, Stamm P, Wen B, Randall RS, Murray JAH, Bassel GW. Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6. Sci Rep 2016; 6:23586. [PMID: 27021201 PMCID: PMC4810365 DOI: 10.1038/srep23586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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] [Received: 12/02/2015] [Accepted: 02/25/2016] [Indexed: 11/09/2022] Open
Abstract
Seeding establishment following seed germination requires activation of the root meristem for primary root growth. We investigated the hormonal and genetic regulation of root meristem activation during Arabidopsis seed germination. In optimal conditions, radicle cell divisions occur only after the completion of germination and require de novo GA synthesis. When the completion of germination is blocked by ABA, radicle elongation and cell divisions occurred in these non-germinating seeds. Conversely under GA-limiting conditions, ABA-insensitive mutants complete germination in the absence of radicle meristem activation and growth. Radicle meristem activation and extension can therefore occur independently of completion of the developmental transition of germination. The cell cycle regulator KRP6 partially represses GA-dependent activation of the cell cycle. Germination of krp6 mutant seeds occurs more rapidly, is slightly insensitive to ABA in dose-response assays, but also hypersensitive to the GA synthesis inhibitor PAC. These conflicting phenotypes suggest the cell cycle uncouples GA and ABA responses in germinating Arabidopsis seeds, and that KRP6 acts downstream of GA to inhibit mitotic cell cycle activation during germination.
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Affiliation(s)
- Jeroen Nieuwland
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK.,School of Applied Sciences, University of South Wales, Pontypridd, CF37 4AT, United Kingdom
| | - Petra Stamm
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Bo Wen
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Ricardo S Randall
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - James A H Murray
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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15
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Sornay E, Forzani C, Forero-Vargas M, Dewitte W, Murray JAH. Activation of CYCD7;1 in the central cell and early endosperm overcomes cell-cycle arrest in the Arabidopsis female gametophyte, and promotes early endosperm and embryo development. Plant J 2015; 84:41-55. [PMID: 26261067 PMCID: PMC5102630 DOI: 10.1111/tpj.12957] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 04/12/2015] [Revised: 07/15/2015] [Accepted: 07/17/2015] [Indexed: 05/27/2023]
Abstract
In angiosperms, double fertilization of the egg and central cell of the megagametophyte leads to the development of the embryo and endosperm, respectively. Control of cell cycle progression in the megagametophyte is essential for successful fertilization and development. Central cell-targeted expression of the D-type cyclin CYCD7;1 (end CYCD7;1) using the imprinted FWA promoter overcomes cycle arrest of the central cell in the Arabidopsis female gametophyte in the unfertilized ovule, leading to multinucleate central cells at high frequency. Unlike FERTILIZATION-INDEPENDENT SEED (fis) mutants, but similar to lethal RETINOBLASTOMA-RELATED (rbr) mutants, no seed coat development is triggered. Unlike the case with loss of rbr, post-fertilization end CYCD7;1 in the endosperm enhances the number of nuclei during syncytial endosperm development and induces the partial abortion of developing seeds, associated with the enhanced size of the surviving seeds. The frequency of lethality was less than the frequency of multinucleate central cells, indicating that these aspects are not causally linked. These larger seeds contain larger embryos composed of more cells of wild-type size, surrounded by a seed coat composed of more cells. Seedlings arising from these larger seeds displayed faster seedling establishment and early growth. Similarly, two different embryo-lethal mutants also conferred enlarged seed size in surviving siblings, consistent with seed size increase being a general response to sibling lethality, although the cellular mechanisms were found to be distinct. Our data suggest that tight control of CYCD activity in the central cell and in the developing endosperm is required for optimal seed formation.
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Affiliation(s)
- Emily Sornay
- Cardiff School Biosciences, Cardiff University, Sir Martin Evans building, Museum Avenue, Cardiff, CF10 3AX, Wales, UK
| | - Céline Forzani
- Cardiff School Biosciences, Cardiff University, Sir Martin Evans building, Museum Avenue, Cardiff, CF10 3AX, Wales, UK
- Institut Jean-Pierre Bourgin, INRA Centre de Versailles-Grignon, Route de Saint-Cyr, 78026, Versailles, Cedex, France
| | - Manuel Forero-Vargas
- Cardiff School Biosciences, Cardiff University, Sir Martin Evans building, Museum Avenue, Cardiff, CF10 3AX, Wales, UK
- Facultad de Ingenieria, Universidad de Ibagué, Calle Barrio Ambalá, Ibagué, 730002, Colombia
| | - Walter Dewitte
- Cardiff School Biosciences, Cardiff University, Sir Martin Evans building, Museum Avenue, Cardiff, CF10 3AX, Wales, UK
| | - James A H Murray
- Cardiff School Biosciences, Cardiff University, Sir Martin Evans building, Museum Avenue, Cardiff, CF10 3AX, Wales, UK
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16
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Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AAR, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JDG, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JAH, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J. Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol 2015; 208:13-9. [PMID: 26171760 DOI: 10.1111/nph.13532] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [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] [Indexed: 05/02/2023]
Abstract
Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.
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Affiliation(s)
- Nicola J Patron
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Avda Tarongers SN, Valencia, Spain
| | | | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstrasse 4, Darmstadt 64287, Germany
| | - Colette Matthewman
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark Youles
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Oleg Raitskin
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Aymeric Leveau
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gemma Farré
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Christian Rogers
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Smith
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Julian Hibberd
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Alex A R Webb
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - James Locke
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Sebastian Schornack
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Jim Ajioka
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - David C Baulcombe
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | | | - Hannah Kuhn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - H Peter Van Esse
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Dale Sanders
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Giles Oldroyd
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cathie Martin
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rob Field
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah O'Connor
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Samantha Fox
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Brande Wulff
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ben Miller
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Andy Breakspear
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Dominique Loqué
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Avda Tarongers SN, Valencia, Spain
| | - Alain Tissier
- Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, 06120, Halle (Saale), Germany
| | - Patrick Shih
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - W Paul Quick
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Heiko Rischer
- VTT Technical Research Centre of Finland, Espoo 02044, Finland
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christine Raines
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Paul F South
- United States Department of Agriculture, Global Change and Photosynthesis Research Unit, ARS 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Jean-Michel Ané
- Departments of Bacteriology and Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Björn R Hamberger
- Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, Denmark
| | - Harro Bouwmeester
- Wageningen UR, Wageningen University, Wageningen 6700 AA, the Netherlands
| | - Michael Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - James A H Murray
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Vardis Ntoukakis
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Katherine Denby
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Keith J Edwards
- BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Anne Osbourn
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jim Haseloff
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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17
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Randall RS, Miyashima S, Blomster T, Zhang J, Elo A, Karlberg A, Immanen J, Nieminen K, Lee JY, Kakimoto T, Blajecka K, Melnyk CW, Alcasabas A, Forzani C, Matsumoto-Kitano M, Mähönen AP, Bhalerao R, Dewitte W, Helariutta Y, Murray JAH. AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins. Biol Open 2015; 4:1229-36. [PMID: 26340943 PMCID: PMC4610221 DOI: 10.1242/bio.013128] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [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] [Indexed: 01/13/2023] Open
Abstract
Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.
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Affiliation(s)
- Ricardo S Randall
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Shunsuke Miyashima
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Tiina Blomster
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Jing Zhang
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Annakaisa Elo
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Anna Karlberg
- Department of Plant Physiology, Umeå University, Umeå SE-901 87, Sweden
| | - Juha Immanen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Kaisa Nieminen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Tatsuo Kakimoto
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Karolina Blajecka
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Charles W Melnyk
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Annette Alcasabas
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Celine Forzani
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Miho Matsumoto-Kitano
- Department of Biological Sciences, Osaka University, Graduate School of Science, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ari Pekka Mähönen
- Department of Biosciences, Institute of Biotechnology, Viikinkaari 1 (P.O.Box 65), 00014, University of Helsinki, Helsinki, Finland
| | | | - Walter Dewitte
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
| | - Ykä Helariutta
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - James A H Murray
- Department of Molecular Biosciences, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales CF10 3AX, UK
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Randall RS, Sornay E, Dewitte W, Murray JAH. AINTEGUMENTA and the D-type cyclin CYCD3;1 independently contribute to petal size control in Arabidopsis: evidence for organ size compensation being an emergent rather than a determined property. J Exp Bot 2015; 66:3991-4000. [PMID: 25948704 PMCID: PMC4473993 DOI: 10.1093/jxb/erv200] [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] [Indexed: 05/03/2023]
Abstract
Plant lateral aerial organ (LAO) growth is determined by the number and size of cells comprising the organ. Genetic alteration of one parameter is often accompanied by changes in the other, such that the overall effect on final LAO size is minimized, suggested to be caused by an active organ level 'compensation mechanism'. For example, the aintegumenta (ant) mutant exhibits reduced cell number but increased cell size in LAOs. The ANT transcription factor regulates the duration of the cell division phase of LAO growth, and its ectopic expression is correlated with increased levels of the cell cycle regulator CYCD3;1. This has previously led to the suggestion that ANT regulates CYCD3;1. It is shown here that while ANT is required for normal cell proliferation in petals, CYCD3;1 is not, suggesting that ANT does not regulate CYCD3;1 during petal growth. Moreover CYCD3;1 expression was similar in wild-type and ant-9 flowers. In contrast to the compensatory changes between cell size and number in ant mutants, cycd3;1 mutants show increased petal cell size unaccompanied by changes in cell number, leading to larger organs. However, loss of CYCD3;1 in the ant-9 mutant background leads to a phenotype consistent with compensation mechanisms. These apparently arbitrary examples of compensation are reconciled through a model of LAO growth in which distinct phases of division and cell expansion occupy differing lengths of a defined overall growth window. This leads to the proposal that many observations of 'compensation mechanisms' might alternatively be more simply explained as emergent properties of LAO development.
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Affiliation(s)
- Ricardo S Randall
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Emily Sornay
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Walter Dewitte
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
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Galletti R, Johnson KL, Scofield S, San-Bento R, Watt AM, Murray JAH, Ingram GC. DEFECTIVE KERNEL 1 promotes and maintains plant epidermal differentiation. Development 2015; 142:1978-83. [PMID: 25953348 DOI: 10.1242/dev.122325] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
During plant epidermal development, many cell types are generated from protodermal cells, a process requiring complex co-ordination of cell division, growth, endoreduplication and the acquisition of differentiated cellular morphologies. Here we show that the Arabidopsis phytocalpain DEFECTIVE KERNEL 1 (DEK1) promotes the differentiated epidermal state. Plants with reduced DEK1 activity produce cotyledon epidermis with protodermal characteristics, despite showing normal growth and endoreduplication. Furthermore, in non-embryonic tissues (true leaves, sepals), DEK1 is required for epidermis differentiation maintenance. We show that the HD-ZIP IV family of epidermis-specific differentiation-promoting transcription factors are key, albeit indirect, targets of DEK1 activity. We propose a model in which DEK1 influences HD-ZIP IV gene expression, and thus epidermis differentiation, by promoting cell adhesion and communication in the epidermis.
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Affiliation(s)
- Roberta Galletti
- Laboratoire de Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, Lyon 69364, Cedex 07, France
| | - Kim L Johnson
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Royal Parade, Parkville, Victoria 3010, Australia
| | - Simon Scofield
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Rita San-Bento
- Laboratoire de Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, Lyon 69364, Cedex 07, France
| | - Andrea M Watt
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Royal Parade, Parkville, Victoria 3010, Australia
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Gwyneth C Ingram
- Laboratoire de Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, Lyon 69364, Cedex 07, France
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Forzani C, Aichinger E, Sornay E, Willemsen V, Laux T, Dewitte W, Murray JAH. WOX5 suppresses CYCLIN D activity to establish quiescence at the center of the root stem cell niche. Curr Biol 2014; 24:1939-44. [PMID: 25127220 PMCID: PMC4148176 DOI: 10.1016/j.cub.2014.07.019] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/09/2014] [Accepted: 07/08/2014] [Indexed: 11/28/2022]
Abstract
In Arabidopsis, stem cells maintain the provision of new cells for root growth. They surround a group of slowly dividing cells named the quiescent center (QC), and, together, they form the stem cell niche (SCN). The QC acts as the signaling center of the SCN, repressing differentiation of the surrounding stem cells [1] and providing a pool of cells able to replace damaged stem cells [2, 3]. Maintenance of the stem cells depends on the transcription factor WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the QC [4]. However, the molecular mechanisms by which WOX5 promotes stem cell fate and whether WOX5 regulates proliferation of the QC are unknown. Here, we reveal a new role for WOX5 in restraining cell division in the cells of the QC, thereby establishing quiescence. In contrast, WOX5 and CYCD3;3/CYCD1;1 both promote cell proliferation in the nascent columella. The additional QC divisions occurring in wox5 mutants are suppressed in mutant combinations with the D type cyclins CYCD3;3 and CYCD1;1. Moreover, ectopic expression of CYCD3;3 in the QC is sufficient to induce cell division in the QC. WOX5 thus suppresses QC divisions that are otherwise promoted by CYCD3;3 and CYCD1;1, in part by interacting with the CYCD3;3 promoter to repress CYCD3;3 expression in the QC. Therefore, we propose a specific role for WOX5 in initiating and maintaining quiescence of the QC by excluding CYCD activity from the QC. WOX5 prevents divisions at the root stem cell niche center to initiate quiescence WOX5 suppresses CYCD expression in the quiescent center to restrict cell divisions WOX5 binds to the CYCD3;3 promoter CYCD3;3 and CYCD1;1 stimulate division during formation of the columella
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Affiliation(s)
- Celine Forzani
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Ernst Aichinger
- Faculty of Biology, BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Emily Sornay
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Thomas Laux
- Faculty of Biology, BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Walter Dewitte
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK.
| | - James A H Murray
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK.
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Patzewitz EM, Salcedo-Sora JE, Wong EH, Sethia S, Stocks PA, Maughan SC, Murray JAH, Krishna S, Bray PG, Ward SA, Müller S. Glutathione transport: a new role for PfCRT in chloroquine resistance. Antioxid Redox Signal 2013; 19:683-95. [PMID: 23256874 PMCID: PMC3739961 DOI: 10.1089/ars.2012.4625] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIMS Chloroquine (CQ) kills Plasmodium falciparum by binding heme, preventing its detoxification to hemozoin in the digestive vacuole (DV) of the parasite. CQ resistance (CQR) is associated with mutations in the DV membrane protein P. falciparum chloroquine resistance transporter (PfCRT), mediating the leakage of CQ from the DV. However, additional factors are thought to contribute to the resistance phenotype. This study tested the hypothesis that there is a link between glutathione (GSH) and CQR. RESULTS Using isogenic parasite lines carrying wild-type or mutant pfcrt, we reveal lower levels of GSH in the mutant lines and enhanced sensitivity to the GSH synthesis inhibitor l-buthionine sulfoximine, without any alteration in cytosolic de novo GSH synthesis. Incubation with N-acetylcysteine resulted in increased GSH levels in all parasites, but only reduced susceptibility to CQ in PfCRT mutant-expressing lines. In support of a heme destruction mechanism involving GSH in CQR parasites, we also found lower hemozoin levels and reduced CQ binding in the CQR PfCRT-mutant lines. We further demonstrate via expression in Xenopus laevis oocytes that the mutant alleles of Pfcrt in CQR parasites selectively transport GSH. INNOVATION We propose a mechanism whereby mutant pfcrt allows enhanced transport of GSH into the parasite's DV. The elevated levels of GSH in the DV reduce the level of free heme available for CQ binding, which mediates the lower susceptibility to CQ in the PfCRT mutant parasites. CONCLUSION PfCRT has a dual role in CQR, facilitating both efflux of harmful CQ from the DV and influx of beneficial GSH into the DV.
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Affiliation(s)
- Eva-Maria Patzewitz
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Scofield S, Dewitte W, Nieuwland J, Murray JAH. The Arabidopsis homeobox gene SHOOT MERISTEMLESS has cellular and meristem-organisational roles with differential requirements for cytokinin and CYCD3 activity. Plant J 2013; 75:53-66. [PMID: 23573875 DOI: 10.1111/tpj.12198] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 03/28/2013] [Accepted: 04/04/2013] [Indexed: 06/02/2023]
Abstract
The Arabidopsis class-1 KNOX gene SHOOT MERISTEMLESS (STM) encodes a homeodomain transcription factor essential for shoot apical meristem (SAM) formation and sustained activity. STM activates cytokinin (CK) biosynthesis in the SAM, but the extent to which STM function is mediated through CK is unclear. Here we show that STM inhibits cellular differentiation and endoreduplication, acting through CK and the CK-inducible CYCD3 cell cycle regulators, establishing a mechanistic link to cell cycle control which provides sustained mitotic activity to maintain a pool of undifferentiated cells in the SAM. Equivalent functions are revealed for the related KNOX genes KNAT1/BP and KNAT2 through ectopic expression. STM is also required for proper meristem organisation and can induce de novo meristem formation when expressed ectopically, even when CK levels are reduced or CK signaling is impaired. This function in meristem establishment and organisation can be replaced by KNAT1/BP, but not KNAT2, despite its activation of CK responses, suggesting that promotion of CK responses alone is insufficient for SAM organisation. We propose that STM has dual cellular and meristem-organisational functions that are differentially represented in the class-1 KNOX gene family and have differing requirements for CK and CYCD3.
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Affiliation(s)
- Simon Scofield
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Walter Dewitte
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Jeroen Nieuwland
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
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Wen B, Nieuwland J, Murray JAH. The Arabidopsis CDK inhibitor ICK3/KRP5 is rate limiting for primary root growth and promotes growth through cell elongation and endoreduplication. J Exp Bot 2013; 64:1135-44. [PMID: 23440171 PMCID: PMC3580825 DOI: 10.1093/jxb/ert009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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] [Indexed: 05/24/2023]
Abstract
The coordination of plant cell division and expansion controls plant morphogenesis, development, and growth. Cyclin-dependent kinases (CDKs) are not only key regulators of cell division but also play an important role in cell differentiation. In plants, CDK activity is modulated by the binding of INHIBITOR OF CDK/KIP-RELATED PROTEIN (ICK/KRP). Previously, ICK2/KRP2 has been shown to mediate auxin responses in lateral root initiation. Here are analysed the roles of all ICK/KRP genes in root growth. Analysis of ick/krp null-mutants revealed that only ick3/krp5 was affected in primary root growth. ICK3/KRP5 is strongly expressed in the root apical meristem (RAM), with lower expression in the expansion zone. ick3/krp5 roots grow more slowly than wildtype controls, and this results not from reduction of division in the proliferative region of the RAM but rather reduced expansion as cells exit the meristem. This leads to shorter final cell lengths in different tissues of the ick3/krp5 mutant root, particularly the epidermal non-hair cells, and this reduction in cell size correlates with reduced endoreduplication. Loss of ICK3/KRP5 also leads to delayed germination and in the mature embryo ICK3/KRP5 is specifically expressed in the transition zone between root and hypocotyl. Cells in the transition zone were smaller in the ick3/krp5 mutant, despite the absence of endoreduplication in the embryo suggesting a direct effect of ICK3/KRP5 on cell growth. It is concluded that ICK3/KRP5 is a positive regulator of both cell growth and endoreduplication.
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Affiliation(s)
- Bo Wen
- Present address: Shanxi Agricultural University, Taigu, Shanxi, 030801, PR China
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Cruz-Ramírez A, Díaz-Triviño S, Blilou I, Grieneisen VA, Sozzani R, Zamioudis C, Miskolczi P, Nieuwland J, Benjamins R, Dhonukshe P, Caballero-Pérez J, Horvath B, Long Y, Mähönen AP, Zhang H, Xu J, Murray JAH, Benfey PN, Bako L, Marée AFM, Scheres B. A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell 2012; 150:1002-15. [PMID: 22921914 DOI: 10.1016/j.cell.2012.07.017] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [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] [Received: 07/05/2011] [Revised: 05/24/2012] [Accepted: 07/11/2012] [Indexed: 12/21/2022]
Abstract
In plants, where cells cannot migrate, asymmetric cell divisions (ACDs) must be confined to the appropriate spatial context. We investigate tissue-generating asymmetric divisions in a stem cell daughter within the Arabidopsis root. Spatial restriction of these divisions requires physical binding of the stem cell regulator SCARECROW (SCR) by the RETINOBLASTOMA-RELATED (RBR) protein. In the stem cell niche, SCR activity is counteracted by phosphorylation of RBR through a cyclinD6;1-CDK complex. This cyclin is itself under transcriptional control of SCR and its partner SHORT ROOT (SHR), creating a robust bistable circuit with either high or low SHR-SCR complex activity. Auxin biases this circuit by promoting CYCD6;1 transcription. Mathematical modeling shows that ACDs are only switched on after integration of radial and longitudinal information, determined by SHR and auxin distribution, respectively. Coupling of cell-cycle progression to protein degradation resets the circuit, resulting in a "flip flop" that constrains asymmetric cell division to the stem cell region.
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Affiliation(s)
- Alfredo Cruz-Ramírez
- Molecular Genetics, Department of Biology, University of Utrecht, 3584 CH Utrecht, The Netherlands
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Collins C, Dewitte W, Murray JAH. D-type cyclins control cell division and developmental rate during Arabidopsis seed development. J Exp Bot 2012; 63:3571-86. [PMID: 22412186 PMCID: PMC3388828 DOI: 10.1093/jxb/ers015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [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: 12/13/2011] [Revised: 12/13/2011] [Accepted: 01/10/2012] [Indexed: 05/20/2023]
Abstract
Seed development in Arabidopsis is characterized by stereotypical division patterns, suggesting that coordinated control of cell cycle may be required for correct patterning and growth of the embryo and endosperm. D-type cyclins (CYCD) are key cell cycle regulators with roles in developmental processes, but knowledge regarding their involvement in seed development remains limited. Here, a family-wide gene expression, and loss- and gain-of-function approach was adopted to reveal additional functions for CYCDs in the development of seed tissues. CYCD genes have both discrete and overlapping tissue-specific expression patterns in the seed as revealed by GUS reporter gene expression. Analysis of different mutant combinations revealed that correct CYCD levels are required in seed development. The CYCD3 subgroup is specifically required as its loss caused delayed development, whereas overexpression in the embryo and endosperm of CYCD3;1 or a previously uncharacterized gene, CYCD7;1, variously leads to induced proliferation, abnormal phenotypes, and elevated seed abortion. CYCD3;1 overexpression provoked a delay in embryonic developmental progression and abnormalities including additional divisions of the hypophysis and suspensor, regions where CYCD3 genes are normally expressed, but did not affect endosperm development. Overexpression of CYCD7;1, not normally expressed in seed development, promoted overgrowth of both embryo and endosperm through increased division and cell enlargement. In contrast to post-germination growth, where pattern and organ size is not generally related to division, results suggest that a close control of cell division through regulation of CYCD activity is important during seed development in conferring both developmental rate and correct patterning.
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Affiliation(s)
- Carl Collins
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
- To whom correspondence should be addressed. E-mail: or
| | - Walter Dewitte
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - James A. H. Murray
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
- To whom correspondence should be addressed. E-mail: or
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Kiddle G, Hardinge P, Buttigieg N, Gandelman O, Pereira C, McElgunn CJ, Rizzoli M, Jackson R, Appleton N, Moore C, Tisi LC, Murray JAH. GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use. BMC Biotechnol 2012; 12:15. [PMID: 22546148 PMCID: PMC3388468 DOI: 10.1186/1472-6750-12-15] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [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] [Received: 11/01/2011] [Accepted: 04/30/2012] [Indexed: 11/12/2022] Open
Abstract
Background There is an increasing need for quantitative technologies suitable for molecular detection in a variety of settings for applications including food traceability and monitoring of genetically modified (GM) crops and their products through the food processing chain. Conventional molecular diagnostics utilising real-time polymerase chain reaction (RT-PCR) and fluorescence-based determination of amplification require temperature cycling and relatively complex optics. In contrast, isothermal amplification coupled to a bioluminescent output produced in real-time (BART) occurs at a constant temperature and only requires a simple light detection and integration device. Results Loop mediated isothermal amplification (LAMP) shows robustness to sample-derived inhibitors. Here we show the applicability of coupled LAMP and BART reactions (LAMP-BART) for determination of genetically modified (GM) maize target DNA at low levels of contamination (0.1-5.0% GM) using certified reference material, and compare this to RT-PCR. Results show that conventional DNA extraction methods developed for PCR may not be optimal for LAMP-BART quantification. Additionally, we demonstrate that LAMP is more tolerant to plant sample-derived inhibitors, and show this can be exploited to develop rapid extraction techniques suitable for simple field-based qualitative tests for GM status determination. We also assess the effect of total DNA assay load on LAMP-BART quantitation. Conclusions LAMP-BART is an effective and sensitive technique for GM detection with significant potential for quantification even at low levels of contamination and in samples derived from crops such as maize with a large genome size. The resilience of LAMP-BART to acidic polysaccharides makes it well suited to rapid sample preparation techniques and hence to both high throughput laboratory settings and to portable GM detection applications. The impact of the plant sample matrix and genome loading within a reaction must be controlled to ensure quantification at low target concentrations.
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Affiliation(s)
- Guy Kiddle
- Lumora Ltd, Bartholomew Walk, Cambridgeshire Business Park, Ely, Cambridgeshire CB7 4EA, UK.
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Umbrasaite J, Schweighofer A, Kazanaviciute V, Magyar Z, Ayatollahi Z, Unterwurzacher V, Choopayak C, Boniecka J, Murray JAH, Bogre L, Meskiene I. MAPK phosphatase AP2C3 induces ectopic proliferation of epidermal cells leading to stomata development in Arabidopsis. PLoS One 2010; 5:e15357. [PMID: 21203456 PMCID: PMC3009721 DOI: 10.1371/journal.pone.0015357] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 11/15/2010] [Indexed: 12/21/2022] Open
Abstract
In plant post-embryonic epidermis mitogen-activated protein kinase (MAPK) signaling promotes differentiation of pavement cells and inhibits initiation of stomata. Stomata are cells specialized to modulate gas exchange and water loss. Arabidopsis MAPKs MPK3 and MPK6 are at the core of the signaling cascade; however, it is not well understood how the activity of these pleiotropic MAPKs is constrained spatially so that pavement cell differentiation is promoted only outside the stomata lineage. Here we identified a PP2C-type phosphatase termed AP2C3 (Arabidopsis protein phosphatase 2C) that is expressed distinctively during stomata development as well as interacts and inactivates MPK3, MPK4 and MPK6. AP2C3 co-localizes with MAPKs within the nucleus and this localization depends on its N-terminal extension. We show that other closely related phosphatases AP2C2 and AP2C4 are also MAPK phosphatases acting on MPK6, but have a distinct expression pattern from AP2C3. In accordance with this, only AP2C3 ectopic expression is able to stimulate cell proliferation leading to excess stomata development. This function of AP2C3 relies on the domains required for MAPK docking and intracellular localization. Concomitantly, the constitutive and inducible AP2C3 expression deregulates E2F-RB pathway, promotes the abundance and activity of CDKA, as well as changes of CDKB1;1 forms. We suggest that AP2C3 downregulates the MAPK signaling activity to help maintain the balance between differentiation of stomata and pavement cells.
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Affiliation(s)
- Julija Umbrasaite
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Alois Schweighofer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Vaiva Kazanaviciute
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- Institute of Biotechnology, University of Vilnius, Vilnius, Lithuania
| | - Zoltan Magyar
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Zahra Ayatollahi
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | | | - Chonnanit Choopayak
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Justyna Boniecka
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Laszlo Bogre
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Irute Meskiene
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- Institute of Biotechnology, University of Vilnius, Vilnius, Lithuania
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Gandelman OA, Church VL, Moore CA, Kiddle G, Carne CA, Parmar S, Jalal H, Tisi LC, Murray JAH. Novel bioluminescent quantitative detection of nucleic acid amplification in real-time. PLoS One 2010; 5:e14155. [PMID: 21152399 PMCID: PMC2994769 DOI: 10.1371/journal.pone.0014155] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [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: 05/24/2010] [Accepted: 10/18/2010] [Indexed: 11/18/2022] Open
Abstract
Background The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. Principal Findings Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs) enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART) continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi) produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi) produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. Conclusions The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a simple light detector, the iNAAT-BART combination is ideal for molecular diagnostic assays in both laboratory and low resource settings.
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Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JAH, Benfey PN. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 2010; 466:128-32. [PMID: 20596025 DOI: 10.1038/nature09143] [Citation(s) in RCA: 289] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 04/28/2010] [Indexed: 12/18/2022]
Abstract
The development of multicellular organisms relies on the coordinated control of cell divisions leading to proper patterning and growth. The molecular mechanisms underlying pattern formation, particularly the regulation of formative cell divisions, remain poorly understood. In Arabidopsis, formative divisions generating the root ground tissue are controlled by SHORTROOT (SHR) and SCARECROW (SCR). Here we show, using cell-type-specific transcriptional effects of SHR and SCR combined with data from chromatin immunoprecipitation-based microarray experiments, that SHR regulates the spatiotemporal activation of specific genes involved in cell division. Coincident with the onset of a specific formative division, SHR and SCR directly activate a D-type cyclin; furthermore, altering the expression of this cyclin resulted in formative division defects. Our results indicate that proper pattern formation is achieved through transcriptional regulation of specific cell-cycle genes in a cell-type- and developmental-stage-specific context. Taken together, we provide evidence for a direct link between developmental regulators, specific components of the cell-cycle machinery and organ patterning.
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Affiliation(s)
- R Sozzani
- Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
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Lee TJ, Pascuzzi PE, Settlage SB, Shultz RW, Tanurdzic M, Rabinowicz PD, Menges M, Zheng P, Main D, Murray JAH, Sosinski B, Allen GC, Martienssen RA, Hanley-Bowdoin L, Vaughn MW, Thompson WF. Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genet 2010; 6:e1000982. [PMID: 20548960 PMCID: PMC2883604 DOI: 10.1371/journal.pgen.1000982] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 05/12/2010] [Indexed: 12/23/2022] Open
Abstract
DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins. During growth and development, all plants and animals must replicate their DNA. This process is regulated to ensure that all sequences are completely and accurately replicated and is limited to S phase of the cell cycle. In the cell, DNA is packaged with histone proteins into chromatin, and both DNA and histones are subject to epigenetic modifications that affect chromatin state. Euchromatin and heterochromatin are chromatin states marked by epigenetic modifications specifying open and closed conformations, respectively. Using the model plant Arabidopsis thaliana, we show that the time at which a DNA sequence replicates is influenced by the epigenetic modifications to the surrounding chromatin. DNA replication occurs in two phases, with euchromatin replicating in early and mid S phase and heterochromatin replicating late. DNA replication time has been linked to gene expression in other organisms, and this is also true in Arabidopsis because more genes are active in euchromatin when compared to heterochromatin. The earliest replicating DNA sequences are associated with acetylation of histone H3 on lysine 56 (H3K56ac). H3K56ac is also abundant in active genes, but the patterns of association of H3K56ac with gene expression and DNA replication are distinct, suggesting that H3K56ac is independently linked to both processes.
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Affiliation(s)
- Tae-Jin Lee
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Pete E. Pascuzzi
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sharon B. Settlage
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Randall W. Shultz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Milos Tanurdzic
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Pablo D. Rabinowicz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Margit Menges
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Ping Zheng
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - James A. H. Murray
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Bryon Sosinski
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - George C. Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Linda Hanley-Bowdoin
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Matthew W. Vaughn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - William F. Thompson
- Departments of Plant Biology, Genetics, and Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Maughan SC, Pasternak M, Cairns N, Kiddle G, Brach T, Jarvis R, Haas F, Nieuwland J, Lim B, Müller C, Salcedo-Sora E, Kruse C, Orsel M, Hell R, Miller AJ, Bray P, Foyer CH, Murray JAH, Meyer AJ, Cobbett CS. Plant homologs of the Plasmodium falciparum chloroquine-resistance transporter, PfCRT, are required for glutathione homeostasis and stress responses. Proc Natl Acad Sci U S A 2010; 107:2331-6. [PMID: 20080670 PMCID: PMC2836691 DOI: 10.1073/pnas.0913689107] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Arabidopsis thaliana, biosynthesis of the essential thiol antioxidant, glutathione (GSH), is plastid-regulated, but many GSH functions, including heavy metal detoxification and plant defense activation, depend on cytosolic GSH. This finding suggests that plastid and cytosol thiol pools are closely integrated and we show that in Arabidopsis this integration requires a family of three plastid thiol transporters homologous to the Plasmodium falciparum chloroquine-resistance transporter, PfCRT. Arabidopsis mutants lacking these transporters are heavy metal-sensitive, GSH-deficient, and hypersensitive to Phytophthora infection, confirming a direct requirement for correct GSH homeostasis in defense responses. Compartment-specific measurements of the glutathione redox potential using redox-sensitive GFP showed that knockout of the entire transporter family resulted in a more oxidized glutathione redox potential in the cytosol, but not in the plastids, indicating the GSH-deficient phenotype is restricted to the cytosolic compartment. Expression of the transporters in Xenopus oocytes confirmed that each can mediate GSH uptake. We conclude that these transporters play a significant role in regulating GSH levels and the redox potential of the cytosol.
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Affiliation(s)
- Spencer C Maughan
- Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, United Kingdom.
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de Jager SM, Scofield S, Huntley RP, Robinson AS, den Boer BGW, Murray JAH. Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc. Plant Mol Biol 2009; 71:345-65. [PMID: 19662336 DOI: 10.1007/s11103-009-9527-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 07/13/2009] [Indexed: 05/10/2023]
Abstract
Activation of E2F transcription factors at the G1-to-S phase boundary, with the resultant expression of genes needed for DNA synthesis and S-phase, is due to phosphorylation of the retinoblastoma-related (RBR) protein by cyclin D-dependent kinase (CYCD-CDK), particularly CYCD3-CDKA. Arabidopsis has three canonical E2F genes, of which E2Fa and E2Fb are proposed to encode transcriptional activators and E2Fc a repressor. Previous studies have identified genes regulated in response to high-level constitutive expression of E2Fa and of CYCD3;1, but such plants display significant phenotypic abnormalities. We have sought to identify targets that show responses to lower level induced changes in abundance of these cell cycle regulators. Expression of E2Fa, E2Fc or CYCD3;1 was induced using dexamethasone and the effects analysed using microarrays in a time course allowing short and longer term effects to be observed. Overlap between CYCD3;1 and E2Fa modulated genes substantiates their action in a common pathway with a key role in controlling the G1/S transition, with additional targets for CYCD3;1 in chromatin modification and for E2Fa in cell wall biogenesis and development. E2Fc induction led primarily to gene downregulation, but did not antagonise E2Fa action and hence E2Fc appears to function outside the CYCD3-RBR pathway, does not have a direct effect on cell cycle genes, and promoter analysis suggests a distinct binding site preference.
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Affiliation(s)
- Sarah M de Jager
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
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Tromas A, Braun N, Muller P, Khodus T, Paponov IA, Palme K, Ljung K, Lee JY, Benfey P, Murray JAH, Scheres B, Perrot-Rechenmann C. The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth. PLoS One 2009; 4:e6648. [PMID: 19777056 PMCID: PMC2744284 DOI: 10.1371/journal.pone.0006648] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 07/13/2009] [Indexed: 12/18/2022] Open
Abstract
Background In plants, the phytohormone auxin is a crucial regulator sustaining growth and development. At the cellular level, auxin is interpreted differentially in a tissue- and dose-dependent manner. Mechanisms of auxin signalling are partially unknown and the contribution of the AUXIN BINDING PROTEIN 1 (ABP1) as an auxin receptor is still a matter of debate. Methodology/Principal Findings Here we took advantage of the present knowledge of the root biological system to demonstrate that ABP1 is required for auxin response. The use of conditional ABP1 defective plants reveals that the protein is essential for maintenance of the root meristem and acts at least on the D-type CYCLIN/RETINOBLASTOMA pathway to control entry into the cell cycle. ABP1 affects PLETHORA gradients and confers auxin sensitivity to root cells thus defining the competence of the cells to be maintained within the meristem or to elongate. ABP1 is also implicated in the regulation of gene expression in response to auxin. Conclusions/Significance Our data support that ABP1 is a key regulator for root growth and is required for auxin-mediated responses. Differential effects of ABP1 on various auxin responses support a model in which ABP1 is the major regulator for auxin action on the cell cycle and regulates auxin-mediated gene expression and cell elongation in addition to the already well known TIR1-mediated ubiquitination pathway.
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Affiliation(s)
- Alexandre Tromas
- Institut des Sciences du Végétal, CNRS UPR2355, Université Paris Sud Orsay, Gif sur Yvette, France
| | - Nils Braun
- Institut des Sciences du Végétal, CNRS UPR2355, Université Paris Sud Orsay, Gif sur Yvette, France
- Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Philippe Muller
- Institut des Sciences du Végétal, CNRS UPR2355, Université Paris Sud Orsay, Gif sur Yvette, France
| | - Tatyana Khodus
- Institut für Biology II – Zellbiologie Universität Freiburg, Freiburg, Germany
| | - Ivan A. Paponov
- Institut für Biology II – Zellbiologie Universität Freiburg, Freiburg, Germany
| | - Klaus Palme
- Institut für Biology II – Zellbiologie Universität Freiburg, Freiburg, Germany
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Sveriges Lantbruksuniversitet, Umeå, Sweden
| | - Ji-Young Lee
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Philip Benfey
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - James A. H. Murray
- Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Ben Scheres
- Department of Molecular Cell Biology, Utrecht University, Utrecht, The Netherlands
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Nieuwland J, Scofield S, Murray JAH. Control of division and differentiation of plant stem cells and their derivatives. Semin Cell Dev Biol 2009; 20:1134-42. [PMID: 19770062 DOI: 10.1016/j.semcdb.2009.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 09/12/2009] [Accepted: 09/14/2009] [Indexed: 01/10/2023]
Abstract
The core mechanism of the plant cell cycle is conserved with all other eukaryotes but several aspects are unique to plant cells. Key characteristics of plant development include indeterminate growth and repetitive organogenesis derived from stem cell pools and they may explain the existence of the high number of cell cycle regulators in plants. In this review, we give an overview of the plant cell cycle and its regulatory components. Furthermore, we discuss the cell cycle aspects of plant stem cell maintenance and how the cell cycle relates to cellular differentiation during development. We exemplify this transition by focusing on organ initiation in the shoot.
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Affiliation(s)
- Jeroen Nieuwland
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
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López-Juez E, Dillon E, Magyar Z, Khan S, Hazeldine S, de Jager SM, Murray JAH, Beemster GTS, Bögre L, Shanahan H. Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis. Plant Cell 2008; 20:947-68. [PMID: 18424613 PMCID: PMC2390750 DOI: 10.1105/tpc.107.057075] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 02/19/2008] [Accepted: 03/24/2008] [Indexed: 05/19/2023]
Abstract
In darkness, shoot apex growth is repressed, but it becomes rapidly activated by light. We show that phytochromes and cryptochromes play largely redundant roles in this derepression in Arabidopsis thaliana. We examined the light activation of transcriptional changes in a finely resolved time course, comparing the shoot apex (meristem and leaf primordia) and the cotyledon and found >5700 differentially expressed genes. Early events specific to the shoot apices included the repression of genes for Really Interesting New Gene finger proteins and basic domain/leucine zipper and basic helix-loop-helix transcription factors. The downregulation of auxin and ethylene and the upregulation of cytokinin and gibberellin hormonal responses were also characteristic of shoot apices. In the apex, genes involved in ribosome biogenesis and protein translation were rapidly and synchronously induced, simultaneously with cell proliferation genes, preceding visible organ growth. Subsequently, the activation of signaling genes and transcriptional signatures of cell wall expansion, turgor generation, and plastid biogenesis were apparent. Furthermore, light regulates the forms and protein levels of two transcription factors with opposing functions in cell proliferation, E2FB and E2FC, through the Constitutively Photomorphogenic1 (COP1), COP9-Signalosome5, and Deetiolated1 light signaling molecules. These data provide the basis for reconstruction of the regulatory networks for light-regulated meristem, leaf, and cotyledon development.
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Affiliation(s)
- Enrique López-Juez
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom.
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Ren H, Santner A, del Pozo JC, Murray JAH, Estelle M. Degradation of the cyclin-dependent kinase inhibitor KRP1 is regulated by two different ubiquitin E3 ligases. Plant J 2008; 53:705-16. [PMID: 18005227 DOI: 10.1111/j.1365-313x.2007.03370.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In animals and fungi, a group of proteins called the cyclin-dependent kinase inhibitors play a key role in cell cycle regulation. However, comparatively little is known about the role of these proteins in plant cell cycle regulation. To gain insight into the mechanisms by which the plant cell cycle is regulated, we studied the cyclin-dependent kinase inhibitor KRP1 in Arabidopsis. KRP1 interacts with the CDKA;1/CYCD2;1 complex in planta and functions in the G1-S transition of the cell cycle. Furthermore, we show that KRP1 is a likely target of the ubiquitin/proteasome pathway. Two different ubiquitin protein ligases, SCF(SKP2) and the RING protein RKP, contribute to its degradation. These results suggest that SCF(SKP2b) and RPK play an important role in the cell cycle through regulating KRP1 protein turnover.
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Affiliation(s)
- Hong Ren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Paponov IA, Paponov M, Teale W, Menges M, Chakrabortee S, Murray JAH, Palme K. Comprehensive transcriptome analysis of auxin responses in Arabidopsis. Mol Plant 2008; 1:321-37. [PMID: 19825543 DOI: 10.1093/mp/ssm021] [Citation(s) in RCA: 212] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In plants, the hormone auxin shapes gene expression to regulate growth and development. Despite the detailed characterization of auxin-inducible genes, a comprehensive overview of the temporal and spatial dynamics of auxin-regulated gene expression is lacking. Here, we analyze transcriptome data from many publicly available Arabidopsis profiling experiments and assess tissue-specific gene expression both in response to auxin concentration and exposure time and in relation to other plant growth regulators. Our analysis shows that the primary response to auxin over a wide range of auxin application conditions and in specific tissues comprises almost exclusively the up-regulation of genes and identifies the most robust auxin marker genes. Tissue-specific auxin responses correlate with differential expression of Aux/IAA genes and the subsequent regulation of context- and sequence-specific patterns of gene expression. Changes in transcript levels were consistent with a distinct sequence of conjugation, increased transport capacity and down-regulation of biosynthesis in the temperance of high cellular auxin concentrations. Our data show that auxin regulates genes associated with the biosynthesis, catabolism and signaling pathways of other phytohormones. We present a transcriptional overview of the auxin response. Specific interactions between auxin and other phytohormones are highlighted, particularly the regulation of their metabolism. Our analysis provides a roadmap for auxin-dependent processes that underpins the concept of an 'auxin code'--a tissue-specific fingerprint of gene expression that initiates specific developmental processes.
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Affiliation(s)
- Ivan A Paponov
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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Menges M, Dóczi R, Ökrész L, Morandini P, Mizzi L, Soloviev M, Murray JAH, Bögre L. Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. New Phytol 2008; 179:643-662. [PMID: 18715324 DOI: 10.1111/j.1469-8137.2008.02552.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
* Mitogen activated protein kinase (MAPK) pathways are signal transduction modules with layers of protein kinases having c. 120 genes in Arabidopsis, but only a few have been linked experimentally to functions. * We analysed microarray expression data for 114 MAPK signalling genes represented on the ATH1 Affymetrix arrays; determined their expression patterns during development, and in a wide range of time-course microarray experiments for their signal-dependent transcriptional regulation and their coregulation with other signalling components and transcription factors. * Global expression correlation of the MAPK genes with each of the represented 21 692 Arabidopsis genes was determined by calculating Pearson correlation coefficients. To group MAPK signalling genes based on similarities in global regulation, we performed hierarchical clustering on the pairwise correlation values. This should allow inferring functional information from well-studied MAPK components to functionally uncharacterized ones. Statistical overrepresentation of specific gene ontology (GO) categories in the gene lists showing high expression correlation values with each of the MAPK components predicted biological themes for the gene functions. * The combination of these methods provides functional information for many uncharacterized MAPK genes, and a framework for complementary future experimental dissection of the function of this complex family.
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Affiliation(s)
- Margit Menges
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
| | - Róbert Dóczi
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - László Ökrész
- Institute of Plant Biology, Biological Research Centre, POB 521, H-6701, Szeged, Hungary
| | - Piero Morandini
- Department of Biology, University of Milan and CNR Biophysics Institute (Milan Section), Via Celoria 26, I-20133 Milan, Italy
| | - Luca Mizzi
- Department of Biomolecular Sciences and Biotechnology, University of Milan and CNR Biophysics Institute (Milan Section), Via Celoria 26, I-20133 Milan, Italy
| | - Mikhail Soloviev
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - James A H Murray
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
| | - László Bögre
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
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Menges M, Murray JAH. Plant D-type cyclins: structure, roles and functions. SEB Exp Biol Ser 2008; 59:1-28. [PMID: 18368915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Margit Menges
- Institute of Biotechnology, University of Cambridge, UK
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Menges M, Pavesi G, Morandini P, Bögre L, Murray JAH. Genomic organization and evolutionary conservation of plant D-type cyclins. Plant Physiol 2007; 145:1558-76. [PMID: 17951462 PMCID: PMC2151690 DOI: 10.1104/pp.107.104901] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 10/06/2007] [Indexed: 05/21/2023]
Abstract
Plants contain more genes encoding core cell cycle regulators than other organisms but it is unclear whether these represent distinct functions. D-type cyclins (CYCD) play key roles in the G1-to-S-phase transition, and Arabidopsis (Arabidopsis thaliana) contains 10 CYCD genes in seven defined subgroups, six of which are conserved in rice (Oryza sativa). Here, we identify 22 CYCD genes in the poplar (Populus trichocarpa) genome and confirm that these six CYCD subgroups are conserved across higher plants, suggesting subgroup-specific functions. Different subgroups show gene number increases, with CYCD3 having three members in Arabidopsis, six in poplar, and a single representative in rice. All three species contain a single CYCD7 gene. Despite low overall sequence homology, we find remarkable conservation of intron/exon boundaries, because in most CYCD genes of plants and mammals, the first exon ends in the conserved cyclin signature. Only CYCD3 genes contain the complete cyclin box in a single exon, and this structure is conserved across angiosperms, again suggesting an early origin for the subgroup. The single CYCD gene of moss has a gene structure closely related to those of higher plants, sharing an identical exon/intron structure with several higher plant subgroups. However, green algae have CYCD genes structurally unrelated to higher plants. Conservation is also observed in the location of potential cyclin-dependent kinase phosphorylation sites within CYCD proteins. Subgroup structure is supported by conserved regulatory elements, particularly in the eudicot species, including conserved E2F regulatory sites within CYCD3 promoters. Global expression correlation analysis further supports distinct expression patterns for CYCD subgroups.
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Affiliation(s)
- Margit Menges
- Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, United Kingdom
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Hannink NK, Subramanian M, Rosser SJ, Basran A, Murray JAH, Shanks JV, Bruce NC. Enhanced transformation of tnt by tobacco plants expressing a bacterial nitroreductase. Int J Phytoremediation 2007; 9:385-401. [PMID: 18246725 DOI: 10.1080/15226510701603916] [Citation(s) in RCA: 17] [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] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The manufacture, disposal, and detonation of explosives have resulted in the pollution of large tracts of land and groundwater. Historically, 2,4,6-trinitrotoluene (TNT) is the most widely used military explosive and is toxic to biological systems and recalcitrant to degradation. To examine the feasibility of enhancing the ability of plants to detoxify the explosive TNT, we created transgenic tobacco (Nicotiana tabacum) constitutively expressing the nsfI nitroreductase gene from Enterobacter cloacae. The product of TNT reduction by the nitroreductase was found to be 4-hydroxylamino-2,6-dinitrotoluene (4-HADNT). Characterization of the transgenic lines in sterile, aqueous conditions amended with TNT demonstrated that these plants were able to remove all of the TNT from the medium at an initial concentration of 0.5 mM (113 mg L(-1)) TNT. In contrast, growth was suppressed in wild-type plants at 0.1 mM (23 mg L(-1)). Following uptake, transgenic seedlings transformed TNT predominantly to 4-HADNT and its high levels appeared to correlate with enhanced tolerance and transformation of TNT. Transformation products of TNT were subsequently conjugated to plant macromolecules to a greater degree in transgenic tobacco, indicating enhanced detoxification compared to the wild type.
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Dewitte W, Scofield S, Alcasabas AA, Maughan SC, Menges M, Braun N, Collins C, Nieuwland J, Prinsen E, Sundaresan V, Murray JAH. Arabidopsis CYCD3 D-type cyclins link cell proliferation and endocycles and are rate-limiting for cytokinin responses. Proc Natl Acad Sci U S A 2007; 104:14537-42. [PMID: 17726100 PMCID: PMC1964848 DOI: 10.1073/pnas.0704166104] [Citation(s) in RCA: 262] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Current understanding of the integration of cell division and expansion in the development of plant lateral organs such as leaves is limited. Cell number is established during a mitotic phase, and subsequent growth into a mature organ relies primarily on cell expansion accompanied by endocycles. Here we show that the three Arabidopsis cyclin D3 (CYCD3) genes are expressed in overlapping but distinct patterns in developing lateral organs and the shoot meristem. Triple loss-of-function mutants show that CYCD3 function is essential neither for the mitotic cell cycle nor for morphogenesis. Rather, analysis of mutant and reciprocal overexpression phenotypes shows that CYCD3 function contributes to the control of cell number in developing leaves by regulating the duration of the mitotic phase and timing of the transition to endocycles. Petals, which normally do not endoreduplicate, respond to loss of CYCD3 function with larger cells that initiate endocycles. The phytohormone cytokinin regulates cell division in the shoot meristem and developing leaves and induces CYCD3 expression. Loss of CYCD3 impairs shoot meristem function and leads to reduced cytokinin responses, including the inability to initiate shoots on callus, without affecting endogenous cytokinin levels. We conclude that CYCD3 activity is important for determining cell number in developing lateral organs and the relative contribution of the alternative processes of cell production and cell expansion to overall organ growth, as well as mediating cytokinin effects in apical growth and development.
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Affiliation(s)
- Walter Dewitte
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Simon Scofield
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Annette A. Alcasabas
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Spencer C. Maughan
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Margit Menges
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Nils Braun
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Carl Collins
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Jeroen Nieuwland
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Els Prinsen
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium; and
| | - Venkatesan Sundaresan
- Section of Plant Biology and Department of Plant Sciences, University of California, Davis, CA 95616
| | - James A. H. Murray
- *Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
- To whom correspondence should be addressed. E-mail:
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Scofield S, Dewitte W, Murray JAH. The KNOX gene SHOOT MERISTEMLESS is required for the development of reproductive meristematic tissues in Arabidopsis. Plant J 2007; 50:767-81. [PMID: 17461793 DOI: 10.1111/j.1365-313x.2007.03095.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In Arabidopsis, the central stem cells of the shoot apical meristem (SAM) are indefinitely maintained, whereas those in floral meristems differentiate into female gametophyte-bearing organs termed carpels. The class 1 KNOX genes encode homeodomain transcription factors that function variously in the establishment and maintenance of the SAM, and have also been implicated in carpel development. Here we show that the KNOX gene SHOOT MERISTEMLESS (STM) induces carpel formation and promotes homeotic conversion of ovules to carpels when ectopically expressed in flowers, as previously reported for the related gene KNAT2. In contrast to KNAT2, loss of which confers no phenotype, we show using inducible RNA interference and mutational analysis that progressive loss of STM causes floral phenotypes ranging from reduced formation of placental tissues and inhibited carpel fusion to complete loss of carpel development. These effects result neither from failure to establish the central stem cell niche nor from reduced floral homeotic gene expression, but rather indicate a specific requirement for STM in carpel initiation, as further supported by the loss of leafy carpelloid features in stm leafy double mutants. Activation of carpel development by STM is independent of LEAFY and WUSCHEL, but requires the function of AGAMOUS. The essential role for STM in carpel development, together with its previous reported role in the SAM, shows that, despite the existence of several partially redundant paralogous genes, STM provides the critical KNOX function in the development of both vegetative and reproductive meristematic tissues.
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Affiliation(s)
- Simon Scofield
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
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Maughan SC, Murray JAH, Bögre L. A greenprint for growth: signalling the pattern of proliferation. Curr Opin Plant Biol 2006; 9:490-5. [PMID: 16877026 DOI: 10.1016/j.pbi.2006.07.010] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 07/17/2006] [Indexed: 05/11/2023]
Abstract
The shoot and root apical meristems (SAM and RAM, respectively) of plants serve both as sites of cell division and as stem cell niches. The SAM is also responsible for the initiation of new leaves, whereas the analogous process of lateral root initiation occurs in the pericycle, a specialized layer of cells that retains organogenic potential within an otherwise non-dividing region of the root. A picture is emerging of how cell division, growth, and differentiation are coordinated in the meristems and lateral organ primordia of plants. This is starting to reveal striking parallels between the control of stem cell maintenance in both shoots and roots, and to provide information on how signalling from developmental processes and the environment impact on cell behaviour within meristems.
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Affiliation(s)
- Spencer C Maughan
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
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Abstract
We have recently described the selection of rapidly dividing Arabidopsis cell suspension cultures MM1 and MM2d that provide a powerful platform for plant cell-cycle research. Here we provide detailed protocols and procedures to achieve high levels of synchronization, either by starving the cell cultures of sucrose or by applying the toxin aphidicolin. Cell-cycle activity during cell-cycle reentry (starvation-induced synchrony) or further cell-cycle progression (aphidicolin-induced synchrony) can be conveniently followed by using various validation procedures, such as determination of labeling index and metaphase/anaphase index or flow cytometry. We also describe a procedure that allows clonal transformed cell-suspension lines to be produced using Agrobacterium-mediated transformation, and an optimized and straightforward method for the cryopreservation and recovery of both parental and transformed lines which is applicable both to Arabidopsis and the tobacco BY2 cell lines. Cell-cycle synchronization capacity of the parental lines is maintained after both transformation and recovery from cryopreservation. The techniques described here require no specialized equipment and are suitable for routine laboratory use, greatly facilitating the handling and maintenance of cell cultures. The ability to store easily large numbers of transformed lines opens the possibility of using Arabidopsis cell suspension cultures for future high-throughput cell-cycle analysis.
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Affiliation(s)
- Margit Menges
- Institute of Biotechnology, University of Cambridge, UK
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Law GHE, Gandelman OA, Tisi LC, Lowe CR, Murray JAH. Mutagenesis of solvent-exposed amino acids in Photinus pyralis luciferase improves thermostability and pH-tolerance. Biochem J 2006; 397:305-12. [PMID: 16551268 PMCID: PMC1513288 DOI: 10.1042/bj20051847] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Firefly luciferase catalyses a two-step reaction, using ATP-Mg2+, firefly luciferin and molecular oxygen as substrates, leading to the efficient emission of yellow-green light. We report the identification of novel luciferase mutants which combine improved pH-tolerance and thermostability and that retain the specific activity of the wild-type enzyme. These were identified by the mutagenesis of solvent-exposed non-conserved hydrophobic amino acids to hydrophilic residues in Photinus pyralis firefly luciferase followed by in vivo activity screening. Mutants F14R, L35Q, V182K, I232K and F465R were found to be the preferred substitutions at the respective positions. The effects of these amino acid replacements are additive, since combination of the five substitutions produced an enzyme with greatly improved pH-tolerance and stability up to 45 degrees C. All mutants, including the mutant with all five substitutions, showed neither a decrease in specific activity relative to the recombinant wild-type enzyme, nor any substantial differences in kinetic constants. It is envisaged that the combined mutant will be superior to wild-type luciferase for many in vitro and in vivo applications.
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Affiliation(s)
- G H Erica Law
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
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Kawamura K, Murray JAH, Shinmyo A, Sekine M. Cell cycle regulated D3-type cyclins form active complexes with plant-specific B-type cyclin-dependent kinase in vitro. Plant Mol Biol 2006; 61:311-27. [PMID: 16786309 DOI: 10.1007/s11103-006-0014-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Accepted: 01/23/2006] [Indexed: 05/10/2023]
Abstract
Tobacco (Nicotiana tabacum L.) cv Bright Yellow-2 (BY-2) cells are the most highly synchronizable plant cell culture, and previously we used them to analyze cell cycle regulation of cyclin-dependent kinases (CDKs) containing the cyclin binding motifs PSTAIRE (CDKA) and PPTA/TLRE (CDKB). Here we describe the analysis of tobacco CycD3 cyclins whose transcripts predominantly accumulate during G2 to M phase, which represents a unique feature of this type of cyclin D in plants. Although protein levels of CycD3s fluctuate with different patterns during the cell cycle, kinase assays revealed that the CycD3-associated kinases phosphorylate histone H1 and the tobacco retinoblastoma related protein (NtRBR1) with two peaks at the G1/S and G2/M boundaries. In vitro pull-down assays revealed that cell cycle-regulated CycD3s bind to CDKA, but more weakly than does CycD3;3, and that they also bind to CDKB and the CDK inhibitor NtKIS1a. Mutations in the cyclin box of the CycD3s showed that two amino acids are required for binding with CDKA and NtKIS1a, but no diminished interaction was observed with CDKB. A reconstituted kinase assay was adapted for use with bacterially produced GST-CycD3s, and kinase activity could be activated by incubation of extracts from exponentially growing BY-2 cells. Such activated complexes contained CDKA and CDKB, and the reconstituted GST-CycD3 mutants, retaining binding ability to CDKB, showed kinase activity, suggesting that these cell cycle-regulated CycD3s form active complexes with both A- and B-type CDKs in vitro.
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Affiliation(s)
- Kazue Kawamura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama, Ikoma, Japan
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Abstract
Homeobox genes encode transcriptional regulators that control development in multicellular eukaryotes. In plants, post-embryonic shoot growth relies on the activity of indeterminate cell populations termed shoot meristems, within which members of the class-1 KNOX sub-family of homeobox genes are expressed. KNOX genes are differentially required for meristem development and function to inhibit cell expansion and differentiation associated with organogenesis. Mechanisms must therefore be employed to prevent KNOX gene expression in developing lateral organs such as leaves. This review focuses on the expression patterns, meristematic functions and regulation of KNOX genes, and how the activities of these genes are integrated within the framework of pathways that control plant development.
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Affiliation(s)
- Simon Scofield
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
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Affiliation(s)
- Simon Scofield
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK,
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