| 1. |
- Ashelford, Kevin, et al.
(författare)
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Full genome re-sequencing reveals a novel circadian clock mutationin Arabidopsis
- 2011
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 12, s. R28-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process,specifically if the phenotype is subtle and scoring labour intensive. An alternative to map basedcloning would be to directly sequence the whole genome of a mutant to uncover the mutationresponsible for the phenotype. Results: Here, we have re-sequenced the 120 Mb genome of a novel Arabidopsis clock mutant earlybird (ebi-1), using massively parallel sequencing by ligation. This process was further complicated by the fact that ebi-1 is in Wassilewskija (Ws-2), not the reference accession ofArabidopsis. The approach reveals evidence of DNA strand bias in the ethyl methanesulfonate(EMS) mutation process. We have demonstrated the utility of sequencing a backcrossed line andusing gene expression data to limit the number of SNP considered. Using new SNP informationwe have excluded a previously identified clock gene, PRR7. Finally, we have identified a SNPin the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype and validated this bycharacterising a further allele. Conclusion: In Arabidopsis, as in other organisms, the (EMS) mutation load can be high. Here wedescribe how sequencing a backcrossed line, using functional genomics and analysing new SNPinformation can be used to reduce the number EMS mutations for consideration. Moreover, theapproach we describe here does not require out-crossing and scoring F2 mapping populations, anapproach which can be compromised by background effects. The strategy has broad utility andwill be an extremely useful tool to identify causative SNP in other organisms.
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| 2. |
- Edwards, Kieron D., et al.
(författare)
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Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees
- 2018
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Ingår i: Plant, Cell and Environment. - : John Wiley & Sons. - 0140-7791 .- 1365-3040. ; 41:6, s. 1468-1482
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Tidskriftsartikel (refereegranskat)abstract
- Trees are carbon dioxide sinks and major producers of terrestrial biomass with distinct seasonal growth patterns. Circadian clocks enable the coordination of physiological and biochemical temporal activities, optimally regulating multiple traits including growth. To dissect the clock's role in growth, we analysed Populus tremula x P. tremuloides trees with impaired clock function due to down-regulation of central clock components. late elongated hypocotyl (lhy-10) trees, in which expression of LHY1 and LHY2 is reduced by RNAi, have a short free-running period and show disrupted temporal regulation of gene expression and reduced growth, producing 30-40% less biomass than wild-type trees. Genes important in growth regulation were expressed with an earlier phase in lhy-10, and CYCLIN D3 expression was misaligned and arrhythmic. Levels of cytokinins were lower in lhy-10 trees, which also showed a change in the time of peak expression of genes associated with cell division and growth. However, auxin levels were not altered in lhy-10 trees, and the size of the lignification zone in the stem showed a relative increase. The reduced growth rate and anatomical features of lhy-10 trees were mainly caused by misregulation of cell division, which may have resulted from impaired clock function.
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| 3. |
- Ibáñez, Cristian, et al.
(författare)
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Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees
- 2010
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Ingår i: Plant Physiology. - : ASPB Publications. - 0032-0889 .- 1532-2548. ; 153:4, s. 1823-1833
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Tidskriftsartikel (refereegranskat)abstract
- This study addresses the role of the circadian clock in the seasonal growth cycle of trees: growth cessation, bud set, freezing tolerance, and bud burst. Populus tremula x Populus tremuloides (Ptt) LATE ELONGATED HYPOCOTYL1 (PttLHY1), PttLHY2, and TIMING OF CAB EXPRESSION1 constitute regulatory clock components because down-regulation by RNA interference of these genes leads to altered phase and period of clock-controlled gene expression as compared to the wild type. Also, both RNA interference lines show about 1-h-shorter critical daylength for growth cessation as compared to the wild type, extending their period of growth. During winter dormancy, when the diurnal variation in clock gene expression stops altogether, down-regulation of PttLHY1 and PttLHY2 expression compromises freezing tolerance and the expression of C-REPEAT BINDING FACTOR1, suggesting a role of these genes in cold hardiness. Moreover, down-regulation of PttLHY1 and PttLHY2 causes a delay in bud burst. This evidence shows that in addition to a role in daylength-controlled processes, PttLHY plays a role in the temperature-dependent processes of dormancy in Populus such as cold hardiness and bud burst.
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| 4. |
- Johansson, Mikael, et al.
(författare)
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Monitoring seasonal bud set, bud burst, and cold hardiness in Populus
- 2014
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Ingår i: Plant Circadian Networks. - New York : Springer Science+Business Media B.V.. - 9781493906994 - 9781493907007 ; , s. 313-324
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Bokkapitel (refereegranskat)abstract
- Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as Arabidopsis thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.
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| 5. |
- Johansson, Mikael, et al.
(författare)
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Monitoring seasonal bud set, bud burst, and cold hardiness in populus
- 2022
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Ingår i: Plant circadian networks. - New York, NY : Humana Press. - 9781071619117 - 9781071619124 ; , s. 215-226
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Bokkapitel (refereegranskat)abstract
- Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.
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| 6. |
- Johansson, Mikael, 1981-, et al.
(författare)
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Partners in time : early bird associates with zeitlupe and regulates the speed of the arabidopsis clock
- 2011
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 155:4, s. 2108-2122
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Tidskriftsartikel (refereegranskat)abstract
- The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a posttranslational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, ZTL counteracts the effect of EBI during the day and increases it at night, modulating the expression of key circadian components. The partnership of EBI with ZTL reveals a novel mechanism involved in controlling the complex transcription-translation feedback loops of the clock. This work highlights the importance of cross talk between the ubiquitination pathway and transcriptional control for regulation of the plant clock.
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| 7. |
- Johansson, Mikael, et al.
(författare)
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Partners in time: EARLY BIRD reveals novel regulatory function of ZEITLUPE in the Arabidopsis clock
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The circadian clock of the model plant Arabidopsis thaliana is made up of acomplex series of interacting feedback loops whereby proteins regulate their ownexpression across day and night. early bird (ebi) is a circadian mutation that causesthe clock to speed up: ebi plants have short circadian periods, early phase of clockgene expression and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a post-translational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, EBI acts in opposition to ZTL, modulating the expression of key circadiancomponents. The partnership of EBI with ZTL reveals a novel mechanism involved incontrolling the complex transcription-translation feedback loops of the clock. Thiswork highlights the importance of cross-talk between the ubiquitination pathway andtranscriptional control for regulation of the plant clock
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| 8. |
- Johansson, Mikael, et al.
(författare)
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Role of the circadian clock in cold acclimation and winter dormancy in perennial plants
- 2015
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Ingår i: Advances in plant dormancy. - Cham : Springer. - 9783319144511 - 9783319144504 ; , s. 51-74
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Bokkapitel (refereegranskat)abstract
- Seasonal variation is a strong cue directing the growth and development of plants. It is particularly important for perennials growing in temperate and boreal regions where woody plants must become dormant to survive freezing winter temperatures. Shortening of the photoperiod induces growth cessation, bud set and a first degree of cold acclimation in most woody plants. The subsequent drop in temperature then produces a greater tolerance to cold and, in deciduous trees, leaf senescence and fall. Trees must time their periods of dormancy accurately with their environment. Circadian clocks underlie this ability, allowing organisms to predict regular, daily changes in their environment as well as longer term seasonal changes. This chapter provides an update on the plant clock in a model annual, thale cress (Arabidopsis thaliana), and further summarizes recent advances about the clock in perennial plants and its involvement in their annual growth cycles, which allows trees to withstand cold and freezing temperatures. Moreover, we outline our views on areas where future work on the circadian clock is necessary to gain insight into the life of a tree.
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| 9. |
- Johansson, Mikael, 1981-
(författare)
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The circadian clock in annuals and perennials : coordination of Growth with Environmental Rhythms
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Since the first signs of life on planet earth, organisms have had to adapt to the daily changes between light and dark, and high and low temperatures. This has led to the evolution of an endogenous time keeper, known as the circadian clock. This biological timing system helps the organism to synchronize developmental and metabolic events to the most favorable time of the day. Such a mechanism is of considerable value to plants, since they in contrast to animals cannot change location when the environment becomes unfavorable. Thus is the ability to predict coming events of central importance in a plants life. This thesis is a study of the molecular machinery behind the clockwork in the small weed plant Arabidopsis thaliana as well as its close relative perennial; the woody species Populus. We have characterized a novel component of the circadian clock, EARLY BIRD (EBI). EBI is involved in transcriptional and translational regulation, via interaction with the known post-translational clock regulator ZEITLUPE (ZTL). In Populus, we describe the role of the circadian clock and its components with respect to entry and exit of dormancy and show that gene expression of the Populus LATE ELONATED HYPOCOTYL (LHY) genes are crucial importance for freezing tolerance and thereby survival at high latitudes. Furthermore, the input to the Populus clock is mediated via the phytochrome A (phyA) photoreceptor.
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| 10. |
- Johansson, Mikael, et al.
(författare)
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The perennial clock is an essential timer for seasonal growth events and cold hardiness
- 2014
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Ingår i: Plant Circadian Networks. - New York : Springer. - 9781493907007 ; , s. 297-311
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Bokkapitel (refereegranskat)abstract
- Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate. To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.
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