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The circadian clock in annuals and perennials: coordination of Growth with Environmental Rhythms
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. (Maria E. Eriksson)
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Abstract [sv]

Liv på jorden har alltid behövt anpassa sig till de dagliga växlingarna mellan främst ljus och mörker. Detta har lett till evolutionen av en intern, biologisk klocka, känd som den circadianska klockan, efter latinets ”circa diem”, som betyder ”ungefär en dag”. Denna inre klocka hjälper organismer att styra biologiska processer till den tid på dygnet som är mest gynnsam för deras utveckling och överlevnad. Denna mekanism är av stort värde för växter, eftersom de inte kan söka skydd på mera lämpliga platser om de blir utsatta för olika former av stress. Det gör att förmågan att förutse kommande händelser är av yttersta vikt för växter. Denna avhandling är en studie av det molekylära nätverk som styr denna biologiska klocka i den lilla örtplantan Arabidopsis thaliana (backtrav), och den besläktade träd-arten Populus (hybrid-asp). Vi har karaktäriserat en ny komponent i den circadianska klockan i Arabidopsis, EARLY BIRD (EBI). EBI är involverad i transkriptionell och translationell reglering av klockan, via interaktion med den kända post-translationella klock-regulatorn ZEITLUPE (ZTL). I Populus har vi beskrivit den interna klockan och dess roll i processer som invintring, vinterdvala och återstart av tillväxt. LATE ELONATED HYPOCOTYL (LHY) generna i Populus är avgörande för förvärv av köld-tolerans och således överlevnad på högre latituder. Dessutom har vi visat att signaler till den circadianska klockan i Populus är medierade via fotoreceptorn phytochrome A (phyA).

Place, publisher, year, edition, pages
Umeå: Umeå Universitet, Institutionen för fysiologisk botanik , 2010. , 61 p.
Keyword [en]
circadian clock, arabidopsis, populus
National Category
Biochemistry and Molecular Biology Plant Biotechnology Botany
Research subject
Molecular Biology
Identifiers
URN: urn:nbn:se:umu:diva-35870ISBN: 978-91-7459-062-3 (print)OAI: oai:DiVA.org:umu-35870DiVA: diva2:349785
Public defence
2010-10-01, KB3B1, KBC-huset, Umeå universitet, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2010-09-10 Created: 2010-09-08 Last updated: 2010-09-10Bibliographically approved
List of papers
1. Partners in time: EARLY BIRD reveals novel regulatory function of ZEITLUPE in the Arabidopsis clock
Open this publication in new window or tab >>Partners in time: EARLY BIRD reveals novel regulatory function of ZEITLUPE in the Arabidopsis clock
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

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

Keyword
Circadian clock, Arabidopsis
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-35860 (URN)
Available from: 2010-09-08 Created: 2010-09-08 Last updated: 2010-11-09Bibliographically approved
2. Full genome re-sequencing reveals a novel circadian clock mutationin Arabidopsis
Open this publication in new window or tab >>Full genome re-sequencing reveals a novel circadian clock mutationin Arabidopsis
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2011 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1465-6914, Vol. 12, R28- p.Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Biochemistry and Molecular Biology Botany
Identifiers
urn:nbn:se:umu:diva-35864 (URN)10.1186/gb-2011-12-3-r28 (DOI)
Available from: 2010-09-08 Created: 2010-09-08 Last updated: 2014-11-17Bibliographically approved
3. ZEITLUPE promoter activity is modulated in an EARLY BIRD dependent manner in response to abscisic acid
Open this publication in new window or tab >>ZEITLUPE promoter activity is modulated in an EARLY BIRD dependent manner in response to abscisic acid
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The newly described clock regulator EARLY BIRD (EBI) was shown to interact with ZEITLUPE (ZTL) and to influence the function of the core circadian oscillator. Studiesof mutants in the EBI locus have earlier been used to ascribe a role for EBI in responsesto abiotic stress.Here, we test the early bird-1 (ebi-1) clock mutant’s response to salt stress. Also, weprobe the effect on the expression and regulation of clock associated genes in response tothe known stress signaling modulator, abscisic acid (ABA). We show that ZTL promoteractivity is under circadian clock control and that these oscillations are stabilized to morerobust rhythms in response to ABA. The clock regulation of ZTL is found to beindependent of EBI and different from the regulation of CAB2 suggesting that they, atleast partially, are driven by separate oscillators. In addition, EBI appears to modulate thestabilization of these oscillations in response to ABA suggesting that it may act as amediator between oscillators and in the clock’s response to stress.

Keyword
Circadian clock, Arabidopsis
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-35867 (URN)
Available from: 2010-09-08 Created: 2010-09-08 Last updated: 2010-11-09Bibliographically approved
4. Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees
Open this publication in new window or tab >>Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees
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2010 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 153, no 4, 1823-1833 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
ASPB Publications, 2010
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-35854 (URN)10.1104/pp.110.158220 (DOI)000280566000031 ()20530613 (PubMedID)
Available from: 2010-09-08 Created: 2010-09-08 Last updated: 2016-12-05Bibliographically approved
5. Alteration of PHYA expression change circadian rhythms and timing of bud set in Populus
Open this publication in new window or tab >>Alteration of PHYA expression change circadian rhythms and timing of bud set in Populus
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2010 (English)In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 73, no 1-2, 143-56 p.Article in journal (Refereed) Published
Abstract [en]

In many temperate woody species, dormancy is induced by short photoperiods. Earlier studies have shown that the photoreceptor phytochrome A (phyA) promotes growth. Specifically, Populus plants that over-express the oat PHYA gene (oatPHYAox) show daylength-independent growth and do not become dormant. However, we show that oatPHYAox plants could be induced to set bud and become cold hardy by exposure to a shorter, non-24 h diurnal cycle that significantly alters the relative position between endogenous rhythms and perceived light/dark cycles. Furthermore, we describe studies in which the expression of endogenous Populus tremula x P. tremuloides PHYTOCHROME A (PttPHYA) was reduced in Populus trees by antisense inhibition. The antisense plants showed altered photoperiodic requirements, resulting in earlier growth cessation and bud formation in response to daylength shortening, an effect that was explained by an altered innate period that leads to phase changes of clock-associated genes such as PttCO2. Moreover, gene expression studies following far-red light pulses show a phyA-mediated repression of PttLHY1 and an induction of PttFKF1 and PttFT. We conclude that the level of PttPHYA expression strongly influences seasonally regulated growth in Populus and is central to co-ordination between internal clock-regulated rhythms and external light/dark cycles through its dual effect on the pace of clock rhythms and in light signaling.

Keyword
growth cessation, dormancy, circadian clock, photoperiodism, phytochrome, populus
Identifiers
urn:nbn:se:umu:diva-33187 (URN)10.1007/s11103-010-9619-2 (DOI)000276440900013 ()20229130 (PubMedID)
Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2016-12-05Bibliographically approved

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