The cautionary tale of ABP1.

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Published on: June 29, 2015

The plant hormone auxin has long been known to play a significant role in plant growth, even featuring in Charles Darwin’s book ‘The Power and Movement of Plants’.

However until the mid-2000s the identity of any receptor for the hormone remained a mystery. Until that time, the site of auxin reception was somewhat of an enigma with the main candidate being a protein named ‘Auxin Binding Protein (ABP)’ that, in many biochemical studies, was shown to bind auxin at physiological concentrations (for review of ABP1 work1). This protein is present in Arabidopsis but investigations into its in vivo function were somewhat stalled by a 2001 publication that demonstrated that an abp1 T-DNA insertion mutant was embryo lethal2. This did not overly surprise the research community given the fundamental and wide-ranging role of auxin in plant development.

Meanwhile researchers at York University in the UK and at Indiana University in the US were working on a novel hypothesis that proposed the auxin receptor was linked to the degradation of AuxIAA proteins, which are negative regulators of the auxin response. Ultimately after years of painstaking research the labs of Ottoline Leyser and Mark Estelle demonstrated that the F-box protein TIR1, when in complex with an AuxIAA protein, was also able to bind auxin3-4. This finding nicely pieced together an elegant pathway of control that involved tightly regulated protein degradation controlling both positive and negative feedback regulation of the hormone signal.

At this time the work on ABP1 had mostly retreated into the long weeds as research in the community revolved around the TIR1-AuxIAA receptor paradigm. However toward the end of the 2000s ABP1 had a renaissance as molecular techniques such as RNAi and cellular immunisation allowed identification of transgenic plants with reduced expression of ABP1. Plants with a deficiency in ABP1 exhibited robust auxin-deficient phenotypes including cell-cycle arrest in tobacco BY2 cells5 and changes in cell-wall composition during cell expansion6. Initially these effects were thought to occur independent of TIR1 but more recently ABP1 was shown to lie genetically upstream of the TIR1-receptor pathway7. In keeping with its initially proposed role in the rapid auxin response, ABP1 was found, by use of a weak abp1-5 allele, to have a defect in auxin-induced transcriptionally-independent clathrin-mediated endocytosis of PIN proteins8 as well as playing a critical role in the activation of ROP proteins that control epidermal cell interdigitation9. Therefore reducing the expression of ABP1 had demonstrated, as would be predicted, that the protein plays a critical and wide-ranging role in cell division and expansion.

Therefore at this time the functional relationship between ABP1 and TIR1 appeared to satisfy researchers…… that was until a paper was published at the start of 2015 that greatly altered perceptions within this research community10.

The labs of Yunde Zhao and Mark Estelle at UC-San Diego initially used a CRISPR-based strategy to generate a null abp1 mutant allele, with the full expectation that the resulting plant would be unable to survive. Surprisingly they discovered that this abp1-c1 allele exhibited a completely wildtype phenotype. This prompted the isolation of a new T-DNA insertion mutant that was an abp1 null mutant. These plants also showed wildtype phenotypes across a range of assays that were thought to be ABP1-dependent. Ultimately the authors concluded that ‘ABP1 is not a key component in auxin signaling or Arabidopsis development’.

The discrepancy between these findings and the previous 15 years of data is striking and inevitably leads to questions about the previous work. In a recent calm editorial comment in the Journal of Integrative Plant Biology, Professor Chun-Ming Liu called for a careful reexamination of the previous data and for experimental materials to be exchanged in order to get to the bottom of this growing controversy11.

Even more recently the lab of Lucia Strader at Washington University in St Louis published a short paper in Plant Cell that questioned the abp1-5 mutant12. As stated above this allele has been used in a number of studies where its many interesting phenotypes include long hypocotyl growth in red light9. The Strader lab were interested in this response but ran into difficulties when characterising the genetic basis of this phenotype. Ultimately they decided to sequence the abp1-5 genome and surprisingly found that it contained significant portions from the Arabidopsis ecotype Wassilewskija, which is known to display mild resistance to auxin. Perhaps most worrying was that they discovered abp1-5 contained a null mutation in phyB, which is likely the causative effect of the long hypocotyl phenotype. The authors conclude by warning that their findings ‘provide a cautionary tale illustrating the need to use multiple alleles or complementation lines when attributing roles to a gene product’.

So what has happened in these experiments? In the Gao et al paper10 the authors took the simple approach of testing abp1 mutants for phenotypes and didn’t find anything different from the wildtype. It would be difficult to imagine where any errors would have occurred in these experiments especially given the nature of the genetic lesion in these new abp1 mutants. Gao et al suggest that the previous work based on ABP1 knock-down lines might have in fact been the consequence of off-target transgenic effects. Given the varied role that auxin plays in Arabidopsis development this is not an impossible conclusion to draw as numerous genes are involved in some aspects of this hormone response.

Most concerning is the initial characteristic of the original null abp1 mutant lines that was found to be embryo-lethal. This work is the cornerstone of the subsequent work that aimed to create plants with reduced ABP1 expression. The characterised abp1 mutant lines in Chen et al and Gao et al have T-DNA insertions close together at the 5’ end of the coding sequence so it is unclear why there are such differing results. It was unusual that in the first study only a single abp1 mutant allele was characterised, especially when the authors claimed embryo-lethality2. It would have been helpful for Gao et al (2015) to reexamine the original abp1 mutant line assessed in Chen et al (2001) but perhaps that might have appeared rather too confrontational.

At it stands the future direction of research into ABP1 is in flux with the onus now on those researchers with a vested interest, of which there are plenty, to try to understand the role of this protein.

In many ways this story is an excellent example of how science should work, where claims are independently tested to ensure that earlier experiments have been conducted or interpreted correctly. However this can be difficult as there is usually little value in retroactive testing of published claims. The plant science community awaits the resolution of the mystery of ABP1 whilst commiserating with those who have been negatively affected by this new development in this story.

 

1- Sauer and Klein-Vehn (2011) Plant Cell 23, 2033-2043

2- Chen et al (2001) Genes and Development 15, 902-911

3- Dharmasiri et al (2005) 435, 441-445

4- Kepinski and Leyser (2005) 435 446-451

5- David et al (2007) Plant Journal 50, 197-206

6- Paque et al (2014) Plant Cell 26, 280-295

7- Tromas et al (2013) Nature Communications 4, 2496

8- Robert et al (2010) Cell 143 111-121

9- Xu et al (2010) Cell 143, 99-110

10- Gao et al (2015) PNAS 112, 2275-2280

11- Liu (2015) JIPB 57, 234-235

12- Enders et al (2015) The Plant Cell Epub

COPO 2015 Meeting

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Published on: June 25, 2015

COPO has big plans…. and if it is to be truly successful and benefit the plant community there needs to be a cultural change! That’s the simple if revolutionary message that came out of the recent COPO meeting held at TGAC on June 23rd-24th.

So the uninitiated will be asking: ‘What is COPO?‘ The answer is the Collaborative Open Plant Omics group which was funded by a BBSRC BBR grant in 2014. This is a >£1m collaboration between The Genome Analysis Centre (TGAC), University of Oxford, the European Bioinformatics Institute (EMBL) and the University of Warwick.

This workshop was to introduce the aims of COPO to a range of stakeholders, from curators of available data repositories to experimentalists who are generating large datasets. By the end of the 2-day session it was hoped that everyone would gain an understanding of what COPO can offer the community with regard facilitating the sharing of large datasets.

White Board Discussions

The workshop was led by Rob Davey (TGAC) and Ruth Bastow (GPC, GARNet, Warwick). Rob kicked off the meeting by describing the aims of COPO which included asking ‘What are the barriers for you and your data and how can COPO facilitate access to the workflows used to analyse data’.

Subsequently a range of stakeholders introduced the fantastic tools that are out there for repositing data of many different types. These included David Salt (University of Aberdeen, Ionomics), Elizabeth Arnaud (Montpellier, CropOntology), David Marshall (James Hutton Institute, Germinate: Plant Genetic Resources), Esther Kabore (INRA, Wheat Data Repository) Reza Salek (EMBL, Metabolights), and finally Tomasz Zielinski (Edinburgh, BioDare) who made the telling observation that ‘data Management is a user interface/user experience problem NOT a software engineering/ data modelling problem’. Many researchers are often reluctant to take the time and effort required to submit their data to an appropriate repository in a reasonable manner, for any number of opaque reasons. However the take-home message from the early talks was very positive as there are a large number of data platforms available for people to use and benefit from. One of the challenges for COPO is to not only to help convince people to use these resources but encourage them to share data in a standardised manner.

Following a useful coffee break it was time for researchers to explain the data they are producing and the challenges for their analysis. Miriam Gifford (Warwick) discussed her generation of transcriptomic data, Christine Sambles (Exeter) talked about developing a workflow for metabolomics data and TGAC group leader Ksenia Krasileva introduced her work on wheat functional genomics. Ksenia also highlighted a new portal for communication between data generators and data users called Grassroot Genomics.

The final three talks of the day highlighted the amount of data that can be produced in different sets of biological experiments. Ji Zhou (TGAC) and Chris Rawlings (Rothamstead) introduced cutting-edge field phenotyping technologies that use large imagers to capture visible and spectral aspects of plant growth. Workshop attendee Professor Peter Murray-Rust summed it up with a tweet: ‘Blown away by the crop monitoring equipment at Rothamstead’. On an opposite end of the spectrum Jim Murray (Cardiff) showed a single fluorescent image of a zebrafish taken on a light-sheet microscope that weighed in at an impressive 23Tb of data. Overall these talks served to highlight the vast amounts of data that can be produced and provided the second take-home message of the day that ‘Getting data is NOT the issue, making any sense of it IS the challenge’……

 

The task of second day discussions was to make sense of what had been presented the previous day and identify the best opportunities for COPO to impact on the process of data sharing. A lively first hour of debate included Dr Philippe Rocca-Serra (COPO Co-PI from Oxford) presenting a somewhat sobering eight slides of ‘Pain Points’ that he had taken out of the previous days presentations! However it was refreshing to observe that the challenge of the task was not underestimated and being tackled with realistic planning.

Pain Points!

Later in the morning discussions turned more specific with a white-board brainstorming session that was divided into ‘Data Collection’.Data Storage’ and ‘Data Analysis’ sections. Most progress was made in the first two sections with a long list of storage repositories identified that bridged the breath of biological data and with which COPO could potentially interact.

It was felt that successful interactions would be predicated on some level of data standardisation so perhaps the most effective initial use of the COPO resources would be to develop a workflow for standard data collection. This would hopefully make experimentalists think about the format of their data submission as they are planning and generating the data. The consensus was that attaching these standards to legacy-data might be a difficult task but that for future data generation, COPO could influence data sharing at this level.

IMG_8241

Ultimately it is clear that plant science has the same generic problems as many other disciplines and the greatest challenge is to change the ‘culture’ of sharing data. The most obvious and direct way to promote this change will be via the funders and publishers. Some progress has been made in this arena with a recent shift towards open access publication in the REF process, and it would only take another small additional step to make it a requirement to share data in any REF-returnable publications. So I hope that those with greater power and influence than me, are reading the GARNet blog!

Regardless of the pace of cultural change, the feeling in the meeting was that the COPO mandate is to encourage data sharing whilst moving to a position to effectively interact with the data that is shared. There is plenty of work to do but at the end of this exploratory workshop the COPO organisers had plenty to think about regarding the direction of the project. Watch their space!

Storify of tweets from the meeting

GARNet-OpenPlant CRISPR workshop

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Published on: June 23, 2015

Please see program in the poster below and register for the meeting here. For more information please contact geraint@garnetcommunity.org.uk

CRISPR Poster

Arabidopsis Research Roundup

This week roundup features a wide range of research topics from two current members of GARNet Advisory board as well as two papers featuring work from the lab of Laszlo Bogre at Royal Hollaway. The studies range from an investigation into the similarity between the barley and Arabidopsis circadian clocks, the role of MYR3R during regulation of organ growth, documenting a novel interaction of a MAPK protein and the development of new fluorescent probes for study of cysteine proteases.

 

Kusakina J, Rutterford Z, Cotter S, Martí MC, Laurie DA, Greenland AJ, Hall A, Webb AA (2015) Barley Hv CIRCADIAN CLOCK ASSOCIATED 1 and Hv PHOTOPERIOD H1 Are Circadian Regulators That Can Affect Circadian Rhythms in Arabidopsis. PLoS One. 10(6):e0127449. http://dx.doi.org/10.1371/journal.pone.0127449

This publication is the result of a multi-site collaboration between the Alex Webb at Cambridge, GARNet Advisory board member Anthony Hall at Liverpool, Andy Greenland at NIAB and David Laurie at the JIC. The focus of this study are the barley CIRCADIAN CLOCK ASSOCIATED 1 and PHOTOPERIODH1 genes, which are involved in regulation of the circadian clock. The authors investigated the circadian rhythms in barley whilst using heterologous expression in Arabidopsis to show that the barley CCA1 is functionally equivalent to AtCCA1 and that barley PHOTOPERIODH1 functions similar to AtPRR7.

 

Kobayashi K, Suzuki T, Iwata E, Nakamichi N, Suzuki T, Chen P, Ohtani M, Ishida T, Hosoya H, Müller S, Leviczky T, Pettkó-Szandtner A, Darula Z, Iwamoto A, Nomoto M, Tada Y, Higashiyama T, Demura T, Doonan JH, Hauser MT, Sugimoto K, Umeda M, Magyar Z, Bögre L, Ito M (2015) Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J. http://dx.doi.org/10.15252/embj.201490899

GARNet advisory board member John Doonan and Royal Hollaway-based Laszlo Bogre are collaborators on this multi-nation publication that looked at the role of three MYB2R3 proteins in cell cycle control. Arabidopsis plants that have mutations in three repressor type-myb3r genes display enlarged organs. In addition, MYB3R3 binds to G2/M-specific genes and associates with the repressor-type E2F and RBR proteins. The authors perform a range of pair-wise interaction studies to identify components of multiprotein complexes, that have also been identified in other organisms. Ultimately they show that these MYC3R genes are important for periodic expression during the cell cycle and for establishing a post-mitotic quiescent state that determines organ size.

 

Kohoutová L1, Kourová H1, Nagy SK2, Volc J1, Halada P1, Mészáros T2,3, Meskiene I4,5, Bögre L6, Binarová P1 (2015) The Arabidopsis mitogen-activated protein kinase 6 is associated with γ-tubulin on microtubules, phosphorylates EB1c and maintains spindle orientation under nitrosative stress New Phytologist. http://dx.doi.org/10.1111/nph.13501

Laszlo Bogre also features as a collaborator in this East European-led study that investigated the interaction of the MAPK-protein MPK6 with microtubules. Immunoprecitations showed that the active form of MPK6 interacted with γ-tubulin, sedimenting with in vitro polymerised microtubules. In addition they identified a novel substrate for MPK6, the microtubule plus-end protein, EB1c. Overall the authors propose that MPK6 plays a significant role in maintaining regular planes of cell division, particularly during stress conditions.

 

Lu H, Chandrasekar B, Oeljeklaus J, Misas-Villamil JC, Wang Z, Shindo T, Bogyo M, Kaiser M, van der Hoorn RA (2015) Subfamily-specific Fluorescent Probes for Cys proteases Display Dynamic Protease Activities During Seed Germination. Plant Physiology http://dx.doi.org/10.1104/pp.114.254466

Renier Van De Hoorn who works in the Department of Plant Chemetics at the University of Oxford, leads this study that investigates the activity of plant cysteine proteases. They developed a novel set of fluorescent probes that specifically target different subfamilies of Cys proteases. In order to test these probes they used Arabidopsis mutant lines alongside transient expression studies in tobacco. In addition they show that these probes have broad applicable across 8 plant species. Finally they use these new tools to reveal the dynamic properties of different protease sub-families during remobilization of seed storage proteins in Arabidopsis.

Arabidopsis Research Roundup: June 10th.

This weeks UK Arabidopsis Research Roundup features work from two members of the GARNet advisory board who are working on very different aspects of how plants response to external stimuli. In addition there is a genetic and biochemical dissection of primary cell wall formation as well as a comment piece that questions recent findings concerning the relationship between auxin, ABP1 and cortical microtubules.

Busoms S, Teres J, Huang X, Bomblies K, Danku J, Douglas A, Weigel D, Poschenrieder C, Salt DE (2015) Salinity is an agent of divergent selection driving local adaptation of Arabidopsis thaliana to coastal habitats Plant Physiology http://dx.doi.org/pp.00427.2015

Current GARNet Chairman David Salt from Aberdeen has collaborated with researchers from Spain, Germany and the USA in this study that looks at the drivers of adaptive evolution of Arabidopsis plants grown in saline conditions. Unusually this is a field-based study using Arabidopsis that naturally grow in coastal or inland areas of NE Span. Plants taken from coastal areas outperform inland plants when grown on highly saline soils, indicating local adaptation to salt tolerance. The authors conclude that the variation in sodium concentration is causing divergent selection between these two populations.

Monaghan J, Matschi S, Romeis T, Zipfel C (2015) The calcium-dependent protein kinase CPK28 negatively regulates the BIK1-mediated PAMP-induced calcium burst Plant Signaling and Behaviour June 2015 http://dx.doi.org/10.1080/15592324.2015.1018497

GARNet advisory board member Cyril Zipfel from the Sainsbury lab led this study looking at the role of the cytoplasmic kinase BIK1 in the plants response to microbial infection. In plants that are mutant for the Ca2+-dependent protein kinase CPK28, BIK1 accumulates, which leads to enhancing immune signaling. In this study the authors add to these previous finding from their lab by showing that CPK28 also contributes to a burst of Ca2+ production following exposure to pathogens.

Mortimer JC, Faria-Blanc N, Yu X, Tryfona T, Sorieul M, Ng YZ, Zhang Z, Stott K, Anders N, Dupree P (2015) An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14 Plant Journal http://dx.doi.org/10.1111/tpj.12898

Paul Dupree from the Biochemistry department at the University of Cambridge led this work that investigated a newly characterised form of Xylan, a little studied component of the plant primary cell wall. Genetic analysis indicates that the IRX9L, IRX10L and IRX14 proteins are necessary for xylan backbone synthesis. Importantly this new xylan is contains GlcA side chains, whose addition only requires the glucuronyltransferase GUX3. This type of xylan has not been observed in secondary cell walls so the authors comment on how differences in xylan structure assist in the formation of primary vs secondary cell walls.

Taken from wikipedia.
Taken from wikipedia.

 

 

 

 

 

T Baskin (2015) Auxin inhibits expansion rate independently of cortical microtubules. Trends in Plant Science http://dx.doi.org/10.1016/j.tplants.2015.05.008

Visiting scholar at CPIB in Nottingham, Tobias Baskin provides a short reply to a publication in Nature that claimed that the control of cell expansion by auxin is caused by reorientation of cortical microtubules. In this paper, Tobias provides evidence from both a simple experiment and from the literature that this might not be the paradigm-shifting observation that it initially appears.

BBC Panorama: GM Food

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Published on: June 9, 2015

On June 8th 2015, BBC Panorama reported on Genetically Modified Crops. I put together a ‘Storify’ taken from the twitter response that occurred during and after the program.

Check it out!

PanoramaPic

 

Genome Resequencing for Mutant Identification

As most biologists will be aware, the cost of DNA sequencing has been falling well in advance of the costs predicted by Moores law (although argued by Neil Hall a few years ago, this might not have been the best thing to happen, intellectually at least).

Instead of simply sequencing many genomes for the sake of it, this also offers opportunities for researchers to use this technology to ‘do-science’ that might previously have been prohibitively laborious or expensive. One such area where this is true is in the identification of novel mutations in plants, especially in Arabidopsis.

Classic approaches to identity the location of an EMS mutation involved mutant identification, backcrossing, selection, rough mapping by PCR or CAPS markers, probably more crossing and then a little guesswork toward the end..…..before using Sanger sequencing to identify what you hope is the causative mutation. Even with a strong following wind this process could take upwards of a year……. many a 1990s PhD thesis was written off the back of mutant identification. In contrast it is now relatively cheap to resequence the Arabidopsis genome so a lot of time can be taken out of this process. In addition, resequencing can remove some of the difficulty involved with selective of mutants that have a subtle phenotypes wherein inaccurate selection of putative mutants would significantly set back the process.

Back in 20111, Anthony Hall’s group in Liverpool University used resequencing in parallel with classic genetics to identify the lesion in the novel early bird1 gene (ebi1), which has a defect in function of the circadian clock. In this case ebi1, which was generated using EMS, was backcrossed 4 times to reduce the number of EMS-induced SNPs not associated with phenotype, and then sequenced alongside the original wildtype plant (from the WS ecotype). The critical part of the protocol came in the power of the software they used to detect homozygous SNPs in the ebi1 line. Indeed the researchers ran into some difficulties due to a high number of SNPs they initially identified. However, when they combined altering the stringency of SNP-calling together with classical rough mapping they were left with approximately 30 SNPs to finally assess. Using a priori knowledge of proposed gene function and by investigating expression changes in these candidates they ultimately identified a novel mutant. Although this process was ultimately successful, it took some extra time due to the difficulty of mutant selection, optimization of the SNP-calling software and subsequent analysis of gene expression.

A recent paper from the lab of Lucia Strader at Washington University in St Louis shows how powerful resequencing can be if you are using a robust method of mutant selection. In their case they isolated mutants with a defect in the root growth response to ABA, which is an unequivocal phenotype to score. They backcrossed their initial mutants, selected for ABA resistance in F2 generation before resequencing these resistant plants. Using this process the authors report that they narrowed their search to between 3-10 candidate genes and that they have subsequently identified novel (unpublished) genes using this method. In addition, as an exemplar of their protocol they used it to isolate novel alleles of known ABA-resistant mutants.

Schematic for mutant identification using NGS. Reproduced from Taylor and Francis PSB http://dx.doi.org/10.1080/15592324.2014.1000167
Schematic for mutant identification using NGS. Reproduced from Taylor and Francis PSB http://dx.doi.org/10.1080/15592324.2014.1000167

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

In parallel they used a similar protocol to the Hall lab where they resequenced non-backcrossed plants and then selected SNPs that only lay within exons.Using this approach they identified between 100-200 homozygous SNPs, a potentially fifty-fold increase compared to their other method. Therefore when you are working with a strong robust phenotype it is probably worth the extra time to obtain a back-crossed population in order to have greater confidence you are isolated your mutant of interest.

The authors importantly note that one limitation of this protocol is that by only selecting for exonic mutations, they are removing the possibility of identifying mutants with splicing or non-coding defects, which may in turn rule out a number of candidate genes.

 

For me the take-home message from this second study is that if you have a robust phenotype to select for and are confident that your mutation is novel then use of ever-improving NGS is now a time and cost effective way of mutant identification.

In fact this technology might inspire a return to the forward genetic screens of the 80s and 90s , with the aim of identifying novel genes involved in well characterised signaling pathways……..except that PhD students might now have to characterise 10 novel genes prior to graduation….

Arabidopsis Research Roundup: June 3rd 2015

We are unashamedly biased in this weeks Arabidopsis Research Roundup which firstly features work from the group of GARNet PI Jim Murray about the genetic interactions that define growth of lateral organs. Elsewhere we highlight papers that investigate a different role for CYCD3 genes in vascular development, the role of TFL1 in the shoot meristem and the ability of Arabidopsis seedling to tolerant a high light environment during ontogenesis.

Randall RS, Sornay E, Dewitte W, Murray JA (2015) 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 Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv200

Jim Murray and Walter Dewitte (Cardiff) lead this study that investigates the relationship between the AINTEGUMENTA (ANT) transcription factor and cyclin CYCD3;1 during lateral aerial organ (LAO) formation. LAO growth is determined by the both the number and size of cells that comprise the organ. During petal development, ant mutants have reduced cell number but increased cell size, demonstrating a ‘compensatory mechanism’ of growth. In contrast cycd3;1 mutants have increased cell size that results in larger petals, showing no compensatory mechanism. Interestingly ant cycd3;1 double mutants do show growth compensation in the same tissue. The authors propose that occurrence of the compensatory mechanism depends on at which time-point during distinct phases of cell division and cell expansion the growth defect occurs.

 

C Collins, Maruthi M.N and C Jahn (2015) CYCD3 D-type cyclins regulate cambial cell proliferation and secondary growth in Arabidopsis. Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv218

Another study that investigates a different role of D-type cyclins is led by former Murray lab member, Carl Collins working at the Natural Resources Institute at the University of Greenwich. The factors that control cambial cell growth are poorly understood but the authors provide a link between the cell cycle and cambial differentiation by showing that CYCD3 subgroup of genes play a role in the process. Three CYCD3 genes are expressed in cambial tissue and the equivalent triple mutant has reduced hypocotyl and stem diameter, which is linked to a reduction in mitotic activity. Conversely, mutant xylem cells increased in size. This shows that CYCD3 genes provide a mechanism for controlling the correct proportions of cell growth during vascular development. This might provide a useful tool in the future study of this important process in woody plants.

 

Carvalho FE, Ware MA, Ruban AV (2015) Quantifying the dynamics of light tolerance in Arabidopsis plants during ontogenesis Plant Cell Environment http://dx.doi.org/10.1111/pce.12574

The group of Professor Alexander Ruban at Queen Marys University London utilise a novel methodology to measure the ‘intactness’ of photosystem II (PSII). In this paper they assess the amount of light required to inhibit PSII activity through the life cycle of Arabidopsis plants grown in short days. They show that maximum light tolerance occurs in 8-week old plants. Interestingly the light tolerance correlates with rates of electron transport yet did not coincide with the chlorophyll a/b ratios or anthocyanin content.

 

Baumann K, Venail J, Berbel A, Domenech MJ, Money T, Conti L, Hanzawa Y, Madueno F, Bradley D (2015) Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture. Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv247

The TFL1 gene is a repressor of flowering in the Arabidopsis shoot meristem. Researchers from the UK, USA, Spain and Italy, led by Desmond Bradley at the JIC show that ecoptocally expressed TFL1 can repress flowering outside of its normal expression domain. By comparing the expression of TFL1 with genes that determine floral identity (APETALA, LEAFY) the authors conclude that the shoot meristem is more sensitive to TFL1, allowing the maintenance of a vegetative state in this tissue.

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