plant molecular biology
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Rewiring of the Fruit Metabolome in Tomato Breeding

Highlights
•Multi-omic analysis of tomato fruits revealed new metabolic genes and pathways
•Selection of fruit mass gene-altered metabolites altered due to nearby hitchhiking genes
•Domestication acted on five major loci that reduced anti-nutritional compounds
•Pink tomato breeding modified hundreds of metabolites, leading to unexpected changes

Via Loïc Lepiniec
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Jonathan Lapleau's curator insight, January 12, 4:34 AM
All you want to know about Tomatoes metabolism is here !
Rescooped by Guojian HU from Plant Sciences
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International Conference SPS 2018 - Plant Sciences for the Future  July 4-6, 2018 Saclay,  Paris 

International Conference SPS 2018 - Plant Sciences for the Future  July 4-6, 2018  Saclay,  Paris  | plant molecular biology | Scoop.it

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Live Confocal Imaging of Developing Arabidopsis Flowers | Protocol

Live Confocal Imaging of Developing Arabidopsis Flowers | Protocol | plant molecular biology | Scoop.it
Live confocal imaging provides biologists with a powerful tool to study development. Here, we present a detailed protocol for th
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A chemical genetic roadmap to improved tomato flavor

A chemical genetic roadmap to improved tomato flavor | plant molecular biology | Scoop.it
Commercially available tomatoes are renowned these days for sturdiness, but perhaps not for flavor. Heirloom varieties, on the other hand, maintain the richer flavors and sweeter tomatoes of years past. Tieman et al. combined tasting panels with chemical and genomic analyses of nearly 400 varieties of tomatoes. They identified some of the flavorful components that have been lost over time. Identification of the genes that have also gone missing provides a path forward for reinstating flavor to commercially grown tomatoes.

Science , this issue p. [391][1]

[1]: /lookup/doi/10.1126/science.aal1556

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Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN. Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.

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A flower is born: an update on Arabidopsis floral meristem formation

A flower is born: an update on Arabidopsis floral meristem formation | plant molecular biology | Scoop.it
"In Arabidopsis, floral meristems appear on the flanks of the inflorescence meristem. Their stereotypic development, ultimately producing the four whorls of floral organs, is essentially controlled by a network coordinating growth and cell-fate determination. This network integrates hormonal signals, transcriptional regulators, and mechanical constraints. Mechanisms regulating floral meristem formation have been studied at many different scales, from protein structure to tissue modeling. In this paper, we review recent findings related to the emergence of the floral meristem and floral fate determination and examine how this field has been impacted by recent technological developments."

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Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. - Science

Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. - Science | plant molecular biology | Scoop.it
Abstract
The determinants that specify the genomic targets of Polycomb silencing complexes are still unclear. Polycomb silencing of Arabidopsis FLOWERING LOCUS C (FLC) accelerates flowering and involves a cold-dependent epigenetic switch. Here we identify a single point mutation at an intragenic nucleation site within FLC that prevents this epigenetic switch from taking place. The mutation blocks nucleation of plant homeodomain-Polycomb repressive complex 2 (PHD-PRC2) and indicates a role for the transcriptional repressor VAL1 in the silencing mechanism. VAL1 localizes to the nucleation region in vivo, promoting histone deacetylation and FLC transcriptional silencing, and interacts with components of the conserved apoptosis- and splicing-associated protein (ASAP) complex. Sequence-specific targeting of transcriptional repressors thus recruits the machinery for PHD-PRC2 nucleation and epigenetic silencing.

Via Loïc Lepiniec
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Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins

Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins | plant molecular biology | Scoop.it
Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins | The auxin-sensitive Aux/IAA transcriptional repressors regulate approximately 35% of the annotated genes in Physcomitrella patens and exhibit complex interactions with both the activating and repressing ARF transcription factors.
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Writing workshop 2016

How to write scientific research articles- from structuring your paper to polishing it, ethical issues in writing and figure preparation, and peer review

Via Mary Williams
Guojian HU's insight:

I ran a two-hour writing workshop for scientists yesterday at the University of Nottingham - here are my slides.

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Mary Williams's curator insight, March 10, 2016 7:28 AM

I ran a two-hour writing workshop for scientists yesterday at the University of Nottingham - here are my slides.

Jennifer Mach's curator insight, March 21, 2016 3:51 PM

I ran a two-hour writing workshop for scientists yesterday at the University of Nottingham - here are my slides.

Thirumurugan's curator insight, March 26, 2016 5:05 AM

I ran a two-hour writing workshop for scientists yesterday at the University of Nottingham - here are my slides.

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Embryonic lethality of Arabidopsis abp1-1 is caused by deletion of the adjacent BSM gene

Embryonic lethality of Arabidopsis abp1-1 is caused by deletion of the adjacent BSM gene | plant molecular biology | Scoop.it
Decades of research have suggested that AUXIN BINDING PROTEIN 1 (ABP1) is an essential membrane-associated auxin receptor, but recent findings directly contradict this view. Here we show that embryonic lethality observed in abp1-1, which has been a cornerstone of ABP1 studies, is caused by the deletion of the neighbouring BELAYA SMERT (BSM) gene, not by disruption of ABP1. On the basis of our results, we conclude that ABP1 is not essential for Arabidopsis development.
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Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate | eLife

Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate | eLife | plant molecular biology | Scoop.it

Reprogramming of cell identities during development frequently requires changes in the chromatin state that need to be restricted to the correct cell populations. Here we identify an auxin hormone-regulated chromatin state switch that directs reprogramming from transit amplifying to primordium founder cell fate in Arabidopsis inflorescences. Upon auxin sensing, the MONOPTEROS transcription factor recruits SWI/SNF chromatin remodeling ATPases to increase accessibility of the DNA for induction of key regulators of flower primordium initiation. In the absence of the hormonal cue, auxin sensitive Aux/IAA proteins bound to MONOPTEROS block recruitment of the SWI/SNF chromatin remodeling ATPases in addition to recruiting a co-repressor/histone deacetylase complex. This simple and elegant hormone-mediated chromatin state switch is ideally suited for iterative flower primordium initiation and orchestrates additional auxin-regulated cell fate transitions. Our findings establish a new paradigm for nuclear response to auxin. They also provide an explanation for how this small molecule can direct diverse plant responses.SWI/SNF chromatin remodeling complexes act as ‘gatekeepers’ for auxin responses and directly interact with the auxin response factor MONOPTEROS.

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A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells - Cell Reports

A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells - Cell Reports | plant molecular biology | Scoop.it

(via T. Lahaye, thx)

Dalvai et al, 2015

Conventional affinity purification followed by mass spectrometry (AP-MS) analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs) to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.


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Very interesting!

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A DEMETER-like DNA demethylase governs tomato fruit ripening

A DEMETER-like DNA demethylase governs tomato fruit ripening | plant molecular biology | Scoop.it

In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DMLs). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only a few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here, we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripening— an important developmental process unique to plants. RNAi SlDML2 knockdown results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato.

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Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers

Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers | plant molecular biology | Scoop.it
Genetic modification plays a vital role in breeding new crops with excellent traits. Almost all the current genetic modification methods require regeneration from tissue culture, involving complicated, long and laborious processes. In particular, many crop species such as cotton are difficult to regenerate. Here, we report a novel transformation platform technology, pollen magnetofection, to directly produce transgenic seeds without regeneration. In this system, exogenous DNA loaded with magnetic nanoparticles was delivered into pollen in the presence of a magnetic field. Through pollination with magnetofected pollen, transgenic plants were successfully generated from transformed seeds. Exogenous DNA was successfully integrated into the genome, effectively expressed and stably inherited in the offspring. Our system is culture-free and genotype independent. In addition, it is simple, fast and capable of multi-gene transformation. We envision that pollen magnetofection can transform almost all crops, greatly facilitating breeding processes of new varieties of transgenic crops.

Via Loïc Lepiniec
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Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene

Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene | plant molecular biology | Scoop.it

Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing “jointless” fruit stems that reduced fruit dropping and facilitated mechanical harvesting. Stacking both beneficial traits caused undesirable branching and sterility due to epistasis, which breeders overcame with suppressors. However, this suppression restricted the opportunity for productivity gains from weak branching. Exploiting natural and engineered alleles for multiple family members, we achieved a continuum of inflorescence complexity that allowed breeding of higher-yielding hybrids. Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms.

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Coordination of auxin-triggered leaf initiation by tomato LEAFLESS

Coordination of auxin-triggered leaf initiation by tomato LEAFLESS | plant molecular biology | Scoop.it
Lateral plant organs, particularly leaves, initiate at the flanks of the shoot apical meristem (SAM) following auxin maxima signals; however, little is known about the underlying mechanisms. Here, we show that tomato leafless (lfs) mutants fail to produce cotyledons and leaves and grow a naked pin while maintaining an active SAM. A similar phenotype was observed among pin-like shoots induced by polar auxin transport inhibitors such as 2,3,5-triiodobenzoic acid (TIBA). Both types of pin-like shoots showed reduced expression of primordia markers as well as abnormal auxin distribution, as evidenced by expression of the auxin reporters pPIN1:PIN1:GFP and DR5:YFP. Upon auxin microapplication, both lfs meristems and TIBA-pin apices activated DR5:YFP expression with similar kinetics; however, only lfs plants failed to concurrently initiate leaf primordia. We found that LFS encodes the single tomato ortholog of Arabidopsis DORNRONSCHEN (DRN) and DRN-like (DRNL) genes and is transiently expressed at incipient and young primordia, overlapping with auxin response maxima. LFS is rapidly induced by auxin application, implying feed-forward activity between LFS and auxin signals. However, driving LFS at auxin response maxima sites using the DR5 promoter fails to fully rescue lfs plants, suggesting that additional, auxin-independent regulation is needed. Indeed, extended GCC-box elements upstream of LFS drove primordia-specific expression in a LFS-dependent but auxin-independent manner. We thus suggest that LFS transiently acts at the site of primordia initiation, where it provides a specific context to auxin response maxima culminating in leaf primordia initiation.
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PRC2 Represses Hormone-Induced Somatic Embryogenesis in Vegetative Tissue of Arabidopsis thaliana

PRC2 Represses Hormone-Induced Somatic Embryogenesis in Vegetative Tissue of Arabidopsis thaliana | plant molecular biology | Scoop.it
Author Summary Somatic embryogenesis provides the strongest support for plant cell totipotency but reprogramming of non-reproductive tissue is problematic or even impossible in many plant species. Here we show that the activity of Polycomb Repressive Complex 2 (PRC2) constitutes a major barrier to hormone-mediated establishment of embryogenic competence in plant vegetative tissue. We identify a conservative set of transcription factors whose expression coincides with the establishment of embryogenic competence in vegetative tissue, among which are key developmental regulators of root, shoot and embryo development. We show that lowering the PRC2-imposed barrier combined with activating hormone treatments establishes embryogenic competence in different tissue types, which opens possibilities for novel strategies to plant cell identity reprogramming.

Via Loïc Lepiniec
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Widespread natural variation of DNA methylation within angiosperms

Widespread natural variation of DNA methylation within angiosperms | plant molecular biology | Scoop.it
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Via Andres Zurita
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The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes - Krogan - 2016 - New Phytologist -

The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes - Krogan - 2016 - New Phytologist - | plant molecular biology | Scoop.it
The regulatory effect auxin has on its own transport is critical in numerous self-organizing plant patterning processes. However, our understanding of the molecular mechanisms linking auxin signal transduction and auxin transport is still fragmentary, and important regulatory genes remain to be identified.
To track a key link between auxin signaling and auxin transport in development, we established an Arabidopsis thaliana genetic background in which fundamental patterning processes in both shoot and root were essentially abolished and the expression of PIN FORMED (PIN) auxin efflux facilitators was dramatically reduced.
In this background, we demonstrate that activating a steroid-inducible variant of the auxin response factor (ARF) MONOPTEROS (MP) is sufficient to restore patterning and PIN gene expression. Further, we show that MP binds to distinct promoter elements of multiple genetically defined PIN genes.
Our work identifies a direct regulatory link between central, well-characterized genes involved in auxin signal transduction and auxin transport. The steroid-inducible MP system directly demonstrates the importance of this molecular link in multiple patterning events in embryos, shoots and roots, and provides novel options for interrogating the properties of self-regulated auxin-based patterning in planta.
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A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop

A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop | plant molecular biology | Scoop.it

Artemisinin-based therapies are the only effective treatment for malaria, the most devastating disease in human history. To meet the growing demand for artemisinin and make it accessible to the poorest, an inexpensive and rapidly scalable production platform is urgently needed. Here we have developed a new synthetic biology approach, combinatorial supertransformation of transplastomic recipient lines (COSTREL), and applied it to introduce the complete pathway for artemisinic acid, the precursor of artemisinin, into the high-biomass crop tobacco. We first introduced the core pathway of artemisinic acid biosynthesis into the chloroplast genome. The transplastomic plants were then combinatorially supertransformed with cassettes for all additional enzymes known to affect flux through the artemisinin pathway. By screening large populations of COSTREL lines, we isolated plants that produce more than 120 milligram artemisinic acid per kilogram biomass. Our work provides an efficient strategy for engineering complex biochemical pathways into plants and optimizing the metabolic output.


Via Loïc Lepiniec
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Auxin response factors - Chandler - 2016 - Plant, Cell & Environment -

Auxin response factors - Chandler - 2016 - Plant, Cell & Environment - | plant molecular biology | Scoop.it
Auxin signalling involves the activation or repression of gene expression by a class of auxin response factor (ARF) proteins that bind to auxin response elements in auxin-responsive gene promoters. The release of ARF repression in the presence of auxin by the degradation of their cognate auxin/indole-3-acetic acid repressors forms a paradigm of transcriptional response to auxin. However, this mechanism only applies to activating ARFs, and further layers of complexity of ARF function and regulation are being revealed, which partly reflect their highly modular domain structure. This review summarizes our knowledge concerning ARF binding site specificity, homodimer and heterodimer multimeric ARF association and cooperative function and how activator ARFs activate target genes via chromatin remodelling and evolutionary information derived from phylogenetic comparisons from ARFs from diverse species. ARFs are regulated in diverse ways, and their importance in non-auxin-regulated pathways is becoming evident. They are also embedded within higher-order transcription factor complexes that integrate signalling pathways from other hormones and in response to the environment. The ways in which new information concerning ARFs on many levels is causing a revision of existing paradigms of auxin response are discussed.
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A proposed regulatory framework for genome-edited crops : Nature Genetics

A proposed regulatory framework for genome-edited crops : Nature Genetics | plant molecular biology | Scoop.it
Sanwen Huang, Detlef Weigel, Roger Beachy and Jiayang Li propose a regulatory framework for precision breeding with genome-edited crops. They argue that society should benefit from the latest advances in plant genetics and genomics.

Via Loïc Lepiniec
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High-frequency, precise modification of the tomato genome - Genome Biol.

High-frequency, precise modification of the tomato genome - Genome Biol. | plant molecular biology | Scoop.it

(via T. Lahaye, thx)

Čermák et al, 2015

The use of homologous recombination to precisely modify plant genomes has been challenging, due to the lack of efficient methods for delivering DNA repair templates to plant cells. Even with the advent of sequence-specific nucleases, which stimulate homologous recombination at predefined genomic sites by creating targeted DNA double-strand breaks, there are only a handful of studies that report precise editing of endogenous genes in crop plants. More efficient methods are needed to modify plant genomes through homologous recombination, ideally without randomly integrating foreign DNA.


Via dromius
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Non-transgenic Plant Genome Editing Using Purified Sequence-Specific Nucleases: Molecular Plant

Non-transgenic Plant Genome Editing Using Purified Sequence-Specific Nucleases: Molecular Plant | plant molecular biology | Scoop.it

(via J. Boch, thx)

Luo et al, 2015

Sequence-specific nucleases, including zinc-finger nucleases, meganucleases, TAL effector nucleases (TALENs), and CRISPR/Cas systems, have been used to introduce targeted mutations in a wide range of plant species (Voytas, 2013; Baltes and Voytas, 2015). However, delivery of these nucleases using traditional transformation methods (e.g., particle bombardment, Agrobacterium or protoplast transformation) may result in undesired genetic alterations due to random insertion of nuclease-encoding DNA into the host genome.


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A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs - Spiegelman - 2015 - The Plant Journal - Wiley Online Library

A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs - Spiegelman - 2015 - The Plant Journal - Wiley Online Library | plant molecular biology | Scoop.it
The plant vascular system serves as a conduit for delivery of both nutrients and signaling molecules to various distantly located organs. The anucleate sieve tube system of the angiosperm phloem delivers sugars and amino acids to developing organs, and has recently been shown to contain a unique population of RNA and proteins. Grafting studies have established that a number of these macromolecules are capable of moving long distances between tissues, thus providing support for operation of a phloem-mediated inter-organ communication network. Currently, our knowledge of the roles played by such phloem-borne macromolecules is in its infancy. Here, we show that, in tomato, translocation of a phloem-mobile cyclophilin, SlCyp1, from a wild-type scion into a mutant rootstock results in restoration of vascular development and lateral root initiation. This process occurs through reactivation of auxin response pathways and reprogramming of the root transcriptome. Moreover, we show that long-distance trafficking of SlCyp1 is associated with regulation of the shoot-to-root ratio in response to changing light intensities, by modulating root growth. We conclude that long-distance trafficking of SlCyp1 acts as a rheostat to control the shoot-to-root ratio, by mediating root development to integrate photosynthesis and light intensity with requirements for access to water and mineral nutrients.
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