What We’re Reading: January 6th

Review: Transport and homeostasis of K and P ($)

luanpkNitrogen (N), phosphorus (P), and potassium (K) are the three macronutrients required in highest amounts for plant growth. N is abundant in the atmosphere, therefore plentiful if we overlook the energetic costs of converting N2 to usable form. By contrast, K and P are present in limited amounts in the Earth’s crust, and their extraction can be challenging. Over the next few decades, achieving good crop yields by applying these macronutrients to soils will become more and more expensive. Luan et al. review current understanding of K and P transporters and the regulatory circuits that control their activities. Ultimately, exploiting this knowledge should lead to greater uptake and use efficiencies of these essential nutrients. J. Exp. Bot.  10.1093/jxb/erw444 Tags: Biochemistry, Ecophysiology, Growth Regulation, Metabolism, Transport

Review: Adaptive strategies for N metabolism in P deficient legume nodules ($)

Plant Science Figures 3May 2016.keyLegume nodules fix N, but their function has a high requirement for P, making nitrogen-fixation highly sensitive to P deficiency. Valentine et al. review how P limitation affects nodule function and also how nodules respond and adapt to P deficiency, drawing largely on studies of Virgilia divaricata, a legume endemic to P-poor soils of South Africa. One way that P deficiency affects nodule function is through the ADP:ATP ratio; N fixation and export from nodules has a high demand for energy.  Although nodules are strong sinks for P, with P limitation NO3 and NH4+ can become preferred N sources (over N2), a switch that impacts amino acid and carbon skeleton availability. Lessons from this tropical legume can point to potential traits for legume crop improvement in other nutrient-poor ecosystems. Plant Science 10.1016/j.plantsci.2016.12.010 Tags: Botany, Ecophysiology, Metabolism, Physiology, Transport

Review: The many roles of AVP1, a H+-PPase ($)

avp1The AVP1 gene encodes a proton-pumping pyrophosphatase (H+-PPase) localized to the vacuolar membrane, which means that it pumps H+ into the vacuole using energy stored in pyrophosphatase (PPi). The direct consequences of its action are the acidification of the vacuole and the removal of PPi from the cytosol. Indirect consequences derived from these direct effects include enhanced salinity tolerance, due to sequestration of Na+ in the vacuole via Na+/H+ exchange. However, other effects, such as enhanced plant size in non-stressed conditions, are not so easy to explain. Schilling et al. review the diverse roles of AVP1, including effects on sucrose transport, inferred from knock-out and overexpression studies, and discuss how this gene can be used to increase crop yields. Trends Plant Sci. 10.1016/j.tplants.2016.11.012 Tags: Bioenergetics, Cell Biology, Growth Regulation, Metabolism, Transport

Perspective: Computational Modeling of Auxin: A Foundation for Plant Engineering

engineeringpatternmulticoloured-800pxAuxins are a class of phytohormones that regulate many aspects of plant development. Morales-Tapia and Cruz-Ramírez review the current status of the available auxin-driven computational models and discuss plausible integration of these into a single model for plant development. Computational modeling of auxin through a single, unified model would enable predictions of plant behavior under diverse physical and biochemical constraints. However, the development of a single model is complicated, because different models incorporate different aspects of auxin function and behaviour including transport, formation of maxima and minima, canalization and cross-talk. Furthermore, different models are built on different platforms. The authors conclude, “Due to its complexity, a model of this nature would have to come from a large collaborative effort among the interested scientific community.” (Summary by Bhavisha Sheth) Frontiers Plant Sci. 10.3389/fpls.2016.01881 Tags: Computational Biology, Systems Biology

Homeodomain protein underpins classically-defined leaf shape variation in cotton ($)

cottonokraHomeodomain transcription factors are well-known as regulators of developmental patterning, including in leaves. Andres et al. examine the molecular basis behind leaf shape in cotton, particularly the Okra locus that was identified by breeders as a regulator of leaf shape. They show that the Okra locus encodes a homeodomain transcription factor, and that different leaf shapes (including normal, okra, super-okra and sub-okra) express allelic variants. Specifically, the narrower okra and super-okra leaves express higher levels of the gene. Suppressing this expression through viral-induced gene silencing transiently switches leaf shape to the broader normal form, demonstrating the importance of this gene in the control of leaf shape. As leaf shape is correlated with water-use efficiency, light interception and susceptibility to insects, these insights provide breeders with new tools. This paper would be a nice addition to a genetics course, especially if provided to students along with some of the classic studies of the Okra locus, such as Shoemaker (1909) and Green (1953). (Update: Author Dan Chitwood also recomments Hammond 1941a and 1941b for teaching).  Proc. Natl. Acad. Sci. USA 10.1073/pnas.1613593114 Tags: Applied Plant Biology, Botany, Development, Education and Outreach, Genetics

The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots

pltDue to plant cells’ shared walls and immobility, cell division, differentiation and expansion must be tightly regulated across space and time. The six members of the PLETHORA (PLT) transcription factor family distribute in gradients through the root tip and are largely responsible for its developmental patterning. Santuari et al. studied the gene set transcriptionally regulated by PLTs and showed that PLT gradients regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. PLTs’ effects are mediated in part through transcriptional control of genes involved in auxin synthesis and transport and other key developmental switches. (Summary by Bhavisha Sheth) Plant Cell 10.1105/tpc.16.00656  Tags: Computational Biology, Development, Genomics, Growth Regulation, Systems Biology

UV-B perceived by the UVR8 photoreceptor inhibits plant thermomorphogenesis

hayes-2017_currbiol_fig4emodel_01-04-17Ambient temperature can influence plant architecture, an effect termed thermomorphogenesis.  In A. thaliana, thermomorphogenesis phenotypes include stem elongation and changes in leaf elevation angles.  Increased auxin biosynthesis involving the transcription factor PIF4 is required for thermomorphogenesis, but the roles of other signals besides auxin remain unknown.  Hayes et al. studied how ultraviolet-B (UV-B) light perceived through the photoreceptor UVR8 influences thermomorphogenesis using duplicate experiments at 20°C & 28°C.  At 20°C & 28°C, PIF4 transcript abundance and thermomorphogenesis are both inhibited by signaling from heterodimers of UVR8 and the E3 ubiquitin ligase COP1.  This is consistent with the decrease in PIF4 protein levels seen at 20°C, but there is no similar decrease for 28°C.  At 28°C, the PIF4 protein is postulated to lose activity, and this loss is attributed to PIF4 binding to the bHLH protein HFR1 to form heterodimers that cannot bind DNA.  UV-B light uses multiple mechanisms to inhibit thermomorphogenesis, and this explains one facet of how a plant interacts with and adapts to its environment. (Summary by Daniel Czerny) Curr. Biol. 10.1016/j.cub.2016.11.004 Tags: Gene Regulation, Growth Regulation, Molecular Biology, Signals and Responses

Two independenent S-phase checkpoints regulate appressorium-mediated plant infection by rice blast fungus

talbot2The rice blast fungus Magnaporthe oryzae causes a devastating disease of rice that can reduce harvests by 30%. Infection of plant tissues by the fungus requires the formation of an appressorium, a specialized structure that builds up sufficient pressure to burst through the plant cuticle. Previous work showed that cell cycle progression is required for appressorium formation and function. Osés-Ruiz et al. identified two indpendent S-phase checkpoints that operate over two successive cell cycles and are both required for infection. Through genetic and inhibitor studies, the authors found that the first checkpoint responds to classic DNA damage signals, but passing through the second checkpoint requires appressorium turgor pressure buildup. Significantly, if this process is blocked, infection cannot occur. Proc. Natl. Acad. Sci. 10.1073/pnas.1611307114 USA Tags: Biotic Interactions, Cell Biology

Genome sequence and genetic diversity of European ash trees

ashgenomeAsh dieback (a fungal disease) and the beetle Agrilus planipennis (a herbivore) are crushing ash tree populations in the Northern Hemisphere. To shed light on the genetic basis of the trees’ susceptibility and to understand the genetic diversity of these trees, Sollars et al. have sequenced one individual from the UK and annotated its genome. Through a deep sequence analysis, they compared the genome structure with other species for which genomes are already available, revealing an interesting set of genes shared among them. They also investigated the genetic diversity between different ash tree populations from Europe with the goal of finding the underlying genetic bases of tree susceptibility to fungal disease and herbivory. The authors found a correlation between ash dieback susceptibility and glycosides production (which defends against herbivory), indicating that it may be difficult to generate trees with resistance to both fungal and herbivore attack. (Summary by Gaby Auge) Nature 10.1038/nature20786 Tags: Applied Plant Biology, Biotic Interactions, Computational Biology, Genomics

Integrating omics reveals insights into grape response to high temperature

grapeasHeat stress is one of the main abiotic stresses plants encounter. Jiang et al. used combined transcriptomic and proteomic data to explore the responses of grape leaves to elevated temperatures (35, 40, 45°C). Using high-throughput sequencing and the iTRAQ (isobaric tags for relative and absolute quantitation) method, they found that non-random posttranscriptional events, particularly alternative splicing, are important heat responses. Notably, heat-shock proteins and transcription factors associated with high temperature were particularly prone to alternative splicing at elevated temperatures. How these differently-spliced transcripts affects plant heat response remains to be explored. Plant Physiol.  10.1104/pp.16.01305 Tags: Abiotic Interactions, Ecophysiology, Gene Regulation, Genomics

Growth-ring studies show no growth enrichment in Canadian boreal forests despite 50 years of CO2 enhancement

borealforestIt has been argued that rising atmospheric CO2 levels might benefit plants by providing them more substrate for photosynthetic carbon-fixation. However, numerous studies have indicated that other factors interfere with a so-called CO2-fertilization benefit. Girardin et al. explore recent tree growth by analysing 873 tree-ring chronologies obtained from Canada’s National Forest Inventory. Although they observed species-related and regional differences, there was no strong overall change in growth over the past 60 years. The authors conclude that increased temperatures and effects on soil moisture have overridden any positive CO2-enrichment effects. They further observe that their data, which measures tree growth directly, shows some significant differences from observations obtained by remote sensing (NDVI: normalized difference vegetation index), supporting the need for continuing ground-based observations. Proc. Natl. Acad. Sci. USA 10.1073/pnas.1610156113 Tags: Botany, Ecophysiology, Environmental Plant Biology, Growth Regulation

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