What We’re Reading: July 28th

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This week’s edition of What We’re Reading is guest edited by Dr. Bhavisha P. Sheth, who is currently working as a DST- Science, Technology and Innovation Policy Postdoctoral Fellow at the Entrepreneurship Development Institute of India (EDII), India. Her current research work focusses on Policy research studies of Science and Technology Entrepreneurship. She pursued a PhD in Plant Biotechnology and her thesis was awarded ‘the Best Life Sciences PhD Thesis’ in the state. During her PhD, she was a recipient of the UGC Junior and Senior Research Fellowships from Govt. of India. She has published 15 papers in national and international journals of high repute as well as presented her research in various conferences in India and abroad.

Differentially regulated orthologs in sorghum and the subgenomes of maize

Gene expression patterns are often used to assign function, but how tight is the correlation between expression and function? Zhang et al. addressed this question by investigating whether orthologous genes in two species (including the two subgenomes of maize) show similar patterns of expression. Specifically, they carried out a genome-wide transcriptional comparison of cold-response in sorghum and maize. They found that most orthologous genes were not similarly regulated in maize and sorghum, although early-expressed cold-response genes showed greater cross-species conservation than later genes. Further, genes with conserved transcriptional regulation patterns had a low ratio of non-synonymous to synonymous substitutions, suggesting stronger selection. The authors suggest that cross-species expression comparisons can reveal functionally important genes. Plant Cell. 10.1105/tpc.17.00354

A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone ($)

By measuring the length of Arabidopsis and rice roots treated with synthetic peptides, Pruitt et al. showed that RaxX, a peptide produced by the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo), mimicked the growth-stimulating activity of plant peptides containing sulfated tyrosine residues (PSYs). They propose that the pathogen produces RaxX to promote growth of infected tissues, and they also show that RaxX-deficient Xanthomonas have decreased virulence. Unlike growth-promoting PSYs, the pathogen-derived peptide induces immune responses, indicating that the plant is able to distinguish between the endogenous and pathogen-derived peptides. New Phytol. 10.1111/nph.14609

 

Rice peroxisomal ascorbate peroxidase knockdown affects ROS signaling and triggers early leaf senescence ($)

Ribeiro et al. describe functional aspects of the rice gene OsAPX4 encoding a peroxisomal ascorbate peroxidase, which shows the highest level of expression in leaves. RNAi silencing of this gene did not lead to an increase in the intracellular H2O2 levels and no change was observed in growing plants. However, a drastic change was seen in  aging plants which exhibited early senescence. The study suggests that OsAPX4 plays a significant role in ROS signalling during leaf senescence Plant Science. 10.1016/j.plantsci.2017.07.009

 

Heterologous expression of two GPATs from Jatropha curcas alters seed oil levels in transgenic Arabidopsis thaliana ($)

Mishra et al. (2017) characterized two GPATs (glycerol-3-phosphate acyltransferase) JcGPAT1 and JcGPAT2 in the biofuel seed oil crop Jatropha curcas. These GPATs showed sequence homology with Arabidopsis acyltransferase-1 (ATS1) and Arabidopsis GPAT (AtGPAT9) respectively. Subcellular localization studies indicated that JcGPAT1 is localized in plastids whereas JcGPAT2 is localized in the endoplasmic reticulum. Overexpression of these enzymes in Arabidopsis thaliana led to an increase in total seed oil content – as much as a 43-60% increase in transgenic lines overexpressing JcGPAT2. This study highlights the role of these GPATs in oil biosynthesis in Jatropha curcas. Plant Science 10.1016/j.plantsci.2017.07.003  Image source: Elitre

 

Phylogenetic analysis of proteins involved in the stringent response in plant cells ($)

The stringent response in bacteria is a global transcriptional response to stress, mediated by the second messenger ppGpp (guanosine 5′-diphosphate 3′-diphosphate) which is synthesized by the action of guanosine 5′-triphosphate 3′-diphosphate pyrophosphatase (GppA) or exopolyphosphatase (Ppx). Recently it was shown that plants also exhibit a stringent response mediated by ppGpp, but the origin of this response in plants has not been resolved.  Ito et al. investigated the distribution of the gppA/ppx gene families as well as the RSH hydrolase gene family. Their data indicate that genes involved in the stringent response were likely introduced to plants from various bacterial phyla by lateral gene transfer events. Moreover, the results suggest that plant RSH homologs likely function in the plastid, whereas the plant gppA/ppx homologs may function in the cytosol. J. Plant Research 10.1007/s10265-017-0922-8

 

Structure and expression patterns of dehydrin gene family in barley ($)

Dehydrins are proteins that have important roles in dehydration stress in plants. Abedini et al. carried out a phylogenetic analysis of barley dehydrins and investigated physiological and gene expression levels in tolerant (HV1), and susceptible (HV2) cultivars and a drought tolerant Iranian wild barley genotype (Spontaneum; HS) subjected to water stress and after recovery. They found notable differences in physiological responses and dehydrin expression levels in the drought tolerant varieties as compared to the susceptible variety, as well as between the wild and cultivated genotypes, supporting the role for dehydrins in vegetative drought tolerance. As barley is an important grain in arid regions, the study will contribute to future breeding efforts for drought tolerance J. Plant Research 10.1007/s10265-017-0941-5.

 

Identification and functional analysis of new peroxygenases in oat ($)

Peroxygenases catalyze the hydroperoxide dependent epoxidation of unsaturated fatty acids. Benaragama et al. identified two novel peroxygenases (AsPXG2 and AsPXG3) in oat (Avena sativa L.) AsPXG2 and AsPXG3 share structural similarity by having a single transmembrane domain, conserved histidines for heme-binding as well as a conserved EF-hand motif. However, they show only 50% amino acid identity with each other, and the activity of heterologously-expressed AsPXG3 is much higher than that of AsPXG2. Site-directed mutagenesis of AsPXG3 showed that replacement of two conserved histidines by alanine resulted in complete loss of activity, and substitution of three conserved residues surrounding the two histidines resulted in reduction of enzymatic activity by more than 80%, suggesting that these conserved residues are located near the catalytic sites, where they coordinate the heme group and define the shape and size of the catalytic site. Planta 10.1007/s00425-017-2729-1.

 

Vesicle dynamics during plant cell cytokinesis reveals distinct developmental phases

The cell plate is a common feature of plant cell divisions, but the mechanisms forming this structure are not completely understood.  The cell plate is made from membrane vesicles carrying polysaccharide cargo, and thousands of tiny vesicles fuse together to form one cell plate.  Observing fluorescence micrographs alone cannot provide a full picture of cell plate biogenesis, so Oostende-Triplet et al. developed FluMOS (Fluorescence Morphological Operators Software).  This program can identify and analyze cell plates within fluorescence confocal images.  The authors identified three distinct phases of cell plate expansion in N. tabacum BY-2 cells based on the growth rate of the cell plate.  FluMOS quantitated vesicle movement towards nascent cell plates.  Initially, the vesicles move quickly to the cell plate when its growth begins.  As the cell plate growth, vesicle movement remains high at the edges, but vesicle movement slows in the center of the cell plate.  Pharmacological inhibition of membrane trafficking and protein synthesis showed both processes contribute to cell plate expansion. (Summary by Daniel Czerny) Plant Physiol. 10.1104/pp.17.00343

Are you interested in contributing to What We’re Reading? We welcome informal, one-off summaries, but you can also formalize your contributions by applying to be a Plantae Fellow, like Daniel and Bhavisha are!

 

From Light to Food – Organization of Photosynthetic Complexes

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MacGregor-Chatwin et al. map the cellular organization of photosynthetic protein complexes http://www.plantcell.org/content/29/5/1119

Life on Earth depends on photosynthesis, the source of all of our food, oxygen, and most of our energy. Two pigment-protein complexes called Photosystems I and II drive photosynthesis. These chlorophyll-protein complexes are housed in the membranes of cyanobacteria, algae, and plants. The two photosystems convert solar energy and water into chemical energy for making carbohydrates and other cell materials from carbon dioxide. The distribution and organization of the photosystems, for example which proteins they sit next to in the membrane, are critical for solar energy capture and conversion. Photosystem I is the dominant photosynthetic complex in cyanobacteria, and we know its detailed structure and how it works. However, prior to this work, we did not know where this photosystem sits in the photosynthetic membrane, or precisely where the photosystem-containing membranes lie within the cell.

MacGregor-Chatwin et al. set out to discover the location of Photosystem I in several types of cyanobacterium, using atomic force microscopy of isolated membranes and high resolution fluorescence microscopy of whole cells. These two advanced microscopy techniques are highly complementary as they detect different features. Atomic force microscopy is a super-high resolution imaging tool that allows the distribution and orientation of individual complexes to be visualized. High resolution fluorescence microscopy reveals the pigments within the membrane domains and so the identity of the complexes. Thus the authors were able to construct detailed models of the orientation of these pigment-protein complexes inside membranes and cells.

They found that Photosystem I complexes form extensive, ordered assemblies in some regions of the photosynthetic membrane in several different cyanobacteria species. They built a structural model of one such region containing 96 Photosystem I complexes and 27,648 chlorophyll molecules, and showed how harvested solar energy moves between the photosystem complexes.

The authors also found that Photosystem I likely sits next to Photosystem II complexes in other parts of the membrane. Here, contact zones between the two photosystems provide sites for docking large protein structures called phycobilisomes, which contain many pigments for absorbing light. The phycobilisomes sit on the membrane and feed harvested energy to both Photosystems I and II.

The aim of understanding photosynthesis requires that we know the structures, amounts, and cellular locations of the machinery that harvests and stores solar energy. The future challenge is to map the distribution and organization of all major photosynthetic complexes within the photosynthetic membrane.

MacGregor-Chatwin,C., Sener, M., Barnett, S.F.H., Hitchcock, A., Barnhart-Dailey, M.C., Maghlaoui. K., Barber, J., Timlin, J.A., Schulten, K., and Hunter, C.N. (2017). Lateral segregation of photosystem I in cyanobacterial thylakoids. Plant Cell ​10.​1105/​tpc.​17.​00071.

Maize Meristem Matters

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Tsuda et al. explore the function of BLH transcription factors in maize meristems

Plants have specialized tissues at the tips of roots and shoots called meristems. Meristem cells are what keep the plant growing; they are undifferentiated cells that continue to divide, providing new cells for growth. The progeny of the cells in the meristem can develop into many different cells types. In many ways plant meristem cells resemble stem cells in animals.

Tsuda et al. identified a mutant in maize that shows defects in all of the shoot meristems as well as the vascular system. The plant vascular system is also critical for growth, as it transports water, sugars and other metabolites throughout the plant. The genes affected in the mutant encode transcription factors, special proteins that regulate the expression of other genes; in other words, they determine when other genes are turned on or off to produce the proteins that they encode. The maize genes identified in this study encode a type of transcription factor known as BELL1-like Homeobox (BLH) transcription factors.

Homeobox genes are present in all multicellular organisms, including plants, animals, and fungi. These genes encode transcription factors that often direct basic anatomy and the formation of body parts. In plants, Knotted1-like homeobox (KNOX) genes encode transcription factors that play an important role in meristem maintenance; they are crucial in determining where and when meristem cells differentiate into other cells that will develop into the different plant organs. In some plants, such as the model plant Arabidopsis thaliana, BLH proteins are known to interact with KNOX proteins in shoot meristem maintenance. Mutants in KNOX genes have known phenotypes in maize, but maize mutants in BLH genes have not been described before.

Maize, like all grasses, is fundamentally different from Arabidopsis in that it is a monocotyledon plant, as opposed to a dicotyledon plant. One of the main differences is that monocots have scattered veins in the stem, whereas dicot stems have a ring of vascular tissue. Many important crop plants, in addition to maize, are monocots, such as rice, wheat, barley, sugarcane, and forage grasses.

The maize mutant identified by Tsuda et al. has abnormally fused veins, suggesting that the BLH genes affected in this mutant normally function to keep veins from fusing. In addition, smaller veins normally located near the surface of the stem are missing in the mutant. The flowering heads and tips of leaves at the top of the mutant plants become dehydrated and die in field conditions, presumably because of these profound differences in the vasculature.

A future challenge is to identify the target genes – those genes that are turned on or off by the BLH transcription factors – that are responsible for the fused veins and missing smaller veins in the mutant.

Tsuda, K., Abraham-Juarez, M.J., Maeno, A., Dong, Z., Aromdee, D., Meeley, R., Shiroishi, T., Nonomura, K., and Hake, S. (2017). KNOTTED1 cofactors, BLH12 and BLH14, regulate internode patterning and vein anastomosis in maize. Plant Cell doi:10.1105/tpc.16.00967.

How Rice Seedlings Emerge from Soil

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Xiong et al. explore the action of plant hormones that control how rice seedlings emerge from the soil http://www.plantcell.org/content/29/5/1053

By Qing Xiong, Bao Ma, and Lu Xiang

Flowering plants begin their life cycle as a seed beneath the soil surface. With adequate water and the right temperature, the seeds germinate and seedlings develop. In rice and other grasses, a sheath called the coleoptile protects the leaves of the emerging shoot. Below the coleoptile, a short stem called the mesocotyl develops in the dark and pushes the base of the coleoptile toward the soil surface. The elongation of these organs is regulated both by genetic and environmental factors that stimulate the emergence of rice seedlings.

The gaseous plant hormone ethylene is known to play an important role in promoting seedling emergence from the soil. Ethylene production is induced if rice seedlings are covered with soil, and this causes elongation of the mesocotyl and coleoptile. We would like to know how ethylene works in this process: what is happening inside the plant that leads to elongation of these parts of the shoot and emergence from the soil? We found that ethylene works together with another plant hormone, jasmonic acid (JA), to control elongation and promote the emergence of rice seedlings from the soil.

We identified a rice mutant, called gaoyao1 (gy1), that has an abnormally long coleoptile and mesocotyl (gaoyao is a Chinese name for “high waisted”), and cloned the gene, called GY1, responsible for these mutant characteristics. We found that GY1 encodes an enzyme that acts at the first step in the biosynthesis of the plant hormone jasmonic acid (JA). This shows that JA normally inhibits the elongation of rice seedlings, since knocking out GY1 function in the gy1 mutant led to the abnormally long shoots. During rice seedling emergence, ethylene production increases and JA content decreases. Our work shows that ethylene signaling inhibits the action of GY1, thus suppressing the biosynthesis of JA and promoting seedling elongation.

Interestingly, although the mesocotyl and colepotile of the gy1 mutant are already abnormally elongated, we found that supplying ethylene to mutant seedlings promoted even further elongation, suggesting that ethylene may also act on shoot elongation through another pathway that is independent of GY1. Future research will focus on uncovering additional factors that work with ethylene to affect the emergence of rice seedlings.

In addition, we made the important discovery that some rice cultivars carry a previously undescribed natural variant of the GY1 gene, and these cultivars have longer stems and shoots compared to common rice seedlings. The discovery of natural variation of the GY1 gene should aid breeding for new rice cultivars that are adapted to growing in dry soil. Through breeding, the GY1 gene variant could be introduced into varieties lacking it to produce new rice cultivars, since the variation does not appear to affect rice yield.

Xiong, Q.,  Ma, B.,  Lu, X., Huang, Y.-H., He, S.-J., Yang, C., Yin, C.-C.,  Zhao, H., Zhou, Y., Zhang, W.-K., Wang, W.-S., Li, Z.-K., Chen, S.-Y., and Zhang, J.-S. (2017). Ethylene-Inhibited Jasmonic Acid Biosynthesis Promotes Mesocotyl/Coleoptile Elongation of Etiolated Rice Seedlings. Plant Cell 29: 1053-1072.

 

Funding Opportunity: NSF Solicits Proposals to Expand INCLUDES National Network

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On July 14, the National Science Foundation (NSF) released a Dear Colleague Letter (DCL) soliciting proposals to expand the Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science (INCLUDES) program.  The DCL invites proposals for Early-concept Grants for Exploratory Research (EAGER), workshops and conferences, and supplements to existing grants to create new on-ramps to the INCLUDES National Network.  INCLUDES is one of the thrusts of the NSF 10 Big Ideas for Future Investment, and efforts through INCLUDES to increase diversity in Science, Technology, Engineering, and Mathematics (STEM) are a top priority for NSF Director France Córdova.

NSF is looking for innovative ways to include new and existing NSF programs in the INCLUDES National Network as part of an effort to create linkages between INCLUDES and all of NSF’s programs to broaden participation.  This solicitation seeks projects to evaluate, aggregate, and implement evaluations and best practices; conduct fundamental research on expanding participation, and scale up programs to increase diversity.

As part of the INCLUDES initiative, NSF has already awarded Design and Development Launch Pilots to develop models for collective action to increase participation in STEM by underrepresented groups.  NSF is expected to release solicitations this year for both a Backbone Organization to help coordinate the INCLUDES network, as well as for an Alliance competition that will be open to those who have previously won pilot awards and their partners.

EAGER awards are limited to $300,000, and maximum conference awards are $250,000.  Both awards may last up to two years.  Proposal submissions for EAGERs and conferences are due either November 13, 2017 or April 16, 2018.  Those who would like to apply should send a one-pager summarizing their project to NSF to ensure relevance and determine the applicable deadline for the particular proposal.  Supplemental funding is available for existing grants in all NSF directorates.

Additional information is available in the DCL which can be found at https://www.nsf.gov/pubs/2017/nsf17111/nsf17111.jsp.  More information on the INCLUDES program is available at https://www.nsf.gov/funding/pgm_summ.jsp.

Using Metabolism to Improve Maize Breeding

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Cañas et al. study the relationships between maize leaf metabolism and grain yield to identify putative markers for breeding http://www.plantcell.org/content/29/5/919

By Rafael A. Cañas, Peter J. Lea and Bertrand Hirel

In crops, several metabolic pathways are involved in the control of biomass production and yield, notably those involved in primary carbon and nitrogen metabolism. For these metabolic pathways, metabolite fluxes and metabolite accumulation strongly depends on the plant genetic background and on the environmental conditions.

Maize is now ranked first among crops, comprising 41% of the total world cereal production. It is mostly used for feeding animals and humans and to a lesser extent the production of  biofuel and starch-derived commercial products. Maize was domesticated more than 7,000 years ago in Mexico and then exported and cultivated in the rest of the world. The worldwide expansion of maize cultivation allowed the creation of a huge reservoir of genetic resources. These genetic resources are now used by breeders to improve maize productivity and by scientists to decipher the genetic and physiological basis of grain and biomass production.

Most scientific approaches developed so far have not been able to link plant metabolism to agronomic traits such as yield. We developed a new modelling approach to investigate whether there was any relationship between leaf metabolism and grain production, by combining metabolomics with analysis and modelling of enzymatic reactions, metabolite flux, and physiological and agronomic traits. Taking advantage of maize genetic diversity, we used this approach to study nineteen genetically distinct maize lines from Europe and America.

During grain filling, leaf metabolic composition appeared to be a reliable marker, allowing a classification matching the genetic diversity of the lines. Both correlation studies and metabolic network analyses allowed the description of a maize ideotype (model of a new variety) with a high grain yield potential. Such an ideotype is characterized by a low accumulation of soluble amino acids and carbohydrates in the leaves and a high activity of enzymes involved in the C4 photosynthetic pathway and in the synthesis of amino acids derived from glutamate. Specific metabolites known as chlorogenates appear to be important markers that can be used to select for maize lines that produce larger kernels.

Genes controlling the synthesis and accumulation of metabolites might also be used as markers for breeding high yielding maize varieties. Optimizing their positive impact on plant productivity will require modifying their level of expression through genetic engineering or marker-assisted breeding in an integrated and coordinated way.

Cañas, R.A., Yesbergenova-Cuny, Z., Simons, M., Chardon, F., Armengaud, P., Quilleré, I., Cukier, C., Gibon, Y., Limami, A.M., Nicolas, S., Brulé, L., Lea, P.J., Maranas, C.D., and Hirel, B. (2017). Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield. Plant Cell 29: 919-943.

Review: Uncovering gene regulatory networks controlling plant cell differentiation ($)

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The transparency and simplicity of the Arabidopsis root apex has made it an excellent model through which to understand the processes that lead from undifferentiated meristem cells to mature root tissues. Drapek et al. review the gene regulatory networks (GRNs) that underlie the development of the endodermis in Arabidopsis root tips. They first summarize the roles of transcription factors including mobile transcription factors (those that move between cells) in the specification of the endodermal cells, and then they discuss the GRNs that control the differentiation of endodermal cells including the proper formation of the Casparian strip.  They conclude by describing outstanding questions and new approaches. Trends Genetics 10.1016/j.tig.2017.05.002

Update: Shining light on the function of NPH3/RPT2-like proteins in phototropin signalling

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Blue light regulates diverse functions including phototropism and chloroplast movements. Christie et al. summarize recent updates in understanding the signalling pathway between light perception by phototropins and downstream responses. They describe the central roles for the 33 members (in Arabidopsis) of the NRL protein family, named for the founding members NON-PHOTOTROPIC HYPOCOTYL (NPH3) and ROOT PHOTOTROPISM 2 (RPT2), and the four members of the  PHYTOCHROME KINASE SUBSRTATE (PKS) protein family. The authors also summarize the evolutionary origins of the blue-light signalling pathway in the green plant lineage and highlight ongoing questions including the need for biochemical characterization of many of these proteins. Plant Physiol. 10.1104/pp.17.00835

Review: The evolution of calcium-based signalling in plants

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Calcium signalling is a ubiquitous process in plants and other organisms. Transporters at the plasma and vacuolar (tonoplast) membranes control entry and exit of calcium ion into the cytoplasm, and it is the cytoplasmic calcium level ([Ca2+]cyt) that affects cellular responses, as calcium-binding proteins alter their activities or binding properties in response to changing calcium levels. Edel et al. review the diversity and distribution of various components of the calcium-based signalling process in plants as compared to animals, and speculate as to the forces that have shaped it in plants, including photosynthesis. Curr. Biol. 10.1016/j.cub.2017.05.020