From Light to Food – Organization of Photosynthetic Complexes

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

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

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

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

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 ($)

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

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

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

What We’re Reading: July 21

Review: The evolution of calcium-based signalling in plants

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

 

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

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

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: Unlocking the potential of plant phenotyping data through integration and data-driven approaches

Coppens et al.  describe the challenges and opportunities for developing integrated data accession and analysis systems for plant phenotyping. They observe that the lack of standardization for ontologies, data forms and structures and metadata collection needs to be resolved, both to increase the value of collected data and also for the application of machine learning. The article includes links to many useful repositories, datasets, projects and platforms. Curr. Opin. Sys. Biol. 10.1016/j.coisb.2017.07.002

 

Single-molecule spectroscopy of LHCSR1 identifies two distinct states responsible for photosynthetic photoprotection

Light-harvesting complex stress-related (LHCSR) proteins catalyze excess-light energy dissipation in green algae and mosses. Kondo et al. used use single-molecule spectroscopy to uncover how LHCSR1 achieves this. The authors find the protein exists in two states, one activated by a change in pH and the other by carotenoid composition (specifically, the xanthophyll cycle). The authors describe how regulated conformational dynamics match LHCSR1 function to different conditions. Nature Chem. 10.1038/nchem.2818 (Here is a plain-language summary about this work).

 

Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis

Previous exposure to stress can sometimes lead to enhanced stress tolerance through memory or priming, but the molecular mechanisms through which this occurs remain uncertain. Crisp et al. investigated how the transcriptome resets itself after high-light stress. They identified a subset of mRNAs that rapidly decay following the alleviation of stress, in an affect that they call Rapid Recovery Gene Downregulation (RRGD). The authors found little evidence for small RNAs or 5ʹ-3ʹ RNA decay contributing to rapid decay of mRNAs, but they do find evidence for ribosome stalling and co-translational decay having a role. They also found little evidence for the involvement of DNA methylation. Although the mechanism of the observed rapid gene downregulation remains unclear, the large datasets of mRNA dynamics during stress recovery should help to elucidate the factors that contribute to memory and priming. Plant Cell 10.1105/tpc.16.00828

 

Novel stress-inducible antisense RNAs of protein-coding loci are synthesized by RNA-dependent RNA polymerase

Previous work showed that many long non-coding RNAs are produced in response to abiotic stress, and that these often show considerable overlap with protein-coding genes. Matsui et al. investigated two of these, fAsRD29A1 and fAsRD29A2, corresponding to (A1) a full-length antisense RNA of the drought-inducible gene RD29A and (A2) one corresponding to the mRNA with the intron spliced out. They examined production of these AS RNAs in several different mutant backgrounds to identify their mechanisms of production; key findings include that endogenous uncapped sense RNA serves as a template for their synthesis, and that although RNA-dependent RNA Polymerases (RDR 1/2/6) are required for their production, this occurs independently of siRNA production. The authors also find that the AS RNAs contribute to turnover of the cognate mRNAs. They summarize, “These data reveal a novel mechanism of RNA regulation during abiotic stress response that involves complex RNA degradation pathways.” Plant Physiol. 10.1104/pp.17.00787

 

Maize YABBY genes drooping leaf1 and drooping leaf2 regulate plant architecture

Strable et al. describe the characterization of two loci that affect leaf morphology and plant architecture. The leaf insertion angle in droopingleaf1 (drl1-R) mutants is larger than that in wild-type, making the leaves appear droopy, an effect that is associated with a reduced midvein. This effect is enhanced in the presence of the drl2-M mutation. Both the DRL genes encode YABBY transcription factors and are located in quantitative trait loci (QTL) regions previously identified as affecting leaf angle. The authors observe that these and related loci are candidates for optimizing leaf-angle effects on light capture for photosynthesis. Plant Physiol. 10.1105/tpc.16.00477

 

A statistical description of plant shoot architecture ($)

Conn et al. analysed nearly 600 three-dimensional scans of three plant species (tomato, tobacco and sorghum) from different developmental stages and environments, and identified three underlying principles. The first they call separability, which indicates that variation in one dimension can occur without affecting the other dimensions. The second they call self-similarity, which indicates that the shapes are fundamentally similar and differ only by stretching and compression. The third is that all plant architectures follow a single form, that of a 3D Gaussian truncated at roughly two standard deviations (SDs) from the center of mass, so that “only four parameters are needed to specify statistically any architecture’s size and shape: its total branch length and the SDs of the Gaussian in the three orthogonal directions.” They finally compare these architectural principles to those of other naturally occurring structures.  Curr. Biol. 10.1016/j.cub.2017.06.009

 

Evolution of the wheat blast fungus through functional losses in a host specificity determinant ($)

We describe plant-pathogen interactions as an “arms race” whereby each new weapon deployed by the pathogen is countered by enhanced host defences. Inoue et al. reveal the molecular footprint of the arms race between a blast fungus and its hosts, in particular how a fungal pathogen of rice, oat and ryegrass (Pyricularia oryzae) evolved to also infect wheat. The authors found that the origins of this host jump correlate with the widespread cultivation of a wheat variety that fails to recognizes certain fungal proteins, which allowed the fungal population to increase and adapt to its new host. As the accompanying summary by Maekawa and Schulze-Lefert concludes, “The dynamics of P. oryzae host range alterations is likely influenced by plant domestication and agricultural practices favoring cultivars with homogenous genetic makeup that carry only a fraction of the resistance gene repertoire present in their wild relatives” – an important reminder that genetically homogenous populations are fertile breeding grounds for pathogens.  Science 10.1126/science.aam9654

 

CRISPR–Cas encoding of a digital movie into genomes of a population of living bacteria ($)

This is a fun and interesting look at how a population of bacteria can serve as a repository for digital data. Shipman et al. generated a code by which graphical information (pixels) could be translated to nucleotide sequences. They then introduced DNA encoding the pixel information into bacterial cells using CRISPR-Cas. Because the amount of data in the encoded images is large, they put a pool of DNA sequences into a population of cells. Sequencing the engineered locus from the pool returned all of the data, which was than decoded into an image strikingly like the starting image. This study demonstrates the potential of engineered bacteria as data storage devices. It is interesting to consider the implications of this work, some of which are described by Gina Kolata in a New York Times article about this work https://www.nytimes.com/2017/07/12/science/film-clip-stored-in-dna.html. Nature 10.1038/nature23017