Chris Surridge

Red but not dead

The photosystems of all plants and almost all cyanobacteria use the pigment chlorophyll a (Chl a) to absorb light energy and convey it to reaction centres where this energy is used to split water. This has led to the idea that light absorption by Chl a sets a lower limit for the energy needed to drive photosynthesis. However, a group led by William Rutherford of Imperial College, London, have shown that the cyanobacterium Chroococcidiopsis thermalis employs an alternative pigment, chlorophyll f, to capture light at the far-red end of the spectrum, well below the ‘red-limit’ of Chl a, and so survive in highly shaded conditions. C. thermalis is an extremophile capable of living in harsh environments such as hot springs, including those at Yellowstone National Park, although the strain used in these experiments was originally isolated in a sample of soil from Greifswald, East Germany in the early 1960s. C. thermalis will also grow under far-red light, that is wavelengths around 750 nm, some 50 nm longer than that absorbed by Chl a. In such conditions, around 10% of its chlorophyll pigments are Chl f. This has the effect of extending the action spectra of both photosystem I and photosystem II to longer wavelengths, compared to C. thermalis grown under white light and so lacking Chl f. Using sophisticated spectroscopy, the researchers were able to see that, in the cyanobaterial phototosystems, Chl f was replacing Chl a as the primary electron donor at the heart of the reaction centre, as well as forming antenna complexes to collect photons of far-red light. C. thermalis is not the only cyanobacterium to operate below the redlimit. Acaryochloris has previously been shown to achieve this feat by replacing all its Chl a molecules with another variant, Chl d. However, C. thermalis can exist on even lower energy light than Acaryochloris, and tune its photosystems to the prevailing light. Further study of C. thermalis may thus provide routes to engineer crops able to grow in a wider range of conditions. Also, by showing that the red-limit is not an absolute barrier this study increases the range of habitats that could perhaps support photosynthetic life, both on Earth and on the multitude of exoplanets increasingly being discovered.

Invasions reduce fire-risk

In grasslands, fire is less an occasional catastrophe and more a regular occurrence. Plant species have evolved to survive fires and even control it by tuning traits such as flammability to promote particular fire regimes. However, ecosystem properties are sensitive to disturbance by invading exotic species, as is shown by a 25-year study in New Zealands south-eastern South Island. By changing the overall flammability of the grasslands, invading plants probably alter the patterns of fires that take place, which can have dramatic effects on subsequent plant community structure. The researchers investigated the morphology and flammability of plant species found along 103 transects across Canterbury and Otago in South Island, New Zealand. These transects were surveyed three times between 1982 and 2007. Of the 334 species found, 51 accounted for more than 86% of the ground cover and were considered the dominant components of the ecosystem. Samples of these species were placed on a ‘plant barbecue’ at ~150 oC before being lit with a blowtorch. The time taken to ignite, the temperature of the flame produced and the length of time that the samples burned were all recorded. Combining the make-up of the communities with the traits of individual species gave a measure of the flammability of the ecosystems over time. In those locations where significant alien invasions had occurred, the general level of flammability decreased, mainly due to highly flammable native tussock grasses being replaced by lower-growing and less-flammable exotic mat-forming forbs. This could act as a positive feedback by changing the fire regime in favour of fewer, shorter and lower-intensity fires that in turn may make further invasions by less fire-tolerant non-native plants easier.

Chinese Spring fervour

Bread wheat, Triticum aestivum, is one of the major sources of food for the world, and as such could have been expected to be an early target of genome sequencing. However, unlike other significant crop plants such as rice and maize whose genomes were decoded by 2002 and 2009, respectively, the size and complexity of the wheat genome has made it an almost intractable challenge. At last this has been rectified with the publication in Science of a fully annotated reference genome of a wheat variety called Chinese Spring, by the International Wheat Genome Sequencing Consortium consisting of researchers from well over 50 institutions. Much of the difficulty for the sequencers stemmed from the fact that T. aestivum is hexaploid, having arisen from the hybridization of domesticated emmer or durum wheat (themselves tetraploid varieties) with another grass species, Aegilops tauschii, well over 3,000 years ago. The result is a genome with 21 pairs of chromosomes containing six copies of most genes. At around 16 billion base pairs in length, it is a little more than 5 times the length of the human genome, and was assembled from Illumina short-read sequences. The researchers achieved 94% coverage, which is impressive given that 85% of the genome was found to consist of repetitive DNA within which nearly 4 million copies of transposable elements from 505 families have been annotated. The consortium also identified with high confidence 107,891 separate genes. Possibly the key feature of this genome sequence, and a mark of its quality, is that 90% of the genome has been placed into large, continuous stretches of greater than 4.1 Mb in length (superscaffolds), the largest of which, at 166 Mb, is longer than the entire genome of Arabidopsis thaliana. Although this project is the result of some 18 years of work, its usefulness is only just beginning. With this sequence in hand it is possible to precisely locate all the currently known genetic markers for agronomically important traits, greatly speeding up the pace of conventional breeding. The sequence will also accelerate gene discovery, and facilitate genome engineering and editing.

Pest control: Reproductive strategy

The wide adoption of transgenic cotton varieties expressing insecticidal proteins from Bacillus thuringiensis (Bt) has greatly reduced the use of broad-spectrum insecticides for this crop, but concerns over long-term off-target effects remain, and in any case not all insects are susceptible to Bt. Luo et al. demonstrate a subtler transgenic approach to control the sap-sucking plant bug Adelphocoris suturalis, using a DNA contraceptive rather than an insecticide. Several species of Adelphocoris have emerged as pests of cotton and other crops in China, America and India, not least because of their resistance to Bt. The researchers had previously identified a fatty acyl-CoA reductase (FAR), which they believed to be involved in pheromone production. However, reducing the expression of the AsFAR gene using RNA interference (RNAi) suppressed the development of ovaries in female A. suturalis and dramatically reduced their fertility. Luo et al. proceeded to create transgenic cotton plants, producing a 432-base-pair fragment of the AsFAR gene. When bugs fed on these plants, the double-stranded AsFAR fragment stimulated RNAi in the insect, suppressing expression of the AsFAR gene. In field experiments conducted over two years, the transgenic cotton showed substantial resistance to A. suturalis infestation while having no detectable effect on other insect populations. Using targeted manipulation of an insect’s reproduction could thus prove an effective and acceptable transgenic approach to limiting losses of crops to herbivory.

Remote phenotyping: Raman reveals stress

The ability to noninvasively determine the physiological status of a plant is important for basic research and agriculture alike. Currently, such phenotyping can only be practically achieved by relatively indirect methods. For example, methods to noninvasively follow the response of plants to various stresses have focused on gross physical features or measurements of the chlorophyll content of plants. Marlan Scully, of Texas A&M University, and colleagues have now developed a high-throughput system that employs Raman spectroscopy to directly follow multiple stress responses of plants. Raman spectroscopy can be used to observe various pigments involved in plant stress responses, such as anthocyanins and carotenoids. The unique spectra of these molecules means that their concentrations can be simultaneously determined from single Raman measurements of leaves. In addition to using a commercially available confocal Raman microscope for this purpose, the researchers custom-built a portable system capable of being operated in the field. To demonstrate the efficacy of their system, they investigated coleus plants (Plectranthus scutellarioides) and various stressors such as high salt and light conditions, drought and cold. The Raman spectra obtained at various time points following the onset of stress clearly showed the different characteristics of the plants’ particular responses to these abiotic stressors. Most striking was a negative correlation in the levels of anthocyanins and carotenoids. The accuracy of the spectroscopic measurements was confirmed by conventional chemical extraction. Destructive analysis of plant material to measure levels of complex chemicals does not meet the needs of researchers who wish to follow physiological processes over time in individual plants. Nor does it provide the high-throughput, fast and easyto-use tools needed by plant breeders and growers. This spectroscopic approach could form the basis of mobile and automated systems for incorporation into precision agricultural applications.

Leaf development: Hole creation

The Madagascan laceleaf plant (Aponogeton madagascariensis) is an aquatic plant popularly used in aquariums due to its decorative leaves consisting of a meshwork of holes. These holes form by the death of regular patches of cells leaving an edge about five cell layers wide around the leaf veins. Adrian Dauphinee of Dalhousie University, Halifax, Canada, and colleagues, have investigated how a balance between antioxidants and reactive oxygen species (ROS) creates this patterning. At first all the cells in an A. madagascariensis leaf are darkly coloured due to the presence of anthocyanins. However, the cells farthest from the veins progressively lose their pigmentation forming transparent ‘windows’ before dying completely leaving the characteristic holes. Cells closer to the veins retain their pigmentation and continue to develop normally creating a sharp boundary at the hole’s edge. Dauphinee et al. discovered that growing A. madagascariensis in the presence of the antioxidants acetic acid and cysteine greatly reduced the number of holes that formed in its leaves and that the presence of holes was somewhat recovered by the further addition of hydrogen peroxide to the growth medium. Staining of developing cells with nitro blue tetrazolium (NBT) revealed higher levels of superoxide in cells destined for death, while immune assays showed that these cells are deficient in two antioxidant enzymes: superoxide dismutase 1 (SOD1) and catalase (CAT). These enzymes, and the high concentrations of anthocyanins that can be seen by eye, protect cells closer to the leaf veins from oxidative stress. Lacking sufficient protection, cells further from the veins mount a programmed cell death response involving breakdown of mitochondria and chloroplasts that further increases the oxidative stress. It remains unclear whether the leaf veins are releasing some form of mobile signal to establish this pattern of antioxidants, but this study establishes that the positive feedback inherent in programmed cell death creates the sharp border around the holes and thus the tracery of these elegant leaves.

Wood from the Heart

That Fiona Stafford loves trees is clear from every page of this deeply evocative book, the paperback version of which was published earlier this year. She not only loves trees but knows them on a personal level. Each of the book’s thirteen chapters is devoted to a different tree, almost all of which are found in the British countryside either as natives such as the oak and ash, or as imports gone native such as the apple and cypress. All are subject to Stafford’s kindly scrutiny as she describes the trees themselves and examines how their particular characters have been taken up by folklore, artists and common culture. Why, for instance in Canova’s statue of Napoleon posing as Mars has he hung his sword on an olive stump? Why did the eighteenth century ceramicist Thomas Minton so prominently feature willow in his faux-Chinese willow pattern crockery? And what tree links hockey sticks, the Morris traveller motor car and the Mosquito bomber? The greatest strength of Stafford’s writing is in the personal. All the chapters begin with anecdotes from her life in which trees have played a part. Whenever possible she talks about individual trees and her excursions to meet them, as if checking up on old friends to find out how the years have been treating them. The book is filled with images of specific trees and sometimes photographs but more often paintings and illustrations from artists stretching back through the centuries. If there is a fault in this book it is in the unquestioning acceptance of each tree’s particular characters. Another writer might have looked at the poplar tree and wondered how a tree so tall could ever provide water to its uppermost branches. Or, when discussing the yew or willow, given more than a passing mention to their medicinal properties and from there uncovered the fascinating biochemistry of their secondary metabolism. A different book could easily have been written using the very same trees to illustrate some of the many aspects of biology that shaped them to be as they are, the problems encountered when living for millennia, how to fight disease without antibodies, symbiosis and the creation of a supportive ecosystem, or how to be both strong and flexible enough to remain standing through a gale. This may be exactly what Stafford would want of her book. Not to satisfy the reader’s appetite for tree lore, but to inspire them to pay more attention to the trees around them and ask what knowledge their experiences can provide from their long, long lives. ❐

Herbicide resistance: Self-preservation.

For the long-term fitness of a population, it is important to reduce the level of inbreeding. However, when faced with extreme threats, there is an advantage for individuals who have genetic resistance to those conditions to mate with others who share that advantage, or even with themselves, to fix such traits in their offspring. Kuester et al. have shown that this is exactly what happens in populations of weeds that develop resistance to herbicides. The researchers investigated 24 populations of the morning glory (Ipomoea purpurea) growing as weeds in the Southeastern and Midwest United States in fields where glyphosate herbicide had been applied over a number of years. By genotyping several thousand individuals from these populations, they were able to determine the level of outcrossing/self-fertilization of the wild populations, as well as test their resistance to herbicide. In populations with higher resistance, there was a noticeable increase in self-fertilization. One of the factors that can affect the level of self-fertilization of a plant is its floral anatomy. If, for example, the flower has its anthers and stigmas close together, there is a higher chance of self-fertilization than if they are more distantly spaced. In the highly herbicide-resistant morning glory flowers, the anthers and stigmas were further apart than in only moderately resistant plants. However, the plants with low resistance also had more closely associated floral organs. Furthermore, this relationship was more marked in plants collected in one year but not significant in plants from another, showing that there are probably multiple mechanisms controlling the mating systems of these plants; any or all of which were responding to the application of herbicide.

Oral vaccines: Papaya salad

A number of plants, including bananas and tobacco, have been proposed as ways to both produce and deliver vaccines. Now, Edda Sciutto of the Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, and colleagues have demonstrated the effectiveness of papaya callus tissue for oral vaccination against the widespread disease cysticercosis. Cysticercosis is caused by the pork tapeworm, Taenia solium. It is not only an intestinal parasite of humans, but its larval form (or cysticerci) can infect tissues throughout the body. The most severe and often fatal form involves infection of the nervous system (neurocysticercosis), but infection of muscle, eye and skin is also common. Pigs are the intermediate host of T. solium, and therefore a simple-toadminister treatment of pig flocks would greatly reduce its prevalence. S3Pvac is an effective vaccine against T. solium, containing three peptides derived from the parasites. The Mexican researchers had previously transformed papaya calli using particle bombardment to produce stable lines expressing all three peptides. They had also shown that extracts from these cells could produce both an antigenic response and protection against T. solium in mice when administered by injection or orally. In the most recent study, the researchers have gone a significant step further. Mice were fed callus tissue expressing the S3Pvac papaya vaccine, either on its own, mixed with corn starch or vegetable oils, or pressed into maize wafers. All of these delivery methods produced high levels of protection against the parasite. In addition, when S3Pvac-expressing calli were fed to pigs with their food they mounted a substantial resistance response. These studies demonstrate the potential usefulness of callus tissue for oral immunization, but it will be some time yet before we are faced with a papaya fruit instead of a hypodermic needle for our winter flu jabs.

Defence: Switching targets

The immune response in plants is costly because every cell defends itself, so it is only induced when pathogen presence is sensed through membrane or cytosolic receptors. NLRs are cellular sensors that perceive the presence or activity of pathogen effectors being delivered into the plant cell, initiating a strong immune response. If this control is lost, defence can be constitutively switched on and plants then suffer from autoimmunity, leading to dwarfed growth. To find new immune regulators that may be difficult to discover in a wild-type background, Shuai Huang, Xin Li and colleagues from the University of British Columbia, Canada, searched for mutations that enhanced the autoimmune phenotype of the mutant snc1, in which the NLR protein SNC1 is stabilized. They identified two redundant TRAF-like proteins named MUSE. TRAFs are major players in animal immunity, and despite the large family in Arabidopsis, these proteins have been seldom studied in plants. A double muse mutant shows very severe autoimmune symptoms, confirming the role of MUSE proteins as negative regulators of immunity. After an elegant series of genetic and molecular experiments, the authors concluded that, just like in animals, the two MUSE proteins mediate the formation of signalling complexes called TRAFasomes, which bring together NLRs and proteasome components. These complexes control NLR homeostasis, so that plants can choose between growth and defence. GT