Friday, July 31, 2015

Tutorial: Mass spectrometry in plant science, part 4 – measuring ethylene gas by GC-MS

In this post I would like to discuss a specific application of mass spectrometry to plant science, that of measuring the concentration of ethylene gas in head space samples. Ethylene gas is a plant hormone with numerous roles in plant development and defense. Climacteric fruits produce ethylene when they enter the ripening phase, and so for agronomists it can be very important to measure ethylene in order to monitor the progression of fruit development. Its chemical structure can be represented as CH2=CH2 and is the simplest alkene in nature. Because it is so volatile and present at such low concentrations, it is difficult to measure. A number of dedicated infrared and laser detectors can be found on the market. They may or may not offer the kind of stability and reproducibility that is required for precision analysis. For labs that do not have the funds to buy a dedicated, high end detector,  the default analytical technique to measure ethylene is a standard GC with a packed column connected to a FID (flame ionization detector). This technique has the virtue of being highly reproducible and sensitive enough for most applications. It takes advantage of the fact that ethylene produces an electrical signal when it burns at the detector, unlike the oxygen and nitrogen in the air which it is dissolved in. This is a tremendous advantage over mass spectrometry in this case because due to an unfortunate cosmic coincidence, both ethylene and nitrogen gas have a molecular mass of 28, meaning they are indistinguishable at unit resolution. This can make it nearly impossible to use mass spectrometry to pick out low levels of ethylene in a head space sample where the nitrogen is a million times as concentrated. And in practice it isn't so easy to separate the two on normal stationary column phases. An aluminum oxide column is probably the best phase currently available. However, nowadays, a GC system hooked up to a mass spectrometer is probably far more common that one connected to a FID, so many labs that might like to analyze ethylene production from plants have an analytical tool that is perhaps too sophisticated to get the job done, at least without a few tricks.  Here I offer a modest technical innovation that makes GC-MS nonetheless a viable technique that is comparable to a GC-FID for this task and represents another way that mass spectrometry can enrich our investigations in the plant sciences.

Conn et al. "Convergent evolution of strigolactone perception enabled host detection in parasitic plants"

Caitlin E. Conn1, Rohan Bythell-Douglas2, Drexel Neumann1, Satoko Yoshida3, Bryan Whittington4, 4, Ken Shirasu3, Charles S. Bond2, Kelly A. Dyer1, David C. Nelson1,*
James H. Westwood
1Department of Genetics, University of Georgia, Athens, GA 30602, USA
2School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia
3RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
4Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
Science 31 July 2015: Vol. 349 no. 6247 pp. 540-543 DOI: 10.1126/science.aab1140

Here's an interesting story on the perception of strigolactones (plant branching hormones) and how the normal physiological process of sensing these hormones has been co-opted  by sneaky parasites. Conn et al. find that a modern day clade of an ancient paralog of the Arabidopsis strigolactone receptor D14 is overrepresented in the genomes of certain parasitic plants. While derived from the same ancient paralog KAI2, the KAI2d clade members are used by obligate parasites to locate host plants. KAI2d induces germination in Orobanchaceae members by sensing strigolactones in host plant root exudates so that these parasites only germinate when a suitable host is near. In other words, while D14 is used by plants like Arabidopsis to sense their own strigolactone production and respond accordingly by initiating branching, parasitic plants use a very similar receptor with a common evolutionary origin to sense the same hormone but in this case to locate a host to parasitize. In a strange case of convergent evolution, both modern day clades (D14 and KAI2d) function as strigolactone sensors but for very different ends.

From the article:
Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, the α/β-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed that KAI2, but not D14, is present at higher copy numbers in parasitic species than in nonparasitic relatives. KAI2 paralogs in parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains the majority of KAI2 paralogs. Homology models predict that the ligand-binding pockets of KAI2d resemble D14. KAI2d transgenes confer strigolactone-specific germination responses to Arabidopsis thaliana. Thus, the KAI2 paralogs D14 and KAI2d underwent convergent evolution of strigolactone recognition, respectively enabling developmental responses to strigolactones in angiosperms and host detection in parasites.

Friday, July 17, 2015

Stapelia asterias in bloom: this flower stinks

I have this beautiful succulent on my balcony, Stapelia asterias, which is currently blooming. I always appreciated the tiger-like pattern to the petals, but as a member of the carrion flower group, its odor is apparently supposed to resemble rotting meat to attract carrion flies, its pollination vector. As a bonus, it also smells like poop. I learned this one day when I cut some freshly opened flowers and brought them inside to admire. It is better to admire them through a closed window as it turns out. Would a carrion flower by any other name smell as putrid?

Wednesday, July 8, 2015

Magnard et al. "Biosynthesis of monoterpene scent compounds in roses"

Jean-Louis Magnard1, Aymeric Roccia1,2, Jean-Claude Caissard1, Philippe Vergne2, Pulu Sun1, Romain Hecquet1, Annick Dubois2, Laurence Hibrand-Saint Oyant3, Frédéric Jullien1, Florence Nicolè1, Olivier Raymond2, Stéphanie Huguet4, Raymonde Baltenweck5, Sophie Meyer5, Patricia Claudel5, Julien Jeauffre3, Michel Rohmer6, Fabrice Foucher3, Philippe Hugueney5,*, Mohammed Bendahmane2,*, Sylvie Baudino1,*

1Laboratoire BVpam, EA3061, Université de Lyon/Saint-Etienne, 23 Rue du Dr Michelon, F-42000, Saint-Etienne, France 
2Laboratoire Reproduction et Développement des Plantes UMR Institut National de la Recherche Agronomique (INRA)–CNRS, Université Lyon 1-ENSL, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France. 
3INRA, Institut de Recherche en Horticulture et Semences (INRA, AGROCAMPUS-OUEST, Université d’Angers), SFR 4207 QUASAV, BP 60057, 49071 Beaucouzé Cedex, France
4Génomiques Fonctionnelles d’Arabidopsis, Unité de Recherche en Génomique Végétale, UMR INRA 1165–Université d’Evry Val d’Essonne–ERL CNRS 8196, Evry, France
5INRA, Université de Strasbourg, UMR 1131 Santé de la Vigne et Qualité du Vin, 28 Rue de Herrlisheim, F-68000 Colmar, France
 6Université de Strasbourg–CNRS, UMR 7177, Institut Le Bel, 4 Rue Blaise Pascal, 67070 Strasbourg Cedex, France

This outstanding report by Magnard, et al addresses the origin of monoterpenoid scent compounds in rose petals. Roses breed for sale as cut flowers are arguably the world's most important ornamental plants, and descriptions of their scents has inspired poets and artists for centuries or longer. However, the aggressive breeding which has improved the color and longevity of cut flowers has also occasionally resulted in hybrids which lack the same aromatic bouquets of more classic cultivars such as Papa Mailland. Magnard and co-workers exploited these induced genetic differences by comparing high and low scent varieties to identify differentially expressed genes that correlated with the accumulation of monoterpene alcohols typical of high quality rose scents. Geraniol, for instance, is an important monoterpene alcohol in rose oil, and geraniol synthase has been identified in basil, cinnamon, and many other plant species.  Ordinarily, we would just look at rose EST databases and look for terpene synthases, which are now some of the best studied catalysts in  the field of natural products with well known signature motifs at the amino acid level.That should lead us to a likely geraniol synthase candidate in rose.

Tuesday, July 7, 2015

Fund my research and win the world cup

I have been seeking a faculty position for the last few years to expand my research activities, hopefully before my current contract runs out. I'm nearly out of time, and it's a little scary. So far, it looks pretty grim. If I start to really think about the statistics behind getting a tenured faculty position, it is depressing. It is a little like becoming a professional athlete in one of the big U.S. sports (football, baseball, and basketball; or soccer in the rest of the world). Starting out in age group play is a little like being an undergraduate, and moving into graduate school and then the first post-doctoral position is perhaps comparable to moving up into more competitive leagues in professional sports. Getting tenure would be like playing in the NFL or NBA. Winning the world cup would, to carry this absurd analogy further, be like winning a Nobel prize. Fortunately, I have a way to virtually guarantee a world cup victory, and all I ask is a mere faculty position.