Bhodi Tims

Plant Root Chemistry is Just an Invitation to Play

September 28, 2018September 28, 2018Bhodi Tims

Plants and organisms in the rhizosphere (area of soil surrounding plant roots) are living organisms and part of a complex ecosystem requiring communication skills. Two different classes of compounds are important communicators – flavonoids and strigolactones – both ubiquitous in plants across multiple taxa. Of note, strigolactones were originally detected (Bouwmeester et al.) in plant root exudate stimulating seed germination of parasitic plants (genera Striga and Orobanche). These weedy species parasites host plant roots for nutrients. Flavonoid basal structures are highly varied, including flavones, flavonols, flavan-3-ols, flavanones, isoflavonoids, isoflavans and pterocarpans. They accumulate at root tips or root cap and makeup a large portion of root exudate. The fact these structures are easily modified and that their biosynthesis can be triggered by a numerous transcription factors points strongly to a role as elicited, signaling compounds. The conversation starters, the deal makers, they patrol the root neighborhood deciding who’s gonna join the party. Hassan and Mathesius (2012) noted in more technical terms that this localization allows them to influence the rhizosphere environment – increasing the bioavailability of both phosphorous and iron, inducing Rhizobium nod genes (for nitrogen fixation), determining host specificity, and influencing bacterial quorum sensing. They also influence soil fungi, both parasite and non-parasite, to investigate their environment by stimulating macronidial germination. These are spore structures that allow the fungus to remain in a dormant state until the surrounding soil supports their growth (Ruan et al.). Plants represent nutrient sources – the internal cell structures for parasites, and the substances released from plant root such as carbohydrates, organic acids, and proteins (root exudate) for non-parasitic fungi. One of the most fascinating chemical conversations involves how both flavonoids and strigolactones trigger AM fungi to investigate the rhizosphere more actively, by stimulating sporulation (breaking out of their dormant state), hyphal branching (similar to send out runners), and root colonization. Interestingly, changes to flavonoid ratios in root exudate can alter the symbiotic relationship and defines how mature the relationship is developmentally. Metabolic pathways in living organisms require dedicated gene expression. They tend to have been around a long time. Plants originated as aquatic organisms. They had no root systems. The prevalent theory on their terrestrial adaptation suggests that root exudate facilitated symbiosis with AM fungi, which allowed primitive land plants to survive by providing them an early “root system”. A paper by Delaux et. al. (2012) tested whether the presence of strigolactones in the aquatic green algae lineage may have helped them adapt to and colonize terrestrial environments. The researchers used a bioassay to detect branching of a AM fungus, Gigaspora rosea, to show strigolactones were present in the green algae Charales corallina. They also applied a synthetic strigolactone to C. coralina, which stimulated rhizoid elongation in the algae. Rhizoids were early “root-like” structures. The results beg the question of whether strigolactone biosynthesis predates AM fungal colonization and reinforces the idea that what survives adapts to changes in habitat, since anchoring to land increased the plant’s ability to acquire water and nutrients.

Strigolactones General Chemical Structure

Experiments on potato found that strigolactone may be involved in resource partitioning by maintaining phosphate and nitrogen homeostasis in plants (Pasare et al., 2013). Researchers reported that strigolactones enhanced plant association with AM fungi by increased branching of the AM hyphae (Giovannetti et al.). We see the effect of this type of chemical conversation, both internally within the plant and externally, with the fungus, to stimulate exploration. Strigolactones do also play a role as a plant hormone and appear to regulate axillary growth, lateral branching, and decreased apical dominance (Delavault et al.). This mimics the biological impact on fungi and suggestions that plants explore their aerial environment of air and sunlight. Rasmussen et al. (2012) noted the ability of strigolactones to impact root exploration in plants, limiting adventitious rooting by inhibiting the initial formative divisions of founder cells. These phenomena may point to the plant directing both the timing and directionality of new root growth in response to the presence/absence of appropriate soil symbionts. So then, what triggers strigolactone or flavonid secretions? What’s the chemical cross talk originating from the fungal side of the conversation?

Spices

September 24, 2018September 28, 2018Bhodi Tims

I was lucky enough to grow up all over the world – Thailand, Hong Kong, Germany, Romania and Greece. Some of my fondest memories are around food. My mom was a fabulous cook, which was a vital part of my father’s work as a cultural affairs officer in the US Foreign Service.

One of my earliest memories was of making a landing in Anchorage Alaska on a return trip from Bangkok to my parents’ home town of Biloxi, Mississippi. I remember the large stuffed polar bear in the lobby, and more importantly, my first taste of vanilla ice cream. Having come from the heat of Bangkok, with my daily food rich in hot peppers and ginger, this cooling fragrant treat was nectar from the gods.

When I started to learn to cook standing over my mom’s pot of gumbo she stressed the importance of simmer with the last ingredients – two bay leaves. They looked so simple – small dried plant material – but an hour later, the aroma of my Nannie’s gumbo was bigger than just the file and seafood, with the bay leaves providing a vibrant top note. Years later, deep into a career researching active molecules in medicinal plants, I realized that the food culture I grew up in was full of medicinal plants in the spices added to our evening meals.

Spices both sense of taste and smell. Our sense of smell, in particular, is influenced by the characteristics of the molecules responsible for odor. How quickly do they volatilize (how easily molecules vaporize)? How soluble are they in water or oil? How acidic is the food (a tomato based food or something with lemon)? Even our genes can influence the sense of smell.

A molecule that we can sense through smell is called a fragrance or odorant. Those molecules need to reach the olfactory system in the upper part of our nose. To do so, generally the molecular weight of these molecules needs to be equal to or less than 300 g/mol (a scientific designation for the mass of a substance divided by the amount of the substance). Ultimately, our sense of smell comes down to a pattern of activity of neurons in the brain responding to the stimulus of odor molecules binding to receptors (Malnic et al., 1999).

We have receptors (a protein in a cell membrane that responds to molecule attaching to it) in our nasal passages that are triggered by these molecules. Each olfactory receptor recognizes more than one odorant, and each odorant can be detected by several different olfactory receptors. This reflects a combinatorial process common to biological systems. Several factors influence the resulting signal sent from the receptor site.

We know that the shape of a molecule is important (Saberi and Seyed-Allaei, 2016), and that as the molecule binds (or sticks to) a receptor, the receptor changes shape, which leads to neural signals reaching the brain. Several theories exist to help us understand how to map the process of detecting odors, based largely on chemical qualities of the odorants.

Mori et al. (1994) suggested that the odor signal are more complex than a single receptor binding event, rather the signal is a product of a series of receptor excitations from numerous receptor sub sites (odotypes). This became known as the Odotope Theory. This theory also explains odor-less molecules as the presence sub sites more numerous than the limit of potential binding sites.

A second important theory, Dyson (1938) originated the Vibrational Theory that Wright (1982) later refined. This theory posits that olfactory receptors might really sense vibrational energy on a quantum level rather than structural shapes of the molecule when detecting odors. Quantum mechanics describes nature at the smallest scales of energy levels of atoms or substances.

Combining the two theories, Turin and Yoshi suggest that the tightness of receptor binding, based on both the physical and charge shape (polarity) of an odorant molecule may influence the intensity of the odor, while the character of the odor is effected by vibrational characteristics of the molecule.

To help visualize the theories, we can take a series of molecules found in medicinal plants that have a common base structure, and explore how their odor characteristics may be influenced by chemical features such as solubility, volatility, molecular shape and size (see Table 1).

Starting with the basic structure, vanillin give vanilla its signature sweet, perfumed, woody aroma. The molecular weight is relatively low, and it volatilizes easily, filling a room with the odor when cooked. The oxygen R-groups (groups that “hang” from the ring) on the benzene ring of vanillin make it highly solubility in water.

Built from the same basic structure, eugenol has a short hydro-carbon tail that gives it a stronger odor than vanillin, the familiar aroma found in bay leaf or allspice. This hydro-carbon tail also makes it more fat soluble and may influence the intensity of receptor binding. The odor threshold of eugenol is also lower than that of vanillin. The less polar binding site on the molecule may influence the strength of binding in this example, and explain why the vanillin odor is not as persistent as that of bay leaf or allspice.

Table 1: Vanillin Based Molecular Structures with Odor Thresholds


Vanillin (Odor Threshold: 20-200ppb)*	Eugenol (Odor Threshold: 6-30ppb)

Zingerone (Odor Threshold: na)	Capsaicin (Odor Threshold: na)

*http://www.leffingwell.com/odorthre.htm

Zingerone has an even longer hydro-carbon tail connected to the basic vanillin shape, making it insoluble in water. Found in ginger and mustard oil, it gives a rich, sweet, warm and woody fragrance. However, the presence of the carbonyl group (C=O) in the tail means that the zingerone molecules tend to attract each other, limiting how easily it volatilizes. Thus, ginger is less likely to fill a room as quickly with its aroma than vanilla.

Even though Capsaicin also has a long, hyrdo-carbon rich tail, the polar amide group (-NHCO-) makes it slightly more soluble in water than zingerone. The size of the tail also limits the molecule’s volatility. Capsaicin has no odor, and given the numerous sites along that long tail with the potential of binding to a receptor sub sites, this may be an example of a molecule with too many binding sites, as the Odotope theory suggests.

So the next time in you are in the kitchen and the aromas are filling your senses, see if you can think about the shapes and characteristics of the molecules influencing that wonderful moment.

References:

Malnic B, Hirono J, Sato T, Buck LB. (1999) Combinatorial receptor codes for odors. 96(5), 713.
Saberi M, Seyed-Allaei H (April 2016). “Odorant receptors of Drosophila are sensitive to the molecular volume of odorants”. Scientific Reports. 6: 25103. doi:1038/srep25103.
Mori, K. and Shepherd, GM. (1994). Emerging principles of molecular signal processing by mitral/tufted cells in the olfactory bulb. Semin Cell Biol 5-1:65-74.
Dyson, G.M. The scientific basis of odour . Chem Ind 57: 647-651.
Wright, R.H. (1982) The sense of smell CRCpress, Boca Raton, Florida, USA.
Turin, L, and Yoshi, F. (2003) Structure-Odor Relations: a modern perspective in Handbook of Olfaction and Gustation Second Edition. Doty RL, Ed. New York Marcel Dekker.

Fire

September 21, 2018September 21, 2018Bhodi Tims

In an issue of New Phytologist, Claire Belcher provides a wonderful summary about work by Bond and Scott (from same issue) on the ecological role of fire in the spread of angiosperms (flowering plants). During the Cretaceous (145.5 to 65.5 mya, ending with extinction of dinosaurs), angiosperms were fast growing, weedy and largely understory herbs, shrubs and small trees more likely to colonize edge or disturbance sites. An improved plant vascular system, including a large increase in leaf vein density, doubled the photosynthetic rate and increased leaf mass in comparison with ferns and gymnosperms, which were the dominant land plants at the time. This adaption allowed angiosperms to work more efficiently fixing carbon from falling CO₂ levels of the period. Fire also appeared to play a vital ecological role in the spread and ultimate dominance of flowering plants on earth.

Fossil charcoal demonstrated the presence of fire in the early ecosystem. The combination of highly flammable detritus from weedy angiosperms and increasing atmospheric oxygen levels created an angiosperm-fire cycle equivalent to modern prairie fire cycles. Once an ecosystem was fire damaged, the faster growing angiosperms out-competed both gymnosperms and ferns. The early fossil records indicate that fire activity was greater during the Cretaceous than in previous epochs. However, when oxygen levels dropped about 56 mya, fire-cycles decreased and angiosperm-dominated forests, such as tropical forests, expanded.

In fact, the resulting layers of charcoal helped preserve the fossil record of dinosaurs’ last days. Researchers were then able to predict what the Cretaceous forests looked like.

Earliest land plants discovered (news.bbc.co.uk)

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