Monday, June 22, 2015

Colorful Carotenoids

One of my professors once said (ok I lied, he actually says this all the time), “Plants are the world’s best biochemists.” And it is very true. Plants produce thousands of different types of phytochemicals, including pigments, toxins, hormones, signaling molecules, the list goes on and on. This is going to be the first in a series called “Best Biochemists” where I’ll highlight different plant produced chemicals. Today’s post is going to scratch the surface of the beautifully colored carotenoids.
Fall Leaves - personal photograph
Carotenoids are probably most well-known by the yellow-orange-red color they provide to fruits, vegetables and flowers, for example the orange in carrots, red in tomatos, or yellow in peaches. They are a huge family with over 600 naturally occurring carotenoids. Most of the coloration, fragrance, and even taste of many flowers and spices come from carotenoids. The bright oranges, reds, and yellows that paint the leaves of trees is due to a build-up of carotenoids as photosynthesis ceases. So where does all of this diversity come from? Biochemically, all carotenoids start as a 40 carbon chain called phytoene.

"Phytoene" by Edgar181. Own work. Licensed under Public Domain via Wikimedia Commons.
 Phytoene is colorless and requires 4 dehydrogenation (loss of hydrogen) and 2 isomerization (rearrangement) reactions to become lycopene, the first colored carotenoid. Lycopene is bright red and gets its name from Lycopersicum, the genus name of tomatoes. Most of the bright red fruits and vegetables we eat are high in lycopene, such as tomato, watermelon, pink grapefruit, red bell peppers, etc. Lycopene is an important branchpoint in carotenoid biosynthesis as in the next step, the ends of lycopene are cyclized (made into rings). These rings can be in several different configurations, the most famous of which is the beta ring, that forms both ends of beta-carotene.

"Beta-Carotin" by NEUROtiker. Own work. Licensed under Public Domain via Wikimedia Commons.
Carotenes are very important to humans as precursors of Vitamin A. Beta-carotene is the most important for this purpose as it is composed of 2 Vitamin A (retinol) molecules linked tail to tail. Alpha and gamma carotene both contain 1 Vitamin A linked to a different ring type (epsilon). Thus, for every molecule of beta-carotene we consume, 2 Vitamin A molecules are produced during digestion, while only 1 is produced by alpha and gamma-carotene. The most famous usage of Vitamin A is in our eye health and development. This is where the idea that eating carrots can increase your night vision originates.  

Obviously, plants do not require Vitamin A for their eye development, so why do plants produce carotenes? All of the carotenoids are produced inside the plastids of plant cells; the most famous plastid is the chloroplast. Chloroplasts are the site of photosynthesis within plants. Inside the photosynthetic apparatus, we find 12 beta-carotenes in photosystem II and 22 beta-carotenes in photosystem I. There they, and all the carotenoids, act as extra light receptors, collecting light at wavelengths that chlorophyll cannot. In addition to capturing light, beta-carotene is a powerful antioxidant. It quenches highly reactive oxygen species that are generated as a by-product of photosynthesis to protect the photosystems. For example, beta-carotene in photosystem II acts as a backdoor for the energy contained in singlet oxygen’s away from the reaction core D1/D2 proteins and into cytochrome b559 cycle electron transport so that the reaction core is not damaged and the energy is not lost.
Beta-carotene backdoor - my silly diagram work
Beta-carotene and alpha-carotene, while used in these forms, are also critical steps in the production of xanthophylls. Xanthophylls are oxygenated carotenoids and appear yellow in coloration. The most common xanthophyll is lutein, which is found in high concentrations in kale and spinach. Lutein is also important for our vision, in our retina it prevents oxidation of lipids and proteins. In plants, lutein quenches damaging reactive oxygen species produced during photosynthesis.

Light capture and antioxidant properties are only a few of the functions of carotenoids. All of the carotenoids can be cleaved at any double bond to produce a wide array of apocartenoids (less than 40 carbon chains) which are found in the fragrances, tastes, and colors of various spices in the world. The interconversion of several forms of xanthophylls play an important role in the state transitions of photosynthesis, a feature called non-photochemical quenching. Plant hormones, such as abscisic acid are formed from carotenoid precursors.

Clearly, carotenoids are too diverse of a group to be summed up in one post. Thus look for future Best Biochemists posts to delve into the apocarotenoids, xanthophyll state transition, and phytohormone formation.


Moise, A., Al-Babili, S., and Wurtzel, E., 2014. Mechanistic Aspects of Carotenoid Biosynthesis. Chemical Review 114(1):164-193. (paywall :( )
Telfer, A. 2002. What is beta-carotene doing in the photosystem II reaction centre? Philosophical Transactions Royal Society of London B Biological Sciences 357(1426):143-139

Monday, June 15, 2015

Drought Resistant Plants?

Water is an essential component to life on this planet. Dehydration is a serious problem; complete lack of water will kill an adult human in only 3 days. Plants also suffer from dehydration, which can also lead to their death, but more important to agriculture is the loss in seed yield. Susceptibility to dehydration varies between plants, for example, cacti store water and thus can go a very long time without water, while impatiens require frequent watering. Drought, lack of water, is occurring worldwide. Right now California is, and has been, experiencing an exceptional drought. In 2014, 5% of the irrigated cropland and over $1 billion in direct agriculture was lost. That's just the losses in one year for one state, imagine the losses worldwide if droughts continue to spread.

Scientists have been studying drought tolerance properties in plants for decades with the hope of being able to translate the knowledge into drought resistant crops. And this month, a new transcription factor was described that might play a major role in regulating drought tolerance (Sakuraba, 2015). A transcription factor is a protein that binds to DNA to activate specific genes, they are the middle men of the cell, passing a signal to activate the work force. When new environmental condition arises, cells need to change the genes that are expressed rapidly and this is accomplished by transcription factors. Once they are activated, transcription factors then activate a suite of genes which produce the proper proteins for survival. This particular transcription factor is designated NAC016. The NAC family of transcription factors is one of the largest known in plants, with 106 NAC genes in the Arabidopsis (the study organism and model species for plant research) genome.

The levels of NAC016 were measured in a variety of abiotic stressors in wild type (aka normal) Arabidopsis by researchers in Dr. Nam-Chon Paek lab at Seoul National University. They found that these levels increased dramatically only during dehydration, not under cold or heat stress which suggested that this transcription factor plays a role in drought tolerance. To fully characterize NAC016, the researchers used two different mutants, a knockout (nac016) which has a non-functional NAC016 and an overexpressor (NAC016-OX) which expresses NAC016 at a very high level regardless of external conditions. After dehydration for 2 weeks, all 3 lines were compared and only the nac016 knockout had a high survival and recovery rate. Additionally, they looked at seedlings moved to dry filter paper and after 12 hours the nac016 again were fine while the other two lines were wilted. All of this means that the loss of NAC016 results in more drought tolerance!

Arabidopsis wild type and nac016 mutant after drought stress. Photo credit: Nam-Chon Paek, Copyright ASPB.

How does this work? The loss of NAC016 resulting in an increase of drought tolerance means that NAC016 is a negative regulator. It depresses the genes required for successful drought survival. The researchers examined several different genes known to be important for drought tolerance and indeed they were increased when NAC016 was knocked out and decreased when NAC016 was increased. One important pathway that NAC016 impacted was that of the hormone abscisic acid, which controls water retention via stomata (little pores on the leaves) opening/closing. Preventing water loss out of the stomata is an important defense against dehydration.

So... why care? Right now, this has only been shown in Arabidopsis. Arabidopsis is the model plant species because it is small, has a quick reproduction time, and has a fully sequenced genome. Most plant research begins in Arabidopsis and then is applied to other species. If NAC016 is shown to be a negative regulator of drought tolerance in agriculturally important species, then that's a target to remove. This removal can be done either by transgenic knockout, RNA interference, or traditional breeding techniques. But none of these avenues can be taken until the targets are established and this paper is a great first step towards identifying these targets.

Sakuraba 2015:
ASPB Press release w/ photo

Monday, June 8, 2015

Giant Kelp

As today is World Ocean Day, I thought I would feature a post about one of my favorite algae, the giant kelp, or more scientifically Macrocystis pyrifera. I learned to SCUBA dive in the kelp forests of Southern California. I have many, many fond memories of fining my way through the fronds. The way the light filters through the blades, the gentle swaying of the stalks, the many creatures darting around, was the epitome of peaceful.
My best pic of kelp, I haven't been back since digital cameras :(
Giant kelp gets its common name because it truly is giant, it can be 150 feet long and grow almost 2 feet a day! Kelp forests are so large they can be seen from space. In fact, Floating Forests takes advantage of this fact by using volunteers to mark the location of kelp in satellite imagines, it's a great little citizen science project which I reviewed here.

The pneumatocysts at the bottom of each blade resulted in the genus name Macrocystis as it means "large bladder." One of the characteristics that distinguish giant kelp from bull kelp or other large brown algae, is the single pneumatocyst found at the end of every single blade. These bladders are full of gas to keep the algae floating in the water column and closer to the sunlight needed for photosynthesis. Looking like a giant tangled knot of roots at the bottom of the kelp is the holdfast. Holdfasts do just what the name implies, hold tight so that the algae is not dislodged in rough conditions, they do not absorb water or nutrients like roots do for land plants. 

Another ancient film photo, this one featuring CA state fish the Garibaldi
Kelp forests resemble the forests you've probably hiked through since they are the base of a large food web, providing both food and habitat. They create a vertical environment, with different species of fish, invertebrates, algae, and even marine mammals inhabiting the various levels. They can be found in the holdfasts, living in the fronds, playing in the canopy. Sea otters have been known to wrap themselves in the canopy to keep themselves in position while sleeping. Encountering macrofauna such as seals, sea lions, giant sea bass, or sharks was common for me when diving the Channel Islands kelp forests, but my favorites were the tiny creatures. Staring closely at the rocks and kelp to find little invertebrates hiding in the fronds/holdfast or fish that mimic the kelp, all of which is easily missed when swimming past, was always exciting for teenage me. Not only do they provide habitat on the shore, when the holdfast breaks down, floating kelp mats bring their nutrients and hitchhikers out to the open ocean where they attract pelagic fish and birds.
Giant kelp is harvested and used to make algin, a thickening agent which is found in a lot of food. It also has been used for fertilizer, gun powder, in cosmetics and many other applications. In California, harvesting kelp is a $40 million dollar industry. To protect the kelp forest environment, only the kelp found in the top 4 feet of the water column are collected, leaving the bulk of the strand in tact to regrow. In addition to harvesting, kelp forests provide other economical advantages to the coasts they cover, such as tourism. Another important feature is shoreline protection, waves are slowed down by the thick kelp forests and thus less energy hits the shore, resulting in less erosion.
Last old scanned, film photos of the kelp forests, this time looking up!

To experience a small taste of the diversity of the kelp forest, Monterey Bay Aquarium features a Kelp Cam in their big kelp forest tank here, as does Scripps Birch Aquarium here.