Category Archives: vocabulary

Cyanothece 51142 by Michelle Liberton, Pakrasi lab

The Dangerous Double Life of a Distinctive Diazotroph

For many people around the world, tonight is one of the most anticipated nights of the year. In that spirit, here’s some new science, not under the sun, but under the moonlight and starlight. New research from Wegener, Nagarajan and Pakrasi* describe something new about the Photosystem II D1 protein, an unexpected source that photosynthesis researchers had long written off as conquered or fully explained.

Why would we care about photosynthesis at night anyway? It all comes down to the distinctive lifestyle of the cyanobacterium Cyanothece, which belongs to an interesting class called unicellular diazotrophs (word of the day). Like all cyanobacteria, they perform oxygenic photosynthesis but they have the bonus biochemical ability of nitrogen-fixation.

Nitrogen-fixers are capable of pulling nitrogen gas (N2) out of the air and turning it into ammonia which the cells can use as a nitrogen source for important molecules like protein and DNA. Other microbes can perform nitrogen-fixation, and you may remember them as the root nodule symbionts of legumes. If you’re not a nitrogen-fixer, you have to rely on ammonia or other nitrate compounds present in the soil, sea or your diet (depending on what kind of organism you are) to make the required nitrogenous biomolecules. Since the Earth’s atmosphere is 78% N2, you don’t have to be great at math to figure out that acquiring the ability to tap into the atmospheric nitrogen source advances your species in the game of life a considerable number of squares.

What does this have to do with photosynthesis? Why don’t more plants and cyanobacteria get in on this nitrogen-fixation biochemistry? There’s a critical fatal flaw in the photosynthesis/nitrogen-fixation biochemical tango. Nitrogenase, the enzyme responsible for the nitrogen-fixation reaction is hopelessly and irreversibly killed by oxygen. Oxygen destroys the protein enzyme that’s already been made and tells the genome not to even bother wasting energy trying to make it new. If you’ve been paying attention to the blog, oxygenic photosynthesizers like cyanobacteria and plants make oxygen via their PSII enzyme every time light shines on them. So for nonphotosynthetic soil bacteria and other microbes, it’s not a big deal to avoid oxygen and go anaerobic to fix nitrogen. Cyanobacteria, however, must lead dangerous double lives to combine these two opposing biochemical processes.

Anabeana spherica via Wikimedia Commons The more round cell in the center of the string is the nitrogen-fixing heterocyst.

Some diazotrophic cyanobacteria solve this problem by separating these two processes in space. Species like Anabeana can go through a special type of development where the cells divide themselves, but incompletely to form a connected network like beads on a string. Every tenth cell (heterocyst) gets an extra layer of cell wall, destroys its photosynthetic machinery, and commits itself to a life of nitrogen-fixation. These cells share their fixed nitrogen compounds with their neighbors, which in turn share their fixed-carbon from photosynthesis. This is a fascinating process still hasn’t given up all of its secrets and remains an active area of research.

Cyanothece 51142 by Michelle Liberton, Pakrasi lab

Cyanothece 51142 by Michelle Liberton, Pakrasi lab

Cyanothece, on the other hand, is a more ruggedly individualistic species that manages to perform both oxygenic photosynthesis and nitrogen-fixation within a single cell. It accomplishes this through a carefully controlled circadian rhythm. During the day, oxygenic photosynthesis occurs. During the night, nitrogen-fixation occurs. It sounds so simple, yet this elegance is far from easy. This is a true circadian process, in that, while some cues are definitely derived from light signals, the cells also have a strong internal clock that keeps the time of day and controls what biochemical machinery is active. Thus, near the hour of dawn and dusk, the cells are actively preparing for the metabolism to come. Also, if you were to train a culture of these cells under a certain day/night cycle for several days then switch them to continuous light, they would still maintain their circadian biochemical cycle for several days after the switch.

One issue that has puzzled researchers for some time is that the photosynthetic machinery, like PSII, is actively shut down at night. It’s not just that it’s dark, so there won’t be any photosynthetic oxygen production. Apparently, that’s not good enough. The cells actively shut it down. When researchers take culture samples of these cells during their dark period and shine light on them to check photosynthetic capability, there is no signal. Sure, there’s probably little chance any significant photosynthesis is occurring at night, but Cyanothece isn’t taking any chances. For these cells, no moonlight, floodlights from passing ships, comets, or even the blessed Eastern Star is going to interfere with their nocturnal nitrogen fixation.

Shutting down photosynthesis is no small feat. Again, if you’ve been paying attention to the blog, you will note that I’ve ranted on numerous occasions about how complex PSII is and how difficult it is to assemble  and reassemble from its individual parts. As far as energetics are concerned, it would be a losing battle for Cyanothece to completely disassemble its PSII at dusk only to resynthesize it again the next morning. I don’t care how hard-up it is for a nitrogen source. As it turns out, Cyanothece and other unicellular diazotrophic cyanobacteria solve this problem in a more graceful way, for which Wegener et al have provided new experimental evidence.

Cyanothece, like all other oxygenic photosynthesizers, contains multiple copies of the psbA gene encoding the D1 protein, which is a core subunit of PSII and critical for function. Since the advent of the genomic era, the genomes of numerous photosynthetic organisms have been sequenced revealing these multiple psbA genes, most of which have little or no protein sequence differences. These subtle changes have been linked to cells’ ability to fine-tune photosynthesis under certain conditions. However, Cyanothece and its cousins have a psbA gene copy that is particularly different- psbA4. If one were to take all of the site-directed mutants that photosynthesis researchers made to sort out PSII function over the last few decades since molecular biology techniques were available and threw them altogether into a single mutant gene, you would get psbA4. If PSII contained the D1 protein encoded by psbA4, there would be no C-terminal processing and no active site for water-splitting and oxygen production.

Why would any self-respecting photosynthetic organism retain such an utterly non-functional PSII subunit? The answer is because it does serve a critical function in the daily cycle of Cyanothece, just not during the day. The D1 protein encoded by the psbA4 gene, called a sentinel D1 protein (sD1), is made only for the night, when it does the only thing it still can do- fit right in the center of the PSII complex and prevent PSII function of any kind. There’s no chance of any oxygen production while sentinel D1 is on duty, but the cells can maintain most of the other PSII components in a stable complex (meaning they don’t have to be degraded and made fresh every morning). Then, Cyanothece can turn photosynthesis back on in the morning by replacing a single protein in its PSII complexes. The report by Wegener et al gives the first biochemical characterization of PSII complexes containing a sentinel D1 protein, providing evidence that this strategy works for controlling PSII oxygen production.


Performing oxygenic photosynthesis and nitrogen-fixation within the same cell is biochemically problematic, but the sentinel D1 protein appears to be the secret weapon for this dangerous double life. Through this strategy oxygenic photosynthesis and nitrogen fixation are “Always together, eternally apart.”** Many questions remain regarding the regulation of the transition from functional D1 to sentinel D1 at dusk and the reverse replacement at dawn. There are still outstanding questions regarding the D1 turnover event for any PSII in any photosynthetic organism, so it’s not at all clear what parts of this process Cyanothece uses or whether new factors are involved. Obviously, there must also be some sophisticated regulation to prevent the synthesis of sentinel D1 during the day.

While this work focuses on an organism you’ve never heard of, it has some interesting biotech implications for the future. As I mentioned, being able to both fix CO2 through photosynthesis and N2 through nitrogenase puts you at a significant metabolic advantage. And no, I don’t mean you. Remember, we’ve been through this- people are not photosynthetic. It would be great if one day we could engineer certain crop plants to combine these traits. Legumes already have this trick covered through symbiosis, but many other staple crops require tons of nitrogen fertilizer. If researchers could unlock the secrets of Cyanothece’s double life and translate it to plants, then it may be possible to engineer versions of crop plants that don’t require so much nitrogen fertilizer. Thus, one night in the future, engineered crop plants may be fixing nitrogen thanks to the addition of a variant gene they already had.


*I know I’ve posted frequently about Pakrasi lab (my thesis lab) research, but this topic was just developing as I was leaving the lab and it’s too cool to pass up.

**Bonus points to you if you get the movie reference.

References and Links:

Corpse Flower: The Living Dead

Corpse Flower Credit: U.S. Botanic Garden via Wikipedia

Today’s plant costume is an odiferous disguise instead of a visual one. Its common name is also appropriate for the Halloween season- The Corpse Flower. It only pretends to be dead by giving off a rank odor of rotting flesh when it blooms. Again the reason is pollination. This horrible smell to us calls to every beetle and fly around that supper’s on. While they root around in the tight dark spaces of the bloom trying to find a decent place to feed and lay their eggs, they become covered in pollen. These pollen-covered insects then fly off to another bloom to pollinate another plant.

This species, Amorphophallus titanum*, is also a superphotosynthesizer in the plant world. As you may have noticed from the pictures and videos, the blooms can be as large as 10 feet tall. This makes the corpse flower the world’s largest inflorescence. Notice I didn’t say flower. Ah, botanical anatomy semantics! The images may look like a giant flower with burgundy petals surrounding a central stigma on steroids. Not so. The ‘petal’ portion of the flower is actually a bract structure called a spathe (plant biology word of the day). The tall central feature is called a spadix (bonus plant biology word of the day), and it is this structure on which the true flowers of the plant (separate male and female flowers) are arranged. The entirety of this plant reproductive structure is the inflorescence and there isn’t a bigger one in the plant world. The world’s record for a corpse flower bloom is nearly 11 feet tall. After flowering, the plant then makes the world’s largest leaf structure. It may look a tree in its own right, but developmentally, it’s just a compound leaf.


* Grossly translated as giant misshapen penis. Yeah. Well, you’ve seen the pictures. Stay classy readers!

References and Links:

For the First Time in Forever: Vernalization


Next up in the Frozen series… we’re talking about flowering for the first time in ‘forever’ (really, just after winter). Here’s the Disney version for your reference.

FRIGIDA’s gone, so’s FLC

Winter is over? Can it be?

We need to transcribe a thousand different genes

For months we’ve waited in dormancy

Halted all pluripotency

Finally, it’s time to make some scenes!

There’ll be actual real live flowers

It’ll be totally great

I’m so ready for this activated state!

‘Cause for the first time in forever

There’ll be flow’ring, there’ll be growth

For the first time in forever

Translating AP1 and LFY both!

It must be the gibberellic acid

There’s active meristematic zones

‘Cause for the first time in forever

FLC is gone

I can’t wait to bloom, everyone!

What if I meet… the one?

This Spring imagine me petals and all,

Fetchingly vining up the wall

My flowers a delicately shaped vase

Ooh! I suddenly see him buzzing by

A striped pollinator that can fly

I’m gonna shove some pollen in his face!

But then we trade pollen and nectar

Which is completely strange

Not like when FLC is in detectable range

For the first time in forever

There’ll be flowers, there’ll be sun

For the first time in forever

I’ll be making AP1

And I know it is totally crazy

Excitement over meristems

But for the first time in forever

There’s activity in them


Don’t let them out, don’t turn them on

Winter could still go on and on and on

Repress, turn off, it’s not time to grow,

Make one wrong move and get killed by snow

[FLC:] Is it only for today?

[FT:] It seems like Spring today!

[FLC:] It’s agony to wait

[FT:] It’s agony to wait

[FLC:] The VRNs are saying open up the gate

[FT:] The gate

[FT:] For the first time in forever

[FLC:] Don’t turn them on, don’t let them out

[FT:] I’m getting what I’ve waited for

[FLC:] Be the regulator the plant needs about

[FT:] A chance to change my stagnant world

[FLC:] Repress

[FT:] A chance to pollinate!

[FLC:] Repress, turn off, don’t let them out

I know it all ends in autumn,

So it has to start today

‘Cause for the first time in forever

For the first time in forever

Nothing’s in my way!

Flowering is important for plants because it’s how they reproduce. So, they need to have ways of ensuring that this process occurs under conditions that are most favorable for seed production. Plant species solve this problem in a variety of ways. Some annual plants avoid harsh conditions altogether and complete their life cycle within a single warm growing season. Others must find ways of going dormant during the freezing winter months and wait out the season until spring comes back. Plants integrate information on both day-length and duration of cold temperatures so they are not fooled into flowering on a random warm day in winter.

Under any conditions, the transition to flowering requires an elaborate set of gene expression changes so that cells achieve the proper developmental fate. The perennials and winter annual plants that require a cold period of dormancy prior to the flowering transition have an extra layer of regulation to ensure the transition occurs at the right time. Plants accomplish this with a set of gene regulators, some promoting the floral transition and others repressing it. These tiered layers of control allow for seemingly binary (on/off) switches to become a way of fine-tuning the development of flowers in these plants.

It’s not unlike the opposing personalities of Anna and Elsa in the movie Frozen. The gene FLC functions to keep plants from flowering, while genes like AP1, SOC1, FT, and LEAFY turn on genes to promote flower production. In perennials and winter annual plants, FRIGIDA serves to keep plants from flowering through the work of FLC until a certain amount of winter temperatures have passed. The genes VIN3, VRN1 and VRN2 act to let the plants know that enough winter weather has occurred and the hold on flower development (via FLC and FRI) can be let go. The way that the repression system works is also an interesting case. It’s not that these proteins physically block transcription of certain genes; these repressors leave covalent marks on the genome and the histone proteins whose job it is to organize the DNA within the cell nucleus. It takes some effort on the part of the activators to undo these marks to subsequently turn on the necessary genes.

Major players controlling flowering in plants. Pointed arrows mean activation or promotion, while blocked lines indicate repression.

Major players controlling flowering in plants. Pointed arrows mean activation or promotion of the next downstream thing, while blocked lines indicate repression of the next step in the pathway.

It’s interesting to note that all of the genes mentioned in the above paragraph are gene transcription regulators of one variety of another. This highlights a continuing theme in how pathways for development or environmental acclimation are controlled. There are a small set of regulators which control sets of other genes that are also regulators or that actually do the necessary biochemical work. These regulators work together to integrate environmental information (in this case-temperature, light, day-length) and keep developmental programs in check. Scientists tend to identify these factors pretty early in their investigations of these big questions, usually because mutants in these important regulators have obvious defects in the process of interest.

However, I have to admit, this drives me crazy as a biochemist. I want to know what’s going on beyond the nucleus in these processes. Sure, we may know a lot about what conditions turn these regulators and other genes on and off, but we know very little about the physical mechanisms by which plants sense the winter temperatures and time how long they’ve persisted. What is the actual ‘winter sensor’ in plants? How is it different from the cold sensor that plants use for cold acclimation on the timescale of hours or just a few days? How does this winter sensor differ among varieties with different ‘chill requirements’ before they flower and make fruit in the spring?* These components remain a mystery, but one that plant scientists are furtively working to solve.

Vernalization (the plant biology word of the day) is the acquired ability of a plant to flower after a cold season. For our perennials and winter annual plants, the passing of sufficient winter (as measured by the mysterious ‘winter sensor’ and regulated by VIN3, VRN1, VRN2, and FRI) gives these plants the ability to burst forth in flowers in the spring. Even though these regulators have a protective role for the plants in keeping them from trying to flower in the freezing winter, once their control is finally released, the flurry of activity associated with flower development is akin to a grand celebration after what seems like a lifetime of seclusion. Upon flowering, it’s all about reproduction. When it comes to plants, there’s not even a pretense of modesty; they have no problems trading pollen grains with a pollinator they have just met.

A number of economically important agricultural crops, like wheat, cabbage, carrots and most fruit trees, have vernalization requirements for flowering. Understanding how this process works is critical for getting the most out of these plants where they are grown and expanding the arable ranges for these crops. It may be some time before plant biologists make a Honeycrisp apple tree I can grow in Louisiana, but even modest adjustments to vernalization requirements to staple crops like wheat may be needed to accommodate predicted climate changes.

For more on how plants remember winter, check out this post over at The Quiet Branches.


*This is why apple trees (with varieties requiring 400 – 1000 chill hours) don’t flower efficiently and produce fruit in a place as far south as Baton Rouge, LA (~200 – 300 chill hours), but figs (requiring only 100 – 200 chill hours) do.

References and Links:

Do you want to make a plastid?

FrozenNext up in the Frozen series… Do you want to make a plastid? Here’s the snowman version from Frozen for your reference.

Plant cells…

Do you want to make a plastid?

Come on, differentiate

Time to photosynthesize

Special things to metabolize

C’mon they need a fate

Those used to be proplastids

And now they’re not

We hope genetics tells us why!

Do you want to make a plastid?

It doesn’t have to be a chloroplast

Do you want to make a plastid?

Some grana stacks green and tall?

I think some development is overdue…

Environment gives you cues

From the nucleus transcription calls!

(Induce there GLKs)

It gets a bit confusing

All these proteins whizzing by



Chromoplasts get lots of color

With all these carotenoids

Amyloplasts store starches

For all the tissues underground!

Do you want to make a plastid?

It could even be a tannosome

Yes, etioplasts are in there

In the dark since who knows when

Shine the light to start,

The nucleus is there for them,

No longer inside meristems,

Time for some changes to begin!

They do so many functions,


What can’t plastids do?

Do you want to make a plastid?

Well, if you are a plant cell, the answer to that refrain is always, “Yes!” Plastids are specialized organelles in plants that perform a wide array of specialized biochemistry. The most well-known and recognized of these are chloroplasts. These subcellular compartments are packed full of the thylakoid membranes and enzymes necessary to convert light into sugars. Chloroplasts perform other important biochemical reactions including the synthesis of starches and fatty acids as well as the assimilation of nitrogen into amino acids.

The chloroplast by User:Miguelsierra, adapted by User:Vossman via Wikipedia

There are other types of plastids made in plant cells for other specialized purposes. There are chromoplasts, which are full of carotenoid and other pigments giving them distinctive colors. The cells of tomato flesh, carrots and rose petals contain this type of plastid. Of course, pigments don’t do much good in root tissues. You may not find chloroplasts or chromoplasts there, but they do contain leucoplasts (loosely defined as non-green plastids used for storage of starches and oils). Storage-type plastids aren’t relegated to the roots. Recently other types of plastids have been identified, which specialize in the synthesis and storage of distinctive metabolites. Tannosomes have recently been characterized as specialists in tannin storage. A phenyloplast was also recently described in vanilla fruit as the storage location for vanillin precursor metabolites. In fact, the range of biochemical specialization that plastids perform strains their traditional nomenclature and definitions. As scientists learn more about them, the divisions between traditional types seems to blur. It seems that plants can make them as specialized as they need to be along a gradient of biochemical functions.

Types of plastids by Mariana Ruiz Villarreal LadyofHats via Wikipedia

Plant cells have definitely capitalized on the versatility of the plastid organelle structure to ensure dedicated locations for all manner of biochemical reactions and/or storage of their products. This is no small task. It requires the coordination of genes in two different genomes (that of the plant cell nucleus as well as a small genome in the plastid), trafficking of proteins throughout the cell, sensing of environmental cues, and synchronization with the overall plant developmental program. It’s enough to make any project manager run out of color-coded post-its and lose track of scheduled task times. Here are the highlights:

First of all, plastids do not exist in their mature forms in plant seeds and developing meristem tissues, but as immature and developmentally-flexible proplastids. These proplastids may not be special biochemists in their own right, but they have the potential to become any kind of plastid the plant cell needs. Consequently, proplastids have to know whether they are inside a root cell, petal cell or leaf cell. This means that plastid differentiation (aka development to maturity) must be coordinated with the development of the rest of the plant. Scientists are beginning to learn more about how this works, but this research is difficult since we’re talking about tiny, unremarkable pro-organelles within small portions of tissue. It’s a universal rule of cell biology that studying on small things is much more difficult than studying large things. Genetics has provided some new insights as to which genes have control over this developmental process. Transcription factors like the Golden-like (GLK) family of proteins have been identified as major players in this process, turning on suites of other genes to trigger proplastid development into mature plastids.

Of course, a lot of plant cell and plastid development is tied to environmental cues like light intensity. For example, plants can develop up to a point in darkness, but that doesn’t mean those cells have the same mature chloroplasts present in light-grown plants. Dark-grown plant cells contain plastids termed etioplasts, which are somewhat more differentiated than proplastids but not quite chloroplasts. Upon illumination, etioplasts quickly whip up thylakoid membranes and the photosynthetic machinery and get to the work of photosynthesis.

Plastid development and maintenance requires a large protein migration within plant cells. While plastid genomes make a number of their proteins, they do not make all of their resident proteins. Many essential proteins must come from genes transcribed in the plant cell nucleus and translated in the cytoplasm or endoplasmic reticulum. Thus, plant cells have an elaborate system of trafficking proteins to the proper cellular destination. This is true for all kinds of eukaryotic cells, but plant cells have extra organelles to distinguish among relative to animal cells. For those proteins with final destinations in the chloroplast, they have signals within their sequences that target them there. When they arrive at the chloroplast, they must pass through the surrounding double membranes using the Translocon of Outer Chloroplast Membrane (TOC) and the Translocon of Inner Chloroplast Membrane (TIC). In addition to the large influx of proteins that must be deposited upon initial development, the nucleus continues to provide essential proteins to the chloroplasts throughout their lifetime. It’s a constant flurry of activity maintained by two-way communication between the nucleus and chloroplast such that each organelle knows the biochemical status of the other.

Development into a mature plastid type isn’t the end of the line. There is still some developmental plasticity allowing certain plastids to convert into other plastid types. I’ve mentioned before that chloroplasts convert to chromoplasts in ripening fruit, as can be seen in the characteristic color change of green, unripe fruits into bright yellows, oranges and reds. Chloroplasts also provide the starting point for the development of other plastids specializing in storage of certain biomolecules. Plant cells also have ways of recycling the valuable contents of their plastids when cells and tissues reach the end of their lives (think autumn leaf color-change). As you might expect, this process requires more changes in gene transcription, protein synthesis and membrane structure orchestrated by the cell nucleus in response to more environmental and developmental cues.

Finally, proplastids and plastids of all types have ways of replicating themselves within plant cells. In this way, as plant cells divide each new daughter cell will contain roughly equal numbers of plastids. It wouldn’t be very good if a certain cell line within a tissue ran out of plastids. As much as plastids rely on the nucleus to full development and function, the nucleus cannot spontaneously create plastids from nothing. This wrinkle adds another layer of complexity to plastid biology. It means plastids must have some way of dividing themselves within the cells, and when plant cells divide, they must have some way of equally segregating the multiple plastids between the two new cells.

Basically, plastids are a lot of work for plant cells to make and maintain. However, these high-maintenance organelles are worth it given the biochemical rewards they offer. Scientists are only beginning to understand how plants make, maintain and recycle their plastids. Pieces of the complex system are studied by plant biologists all over the world and will likely keep them busy for many years to come.




References and Links:

Blackberries: Jewels of Spring

101016Southern springtime brings many botanical treasures, which are usually proudly displayed in orderly fashion in well-kept garden beds. However, the jewels I cherish most are found along overgrown fence lines and creeping into unkempt pastures. I’m talking about wild blackberries or dewberries or whatever you would like to call species of the Rubus genus. In early spring, X’s can be marked on treasure maps when a profusion of white flowers bloom almost synchronously on two-year old canes. After this display, the plants blend into the background greenery nearly lost and relegated to the shadows of honeysuckle and other trees that finally decide to leaf out. Persistent foragers are rewarded several weeks later when ripening berries can be seen in flashes of red, purple and ultimately black.


Like all precious treasures, blackberries are heavily guarded by barbed brambles. Personally, I’m as at home in a briar patch as Br’er Rabbit and won’t let the snags and sticks of the berry canes keep me from my delicious prize. I’ll endure encounters with bugs of all kinds- mosquitos, fire ants, chiggers, ticks, spiders, and stinging caterpillars. Larger animals will elicit a stronger startle response from me- the flutter of birds, the scurry of rabbits or field mice, the scamper of feral cats and even once the bustle of an extremely near-sighted armadillo. There is only one thing that will cause my stomach to pucker and lead me to call it a day on blackberries- the slither of a snake. This time of year in Louisiana, a snake encounter is a statistical certainty during blackberry picking. Even if I don’t see them, I accept that they are there. I will even go so far as to acknowledge their right to exist in my berry patches.* I would just never like to confront them. So, I tromp heavily in boots and use a cane knife to shake the briars a bit before plunging into them up to my elbows. When I do happen upon the fearsome reptiles, the encounters are never lethal despite my cane knife, but I do lose the nerve for berry-picking for the day.

Blackberry bucket

Blackberry bucket Credit: Johnna Roose

Dewberry canes

Dewberry canes Credit: Johnna Roose

The internet tells me that there are some cultivated varieties without thorns at all that can be grown orderly-like vineyard-style, but it is difficult for this southern girl to reason why you would take the effort to tend such plants when wild varieties produce such deliciousness for free with no aid from a gardener. Nevertheless, several links at the end of this post provide details on blackberry cultivation if you are not a wild-blackberry purist like me. For many wild varieties, some have prominent prickles on the stems and spines on the leaves, while others have additional sharp hairs along their stems. This brings us to an issue of nomenclature dear to some people’s hearts. (No, I’m not talking about thorns vs. prickles vs. spines. I’ve covered that previously.) I’m talking about blackberries vs. dewberries. While blackberries may be an umbrella term for this type of fruit, I’ve noticed that southerners prefer to make the distinction when dewberries are what you are really talking about. I am an equal opportunity berry picker and eater, but here are the highlights when it comes to dewberries. Dewberries, Rubus trivialis**, are slightly larger than most wild blackberries and ripen a few weeks earlier. Their canes are red and contain hairy bristles in addition to prickles, while blackberry canes are green and lack the extra layer of hairy bristles. Blackberry plants have a more upright form, while the dewberry canes bend and creep along the ground with tips that root easily to conquer more ground.

Blackberry, an aggregate fruit of drupelets. Credit: Johnna Roose

Blackberry, an aggregate fruit of drupelets.
Credit: Johnna Roose

While we’re on the subject of nomenclature, there’s something more fundamental we need to talk about. //looks over both shoulders and whispers// They aren’t really berries, botanically speaking. Yes, it’s true. This is another instance when common or culinary usage of a term differs from the strict scientific definition. In the world of plant science, a simple berry is a fruit containing the seeds and pulp from a single ovary. So, things like blueberries and cranberries are examples of fruit both commonly and scientifically referred to as berries. Other believable berries include grapes and currants. You may not believe me, but based on the botanical definition avocados, tomatoes and watermelons are also berries. Incidentally, strawberries are not berries either, but that is a subject for another post. Blackberries, dewberries and raspberries are aggregate fruit, in which each tiny round fleshy piece (a drupelet) is derived from a separate ovary in the flower but bound together in the form we commonly refer to as a berry. Don’t worry, I’ll still call them blackberries because blackaggregatefruit just doesn’t have the same ring to it.

After all, when it comes to food plants, being scientifically accurate takes a backseat to culinary use. ‘Berry cobbler’ just triggers a Pavlovian salivation response that ‘Aggregate fruit cobbler’ doesn’t. I know this isn’t really a food blog, but I feel strongly about wild blackberries, and it’s my blog and I can do what I want. Blackberries should be eaten out of hand using sunshine and dew as the only condiments. If there are any surplus berries, then you should bake them into a cobbler, tart or pie. There are many pastry recipes with berry ingredients, and I’m sure many are delicious. However, I am a minimalist. I rely on the berry cobbler recipe from the ‘Quick-N-Easy’ section of the 1981 Istrouma Baptist Church cookbook. Ingredients: 1 stick of salted butter, 1 cup of flour, 1 cup of sugar, 1 cup of milk and 2 cups of berries. Melt butter in baking dish. Mix other ingredients (except berries) together in bowl and pour over melted butter in baking dish. Pour berries over entire mixture and bake at 400 F until golden brown. It’s not fancy, but the simple gooey batter is the perfect medium for the tart flavorful berries. If you’ve really gotten more berries than you can handle in a single dessert preparation, then cook them for juice to make into jelly. Check out this resource from the LSU AgCenter for more information and recipes.


Blackberry cobbler and vanilla ice cream Credit: Johnna Roose

Blackberry cobbler and vanilla ice cream
Credit: Johnna Roose

The good thing about this treasure is that there is plenty to go around for all determined prospectors. Grab your boots and bucket. It’s berry pickin’ time (or soon will be for those of you just a bit further north).




*My brother would disagree with me. He is convinced that all snakes are copper-headed rattle moccasins. It’s either kill or be killed, and he will put down a layer of cover fire from his handy sidearm at the first sound of scales.

**trivialis, as in trivial. Really, botanical nomenclature, really? I find it hard to believe that anyone that has tasted dewberries would have called them trivial in terms of flavor. They probably should have been named Rubus heavenlyflavorexplosiononmypalate.

References and links:

So, this link provides an unbelievably detailed 15-step protocol (15!) for blackberry picking.

Here’s my version:

  1. Put on boots.
  2. Grab cane knife and bucket with handle.
  3. Tromp to back pasture and walk along fence line.
  4. After unripe red berries catch your eye, look for fully ripe blackberries nearby. For every ripe blackberry in the sun, there’s five more hiding under the shade of the leaves.
  5. Be careful not to step on ant piles, field mice, or snakes.
  6. Curse birds and small mammals that scurry out of the berry patch as you approach.
  7. Pick ripe blackberries and eat one for every five you toss in your bucket.
  8. Use yoga breathing techniques, balance and poses to reach ripe berries deeper in the patch.
  9. Curse the perfectly ripe succulent berries that fall from your grip into the dark depths of the ground below the briar patch.
  10. Curse the thorns, prickles and spines of the brambles as they get caught in your clothing, hair and flesh.
  11. Enjoy the morning sunshine until you remember you didn’t put any sunscreen on your neck.
  12. Curse because you forgot to put on insect repellent.
  13. See two inches of what must be a six-foot-long venomous snake. Shriek curses and defy gravity to escape blackberry patch.
  14. Upon entering a human dwelling, pick the ticks off of yourself. (Ironically, this step is unnecessary for any canine companions that have been adequately treated with flea and tick preventatives.)
  15. Cook and eat blackberry cobbler, served with vanilla ice cream.

May Bouquet: Alstroemeria

April showers have brought May flowers… to the blog. Today’s post is part of a May Bouquet series focused on flowers one might find in a bouquet. Y’know, leading up to Mother’s Day next Sunday. Think of these posts as daily reminders with wonderful suggestions on ways to honor the mothers in your lives.

Alstroemeria aurea ‘Saturne’ in southern Tasmania, Australia Credit: JJ Harrison via Wikipedia

Today we’ll have a look at the flower prevalent in many mixed-flower bouquets whose name you never learned- alstroemeria or Lily of the Incas. There are numerous species and cultivars, but they are native to South America. The different cultivars sport a variety of bloom sizes and markings. Alstroemeria are far more popular as cut flowers than garden plants, but they can be safely grown outdoors in USDA hardiness zones 8 – 11. They may tolerate the southern part of Zone 7 if the bulbs or rhizomes are adequately protected with layers of mulch during the winter months. Everyone else will just have to enjoy them as cut flowers or be prepared to host them indoors during winter.

Alstroemeria aurea in southern Tasmania, Australia Credit: JJ Harrison via Wikipedia

The pictures provide ample evidence as to why alstroemeria are popular cut flowers. They come in all colors and have beautiful spot patterns on the petals. Take a closer look at some of the flowers. There is a method to the madness when it comes to the spot pattern for many alstromeria blooms. Notice how (at least for these varieties) only three of the petals have the spotted pattern, two on the top half of the flower and one on the bottom? How do you think the flowers know their orientation and produce those markings?

Alstroemeria magnifica Credit: Pato Novoa via Wikipedia

Well, the truth involves knowing a little bit more about plant flower development. You’re not really looking at a flower with six true petals. Only three of them are petals (the ones with the spots). The other three are derived from tissue that would normally be sepals (special leaves at the base of most flowers that appear to hold the buds and blossoms together). In the case of alstroemeria blossoms, the sepals follow a developmental program that makes them look more like petals than leaves. Of course, botany has a name for this situation- tepals (when the sepals and petals cannot really be distinguished from one another as flower components in the perianth). If you would like an even closer look, check out this link with stunning photos and microscopic images of alstroemeria flowers.

The main parts of a mature flower Credit: Mariana Ruiz LadyofHats via Wikipedia

Alstroemeria pelegrina L. Credit: Pato Novoa via Wikipedia


References and Links:

Prokaryotic Picassos

Photosynthetic organisms are brilliant artists when it comes to their use of colors. Most people are familiar with the wide range of colors plants display. Roses are red, violets are blue, anyone? Well, cyanobacteria package prodigious amounts of pigments in prokaryotic form. Their name is derived from their blue-green color. It’s kinda their trademark. As photosynthetic organisms, they have plenty of chlorophyll in their photosynthetic machinery. Their blue color comes from their light-harvesting antenna, the phycobilisomes (PBS), which are comprised of proteins with blue pigments.

Phycocyanoobilin from Wikipedia

Phycocyanin from Wikipedia

Phycobiliproteins bind blue bilin pigments and assemble into discs; these discs assemble into the large phycobilisome complexes that sit on top of the photosystems and funnel light energy to them. The PBS looks like a giant blue octopus with a central core and a number of ‘arms’ of phycobiliprotein discs that extend out in all directions. Because these complexes are particularly good at absorbing orange light, which chlorophyll does not, the PBSs extend the wavelengths of light (and therefore the energy) available to cyanobacterial photosystems.


Phycobilisome General Structure

Some cyanobacteria like Fremyella diplosiphon can take color to another level. They can change the composition of their PBSs according to the color of light available to them in a process called complementary chromatic adaptation (CCA). This is possible because some species of cyanobacteria have two varieties of phycobiliproteins, each of which coordinates a distinct pigment. Phycocyanin binds the blue phycocyanobilin chromophore, which efficiently absorbs orange and red light and appears blue in color. Phycoerythrin binds the pigment phycoerythrobilin, which efficiently absorbs green light and appears pink to red in color. Thus, these cyanobacteria have blue PBSs in red light and have a typical blue-green appearance. However, in green light, they produce PBSs containing phycoerythrin and have a rose or red-colored appearance.

Phycobiliproteins, bilin variation, and group III CA regulation. (A) Phycocyanin and phycoerythrin (blue and red lines, and in vials) absorb in regions of the visible spectrum not well absorbed by chlorophyll or carotenoids. Attached bilins: PEB, phycoerythrobilin; PCB, phycocyanobilin. (B) Natural diversity in coloration of many different cyanobacterial species due to variation in their bilin content [photograph by Christophe Six. Reproduced with permission from Six et al. (2007) (Copyright 2010, Biomed Central Ltd.)]. (C) Group III CA regulation model for F. diplosiphon in red light, showing the asymmetric regulation of red-light active genes (orange) and green-light active genes (yellow) by the Rca and Cgi systems. Dashed line represents proposed repression by the Cgi system; yellow balls, phosphoryl groups; blue boxes, RcaC binding sites.

Phycobiliproteins, bilin variation, and group III CA regulation. (A) Phycocyanin and phycoerythrin (blue and red lines, and in vials) absorb in regions of the visible spectrum not well absorbed by chlorophyll or carotenoids. Attached bilins: PEB, phycoerythrobilin; PCB, phycocyanobilin. (B) Natural diversity in coloration of many different cyanobacterial species due to variation in their bilin content [photograph by Christophe Six. Reproduced with permission from Six et al. (2007) (Copyright 2010, Biomed Central Ltd.)]. (C) Group III CA regulation model for F. diplosiphon in red light, showing the asymmetric regulation of red-light active genes (orange) and green-light active genes (yellow) by the Rca and Cgi systems. Dashed line represents proposed repression by the Cgi system; yellow balls, phosphoryl groups; blue boxes, RcaC binding sites.

To achieve this dramatic color change, the cells have elaborate systems for sensing the incident light wavelengths in their environment and eliciting the appropriate response. Changing out the PBS antenna requires changes in gene expression of the protein components as well as the pathways that synthesize the necessary pigment (phycocyanin vs. phycoerythrin). It also means that the existing phycobiliproteins and their pigments must be degraded and their components recycled. The PBS antenna complexes comprise a significant portion of soluble protein within cyanobacterial cells, so it is important that the pieces be reused, no matter the light condition. All of these requirements add up to a sophisticated system of multiple players working to make this simple-looking color change happen on cue. This phenomenon is the research area of a number of groups working on cyanobacteria and photosynthesis.

greenlightPBS RedlightPBS

In this way, cyanobacteria are similar to Picasso, going through a blue period and later a rose period. In the case of Fremyella, the change is not due to swings in mood from melancholy to cheer, nor is it purely aesthetic. In biology, even beauty is functional. In the case of complementary chromatic adaptation, it allows cyanobacteria to most efficiently harvest the wavelengths of light available to them. You may be wondering when cyanobacterial cells would be exposed to differently colored light sources outside of an elementary school science fair project. Well, this scenario is more commonplace than you would think. For example, cyanobacteria cells close to the surface of a pond or ocean would be exposed to higher amount of red light compared to those deeper in the water column.* Those cyanobacterial cells that find themselves deeper in the water column would have much less red light because it does not penetrate as well as green light and other photosynthetic organisms living closer to the surface have already absorbed all of the red wavelengths of light allowing only green to pass through.**

Light microscopy image of a normal 'Fremyella diplosiphon' colony (green, left side) adjacent to a 'F. diplosiphon' mutant capable of only producing the light-harvesting pigment phycoerythrin (red, right side), growing on an agar plate in red light.

Light microscopy image of a normal ‘Fremyella diplosiphon’ colony (green, left side) adjacent to a ‘F. diplosiphon’ mutant capable of only producing the light-harvesting pigment phycoerythrin (red, right side), growing on an agar plate in red light. Credit: David Kehoe, used with permission

The image on the left may appear to be some kind of impressionism masterpiece or abstract work by a yet-to-be-discovered artist, but really it’s the combination of two cultures of Fremyella. The green side is the normal strain, while the red side is a mutant that contains only the red phycoerythrin pigment.

This post was written for the April Berry Go Round blog Carnival. Plants aren’t the only photosynthetic organisms that use color beautifully and efficiently.





*For those of you paying attention, this means they would use the blue phycocyanin-pigmented PBSs and appear blue-green.

**This means that cyanobacterial cells deeper in the water would adapt to use phycoerythrin in their PBSs and appear red.

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