Sunday, April 27, 2014

Astrobiology : Follow the Water

The more we've learned about life on our planet, the more we've come to realize the conditions that we consider livable are only a small fraction of the conditions that living things on this planet are happy to have. The two factors which remain are the need for an energy source and the presence of at least some liquid water.

Almost any sort of energy can be utilized by living things (Light, organic chemical, inorganic chemical, ion gradient, electrical, radiation) even when present in minimal amounts. Energy isn't the limiting factor on our planet

Water is ubiquitous on Earth, from the upper atmosphere to miles below the surface. We find life everywhere we find water, even if that water is horrendously toxic (acid/alkali/heavy-metal/etc.) to us. We find life subsisting between grains of sand subsisting on the trace of moisture provided by dew. We find life in the deepest mines we've dug. We find life living in lakes isolated from the surface for thousands of years of ice.

On Earth, wherever there is water, there is life.

The name of our planet is synonymous with solid ground, but most of the surface of our world is covered in water. From a distance, a glance at our home reveals it to be a water-world first. No other planet (under any definition of 'planet') in our system is anything like it. However, water is common in our part of the universe.

During the formation of a planetary system, volatile elements and compounds are pushed out from the star until ambient space cools enough for those volatiles to condense and freeze. The place where water freezes is referred to as the ice-line and represents the start of the region where icy bodies are formed.

The formation of planets produces a great deal of heat. The kinetic energy of rocky/icy bodies as they merge under gravitational attraction is converted to heat. If the resulting bodies are large enough, they melt and the different components form layers ranging from densest to lightest going from the core to the surface. Water is very low density and so ends up largely on the surface of such bodies. Because they formed far enough out from the sun for water to freeze, the surfaces begin to cool and freeze soon after they form. The residual heat of formation is tremendous, and combined with new heat generated through radioactive decay and tidal interactions can keep temperatures below the surface elevated above the freezing point of water for quite some time.

Several bodies in our solar system appear to have under-ice oceans.

Calisto :
Enceledus :
Europa :

There are potentially living things on these moons, prospering in the warm water of thermal vents or creeping along in the cold waters near the ice.

I can't wait until we go and look.

References :
  1. Follow-the-water.
  2. Light energy for biology.
  3. Electrical energy for biology.
  4. Radiation energy for biology.
  5. Ice-line.
  6. Oxygenation of Earth.
  7. Snowball-Earth.

Friday, April 18, 2014

Oxalis and the Red Queen
Breeding in the genus Oxalis is complicated by the presence of multiple flower types, referred to as heterosytly because of differences in the arrangement of styles (the female part of a flower). Oxalis generally have three forms, so they are specifically described as being tristylous.

The physical differences between the flower types match hidden differences in chemistry which limit the effectiveness of pollination between like types. These differences, both physical and chemical, discourage inbreeding.

With three forms, the odds that a vegetatively related plant will have the same form is 1/1 while the odds that any random plant will have the same form is 1/3. Failure of pollination from the same form to succeed results in a strong preference against inbreeding.

Inbreeding reduces genetic diversity and increases the odds of revealing deleterious recessive alleles. Some plants, like Oxalis, have systems to discourage inbreeding, others don't. It isn't clear what drives some species to evolve these systems while others don't, but there is related theory that might be informative…

Why do most plants/animals reproduce by sexual means? Any asexual progeny will get 100% of their
DNA from their mother. Any sexual progeny will get only 50% of their DNA from their mother. Basic evolutionary theory suggests there would be a strong bias towards species reproducing by asexual means. So, why…?

The current theory, backed by years of experimental evidence in different systems (fish, snails, nematodes) is that sexual reproduction allows a species to mix its genome up and keep ahead of parasites, which have much shorter generation times and are rapidly evolving to overwhelm the host immune system.

This is referred to as the "Red Queen Hypothesis", in reference to Lewis Carol's character in "Through the Looking-Glass".

"Now, here, you see, it takes all the running you can do, to keep in the same place."

From a theoretical stance, the same pressures which lead to the prevalence of sexual reproduction are likely to be involved in why some plant species have evolved heterostyly. That is to say, a high level of parasitism over evolutionary time periods likely provided the selection pressure leading to the evolution of heterostyly and other mechanisms to minimize inbreeding. Proving this experimentally is a bit harder to do, however, and researchers are actively working on the subject.

What got me interested in this system is that I have two Oxalis triangularis plants I got from a friend. One plant has dark purple leaves with a central lighter mark and pink flowers. The second plant has green leaves and white flowers. I opened up a flower from each plant and discovered they were structured differently.

Plant #1
  • Purple leaves, light mark.
  • Pink flowers.
    • 1' : styles
    • 2' : stamens
    • 3' : stamens
Plant #2
  • Green leaves, smaller.
  • White flowers.
    • 1' : stamens
    • 2' : styles
    • 3' : stamens
If my two plants had happened to have the same flower structure, I wouldn't have looked into the topic of heterostyly. I would have tried crossing the flowers and had the cross fail. I would have assumed the plants were incompatible and not thought to look into it further.

I lucked out and my plants have different flower forms, so my attempts to cross them will likely result in the production of seed. I still have to ponder on the subject of what I might want to breed this species for, but at least I will probably get some interesting combinations of traits in the offspring.

  1. Dercole F, Ferriére R, and Rinaldi S. (2010) Chaotic Red Queen coevolution in three-species food chains. Procedings of the Royal Society of Biologists 277:2321-2330.
  2. King KC, Delph LF, Jokela J, and Lively CM. (2009) The Geographic Mosaic of Sex and the Red Queen. Current Biology 19:1438-1441.
  3. Marco DE and Arroyo MTE. (2014) The Breeding System of Oxalis squamata, a Tristylous South American Species. Botanica Acta 111:497-504.
  4. Moran LT, Schmidt OG, Gelarden IA, Parrish RCII, and Lively CM. (2011) Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex. Science 333:216-218.
  5. Quental TB and Marshall CR. (2013) How the Red Queen Drives Terrestrial Mammals to Extinction. Science 341:290-292.
  6. Weller SG, Dominguez CA, Molina-Freaner FE, Fornoni J, and Lebuhn G. (2007) The evolution of distyly from tristyly in populations of Oxalis alpina (Oxalidaceae) in the Sky Islands of the Sonoran Desert. American Journal of Botany 94:972-985.

Tuesday, April 1, 2014

The Color of Tomatoes

Tomatoes can be found in a wide range of colors (red, pink, orange, yellow, white, green, brown, purple, blue) at your local farmers' market or grocer. Those color differences represent differences in the types and proportions of biologically synthesized pigments. Because tomatoes are such an important crop and adding those pigments to our diet has been shown to give us positive health impacts, researchers have spent some time studying the pathway they use to build the various pigments.

Information about the pathway is spread across numerous papers encompassing decades of research. Not every paper examining the topic will contain all the details of the pathway and there are sometimes conflicting results that have to be negotiated.

The fortunate thing is that these days, more and more of the research behind any particular topic is being placed online. This gives amateur and professional researchers alike access to the same information and either can learn a great deal about many different subjects that may interest them. In general you shouldn't put too much stock in the results of any one paper, but when the results of multiple independent lines of inquiry happen to align, you can be more confident in the inferences you gain.

You might say I'm somewhat interested in the biology of the things I find around me. I decided to look into what was known about the interesting colors found in tomatoes.

The majority of pigments in the tomato are carotenoids. After a bit of research, I generated the figure (at right) to show the biosynthesis pathway which produces these pigments. It illustrates most of what I've learned about the pathway. The figure is probably not entirely comprehensive, as all biological systems are intricate, but it contains sufficient detail to help explain the range of fruit colors seen in tomatoes.

You can dig through the references at the end of this post if you're interested in where I got the information. In fact, I would highly recommend you do so, if you're interested in the biology of tomato color. If you've never read primary literature, you should be aware that you may have to read through dozens (or hundreds) of papers to get a solid grasp of a new topic in this way.

In my figure, I use double arrows to indicate higher reaction rates, as inferred from preferred branches of the reaction pathway or intermediates which are known but don't appear in large amounts. The colored components of the pathway are highlighted in something approaching their true colors in chromatography experiments (and in the fruit) to make it simpler to visualize how mutations might impact fruit color.

Energy flows through biosynthetic pathways. Though each enzymatic reaction is reversible, the overall progression of the pathway is driven by the enthalpy gradient across its components. When a mutation breaks part of a pathway, it blocks that flow of energy, resulting in a build-up of the chemical intermediates just before the break as well as a reduction or absence of those intermediates after the break.

The following figures are close-up versions of the main figure above, highlight the placement of a series of mutations in the pathway which result in color changes in the flesh of tomatoes. The mutations are indicated by a large negative or positive sign, highlighted in red, at the location of the change to the pathway.

Mutant : 'r'
The first major mutation (left) is responsible for the difference between red and yellow tomatoes. The wild-type dominant allele of the gene leads to the production of lycopene, so the gene is named 'red' ('R'). The recessive allele ('r') results in an overall decrease in the production of carotenoids. The decrease is not uniform; some carotenoids are suppressed more than others, resulting in an overall yellow appearance.
Mutant : 'gf'

The second major mutation (right), in combination with the 'r' mutation just described, is the most common cause of green-fleshed tomatoes. The recessive mutant allele leads to green flesh, so it is named 'green-flesh' ('gf'). The wild-type dominant allele of the gene ('Gf') allows the breakdown of chlorophyll and other photosynthetic components during the ripening process.

A minor mutation produces green ripe fruit by interfering with the ability of the fruit ripening system to respond to ethylene. Ethylene is a common plant hormone involved in maturation/ripening/senescence, so this mutation keeps some aspects of the normal fruit ripening from happening. This dominant mutant allele is called 'Green-ripe' ('Gr') and results in a green tomato with a red heart. This mutation doesn't impact the pigment pathway, but instead where different components of it are activated. It is not clear if it interacts with the 'red' ('r') locus in a similar way to the more common 'gf' mutation.

Mutant : 't'
The third major mutation (left) is responsible for the most common form of orange tomato. The recessive mutant allele is named 'tangerine' ('t') (after the orange variety "Tangerine" where the gene was found). The wild-type dominant allele of the gene ('T') allows the final synthesis of lycopene. The mutation results in the build-up of orange prolycopene, as well as zeta-carotene in smaller amounts.
Mutant : 'B'

Another minor mutation (right) results in a less common types of orange tomato. The dominant allele is named 'beta-carotene' ('Beta', 'B') because it leads to a large increase in beta-carotene and a decrease in lycopene. The position of this gene in the pathway and the mechanism of the mutation isn't entirely clear, but the data seems to suggest the gene is involved in the conversion of lycopene to gamma-carotene and the mutation results in increased activity.

The color of the epidermis also impacts the apparent color of tomatoes, but the mutations impacting this system are less well-understood. The typical red tomato has a transparent-yellow epidermis, giving the associated gene its name 'yellow' ('Y'). A common recessive mutation ('y') results in a clear epidermis. The epidermis color overlaid on the flesh color results in the perceptual differences is red/pink and brown/purple tomatoes.

Recently, breeders have been been working with genes that result in the production of dark purple anthocyanins in the skin of tomatoes. The two genes 'anthocyanin-fruit' ('Aft') and 'atroviolaceum' ('atv') were introgressed into cultivated tomatoes from Solanum chilense and Solanum cheesmaniae, respectively. A less common gene 'Abg' was introgressed into cultivated tomatoes from Solanum lycopersicoides, but is less useful/available because it has a recessive lethal character. All three genes are described in Mes et al, 2008.

Frogsleep Farms
There is evidence for lycopene production in the skin of some tomatoes, resulting in an opaque-red skin. The details of the genetics have yet to be worked out and published, but Frogsleep Farms has found some lovely examples. The fruit at right appears to have the genotype 'r' for yellow fruit flesh color, but has intense lycopene-red in the epidermis. (The first photo on this page shows another fruit, illustrating high-lycopene opaque-red skin.)

In my personal gardening, I've noticed an opaque-red epidermis in fruit produced by the micro-tomato variety 'Tiny Tim'. This variety was derived in part from the wild tomato Solanum pimpinellifolium, which also seems to have an opaque-red fruit epidermis. Potential variations might eventually be found which have opaque-yellow or opaque-orange skin, so I find the idea of exploring the traits of fruit skin color to be exciting.

Another set of genes impact where pigment is produced in the fruit. A wild-type tomato has a dark-green shoulder when immature, which delays ripening at the top of the fruit. Common modern market tomatoes have the 'uniform ripening' ('u') trait which shows even ripening, but reduced overall color. This gene is a transcription factor which normally guides chlorophyll distribution and abundance in unripe fruit.

[dgdg] vs. [uu]
The 'dark green' ('dg') mutation produces a dark green immature fruit and increased levels of carotenoids in the ripe fruit. The 'high pigment 2' ('hp2') mutant is now considered to be a different allele of the same gene as 'dg', which is now known to be the tomato homolog of the Arabidopsis DEETIOLATED1 gene. This gene is involved in the perception of light levels and impacts morphogenesis.

The cause of bicolor, striped, and spotted tomatoes are less well understood. Striped tomatoes using the 'green stripe' ('gs') mutation are pretty common these days. Another type of striping is due to a dominant allele ('Ufs') of the 'uniform ripening' gene. Spotting is generally considered a commercial defect, but the 'gold fleck' ('Gfk') trait is an interesting look when it is highly expressed.

In the following section, I give limited descriptions of the different color categories of tomatoes. This description includes the genotypes and example varieties associated with them when they're commercially available.

 'RR' (Kachanovsky et al, 2012)
Red Tomatoes

The typical red tomato is pigmented by a large amount of lycopene and lesser amounts of beta-carotene, driven by the 'red' ('R') gene. The skin of these tomatoes also has a yellow pigment driven by the 'yellow' ('Y') gene.
genotype = [RR; YY]
example = "Red Barn".

Pink Tomatoes

These have the lycopene (red) and beta-carotene (orange) of typical tomatoes, but they have clear skin from a recessive allele 'y'. This results in the tomatoes appearing pink when compared to the typical red tomato.
genotype = [RR; yy]
example = "Dwarf Champion Improved".

Orange Tomatoes
 'RR; tt' & 'rr; tt' (Kachanovsky et al, 2012)

The most common type of orange tomato is caused by the 'tangerine' ('t') mutation. The skin can be clear or yellow.
genotype = [RR; YY/yy; tt] or [rr; YY/yy; tt]
example = "Earl of Edgecombe", "Elbe""Tangerine".

A less common type of orange tomato is caused by the 'Beta-carotene' ('Beta','B') mutation. The skin can be clear or yellow.
genotype = [RR; YY/yy; BB]
 'rr' (Kachanovsky et al, 2012)
example = "Caro-Rich","Jaune Flammée".

Yellow/White Tomatoes

Yellow tomatoes are caused by a recessive allele ('r') of the 'red' gene. The skin can be clear or yellow.
genotype = [rr; YY/yy; TT]
examples = "Yellow Pear".

White tomatoes appear to be caused by a stronger recessive allele ('r-') of the 'red' gene.
genotype = [r-r-; YY/yy; TT]
example = "Dr Carolyn", "White Queen".

Green Tomatoes

The most common type of green tomato is caused by the recessive 'green-flesh' ('gf') mutation in combination with the 'r' mutation.
genotype = [rr; YY/yy; TT; gfgf]
example = "Green Zebra".

A less common type of green tomato is caused by the dominant 'Green-ripe' ('Gr') mutation. This mutation leaves the center of the fruit to ripen normally, resulting in green/'purple' outer regions and a yellow/red center. There are heirloom varieties around with this trait, but I haven't been able to find any specific names.
genotype = [GrGr]
example = ???

Brown Tomatoes

These are pigmented by a large amount of lycopene and lesser amounts of beta-carotene, driven by the 'red' ('R') gene, as well as by chlorophyll from the 'green-flesh' ('gf') gene. The skin of these tomatoes has a yellow pigment driven by the 'yellow' ('Y') gene.
genotype = [RR; YY; TT; gfgf]
example = "Black Russian", "Brazilian Beauty".

Purple Tomatoes

These are pigmented by a large amount of lycopene and lesser amounts of beta-carotene, driven by the 'red' ('R') gene, as well as by chlorophyll from the 'green-flesh' ('gf') gene. The skin of these tomatoes is clear driven by the mutant allele ('y') of the 'yellow' gene.
genotype = [RR; yy; TT; gfgf]
example = "Black Cherry""Black Krim".

"Indigo Rose" showing 'Aft' and 'atv'.
Blue Tomatoes 

These have anthocyanin expression in the skin, driven by the combination of 'anthocyanin fruit' ('Aft') and 'atroviolaceum' ('atv') genes.
genotype = [AftAft; atvatv]
example = "Indigo Rose".

Black Tomatoes

There is no specific genetics to describe for this category. 'Black' is often used to describe those that I would call 'brown' or 'purple'. (The example varieties I list for the 'brown' and 'purple' groups have names starting with 'black'.) I wouldn't be surprised if the 'blue' tomatoes end up being described this way, since they're actually the closest to black we're likely to get.

Bicolor Tomatoes

The 'bicolor' trait is caused by an allele ('ry') of the 'R' gene which activates of the carotenoid pathway in some parts of the fruit and not others. This results in streaks of red and yellow throughout the fruit and skin.
genotype = [ryry]

Striped Tomatoes

"Green Zebra" showing 'gs'.
Dark green stripes on immature fruit, driven by the recessive 'green-stripe' ('gs') gene. This trait has become very popular lately and is responsible for the stripes seen on many heirloom-type varieties available in markets.
genotype = [gsgs]
examples = "Green Zebra", "Striped Roman".

tomato showing 'UFs'
Dark green radial stripes, opposite of each locule, driven by a dominant allele ('UFs') of the 'uniform-ripening' gene. Frogsleep Farm has some nice photos of fruit with the pattern mixed with anthocyanin production, as well as a nice bit of discussion of the trait, but there seem to be few commercially available varieties with this form of striping.
genotype = [UFsUFs]
examples = "Siberian Tiger", "Arbuznyi".
Spotted Tomatoes

Yellow spots on ripe fruit, driven by the dominant 'gold-fleck' ('Gdf') gene.   Frogsleep Farms has some interesting images showing this trait.
genotype = [GdfGdf]
examples = "Scabitha".

  1. Apel W & Bock R. (2009) Enhancement of Carotenoid Biosynthesis in Transplastomic Tromatoes by Induced Lycopene-to-Provitamin A Conversion. Plant Physiology 151:59-66. 
  2. Barry CS, McQuinn RP, Thompson AJ, Seymour GB, Grierson D, and Giovannoni JJ. (2005) Ethylene Insensitivity Conferred by the Green-ripe and Never-ripe 2 Ripening Mutants of Tomato. Plant Physiology 138:267-275.
  3. Barry CS, McQuinn RP, Chung M, Besuden A, & Giovannoni JJ. (2008) Amino Acid Substitutions in Homologs of the STAY-GREEN Protein are Responsible for the green-flesh and chlorophyll-retainer Mutations of Tomato and Pepper. Plant Physiology 147:179-187.
  4. Fantini E, Falcone G, Frusciante S, Giliberto L, & Giuliano G. (2013) Dissection of Tomato Lycopene Biosynthesis Through Virus-Induced Gene Silencing. Plant Physiology 163:986-998.
  5. Gonzali S, Mazzucato A, & Perata P. (2009) Anthocyanin pathway in tomatoes. Trends in Plant Science 14:237-241.
  6. Issacson T, Ronen G, Zamir D, and Hirschberg J. (2002) Cloning of tangerine from Tomato Reveals a Carotenoid Isomerase Essential for the Production of Beta-Carotene and Xanthophylls in Plants. Plant Cell 14:333-342.
  7. Jenkins JA & Mackinny G. (1951) Color in Tomatoes. California Agriculture  Feb 13-14.
  8. Jenkins JA & Mackinny G. (1953) Inheritance of Carotenoid Differences in the Tomato Hybrid Yellow x Tangerine. Genetics 38:107-116.
  9. Jenkins JA & Mackinny G. (1955) Carotenoids of the Apricot Tomato and its Hybrids with Yellow and Tangerine. Genetics 40:715-720.
    2. Carotenoid characterization of 'apricot' ('at') mutation.
    3. Data suggests alternate pathway to generate beta-carotene.
  10. Kachanovsky DE, Filler S, Isaacson T, & Hirschberg J. (2012) Epistasis in tomato color mutations involves regulation of phytoene synthase 1 expression by cis-carotenoids. Proceedings of the National Academy of Science USA 109:19021-19026.
  11. Levin I, Frankel P, Gilboa N, Tanny S, and Lalazar A. (2003) The tomato dark green mutation is a novel allele of the tomato homolog of the DEETIOLATED1 gene. Theoretical Applied Genetics 106:454-460.
  12. Lesley JW and Lesley MM. () Linkage of sh (sherry).
  13. Ma Q, Du W, Brandizzi F, Giovannoni JJ, & Barry CS. (2012) Differential Control of Ethylene Responses by GREEN-RIPE and GREEN-RIPE LIKE1 Provides Evidence for Distinct Ethylene Signaling Modules in Tomato. Plant Physiology 160:1968-1984.
  14. Mes PJ, Boches P, & Myers JR. (2008) Characterization of Tomatoes Expressing Anthocyanin in the Fruit. Journal of American Society of Horticultural Science 133:262-269.
  15. Paran I, van der Knaap E. (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. Journal of Experimental Botany 58:3841-3852.
    • 'Del' has increased expression of lycopene-delta-cyclase, resulting in conversion of lycopene to delta-carotene.
    • 'Del' was introgressed from Solanum pennelii.
    • 'Beta' was introgressed from Solanum cheesmaniae.
    • 'old gold' is allelic to 'Beta', but eliminates Beta-carotene production.
  16. Powell ALT, Nguyen CV, Hill T, Cheng KL, Figueroa-Balderas R, Aktas H, Ashrafi H, Pons C, Fern ández-Muñoz R, Vicente A, Lopez-Baltazar J, Barry CS, Liu Y, Chetalat R, Granell A, Deynze AV, Giovannoni JJ, and Bennett AB. (2012) Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development. Science 336:1711-1715.
  17. Tomes ML, Quackenbush FW, Nelson OE Jr, & North B. (1953) The Inheritance of Carotenoid Pigment Systems in the Tomato. Genetics 38:117-127.
    • Identification of pigments found in red/yellow/B-orange/tangerine fruit.
    • Yellow skin is a non-carotenoid pigment.
    • Yellow differs from red mostly in across-the-board reduction in pigment.
    • Tangerine fruit contains mostly zeta-carotene and prolycopene.
    • Red fruit contains mostly lycopene and less beta-carotene.
    • 'Beta'-orange fruit contains mostly beta-carotene and less lycopene.
    • [r locus < t locus < Beta locus] in pathway.
  18. Tomes ML. (1966) The Competitive Effect of the Beta- and Delta-Carotene Genes on Alpha- and Beta-Ionone Ring Formation in the Tomato. Genetics 56:227-232.
  19. Wann EV. Reduced Plant Growth in Tomato Mutants high pigment and dark green Partially Overcome by Gibberelin. (1995) HortScience 30:379.
    • Mention of 'B' mutant variety.
    • List of several varieties with high prolycopene => 'tangerine' mutant varieties.
    • Data suggests secondary pathway to beta-carotene.
    • Bicolor trait.
    • Bicolor trait.