As Many Exceptions As Rules: taxonomy

Showing posts with label taxonomy. Show all posts

Thursday, November 16, 2017

On Geometry And Genomes

Biology concepts – linear chromosomes, circular chromosomes, taxonomy, replication, telomere

Organization is helpful in learning and work,

and apparently in crafts. But there is a fine

line between organization and obsessive

compulsive disorder.

Everyone (teenagers excepted) knows that getting organized helps you to learn and work. When you group tasks, items, or facts, it helps in remembering or working with them. In biology, grouping organisms has a history as old as language.

In the older grouping systems, the name of an organism was a phrase that described some characteristic of the organism. When a new relative was identified, the name phrase had to be lengthened to separate this new organism from those similar to it. As you can imagine, the names got very long very fast.

In the 1750’s, Carolus Linnaeus developed a much easier system of naming. In his “trivial system,” each organism had two descriptors in its name; a binary naming system. Linnaeus’ system (and others) of taxonomy (taxis is Greek for “arrangement”) is based on shared characteristics.

Carolus Linnaeus (he let me call him Carl) had many

names. His knighthood name was Carl von Linne, his

born name was Carl Nilsson Linnaeus. In his naming

system Linne came up with the name mammal, so I guess

he named himself again.

At first, it was the characteristics people could see that were used to group organisms. Then it was the characteristics on the macroscopic and the microscopic levels. Now it is based on molecular characteristics, forming both a taxonomic classification and an evolutionary tree; this is now called the science of phylogenetics.

Molecular characteristics usually mean DNA. Differences in DNA sequence and in the number of mutations that have occurred provide a relationship between organisms. Using these factors, a time line for their divergence can be estimated. We changed the ways we determine similarity, and that changed the rules. With new rules come new exceptions.

Many of the DNA rules start with chromosomes (chromo = color and soma = body, this comes from the dark and light banding pattern of stained DNA). Cellular DNA is very long and very thin, perhaps only 12-22 nanometers wide (about 1/5000 the width of a human hair). In this form, it can only be seen with an electron microscope.

In eukaryotes, this DNA becomes complexed with many proteins during cell division so that all the DNA can be packed up and moved more easily to the daughter cells. Called chromosomal packaging, the DNA is wound around proteins called histones, then folded many times over, so that the finished chromosome is packed 10,000 times more compact than the original DNA helix. This is the packed DNA that we see as dark and light bands and gives it its name.

DNA packaging with proteins is a eukaryotic characteristic, unless

I find an exception! The DNA wraps around the histones, then the

histones line up into a coil, then the coils fold up into the

chromatid. Total packing – about 10,000 fold; it takes a piece of

DNA 1.5 cm long and makes it 0.0000002 cm long!

By definition, a chromosome is a piece of DNA that contains genes that are essential for the survival and function of the organism. This implies that there may be other pieces of DNA that contain genes that are not necessary for survival.

The molecular rules of biology state that prokaryotes have one chromosome, a single piece of double stranded DNA that contains all the genes that the prokaryote (archaea or bacteria) needs. This is efficient for the organism; it is one stop shopping for replication of all its instructions and only two chromosomes (after replication) need to be segregated to the two daughter cells that are being made.

And here begins our exceptions. There are several prokaryotic organisms that have more than one chromosome. That is to say, their essential genes are located on more than one piece of DNA.

The first identified example of multiple chromosomes in a prokaryote was Rhodobacter sphaeroides, a photosynthetic species of true bacteria that can also break down carbohydrates it takes up. This bacterium was found to have two chromosomes, although one was more than three times the size of the other.

Genes encoding essential products for making proteins and carrying out day-to-day functions are located on each of the two R. sphaeroides circular chromosomes. There are other genes that exist on both of the chromosomes, but appear to be turned on and off via different signals. This implies that the same gene may serve its function at different times in the organism's life, or under different environmental conditions.

R. sphaeroides is by no means the only prokaryote that possesses multiple chromosomes. More than a dozen different groups of bacteria have at least some members with more than one chromosome. This includes Vibrio cholerae, the causative organism of the disease cholera. V. cholerae is responsible for a diarrheal infection that affects more than 3-5 million people per year and causes 130,000 deaths each year.

This is a crown gall in a birch tree caused by R. radiobacter.

Like in cancer tumor in animal tissues, a gallis unregulated
growth. In grape vines, it has been responsible for the ruin
of entire Kentucky vineyards. Kentucky makes wine?

In addition to these organisms there is Agrobacterium tumefaciens, whose name was recently changed to Rhizobium radiobacter. This is a very interesting two chromosome bacterium. It usually is a pathogen of plants, forming galls (tumors) on several cash crops, such as nut trees and grape vines. This is an important tool in the molecular biologist’s toolbox, since it has been found that R. radiobacter easily transfers DNA between itself and the plants it infects, via lateral gene transfer (a subject we have discussed in depth, When Amazing Isn’t Enough and Evolution of Cooperation). But R. radiobacter goes further, it can also cause disease in humans who have poorly functioning immune systems. For folks battling cancers, HIV, or other diseases that wreak havoc with their ability to fight off infections, R. radiobacter can cause bacteremia (bacteria colonizing the blood) or endopthalmitis (infection of the two hollow cavities of the eye).

The second molecular rule of biology is that prokaryotic chromosomes take the shape of a circle; the DNA forms a single loop. This shape is helpful in terms of replicating the prokaryotic chromosome prior to cell division. Start anywhere, and you can keep going to replicate the entire thing. In point of fact, they don’t start just anywhere, but one start point (called an origin of replication) leads to complete replication.

There are advantages to having a circular chromosome. Prokaryotic chromosomes do not complex with proteins to become more densely packed, so it remains as a thin, long molecule. This means that fewer proteins are needed to maintain a circular, prokaryotic chromosome. In addition, since replication requires the doubling of just one piece of DNA from one origin of replication, this takes less time and fewer proteins to accomplish. Together, these features of a circular chromosome result in a more efficient and simpler process, with fewer chances for mistakes to be made.

Borrelia burgdorferi, a spirochete (spiral) bacterium was

Named for the researcher who discovered, it in 1982, Willy

Burgdorfer. It is one of the few pathogens that can function

without iron; it uses manganese instead. The ways this bug

gets around the rules is astounding.

However, there are exceptions in which prokaryotes have linear chromosomes. The Borrelia burgdorferi bacterium has a single chromosome, but it has the geometry of eukaryotic chromosomes, a line segment with two ends. This was the first prokaryote found to have a linear genome, way back in 1989. This lyme disease pathogen has one major linear chromosome and other pieces of smaller DNA that are circular or linear (which we will discuss in the next post); you just can’t trust a pathogen to follow the rules. Other prokaryotes that have linear chromosomes include our friend R. radiobacter. Even more interesting, while this pathogen has two chromosomes; one is circular and one is linear. How does that happen?

The previous discussions do not mean that all prokaryotes with multiple chromosomes or linear chromosomes are disease-causing agents, just the interesting ones. Since they cause pathology in animals or crops, they hit us in the wallet. It makes sense that we have studied them in more detail and have discovered their hidden exceptions. There are probably thousands of innocuous prokaryotes that have more than one chromosome or have linear chromosomes, we just don’t have a reason to look at them in that much detail.

There may be more than one way that prokaryotes end up with linear chromosomes. In some cases, the linear chromosomes still have bacterial origins of replication, indicating that they may have evolved from circular chromosomes. There is also evidence that some linear chromosomes might have developed from other linear DNAs in the cell, something we will talk about next time.

The rules of defining prokaryotes and eukaryotes also state that eukaryotes have linear chromosomes. The essential genes are stored on more than one piece of DNA, and these pieces have two ends apiece, like a line segment in geometry.

Linear chromosomes are a disadvantage because it is hard to replicate the ends. Because of the way that DNA replicates, the ends of the chromosomes, called telomeres, end up being shortened every time the DNA is replicated. Over time, this leads to shorter chromosomes that might lose DNA sequences that the cell needs in order to function.

Some lines of evidence suggest that telomere shortening is a direct cause of ageing. The loss of important sequences at the ends of chromosomes cases cells to perform at less than optimal levels, and mistakes and toxic products then build up and lead to larger dysfunctions of cells, organs, and systems, ie. getting old.

This is a very simple cartoon depicting recombination. When

sequences are exchanged, it isn’t necessarily a 1:1 exchange.

Sometimes parts of genes are sent one way but not the other,

So new genetic sequences can result. Some help, some hurt, and

some have no effect until the environmental conditions show

them for what they are. Most exchanges do not increase diversity

to any great degree, but the fact that some do has helped move

evolution along.

On the other hand, linear chromosomes may promote genetic diversity. In eukaryotes, the division of the cell requires each chromosome to be replicated, then the matching chromosomes of a pair (one from mom and one from dad) line up together. This is a prime opportunity for the chromosome to exchange some sequences in a process called homologous recombination; a mixing of genes beyond just getting one from each parent.

However, a study published in 2010 indicates that the geometry of the chromosome doesn’t matter when it comes to recombination rates. Scientists took a circular chromosome organism and linearized its genome (they cut it so it had ends). They also did the reverse experiment, taking a linear chromosome organism and circularizing its DNA.

In both cases, there was no change in the rate that its DNA recombined and produced slightly different offspring (the two circular chromosomes after replication can swap some pieces). So geometry does not appear to affect genetic diversity – so why did each type evolve? Good question – that can be your Nobel Prize project.

Next week we will continue the discussion of exceptions in DNA structures, including DNA that isn’t part of a chromosome, and mitochondrial and chloroplast genomes that don’t look like they should.

Casjens SR, Mongodin EF, Qiu WG, Luft BJ, Schutzer SE, Gilcrease EB, Huang WM, Vujadinovic M, Aron JK, Vargas LC, Freeman S, Radune D, Weidman JF, Dimitrov GI, Khouri HM, Sosa JE, Halpin RA, Dunn JJ, & Fraser CM (2012). Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids. PloS one, 7 (3) PMID: 22432010

Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, & Muller D (2014). Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Molecular phylogenetics and evolution, 73, 202-7 PMID: 24440816

Suwanto A, & Kaplan S (1989). Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. Journal of bacteriology, 171 (11), 5850-9 PMID: 2808300

For more information or classroom activities on prokaryotic chromosomes or eukaryotic chromosomes, see:

Prokaryotic chromosomes –

http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/chromosomes.html

http://www.news-medical.net/health/Chromosomes-in-Prokaryotes.aspx

http://www.biog1105-1106.org/demos/106/unit01/17b.eukchroms.html

http://www.nature.com/scitable/topicpage/genome-packaging-in-prokaryotes-the-circular-chromosome-9113

http://biology.kenyon.edu/courses/biol114/Chap01/chrom_struct.html

http://www.tusculum.edu/faculty/home/ivanlare/html/genetics/chromosome1-master.html

http://en.wikipedia.org/wiki/Nucleoid

http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter4/bacterial_chromosome_compaction.html

Eukaryotic chromosomes –

http://biology.kenyon.edu/courses/biol114/Chap01/chrom_struct.html

http://www.ndsu.edu/pubweb/~mcclean/plsc431/eukarychrom/eukaryo3.htm

http://ocw.mit.edu/high-school/biology/heredity/eukaryotic-chromosomes/

http://studentreader.com/eukaryotic-chromosome/

http://www.ndsu.edu/pubweb/~mcclean/plsc431/eukarychrom/eukaryo3.htm

http://www.nature.com/scitable/topicpage/chromosomes-14121320

http://www.emunix.emich.edu/~rwinning/genetics/chrom.htm

http://www.pbs.org/wgbh/nova/teachers/activities/2809_genome_04.html

www.indiana.edu/~ensiweb/lessons/chr.con2.tchr.pdf

http://www.windows2universe.org/earth/Life/genetics_intro.html

Wednesday, October 29, 2014

Almost This Or Almost That? Must Be The Other

Biology concepts – Protista, taxonomy, phylum, kingdom, monophyletic, paraphyletic, cladistics, algae, diatom, dinoflagellate

Euglena gracilis is an organism in the Kingdom Protista. It has

one long flagellar undulipodium, but it can also move by

amoeboid movement. It has chloroplasts and can do

photosynthesis, but it also can eat other organisms. Is it any

wonder that classifying protists is so hard?

Classifying living organisms is self-perpetuating job. Imagine if the dentist sold candy in his/her office, “Here’s your root canal and your Laffy Taffy.” Scientists try their best, but whenever you start sorting things out, you always have that pile left over that doesn’t seem to fit anywhere. So you have to rethink your categories and try again.

The best example of the inanity of classification is Kingdom Protista. The word means, “the very first,” probably because it is supposed that these were the first eukaryotes. How do we define the organisms of this Kingdom? The best we can manage is to say that they are the eukaryotes that aren't animals, plants, or fungi. Really, is that the best we can do?

In a perfect system, all the organisms of one kingdom would be descended from a single common ancestor (be monophyletic, mono = one, and phulon = tribe). But it don’t work like that. And this is where Kingdom Protista serves as a good example.

There are protists that look a lot like animals, those that resemble plants, and those that share features of fungi. No way did they all come from a single ancestor. Protista is a paraphyletic (para = near) kingdom, the group may exclude a member with a common ancestor. As such, the protists are a catch-all, those that don’t fit in some other kingdom. Protists are like pornography – hard to define, but you know it when you see it.

Classification isn’t perfect, some groups come from

different ancestors. A shows a group (in yellow) that

is monophyletic, they all come from one ancestor.

The paraphyletic group (B) shows that some groups

can’t include all descendents of a common ancestor.

And if a group is made from descendents of different

ancestors, it is called polyphyletic (C).

We already said that some behave like animals, plants, or fungi. Some are unicellular, some are multicellular, and some can be either. Some do photosynthesis, while some eat other organisms. How can you break these up into phyla, classes, orders, families, genera, and species when they are all so different?

You might do it by common ancestor; let their genes do the talking. We are learning more and more about who begot who – this is the study of cladistics. But if you break down protists into their clades – they don’t seem to make sense. Organisms that look or act similar might be in different clades, with wildly different organisms linked close together.

Alternatively, you might divide them up based on the characteristics, as Linneaus did - the animal-like protists in one phylum, the plant-like protozoans in another. But this may separate genetically related organisms into very different phyla. Same problem. How about by the way they get around? Some use flagella-like undulipodia, some use undulipodia called cilia, some use cytoplasmic crawling called pseudopodia, and others are immotile. Again, disparate organisms may be lumped together just based on their preferred mode of travel.

The idea of the "phylum" is to place the organisms in categories so that they are “more related to each other than they are to any other group.” Wow, that sounds scientific. Related based on what? We just discussed motility, genetics, and physical characteristics or behaviors.

The Kingdom Protista sits between the modern plants,

animals, and fungi, and the ancient prokaryotes. As such,

they end up being a catch all group. The right image

shows how some people group the protists based on

undulipodia characteristics, not ancestry.

And this assumes that we even know how related they are to each other and to organisms outside each phylum. Genome studies haven’t even begun to get close to establishing the ancestral relationships between all the organisms.

So we guess. And then we change things as new information becomes available. The work never ends, and the students never get to just memorize the categories.

As of today, some scientists classify protists based on a combination of the characteristics above. In the system I like best, there are 15 phyla, and we can roughly divide them as we show below. But there are six different phyla just for the protists that perform photosynthesis! The reason I like this system best -it roughly mimics the way they use undulipodia. And this is what we’re interested in today.

Kingdom Protista contains the organisms that seem to have made the most obvious uses of undulipodia. Eukaryotic flagella and cilia abound, some protists have both, and some have them only part of the time. There are six phylums of plant-like protists. Many have flagella, none that I could find have cilia. Here are some examples:

Pyrrophyta organisms will bloom and then bioluminesce

in order to scare predators away. Movement in the water

causes vesicles in the dinoflagellate to rupture via action

potential and release the reagents to make light. It’s exactly

the same system that fireflies use.

Phylum Pyrrhophyta – The dinoflagellates are in this phylum; they have two flagella, one from that side that beats and one on the posterior that whips more traditionally. Some species of this protist are responsible for the red tides that poison fish and can (and have) killed humans who eat the fish. Other dinoflagellates are bioluminescent and make the water appear to be on fire (hence the phylum pyrro = fire).

Phylum Euglenophyta – This phylum includes the Euglena gracilis organism shown in the animation at the beginning of the post. These protists also have two flagella, but one of them is reduced and doesn’t stick out. They have an eyespot, perhaps the genesis of our own eye. The eyespot helps them to move away from strong light sources, sources that would overheat them.

Euglena are common model organisms, on this world and in (near) space. They traveled on the parabolic flights to have their flagellar motions studied in zero gravity. The 2010 publication that resulted from the experiments showed that the process of beating is regulated and physiologic, as the change from hypergravity to microgravity stopped the flagellum from moving. The opposite change in gravity reoriented the cells and they started swimming to the bottom of their tank again.

The remaining phyla of plant-like protists can be included in a supergroup called the Chromista (colored organisms). In terms of their undulipodia, the chromists tend to have two flagella, one on each end. The forward flagellum is usually longer and has lateral growths called mastigonemes. The best description for this type of flagellum is that it looks like Christmas tinsel. The back flagellum is shorter and smooth.

These are the phyla of the Chromista; the colored protists.

Problem is, not all of them are colored and some colored

protists aren’t included in this group. Top right and bottom

left are the chlorophyta, the green algae. These are the most

recognizable algae. The bottom right is the diatoms, they have

the most interesting shapes. Look them up.

The Chrysophyta are the golden algae and diatoms. The diatoms are only flagellated when undergoing sexual reproduction, and is just the male gametes that have the flagella, sounds like male gametes in mammals doesn’t it?

Green algae are the ones we recognize; they belong to the Chlorophyta phylum. These are the ancestors of the land plants, and some have flagella in all stages, while others only have flagellated gametes. We will see soon how some land plants still have flagellated gametes.

Brown algae belong to the Phaeophyta phylum. They are exceptional amongst the protists because every organism in this phylum is multicellular. No brown algae live as individual cells. Kelp is an example of brown algae. Kelp forests are multicellular example of brown algae thalli, growing to 40-60 m (130-200 ft) in height! Kelp forests are some of the most productive ecosystems on earth.

The gametes of the brown algae are flagellated like in most of the other chromists. A 2014 study has started to look at the flagella of the chromists, using brown algae as the model organism. The study found that the flagella have functions in motility, signal transduction, and even metabolic activities. The two different types of flagella had common proteins and proteins specific to each form, for a total of 495 different proteins associated with flagellar function and structure. For instance, only the posterior flagellum has a protein that senses blue light, and may be used for steering the organism.

The Rhodophyta are where we get food stuffs. On the left

represents agar that can be used to make things that are like

Jello, it fills the role of the gelatin. In the middle, agar is also

used as a polysaccharide source of nutrition for growing

bacteria in the lab. On the right, nori is a rhodophyta

seaweed used in sushi.

Finally, Phylum Rhodophyta is the last of the Chromists. They are known as red algae, but you may know this protist better as seaweed. We saved them for last because they are the biggest exception in the plant-like protists.

If you’ve eaten Japanese sushi rolls, then you’ve eaten red algae in the nori that the rice and fish are wrapped in. Nori is made from several species of red algae of the genus Porphyra. Not a sushi fan? How about ice cream? Carageenans that make ice cream smooth also come from red algae.

Ice cream is reason enough to love the red algae, but there’s more. A 2014 study indicates that one compound found in the Porphyra is a strong antibiotic. Studies of 1,8-dihydroxy-anthraquinone from this red algae genus can disrupt the cell wall of Staphylococcus aureus. This is hugely important, since many strains of S. aureus (like MRSA and VRSA) are now resistant to most existing antibiotics.

Rhodophyta algae are red because although they use some chlorophylls for photosynthesis, they also use phycoerythrins and phycocyanins. Interestingly, these are the same pigments that are present in the cyanobacteria. This suggests that there is an ancestral link. The link is supported by one other factoid. Both cyanobacteria and red algae lack undulipodia!

The seaweed Rhodophyta organisms often live in the tidal

pools. The spongy material in the stalks and “leaves” is the

agar and is related to the mucin product that attaches to the

male gametes as they are released. I couldn’t find a picture of

the gametes with their mucin tails, so this will have to do.

The male gametes of red algae are at a deficit; they don’t have flagella to swim toward the female eggs. They must relay on water movement to disperse them. An older study showed that when the male spermatia are released by the discharge from vesicles, the vesicle contents can hang on to the gametes and form mucin appendages. These are then more likely to be moved around by the water.

Whatever it is, the system seems to work. A 2014 study found that fertilization success was dependent on male organism biomass, but neared 100% when there were relatively few male gametes present. This was hypothesized to be possible because low tides in the tidal pools where the organisms live greatly increase the chances of male/female interaction and fertilization. Seaweed takes advantage of the moon’s effect on the tides to ensure reproductive success – who needs flagella!?

So far we have met protists that use flagella at some point in their life cycle (except for the red algae). Notice that none of them have used cilia. Next week, how about the animal-like protists? I bet there are some exceptions there as well.

Fu G, Nagasato C, Oka S, Cock JM, & Motomura T (2014). Proteomics Analysis of Heterogeneous Flagella in Brown Algae (Stramenopiles). Protist, 165 (5), 662-675 PMID: 25150613

Wei Y, Liu Q, Yu J, Feng Q, Zhao L, Song H, & Wang W (2014). Antibacterial mode of action of 1,8-dihydroxy-anthraquinone from Porphyra haitanensis against Staphylococcus aureus. Natural product research, 1-4 PMID: 25259418

Maggs CA, Fletcher HL, Fewer D, Loade L, Mineur F, & Johnson MP (2011). Speciation in red algae: members of the Ceramiales as model organisms. Integrative and comparative biology, 51 (3), 492-504 PMID: 21742776

Strauch SM, Richter P, Schuster M, & Häder DP (2010). The beating pattern of the flagellum of Euglena gracilis under altered gravity during parabolic flights. Journal of plant physiology, 167 (1), 41-6 PMID: 19679374

For more information or classroom activities, see:

Kingdom Protista –

http://www.biologycorner.com/lesson-plans/phyla/kingdom-protista/

http://www.lessonplanet.com/article/biology/discovering-the-forgotten-kingdom-protista

http://www.slideshare.net/sciencepowerpointcom/kingdom-protista-protist-biology-lesson-powerpoint

http://sciencestuffbyamy.blogspot.com/2011/12/excellent-resources-for-teaching.html

http://science.lotsoflessons.com/protists.html

http://sciencenetlinks.com/lessons/organisms-motion-practical-applications-biological-research/

https://www.youtube.com/watch?v=0-6dzU4gOJo

http://www.google.com/search?q=pyrrophyta&bih=908&biw=1676&source=lnms&sa=X&ei=s5cpVKPbAYanyQTiu4GwCA&ved=0CAUQ_AUoAA&dpr=1#q=kingdom+protista+ppt

http://biology.clc.uc.edu/courses/bio106/protista.htm

http://www.google.com/search?q=pyrrophyta&bih=908&biw=1676&source=lnms&sa=X&ei=s5cpVKPbAYanyQTiu4GwCA&ved=0CAUQ_AUoAA&dpr=1#q=kingdom+protista