Wednesday, August 14, 2013

How Prokaryotes Shape Up

Biology concepts – morphology, eubacteria, coccus, rod, bacillus, spirilla, spirochete, prosthecae, halotolerant,

The standard menu of prokaryotic shapes may seem boring, but they
really perform specific functions. The underlined types are those we
hear about most often, perhaps you’ve heard of “bacillus” more often
called “rod.” Bacillus is actually the name of one genus of rod-shaped
bacteria, but the name has taken over in many circles, like Kleenex for
facial tissue. Most likely, all the forms evolved from rods, and you can
see how this might be possible from the cartoon.
Most prokaryotes are small - really small. At best they show up as small dots in most microscopes. But we know they have definite shapes. The question is, is the shape of a bacterium an important detail?

Question of the Day – What shapes can prokaryotes take and are their shapes important?

We are taught in school that bacteria have three shapes; spheres, rods, and spirals, but there are actually many more. The second part of our question is just as important to think about. Does it matter what shape a bacterium takes? Do you really think it’s random… really? After all the things we have discussed in this blog?

A 2007 paper summarized the evidence for why scientists believe the morphology (shape) of bacteria must be important. Here's a brief summary. One - genera of bacteria will always show the same subset of shapes. Why spend the energy to maintain the genetic blueprint if it isn’t important? We have talked before about how genes that are not necessary are allowed to drift, but morphology genes don’t drift.

Two - changes in environmental conditions or pressures will bring changes in the morphology of many prokaryotes. What is more, the same change will be bring the same morphology alteration again and again. This implies both regulation and specific functions for different shapes. Shape must be important if it is worthy of controlled regulation.

And three - archaea and eubacteria are very different, as different as you and a pine tree, but they tend to fall within the same types of morphologies. Each representative morphology must be adaptive (important for survival and propagation) if they turn up again and again in very unrelated organisms.

This and other papers by Dr. Young also discuss the ways morphology confer advantages. Our morphology discussion should also include size. Small bacteria usually have shorter generation times. This is important because faster developing bacteria usually out-compete larger ones for limited resources and nutrients. Therefore, most bacteria are very small.

The typical classroom answer for small size is that bacteria do not have intracellular transport systems, so all movement of nutrients and important molecules must be by diffusion. A big cell means too slow a transit time and death. Also, being small is a good way to maximize surface area to volume, so lots of room is given for possibly contacting food, while keeping diffusion time fast.

These are valid reasons to be small, but size is just as important in reducing the chances of being eaten. There probably hundreds of thousands of different single-celled eukaryotes that feed exclusively or mostly on bacteria. But bacteria are cannibals as well. They'll eat other bacteria, and if times are bad enough, may feed on their own kind.

To avoid being the midnight snack of some protozoan, bacteria have several choices. You can be small and fast, or you might opt to become huge - too large to ingest or even be recognizes as food.

There is a lot going on in this collage. On the left is the aggregates that
cocci can form based on the plane in which they divide. The only form
possible for rods is the strepto- form since they always divide through
their short side. The pictures on the right are to illustrate the size
difference between E. coli and T. nambibiensis. If E.coli were the size of
a tic tac candy, the crater seen below could not hold T. nambibiensis.
Bacteria can also join forces by attaching to one another and become too large to consume, either in long chains, large masses, or complex biofilms. Would you pull out a fork and spoon and try to choke down an elephant in the wild – what about a herd of elephants all stuck together?

But back to shape - what might different shapes do for different bacteria? Let’s look at some amazing prokaryotic shapes in terms of several factors: nutrient acquisition; predators; cell division; attachment; dispersal; motility; and differentiation of function.

Cocci (the plural of coccus, from the Greek kokkus = berry) are round bacteria. Spherical is a safe shape since it gives the maximum surface area for a given volume. However, spherical doesn’t necessarily mean small. Thiomargarita namibiensis is a spherical bacterium, but it is the second largest prokaryote we know of. If an E. coli cell was the size of a tic tac, T. namibiensis would have a diameter a bit larger than the Barringer Meteor crater in Arizona (see picture above).

The rod is probably the oldest prokaryotic morphology. It is most probable that cocci were short rods that kept getting shorter, and that other shapes we will talk about are also modifications of rods. So give the rods (of which E. coli is one) the respect they deserve – it may seem mundane later when we talk about weird shapes, but the rod is the mother of all shapes.

Rods show that motility comes into play as a reason for shape. The rod shape, longer than wide, is the fastest mover in response to chemical signals (chemotaxis, chemo = chemical and taxis = arrangement), the chemical trail left by a potential meal for example. Becoming longer and thinner is also a good way to increase apparent size (reduce predation) and provide more surface area (for food collection).

Spiral shaped bacteria are faster through viscous fluids – so this shape is probably an adaptation to allow movement in different fluids. Many spiral bacteria live in environments thicker than water, so moving faster than predators would be important.

The spiral shape of spirilla is usually thicker and flatter than that of spirochetes, and another difference is that spirochetes often have different attachments for their flagella (whip-like oars for movement).

Predation may also play a different role in spiral shape development. Arthrospira platensis (a cyanobacteria) grows as a spiral.  It also known as spirulina, a potential superfood, but promoters usually say it’s a blue-green algae, not a bacterium.

Spirulina is eaten by a protist that can turn left on its long axis up to six times to ingest the A. platensis. Low and behold - A. platensis can reverse it spiral direction in the face of predation so that the ciliate would have to spin right to eat it, and it can’t do that. 

On the left is Caulobacter crescentus, a crescent shaped prokaryote. It
takes two forms, a swarming crescent with flagella for times of
plenty and a stalked crescent for times when food is scarce. In some
parts of the image, you can see the stalk. Atopobium rimae is on the
right, a coccobacillus. A. rimae is a constituent of normal oral flora,
but can cause periodontal disease as well. Its looks remind me of a
microscopic Easter egg hunt.

I call these bacteria elliptical; one nice example is Atopobium rimae. They look like footballs, not quite a rod (bacilli are one genus of rod shaped bacteria), and not yet reduced to a sphere.

Many coccobacilli are pathogenic, including the organisms that cause chancroid STDs, brucellosis, pneumonia, infectious blindness, bacterial flu, and whooping cough. However, a link between shape and disease causation escapes me. I haven’t found any evidence that someone has even asked the question. Maybe you can.

Crescent shaped
These are rod shaped bacteria that have become curved. Vibrio bacteria are an important group of crescents (named because they looked like they vibrated as they moved)….. oh, and because they cause a lot of disease.

The crescent shape can be important for movement. Vibrio alginolyticus swims forward just fine, but when it encounters a flat surface – an area where food might be gathered – it swims backward. Its crescent shape keeps it bumping into the flat surface. This keeps it longer in the area of food. In some crescents, a mutation making them straight means that they lose their motility and ability to find food, so it must be important.

Triangular and square
Yes, there are prokaryotes that look very much like triangles or squares. I am listing them together because the thing they have most in come is that they are usually halophiles (halo = salt, and philic = loving) or are halotolerant.
Both of the bacteria above are halophilic, meaning they love salt.
Haloarcula japonica (left) and Holoquadratum walsbyi (right)
for perfectly shaped to form contiguous sheets of cells. This
helps them float parallel to the surface of the water they live in.
These are archaeal extremophiles, but it is interesting that
archaea and bacteria use the same sets of shapes.

The triangular example I have for you is Haloarcula japonica, so named because it was discovered in a Japanese salt evaporation field. Another member of the same genus is H. quadratum, which you might guess, is square.

But it isn’t just this genus that take on definite geometric shapes, there is another salt-loving arachaean called Haloquadratum walsbyi that is also square. Mind you, these are not cubiodal bacteria, and the H. japonica is not a triangular prism. They are very flat; H. walsbyi, for example, is 5 µm square but only 0.1 µm thick. The same can be said for the triangular H. japonica.

They all tend to grow as flat masses, like little floating mosaics. Their flat shapes keep them buoyant and floating parallel to the water’s surface. Their geometry then provides the largest surface toward the sun, in order to pick up the most heat and energy. Sounds logical to me.

These are my favorites, the stars of the bacterial world. The far left is
Stella vacuolata. Those bubbles in the middle are gas – yes, bacteria get
gas too. The middle photomicrograph is Prosthecomicrobium.
Prostheacae are the arms, and are right in the name, even though these
are very short prosthecae. On the right is Ancalomicrobium adetum. Its
prosthecae are much longer and are used to deter predators, amongst
other things. There is even one very long rod bacterium that has a
star cross section.
It must take quite a bit of regulation to build and maintain a star shape. The ones I have seen come in a couple of varieties. Some are definitely star-shaped because of their cell body. Stella vacuolata is star-shaped, as are Prosthecomicrobium species. The reason for a star-shaped adaptation--- I don’t know - patriotism maybe?

There are also bacteria that have projections from their cell body that make them look like fireworks as they explode; see the picture of Ancalomicrobium adetum. The projections are called prosthecae (Greek for appendage), and can serve many functions. They can increase surface area without increasing mass for better diffusion. They can make a bacterium large enough to not be eaten. They may also catch more water, to help non-motile bacteria be moved along by the current.

We have only touched the surface of the morphologies that prokaryotes can assume. There are others that look like Y’s (bifid bacteria), some that look like connected lollipops, some that look like segmented worms, and at least one that builds a net of connected tubules near black smokers at the bottom of the ocean (Pyrodictum abyssi).

Among the many other shapes possible for bacteria, the bifids are
interesting (left). Certain proteins are produced only in the ends of
the bacteria, and if they need more of that protein, especially for
attachment, one way to get it is to have more ends. On the
right is an archaea found at the bottom of the ocean. The fine lines
are actually tubular projections with fine nets of bacteria cell
inside. The cell bodies are the nodular areas seen nonsymmetrically.
Just how do prokaryotes construct and control their shape? This is an active area of research and may be important for medicine. We have seen that shape affects function and survival, so new antibiotics might just work to turn rods into cocci or stars into blobs.

A 2011 paper shows that zinc metal is essential for proper morphology. Zinc is an important part of several proteins that control which DNA is read to make proteins (zinc finger transcription factors), so this is evidence that discrete controls are in place to define a bacterium’s morphology.

A 2013 study shows that E. coli rod shape is determined mostly by its cell wall. If the cell wall was removed, it took 4-6 generations for the rod shape to be recovered. If mutations in certain lipoproteins or penicillin binding proteins were present, the bacteria progeny would always remain spherical. These genes are not even used in producing the cell wall, so it is apparent that many genes are needed just to maintain cell shape. My current research concerns the ability to bend rod bacteria into tiny balloon animals.

Next week we will start our series of exceptions and core concepts for the year. We begin by looking at the elements of life - there's more than you think, and then we'll look at the four types of biomolecules. 

Ranjit DK, & Young KD (2013). The Rcs stress response and accessory envelope proteins are required for de novo generation of cell shape in Escherichia coli. Journal of bacteriology, 195 (11), 2452-62 PMID: 23543719

Bayle L, Chimalapati S, Schoehn G, Brown J, Vernet T, & Durmort C (2011). Zinc uptake by Streptococcus pneumoniae depends on both AdcA and AdcAII and is essential for normal bacterial morphology and virulence. Molecular microbiology, 82 (4), 904-16 PMID: 22023106  

Young KD (2007). Bacterial morphology: why have different shapes? Current opinion in microbiology, 10 (6), 596-600 PMID: 17981076


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