Wednesday, July 30, 2014

Does Life Come In XXXS?

Biology concepts – characteristics of life, archaea, bacteria, mycoplasma, synthetic biology, symbiosis, parasitism, nanobacteria, genome

As part of this blog, we have talked about some pretty small life. Wolffia globosa is the smallest flowering plant, only 0.6 mm long. We also talked about archaea, a different kingdom than bacteria, but still on the smallish side of life. The tardigrade is the toughest animal, but is also one of the smallest, at 100 µm (0.00394 inch).

The organism on the top is T. dieteri, and arthropod, just
as is any crab or spider. The size is deceiving. The pictures
on the bottom are to scale and are copepods, also
arthropods. The organism on the top is a parasite of the
organisms on the bottom. The small blue line? That would
be the scaled size of T. dieteri. So…. it’s SMALL.
The question for today is – is there a minimum size for life? Candidates might include bacteria or archaea; heck there’s an arthropod, Tantulacus dieteri, that's only 85 µm long! As long as we can keep finding smaller and smaller cells, we know that the minimum size for life is that small or smaller. So we keep looking – you’d be surprised how important it is to keep looking for smaller life.

Here’s one thing we should be able to agree on, viruses don’t get to play in our game. Viruses are very small, but they're not life! We’ve talked about this before - the seven characteristics of life (see this post). Viruses need a host in order to replicate, they don’t manage homeostasis, and they aren’t cells, so they aren’t life.

So how small has actual life become? Let’s assume that since tardigrades and T. dieteri are over 50 µm, huge when compared to some bacteria, our current minimum for life is probably a bacterium or archaea.

Let’s go straight to the genus of smallest bacteria we know about – the mycoplasma (from mykes = fungus, and plasma = formed). They were first described in 1898, but the observer didn’t have a clue what he was looking at; hence the fungal part of the name.

Mycoplasma don’t have the traditional cell wall of many bacteria, so they look different and this might be why they were mistaken for fungi. Whatever the scientists thought of them, they were confusing enough to be roundly ignored for 50 years. Rediscovered in the 1950’s-1960’s, this time they were thought to be L-forms of bacteria. L-forms are organisms that for some reason have lost their cell wall.

There are stable forms of L-bacteria; they can live divide and live on without their cell wall. There are also unstable L-forms as well; those that may revert to walled bacteria at any moment. Are mycoplasma simply bacteria that have lost a cell wall? Nope. They didn’t have a cell wall to lose. They have no cell wall genes, so if they had a cell wall, it was millions of years ago, before they became their own genus.

The difference between some free living cells. You can
probably see the E. coli in bright green, but you may have
to squint to see the mycoplasma above it. It’s pink. Really,
it’s there. Compare these sizes to those of the arthropods
above. 1 mm is equal to 1000 µm.
Mycoplasma is really, really, SMALLLLLLL.
Mycoplasma are generally described in the range of 0.2-0.8 µm in diameter. But this is a little misleading, because they are often not spherical. Even without a cell wall, they can take interesting three-dimensional forms and maintain them. Mycoplasma pneumoniae, which causes a form of …..….. anyone?…….. right, pneumonia, is pear shaped, so its 0.25 µm diameter is actually the measurement on its short side.

So mycoplasma are small, but they still have to play by the rules. They contain DNA and salts and proteins and ribosomes and other things that take up room. A single ribosome is about 50 nm in diameter (0.05 µm or 0.00000005 m), so there must be a certain volume required for the cell to function – a minimum size for life.

Which of the mycoplasma species is the smallest? Mycoplasma genitalium is considered to be the smallest mycoplasma known, and the smallest form of free-living organism - my gosh – you can fit about 400 M. pneumoniae inside one E. coli! As such, it is the current minimum size for life that we have. M. genitalium is 200 nm (0.2 µm) x 600 nm (0.6 µm), so they’re pretty dawg on small. Let’s put it this way, there are 25,400,000 nm in one inch – mucho small.

It is important to note that M. genitalium is free living, but does need some help. It uses cholesterol in its membrane but doesn’t make it itself. It picks it up from the cells that it lives near……wait for it….. your genital epithelium.

One of the human diseases that is becoming more
convincingly associated with M. genitalium is pelvic
inflammatory disease (PID). Resulting when many
different sexually transmitted diseases go untreated,
PID can cause permanent damage to the reproductive
organs of women. It is important to get treatment early.
The inflammation of PID may be associated with the
fallopian tubes or ovary, and will cause a chronic pain
in the lower abdomen, bleeding and pain on urination.
M. genitalium is a cause of non-gonococcal urethritis (inflammation of the urethra). A late 2013 review states that 1-3% of the general population is infected with M. genitalium, more than with gonorrhea. It is linked to pelvic inflammatory disease, and the review cites studies showing that people infected with this mycoplasma are more at risk for HIV and have more dual infections. It’s a sexually transmitted organism, just another reason for proper restraint. But even though it's helped out by your genital epithelium, it can live on its own and divide outside a host, so it's considered a free-living organism.

The idea of free-living is important because M. genitalium also has a very small genome (amount of DNA in one cell, including the list of all its genes). M. genitalium has about 580 kbp of DNA where kbp = kilobase pairs. Remember that DNA is doubled stranded (usually) so each base is paired with another. Knowing this, we count them as a unit. In all, M. genitalium has just 520 or so genes; it can make about that many proteins.

Genome size could be another way of determining the minimum size of life - what's the minimum number of genes or number of base pairs of DNA for an organism to still meet all seven characteristics of life? As of summer 2014, no organism smaller in size than M. genitalium has been described, but there have been some other organisms discovered with smaller genomes.

Nanoarchaeum equitans was thought to have the smallest gene for a while, with only 491 kbp of DNA. It is an archaea that lives on the edge of hydrothermal vents at the bottom of the ocean. But it is an obligate symbiont with another archaea; it can’t survive without its partner, so can you say it has the minimal genome? It relies on another organism’s DNA.

On the left is the leafhopper in which N. deltocepahlinicola makes
his home. Well inside its cells that is. The leafhopper survives on
phloem and xylem; high in carbs but little protein. The bacterium
makes the amino acids the leafhopper can’t in exchange for energy
in the form of ATP. On the right is a colored photomicrograph of
the abdomen. The red is one type of endosymbiont bacteria,
the green is N. deltocephalinicola.
This is also true of Carsonella ruddii (159 kbp, 182 genes) and Nasuia deltocephalinicola. They are bacteria that must live inside insect cells, like those of grasshoppers. N. deltocephalinicola has the smallest known genome (112 kbp, 137 genes), but it doesn’t even make ATP, it steals it from the arthropod cells. This could hardly be considered free living, and so it can’t be considered the minimal genome for life. And even at that, their cell sizes are still bigger than M. genitalium.

So why is it important to find the minimal size and minimal genome for life? So we can use the information. J. Craig Venter (of the human genome project) wanted to develop a synthetic form of life (synthetic biology); a bacterium that could be developed to provide hydrogen for energy or eat waste to reduce pollution. Others say we need to know so that we can better recognize life on other planets, or life that may have come here from other planets (astrobiology).

Being J. Craig Venter, develop a synthetic form of life is exactly what he and his research institute did. It’s interesting that Venter was one of the scientists that first sequenced the entire M. genitalium genome in 1995. Some 15 years later, Venter’s JCVI-syn1.0 (2010) was the first synthetic life, housing 1000 kbp and 500 or so genes. The genome was based on that of another mycoplasma, M. mycoides. They modified the genome, and introduced it into a cell membrane that had been evacuated of all its constituents. The resulting cell was capable of growing, dividing, you know…. living.

If M. genitalium represents our current estimate for the minimum size of life, it’s only because we’re thinking of life as we know it. Perhaps we have already found life that is smaller, and the minimum size is actually much smaller than M. genitalium.

This is a photomicrograph of a meteorite from Mars. The
small spheres (like the ones the arrows point to, are
supposedly nanobacteria. Proof of life on Mars,
contamination from Earth nanobacteria, or just mineral
spheres that look a little like incredibly tiny bacteria?
The answer is C.
Something termed a nanobe and something else called a nanobacterium were described 20-30 years ago. Nanobes were first found in the rocks that came up during oil drilling in Australia, while nanobacteria were also found in surface rocks.  The size of both (about 1/20 size of M. genitalium) negates their use of ribosomes and DNA. They stain for DNA, but this may be artifact, the artificial result of other things picking up the stain.

But nanobes/nanobacteria have their proponents. Some scientists say that since no DNA has been exhibited, they are a completely different form of life, so size restriction (big enough to hold ribosomes) doesn’t apply. Nanobacteria are also claimed to be important in human disease, as these structures are found in many calcifications of diseased tissues.

On the other hand, nanobacteria are probably just mineral formations. A 2013 study showed that they form spontaneously from many different biological fluid samples, and their appearance in diseased tissues is more a sign of disease than a cause of it. We’ll just have to keep looking for something smaller.

Next week, another question tackled and dissected - think pink.

Manhart LE (2013). Mycoplasma genitalium: An emergent sexually transmitted disease? Infectious disease clinics of North America, 27 (4), 779-92 PMID: 24275270

Wu CY, Young L, Young D, Martel J, & Young JD (2013). Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids. PloS one, 8 (9) PMID: 24086546

Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, & Venter JC (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science (New York, N.Y.), 329 (5987), 52-6 PMID: 20488990