Diverse uncultivated ultra-small bacterial cells in groundwater
Nature has taken the praise-worthy step of making content available to a wider readership, via active links to ReadCube versions of the papers in media partners, like “The Huffington Post” in this case.
This particular paper reports on the characterisation of ultra-small organisms, which otherwise have proven impossible to culture. To make them available for study, samples were put into a rapid cryogenic freezer “snap freezing” them for electron microscopy. The results are fascinating, as the organisms are abundant and close to the smallest theoretical size for viable lifeforms.
A bare minimum for any living thing, based on DNA, is a cell-wall, a means of making proteins (i.e. a ribosome, which translates the DNA chain into amino-acid chains that then fold into proteins) and the raw materials to make them from. That minimum size is around 200 nanometres – 0.2 millionths of a metre. These new organisms are as follows in this table:
They’re so small that the volume taken up by their intra-cellular space and their cell-walls are of comparable size. A cubic micrometre is a volume of just 1E-18 cubic metres, or a water mass of just 1E-15 kilograms. Thus the smallest cell in the table masses ~4E-18 kg – in atomic masses that’s 2.4 billion amu. As the average atomic mass of living things is ~8 amu, that means a cell composed of just ~300 million atoms. The cell walls look crinkled because we’re seeing their molecule structure up-close.
Regular bacteria can contain thousands of ribosomes, but these newly characterised micro-bacteria contain ~30-50. This indicates that they reproduce very slowly. Their genomes are also very short. Escherichia coli, a common bacteria in the human enteric system, has over 4.6 million base-pairs in its genome (humans have 3.2 billion) – but these new species range in length from a million to just under 700,000.
Genomes under a million base-pairs usually mean the organisms are obligate “parasites”, living around or inside larger organisms to source genes and metabolites that they can’t make themselves. Larger genomes mean they’re able to make all the required proteins, although they may live very slowly since they have so few ribosomes.
A key question, in molecular biology and astrobiology alike, is how the simple biomolecules produced by chemistry [as reviewed in this recent blog-post] came together to produce the “simplest” organisms. If we imagine a ‘soup’ of simple biomolecules, massing ~300 amu each, then about 8 million of them are required to produce the smallest organism described above. Merely throwing them together will not produce a living organism – the probability is something like 10-8,000,000. This is the chief puzzle faced by “Origins of Life” researchers.
There have been many clever proposals, with simplified metabolic cycles controlled by ribozymes (RNA enzymes) using an RNA based genetic code being a contender for an even smaller, simpler life-form. From the other direction, we know that plausible chemistry can concentrate and link up monomers of RNA nucleotides, forming quite long oligomers of RNA. Surprisingly short sequences show ability to work as ribozymes, thus a ready pool of ribozymes could conceivably form. From such a pool, some self-replicating set could form, which evolution could amplify into ever greater degrees of complexity. Just which particular ribozymes started down that road in the case of terrestrial life we don’t yet know. We might never know, since we have no clear molecular fossils from so deep in our past. Or do we? There’s a hint of that RNA past in the structure of ribosomes themselves. As we learn more about those “molecular assemblers” that produce all living things from raw amino acids, we will gain more insights into the rise of Life from molecules.
A thing to remember is that living things, at a biomolecular level, are continually converting simple molecules into incredibly complex ones, via ‘simple’ chemistry all the time. And those complex molecules show a particular ‘intelligence’ of their own. A good example is protein folding – to work, proteins fold up into specific 3-D configurations. Just how they do so has puzzled physical biochemists for years. It can’t be via simply twisting around at random. To see why, consider a short protein just 300 amino acids long. If, in each connection between amino acids, there are just 2 possible positions they can take, then the total number of possible positions is (2)300 ~2E+90 – a ridiculously large number of options to search through one-by-one. Thus it is impossible to jiggle an amino acid string randomly into the correct configuration of a protein in the mere minutes that protein folding is observed to take. The process is non-random and the way the sequence folds up is driven by the electromagnetic properties of each amino acid, so that they’re driven to form a protein’s structure through their mutual attractions and repulsions. Proteins are also very resilient to random changes in the amino acid sequence – only very rarely do single amino acid mutations produce a totally malfunctioning protein. Fortunately for us, as we depend on properly functioning proteins!
