Whether it is “Keeping Precious Creatures Organized For Grumpy Scientists”, “Kids Prefer Cheese Over Fried Green Spinach” or “King Phillip Came Over For Good Spaghetti”, many of us probably used some sort of silly phrases to memorise the following: Kingdom, Phylum, Class, Order, Family, Genus Species. At least, that was what I learnt back at school. Little did I know that it gets better (or worse depending on your view), you can put Domain on top of Kingdom and potentially fit in strain below species. So, since we are discussing about a microorganism, I think it is appropriate and educational to talk a little bit about evolution too. The concept of evolution Creationists should probably cover their eyes about this bit. One of the processes that govern the concept evolution is natural selection. But to understand that, I will first, VERY briefly explain the production of protein in simple terms. Many of you will be familiar with this already, but hopefully this is a nice refresher. The deoxyribonucleic acid (DNA) of an organism is encoded by 4 different bases ATCG in multiple of orders. ATCG is read and transcribed into the 4 different ribonucleic acid (RNA) AUCG (N.B. T has been replaced by U from DNA to RNA). Amino acids are directed by 3 RNA bases (e.g. AGA for arginine, AAA for lycine, GGU for glycine plus many others). So, the order RNA bases line up will affect the amino acid that will line up with one another. Then lastly, it is the sequence of amino acids lined up that will dictate which protein will be produced by the body. In a living organism, a random mutation occurs in the genes of an organism resulting a change in the genotype. However, not all changes in genotypes will bring about a physical manifestation or phenotype. This is because the sequence of RNA encoding the amino acid is redundant, e.g. AGA, AGG, CGU, CGC, CGA and CGG will all result in arginine. These are the silent mutations that will have no effect on the protein structure. BUT occasionally, a mutation will occur that will actually cause a change in amino acid in a protein, this is more complicated, whether the mutation will have any functional effect on the protein is dependent on the amino acid that has been substituted and where in the protein this change is. Seeing there are many MANY scientists that have dedicated their whole life researching structural changes in proteins and how that impacts on organisms and diseases, all you need to know is, it depends. In natural selection, this random mutation by chance can bring about a change that will allow an organism to survive or reproduce better. For example, resistance to a particular disease in an area, physical adaptations that allows improvement on hunting, movement or mating. However, it is sometimes misunderstood that a significant change can occur instantaneously, I’m not saying it doesn’t happen, but it’s just not that common. No, really, it’s pretty damn rare. If it’s that common, half of the paper on the planet will probably have “superpowers” by now. Furthermore, what we describe as an advantageous mutation may not ALWAYS be advantageous. The best example I can think of is acquiring a resistance to a specific bacterial infection. Normally, you would think it’s good, but that is only if the bacteria is there in the first place. Who cares if you are resistant to this infection if nobody gets it right? Getting a mutation does not make you a different species, divergent in the phylogenetic tree takes tens and hundreds of millions of years. This is due to the fact you need to acquire many mutations before you are sufficiently “different” to your ancestors. Yeast Many of you know yeast as a tiny tiny organism (or microorganism). It is a unicellular fungus. So it belongs to the domain of Eukaryota and the Kingdom of Fungi. Many of you would have arrived at this blog wanting learn more about bakers’ yeast, so I will cover this first in the good yeast section (but if you are The good yeast Microorganisms receive such bad publicity and is often associated with infections whenever we hear it. However, the human gut actually becomes inhabited by microorganisms almost immediately after birth. These normal microbes pose no threat to us and in fact can be beneficial to the body. These microorganisms that naturally inhabit an animals body help with nutrients uptake, turnover of cells in the gut and also help shape the immune system (and In this particular, the good yeasts I refer to are the ones that we use for baking bread and alcohol, also known as baker’s yeast and brewer’s yeast. Baker’s yeast is almost entirely formed by the species Saccharomyces cerevisiae. The “Saccharo” part means sugar and “myces” refers to fungus. The species name, cerevisiae, is derived from the name Ceres, the roman goddess of agriculture. But it is important to know that yeast is not only involved in bread making, it is also used in the production of alcohol, cheese and various recombinant human proteins and antibiotics. This very useful organism ferments sugar (or fermentable sugar) to form ethanol and carbon dioxide (see Figure below).
All species under the animal kingdom can carry out that aeriobiosis reaction following glyolysis into the Kreb’s cycle and the electron transport chain to generate ATP (a form of energy used by biological systems). However, unlike mammals, which produces lactic acid in the absence of oxygen, yeasts are capable of alcoholic fermentation. This is why you have to wrap the container with cling film or with a wet towel, to allow oxygen to be used up and so the yeast starts going through anaerobic respiration. In this scenario, yeasts use the pyruvate generated from glycolysis to form ethanol and Carbon dioxide (Diagram taken from Alba-Lois and Sega-Kischinevzky., 2010. We see that yeast is capable of producing carbon dioxide. It is precisely this production of carbon dioxide that becomes trapped in the bread dough formed by gluten, causing the dough to rise. This biochemical reaction requires glucose, but glucose is not actually readily available in the mixture of flour, water, salt and yeast. However, flour contains starch, which is a large complex polysaccharide, containing many monosaccharides joined together. Glucose and fructose are released from the breakdown of starch. Glucose can then be used in glycolysis, but fructose must be converted to glucose first before it can be used. As mentioned, S. cerevisiae is the dominant species used in both baking and brewing, but there are actually different strains of the same species of yeast that can be used. Strain is used to distinguish microorganisms of the same species, which have very similar genetic make up, except there are specific changes in the genes (either naturally occurring or scientifically manipulated). It has been described that a species is a collection of different strains that show at least 70% cross-hybridisation. But what does it mean? It means that when we melt the double stranded DNA from 2 different organisms into single strands, then at least 70-80% of the DNA from one organism will anneal and bind to the DNA of the other organism (Wayne et al., 1987; Meier-Kolthoff et al., 2014) and this concept is generally applicable to the bacterial domain (Brenner et al., 2000). Each strain is slightly better adapted to a specific environment or use. So, it is perhaps not surprising that although both baker’s and brewer’s yeast belong to the same species, they are actually of different strains. The bad yeast After learning about the good yeast, it’s time to move on to the not so good ones (at least from a human’s point of view). One of the most well known and common yeast infection comes from the gens Candida and amongst the members of this genus, Candida albicans is the most commonly associated with diseases. But under normal conditions, C. albicans won’t actually cause many problems, some scientists have actually termed it as an opportunist, i.e. it will only thrive and cause problems under the right conditions. These yeasts will grow especially well if one’s immune system has been compromised, e.g. patients with AIDS, cancer or undergoing immune suppression for transplantation to name a few. But what some people don’t consider often is that the use of broad spectrum antibiotics can potentially promote the growth of C.albicans. When the normal gut microorganisms have been killed off, C.albicans can then populate the area to replace the lost microbes. The common places C.albicans infect include the mouth, the oesophagus and the vagina. C.albicans form a white patch over certain regions in the mouth and can cause burning sensations, difficulties in drinking and eating and in some case, the patient can also lose the sense of taste. Vagina thrush can also present with white patches and the symptoms associated with this include itchiness, pain during urination or intercourse. However, unless one’s immune system has been compromised, one is unlikely to “catch” a thrush from an infected individual. In the more extreme (but rarer) cases, Candida species can invade the blood stream or introduced into the blood stream by contaminated needles and catheters (Invasive candidiasis). In these cases, Candida species can cause general symptoms associated with sepsis such as shock and shutdown of the kidneys. References
Alba-Lois, L. & Segal-Kischinevzky, C (2010). Yeast Fermentation and the Making of Beer and Wine. Nature education. 3(9): 17 Brenner D, Staley J, Krieg N (2000). Classification of prokaryotic organisms and the concept of Bacterial speciation. Springer; New York, NY: Bergey’s manual of systematic bacteriology Wayne L.G, et al (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol.37: 463–464