Microbial Evolution

Microbial Evolution Biological diversity is usually thought of in terms of plants and animals; yet, the assortment of microbial life forms is huge and largely uncharted. Consider the metabolic diversity of microorganisms this alone suggests that the number of habitats occupied by microbes vastly exc...

Microbial Evolution Biological diversity is usually thought of in terms of plants and animals; yet, the assortment of microbial life forms is huge and largely uncharted. Consider the metabolic diversity of microorganisms this alone suggests that the number of habitats occupied by microbes vastly exceeds that of all larger organisms. How has microbial life been able to radiate to such a bewildering level of diversity? To answer this question, one must consider microbial evolution. The field of microbial evolution, like any other scientific endeavor, is based on the formulation of hypotheses, the gathering of data, the analysis of the data, and the reformation of hypotheses based on newly acquired evidence. That is to say, the study of microbial evolution is based on the scientific method. The Origin of Life Dating meteorites through the use of radioisotopes places our planet at an estimated 4.5 to 4.6 billion years old. However, conditions on Earth for the first hundred million years or so were far too harsh to sustain any type of life. The first direct evidence of cellular life was discovered in 1977 in a geologic formation in South Africa known as the Swartkoppie chert, a granular type of silica. These microbial fossils as well as those from the Archaean Apex chert of Australia have been dated at about 3.5 billion years old. Despite these findings, the microbial fossil record is understandably sparse. Thus to piece together the very early events that led to the origin of life, biologists must rely primarily on indirect evidence. Each piece of evidence must fit together like a jigsaw puzzle for a coherent picture to emerge. The First Self-Replicating Entity: The RNA World The origin of life rests on a single question: How did early cells arise? No one can say for certain; however, it seems likely that the first self-replicating entity was much simpler than even the most primitive modern, living cells. Before there was life, Earth was a cauldron of chemicals that reacted with one another, randomly “testing” the stability of the resulting molecules. This means that the first cells evolved when Earth was a very different place: hot and anoxic, with an atmosphere rich in gases like hydrogen, methane, carbon dioxide, nitrogen, and ammonia. To account for the evolution of life, one must consider the three essential cellular molecules: DNA, RNA, and proteins—one of these molecules presumably developed first and holds the key to understanding all that followed. Proteins are capable of performing cellular work but cannot replicate, while just the opposite is true of DNA. For life to evolve, a molecule was needed that could both replicate and perform cellular work. A possible solution to this problem was suggested in 1981 when Thomas Cech discovered self- splicing RNA in the eucaryotic microbe Tetrahymena. Three years later, Sidney Altman found that RNase P in Escherichia coli is an RNA molecule that cleaves phosphodiester bonds. RNA molecules that possess catalytic activity are called ribozymes and to some, the ability of RNA to catalyze biochemical reactions suggests a precellular RNA world, a term coined by Walter Gilbert in 1986. This hypothesis suggests that the first self-replicating molecule was RNA, which is capable of storing, copying, and expressing genetic information, and possesses enzymatic activity as well. In this version of early life, various forms of molecules were assembled and destroyed over roughly half a billion years, until ultimately an entity something like modern RNA enclosed in a lipid vesicle was generated. Apart from its ability to replicate and perform enzymatic activities, the function of RNA suggests its ancient origin. Consider that much of the cellular pool of RNA in modern cells exists in the ribosome, a structure that consists largely of rRNA and it uses mRNA and tRNA to construct proteins. In fact, rRNA itself catalyzes peptide bond formation during protein synthesis. Thus RNA seems to be well poised for its importance in the development of proteins. Because RNA and DNA are structurally similar, RNA could have given rise to double-stranded DNA. It is posited that once DNA evolved it became the storage facility for cellular functions because it provided a more chemically stable structure. Two other pieces of evidence support the RNA world hypothesis: the fact that the energy currency of the cell, ATP, is a ribonucleotide, and the more recent discovery that RNA can regulate gene expression. Others are skeptical of the RNAworld hypothesis. They claim conditions on Earth 4 billion years ago would have prevented the stable formation of ribose, phosphate, purines, and pyrimidines, all needed to construct RNA. In fact, while purine bases have been generated abiotically in a heated mixture of hydrogen cyanide and ammonia, scientists have so far been unable to make pyrimidines in a similar fashion. Another problem with the RNA world hypothesis is the instability of RNA once it is assembled. In 1996, James Ferris and colleagues were able to overcome the problem of RNA degradation by adding the clay mineral montmorillonite to a solution of chemically charged nucleotides. They showed that the rate of RNA synthesis was faster than its degradation. Early cellular life, although primitive compared to modern life, was still relatively complex. Cells had to derive energy from a harsh, anoxic environment. When scientists attempt to reconstruct the nature of very ancient life, they look to extant (living) microbes for clues. For instance, it is thought that the FeS-based metabolism seen in some hyperthermophilic archaea may be a remnant of the first form of chemiosmosis. Here it is suggested that the energy- yielding reaction FeS + H2S →FeS2 +H2 provided the reducing power (H2) to produce a proton motive force. Photosynthesis also appears to have evolved early in Earth’s history. There is fossil evidence to place the evolution of cyanobacteria and oxygenic photosynthesis at about 3 billion years ago. Stromatolites are layered rocks, often domed, that are formed by the incorporation of mineral sediments into microbial mats dominated by cyanobacteria. Recent evidence has shown that some fossilized stromatolites formed in a similar fashion. The Endosymbiotic Origin of Mitochondria and Chloroplasts In contrast to the unresolved origin of the nucleus, the endosymbiotic hypothesis is generally accepted as the origin of mitochondria and chloroplasts. That endosymbiosis was responsible for the development of these organelles (regardless of the exact mechanism) is supported by the fact that both organelles have bacterial-like ribosomes and most have a single, circular chromosome. Indeed mitochondria and chloroplasts belong to the bacterial lineage. Important evidence for the origin of mitochondria comes from the genome sequence of the α-proteobacterium Rickettsia prowazekii, an obligate intracellular parasite. Its genome is more closely related to that of modern mitochondrial genomes than to any other bacterium. Mitochondria are believed to have descended from such an α proteobacterium that became engulfed in a precursor cell and provided a function that was essential to the host cell. It may be that oxygen toxicity was eliminated because the intracellular bacterium used aerobic respiration to generate ATP. In return, the host provided nutrients and a safe place to live. These bacterial endosymbionts evolved to become mitochondria. This hypothesis also accounts for the evolution of chloroplasts from an endosymbiotic cyanobacterium. Presently the cyanobacterium Prochloron has become a favorite candidate as the extant relative of the endosymbiotic cyanobacterium that gave rise to green algae and plant chloroplasts. This microbe lives within marine invertebrates and is the only procaryote to have both chlorophyll a and b, but not phycobilins. This makes Prochloron most similar to chloroplasts. Finally, the endosymbiotic theory put forth by Lynn Margulis and her colleagues combines elements of the endosymbiotic origin of mitochondria with the genome fusion hypothesis. The serial endosymbiotic theory (SET) calls for the development of eucaryotes in a series of discrete endosymbiotic steps. This theory suggests that motility evolved first through endosymbiosis between anaerobic spirochetes and another anaerobe. Next, nuclei are thought to have formed by the development of internal membranes. These early nucleated forms would have been similar to modern protists with hydrogenosomes. The endosymbiotic events needed for the evolution of mitochondria are thought to have occurred later, giving rise to early fungi and animal cells, with subsequent endosymbiotic events leading to the development of chloroplasts and plants.