Microcosm by Carl Zimmer

Microcosm: E. coli and the New Science of Life by Carl Zimmer

Discovery
Escherichia coli bacteria was discovered by the German-Austrian pediatrician Theodor Escherich. He found it in baby diapers.

Beneficial Bacteria
E. coli inhabit the human colon and most strains of E. coli are beneficial, not pathogens. In fact, most of the bacteria in your colon are non-pathogenic. When you take antibiotics to kill pathogenic bacteria, the antibiotics often also kill friendly bacteria, resulting in diarrhea.

Cadaverine
E. coli bacteria in the intestines neutralize acid by producing an alkaline, foul-smelling substance called cadaverine.

Iron
E. coli makes proteins called siderophores that grab iron atoms in the environment and move it inside the E. coli bacterium, where it is held by an iron storage protein until it is needed by the cell.

Biofilm
Biofilm is an extracellular matrix, largely made up of polysaccharide mucus, that helps the E. coli bacteria to cooperate to promote their group survival. It protects the bacteria from antibiotics, predators, and dehydration.

Evolutionary Cooperation
The author discusses recent theories of evolution that assert that natural selection favors not just traits that help an individual organism survive, but also traits that help the survival of their close genetic relatives, from its immediate family to its species. An E. coli bacterium will often perform acts that harm itself, but help neighboring E. coli bacteria survive, by improving their shared environment.

Oxygen
The E. coli bacteria in the gut are called facultative anaerobes, which means that they can live in either the presence or the absence of oxygen. The E. coli bacteria scavenge oxygen in the gut to maintain the colon in an anaerobic state. This makes the colon hospitable for anaerobic microbes.

Regulation of Heat-Shock Proteins
E. coli produces proteins called heat-shock proteins that help the bacterium to handle proteins that have been partially denatured (unfolded) by heat. There are two kinds of such helpers: (a) ones that help repair (refold) the damaged proteins, and (b) ones that help destroy the proteins which cannot be repaired. The level of production of these heat-shock proteins is regulated in an interesting way. The messenger RNA for the sigma 32 regulatory protein assumes a functional shape for transcription on the ribosome only when bacterium is hot. After the sigma 32 protein is synthesized, it turns on the transcription of the genes for the heat-shock proteins. There is also a feedback loop where excessive amounts of heat-shock protein will shut down their production.

Colicin
E. coli produce toxic proteins called colicins that kill neighboring bacteria of other species. The colicins have three mechanisms of action. Some colicins form pores in the membranes of the enemy bacteria, some prevent protein synthesis, and some attack DNA. E. coli also produce other proteins, called immunity proteins, that protect them from harm by their own colicins.

Type III Secretion System
This is a needle-like structure on the outside membrane of E. coli cells that allows them to inject toxins into the host cell.

Flagella

E. coli have complex structures on their outer membranes called flagella that help them move. Flagella evolved from the more primitive structure described above, the Type III secretion system.

Prophage
A virus that attacks (eats) bacteria is called a bacteriophage (or just phage, for short). If the DNA of the virus integrates into the host chromosome, that DNA segment is called a prophage. It can be passed down to the descendants of the bacterium, and sometimes can cause a viral infection in the descendent bacteria. Many prophages develop mutations that prevent them from ever escaping the host chromosome back into a virus capsid. They are called defective prophages.

Shigella
This form of diarrhea was discovered by Kiyoshi Shiga. Only recently was it discovered that the shigella bacterium is actually a group of strains of E. coli that have developed the ability to move around inside eukaryotic cells. The Shigella bacterium spreads from host cell to cell by loosening the tri-cellular tight junction of intestinal epithelial cells. The Shiga toxin attacks the RNA part of the bacterial ribosomes, halting protein synthesis. Shiga toxin is encoded by a gene in a lambdoid prophage integrated into the bacterial chromosome. These shigella strains also differ from normal E. coli in that they do not have flagella and do not produce cadaverine.

E. coli Strain O157:H7
The pathogenic O157:H7 strain of E. coli occasionally found in undercooked, contaminated ground beef produces a shiga-like protein toxin that is coded for by a defective prophage gene.

Riboswitch Sensors
Recently, it has been discovered that the synthesis of vitamin B12 (cobalamin) by E. coli is regulated in a novel way. This regulatory mechanism involves the messenger RNAs that code for coenzyme B12 biosynthesis and transport proteins. When vitamin B12 binds to a nucleotide sequence of such a messenger RNA, the mRNA changes its shape. In this new conformation, the mRNA will no longer bind to the ribosome and so will not be translated into a biosynthesis or transport protein for vitamin B12. Ron Breaker of Yale University gave the name riboswitch to the nucleotide sequence of the mRNA that binds the vitamin molecule.

RNA World
Starting in 1968, a number of scientists have speculated that the earliest life on earth consisted not of DNA and proteins, but rather of RNA only. These RNA molecules acted as both holders of genetic information (like DNA) and as performers of chemical reactions (like proteins). In the 1980s there were discoveries supporting this theory. It was discovered that there are RNA molecules that act as enzymes, that is, they catalyze chemical reactions. They are called ribozymes. More recently, French virologist Patrick Forterre has proposed the theory that the switchover from RNA-based life to DNA-based life happened independently for each of the three domains: archaea, bacteria, and eukaryote. He has further proposed that the DNA of cells was first introduced by DNA viruses.

Genetically Modified Organisms (GMO)
The author is an advocate of genetic engineering, which started with E. coli, but which has now spread to higher forms of life. He goes into some detail on a particular plant GMO called “Golden Rice”. Golden Rice was developed by Ingo Potrykos of the Swiss Federal Institute of Technology and Peter Beyer of the University of Freiburg. This rice GMO makes vitamin A, which is needed for vision. Millions of poor children go blind every year, because do not eat enough vitamin A.

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