Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin
must be transported through the nuclear membrane before it can be translated into protein in the cytoplasm, where the ribosomes reside, and transcription and translation do not occur simultaneously.
Besides lacking a nucleus, bacterial and archaeal cells lack many other cellular constituents common to eukaryotes, including mitochondria and chloroplasts. They also lack such visible organelles as the Golgi apparatus and the endoplasmic reticulum. While bacteria can possess compartmentalized features for a wide variety of purposes such as the storage of carbon and nutrients and for specialized enzymatic processes, the absence of most organelles generally gives bacterial and archaeal cells a much simpler appearance under the microscope than eukaryotes.
Extremophiles (or “extreme-condition-loving” organisms), as their name implies, live under extreme conditions where other types of organisms cannot survive, such as at very high temperatures, in highly acidic environments, and at very high osmolality, such as in the Dead Sea. Most extremophiles are archaea. However, it is becoming clear that archaea also are important components of many less extreme environments; for example, archaea perform unique biochemical functions, such as making methane, and can be normal inhabitants of the human microbiome.
The archaea themselves are a very diverse group of organisms, and our understanding of the phylogeny of archaea is an area of intense research that is currently in flux. One exciting update to our understanding is that it is now clear that eukaryotes branch out of the archaea and, more specifically, out of the TACK superphylum (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota). Perhaps the most exciting area of research involves the discovery of uncultured archaeal lineages like the Lokiarchaeota that possess numerous molecular systems that were previously only associated with eukaryotes, providing a clear link bet ween archaea and eukaryotes (see Spang et al., Suggested Reading). Excitingly, an archaeon that appears to be on the border between prokaryotes and eukaryotes has now been isolated and is pictured at the start of this chapter (see Imachi et al., Suggested Reading). The relationship between the superphylum TACK archaea and two other large divisions with the archaea, the Euryarchaeota and the superphylum DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota), is currently under investigation. While the basic molecular processes of archaea are an active area of investigation, much less is known about the archaea than about the bacteria.
The Eukaryotes
The eukaryotes are members of the third domain of organisms on Earth, which branches out of the archaea. This domain includes organisms as variable as plants, animals, fungi, and the highly diverse protists. The name “eukaryote” is derived from the presence of their nuclear membrane. Eukaryotic cells usually have a nucleus, and the word karyon in Greek means “nut,” which is what the nucleus must have resembled to early cytologists. The eukaryotes can be unicellular, like yeasts, protozoans, and some types of algae, or they can be multicellular, like plants and animals. In spite of their widely diverse appearances, lifestyles, and relative complexity, however, all eukaryotes are remarkably similar at the biochemical level, particularly in their pathways for macromolecular synthesis.
MITOCHONDRIA AND CHLOROPLASTS AND THE ROLE OF ENDOSYMBIOSIS IN EVOLUTION
Essentially all eukaryotic cells contain something, the mitochondria, that ties them to the world of bacteria. The mitochondria of eukaryotic cells are the sites of efficient adenosine triphosphate (ATP) generation through respiration. Evidence, including the sequences of many genes in their rudimentary chromosomes, indicates that the mitochondria of eukaryotes are descended from free-living bacteria from the Alphaproteobacteria that formed a symbiosis with a primitive ancestor of eukaryotes. A specialized type of symbiosis, where the symbiont resides entirely within another organism, is called endosymbiosis.
Plant cells and some unicellular eukaryotic cells also contain chloroplasts, the site of photosynthesis. Like mitochondria, chloroplasts are also descended from free-living bacteria, in this case Cyanobacteria. Mitochondria and chloroplasts resemble bacteria in many ways. For instance, they contain DNA that encodes the components of oxidative phosphorylation and photosynthesis, as well as rRNAs and transfer RNAs (tRNAs). Even more striking, the mitochondrial and chloroplast rRNA and ribosomal proteins, as well as the membranes of the organelles, more closely resemble those of bacteria than they do those of eukaryotes. Comparisons of the sequences of highly conserved organelle genes, like the rRNAs, with those of bacteria also support this view of chloroplasts and mitochondria (see Yang et al., Suggested Reading).
Mitochondria and chloroplasts may have come to be associated with early eukaryotic/archaeal cells when these cells engulfed bacteria to take advantage of their superior energy-generating systems or their ability to obtain energy from light through photosynthesis. The engulfed bacteria eventually lost many of their own genes, which moved to the chromosome, from where they are expressed and their products are transported back into the organelle. The organelles had by then lost their autonomy and had become permanent endosymbionts of the eukaryotic cells. In one view, the role of endosymbiosis in the evolution of eukaryotes calls into quest ion the use of phylogenetic trees as a tool to describe the interrelationship of entire organisms, given that many organisms represent a conglomeration of genomes (see Koonin, Suggested Reading).
Interestingly, members of a large newly identified group within bacteria with no cultured representatives, called the Candidate Phyla Radiation (Figure 1), have relatively small genomes and, to varying degrees, limited metabolic capacities. This has led to the idea that many of these lineages may be symbionts, something that has been shown in some cases.
What Is Genetics?
Genetics can be simply defined as the manipulation of DNA to study cellular and organismal functions. Since DNA encodes all of the information needed to make the cell and the complete organism, the effects of changes in DNA can give clues to the normal functions of the cell and organism.
Before the advent of methods for manipulating DNA in the test tube, the only genetic approaches available for studying cellular and organismal functions were those of classical genetics. In this type of analysis, mutants (i.e., individuals that differ from the normal, or wild-type, members of the species by a certain observable attribute, or phenotype) that have alterations in the function being studied are isolated. The changes in the DNA, or mutations, responsible for the altered function are then localized in the chromosome by genetic crosses. The mutations are then grouped into genes to determine how many different genes are involved. The functions of the genes can then sometimes be deduced from the specific effects of the mutations on the organism. The ways in which mutations in genes involved in a biological system can alter the biological system provide clues to the normal functioning of the system.
Classical genetic analyses continue to contribute greatly to our understanding of developmental and cellular biology. A major advantage of the classical genetic approach is that mutants with an altered function can be isolated and characterized without any a priori understanding of the molecular basis of the function. Classical genetic analysis also is often the only way to determine how many gene products are involved in a function and, through suppressor analysis, to find other genes whose products may interact either physically or functionally with the products of these genes.
The development of molecular genetic techniques has greatly expanded the range of methods available for studying genes and their functions. These techniques include methods for isolating DNA and identifying the regions of DNA that encode particular functions, as well as methods for altering or mutating DNA in the test tube and then returning the mutated DNA to cells to determine the effect of the mutation on the organism.
The approach of first cloning a gene and then altering it in the test tube before reintroducing it into the cells to determine the effects of the alterations is sometimes called reverse genetics and is essentially the reverse of a classical genetic analysis. In classical genetics, a gene is known to