Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin

      SEM images of the archaeon “Candidatus Prometheoarchaeum syntrophicum” strain MK-D1. Reprinted from Imachi H, et al, ©2020, Springer Nature, CC-BY 4.0, http://creativecommons.org/licenses/by/4.0/.

THE GOAL OF THIS TEXTBOOK is to introduce the student to the field of bacterial molecular genetics. From the point of view of genetics and genetic manipulation, bacteria are relatively simple organisms. There also exist model bacterial organisms that are easy to grow and easy to manipulate in the laboratory. For these reasons, most methods in molecular biology and recombinant DNA technology that are essential for the study of all forms of life have been developed around bacteria. Bacteria also frequently serve as model systems for understanding cellular functions and developmental processes in more complex organisms. Much of what we know about the basic molecular mechanisms in cells, such as transcription, translation, and DNA replication, has originated with studies of bacteria. This is because such central cellular functions have remained largely unchanged throughout evolution. Core parts of RNA polymerase and many of the translation factors are conserved in all cells, and ribosomes have similar structures in all organisms. The DNA replication apparatuses of all organisms contain features in common, such as sliding clamps and editing functions, which were first described in bacteria and their viruses, called bacteriophages. Chaperones that help other proteins fold and topoisomerases that change the topology of DNA were first discovered in bacteria and their bacteriophages. Studies of repair of DNA damage and mutagenesis in bacteria have also led the way to an understanding of such pathways in eukaryotes. Excision repair systems, mutagenic polymerases, and mismatch repair systems are remarkably similar in all organisms, and defects in these systems are responsible for multiple types of human cancers.

In addition, as our understanding of the molecular biology of bacteria advances, we are finding a level of complexity that was not appreciated previously. Because of the small size of the vast majority of bacteria, it was impossible initially to recognize the high level of organization that exists in bacteria, leading to the misconception that bacteria were merely “bags of enzymes,” where small size allowed passive diffusion to move cellular constituents around. However, it is now clear that movement and positioning within the bacterial cell are highly controlled processes. For example, despite the lack of a specialized membrane structure called the nucleus (the early defining feature of the “prokaryote” [see below]), the genome of bacteria is exquisitely organized to facilitate its repair and expression during DNA replication. In addition, advances facilitated by molecular genetics and microscopy have made it clear tha many cellular processes occur in highly organized subregions within the cell. Once it was appreciated that bacteria evolved in the same basic way as all other living organisms, the relative simplicity of bacteria paved the way for some of the most important scientific advances in any field, ever. It is safe to say that a bright future awaits the fledgling bacterial geneticist, where studies of relatively simple bacteria, with their malleable genetic systems, promise to uncover basic principles of cell biology that are common to all organisms and that we can now only imagine.

      However, bacteria are not just important as laboratory tools to understand other organisms; they also are important and interesting in their own right. For instance, they play essential roles in the ecology of Earth. They are the only organisms that can “fix” atmospheric nitrogen, that is, convert N₂ to ammonia, which can be used to make nitrogen-containing cellular constituents, such as proteins and nucleic acids. Without bacteria, the natural nitrogen cycle would be broken. Bacteria are also central to the carbon cycle because of their ability to degrade recalcitrant natural polymers, such as cellulose and lignin. Bacteria and some types of fungi thus prevent Earth from being buried in plant debris and other carbon-containing material. Toxic compounds, including petroleum, many of the chlorinated hydrocarbons, and other products of the chemical industry can also be degraded by bacteria. For this reason, these organisms are essential in water purification and toxic waste clean-up. Moreover, bacteria produce most of the naturally occurring so-called greenhouse gases, such as methane and carbon dioxide, which are in turn used by other types of bacteria. This cycle helps maintain climate equilibrium. Bacteria have even had a profound effect on the geology of Earth, being responsible for some of the major iron ore and other mineral deposits in Earth’s crust.

      Another unusual feature of bacteria and archaea (see below) is their ability to live in extremely inhospitable environments, many of which are devoid of life except for microbes. These are the only organisms living in the Dead Sea, where the salt concentration in the water is very high. Some types of bacteria and archaea live in hot springs at temperatures close to the boiling point of water (or above in the case of archaea), and others survive in atmospheres devoid of oxygen, such as eutrophic lakes and swamps.

      Bacteria that live in inhospitable environments sometimes enable other organisms to survive in those environments through symbiotic relationships. For example, symbiotic bacteria make life possible for Riftia tubeworms next to hydrothermal vents on the ocean floor, where living systems must use hydrogen sulfide in place of organic carbon and energy sources. In this symbiosis, the bacteria obtain energy and fix carbon dioxide by using the reducing power of the hydrogen sulfide given off by the hydrothermal vents, thereby furnishing food in the form of high-energy carbon compounds for the worms, which lack a digestive tract. Symbiotic cyanobacteria allow fungi to live in the Arctic tundra in the form of lichens. The bacterial partners in the lichens fix atmospheric nitrogen and make carbon-containing molecules through photosynthesis to allow their fungal partners to grow on the tundra in the absence of nutrient-containing soil. Symbiotic nitrogen-fixing Rhizobium and Azorhizobium spp. in the nodules on the roots of legumes and some other types of higher plants allow the plants to grow in nitrogen-deficient soils. Other types of symbiotic bacteria digest cellulose to allow cows and other ruminant animals to live on a diet of grass. Bioluminescent bacteria even generate light for squid and other marine animals, allowing illumination, camouflage, and signaling in the darkness of the deep ocean.

      Bacteria are also important to study because of their role in disease. They cause many human, plant, and animal diseases, and new diseases are continuously appearing. Knowledge gained from the molecular genetics of bacteria helps in the development of new ways to treat or otherwise control old diseases that can be resistant to older forms of treatment, as well as emerging diseases.

      Some bacteria that live in and on our bodies also benefit us directly. The role of our commensal bacteria in human health is only beginning to be appreciated. It has been estimated that of the 10¹⁴ cells in a human body, only half are human! Of course, bacterial cells are much smaller than our cells, but this shows how our bodies are adapted to live with an extensive bacterial microbiome, which helps us digest food and avoid disease, among other roles, many of which are yet to be uncovered.

      Bacteria have also long been used to make many useful compounds, such as antibiotics, and chemicals, such as benzene and citric acid. Bacteria and their bacteriophages are also the source of many of the useful enzymes used in molecular biology.

In spite of substantial progress, we have only begun to understand the bacterial world around us. Bacteria are the most physiologically diverse organisms on Earth, and the importance of bacteria to life on Earth and the potential uses to which bacteria can be put can only be guessed. Thousands of different types of bacteria are known, and new insights into their cellular mechanisms and their applications