Bacteriophages
Bacteriophages, or phages, are a type of virus that specifically infects bacteria. Unlike other organisms, viruses are noncellular and consist of a protein shell (capsid) enclosing either DNA or RNA. Bacteriophages are categorized based on their reproductive cycles, primarily the lytic and lysogenic cycles. In the lytic cycle, phages attach to a bacterial host, inject their nucleic acid, and hijack the host's cellular machinery to produce new phage particles, ultimately causing the host to burst and release these new viruses. In contrast, lysogenic phages integrate their DNA into the host's genome, allowing the host cell to replicate normally while carrying the phage DNA, which can later enter the lytic cycle.
Phages are studied extensively due to their simplicity and the fact that they can provide insights into fundamental biological processes. Research involving bacteriophages has significantly advanced our understanding of molecular genetics, including the nature of DNA as genetic material and the mechanisms of mutation. Additionally, the knowledge gained from phage studies has potential applications in medicine, veterinary practices, and agriculture, as scientists continue to explore their utility in combating bacterial infections and improving plant resilience.
Bacteriophages
Categories: Diseases and conditions; genetics; microorganisms
Bacteriophages, or phages for short, are viruses that parasitize bacteria. Viruses are an extraordinarily diverse group of ultramicroscopic particles, distinct from all other organisms because of their noncellular organization. Composed of an inert outer protein shell, or capsid, and an inner core of nucleic acid—either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) but never both—viruses are obligate intracellular parasites, depending to a great extent on host cell functions for the production of new viral particles.
There is considerable variation in size and complexity among viruses. Some have fewer than ten genes and depend almost entirely on host functions. Others are known to contain from thirty to one hundred genes and rely more on proteins encoded by their own DNA. Even the largest viruses are too small to be seen under the light microscope, so studies on viral structure rely heavily on observation with the transmission electron microscope.
The Study of Bacteriophages
Because scientists know more about the molecular and cell biology of the common bacterium Escherichia coli than about any other cell or organism, it is perhaps not surprising that the best-known phages are those that require E. coli as a host (coliphage). It is not possible to observe phage growth directly (as bacterial growth can be detected by the appearance of colonies on an agar plate), but phage growth can be indirectly observed by the formation of plaques, small clear areas in an otherwise continous lawn of host bacteria growing on a solid growth medium in a petri dish.
Reproductive Cycles
Bacteriophages can multiply by two different mechanisms, termed the lytic cycle and the lysogenic cycle. Some phages are capable only of lytic growth, while others retain the ability to reproduce by either lytic growth or entry into the lysogenic cycle. In the lytic cycle, phages first attach themselves to specific receptor sites on the host cell wall. The phage nucleic acid (DNA or RNA) is injected inside the host, while the protein capsid of the infecting particle remains outside of the host cell at all times. Once the DNA or RNA is inside, transcription of phage genes begins, and phage-encoded proteins begin to be made. Some of these proteins serve to inactivate and destroy the host cell DNA, ensuring that the cell’s energy resources will be directed exclusively toward the production of phage proteins and the replication of phage nucleic acid. Phage DNA or RNA replication ensues quickly and is followed by the packaging of this genetic material into the newly synthesized capsids of the progeny phage particles. The final step is host cell lysis—the bursting of the host cell to release the completed and infective phage progeny. The number of phages released in each burst varies with growth conditions and species, but ideal conditions often result in a burst size of one hundred to two hundred per host cell.
For temperate bacteriophages, those capable of entering the lysogenic cycle, infection of the host cell only rarely causes lysis. Injection of the phage DNA into the host is followed by a brief period of messenger RNA (mRNA) synthesis, necessary to direct the production of a phage repressor protein, which inhibits the production of phage proteins involved with lytic functions. A DNA-insertion enzyme is also made, allowing the phage DNA to be physically inserted into the DNA of the host. The cell then can continue to grow and multiply, and new copies of the phage genes are replicated every cell generation as part of the bacterial chromosome. The host cell is said to be lysogenic, for it retains the potential to be lysed if the prophage pops out of the host DNA and enters the lytic cycle. The integrated prophage does confer a useful property on the host cell, however, for the cell will now be immune to further infection from the same phage species.
T4 Coliphage
One of the best-known lytic phages, which is often used in genetic studies, is the coliphage T4. Its protein capsid consists of three major sections—the head, the tail, and the tail fibers. The double-stranded circular DNA molecule of T4 is packaged into the icosahedral-shaped head, and during the infection process it is forced through the hollow core of the cylindrical tail and then directly into the host cell. Contact with the cell is established and maintained throughout the infection process by the tail fibers.
Self-assembly of progeny phages occurs in at least three distinct cellular locations, as complete heads, tails, and tail fibers are first assembled separately and then pieced together in one of the last phases of the infection cycle. Packaging of the replicated T4 DNA is an integral part of the head assembly process. Each of the three subassemblies involves a reasonably complex and highly regulated sequence of assembly steps. For example, head assembly is known to require the activity of eighteen genes, even though only eleven different proteins are found as structural components of mature heads. Identification of the number and sequence of genes involved with each subassembly process has been facilitated by the analysis of artificial lysates from ts mutants.
For those temperate phages capable of entering the lysogenic cycle, many additional strategies for genetic control and regulation have evolved. The most thoroughly studied of the temperate coliphages is phage lambda (?). Genes controlling phage DNA integration, excision, and recombination, and those involved with repressor functions, have been identified in phage ? as well as structural genes involved with lytic functions that are similar to those studied in T4.
Research Tool
One of the most important conclusions to be drawn from studies on bacteriophages, and viral genetics in general, is that many of the results have universal implications. For example, the physical properties of DNA and RNA are remarkably identical in all organisms, and these are perhaps easiest to study in bacteriophage systems. The experiment that provided the final proof that DNA was the genetic material was performed using a coliphage very similar to T4. Studies on the origin of spontaneous mutations, first performed in phage, have extended to higher forms of life as well. Some of the most basic questions concerning protein-DNA interactions are best addressed in viral systems, and the principles that emerge seem to hold for all other experimental systems. There is every reason to believe that many basic questions in cell and molecular biology will continue to be best studied in viruses such as bacteriophages, and that some of these investigations will spawn applications that can directly benefit humankind.
It is certain that advances in molecular biology that have revolutionized the understanding of cell biology and the molecular architecture of cells will continue to expand the frontiers of knowledge in the study of viral genetics. Applications in human medicine, veterinary medicine, and plant breeding are sure to follow, as scientists continue to unravel the complexities of these simplest of organisms.
Bibliography
Birge, Edward A. Bacterial and Bacteriophage Genetics: An Introduction. 4th ed. New York: Springer-Verlag, 2000. An excellent supplementary text for a college student studying viral genetics for the first time. Some useful illustrations. References at end of each chapter are designated either “general” or “specialized.”
Maloy, Stanley R., John E. Cronan, Jr., and David Freifelder. Microbial Genetics. 2d ed. Boston: Jones and Bartlett, 1994. An intermediate-level college textbook focusing on the genetics of bacteria and their bacteriophages. Provides an excellent summary of the properties and life cycles of phages that is accessible to readers with a limited background in biology. The text is well illustrated throughout, with many references for each chapter.
Russell, Peter J. Genetics. 5th ed. Menlo Park, Calif.: Benjamin Cummings, 1998. An introductory college text that is particularly well suited to the problem-solving approach to genetics. Presents a fine overview of gene regulation in phages. Well illustrated with a carefully conceived glossary and reference list.
Stahl, Franklin W. Genetic Recombination: Thinking About It in Phage and Fungi . San Francisco: W. H. Freeman, 1979. Probably the most technical of the references listed, this book might nevertheless be useful to interested readers. Chapter 4 provides a nice treatment of phage replication and the single burst experiment. Some illustrations, glossary, references.
Suzuki, D., A. Griffiths, J. Miller, and R. Lewontin. An Introduction to Genetic Analysis. 4th ed. New York: W. H. Freeman, 1989. Chapters 10-12 of this intermediate-level college text provide a historical perspective on the development of phage genetics and its applications to DNA structure and mutation. The summary of genetic fine structure and complementation is well described and illustrated. Includes glossary and references.