Bacteriophage: Genetics and Molecular Biology

Bacteriophages (viruses that infect bacteria) are fascinating organisms that have played and continue to play a key role in bacterial genetics and molecular biology. Phage can confer key phenotypes on their host, for example converting a non-pathogenic strain into a pathogen, and they play a key role in regulating bacterial populations in all sorts of environments. The phage-ba...

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Bacteriophages (viruses that infect bacteria) are fascinating organisms that have played and continue to play a key role in bacterial genetics and molecular biology. Phage can confer key phenotypes on their host, for example converting a non-pathogenic strain into a pathogen, and they play a key role in regulating bacterial populations in all sorts of environments. The phage-bacterium relationship varies enormously: from the simple predator-prey model to a complex, almost symbiotic relationship that promotes the survival and evolutionary success of both. While infection of bacteria used in the fermentation industry can be very problematic and result in financial losses, in other senarios phage infection of bacteria can be exploited for industrial and/or medical applications. In fact interest in phage and phage gene products as potential therapeutic agents is increasing rapidly and is likely to have a profound impact on the pharmaceutical industry and biotechnology in general over the coming years. One potential application is the use of phage to combat the growing menace of antibiotic-resistant infections.

Written by eminent international researchers actively involved in the disparate areas of bacteriophage research this book focuses on the current rapid developments in this exciting field. The book opens with an excellent chapter that provides a broad overview of the topics and also highlights the multifaceted nature of bacteriophage research. This is followed by a series of reviews that focus on the current most cutting-edge topics including bioinformatics and genomics, phage in the environment, bacteriophage in medicine, transfer of phage DNA to the host, contribution to host phenotype and much more.

Essential reading for all phage researchers and of interest to molecular biologists and microbiologists working on bacteria in academia, biotechnology and pharmaceutical companies, and in the food and other industries

Chapter 1 The New Phage Biology: From Genomics to Applications
Olivia McAuliffe, R. Paul Ross, and Gerald F. Fitzgerald
Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and diverse entities in the biosphere. From initial research defining the nature of viruses, to deciphering the fundamental principles of life, to the development of the science of molecular biology, phages have been 'model organisms' for probing the basic chemistry of life. With more recent advances in technology, most notably the ability to elucidate the genome sequences of phages and their bacterial hosts, there has been a resurgence of interest in phages as more information is generated regarding their biology, ecology and diverse nature. Phage research in more recent years has revealed not only their abundance and diversity of form, but also their dramatic impact on the ecology of our planet, their influence on the evolution of microbial populations, and their potential applications. This review focuses on this new post-genomic era of phage biology, from information emerging from genomics and metagenomics approaches through to applications in agriculture, human therapy and biotechnology.
Chapter 2 Bacteriophage Bioinformatics and Genomics
Carlos A. Canchaya, Marco Ventura, and Douwe van Sinderen
Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology. Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced was a bacteriophage. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome.
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Chapter 1 The New Phage Biology: From Genomics to Applications
Olivia McAuliffe, R. Paul Ross, and Gerald F. Fitzgerald
Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and diverse entities in the biosphere. From initial research defining the nature of viruses, to deciphering the fundamental principles of life, to the development of the science of molecular biology, phages have been 'model organisms' for probing the basic chemistry of life. With more recent advances in technology, most notably the ability to elucidate the genome sequences of phages and their bacterial hosts, there has been a resurgence of interest in phages as more information is generated regarding their biology, ecology and diverse nature. Phage research in more recent years has revealed not only their abundance and diversity of form, but also their dramatic impact on the ecology of our planet, their influence on the evolution of microbial populations, and their potential applications. This review focuses on this new post-genomic era of phage biology, from information emerging from genomics and metagenomics approaches through to applications in agriculture, human therapy and biotechnology.
Chapter 2 Bacteriophage Bioinformatics and Genomics
Carlos A. Canchaya, Marco Ventura, and Douwe van Sinderen
Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology. Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced was a bacteriophage. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome.

Chapter 3 Bacteriophage in the Environment
Markus G. Weinbauer, Martin Agis, Osana Bonilla-Findji, Andrea Malits and Christian Winter
One and a half decades ago, it was detected that phages are much more abundant in the water column of freshwater and marine habitats than previously thought and that they can cause significant mortality of bacterioplankton. Methods in phage community ecology have been developed to assess phage-induced mortality of bacterioplankton and its role for food web process and biogeochemical cycles, to genetically fingerprint phage communities or populations and estimate viral biodiversity by metagenomics. The release of lysis products by phages converts organic carbon from particulate (cells) to dissolved forms (lysis products), which makes organic carbon more bio-available and thus acts as a catalyst of geochemical nutrient cycles. Phages are not only the most abundant biological entities but probably also the most diverse ones. The majority of the sequence data obtained from phage communities has no equivalent in data bases. These data and other detailed analyses indicate that phage-specific genes and ecological traits are much more frequent than previously thought. In order to reveal the meaning of this genetic and ecological versatility, studies have to be performed with communities and at spatiotemporal scales relevant for microorganisms.

Chapter 4 Bacteriophages and Food Fermentations
Eric Emond and Sylvain Moineau
A broad number of food products, commodity chemicals, and biotechnology products are manufactured industrially by large-scale bacterial fermentation of various organic substrates. Because enormous amounts of bacteria are being cultivated each day in large fermentation vats, the risk that bacteriophage contamination rapidly brings fermentations to a halt and cause economical setbacks is a serious threat in these industries. This chapter describes the relationship between bacteriophages and their bacterial hosts in the context of the food fermentation industry. Sources of phage contamination, measures to control their propagation and dissemination, and biotechnological defence strategies developed to restrain phages are discussed. The primary focus will be given to the dairy fermentation industry because it has openly acknowledged the problem of phage and has been working with academia and starter culture companies to develop defence strategies and systems to curtail the propagation and evolution of phages for decades. Other industries will be discussed where appropriate to highlight their similarities and specificities.

Chapter 5 Bacteriophages in Medicine
Andrzej Górski, Jan Borysowski, Ryszard Międzybrodzki, and Beata Weber-Dąbrowska
Bacteriophages, or phages, are viruses of bacteria. Thus, by their very nature, they can be considered as potential antibacterial agents. Over the past decade or two, the idea of phage therapy, i.e. the use of lytic bacteriophages for both the prophylaxis and the treatment of bacterial infections, has gained special significance in view of a dramatic rise in the prevalence of highly antibiotic-resistant bacterial strains paralleled by the withdrawal of the pharmaceutical industry from research into new antibiotics. As an alternative to "classic" phage therapy, in which whole viable phage particles are used, one can also employ bacteriophage-encoded lysis-inducing proteins, either as recombinant proteins or as lead structures for the development of novel antibiotics. Two additional, rather less-recognized potential medical applications of phages are the treatment of viral infections and their use as immunizing agents in diagnosing and monitoring patients with immunodeficiences. We also discuss very interesting novel findings demonstrating the immunomodulatory activity of bacteriophages, suggestive of a potential role of endogenous phages in maintaining the homeostasis of the immune system.

Chapter 6 Phage Therapy: The Western Perspective
Harald Brüssow
Phage therapy has a long and colourful history. Phages have been explored as means to eliminate pathogens like Campylobacter in raw food and Listeria in fresh food or to reduce food spoilage bacteria. In agricultural practice phages were used to fight pathogens like Campylobacter , Escherichia and Salmonella in farm animals, Lactococcus and Vibrio pathogens in fish from aquaculture and Erwinia and Xanthomonas in plants of agricultural importance. The oldest use was, however, in human medicine. Phages were used against diarrheal diseases caused by E. coli, Shigella or Vibrio and against wound infections caused by facultative pathogens of the skin like staphylococci and streptococci. Phage therapy therefore looks like a platform technology. This impression is reinforced by recent extension of the phage therapy approach to systemic and even intracellular infections and the addition of non-replicating phage and isolated phage enzymes like lysins to the antimicrobial arsenal. However, despite some hope and hype in recent editorials on phage therapy, the current review documents that definitive proof for the efficiency of these phage approaches in the field or the hospital is only provided in a few cases.

Chapter 7 Bacteriophage Host Interaction in Lactic Acid Bacteria
Christina Skovgaard Vegge, John Gerald Kenny, Lone Brøndsted, Stephen Mc Grath, and Douwe van Sinderen
The first contact between an infecting phage and its bacterial host is the attachment of the phage to the host cell. This attachment is mediated by the phage's receptor binding protein (RBP), which recognizes and binds to a receptor on the bacterial surface. RBP's are also referred to as: host specificity protein, host determinant, and anti-receptor. For simplicity, the RBP term will be used here. A variety of molecules have been suggested to act as host receptors for bacteriophages infecting lactic acid bacteria (LAB); among those are polysaccharides, (lipo)teichoic acids as well as a single membrane protein. A number of RBPs of LAB phages have been identified by the generation of hybrid phages with altered host range. These studies, however, also found additional phage proteins to be important for successful a phage infection. Analysis of the crystal structure of several RBPs indicated that these proteins share a common tertiary folding as well as supporting previous indications of the saccharide nature of the host receptor. The Gram-positive LAB have a thick peptidoglycan layer, which must be traversed in order to inject the phage genome into the bacterial cytoplasm. Peptidoglycan-degrading enzymes are expected to facilitate this penetration and such enzymes have been found as structural elements of a number of LAB phages.

Chapter 8 Transfer of DNA From Phage to Host
Lucienne Letellier, Laure Plançon, and Pascale Boulanger
Phage DNA transport is atypical among membrane transport and thus poses a fascinating problem: transport is unidirectional; it concerns a unique molecule the size of which may represent 50 times that of the bacterium. The rate of DNA transport can reach values as high as 3 to 4 thousands base pairs / sec. This raises many questions, which will be addressed in this chapter. Is there a single mechanism of transport for all types of phages? How does the phage genome overcome the hydrophobic barrier of the host envelope? Is DNA transported as a free molecule or in association with proteins? Is such transport dependent on phage and / or host cell components? What is the driving force for transport? Data will be presented for a few selected tailed phages for which DNA transport has been most extensively studied.

Chapter 9 Prophages and Their Contribution to Host Cell Phenotype
W. Michael McShan and Joseph J. Ferretti
In many bacterial species, prophages figure prominently in the biology of these cells, often conferring key phenotypes that can convert a non-pathogenic strain into a pathogen. The source of these phenotypic changes can be through prophage-encoded toxins, bacterial cell surface alterations, or resistance to the human immune system. Further, prophage integration into the host genome can inactivate or alter the expression of host genes. In addition to these direct genetic alterations associated with the addition or inactivation of genes, prophages can also alter the phenotype of bacteria at the population level by facilitating the spread of favorable genes through transduction.

Chapter 10 Prophage Induction of Phage λ
John W. Little
The gene regulatory circuitry of phage λ is among the best-understood circuits at the mechanistic level. This circuitry involves several interesting regulatory behaviors. An infected cell undergoes a decision between two alternative pathways, the lytic and lysogenic pathways. If the latter is followed, the lysogenic state is established and maintained. While this state is highly stable, it can switch to the lytic pathway in the process of prophage induction, which occurs when the host SOS response is triggered by DNA damage. We first review events that stabilize the lysogenic pathway and that affect the lysis-lysogeny decision. This is followed by a more extensive description of prophage induction. This process displays threshold behavior, and a model for this behavior is presented. Other aspects of systems behavior in the l circuitry are briefly described. Finally, we discuss insights into the evolution of complex regulatory circuits afforded by studies with the λ circuitry.

Chapter 11 Phage Φ29: Membrane-associated DNA Replication and Mechanism of Alternative Infection Strateg
Wilfried J.J. Meijer, Daniel Muñoz-Espín, Virginia Castilla-Llorente and Margarita Salas
Continuous research, spanning a period of more than three decades, has made the Bacillus bacteriophage Φ29 a paradigm for the study of several molecular mechanisms of general biological processes, including DNA replication and regulation of transcription. The genome of Φ29 consists of a linear double-stranded (ds) DNA, which has a terminal protein covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail in vitro and is considered to be a model system that is also used by other linear genomes with a terminal protein linked to their DNA ends. Phage Φ29 has also been proven to be a versatile system to study in vitro transcription regulation in general and the switch from early to late phage transcription in particular. The detailed knowledge of in vitro phage Φ29 DNA replication and transcription regulation makes it an attractive model to study these processes in vivo. For many years it has been known that (i) phage Φ29 DNA replication, as well as that of other prokaryotic genomes, occurs at the cytosolic membrane, and (ii) the lytic Φ29 cycle is suppressed in early sporulating cells and under these conditions the infecting phage genome becomes trapped into the spore. The molecular mechanisms involved in these processes were largely unknown. We review here the advances recently obtained in our understanding of membrane-associated organization of Φ29 DNA replication and the mechanisms underlying the alternative infection strategy.

Chapter 12 Release of Progeny Phages from Infected Cells
Carlos São José, João Nascimento, Ricardo Parreira and Mário A. Santos
Progeny release from phage-infected cells can occur either by lysis of the host or by a singular secretion mechanism, which has been only documented so far for filamentous phages. All known double stranded DNA phages synthesize two lysis effectors, an endolysin and a holin, the first providing a muralytic function and the second a lysis timing device. Endolysins and holins from different phages can be structurally very diverse in spite of their functional similarities. In its export to the cell wall, the endolysin can either be dependent on holin-formed membrane lesions or use the general secretion pathway of the host. In several known cases an antiholin is also produced. This protein can be either soluble or membrane-bound. In T4, the anti-holin is crucial in the response to superinfecting phage, in a process known as lysis inhibition (LIN). Phage members of the Microviridae and Leviviridae families are also bacteriolytic but use a single gene lysis strategy to release their progeny. The mechanism employed relies on the production of murein synthesis inhibitors and thus lysis by such phages is akin to lysis mediated by antibiotics which target the cell wall. The Inoviridae, filamentous phages, do not lyse their hosts. They are assembled during export, using transmembrane channels formed by at least one inner membrane phage-encoded protein and an outer membrane secretin.
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