Hans-W. Ackermann

5500 Phages examined in the electron microscope

Summary.“Phages” include viruses of eubacteria and archaea. At least 5568 phages have been examined in the electron microscope since the introduction of negative staining in 1959. Most virions (96%) are tailed. Only 208 phages (3.7%) are polyhedral, filamentous, or pleomorphic. Phages belong to one order, 17 families, and three “floating” groups. Phages are found in 11 eubacterial and archaeal phyla and infect 154 host genera, mostly of the phyla Actinobacteria, Firmicutes, and Proteobacteria. Of the tailed phages, 61% have long, noncontractile tails and belong to the family Siphoviridae. Convergent evolution is visible in the morphology of certain phage groups.

Bacteriophage observations and evolution.

Bacteriophages are classified into one order and 13 families. Over 5100 phages have been examined in the electron microscope since 1959. At least 4950 phages (96%) are tailed. They constitute the order Caudovirales and three families. Siphoviridae or phages with long, noncontractile tails predominate (61% of tailed phages). Polyhedral, filamentous, and pleomorphic phages comprise less than 4% of bacterial viruses. Bacteriophages occur in over 140 bacterial or archaeal genera. Their distribution reflects their origin and bacterial phylogeny. Bacteriophages are polyphyletic, arose repeatedly in different hosts, and constitute 11 lines of descent. Tailed phages appear as monophyletic and as the oldest known virus group.

Frequency of morphological phage descriptions in the year 2000

Summary. Over 5100 bacterial viruses have been examined in the electron microscope since 1959. About 4950 phages (96%) are tailed and only 186 phages (3.6%), are cubic, filamentous, or pleomorphic. Phages belong to 13 virus families and occur in over 140 bacterial genera. Phages are listed by morphotypes and host genera. Siphoviridae or phages with long, noncontractile tails comprise 61% of tailed phages. The distribution of phages in different bacterial phylogenetic divisions is shown.

Tailed Bacteriophages: The Order Caudovirales

Publisher Summary This chapter discusses the common properties of tailed phages and potential criteria for their classification as an order and situating tailed phages with respect to other viruses. Tailed bacteriophages have a common origin and constitute an order with three families, named Caudovirales. Their structured tail is unique. Tailed phages share a series of high-level taxonomic properties and show many facultative features that are unique or rare in viruses—for example, tail appendages and unusual bases. They share with other viruses, especially herpesviruses, elements of morphogenesis and lifestyle that are attributed to convergent evolution. Tailed phages present three types of lysogeny, exemplified by phages λ, Mu, and P1. Lysogeny appears as a secondary property acquired by horizontal gene transfer. Amino acid sequence alignments (notably of DNA polymerases, integrases, and peptidoglycan hydrolases) indicate frequent events of horizontal gene transfer in tailed phages. Common capsid and tail proteins have not been detected. Present-day tailed phages appear as chimeras, but their monophyletic origin is still inscribed in their morphology, genome structure, and replication strategy. It may also be evident in the three-dimensional structure of capsid and tail proteins. It is unlikely to be found in amino acid sequences because constitutive proteins must be so old that relationships were obliterated and most or all replication-, lysogeny-, and lysis-related proteins appear to have been borrowed.

Phage Classification and Characterization

Prokaryote viruses include 14 officially accepted families and at least five other potential families awaiting classification. Approximately 5,500 prokaryote viruses have been examined in the electron microscope. Classification has a predictive value and is invaluable to control experimental techniques and results. In describing viruses, the choice of methods depends on structure and taxonomical position of viruses. The study of isometric, filamentous, and pleomorphic viruses requires more detailed investigations than that of tailed species.

Basic Phage Electron Microscopy

Negative staining of purified viruses is the most important electron microscopical technique in virology. The principal stains are phosphotungstate and uranyl acetate, both of which have problems and advantages. Particular problems are encountered in photography, calibration of magnification, measurements, and interpretation of artifacts.

The present state of phage taxonomy.

Characteristics of over 1,150 phages have been categorized into 17 groups, based upon morphology and nucleic acid content. A scheme is presented for cataloging phage data for computer storage, retriev

Guidelines for Bacteriophage Characterization

Publisher Summary Bacteriophages or phages occur in a wide range of prokaryotes, including bacteria and blue-green algae. With an estimated 1650 isolates studied by electron microscopy, they are the largest viral group described. This group is expanding at a rate of about 130 to 150 virus descriptions per year. These large numbers reflect the relative ease, with which the phages are isolated and their enormous importance for molecular biology, genetics, and epidemiology. For example, a recent review lists typing sets for about 70 bacterial species and serotypes. Although most work has been done on the phages of bacteria pathogenic to humans, there is presently a trend toward studying the phages of nonmedical and sometimes arcane bacteria. The isolation of the new phages raises problems for the investigators, the journal editors, and the scientific public alike. At present, there is no agreement on parameters, methods, and nomenclature. This has led to widely different, often unsatisfactory, phage descriptions and many identical names for different phages. In addition, much effort seems to be devoted to the study of obsolete parameters or properties that, for the lack of standard methods, cannot be compared with existing data. Such a situation is detrimental to comparative virology. The purpose of this chapter is to suggest the guidelines for phage characterization and nomenclature, and to set forth the minimum requirements for their description.

Comparative biology and evolution of bacteriophages.

Publisher Summary Viruses have left no fossil record yet evolutionary relationships among certain viruses can now be assessed with a high degree of confidence. The chapter presents an understanding of the mechanisms likely to have been involved in virus evolution particularly bacteriophages. It is found that tailed phages and the various families of cubic, filamentous, and pleomorphic phages have little in common are most probably polyphyletic in origin and arose at different times. Cubic phages and thelnovirus genus may have appeared about 2 x l09 years ago or later. On the other hand, the presence of tailed phages in archaebacteria, eubacteria, and cyanobacteria and the remarkable coincidence of G-C values between the DNAs of tailed phages and those of their hosts suggest that tailed phage genes predate the common ancestor of the three major divisions of the prokaryotic world. From the study it is concluded that the genomes of temperate phages are part of the vertically inherited survival kit of bacterial DNA, subject to the same selective pressures as other chromosomal genes. Thus the traditional view of phages as intracellular parasites or bacteria-eaters is misleading.

Frequency of morphological phage descriptions.

SummaryBacteriophages are listed by morphotypes and host genera. At least 4.007 phages, belonging to 13 virus families, have been described since 1960. About 3,850 phages (96%) are tailed and 154 phages (4%) are cubic, filamentous, or pleomorphic.Siphoviridae or phages with long noncontractile tails constitute 60% of tailed phages. Phages are found in over 100 bacterial genera including archaebacteria and rickettsiae. Their distribution is very uneven and probably reflects the evolutionary history of bacteria.