Chapter 19. Gene creatures, Part 1: viruses, viroids and plasmids Prepared by Woojoo Choi
Dead or alive? 1) In this chapter we will explore the twilight zone of biology and the gene creature who live there. 2) Gene creature: life from consisting primarily of genetic information, sometimes with a protective covering, but without its own machinery to generate energy or replicate macromolecules 3) Vary in their level of independence, from viruses, which can survive outside the host cell as virus particles, down to mere stretches of DNA or RNA that replicate according to their own whims, yet are never found outside the cell
Dead or alive?
Viruses are not living cells 1) We should start by noting that being alive and being a living cell are not necessarily the same. 2) Living cell: an independent unit of life surrounded by a membrane; contains genes made of DNA, and possesses its own machinery to generate energy and synthesize proteins, DNA and RNA
Viruses are not living cells 3) Virus: subcellular parasite with genes of DNA or RNA and which replicates inside the host cell upon which it relies for energy and protein synthesis. In addition, it has an extracellular form in which the virus gene are contained inside a protective coat.
What defines a Virus? 1) A virus alternates between two forms, an inert virus particle, the virion, which survives outside the host cell, and an active intracellular stage. 2) The virus particle consists of a capsid surrounding either RNA or DNA. Capsid: protein shell surrounding the DNA or RNA of a virus particle
What defines a Virus? 3) Viral genome: the nucleic acid, either DNA or RNA, that carries the genetic information of a virus 4) The life cycle of a typical virus has the following stages: Attachment to the correct host cell A protein on the virus particle must recognize a molecule such as a protein and a carbohydrate on the surface of the target cell
What defines a Virus? Entry of the virus genome Replication of the virus genome Manufacture of the virus proteins Assembly of new virus particles Release of new virus particles from the host cell
What defines a Virus? 5) Many animal viruses have an extra envelope, stolen from the previous host cell, outside the protein shell.
What defines a Virus? 6) Once inside, the protein shell disassembles, exposing the genome.
What defines a Virus? 7) Bacteria have a cell wall protecting their cell membrane and so bacterial viruses cannot simply merge with the membrane as do animal viruses. They just have a protein shell surrounding the DNA or RNA. They inject DNA or RNA into the bacterial cell and protein shell is left behind.
What defines a Virus? 8) Once inside the host cell, the virus genome has two major functions. It must replicate to produce more virus genomes. It must persuade the cell to manufacture lots of virus proteins. 9) Then, new virus particles are assembled from components manufactured by the host cell.
The great diversity of viruses 1) There is colossal variation in the structure of viruses and the detailed way in which they take over the cells they invade. 2) Some have DNA genome while others have RNA. 3) The nucleic acid may be either single or double stranded and either linear or circular. 4) Some viruses have segmented genomes made up of several pieces of DNA or RNA.
The great diversity of viruses 5) DNA viruses replicate using DNA polymerase borrowed from the host cell. 6) However, RNA viruses need a special enzyme, RNA replicase. RNA replicase: enzyme that synthesizes new RNA using an RNA template and encoded by RNA viruses
Bacterial RNA viruses have very few genes 1) A back-to-nature minimalist virus can get by with only three genes. 2) Male-specific bacteriophage: only infect male bacteria. In the case of E. coli, those bacteria containing the F-plasmid which confer the ability to conjugate(eg, Qβ or M13)
Bacterial virus ΦX174-A small single stranded DNA virus 1) Bacterial virus ΦX174: a small spherical bacterial virus containing single stranded DNA which infects E. coli 2) They have 20 triangular face and are eicosahedrons.
Bacterial virus ΦX174-A small single stranded DNA virus 3) It has so little DNA that five of its genes overlap others.
Bacterial virus ΦX174-A small single stranded DNA virus 4) Some other bacterial viruses are filamentous rather than spherical. 5) Bacterialphage M13: a small filamentous bacterial virus containing single stranded DNA that only infect male E. coli and is used to make single stranded DNA for sequencing
Complex bacterial viruses with double stranded DNA 1) These viruses all have a complex form made up of a head, tail, and tail fibers. 2) The head contains a large molecule of linear dsdna. 3) They include bacteriophages T4, Lambda, P1 and Mu, which are all used in bacterial genetics and molecular biology.
Complex bacterial viruses with double stranded DNA 4) Attached to the head is a tail with tail fibers that act as landing legs. 5) These viruses bind to bacterial cells by means of recognition proteins on the end of their tail fibers. 6) After setting down, their tails contract and they inject their DNA.
Plant viruses 1) Cauliflower mosaic virus: a double stranded DNA virus that infects and kills cauliflower and related plants
Plant viruses 2) Most plant viruses are small with just a handful of genes and contain single stranded RNA. 3) Some are spherical while others are rod-shaped like tobacco mosaic virus which makes yellowish blotches on the leaves.
Plant viruses
Viroids 1) Viroids are small circular pieces of naked RNA which are only 250 to 400 bases long. 2) They are single stranded but base pairing occurs between bases on opposite halves of the circle to produce a rod-like structure.
Viroids 3) The viroid RNA does not have any genes that encode protein. 4) It carries signals for its own replication by the host. 5) The viroid RNA is probably catalytically active itself, a ribozyme. 6) They cannot recognize and penetrate healthy cells due to the absent of protein coat. 7) They prey only on the weak and injured.
Plasmid 1) Plasmid: circular molecule of double stranded DNA which replicates independently of the host cell s chromosome 2) Although they rely on the cell both for the machinery of DNA replication and the energy to make their own DNA, they are regarded as autonomous because they control their own replication 3) A more sensitive approach is to consider plasmids as creatures in their own right
Plasmid 4) Some cells may have plasmids living inside them; others may not 5) So, although the plasmid is not alive in the same as a cell, it is not just part of the cell
Plasmid 6) Plasmids resemble viruses in requiring a host cell 7) The plasmid genome is replicated by the host cell machinery and at the cell s expense in energy and raw materials 8) Unlike viruses, plasmids do not possess protein coats and since they cannot leave the cell they live in, they do not vandalize it 9) When the cell divides, the plasmid divides and each daughter cell gets a copy of the plasmid
Plasmids help their host cells 1) Most plasmids provide useful properties to their host cells. 2) They often protect bacteria from anitibiotics.
Plasmids help their host cells 3) They also protect bacteria from industrial pollution. 4) Some plasmids provide their bacterial owners with aggressive weaponry. Virulence plasmid: plasmid which carries genes involved in aiding infection or causing symptoms of disease Ti-plasmid: plasmid which carries the gene necessary for causing tumors in plants
Plasmid DNA replicates by two methods 1) Plasmids use two mechanisms for replicating their DNA, though not both at once. Bidirectional replication of plasmid (see Ch. 5)
Plasmid DNA replicates by two methods Rolling circle replication Mechanism of replicating double stranded circular DNA that starts by nicking and unrolling one strand and using the other, still circular strand, as a template for DNA synthesis (eg, F-plasmid, see Ch. 8)
Plasmid DNA replicates by two methods
Plasmid DNA replicates by two methods Rolling circle replication is also used by many viruses.
Plasmid DNA replicates by two methods
Lysogeny and latency 1) Lytic growth: mode of virus growth that results in destruction of the infected host cell
Lysogeny and latency 2) Lysogeny: mode of virus growth in which duplication of the virus genome keeps in step with division of the host cell, which is therefore not destroyed Lysogen: cell containing a virus in harmless, lysogenic mode Latency: another name for lysogeny, normally applied to animal viruses (eg, herpesvirus)
Lysogeny and latency 3) Changing conditions may stimulate a lysogenic virus to stop being the plasmid and go back to being the virus.
Lysogeny or latency by integration 1) Some cases of lysogeny or latency are caused by integration of the virus DNA into a host cell chromosome. 2) Provirus: form of a virus in which the viral DNA is integrated into the host chromosome (eg, bacterial virus lambda, some retroviruses)
Replicons 1) Replicon: molecule of DNA or RNA which contains an origin of replication (chromosomes, plasmids, virus genomes, and viroids) 2) Not all gene creatures are replicons. 3) Some cannot replicate themselves (Transposable element). 4) Transposable element (transposon): segment of DNA that can move from one location to another, but which always remain part of another DNA molecule and do not have own origin of replication