Viral Replication Cycles PDF

VIRUS REPLICATION CYCLES CATHERINE MWANGI INTRODUCTION TO MEDICAL VIROLOGY HPA217  VIRUS REPLICATION  The formation of biological viruses during the infection process in the target host cells.  Viruses must first penetrate and enter the cell before viral replicati...

VIRUS REPLICATION CYCLES CATHERINE MWANGI INTRODUCTION TO MEDICAL VIROLOGY HPA217  VIRUS REPLICATION  The formation of biological viruses during the infection process in the target host cells.  Viruses must first penetrate and enter the cell before viral replication can occur.  From the perspective of the virus, the purpose of viral replication is to allow reproduction and survival of its kind.  By generating abundant copies of its genome and packaging these copies into viruses, the virus is able to continue infecting new hosts.  BACTERIOPHAGE LIFE CYCLE  Bacteriophages have been the most intensely studied viruses and are the replication life cycle is best understood  Bacteriophages are viruses that infect and replicate within a bacteria  They are important in medical and pharmaceutical industry  BACTERIOPHAGE LIFE CYCLE  Potential antibacterial agents in phage therapy  Bacteriophages (lambda, M13), used for the construction of cloning and expression vectors  Bacteriophages used in industrial production:  Expression of heterologous proteins by viruses is used for the production of various pharmaceutical proteins, vaccine antigens and antibodies  BACTERIOPHAGE REPLICATION  The genetic material may be either DNA or RNA;  Most known bacteriophages have double-stranded DNA.  Virulent bacteriophages reproduce within the host cell and many progeny are released when the cell is destroyed by lysis.  A phage life cycle that culminates with the host cell bursting and releasing virions is called a lytic cycle.  BACTERIOPHAGE REPLICATION  The phage infects a bacterium and inserts its DNA into the bacterial chromosome  The phage DNA integrates with the chromosome to form a Prophage  The bacteriophage DNA in the prophage is copied and passed on along with the cell's own and this is called lysogenic cycle  Temperate phages may undergo lytic or lysogenic cycles  BACTERIOHAGE(LAMBDA PHAGE) LYTIC CYCLE  In the lytic cycle, a phage acts like a typical virus:  It hijacks its host cell and uses the cell's resources to make lots of new phages, causing the cell to lyse (burst) and die in the process.  Stages of the lytic cycle are:  Attachment  Entry/Penetration  Replication/Protein synthesis  Assembly  Lysis  BACTERIOHAGE(LAMBDA PHAGE) LYTIC CYCLE  Attachment: Proteins in the "tail" of the phage bind to a specific receptor (in this case, a sugar transporter) on the surface of the bacterial cell.  Entry: The phage injects its double-stranded DNA genome into the cytoplasm of the bacterium.  Replication and protein synthesis: Phage DNA is copied, and phage genes are expressed to make proteins, such as capsid proteins.  BACTERIOHAGE(LAMBDA PHAGE) LYTIC CYCLE  Assembly of new phage: Capsids assemble from the capsid proteins and are stuffed with DNA to make lots of new phage particles  Lysis: Late in the lytic cycle, the phage expresses genes for proteins that poke holes in the plasma membrane and cell wall.  The holes let water flow in, making the cell expand and burst like an overfilled water balloon.  Cell bursting, or lysis, releases hundreds of new phages, which can find and infect other host cells nearby. In this way, a few cycles of lytic infection can let the phage spread like wildfire through a bacterial population.. BACTERIOHAGE(LAMBDA PHAGE) LYSOGENIC CYCLE  The lysogenic cycle allows a phage to reproduce without killing its host.  Some phages can only use the lytic cycle, but the phage we are following, lambda (\lambdaλlambda), can switch between the two cycles  In the lysogenic cycle, the first two steps (attachment and DNA injection) occur just as they do for the lytic cycle.  However, once the phage DNA is inside the cell, it is not immediately copied or expressed to make proteins.  BACTERIOHAGE(LAMBDA PHAGE) LYSOGENIC CYCLE  Instead, it recombines with a particular region of the bacterial chromosome.  This causes the phage DNA to be integrated into the chromosome.  The integrated phage DNA, called a prophage, is not active and it doesn't drive production of new phages.  However, each time a host cell divides, the prophage is copied along with the host DNA BACTERIOHAGE(LAMBDA PHAGE) LYSOGENIC CYCLE  The prophage can be transmitted to daughter cells at each subsequent cell division  Later events (such as UV radiation or the presence of certain chemicals) can cause proliferation of new phages via the lytic cycle  Replication  Protein synthesis  Phage assembly  Lysis..  BACTERIOPHAGE LYSOGENIC CYCLE  Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome  Corynebacterium diphtheriae produces the toxin of diphtheria only when it is infected by the phage β.  In this case, the gene that codes for the toxin is carried by the phage, not the bacteria.  Vibrio cholerae is a non-toxic strain that can become toxic, producing cholera toxin, when it is infected with the phage CTXφ.  ANIMAL VIRUS REPLICATION CYCLE  Viral populations do not grow through cell division, because they are acellular.  Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.  Animal viruses tend to be species- and cell-specific  ANIMAL VIRUS REPLICATION CYCLE  Replication between viruses is varied and depends on the type of genes involved.  Most DNA viruses assemble in the nucleus; most RNA viruses develop solely in cytoplasm.  The life cycle of viruses differs greatly between species but there are six basic stages in the life cycle of viruses  VIRUS REPLICATION CYCLE  Virus replication also depends on virus–host cell interaction such as the type of cells it infects—whether permissive or nonpermissive cells.  Permissive cells are those that permit production of progeny virus particles and/or viral transformation.  However, nonpermissive cells do not allow virus replication, but may allow virus transformation.  VIRUS REPLICATION CYCLE  Virus transformation is change in growth or phenotype of the host cell.  Viruses that can enter only into a productive relationship are called lytic or virulent viruses.  Viruses that can establish either a productive or a nonproductive relationship with their host cells are referred to as temperate viruses.  VIRUS REPLICATION CYCLE  Animal virus reproduction may be divided into several stages:  Adsorption or attachment to the host cell  Penetration or entry  Un-coating  Replication of virus nucleic acids and protein synthesis  Assembly of virion components  Maturation  Release of mature viruses  The above series of events describes a productive or lytic response though sometimes it has slight variations in some viruses  VIRUS REPLICATION CYCLE  Lytic cycle in animal viruses however does not necessarily result in the lysis of the animal cell  Lytic response is not the only possible outcome of a virus infection.  Some viruses can enter a latent state where no new virus is produced, the cell survives and divides, and the viral genetic material persists indefinitely.  This outcome of an infection is referred to as the non-productive response.  The nonproductive response is called lysogenic cycle or Viral Latency for animal virus  ADSORPTION/ATTACHMENT  The first step in the animal virus cycle is adsorption to the host cell surface.  This occurs through a random collision of the virion with a plasma membrane receptor site protein, frequently a glycoprotein.  Surface of the virion called virion attachment proteins attach to host cell receptors.  Highly specific reaction between the virion attachment proteins and receptors  ADSORPTION/ATTACHMENT  The specific host cell receptor proteins to which viruses attach vary greatly but they are always surface proteins necessary to the cell.  Host cell surface proteins usually are receptors that bind hormones and other important molecules essential to the cell’s function and role in the body e.g.  Immunoglobulin superfamily, Chemokine receptors, Growth factor receptors  ADSORPTION/ATTACHMENT  Virion attachment proteins are often associated with conspicuous features on the surface of the virion. For example, Spikes on adenovirus  Some attachment protein sites consist of capsid structural protein e.g.  The poliovirus and rhinoviruses—the binding site is at the bottom of a surface depression or valley.  The site can bind to host cell surface projections but cannot be reached by host antibodies..  ADSORPTION  Enveloped viruses have receptors (glycoproteins), spikes or projections distributed on the surface  A particular kind of virus is capable of infecting only a particular hosts and host tissues is called host range.  Human viruses infect only a particular subset of the cells found in their host organism this is Tissue tropism  Adsorption is enhanced by presence of multiple attachment and receptor proteins  Viruses often enter cells by endocytosis.  They trick the host cell by attaching to surface molecules that are normally taken up by endocytosis. ADSORPTION ADSORPTION.  PENETRATION AND UNCOATING  Viruses penetrate the plasma membrane and enter a host cell shortly after adsorption.  The entire process from adsorption to final uncoating may take from minutes to several hours.  Uncoating, involves the release of the nucleic acid from the capsid and is apparently activated by cellular enzymes (except Poxviruses), possibly with a contribution from cell membranes as well.  The detailed mechanisms of penetration and uncoating are still unclear.  PENETRATION AND UNCOATING  It is possible that three different modes of entry may be employed: 1. At least some naked viruses such as the poliovirus undergo a major change in capsid structure on adsorption to the plasma membrane, so that only their nucleic acids are released in the cytoplasm. 2. The envelope of some enveloped viruses, seems to fuse directly with the host cell plasma membrane e.g. Paramyxoviruses (e.g. measles), some retroviruses (eg, HIV-1), and herpesviruses  The envelopes of these viruses contain protein spikes that promote fusion of the viral membrane with the plasma membrane  Because the viral envelope becomes incorporated into the plasma membrane of the infected cell and still possesses its fusion proteins, infected cells have a tendency to fuse with other uninfected cells.  PENETRATION AND UNCOATING 3. Engulfment of the virus by receptor-mediated endocytosis as it involves viruses it is called Viropexis  Pinching off of the cellular membrane by fusion encloses the virion in a cytoplasmic vesicle termed the endosomal vesicle.  Nucleopsid of enveloped viruses seem to be surrounded by two membranes and surface receptors are recycled to plasma membrane  Naked virus may escape endosome by dissolution of the vesicles due to low pH and not membrane fusion  Lysosomal enzymes may aid in virus uncoating and low endosomal pHs often trigger the uncoating process through degradation of the capsid PENETRATION AND UNCOATING.  VIRION COMPONENT SYNTHESIS  This involves genome replication and protein synthesis of enzymes and proteins required for replication and capsid structure and synthesis  These are used for assembly of progeny  Most RNA viruses with the exception of influenza viruses & the retroviruses replicate in the cytoplasm  Retroviruses, influenza viruses, and all the DNA viruses, except the poxviruses move from the cytoplasm to the nucleus to replicate.  VIRION COMPONENT SYNTHESIS  The larger DNA viruses, such as herpesviruses and adenoviruses uncoat at nuclear membrane before entry into the nucleus.  Smaller DNA viruses e.g. parvoviruses and the papillomaviruses, enter the nucleus intact through the nuclear pores and uncoat inside.  Poxviruses, carry out their entire replicative cycle in the cytoplasm of the infected cell.  PROTEIN SYNTHESIS (TRANSCRIPTION)  Viral proteins are synthesized by cellular ribosomes through translation of viral specific mRNA  Viral proteins include structural proteins, enzymes and other specialized proteins required for genome replication, gene expression, and virus assembly and release.  Production of the first viral mRNAs at the beginning of the infection is a crucial step in the takeover of the cell by the virus.  PROTEIN SYNTHESIS (TRANSCRIPTION)  DNA viruses are transcribed by the host DNA-dependent RNA polymerase (RNA polymerase II) to yield the viral mRNAs except for Poxvirus  Poxvirus synthesis m RNA using viral DNA dependent RNA polymerase  Sense-strand ssRNA viruses, the genome can function directly as mRNA.  One of these viral proteins is RNA dependent RNA polymerase required in order to synthesize new mRNA.  Antisense-strand ssRNA viruses an ds RNA carry virion-associated RNA-dependent RNA polymerase to produce initial mRNAs  PROTEIN SYNTHESIS (TRANSCRIPTION)  Retroviral RNA virus is copied to DNA by virion reverse transcriptase enzyme; host RNA polymerase transcribes viral DNA into more genomic RNA and m RNA  The actual protein synthesis procedure is implemented, coded by the viral mRNA, with the help of cellular components such as tRNA, ribosomes etc.  Two functionally different protein types occur in viruses:  The “noncapsid viral proteins” (NCVP) that do not contribute to capsid assembly. These proteins frequently possess enzymatic properties (polymerases, proteases) and must therefore be produced early on in the replication cycle (EARLY PROTEINS)  The capsid proteins, also known as viral proteins (VP) or structural proteins, appear later in the replication process; LATE PROTEINS.  REPLICATION  DNA replication usually occurs in the host cell nucleus; poxviruses are exceptions since their genomes are replicated in the cytoplasm.  RNA replication usually occurs in the cytoplasm with the exception of retroviruses and Influenza viruses  REPLICATION DNA VIRUSES  Some DNA viruses are dependent on host DNA polymerase  Several complex DNA viruses such as adenoviruses and herpesviruses encode their own DNA polymerase  Parvoviruses depend exclusively on host DNA replication machinery (DNA dependent RNA polymerase, DNA polymerase)  Hepadnaviruses such as hepatitis B virus are quite different from other DNA viruses with respect to genome replication. ADENOVIRUS REPLICATION. HERPES VIRUS LYTIC CYCLE HERPES VIRUS REPLICATION  HERPES VIRUS REPLICATION  Have large DNA molecule as they infect non dividing cells and encode enzymes used for DNA replication  The virus glycoproteins attach to host cell receptors and result in fusion of the envelop with host cell membrane  Fusion delivers the nucleocapsid into the cytoplasm  It migrates to the nuclear membrane where it uncoats and DNA translocates into the nucleus  Early transcription phase occurs using host RNA polymerase to synthesize m RNA that encode for non structural proteins required for DNA replication(DNA polymerase, DNA binding proteins, Thymidine Kinase e.t.c.)  Replication of the DNA molecule follows using virus DNA polymerase produced as an early protein  HERPES VIRUS REPLICATION  Late transcription phase produces mRNAs that encode major structural protein e.g. capsid subunits, tegument proteins and envelope glycoproteins.  Replicated DNA molecules are then packaged into preassembled capsids in the nucleus  Herpes viruses assemble in the nucleus and proteolytic event is necessary for the maturation of the virus  Viral protease cleaves long protein strands required for formation of capsid/maturation of capsid  Envelope is acquired from inner lamella of nuclear membrane during budding from nucles  Virions then transported through the ER and Golgi apparatus  Re-envelopment and de-envelopment of virions in ER and Golgi is thought to occur  Virions are released through exocytosis. POX VIRUS REPLICATION VACCINIA REPLICATION  POXVIRUS REPLICATION CYCLE  All the events in sequence are:  Attachment of the virus on the host cell  Penetration; Fusion or Endocytosis  Early mRNA synthesis  Uncoating  Genome replication  Intermediate mRNA synthesis  Late mRNA synthesis,  Assembly  DNA genome packaging  Maturation  Envelope wrapping from Golgi  Exit or virus release. Lysis of Mature Virus (MV), Exocytosis of EEV, extracellular enveloped virus; POX VIRUS PARVOVIRUS B19 REPLICATION  PARVOVIRUS B19 REPLICATION  Parvovirus enters the cells after binding to P antigen (globoside)  Followed by internalization through coated pits into cytoplasm  Uncoating and delivery of single-stranded DNA in the the nucleus.  The singlestranded DNA genome is converted to double-stranded DNA by host DNA polymerase,  dsDNA is transcribed by host RNA polymerase to produce viral mRNAs, followed by synthesis of viral proteins.  After synthesis of single-stranded DNA genomes by host DNA polymerase, progeny viruses are assembled in the nucleus and released upon cell lysis. PARVOVIRUS B19  REPLICATION  Hep B have circular dsDNA genomes but replicate their DNA using reverse transcriptase  Transcription occurs in the nucleus using host RNA polymerase & yields several mRNAs and pre-genomic RNA (pgRNA)  The RNAs move to the cytoplasm & translated to produce virus proteins (core proteins & a polymerase having 3 activities (DNA polymerase, reverse transcriptase, RNase H).  REPLICATION  Reverse transcriptase subsequently transcribes the pgRNA to –DNA  DNA polymerase to copy the antisense DNA and form a dsDNA genome.  Rnase H degrades the pgRNA in the assembled nucleocapsid. HEPATITIS B REPLICATION HEPATITIS B STRUCTURE  REPLICATION RNA VIRUSES  The RNA viruses are much more diverse in their reproductive strategies than are the DNA viruses.  RNA viruses must encode their own polymerase or transcriptases  Transcription and replication must be separated for most RNA viruses  Most RNA viruses can be placed in one of four general groups based on their modes of replication  REPLICATION A. ssRNA viruses (sense-strand): the virus-coded RNA polymerase transcribes the viral genome (+) into complementary strands (–) and these into new genomic RNA (+).  The latter is then integrated in the viral progeny. B. ssRNA viruses (antisense-strand genome): the RNA polymerase in the virion transcribes the viral genome (–) into complementary strands (+), which a virus-coded polymerase then transcribes into new genomic RNA (–).  REPLICATION C. dsRNA viruses: the virus-coded polymerase transcribes complementary strands (+) from the antisense strand of the (segmented) double-stranded viral genome; these complementary strands are complemented to make the new double stranded viral genome. D. RNA replication in retroviruses: the reverse transcriptase (RT) carried by the virion transcribes the viral genome (sense-RNA strands) into complementary DNA (–), which is complemented to produce dsDNA and integrated in the cell genome. -The viral RNA is first degraded. -Cellular enzymes produce new genomic RNA (+). REOVIRUS REPLICATION ROTAVIRUS REPLICATION. CORONAVIRUS REPLICATION CORONAVIRUS..  INFLUENZA VIRUS REPLICATION  Hemagglutinin binds to sialic acid receptor on host cell for attachment  The virus then penetrates the host cell through endocytosis; lowpH within the endosome  Low pH activates the fusion of the virus envelope with the endosome membrane facilitated by Neuraminidase  Virus genome is released into the cytoplasm and migrates to the nucleus  Once it gets to the nucleus it uses hosts components and its own virus RNA polymerase to produce viral proteins and genomic RNA  Assembly takes place in the cytoplasm, Matrix protein migrate to the cell membrane;site of budding  It attracts the virions towards the cell membrane where they bud acquiring an envelope  Neuraminidase also aids in the release of the newly formed virions INFLUENZA VIRUS HIV VIRUS REPLICATION..  ASSEMBLY  In this step, the viral capsid proteins and genomes (present in multiple copies after the replication process) are assembled into new, infectious virus particles.  In some viral species these particles are also covered by an envelope  Some late genes direct the synthesis of capsid proteins, and these spontaneously self-assemble to form the capsid just as in bacteriophage morphogenesis.  Most DNA viruses assemble in and are released from the nucleus into cytoplasm  Most RNA viruses assemble solely in the cytoplasm  ASSEMBLY  In helical symmetry viruses, structural subunits are preformed and added stepwise to the growing structure along the genome (RNA)  The assembly process ceases when the ends of the RNA are reached.  The structural subunits as well as the RNA trace out a helical path in the final virus particle.  Icosahedral capsids are generally preassembled and the nucleic acid genomes, usually complexed with condensing proteins, are threaded into the empty structures. ASSEMBLY ASSEMBLY  RELEASE  Some enveloped viruses are released when the particles “bud off” of the cytoplasmic membrane and are expelled from the cell  In non-enveloped viruses, release of viral progeny is realized either by means of lysis of the infected cell or more or less continuous exocytosis of the viral particles.  Naked capsid viruses lacking specific lysis mechanisms are released with cell death  Some viruses block or delay apoptosis to allow completion of the virus replication cycle  RELEASE  Poxviruses program the formation of envelope membranes in the endoplasmic reticulum  The membrane site for budding first acquires virus-specified spikes and matrix protein  At the site of the glycoprotein cluster, the inside of the membrane becomes coated with a virion structural protein called the matrix or M protein  The matrix protein attracts the completed nucleocapsid that triggers the envelopment process leading to the release of the completed particle to the outside  RELEASE  The initial budding process rarely causes cell death; however, too many daughter viruses released may result in loss of cell membrane permeability  Most retroviruses (except HIV) reproduce without cell death. BUDDING  ANIMAL VIRUS LYSOGENIC CYCLE  The lysogenic cycle is complementary to the Lytic cycle for viral entry and reproduction within cells.  While the Lytic cycle is common to both animal viruses and bacterial phages, the lysogenic cycle is more commonly found in animal viruses.  The following are the steps of the lysogenic cycle: 1. Viral genome enters cell 2. Viral genome integrates into Host cell genome 3. Host cell DNA Polymerase copies viral chromosomes 4. Cell divides, and virus chromosomes are transmitted to cell's daughter cells  ANIMAL VIRUS LYSOGENIC CYCLE  At any moment when the virus is "triggered", the viral genome detaches from the Host cell's DNA and enters stage 2 of the Lytic cycle.  While it is unclear as of yet what exactly constitutes a "trigger" that activates the viral DNA from the latent stage entered in Step 4, common symptoms that appear to "trigger" the viral DNA are;  Hormones, high stress levels (adrenaline), and free energy within the infected cell.  ANIMAL VIRUS LYSOGENIC CYCLE  An example of a virus that enter the lysogenic cycle is herpes, which first enters the Lytic cycle after infecting a human, then the lysogenic cycle before travelling to the nervous system where it resides in the nerve fibers as an episomal element.  After a long period of time (months to years) in a latent stage, the herpes virus is often reactivated to the Lytic stage during which it causes severe nervous system damage.  ABNORMAL REPLICATIVE CYCLES INCOMPLETE VIRUSES  This is a result of defective assembly or deficiency in some aspects of replication ABORTIVE INFECTION  When a virus infects a host cell (non-permissive) but cannot complete the full replication cycle  Viral components may be synthesized but maturation or assembly is defective and either release does not occur or the progeny is non infectious