BIO3124 - Viruses (Student) (PDF)

BIO3124 - Viruses BIO3124 General Microbiology Textbook (Norton) Chapter 6 OpenStax Chap.6 Image by David Goodell Zika virus unique to Archea->4sevdopeptogix can Haloarchea-D light Carl criven pumps Chapter Overview to wosse :cutify Archea compared new resembles life ribos and RNA...

BIO3124 - Viruses BIO3124 General Microbiology Textbook (Norton) Chapter 6 OpenStax Chap.6 Image by David Goodell Zika virus unique to Archea->4sevdopeptogix can Haloarchea-D light Carl criven pumps Chapter Overview to wosse :cutify Archea compared new resembles life ribos and RNA Sequences with Bacteria Form Enkayote in How PNA:s replicated § What is a virus? § The ecology of viruses § The structure of viruses § What agents are even smaller than a virus? § How viruses are classified § The life cycles of bacteriophages § The life cycles of animal and plant viruses § How viruses are cultured 2 What is a virus? § A virus is a noncellular particle that infects a host cell and directs it to produce progeny particles (more viruses). § The virus particle, or virion, generally consists of a viral genome (DNA or RNA) contained within a protein capsid. 3 Viruses Infect Specific Hosts § Viruses are typically specific to their hosts and a range of cells within these hosts. • Bacteriophages (or phages) are viruses that infect bacteria. Their replication is observed as a plaque of lysed cells on a lawn of bacteria growing in a Petri dish. • An example of a human virus is the measles virus. • An example of a plant virus is the tobacco mosaic virus. Plaques Measles TMV 4 We have more degenerate viral sequences then protein coding sequences in our genome “Ghost of infections past” – Dr Paul Turner Integrated Viral Genomes § Some viruses do more than replicate within a cell; they integrate their genomes into that of the host. • In effect, such viruses become a part of the host organism. § A bacteriophage that integrates its genome into its bacterial host’s genome is called a prophage. § Within a human cell, an integrated viral genome is called a provirus. § A permanently integrated provirus transmitted from one human to another via the germ line is called an endogenous virus. Source: Wikipedia 6 Dynamic Nature of Viruses § We now know that a virus may interconvert among three very different forms: • Virion, or virus particle – An inert particle that does not carry out any metabolism or energy conversion. • Intracellular replication complex – Within a host cell, the viral gene products direct the cell’s enzymes to assemble progeny virions at “virus factories” called replication complexes. • Viral genome integrated within host DNA – Some types of viral genomes may integrate within a host chromosome as a prophage or provirus. This may be a permanent condition. 7 Dynamic Nature of Viruses § The inert nature of the virion particle, which lacks metabolism and the ability to reproduce independent of its host, argues that viruses are nonliving. § The virion assembly process argues that viruses are living organisms. § The genomes of large viruses show evidence of reductive evolution (evolutionary loss of genes) from a cellular origin § Genomes of small RNA viruses indicate they may have been built up from mere parts of a cell. • These claims are debated regularly by virologists. Would you like to know more? Dr Paul Turner Yale University https://www.ibiology.org/speakers/ paul-turner/ 8 Size of viruses Most viruses are smaller than prokaryotic cells; range from 0.02 to 0.3 µm. Size of viruses Giant viruses Up to 2500 genes! Bigger the some bacteria. Infect like micellular amoebad algae Viral structure capsid: the protein shell that surrounds the genome of a virus particle Naked viruses (e.g., most bacterial viruses) have no other layers. Enveloped viruses (e.g., many animal viruses) have an outer layer consisting of a phospholipid bilayer (from host cell membrane) and viral proteins. Nucleocapsid: nucleic acid + protein in enveloped viruses Brock Microbiology, Pearson. Virion morphology: Spherical Complex Spherical Icosahedral Helical Filamentous Image Source: Pinterest 6.3 Viral Genomes and Classification § Viral genomes can be: • DNA or RNA Strains • Single- or double-stranded (ss or ds) • ~ recombinance Linear, circular, or segmented § The form of the genome has key consequences for the mode of infection, and for the course of a viral disease. § Viral genomes are used as the basis of virus classification. 13 6.4 Viral replication § Viruses display a remarkable diversity of ways to replicate within a host cell. § Bacteriophage replication § Animal virus replication § Naked virus § Enveloped virus 14 Overview of the Virus Life Cycle Major difference between prokaryotic and eukaryotic viruses is nucleic acid entry in prokaryotes and virion entry in eukaryotes. The replication cycle of a bacterial virus. In - In bacteria only geno .g animal whole Virus Source: Brock Microbiology, Pearson. Phases of viral replication in a permissive (supportive) host attachment (recognition) of the virion penetration (entry, injection) of the virion nucleic acid synthesis of virus nucleic acid and protein by host cell metabolism as redirected by virus assembly of capsids and packaging of viral genomes into new virions release of mature virions from host cell Bacteriophages Infection § Bacteriophages exhibit two different types of replication cycles: 1. Lytic cycle -> 2. Lysogenic cycle make -> new variants coormant in Cell bust out & replicated with cell § The “decision” of which replication cycle to utilize is dictated by environmental cues that either activate or repress transcription of genes for virus replication. Stress triggers lytic burst • In general, events that threaten host cell survival trigger a lytic burst. 16 Entry mechanism of bacteriophage Attachment: major factor in host specificity Microbiology, Wessner, Dupont, Charles and Neufeld, 2nd ed, Wiley, Chap.5, p.139. The bacteriophage injects its genetic material with a spring-like needle into the host cell! • Virions attach to cells via tail fibers that interact with polysaccharides on E. coli LPS layer. • Tail fibers retract, and tail pins contact cell wall. • T4 lysozyme forms small pore in peptidoglycan. • Tail sheath contracts, and viral DNA passes into cytoplasm. • Capsid stays outside. Source: Brock Microbiology, Pearson. Video of bacteriophage infection Video by Biolution no Viral life cycle ~ lysogen pathway Virulent: Viruses always lyse and kill host after infection. Temperate: Viruses replicate their genomes in tandem with host genome and without killing host, establishing long-term, stable relationship. • • • • can be lytic/virulent can enter lysogeny: most viral genes are not transcribed, viral genome is replicated with host chromosome and passed to daughter cells lysogen: host cell that harbors temperate virus can result in lysogenic conversion with new properties (e.g., virulence in pathogens) The lytic cycle of a bacteriophage Rice Uni chap 6.2 The lysogenic cycle of a bacteriophage Rice Uni chap 6.2 Bacterial Defenses § Bacteria have evolved several forms of defense against bacteriophage infection: • Genetic resistance – • 3 Surface protein Restriction endonucleases – • Altered receptor proteins Change Cleave viral DNA lacking methylation CRISPR integration of phage DNA sequences – Clustered regularly interspaced short palindromic repeats – A bacterial immune system 23 Bacterial Defenses – Genetic resistance Modification of cell-host recognition Bacteriophage resistance mechanisms. Labrie SJ et al, Nature Reviews Microbiology volume 8, pages 317–327 (2010) Bacteria changes cell surface molecule recognized by phage Phage adapts to recognize new surface molecule Bacteria can produce a molecule that masks the phage target 24 Ins ! de cell Virus genome recognized by infection Bacterial Defenses – Restriction enzymes = no Restriction enzymes cat and mouse Going from a to i: restriction enzyme is art - a. Normal infection b. Bacteria digest viral DNA/RNA using restriction enzymes c. Virus counteract with undigestible modified nucleic acid d. Bacteria finds a way to digest modified nucleic acids e. Virus finds another way to protect its nucleic acids f. Bacteria finds another way to get around it g. Etc… h. Etc… i. Etc… Bacteriophage resistance mechanisms. Labrie SJ et al, Nature Reviews Microbiology volume 8, pages 317–327 (2010) 25 recognizes cus DAM ↑ Bacterial Defenses – CRISPR CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats Protect from bacteriophage infection • Regions contain short repeats of DNA sequences alternating with short variable spacers corresponding to “memory” of viral or other foreign DNA. Cur Proter I use DNA W ↑ take On 7 DNA Ai sequence virus put into genome Some viruses have evolved to avoid CRISPR. • • [aS Cu Pruckuse regorize viral infetter infa all the fore mutation of PAM regions production of Cas inhibitors When immunized cell encounters same virus, Cas proteins destroy incoming DNA. PAM: protospacer adjacent motif, crRNA: CRISPR RNA has to survive virus First time in Brock Microbiology, Pearson or to work 6.5 Animal and Plant Viruses § Animal and plant viruses solve problems similar to those faced by bacteriophages: • Host attachment, genome entry and gene expression, virion assembly, and virion release § However, eukaryotic cells have a more complex structure than prokaryotic cells. • Therefore, animal and plant viruses have greater complexity and diversity of viral replication cycles than we see in bacteriophages. § Animal viruses bind specific receptor proteins on their host cell. • Receptors determine the viral tropism, or ability to infect a particular tissue type within a host. • For example, Ebola virus exhibits broad tropism by infecting many kinds of host tissues, whereas papillomavirus shows tropism for only epithelial tissues. 27 Entry mechanism of animal viruses A. Endocytosis of non-enveloped virus B. Membrane fusion of an enveloped virus C. Endocytosis of an enveloped virus Two key differences with bacterial viruses: • Entire virion enters the animal cell. • Eukaryotic cells contain a nucleus, the site of replication for many animal viruses. leave before digested by lysosome Microbiology, Wessner, Dupont, Charles and Neufeld, 2nd ed, Wiley, Chap.5, p.138. Animal Virus Replication Cycles § The primary factor that dictates the details of a replication cycle of an animal virus is the form of its genome. § DNA viruses • Utilize some or all of the host replication machinery § RNA viruses • sense - stand replicated :e - RNA than replicated = Use an RNA-dependent RNA polymerase to transcribe their mRNA § Retroviruses • ↓ - Sense Use a reverse transcriptase to copy their genomic sequence into DNA for insertion in the host chromosome (Most human viral diseases are caused by RNA viruses) 29 +RNA Lytic cycle in animal cells doesn'tfill Cell salt U But Rice Uni Openstax Chap 6.2 cr Budding ex Lositusi I Lysogenic cycle in animal cells HIV infection: • The adhesion of the virus gp120 envelop protein to the cell surface marker CD4 (only present on T helper cells) and its coreceptor is mandatory for infection. • The viral envelop fuses with the lipid bilayer of the host cell, the viral capsid is delivered in the cytoplasm. • The capsid is digested by proteases and the ssRNA genome delivered into to the nucleus with the reverse transcriptase enzyme necessary to convert ssRNA in cDNA which can then be converted to dsDNA by the host cell. • An integrase, also delivered with the virus, helps the transduction of the virus into the host genome. • New viral mRNA and proteins are produced by the host cells, virions assemble within the cytoplasm and envelop proteins are integrated into the host plasma membrane. • Encapsulated new viral particles exocytose, the vesicle with which they exocytose forms the new envelop, the virions are mature and can infect new cells. attech Fusiu with cell Rice Uni Openstax Chap 6.2 HIV life cycle (vimeo in collab with David Goodsell) Animal and Plant Host Defenses § Since viruses are ubiquitous, a wide range of defense mechanisms have evolved in animals and plants. § Genetic resistance – Hosts continually experience mutations. § Immune system – “Innate immunity”— interferons – “Adaptive immunity”— antibodies § RNA interference (RNAi) – Alters gene expression and degrades viral RNA 33 Chapter Summary – 1 § Viruses fill important niches in all ecosystems. § A virus is a noncellular particle that can reproduce only within a living cell. § An infectious viral particle, or virion, is composed of a nucleic acid genome surrounded by a protein capsid and, in some cases, an envelope. § Viruses can be divided into two main types: • Symmetrical • Asymmetrical § The Baltimore system classifies viruses mainly on their means of mRNA synthesis. 34 Chapter Summary – 2 § Phages may undergo a lytic or lysogenic cycle. § The more complex structure of eukaryotic cells leads to greater complexity and diversity of life cycles in animal and plant viruses than in phages. § The life cycles of retroviruses and pararetroviruses are especially complex. § Plant viruses enter host cells mechanically and are transmitted to other cells via plasmodesmata. § Both bacterial and animal viruses can be cultured. • Plaque assays are employed for this purpose. 35