Viral Genetics Lecture 1 & 2 PDF

Potential futuristic Scenario Are We Ready? Copyright © McGraw-Hill Education. Permission required for reproduction or display. 1 Is that true?! WHO Meeting Yesterday  Potential Threats Antimicrobia Resistance (AMR) (De Oliveira et al., 2020) 4 ...

Potential futuristic Scenario Are We Ready? Copyright © McGraw-Hill Education. Permission required for reproduction or display. 1 Is that true?! WHO Meeting Yesterday  Potential Threats Antimicrobia Resistance (AMR) (De Oliveira et al., 2020) 4 There were 4.95 million deaths globally in 2019 (Thompson, 2022) 5  Course Objectives 1- Study the genome structure of prokaryotic, eukaryotic Microbial cells as well as viruses. 2- Differentiate between prokaryotic and eukaryotic cells on the level of replication, transcription and translation. 3- Study the gene regulation in prokaryotes 4- study the genetic exchange mechanisms in prokaryotes  Course Objectives (Cont.) 5- Study the mutation types 6- Study the viral genetics 7- Study the Eukaryotic microbial genetics  Course Objectives (practical level) 1- DNA extraction from gram positive, gram negative and eukaryotic microorganisms. 2- Plasmid DNA extraction 3- Plasmid curing 4- Transformation 5- Conjugation 6- Bioinformatics  INTRODUCTION ▪ Viruses are nonliving particles with nucleic acid genomes ▪ Viruses vary with regard to their structure and their ability to infect different hosts. ▪ They must infect living cells in order to proliferate ▪ Virus. ▪ Virion. ▪ Viroid. ▪ Prion. ▪ Virusoid. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-2 New Expressions  17.1 VIRUS STRUCTURE AND GENETIC COMPOSITION ▪ Viruses differ in several ways (see Table 17.1) ▪ Host range- a cell that is infected by a virus is called a host cell. The host range is the number of species that a particular virus can infect. ▪ Structure- all viruses have a nucleic acid genome (DNA or RNA) surrounded by a protein capsid. Some viruses have a viral envelop, which is derived from the plasma membrane of the host cell and also contains viral spike glycoproteins. Refer to Figure 17.1. ▪ Genome composition- the genome of a virus can be DNA or RNA; it can be single- or double-stranded; and it can carry a few genes or many genes. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-3 17-4 Figure 17.1 Variations in the structure of viruses, as shown by transmission electron microscopy. 17-5  17.2 OVERVIEW OF VIRAL REPRODUCTIVE CYCLES ▪ A viral reproductive cycle is a series of steps that results in the production of new viruses ▪ This cycle occurs after a virus has infected a host cell ▪ The details of viral reproductive cycles vary from one type of virus to another, but they all follow 5 or 6 basic steps Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-10 Steps of Viral Reproductive Cycles 1. Attachment- A virus attaches to the surface of a host cell 2. Entry- the virus or viral genome enters the host cell 3. Integration- some but not all viruses integrate their genome into the genome of the host cell 4. Synthesis of Viral Components- viral proteins and DNA or RNA are made by the host cell 5. Viral Assembly- the viral components assemble into virus particles 6. Release- viruses are released from the host cell Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-11 Steps of Viral Reproductive Cycles ▪ Figure 17.3 shows the viral reproductive cycles for two viruses ▪ Part (a) shows the reproductive cycles for phage , which is a bacteriophage with a DNA genome ▪ Part (b) shows the reproductive cycle for human immunodeficiency virus (HIV), which infects humans and causes acquired immune deficiency syndrome (AIDS) Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-12 Figure 17.3a Comparison of the steps of two viral reproductive cycles. 17-13 to 17-16 Figure 17.3a Comparison of the steps of two viral reproductive cycles. 17-13 to 17-16 Figure 17.3b Comparison of the steps of two viral reproductive cycles. 17-13 to 17-16 Figure 17.3b Comparison of the steps of two viral reproductive cycles. 17-13 to 17-16  Latency in Viruses ▪ Viruses may remain inactive or latent, during which new viruses are not made ▪ Some bacteriophages are latent when they are in the lysogenic cycle (see Figure 17.4) ▪ HIV usually remains latent for a long time after the RNA genome is reverse transcribed into DNA and integrated into the host chromosome. ▪ Some viruses, such as herpesviruses, can remain latent as episomes, a gene genetic element that can replicate independently of the host genome Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-17 Figure 17.4 The lytic and lysogenic reproductive cycles of certain bacteriophages. 17-18  Emerging Viruses ▪ Emerging viruses are viruses that have arisen recently and are more likely to cause infection than previous strains ▪ Examples include new strains of influenza, such as the swine flu strain, and HIV; refer to Figures 17.5 and 17.6 ▪ HIV-causes acquired immune deficiency sydrome (AIDS) ▪ Because HIV damages the immune system, it makes people more susceptible to opportunistic infections, such pneumonia caused by the fungus, Pneumocystis jiroveci ▪ By 2013, caused over 30 million deaths ▪ Worldwide, about 1 in 100 people between the ages of 15 and 49 are infected Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-20  Figure 17.6 Micrograph of HIV invading a human helper T cell. Figure 17.5 A micrograph of influenza virus, strain H1N1. 17-21 Influenza A  17.4 HIV REPRODUCTIVE CYCLE ▪ HIV (human immunodeficiency virus) is a human virus that causes AIDS; it infects human T cells, which play an important role in immunity ▪ HIV has an RNA genome ▪ During the reproductive cycle, HIV RNA is reverse transcribed into DNA and integrated into a host chromosome; it may remain latent for a long time ▪ New HIV particles are made by the transcription of HIV RNA and production of new HIV proteins that assemble at the plasma membrane and bud from the cell ▪ These steps will be considered in detail Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-36  Genome of HIV ▪ Researchers have identified two different strains of HIV, called HIV-1 and HIV-2; HIV-1 is described here ▪ The HIV genome is relatively small, only 9749 nucleotides long ▪ It carries nine genes, but some of them encode polyproteins that are cut into multiple proteins Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-37  Genome of HIV ▪ The nine genes of HIV can be divided into 5 different categories (also refer to Figure 17.11a) ▪ gag: Proteins used for viral assembly and capsid formation; the gag gene encodes a polyprotein this is cleaved into four different proteins ▪ Matrix protein, capsid protein, nucleocapsid protein, and p6 ▪ pol: Enzymes needed for viral replication and viral assembly; the pol gene encodes a polyprotein that is cleaved into three enzymes ▪ HIV protease, reverse transcriptase, and integrase ▪ vif, vpu: Proteins that promote infectivity and budding ▪ vpr, rev, tat, nef: Proteins with regulatory functions ▪ env: Proteins that are part of the viral envelop; the env gene encodes a polyprotein this is cleaved into two proteins ▪ gp41 and gp120 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-38 Figure 17.11a Structure of HIV. 17-39  Structure of HIV ▪ HIV has two copies of the RNA genome that is surrounded by a capsid (refer to Figure 17.11b) ▪ The capsid is surrounded by an envelop that is derived from the host cell plasma membrane with viral spike glycoproteins ▪ Many of the HIV proteins are contained within the virus, including reverse transcriptase and integrase, which are needed during early steps in the viral reproductive cycle Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-40 Figure 17.11b Structure of HIV. 17-41  Reverse Transcription ▪ After HIV enters the host cell, the single-stranded RNA is reverse transcribed into double-stranded DNA by reverse transcriptase (refer to Figure 17.12) ▪ The process begins when a host-cell tRNA binds to the HIV RNA; the tRNA acts as a primer ▪ In a series of steps, portions of the viral RNA are reverse transcribed into DNA; the viral DNA is also used as a template to make a complementary DNA strand ▪ During this process, the viral RNA is degraded by RNase H, which is a component of reverse transcriptase Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-42 Figure 17.12a Synthesis of doublestranded DNA from HIV RNA via reverse transcriptase. 17-43 to 17-44 Figure 17.12b Synthesis of doublestranded DNA from HIV RNA via reverse transcriptase. 17-43 to 17-44  Integration of HIV DNA into a Host-Cell Chromosome ▪ After HIV DNA is made, it binds to integrase, which makes small cuts at the 3’ ends (refer to Figure 17.13) ▪ Vpr and other proteins then bind to the HIV DNA to form a preintegration complex ▪ The preintegration complex enters the nucleus and binds to a site in a host cell chromosome ▪ In a series of steps, the host-cell chromosome is cut and the HIV DNA is integrated into the chromosome. ▪ After integration, the HIV DNA is called a provirus Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-45 Figure 17.13a Integration of the double-stranded HIV DNA into the host-cell genome. 17-46 to 17-47 Figure 17.13b Integration of the double-stranded HIV DNA into the host-cell genome. 17-46 to 17-47  Synthesis of HIV RNA and Viral Proteins ▪ After a long period of latency, the HIV provirus may become active ▪ The activation of the provirus occurs via NF-B, which a transcription factor made by T cells; NF-B becomes active when the T cell is stimulated by an antigen ▪ The active form of NF-B enters the nucleus, binds to the HIV proviral DNA, and stimulates transcription Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-48  Synthesis of HIV RNA and Viral Proteins ▪ Three types of HIV RNAs are made ▪ Fully spliced HIV RNA- early in this process, the HIV RNA is fully spliced; this RNA exits the nucleus and is used to translate Nef, Tat, and Rev proteins ▪ Incompletely spliced HIV RNA- incompletely spliced RNA exits the nucleus with the help of the Rev protein; this RNA is translated into Vif, Env, Vpu and Vpr proteins ▪ Unspliced HIV-RNA- unspliced HIV RNA also exits the nucleus with help of the Rev protein. Unspliced HIV-RNA is translated to make Gag polyprotein and Gag-pol polyprotein. The unspliced HIV RNA is also incorporated into new virus particles Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-49 Figure 17.14 Synthesis of new HIV components: HIV RNA and proteins. 17-50  Assembly, Budding, and Maturation of HIV Particles ▪ The final event in the HIV reproductive cycle is the formation of new HIV particles that are released from the host cell; this process occurs in three overlapping stages called assembly, budding, and maturation ▪ Assembly- HIV components assemble at the plasma membrane; the Gag polyprotein plays a central role in the assembly of the various components ▪ MA domain (later becomes the matrix protein)- binds to the plasma membrane and to gp41 ▪ CA domain- helps with assembly and later becomes the capsid protein ▪ NC domain- captures the HIV RNA ▪ P6 domain- contains binding sites for several other other proteins that are either contained with HIV particles or needed for budding Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-51  Assembly, Budding, and Maturation of HIV Particles ▪ Budding- The immature virus begins to bud from the host cell. ▪ The neck of the bud is broken by host proteins, including those that are components of the ESCRT pathway ▪ Vpu enhances the release of the immature virus particle by inhibiting a host protein called tetherin, which tethers the immature virus particle to the plasma membrane ▪ Maturation- HIV protease cleaves the gag polyproteins and gag-pol polyproteins into their individual components, which promotes the formation of mature viral particles ▪ The matrix protein lines the inside of the HIV envelop and anchors the gp41/gp120 spikes ▪ The capsid protein forms a capsid structure that encloses two molecules of HIV RNA along with several proteins Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 17-52 Figure 17.15 Assembly, budding, and maturation of new HIV particles. 17-53