The Genetics of Viruses and Bacteria

1. The Genetics of Viruses and Bacteria By: Stefanie Vorleiter

2. Molecular biology was started by the study of viruses and bacteria. • E. Coli and other microbes are model systems. • Provides great support that genes are made of DNA. A T4 bacteriophage is infecting the bacterium Escherichia Coli (E. coli), in this SEM.

3. Model Systems mechanisms: • Useful for understanding how bacteria and viruses cause disease. • Another use is to manipulate genes and transfer them to other organisms. • Remember bacteria are prokaryotes, their cells are much smaller and simply organized. • Viruses are even smaller and more simple, they are no more than genes packages in protein coats.

4. Discovery of Viruses: Scientific Inquiry A virus has a genome but can reproduce only within a host cell. Viruses were detected before they were able to be seen. 19th century Tobacco mosaic disease stops or shortens the growth of tobacco and gives their leaves a discoloration. Adolf Mayer, discovered that one could transmit the disease from plant to plant by rubbing sap onto the healthy plants. Mayer concluded that the disease was caused by small bacteria that you cannot see with a microscope.

5. Extracted sap from tobacco plant with tobacco mosaic disease Passed sap through a porcelain filter known to trap bacteria Rubbed filtered sap on healthy tobacco plants Healthy plants became infected

6. Discovery of Viruses This hypothesis was proved a decade later when Dimitri Ivanowsky, passed sap from the infected tobacco plant through a filter, designed to remove bacteria. • After filtering the sap still created the mosaic disease. • Ivanowsky hypothesized that bacteria cause tobacco mosaic disease. It might be that the bacteria was too small and so they filtered through. • This was proven wrong when Martinus Beijerinck, a Dutch botanist, discovered that the infectious agent of the sap could reproduce. • He rubbed plants with the filtered sap, and from these he infected plants, continuing this process through a series of infections.

7. Discovery of Viruses • The bacteria must have been reproducing because the disease was undiluted after several transfers. • The pathogen had only reproduced within the host it infected. • Unlike bacteria, this disease could not be cultivated in test tubes or Petri dishes. • Beijerinck believed the mosaic disease was much smaller and simpler than bacteria. • This was confirmed by Wendell Stanley, who crystallized the infectious particles, known as tobacco mosaic virus (TMV).

8. Structure of Viruses • The tiniest are only 20nm in diameter, where millions could fit on a pinhead. • The largest are barely visible in light microscopes. • The crystallization of a virus by Stanley was exciting news. • The simplest cells can’t even aggregate into crystals. -If viruses aren’t cells, what are they? >Viruses are infectious particles consisting of nucleic acid enclosed in a protein coat.

9. Structure of Viruses: Viral Genome • Viruses defy DNA’s double helix structure, they contain double stranded DNA, single stranded DNA, double stranded RNA, and singe stranded RNAdepending on their nucleic acids. • The smallest virus has only 4 genes, while the largest has several hundreds. • Depending on the size and shape of the genomes capsid, will be how many genes it contains.

10. Structures of Viruses: Capsids and Envelopes • Protein shells enclosing the viral genome is the capsid. • Depending on the type they are: capsids can be rod-shaped, polyhedral, or more complex (T4). • Capsids are made from protein subunits, capsomeres. • The most complex Capsids are those viruses that infect bacteria, called bacteriophages.—E. Coli • Viral Envelopes are derived from the membrane of the host cell and made up of proteins and glycoproteins.

12. General Features of Viral Reproductive Cycles Viruses reproduce only within a host cell. An isolated virus cannot do anything but infect its appropriate host cell. Viruses lack metabolic enzymes, ribosome's, etc.. Each virus can only infect a limited amount of host cells called its host range. The host range is determined by the proteins on its surface and that of the host.

13. Features of Reproductive Cycle • “lock and key” system is detected between proteins on the outside of the virus and receptor molecules on the cells. -The West Nile virus can infest mosquitoes, birds, and humans. -The equine encephalitis virus can infect mosquitoes, birds, horses, and humans. -The measles and poliovirus only infect humans. -Human cold virus infects only cells lining the upper respiratory tract. -Aids virus bind to specific receptors on certain white blood cells. (these two are limited to particular tissues.)

14. Simplified viral reproductive cycle. Mechanisms of reproductive cycle depends on the type of virus and cell.

15. The genome commands the host, reprogramming it to make viral proteins. • Assembly into new viruses is a spontaneous process of self-assembly. • Hundreds of thousands of viruses exit from the host cell, which usually damages or kills the host cell. • This along with the body’s response to destruction, is what causes the symptoms associated with viral infections. • The viral prodigies that exit the cell, have the ability to infect other cells, spreading the virus.

16. Reproductive Cycle of Phages • Two reproductive cycles.. • A phage reproduction which causes the death of the host cell is the lytic cycle. • Lytic refers to the last stage of infection, in which the bacterium lyses (breaks open) and releases a large number of phages. • Each phage can then infect a cell and a few lytic cycles can destroy an entire bacterial population in just a few hours. • A phage that can only reproduce through the lytic cycle is called a virulent phage.

17. Attachment

18. Attachment Entry of phage DNA and degradation of host DNA

19. Entry of phage DNA and degradation of host DNA Synthesis of viral genomes and proteins

20. Entry of phage DNA and degradation of host DNA Phage assembly Assembly Synthesis of viral genomes and proteins

21. Entry of phage DNA and degradation of host DNA Release Phage assembly Assembly Synthesis of viral genomes and proteins

22. Lytic Cycle -phages have been used medically • Bacteria isn’t defenseless. • When phage DNA successfully enters a bacterium, the DNA is often recognized as foreign and cut up by restriction enzymes. The bacteria's cells DNA is altered so that is prevents attacks by the restriction enzymes. Why haven ‘t phages gotten rid of all bacteria?

23. Lysogenic Cycle • A virus that replicates the phage without destroying the host undergoes the lysogenic cycle. • Phages capable of using both modes of reproducing within a bacterium are called temperate phages. • Infection of an E. coli cell by λ begins when the phage binds to the surface of the cell and injects its DNA. • Within the host, the λ DNA molecule forms a circle. • Next, depending whether its lytic or lysogenic, in lytic, the viral genes immediately turn the host cell into λ producing factory, and the cell lyses and releases its viral products. • During a lysogenic cycle, the λ DNA molecule is incorporated by genetic recombination( crossing over) into a specific site on the host cells chromosome. • If this integrates, the viral DNA is a prophage, of which one gene codes for a protein that prevents transcription of other prophage genes.

24. Daughter cell with prophage Phage DNA The phage injects its DNA. Cell divisions produce population of bacteria infected with the prophage. Phage DNA circularizes. Phage Bacterial chromosome Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Lytic cycle Lysogenic cycle The bacterium reproduces, copying the prophage and transmitting it to daughter cells. The cell lyses, releasing phages. Lytic cycle is induced Lysogenic cycle is entered or Prophage Phage DNA integrates into the bacterial chromosome, becoming a prophage. New phage DNA and proteins are synthesized and assembled into phages.

25. Lysogenic Cycle • Every time the E. coli cells divide, it replicates the phage DNA along with its own and passes the copies onto the daughter cells. • A single cell can quickly produce a large population of bacteria carrying the virus • Lysogenic implies that prophage are capable of giving rise to active phages that lyse their host cells. • Expression of the genes may alter the hosts phenotype, which can cause medical significance.

26. The phage attaches to a host cell and injects its DNA Phage DNA Bacterial chromosome Prophage Lytic cycle Lysogenic cycle • Virulent or temperate phage • Destruction of host DNA • Production of new phages • Lysis of host cell causes release • of progeny phages • Temperate phage only • Genome integrates into bacterial • chromosome as prophage, which • (1) is replicated and passed on to • daughter cells and • (2) can be induced to leave the • chromosome and initiate a lytic cycle

27. Lytic Cycle and Lysogenic Cycle

28. Reproductive Cycle of Animal Viruses • Many variations on the basic scheme of viral infection and reproduction are represented among animal viruses. • One key variable is the nature of the viral genome: It is composed of DNA or RNA? Is it double stranded or single stranded? The nature of the genome is the basis for the common classification of viruses. • Another characteristic is the presence of absence of a membranous envelope derived from the host cell membrane. -Nearly all animal viruses with RNA genomes have an envelope, as do some with DNA genomes.

29. Viral Envelopes • An animal is equipped with an outer membrane, or a viral envelope, which it uses to enter the host cell. • Protruding from the outer surface of this envelope are viral glycoproteins that bind to specific receptor molecules on the surface of a host cell. • This reproductive cycle does not necessary kill the host, unlike the lytic cycle.

30. Capsid and viral genome enter the cell Capsid RNA HOST CELL Envelope (with glycoproteins) Viral genome (RNA) Template mRNA Capsid proteins ER Copy of genome (RNA) Glyco- proteins New virus

31. Viral Envelopes • Some viruses have envelopes that are not derived from the plasma membrane. • The envelopes of herpes viruses are derived from the nuclear membrane of the host. These viruses have a double stranded DNA genome and reproduce within the host cell nucleus. • The infection of other cells by these new viruses causes the blisters characteristic of herpes, such as cold sores or genital sores.

32. Viral envelope Glycoprotein Capsid RNA (two identical strands) HOST CELL Reverse transcriptase Reverse transcriptase Viral RNA RNA-DNA hybrid DNA NUCLEUS Provirus Chromosomal DNA RNA genome for the next viral generation mRNA New virus

33. RNA as Viral Genetic Material • The RNA animal viruses with the most complicated reproductive cycles are the retroviruses. • These viruses contain the enzyme, reverse transcriptase, which transcribes a single stranded RNA template into DNA. • HIV contains two identical molecules of single stranded RNA and two molecules of reverse transcriptase. • After HIV enters the host cell, its reverse transcriptase molecules are released into the cytoplasm and catalyze synthesize viral DNA. • The new DNA enters the cells nucleus and integrates which is called a provirus, which then never leaves the genome.

34. Evolution of Viruses • Viruses don’t fit our description of living organisms • A virus is biologically inert, it cannot replicate its genes, or regenerate its own supply of ATP. • Even though viruses are obligate intracellular parasites that cant reproduce, their use of the genetic code makes it hard to deny them evolutionary connection to the living world. • How did viruses originate? • Because they depend on cells for their own propagation • viruses originate from cellular nucleic acids that could move from one cell to another. • A viral genome usually has more in common with the genome of its host, while other viral genomes have more in common with their seemingly distant related viruses. Evolution is still a great topic of debate.

35. Viruses, viroids, and prions are formidable pathogens in animal and plants • Viruses can damage or kill cells by the release of hydrolytic enzymes from lysosomes. • Some cause infected cells to produce toxins that lead to disease symptoms. • People recover from cold because the epithelium of the respiratory tract, which the virus infects, can repair itself. • The immune system is the basis for the major medical tool for preventing viral infections--vaccines

36. Vaccines are harmless variants of pathogenic microbes that stimulate the immune system to build defenses against the actual pathogen. • Vaccination has eradicated smallpox, which was once a devastating scourge in many parts of the world. • Similar worldwide vaccination campaign are currently going on to eradicate other viruses.

37. Even vaccines can’t prevent certain illnesses, once they occur, medical technology can do little. • The antibiotics are powerless against viruses. Antibiotics kill bacteria by inhibiting enzymes, yet viruses contain little or no enzymes. • Still, a few drugs combat viruses.Antiviral drugs resemble nucleosides and therefore interfere with viral nucleic acid synthesis. • Acyclovir, impedes herpes virus reproduction by inhibiting the viral polymerase that synthesizes DNA. • AZT curbs HIV by interfering with the synthesis of DNA reverse transcriptase. • “cocktails” are now effective, a combination of two nucleoside mimics and a protease inhibitor.

38. Emerging Viruses • Emerging Viruses are those that appear suddenly or come to the attention of medical scientists. • Examples are: HIV, the AIDS virus; appeared in San Francisco in the early 1980’s out of nowhere. • The Ebola virus, recognized first in 1976 in Central Africa, which caused hemorrhagic fever, often fatal. • A number of dangerous new viruses cause encephalitis (inflammation of the brain) • West Nile virus, appeared 1999 and spread to all 48 states • A more recent is the sever acute respiratory syndrome (SARS) which started in China in 2002. Between Nov. 2002, and July 2003, 8,000 people were known to be infected of which 700 died. The cause was the corona virus, a virus unknown to humans.

39. Emerging Viruses • Three processes contribute to the emergence of viral diseases: • 1st, the mutation of existing viruses is a major source of these new diseases. • RNA virus has a high rate of mutation because errors in replication their RNA are not corrected. • Mutation enable existing viruses to evolve, where the body is not immune to them anymore. • 2nd, the spread of existing viruses from one host species to another. • Example—The hantavirus • 3rd, Dissemination of a viral disease from a small, isolated population can lead to widespread epidemics. • AIDS went unnamed and unnoticed for decades before it began to spread around the world. • Technology, travel, sexual promiscuity, etc., all allowed this disease to rapidly become a global scourge. • Emerging viruses are not new, but existing viruses that mutate, spread to new host species, or disseminate widely

40. Viral Disease in Plants • There are more than 2,000 types of viral disease known for plants and they account for about $1.5 billion loss each year in agricultural and horticultural crop destruction. • Common symptoms of viral destruction are: bleached or brown spots on leaves and fruits, stunted growth, and damaged flowers or roots. • Plant viruses are basically the same as animal viruses. Most plant viruses discovered, including the tobacco mosaic virus, have an RNA genome.

41. Virus Diseases in Plants • Plant viral disease spread by two major routes; • Horizontal transmission-where a plant is infected from an external source of the virus and spreads to another plant. The plant is more susceptible to damages by wind, injury, and insects. • Vertical transmission-in which a plant inherits a viral infection from a parent. Asexual propagation or sexual reproduction. • Once a virus enters a plant cell and begins reproducing, viral components can spread throughout the plant by passing through cytoplasmic connection.

43. Viroids and Prions: The Simplest Infectious Agents. • Circular RNA molecules that infect plants, are known as viroids. • One viroid disease has killed over 10 million coconut palms in the Philippines. • Viroids do not encode proteins but can replicate in host plant cells, using cellular enzymes. These small RNA molecules cause errors in regulatory systems that control plant growth. • Prions, whichcause degenerative brain disease, include scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans. • Prions are most likely transmitted in food

44. How can a protein which cannot replicate itself, be a transmissible pathogen? • A prion is a misfolded form of a protein normally present in brain cells. • The prion converts normal protein to prion version, triggering chain reactions, eventually leading to an increase in numbers.

45. Note that all my information and data, I used from the book, Biology-seventh edition, as well as from the pictures and figures from the power points.