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Lecture 11 (5 1-2018) acellular life

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Unit 11: Viruses and Prions
LECTURE LEARNING GOALS
1. Define what is a virus, and describe a few examples. Contrast two methods for classifying viruses, and explain the drawbacks for each method.
2. Describe prions, how they function as infectious agents, and what diseases they cause.
3. Describe subviral agents, and name a few examples.

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Lecture 11 (5 1-2018) acellular life

  1. 1. VIRUSES AND PRIONS Unit 11, 5.1.2018 Reading for today: Brown Ch. 7 Review Session: Mon May 7, 2018, 11:30 am – 1:00 pm, LSL N610 Final Exam Wed May 9, 2018, 10:30 am – 12:30 pm, 222 Morrill 2 1 Dr. Kristen DeAngelis Life Science Labs (LSL) N435 Office Hours Tu & Th 12:30 to 1:30 pm OR by appointment (RSVP appreciated) deangelis@microbio.umass.edu, 413-577-4669
  2. 2. Unit 11: Viruses and Prions LECTURE LEARNING GOALS 1.  Define what is a virus, and describe a few examples. Contrast two methods for classifying viruses, and explain the drawbacks for each method. 2.  Describe prions, how they function as infectious agents, and what diseases they cause. 3.  Describe subviral agents, and name a few examples. 2
  3. 3. Unit 11: Viruses and Prions LECTURE LEARNING GOALS 1.  Define what is a virus, and describe a few examples. Contrast two methods for classifying viruses, and explain the drawbacks for each method. 2.  Describe prions, how they function as infectious agents, and what diseases they cause. 3.  Describe subviral agents, and name a few examples. 3
  4. 4. Virus •  Segments of DNA or RNA encapsulated by a protein and/or membrane •  To reproduce, it needs to infect a cellular host, merge with its cytoplasm or nucleoplasm, and use the host’s cellular machinery for replication •  Cells from all three domains of life are susceptible to viral infections 4 Fig  17.1.  E.  coli  being  infected  by  bacteriophage  lambda    
  5. 5. Viral diversity •  Enormous range in size and complexity –  Genome size can range from hundreds to millions of base pairs •  Classification is challenging because most viruses lack ribosomes –  Any shared genes can be used to generate a phylogeny –  If they are conserved evolutionarily, this tree makes a plausible model for evolutionary history –  Because viruses are agents of horizontal gene transfer, this is a risky assumption! •  Two methods –  Evolutionary classification •  Introduced in Microbiology of Early Earth –  Physiological classification •  “the Baltimore method” 5
  6. 6. Hypotheses on the origin of viruses •  virus-first hypothesis •  progressive hypothesis •  regressive hypothesis 6
  7. 7. Hypotheses on the origin of viruses •  virus-first hypothesis –  Perhaps simple replicating RNA molecules, existing before the first cell formed, developed the ability to infect the first cells. –  E.g., single-stranded RNA viruses •  progressive hypothesis –  Viruses arose from genetic elements that gained the ability to move between cells –  E.g., Retroviruses like HIV •  regressive hypothesis –  Viruses are remnants of more complex cellular organisms –  Mimiviruses are dsDNA viruses with genomes as large as some bacteria, and can live independent of hosts –  May be evidence of life forms after the protocell and before LUCA 7
  8. 8. Virus-first hypothesis on the origin of viruses •  viruses predate or coevolved with their current cellular hosts, consistent with the RNA World idea •  Remnants of pre-cellular life •  ssRNA viruses •  Rhinovirus (at right) –  the common cold –  ssRNA virus –  no DNA stage –  Capsid protein coat 8
  9. 9. Rice yellow mottle virus-associated viroid •  ssRNA •  Directs its own replication without DNA intermediate •  Performs some replication-associated functions – Self-cleavage – ligation 9Brown  Figure  17.6  
  10. 10. RNA-S replication •  Example from tobacco ringspot virus •  Protein-free replication of RNA-only genome! 10 Brown  Figure  17.7  
  11. 11. Progressive hypothesis on the origin of viruses •  viruses arose from genetic elements that gained the ability to move between cells •  HIV •  Bacteriophage Mu –  Essentially a transmissible out-of- control transposon 11
  12. 12. Transposons •  Mobile genetic elements (DNA) •  Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms •  Retrovirus is an ssRNA virus with a DNA intermediate, made with its own reverse transcriptase inside the host •  Supports the progressive hypothesis 12
  13. 13. HIV 13
  14. 14. Human Immunodeficiency Virus (HIV) •  ssRNA genome •  Double-stranded DNA form can act as a retrotransposon •  act like retrotransposons, mobile genetic elements that make up 42% of the human genome & can move within the genome via an RNA intermediate 14
  15. 15. Bacteriophage •  Plasmids are secondary chromosomes •  Bacteriophage M13 has an infective transfer like conjugative transfer of the F plasmid, but does not require cell-cell contact 15Brown  Figure  17.2   Brown  Figure  17.3   Brown  Figure  17.4  
  16. 16. Viruses as genetic offshoots of their hosts •  Plasmids are secondary chromosomes, differing from chromosomes in that they usually only house non-essential genes •  Many plasmids can transfer by conjugation, which requires direct contact between cells •  Some plasmids are transferred via encapsidated intermediate, and include genes that encode for capsid proteins and replication 16
  17. 17. Regressive hypothesis on the origin of viruses •  viruses are remnants of more complex cellular organisms •  Originally cellular parasites that degenerated –  E.g., mimivirus-infected amoeba (right) –  Similar to the obligate intracellular bacteria Bdellovibrio, Chlamydia, or Rickettsia •  May be evidence of life forms after the protocell and before LUCA 17 Brown  Figure  17.9  
  18. 18. Mimivirus •  dsDNA virus •  1.2 million base (Mb) genome –  As big as bacteria! •  Can live independent of hosts •  Klosneuvirus is another example of the regressive hypothesis… 18 Brown  Figure  17.8  
  19. 19. Klosneuviruses •  a fourth domain of viruses? •  Phylogenetic analysis supports origins of this group with the escape hypothesis 19
  20. 20. Genome architecture and gene content of the Klosneuviruses Schulz  et  al.  2017   20
  21. 21. •  The left panel illustrates genome bins of the Klosneuviruses. •  From outside to inside: In the first ring, solid circles indicate genes exclusively shared with nucleocytoplasmic large DNA viruses (NCLDVs) (blue), genes specific for Klosneuviruses ( ), genes shared with eukaryotes (red), genes shared with Bacteria (green), genes represented in all three domains of cellular life (yellow), and singletons (gray). •  The second ring displays positions of genes (gray) either on the minus or the plus strand. •  The next track depicts GC content in shades of gray ranging from 20% ( ) to 50% (dark gray). Links connect paralogs (gray) and nearly identical repeats (orange). Genome architecture and gene content of the Klosneuviruses 21
  22. 22. Virus phylogeny •  Based on core nucleocytoplasmic virus orthologous genes (NCVOGs) –  There are dozens to hundreds of NCVOGs, depending on the group of organisms you choose to analyze –  Mostly useful for large, dsDNA viruses 22 Schultz  et  al.  Science  2017.  Transmission  electron  microscopy  image  of  a  candidate   Klosneuvirus  parGcle  detected  in  the  Klosterneuburg  waste  water  treatment  plant  biomass.   Bar  is  50  nm  
  23. 23. Virus taxonomy 23 •  The Baltimore Classification of viruses is based on the method of viral mRNA synthesis (Wikipedia)
  24. 24. Virus taxonomy 24 •  The Baltimore Classification, Wikipedia By  Sara  Confalonieri  -­‐  Own  work,  CC  BY-­‐SA  3.0,  hPps://commons.wikimedia.org/w/index.php? curid=32198313  
  25. 25. Activity for Review of

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