Comparative Virology as Context. Loy Volkman Professor Emerita Plant & Microbial Biology University of California, Berkeley

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1 Comparative Virology as Context Loy Volkman Professor Emerita Plant & Microbial Biology University of California, Berkeley

2 LEFT FIELD

3 Oxygen Accumulation and Evolutionary History of Life on Earth PHOTOSYNTHESIS 6 CO2 + 6 H2O + light energy > C6H12O6 +6 O2 * Albertset al., Molecular Biology of the Cell, 1994.

4 Oxygen Accumulation and Evolutionary History of Life on Earth RESPIRATION 6 O2 + C6H12O6 > yields 6 CO2 + 6 H20 + energy ( stored in ATP) * Albertset al., Molecular Biology of the Cell, 1994.

5 A Plant Cell 25 to 30 nm

6 Historical context in which we and our viruses evolved: The earth: 4.6 billion years old Microbial life: 3.7 billion years Multicellular life: billion years Sparked by the O 2 disaster Vertebrates: 0.5 billion years Insecta : 0.4 billion years Origin of primates 60 Mya: Hominid split with chimpanzee: 6-7 Mya Multiple hominid species: Mya H. sapiens: 0.2 Mya Next: Resultant eucaryotic cell

7 Transcription

8 Translation

9 Three Domains of Life on Earth (based on ribosomal RNA sequence) 276, 1997

10 Life on Earth (based on ribosomal RNA sequence) 276, 1997

11 Oxygen Accumulation and Evolutionary History of Life on Earth RESPIRATION 6 O2 + C6H12O6 > yields 6 CO2 + 6 H20 + energy ( stored in ATP) * Albertset al., Molecular Biology of the Cell, 1994.

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13 Billions 1 ex 9 Human Population Billions billion Our Time billion Renaissance

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15 Packets of nucleic acid -no way to generate energy -no way to translate mrna

16 VIRUSES

17 Translation host virus

18 SIZE MATTERS Alive Not Alive

19 SIZE MATTERS Alive Not Alive Prions&Viroids Satellite viruses

20 Relative Number of Species (based on morphology [before molecular biology]) 4,200 species per degree

21 Relative Number of Species (based on morphology [before molecular biology]) Three families of ds DNA viruses 4,200 species per degree

22 Baculovirusturns caterpillars to mush Day 0 Day 5 Day 12

23 Baculovirus Expression Vector (BEVS) Occlusions Scanning EM Transmission EM

24 Developmental Resistance (Briese, 1986)

25 Nudivirus Non-occluded, sexually transmitted among Helicoverpazeamoths Infected individuals become sterile or asymptomatic carriers. Infection usually not lethal. Productive infection limited to reproductive tissues. Infected females produce: Virus plug 5-7x more sex pheromone Mate with 2x number of males

26 Parasitoid wasp and tomato hornworm

27 Bracoviruses only produced in calyx cells of pharate and adult female wasps Calyx fluid contains bracovirus that accompanies eggs into caterpillar Considered a mutualist with its wasp host

28 Parasitoid C. congregatalarvae on M. sextalarva after emerging

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30 Insect dsdna virus phylogeny obtained from maximum likelihood and Bayesian inference analyses of thirteen orthologous genes Thézé J et al. PNAS 2011;108: by National Academy of Sciences

31 Evolutionary timeline of insect dsdna virus and their associated host species. Thézé J et al. PNAS 2011;108: by National Academy of Sciences

32 Summary of Thézé J et al. PNAS 2011;108: Analysis based on a concatenated alignment of 13 genes shared by 3 bracoviruses.mutualists of braconid wasps 4 baculoviruses lethal pathogens of caterpillars 4 nudiviruses.chronic facultative pathogens H. zea 2 hytrosaviruses (adult fly salivary gland specialists out group) Age calibrated by parasitoid wasp of microgasteroid complex in amber Baculosplit off from Nudi312Mya ~40Mya after advent of holometabolous insects. Nudi Hz2V infects adult reproductive cells Baculo specializes in oral infection of developing larvae Braco split off from Nudi 190 Myaand threw its lot in with the wasp. Did it become an organelle? A symbiont? Is there a difference?

33 ALL HAVE NEGATIVELY-SUPERCOILED GENOMES

34 Supercoiledds DNA Ds DNA with more or less turns per unit length compared to linear or circular dsdna. Ends must be constrained to capture torsional stress Positive supercoil Negative supercoil Undertwisted DNA can make open forms that bind proteins and protein complexes more easily than +SC or linear DNA Primary regulator of transcription

35 Animal Virus Families with Supercoiledds DNA Genomes SV40 (polyoma) is Best Studied

36 Nucleosomes form spontaneously on NEGATIVELY SUPERCOILED DNA

37 NEGATIVELY SUPERCOILED, NUCLEAR REPLICATING VIRUSES OF EUCARYOTES ALL HAVE TO MANAGE NUCLEOSOMES to replicate viral DNA to transcribe early & late genes

38 Four Major Classes of Nucleosome Movers (ATP-dependent chromatin remodelers) Named after the ATPases that do the work Consist of 8-15 subunits combinatorially assembled Core group of essential subunits; others switch in and out during development and differentiation Viral gene products could join and/or recruit

39 The SWI/SNF complex (BAP in insects; BAF in vertebrates) Brahma has an actin-binding domain Polymerizableactin essential subunit of of SWI/SNF Essential for development and differentiation

40 Replication of SUPERCOILED DNA requires that the progeny concatenates be separated by Topoisomerase 2.

41 Nature 624 May 30, 2013 Latrunculin (sequesters actin monomers) prevents BAF function

42 SWI/SNF Complexes Facilitate the resolution of concatenated progeny genomes of viruses with covalently-closed, circular DNA genomes. May account for the exquisite cellular & developmental specificity of papillomaviruses

43 Summary The major form of life on earth is and always has been microbial. Homo sapiens are derivatives of microbes. Size matters when it comes to life. Viruses are nucleic acids with housing. Genomic structure, as well as sequence, may play an important role in viral activities.

44 Thank you for your attention