(RNA-) Structuredness in Viruses ... Viruses I Minimal Life Forms Obligate intracellular parasites...

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  • (RNA-) Structuredness in Viruses

    Roman Ochsenreiter

    TBI Wien University of Vienna

    16.2.2017 / TBI Winterseminar

    Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viruses I Minimal Life Forms

    Obligate intracellular parasites

    No organelles

    (Very) small size

    DNA/RNA genomes

    Electron micrograph of an Ebola Virion, size: 1000 nm (image source: wikipedia)

    Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viruses II Minimal Life Forms

    Figure: Crystal Structure and Schematic of Rhinovirus A 1

    Genome size (nt): Human: 3.2 × 109 Rhinovirus: 7 × 103

    1Zhao et al. 1996 Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viruses and RNA Structure

    Viruses have tightly packed genomes Specific Functions are often provided by RNA Structures

    Figure: Pestivirus IRES1, Rhinovirus CRE-Element

    1Rfam IDs: RF00209, RF00220 Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viral Diversity Baltimore Classification

    Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viral Diversity Baltimore Classification

    Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viral Diversity Viral Phylogeny

    1957. 79 Kokober a_vi r us 3165. 21 Banzi _vi r us_st r ai n_SAH_336_pol ypr ot ei n_gene 3106. 79 Edge_Hi l l _vi r us_st r ai n_YMP_48_pol ypr ot ei n_gene

    645. 80

    913. 37 Wessel sbr on_vi r us 952. 63 Sepi k_vi r us

    2326. 73

    3252. 77 Yel l ow_f ever _vi r us 303. 82

    753. 11

    1588. 25 Sokol uk_vi r us_st r ai n_LEI V- 400K 1624. 75 Ent ebbe_bat _vi r us

    1044. 84

    2686. 66 Yokose_vi r us 2225. 58

    226. 98

    4589. 77 Par ai so_Escondi do_vi r us_i sol at e_Ecuador 2012

    431. 84

    2329. 70 Par r amat t a_Ri ver _vi r us_i sol at e_92- B115745 2296. 30 Hanko_vi r us_pol ypr ot ei n_gene

    3246. 44

    2703. 05 Aedes_f l avi vi r us_genomi c_RNA 2650. 95 Kami t i _Ri ver _vi r us

    2955. 81 619. 84

    6323. 23 Mer cadeo_vi r us_i sol at e_ER- M10 599. 73 Quang_Bi nh_vi r us 593. 27 Mosqui t o_f l avi vi r us_i sol at e_LSFl avi V- A20- 09

    2128. 45

    2700. 05 Cul ex_f l avi vi r us 3303. 02

    501. 91

    2744. 36

    11426. 33 Tamana_bat _vi r us

    2278. 26

    325. 03Spani sh_goat _encephal i t i s_vi r us_i sol at e_Ast Goat I REC2011 445. 97 Loupi ng_i l l _vi r us

    90. 87

    411. 63 Ti ck- bor ne_encephal i t i s_vi r us 381. 34

    795. 91 Omsk_hemor r hagi c_f ever _vi r us 448. 57

    1274. 93 Langat _vi r us

    435. 04

    1681. 96 Al khur ma_vi r us

    263. 67

    1951. 24 Powassan_vi r us

    489. 77

    2494. 68 Kar shi _vi r us

    1599. 66

    2148. 99 Kama_vi r us_st r ai n_LEI V- 20776Tat _pol ypr ot ei n_gene 2085. 01 Tyul eni y_vi r us_st r ai n_LEI V- 6C_pol ypr ot ei n_gene

    1812. 66

    1237. 18

    2929. 92 J ut i apa_vi r us_st r ai n_J G- 128 2982. 08 Modoc_vi r us

    859. 26

    3670. 74 Ri o_Br avo_vi r us 433. 36

    4304. 39 Apoi _vi r us 1962. 39

    472. 20

    709. 24

    652. 03

    2786. 86 Chaoyang_vi r us 2778. 14 Donggang_vi r us

    1763. 85

    633. 00

    451. 44 West _Ni l e_vi r us_l i neage_1 465. 56 West _Ni l e_vi r us_l i neage_2

    1381. 70

    1314. 02 Mur r ay_Val l ey_encephal i t i s_vi r us 1354. 46 J apanese_encephal i t i s_vi r us 1311. 54 Usut u_vi r us 34. 98

    499. 30 422. 01

    2331. 87 Caci pacor e_vi r us_st r ai n_BeAn_3276000

    529. 11

    2575. 20 St . _Loui s_encephal i t i s_vi r us

    174. 44

    854. 63 Bagaza_vi r us 783. 37 Nt aya_vi r us_i sol at e_I PDI A

    603. 37

    1423. 13 Tembusu_vi r us_st r ai n_J S804 1563. 28

    3020. 28 I l heus_vi r us

    1004. 46

    41. 57

    2519. 16 Dengue_vi r us_4 2253. 04 Dengue_vi r us_2

    1686. 38 Dengue_vi r us_1 1693. 62 Dengue_vi r us_3

    594. 96 328. 09

    2010. 88

    150. 08

    2001. 12 Spondweni _vi r us 2055. 88 Zi ka_vi r us

    1381. 72

    3926. 61 Kedougou_vi r us

    276. 39

    3689. 41 Bussuquar a_vi r us

    1957. 79 Spondveni (Zika) Virus Dengue Virus

    West Nile Virus / Japan Encephalitis Virus

    Tick-borne Flaviviruses

    Mosquito- borne FVs

    Yellow Fever Virus

    Figure: Picorna-like Viruses (left)1, Flavivirus (right

    1Fauquet, Schrock; 2006 Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Viral Diversity Viral Phylogeny

    Phylogenetic Tree of Viruses

    Grüne Filamentöse

    BakterienSpirochäten Gram-

    positive Proteobakterien

    Cyanobakterien

    Planctomyceten

    Bacteroides Cytophaga

    Thermotogae

    Aquifex

    Halophile Methanosarcina

    Methanobacterium Methanococcus

    T. celer Thermoproteus

    Pyrodicticum

    Entamoebae Schleim-pilze TierePilze

    Pflanzen

    Wimperntierchen

    Flagellaten

    Trichomonaden

    Microsporidien

    Diplomonaden

    Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Virus Ortholog Groups

    Viral Clusters of Ortholog Groups

    Groups of Ortholog proteins Calculated on Protein alignments Based on newest RefSeq Virus Genomes Includes all annotated viral species

    Roman Ochsenreiter (RNA-)Structuredness in Viruses

  • Virus Ortholog Groups

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