MORFOLOGI, KOMPONEN DAN STRUKTUR VIRUS TUMBUHAN Kuliah ke-3 MORFOLOGI, KOMPONEN DAN STRUKTUR VIRUS TUMBUHAN

Keutamaan Ilmu yang mempelajari struktur virus penting untuk memahami berbagai aspek virologi, seperti bagaimana virus bertahan hidup, menginfeksi, menyebar, bereplikasi dan bagaimana mereka berhubungan atu sama lain. Ilmu tentang struktur virus telah meningkat sejak penemuan mikroskop elektron dan prosedur X-ray crystallography seperti; Teknik molekuler Informasi kimia tentang virus

Ultrastruktur Virus Istilah pada komponen virus Kapsid: kulit luar protein yang melingkupi asam nukleat Kapsomer: unit morfologi yang dilihat dari permukaan partikel dan mewakili klaster unit struktur Virion : partikel lengkap partikel virus

Istilah pada komponen virus Amplop (envelope/viral membrane): zat lemak berlapis yang mengandung glikoprotein virus. Tidak semua virus memiliki amplop, beberapa virus hanya terdiri dari nuklekapsid. Nukleokapsid (core): asam nukleat virus yang dibungkus oleh pelindung kapsid protein

Viruses Figure 13.1

Virus Structures 1. contain DNA or RNA 2. contain a protein coat (capsid) 3. Receptor – on capsid determines what cell can be infected and how the virus infects the cell

Virus Structures Inner core nucleic acid  Contains genetic materials (DNA or RNA) Outer core nucleic acid Surrounds virus (Capsdi) Contains receptors

Structures not found on every viruses Envelope Surround some animal viruses Made from host membranes Tail, end plate, tail fibres Bacteriophage only

Struktur Virus Characteristic size scale is 30-100 nm. Structures are known at “atomic resolution” - see Viper website (http://viperdb.scripps.edu/ Highly symmetric (Baker et al.)

Organization of Viral Particles •Contains RNA or DNA •Form a protective package •Transmit genetic material •Entry, multiply and exit the host •Redirect cellular machinery Streptococcus E. coli Yeast Cell

Principles of Viral Architecture •Viral capsid are made of repated protein subunits •Capsids are self assembled •Fraenkel-Conrat and Williams (1955): self-assembly of TMV •Proteins and nucleic acids are held together with non- covalent bonds •Protein-protein, protein-nucleic acid, protein-lipid •Helical or icosahedral symmetry

General Structure of Viruses Capsids All viruses have capsids - protein coats that enclose and protect their nucleic acid. Each capsid is constructed from identical subunits called capsomers made of protein. The capsid together with the nucleic acid are nucleoscapsid.

The Viral Capsid Capsid functions Protect genome from atmosphere (May include damaging UV-light, shearing forces, nucleases either leaked or secreted by cells). Virus-attachment protein- interacts with cellular receptor to initiate infection. Delivery of genome in infectious form. May simply “dump” genome into cytoplasm (most +ssRNA viruses) or serve as the core for replication (retroviruses and rotaviruses).

Viral Capsids If 1 protein for 1 capsid: Need > 18,000 amino acids. Need > 54,000 nucleotides. Small viruses hold max. of 5,000 nucleotides. Must use many copies of 1 (or a few) protein(s). High symmetry Minimizes # different subunit interactions involved with assembly. Simpler protein. Self assembly: Self-contained assembly "instructions".

Capsid and Envelope Non-enveloped Enveloped Capsid: Envelope: Helical •Protect viral nucleic acid •Interact with the nucleic acid for packaging •Interact with vector for specific transmission •Interact with host receptors for entry to cell and to release of nucleic acid Icosahedral Enveloped Envelope: •Made from host cell membrane (plasma, ER or Golgi) •Fuse for Entry

Bentuk Virus Kira-kira ½ dari semua virus tumbuhan yang telah diketahui berbentuk memanjang (benang berputar atau batang keras). Kira-kira ½ dari semua virus tumbuhan berbentuk bola (isometris atau polyhedral). Beberapa virus berbentuk basilus silindris-menyerupai batang.

Bentuk Virus CUBIC (Icosahedral/polyhedral): Spherical, amount of nucleic acid that can be packaged is limited by the number of capsomers and the size of the viral particle E.g. Papilloma virus

Bentuk Virus HELICAL: Rod shaped, varying widths and specific architectures; no theoretical limit to the amount of nucleic acid that can be packaged

Bentuk Virus BACTERIOPHAGE Polyhedral-shape head cylindrical tail leglike fibres

Cubic (Icosahedral) Susunan Icosahedral adalah struktur virus yang khas Suatu cosahedron memiliki 20 sisi segitiga, 12 sudut, dan 5:3:2 axis simetri rotasi

Helical Organized around a single axis (the “helix axis”) Probably evolved along with other helical structures like DNA, -helix, etc. Allow flexibility (bending) Helical viruses form a closely related spring like helix instead. The best studied TMV but many animal viruses and phage use this general arrangement. – Note-all animal viruses that are helical are enveloped, unlike many of the phage and plant viruses. Most helixes are formed by a single major protein arranged with a constant relationship to each other (amplitude and pitch).

Helical symmetry Tobacco mosaic virus is typical, well-studied example Each particle contains only a single molecule of RNA (6395 nucleotide residues) and 2130 copies of the coat protein subunit (158 amino acid residues; 17.3 kilodaltons) – u=16.33 subunits/turn – p=1.4 Å – P= 23 Å TMV protein subunits + nucleic acid will self-assemble in vitro in a energy-independent fashion Self-assembly also occurs in the absence of RNA TMV rod is 18 nanometers (nm) X 300 nm n

Komposisi Virus Protein  adalah 60-95% terdiri dari virion Sama untuk setiap jenis virus tetapi bervariasi dari satu virus dgn virus lain Subunit TMV - 158 asam amino dgn massa 17,600 Dalton (17.6 kDa, kd atau K) TYMV – 20,600 Dalton protein 2. Asam nukleat  adalah 5-40% virion Sphererical viruses: 20-40% Helical viruses : 5-6%

Komposisi Virus Asam Nukleat (5-40%) mewakili bahan genetika, sangat diperlukan untuk replikasi Asam Nukleat sendiri cukup untuk replikasi virus Protein (60-95%) melindungi genom virus dari: degradasi Fasilitasi pergerakan melalui inang dan transmisi dari satu inang ke inang lainnya.

Persentase protein pada beberapa virus n/a (%) Protein (%) TMV 5 95 PVX 6 94 PVY CpMV 31-33 67-69 CMV 18 82 TRSV 40 60

Watson and Crick Pada tahun 1956 mengemukakan: Jumlah asam nukleat virus tidak cukup untuk meng-kodekan lebih dari sejumlah protein Oleh karena itu kulit luar protein harus merupakan subunit yang sama. Subunit harus disusun untuk menyediakan setiap subunit dengan lingkungan yang sama, seperti pembungkusan simetris.

Berbagai fitur virus dapat di-estimasi dengan mempelajari: 1. Kimia dan Biokimia 2. Ukuran partikel Hidrodinamika Pemancaran laser telah digunakan untuk menentukan radius virus yang berbentuk bola (spherical virus) Mikroskop elektron X-ray crystallography Dapat memberi estimasi akurat radius virus isokahedral (icosahedral virus), tapi dgn kondisi virus harus mampu membentuk kristal yang stabil.

Mikroskop Elektron Pada tahun 1924 L. de BROGLIE menemukan cahaya elektron dengan karakter panjang gelombang, yang kemudian menjadi syarat konstruksi mikroskop elektron. Ditemukan oleh M. KNOLL & E. RUSKA (Technische Universität Berlin, 1932). Salah satu objek biologi yang pertama diamati adalah : tobacco mosaic virus (TMV). Gambar sel pertama dipublikasi tahun 1945 oleh K. R. PORTER, A. CLAUDE dan E. F. FULLAM (Rockefeller Institute, New York). The Transmission Electron Microscope (TEM) The Scanning electron microscope (SEM)

The Transmission Electron Microscope (TEM) A 1973 Siemens electron microscope EM developed by E. Ruska 1933

The Transmission Electron Microscope (TEM)

Flu virus by TEM Avian Flu virus by TEM Swine Flu virus by TEM

TMV by TEM TMV by SEM

Tobacco necrosis virus, 26 nm in diameter

Type member Bromovirus genus, Bromoviridae of the family BROME MOSAIC VIRUS Type member Bromovirus genus, Bromoviridae of the family Virions are nonenveloped icosohedrals (T=3), 26 nm in diameter, contain 22% nucleic acid and 78% protein BMV genome is composed of three positive sense RNAs separately encapsidated RNA1 RNA2 RNA3 RNA4 RNA1 (3.2 kb), RNA3 (0.9 kb) kb), RNA2 (2.9 (2.1 kb), RNA4

Francki, Milne & Hatta. 1985 Atlas of Plant Viruses, vol. I. Three-dimensional image of Turnip yellow mosaic virus (TYMV) reconstructed from EM

Tobacco mosaic virus First virus crystallized (1946 Stanley was awarded the Nobel prize) First demonstration of infectious RNA (1950s) First virus to be shown to consist of RNA and protein First virus characterized by X-ray crystallography to show a helical structure First virus genome to be completely sequenced

Tobacco mosaic virus (TMV), 300 nm Potato virus Y (PVY), 740 nm

Maize streak virus, Geminiviridae Cocoa swollen shoot virus, Badnavirus