40 (SV40), human adenovirus type...Figure 7.16 Organization and regulation of the Epstein-Barr virus Zta gene promo...Figure 7.17 Models for transcriptional activation by the herpes simplex virus ty...Figure 7.18 Conformational changes and recruitment of VP16 to herpes simplex vir...Figure 7.19 The adenoviral E1A proteins bind to multiple transcriptional regulat...Figure 7.20 Indirect stimulation of transcription by adenoviral E1A proteins. Figure 7.21 Cellular repressors regulate the activity of the simian virus 40 lat...Figure 7.22 The latency-associated transcripts of herpes simplex virus type 1. ...Figure 7.23 Organization of viral RNA polymerase III promoters. (A) The human ...Figure 7.24 Assembly of an initiation complex on a vaccinia virus early promoter...8 Chapter 8Figure 8.1 Processing of a viral or cellular pre-mRNA synthesized by RNA polymer...Figure 8.2 The 5′ cap structure and its synthesis by cellular or viral enzymes. ...Figure 8.3 A viral unimolecular assembly line for capping. The structure of th...Figure 8.4 Cleavage and polyadenylation of vertebrate pre-mRNAs. The 3′ end of...Figure 8.5 The vaccinia virus capping enzyme and 2′-O-methyltransferase process ...Figure 8.6 Reversible N6 methylation of internal adenosine nucleosides. Intern...Figure 8.7 Inhibition of assembly and release of virus particles by N6 A methyla...Figure 8.8 Splicing of pre-mRNA. (A) Consensus splicing signals in cellular an...Figure 8.9 The conserved mechanism of eukaryotic pre-mRNA splicing. (A) Pathwa...Figure 8.10 Constitutive and alternative splicing. (A) In constitutive splicin...Figure 8.11 Alternative polyadenylation and splicing control the production of b...Figure 8.12 Control of RNA-processing reactions during retroviral gene expressio...Figure 8.13 Alternative polyadenylation and splicing of adenoviral major late tr...Figure 8.14 Cotranscriptional editing of measles virus mRNAs. (A) Proposed mec...Figure 8.15 Editing of hepatitis delta virus RNA by double-stranded RNA adenosin...Figure 8.16 Regulation of export of human immunodeficiency virus type 1 mRNAs by...Figure 8.17 Features and mechanism of Rev protein-dependent export. (A) The fu...Figure 8.18 Export of unspliced RNA of retroviruses with simple genomes and cell...Figure 8.19 Regulation of alternative splicing of viral pre-mRNA. (A) The poly...Figure 8.20 Inhibition of cellular pre-mRNA processing by viral proteins. The ...Figure 8.21 Mechanisms of intrinsic cellular and viral mRNA decay. A major pat...Figure 8.22 Viral proteins initiate mRNA degradation by different mechanisms. ...Figure 8.23 Major pathways of nonsense-mediated mRNA degradation. Nonsense-med...Figure 8.24 Synthesis and function of miRNAs. The precursors of miRNAs (pri-mi...Figure 8.25 The miRNAs of simian virus 40. The circular simian virus 40 genome...Figure 8.26 Cellular lncRNAs that facilitate or impair virus reproduction. Cel...
9 Chapter 9Figure 9.1 Viral and cellular proteins that synthesize viral DNA genomes. The ...Figure 9.2 Properties of replicons. (A) Electron micrographs of replicating si...Figure 9.3 Semidiscontinuous DNA synthesis from a bidirectional origin. Synthe...Figure 9.4 The 5′-end problem in replication of linear DNAs. (A) Incomplete sy...Figure 9.5 The origin of simian virus 40 DNA replication. The positions in the...Figure 9.6 Model of the recognition and unwinding of the simian virus 40 origin....Figure 9.7 Synthesis of leading and lagging strands. The DNA polymerase (POL) ...Figure 9.8 A model of the simian virus 40 replication machine. A replication m...Figure 9.9 Function of topoisomerases during simian virus 40 DNA replication. ...Figure 9.10 Replication of parvoviral DNA. (A) Sequence and secondary structur...Figure 9.11 Replication of adenoviral DNA. Assembly of the viral preterminal p...Figure 9.12 Features of the herpes simplex virus type 1 genome. The long (L) a...Figure 9.13 Common features of viral origins of DNA replication. The simian vi...Figure 9.14 Functional organization of simian virus 40 LT. The domains of LT a...Figure 9.15 Structural homology among DNA-binding domains of viral origin recogn...Figure 9.16 Model of origin loading of the papillomaviral E1 initiation protein ...Figure 9.17 Crystal structure of the adenoviral single-stranded-DNA-binding prot...Figure 9.18 Regulation of production of cellular and viral replication proteins....Figure 9.19 Discrete sites of viral replication. (A) Cytoplasmic vaccinia viru...Figure 9.20 Reorganization of PML bodies by the adenoviral E4 Orf3 protein. Mo...Figure 9.21 Common features of the adenovirus-associated virus type 2 lTR and th...Figure 9.22 Licensing of replication from Epstein-Barr virus OriP. (A) Organiz...Figure 9.23 Regulation of papillomaviral DNA replication in epithelial cells. ...Figure 9.24 Proofreading during synthesis. If permanently fixed into the genom...Figure 9.25 The DNA damage response. Damage to the DNA genome, such as a doubl...Figure 9.26 Association of cellular DNA damage response proteins with herpesvira...Figure 9.27 General model for initiation of recombination-dependent replication....Figure 9.28 Isomers of the herpes simplex virus type 1 genome. The organizatio...
10 Chapter 10Figure 10.1 Human immunodeficiency type 1 capsid hexamers showing open and close...Figure 10.2 The diploid retroviral genome and a dimerization domain. (A) The d...Figure 10.3 Primer tRNA binding to a retroviral RNA genome. (Top) Linear repre...Figure 10.4 Retroviral reverse transcription: initiation of (–) strand DNA synth...Figure 10.5 Retroviral reverse transcription: first template exchange, mediated ...Figure 10.6 Retroviral reverse transcription: (+) strand DNA synthesis primed fr...Figure 10.7 Retroviral reverse transcription: the second template exchange and f...Figure 10.8 Two models for recombination during reverse transcription. Virtual...Figure 10.9 Domain and subunit relationships of the RTs of different retroviruse...Figure 10.10 Ribbon representation of HIV-1 RT bound to a model RNA template-DNA...Figure 10.11 Model for a DNA-RNA hybrid bound to HIV-1 RT. The RNA template-DN...Figure 10.12 Evolutionary relatedness of RT-like enzymes in bacteria, archaea, e...Figure 10.13 Retroelements resident in eukaryotic genomes and their representati...Figure 10.14 Comparison of the structures of two RTs. (A) The DNA polymerase d...Figure 10.15 Characteristic features of retroviral integration. Unintegrated l...Figure 10.16 Three steps in the retroviral DNA integration process. Endonucleo...Figure 10.17 Sequence preferences of integration sites. The figure shows the 5...Figure 10.18 Models for chromatin tethering of retroviral preintegration complex...Figure 10.19 Host proteins affect the integration process. The abundant host b...Figure 10.20 Domain maps of integrase proteins from different retroviral genera,...Figure 10.21 Crystal structure of the prototype foamy virus integrase tetramer b...Figure 10.22 Arrangement of HIV-1 IN dimer interfaces in the absence of DNA and ...Figure 10.23 Hepadnaviral DNA. The DNA in extracellular hepadnavirus particles...Figure 10.24 Single-cell reproduction cycle for hepadnaviruses. Pathway 1 prov...Figure 10.25 Essential cis-acting signals in pregenomic mRNA. The viral pregen...Figure 10.26 Comparison of hepadnaviral and retroviral RTs. Linear maps of the...Figure 10.27 Model for the assembly of hepadnavirus nucleocapsids. P protein i...Figure 10.28 Critical steps in the pathway of hepadnavirus reverse transcription...Figure 10.29 Model for (+) strand priming. Formation of a hairpin in the (–) s...Figure 10.30 Comparison of the genome replication cycles of cauliflower mosaic v...
11 Chapter 11Figure 11.1 Structure of eukaryotic and bacterial/archaeal mRNAs. UTR, untrans...Figure 11.2 Ribosomes and tRNAs. (A) Model of a eukaryotic ribosome. The 80S r...Figure 11.3 5′-cap-dependent assembly of the initiation complex. Initiation pr...Figure 11.4 5′ -end-dependent initiation. (A) Schematic of eIF4G protein. Data...Figure 11.5 Two mechanisms of methionine-independent initiation. (A) A sequenc...Figure 11.6 Hypothetical model of ribosome shunting. The 40S ribosomal subunit...Figure 11.7 Six types of IRES. The 5′ untranslated regions from genome RNAs of...Figure 11.8 5′-end-independent initiation. (Top) Initiation on the type 1 or 2...Figure 11.9 Long-range RNA-RNA interactions aid translation. (A) Activity of t...Figure 11.10 Translation elongation. There are three tRNA-binding sites on the...Figure 11.11 Translation termination. (A) Overview of termination. When a term...Figure 11.12 Ribosome recycling. After peptide release, ABCE1 binds to eRF1 on...Figure 11.13 Juxtaposition of mRNA ends. Shown is a juxtaposition of mRNA ends...Figure 11.14 The diversity of viral translation strategies. Figure 11.15 Polyprotein processing of picornaviruses and flaviviruses. (A) Pr...Figure 11.16 Leaky scanning in the Sendai virus P/C gene. P and C protein open...Figure 11.17 Reinitiation of translation. (A) (Top) Some mRNAs contain one or ...Figure 11.18 Proposed mechanism of StopGo translation. A model for the site-sp...Figure 11.19 Suppression of termination codons of retroviruses and alphaviruses....Figure 11.20 Frameshifting
