Viral Hepatitis - part 3 pps

Chapter 10168 don. A purine at the +4 and/or –3 position is usually found in initiation codons, but not in internal codons for methionine. 251 Additionally, a stem-loop structure on the RNA, about 30 bases downstream of the start codon, can enhance the start of protein synthesis. 252 Synthesis stops at one of the three possible stop codons UAA, UAG or UGA, which occurs fi rst in this particular ORF. Thus, the position of the 5′ ends of the mRNAs in the HBV genome determines which gene product is expressed. Exceptions to this rule are internal ribosome entry sites (IRES), leaky scanning for start codons, usage of atypical start codons, read-through of stop codons, frame shifting and re- initiation. Some of these exceptions may apply to the translation of certain HBV proteins. An important early step in protein biosynthesis is the distribution of the protein synthetic complex between the cytosol and the ER. Nascent protein chains that contain a hydrophobic α-helical stretch of 16–20 amino acids bind to a signal recognition particle that attaches the ribosome to a pore-like structure at the ER. The growing peptide is transported through this pore to the lumen of the ER. The particular structure and number of such hydrophobic signal sequences determine the intracellular distribution, membrane topology or secretion of the protein. Proteins without signal sequence are synthesized by free ribosomes and released after completion to the cytosol. Enveloped viruses with subgenomic mRNAs such as HBV normally use free ribosomes for synthesis of their nucleocapsid proteins, and ER-bound ribosomes for synthesis of the enveloped protein (Fig. 10.5). HBe protein The HBe protein is translated from the longest mRNA. As mentioned above, this RNA differs from the pregenomic mRNA in that it comprises an additional start codon at its 5’ end. The translation initiation at this precore start suppresses the use of downstream-located AUGs. 253 This includes the core start codon that is ‘in frame’ with the precore AUG. In consequence, the primary translation product comprises a 29 amino acid signal sequence amino-terminally of the core protein. The precore targets this 25-kDa protein to the ER lumen where a cellular signal peptidase at the ER lumen removes the fi rst 19 amino acids of the precore region. 125 The remaining 10 amino acids of the precore cause a folding different to that of the core protein, allowing dimerization but no further assembly of these dimers to capsids. Further proteolytic processing of the HBe-protein probably occurs in the trans-Golgi apparatus. 126 This cellular compartment contains proteases that cleave within the arginine-rich carboxy-terminal domain of the HBe protein so that the processed protein has a molecular weight of only 15 kDa. However, as the signal peptide of HBe protein is not particularly strong, a signifi cant part of the HBe protein remains cytoplasmic. 127 The amount of synthesized HBe protein relative to other HBV proteins is probably regulated by the level of mRNA containing the start codon of an un- interrupted HBe gene. Many patients have HBV variants where little or no HBe mRNA is made because of mutations in enhancer II or the HBc/e promoter. Even more frequent are variants with a stop codon in the pre-C sequence (see Chapter 11). HBc protein The start codon of HBc protein has two guanosines at position –3 and +4, which is a relatively good but not optimal context for initiation because it is localized within the stem of the encapsidation signal ε. Neverthe- less, a highly effi cient translation of the HBc mRNA is necessary, because at a critical level of HBc protein and polymerase protein, this mRNA is encapsidated into core particles and is no longer available for protein synthesis. 140 The overlapping use of this mRNA could suggest that core and polymerase are translated from the same RNA species but from different RNA molecules. However, recent data showed cis-preferential recruit- ment of duck hepatitis B virus core protein to the RNA/ polymerase preassembly complex. 254 Polymerase An intensive search for an mRNA containing a 5′ end slightly upstream of the presumed amino end of the polymerase sequence was not successful, although a very low abundant mRNA for polymerase cannot strictly be excluded. Most members of the orthoret- roviridae express their polymerase via a frame shift between the ORFs of gag (i.e. the analogue of HBc protein) and pol, thus generating a gag-pol fusion protein. Mutational analysis excluded this possibil- ity for HBV. Instead, an unusual internal initiation of the pol protein synthesis at the HBc mRNA is implied. This would generate a full-length non-fused HBV polymerase by translation initiation. 132,255 A leaky scanning mechanism appears possible, because an optimal start codon of ORF C seems to reduce the effi - ciency of pol expression. 256 There are, however, several initiation codons upstream in the HBc mRNA, which should be even stronger. The existence of a weak IRES in proximity to the pol start codon would be another obvious explanation. 257 Ideally, the relative frequency of initiation at the HBc or pol start should regulate the required proportion of HBc to pol protein, which is probably 240:1. However, recent analysis revealed that the polymerase is relatively overexpressed and 1405130059_4_010.indd 1681405130059_4_010.indd 168 01/04/2005 11:57:2701/04/2005 11:57:27 Structure and molecular virology 169 that the majority of hepatitis B virus reverse transcriptase in cells is non-encapsidated but is bound to a cytoplasmic structure, 258 as was determined for DHBV. Polymerase was translated at a rate of 10% compared to core, whereas the half-life of non-encapsidated polymerase was very short, indicating that the translation rate of the polymerase is not limiting for encapsidation. 259 The inability of the polymerase to act on exogenous substrates lacking epsilon prevents massive interference with host RNAs. 135,260 LHBs Initiation of LHBs protein synthesis follows the usual rules. 261 It occurs initially in the cytosol because the pre-S domains do not contain an ER translocation signal peptide. The signal peptides I and II of the S domain insert into the ER membrane, but the entire pre-S domain is too long to be translocated to the ER lumen during protein synthesis 86 and interacts with cytosolic factors. In agreement with this conclusion is the absence of glycoside in the pre-S2 domain of LHBs. The amino-terminal methionine is substituted by myristic acid. The central hydrophilic part of the S domain, however, is in the lumen of the ER and more effi ciently glycosylated than the S domain of MHBs or SHBs. 262 The mRNA for LHBs is not translated into MHBs or SHBs. 261,263 MHBs and SHBs These two gene products are usually co-expressed because of the common promoter for their mRNAs. It is not clear which factors control the relative ratio between the mRNAs containing a start for MHBs or only for SHBs. Irrespective of this transcriptional regulation, the ratio between MHBs and SHBs is also regulated at the translational level. The start codon of MHBs does not have the optimal fl anking bases, whereas that of SHBs is optimal for initiation of protein synthesis. Thus, mR- NAs for MHBs also always express some SHBs unless the start codon of SHBs has been mutated. Signal I of the S domain is obviously able to trans- locate the pre-S2 domain of MHBs to the ER lumen, because most of the MHBs is glycosylated in secreted HBs particles. 264 However, the folding of the nascent S domains seems to be slightly different in MHBs and SHBs, because the S domain is only rarely glycosylated in MHBs. 262 Truncation of MHBs at the predicted transmembrane helix III leads to a topology where pre-S2 is not translocated to the ER lumen. 238 HBx Translation of HBx protein(s) may occur also from mR- NAs that contain or do not contain the fi rst start codon of ORF X, 213 but the size of naturally occurring HBx proteins has not yet been reliably elucidated. Sequence predictions suggest that it is a cytosolic protein. Overex- pression of HBx protein using vaccinia vectors suggests that it is a very labile phosphoprotein within the cell, with a half-life of 20 minutes. 155 The high insolubility of HBx protein suggests that it oligomerizes rapidly or binds to other cellular proteins. Assembly of HBV General strategy of genome maturation The actual multiplication of the HBV genome occurs in the nucleus of the infected cell by the cellular RNA polymerase II, which transcribes the circular HBV DNA to more than genome-length mRNA with redundant ends (see Plate 10.1b, found between p.786–7). All gene products of HBV (probably with the exception of HBx protein) are used to encapsidate that RNA, transcribe it to a circular DNA, and secrete it as an enveloped virion with attachment sites for new target cells. An overview is shown in Fig. 10.8. Encapsidation of pregenomic RNA After translation of suffi cient amounts of HBc and polymerase proteins, these proteins assemble together with their mRNA, and cellular proteins, including the heat shock protein Hsp90, the co chaperone p23, and additional, as yet unknown, factors. 143–147 Core particle formation includes the encapsidation of a cellular protein kinase, the identity of which is controversially dis- cussed. Encapsidation occurs only when the polymerase interacts with a specifi c RNA sequence present at the 5′ end (base 1846 to base 1907) of the HBc mRNA. 141 This signal is termed ε (for encapsidation) and acts predomi- nantly in cis to the polymerase. ε is characterized by a secondary structure consisting of a stem, a bulge, a loop and a non-paired U (see also Fig. 10.9), 265–267 but binding of the polymerase alters the structure of ε 268 and binding to ε is required for activation of the polymerase. 260 How- ever, fusions of ε to heterologous RNAs failed to cause encapsidation. This observation initiated a search for additional sequences required for packaging. Indeed, a second region – termed ε II that is 900 nucleotides 3’ of ε I – was found to be essential at least in avian hepadnaviruses. 269 In addition, this observation may explain why only the pregenomic RNA is encapsidated, although the signal sequence ε is present on the 3’ ends of all hepadnaviral RNAs. Initiation of reverse transcription In HBV-expressing cells genome maturation (e.g. re- 1405130059_4_010.indd 1691405130059_4_010.indd 169 01/04/2005 11:57:2701/04/2005 11:57:27 Chapter 10170 verse transcription to minus-strand DNA and plus- strand DNA synthesis) is a tightly coupled event and seems to occur exclusively within the core particles. However, expression of an active DHBV polymerase in a cell-free system showed that in these systems the fi rst steps of DNA synthesis may occur in the absence of core protein. Using this system, it could be shown that minus-strand DNA synthesis starts in the bulge of the ε-signal. In contrast to that of retroviruses, hepadnavirus replication is initiated de novo, i.e. without a nucleic acid primer. Instead, the –OH group of a tyrosine in the amino-terminal domain of the polymerase (Tyr 96 in DHBV, 270 Tyr 63 in HBV 41 ) is used for formation of a phosphodiester linkage to the fi rst nucleotide. Due to this mode of initiation, the polymerase becomes and remains covalently linked to the DNA minus-strand. Elongation of DNA minus-strand After synthesis of the fi rst four nucleotides within the bulge (DHBV), the polymerase together with its covalently bound nucleotides dissociates from its template and re-anneals with a complementary sequence in the DR1 close to the 3′ end, which was previously named signal for reverse transcription (see Plate 10.1b [found between p. 786–7] and Fig. 10.8). Experiments on the expression of the HBV polymerase confi rmed this initiation model for the human hepatitis B virus, 271 although the homology between the bulge and DR1 in all human HBV genomes is restricted to three nucleotides. Because there are many sequences complementary to the three or four initial bases of the minus-DNA strand within the hepadnavirus genome, an additional process must be involved in correct transfer of the polymerase nucleotide complex. Using mutagenesis analysis, a sequence element designated phi located upstream of the 3’ DR1 sequence was identifi ed that is complementary to ε and is important for effi cient viral replication. It was hypoth- esized that this element brings the 3' DR1 sequence into proximity with the three nucleotide primer synthesized at the bulge of ε. 272 Minus-strand DNA synthesis continues after priming and translocation to the 3′ terminal DR1 of the pregenomic RNA. From mapping the 3′ end of the minus-DNA strand, it appears that this strand nearly coincides with the 5′ end of the pregenomic RNA. Thus, the 3′ end of the minus-DNA strand is specifi ed by ‘run off’, when the polymerase reaches the end of its RNA template, resulting in a terminal redundancy of the minus-DNA strand of 8–10 nucleotides. RNase H and priming of the DNA plus-strand All reverse transcriptases are associated with an RNase H activity, which cleaves the RNA of RNA–DNA hy- brids into oligoribonucleotides. Mutational inactivation of the RNase H domain in the HBV polymerase results in a block of DNA plus-strand strand synthesis. 273 How- ever, the RNase H domain of HBV polymerase is not able to cleave the last RNA nucleotides, bound to minus-strand DNA. Thus, an 18-base-long capped RNA fragment from the 5′ end of the pregenome is generated. This fragment dissociates by unknown reasons from its 5′ terminal DR1 in the DNA minus-strand and is translocated to DR2. Here, it functions as a primer for the DNA plus-strand. The DNA begins with the last base of DR2 274,275 and continues towards the 5’ end on the minus DNA strand. Here, the plus-DNA strand synthesis crosses the discontinuity at the 3′ and 5′ ends of the minus-DNA strand leading to a circular DNA genome. Obviously, the specifi c primer translocation and the circularization processes are complex. In addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M and 5E, contribute to both processes. By disrupting base-pairing between 3E and M3, and between 5E and M5, evidence was obtained that the ends of the minus-strand template are juxtaposed G G G G G G C C C C GU UU U U U U U U U U U U U U U U U U U U U A A A A A A A A A C C C C C C C G G G G G G G U – – – – – – – – – – – – – – – – – – — — — 2589 2605 2568 > > > > (a) G G G G G G C C C C GU U U U U U U U U U U U U U U U U U U U U U A A A A A A A A A C C C C C C C G G G G G G G U – – – – – – – – – – – 2589 2605 2568 > > (b) Tyr 96 O dA dA dT dG Figure 10.8 Structure of the DHBV ε as the free form (a) and after binding of the polymerase (b) (modifi ed from Beck and Nassal 268 ). Sites of ε interacting with the polymerase are shown as grey shadows. The priming of the DHBV DNA minus-strand starts within the bulge region in the 5′ terminal ε. Priming is initiated by covalent linkage of the fi rst nucleotide with Tyr96 of the DHBV polymerase. After synthesis of the fi rst four deoxynucleotides, the polymerase- oligonucleotide complex switches to DR1 (see Fig. 10.8). 1405130059_4_010.indd 1701405130059_4_010.indd 170 01/04/2005 11:57:2701/04/2005 11:57:27 Structure and molecular virology 171 via base-pairing to facilitate the two template switches during plus-strand DNA synthesis. 276 However, a small terminal redundancy (5’r and 3’r) on the ends of the minus-strand DNA has also been shown to be important, but not suffi cient, for circularization. 277,278 Re-entry of mature HBV DNA to the nucleus Tuttleman et al. 174 showed that the amplifi cation of cccDNA in DHBV-infected primary hepatocytes occurs after the cells have lost their susceptibility for viral uptake. These data were confi rmed in the non-susceptible, HBV genome-carrying cell line HepG2.2.15, indicating also that nuclear transport of the genome is not linked to viral uptake. These observations were surprising as they described the fi rst time that a progeny viral particle ‘reinfects’ a cell without having left the cell. Beside hepadnaviruses, this internal amplifi cation has only been described for other pararetreoviruses such as caulimoviruses and potentially for foamyviruses. In all other viral studied infections, the entry pathway of an incoming virus is strictly separated from the exit pathway of the progeny virion. It must be assumed that in hepadnaviruses this strategy plays an important role in establishment of infection. Early in infection, when viral surface proteins are not yet signifi cantly synthesized, the entry of progeny genomes into the nucleus results in accumulation of the cccDNA. However, due to the lack of a suitable infection system all data on the nuclear transport were obtained in artifi cial systems such as the digitonin-permeabilized cells. These experiments show that the progeny capsids harbour the nuclear transport competence and mediate the transport of the progeny genome into the nucleus (Fig. 10.6). Interestingly, exposure of the nuclear localization signal – present on the C-terminus of the core proteins – is associated with phosphorylation of the core proteins. 115 Release of the genome from the capsids was linked to genome maturation, implying a tight regulation. 115 In fact, a defi ned order of genome maturation, localization and release appears to be essential. If the genome was released outside the nucleus it could not Immat-capsid RNA-capsid (2) Transport along MT Cellular RNA Genome-negative capsid Genome release (8) Nuclear basket NPC Viral DNA Karyoplasm Arrest (6) Translocation to the NPC (3) Cytoplasm Translocation to the NPC (3) (2) Transport along MT Infecting virus/capsid (1) Viral entry capsid release Progeny capsid (1a) (–)–DNA synthesis phosphorylation structural change Mat-capsid Microtubules (MT) MTOC Importin α + importin β (4) Translocation through the nuclear pore (5) Maturation (7) Capsid disintegration, genome release Reassembly (9) Figure 10.9 Intracellular transport of HBV capsid and genome. Infection starts with the release of the capsid from the surface proteins (1). The capsid is transported though the cytoplasm towards the microtubules organizing centre (MTOC) using the cellular microtubule network (2), followed by translocation to the cytosolic side of the nuclear pore (3). It exposes nuclear localization signals (NLS) on its surface, allowing the binding of importin β via the importin α adaptor protein (4). Importin β mediates the transport through the nuclear pore into the nuclear basket (5). There, the capsids disassemble and genome becomes released (8). The core proteins can reassemble to capsids (9). At least a part of the newly formed capsids contain cellular RNA. Cytosolic progeny capsids have to undergo phosphorylation of core proteins to induce a conformational change (1a). As infecting capsids, they are actively transported towards the nuclear pore (2, 3). The conformational change allows the binding of importin α and β and the transport into the nuclear basket (4, 5). If the genome maturation has not fi nished at that time, the capsid remains arrested within the basket (6) and genome maturation can proceed (7). As with the infecting capsids, disassembly and genome release occurs (8). 1405130059_4_010.indd 1711405130059_4_010.indd 171 01/04/2005 11:57:2701/04/2005 11:57:27 Chapter 10172 be transported into the karyoplasms, thus not allowing transcription and further genome multiplication. A premature genome release before genome maturation is fi nished would prevent synthesis of replication-competent viral DNA as the polymerase depends on the presence of the core proteins for plus-strand DNA synthesis. 110 Hepadnaviral cccDNA in the nucleus is subject to degradation, with a half-life of 35–57 days in vivo. 279 Thus, the pool of intranuclear HBV genomes has to be permanently restored to ensure viral persistence. Envelopment of core particles After establishment of infection and suffi cient surface protein synthesis, mature core particles are primarily targeted to form progeny virion instead of increasing the pool of intracellular cccDNA. Both pathways over- lap as determined for DHBV mutants being incompe- tent for virion secretion. In these mutants intranuclear cccDNA accumulated up to 50-fold over the natural copy number. 280 The assembly of core particles occurs in the cytosol, but after assembly and genome maturation HBc protein seems to exhibit an affi nity for intracellular membranes, which contain inserted LHBs molecules. 95 It has been shown that signifi cant minus-strand DNA synthesis must have occurred before encapsidation of the core particles. 281 It is presently unsolved whether the confor- mation change of the particles during genome maturation, which is implied by this observation, is the same as is responsible for exposure of the nuclear localization signal. For secretion of enveloped virions, an excess of SHBs protein is necessary. 68,282 It appears that the envelope is formed by mixed aggregates of LHBs, MHBs and SHBs, but MHBs seems to be dispensable. For secretion, virions and accompanying HBs particles move from the ER via the Golgi apparatus to the cell surface. 283 During this migration within transport vesicles, the HBs protein is further modifi ed similar to normal cellular secreted proteins. The glycoside side chains of the HBs proteins are trimmed and modifi ed. Covalent disulfi de bridges are formed within and between HBc or HBs subunits. It appears that the release of virions and HBs particles from secretory vesicles does not require any specifi c signal and follows the constitutive pathway of secretion. However, secretion requires trimming of the immature N-linked glycan bound to the HBs protein. Inhibition of that trimming by the glucosidase I inhibitor N-butyld- esoxynojirimycin also inhibits the appearance of HBV particles in the supernatant of transfected HBV-produc- ing cell lines. 284 The secretion of HBs particles is not as strongly inhibited, probably as a result of the lower con- tents of glycoside in HBs proteins. Somewhere between envelopment of core particles and secretion, part of the LHBs molecules is refolded in the pre-S domain from the internal face of the envelope to the surface. Low pH, as it occurs before secretion in the trans-Golgi network seems to favour this refolding, because low pH also induced the in vitro appearance of additional pre-S1 epitopes on the surface of HBV particles. 85 Human hepatoma cell lines such as HepG2 and Huh7 express a suitable ratio of all HBV proteins to allow for virion assembly and secretion. Immortalized mouse hepatocyte cultures 285 are also able to produce HBV. 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Spontaneous development of anti-hepatitis B virus envelope (anti-idiotypic) antibodies in animals immunized with human liver endonexin II or with the F(ab’)2 fragment of anti-human liver endonexin II immu- 1405130059_4_010.indd 1771405130059_4_010.indd 177 01/04/2005 11:57:2801/04/2005 11:57:28 [...]... 425 1.245 455 1.2255 476 1.2424 40–459 1.169 275 1 .34 5 275 1 .34 25 30 6 1 .34 20 279 1 .34 24 (with spikes) 225 1.19–1.2022 Present5 20–255 1.1825 Present5 15–256 1.1822 Present6 (long, abundant) 40–609 1.149 Absent9 31 82 31 88 100 4 33 08 33 20 70 4 33 11 55 4 30 21 30 27 40 4 1 63 226 29 1 83 838 145 204–205 222 30 187 879 141 206 222 30 188 881 138 161–1 63 167 43 262 786–788 11419 CsCl, caesium chloride; ORF open... , 1405 130 059_4_012.indd 194 30 / 03/ 2005 12:26 :35 Avihepadnaviridae (b) (a) 195 Pre-S/S protein (p36) Envelope or surface proteins S protein (p17) Pre-S/S protein S protein S ORF (nt 80 1-1 7 93) DHBV DHBV P ORF (nt 17 0-2 536 ) 30 27 bp 30 27 bp DR1 DR2 C ORF (nt 25 63 414) Nucleocapsid or core protein Core protein (p30) Precore protein Polymerase X ORF (nt 229 5-2 639 ) 114 AA protein DHBeAg (p27, gp3 0 -3 3) Figure... molecular virology 230 231 232 233 234 235 236 237 238 239 240 241 242 2 43 244 245 B virus DNA causing increased activity of the HBV enhancer Virology 1988;167: 630 3 Lopez-Cabrera M, Letovsky J, Hu KQ, Siddiqui A Transcriptional factor C/EBP binds to and transactivates the enhancer element II of the hepatitis B virus Virology 1991;1 83: 825–9 Bock CT, Tillmann HL, Manns MP, Trautwein C The pre-S region determines... 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