De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus.

Hepatitis C virus (HCV) NS5B protein possesses an RNA-dependent RNA polymerase (RdRp) activity, a major function responsible for replication of the viral RNA genome. To further characterize the RdRp activity, NS5B proteins were expressed from recombinant baculoviruses, purified to near homogeneity, and examined for their ability to synthesize RNA in vitro. As a result, a highly active NS5B RdRp (1b-42), which contains an 18-amino acid C-terminal truncation resulting from a newly created stop codon, was identified among a number of independent isolates. The RdRp activity of the truncated NS5B is comparable to the activity of the full-length protein and is 20 times higher in the presence of Mn(2+) than in the presence of Mg(2+). When a 384-nucleotide RNA was used as the template, two major RNA products were synthesized by 1b-42. One is a complementary RNA identical in size to the input RNA template (monomer), while the other is a hairpin dimer RNA synthesized by a "copy-back" mechanism. Substantial evidence derived from several experiments demonstrated that the RNA monomer was synthesized through de novo initiation by NS5B rather than by a terminal transferase activity. Synthesis of the RNA monomer requires all four ribonucleotides. The RNA monomer product was verified to be the result of de novo RNA synthesis, as two expected RNA products were generated from monomer RNA by RNase H digestion. In addition, modification of the RNA template by the addition of the chain terminator cordycepin at the 3' end did not affect synthesis of the RNA monomer but eliminated synthesis of the self-priming hairpin dimer RNA. Moreover, synthesis of RNA on poly(C) and poly(U) homopolymer templates by 1b-42 NS5B did not require the oligonucleotide primer at high concentrations (>/=50 microM) of GTP and ATP, further supporting a de novo initiation mechanism. These findings suggest that HCV NS5B is able to initiate RNA synthesis de novo.

Establishment of an in vitro assay to characterize hepatitis C virus NS3-4A protease trans-processing activity.

An in vitro cleavage system was established to measure HCV NS3 protease trans-processing activity. This system utilizes purified NS3-4A protein from baculovirus, purified substrates expressed by in vitro transcription and translation and defined buffer components. The 41-residue substrates, 5A/5B and 4A/4B, were processed efficiently in trans by wild-type NS3 but not by a catalytically inactive mutant protease; radiolabel sequencing confirmed that NS3-mediated cleavage occurred at the correct cysteine/serine sites, thereby authenticating this system. Two striking features of this in vitro assay are: (1) analogous 4B/5A and 3/4A substrates cannot be processed in trans under the same conditions, and (2) in vitro cleavage of the 5A/5B and 4A/4B sites is highly dependent on the presence of NS4A, which we show is not the case in vivo.

Partial characterization of ovine skeletal muscle proteoglycans and collagen.

Ovine longissimus dorsi and biceps femoris muscles were analyzed for proteoglycan content, collagen and lysine aldehyde-derived collagen crosslinking concentrations at 2-4 days, six-month-old, and six-year-old stages of development. Tissue extracted proteoglycan molecular sieve distribution on a Sephacryl S-200HR column revealed two proteoglycan populations with estimated relative molecular weight ranges of 200,000 to 250,000 daltons and 23,000 to 70,000 daltons. The molecular sieve distribution was similar between the two muscles within a developmental age, but changed as a function of developmental age. Primary culture from both the longissimus dorsi and biceps femoris muscle liberated proteoglycans into the culture medium. In contrast to the tissue extracted proteoglycans, at the six-year-old stage of development, culture medium liberated proteoglycan Sephacryl S-200HR molecular sieve distribution differed between the two muscles. In both the tissue extracted and medium liberated proteoglycans at all developmental stages, nitrous acid deamination demonstrated the presence of heparan sulfate. Immunoblot analysis of the tissue extracted proteoglycans indicated the presence of decorin at each developmental stage. Longissimus dorsi and biceps femoris collagen concentrations (5.13 +/- 0.9 vs. 5.53 +/- 1.5%, respectively) and crosslink concentrations (0.07 +/- 0.01 moles HP/mole collagen) were initially similar between the two muscles; however, by six-months the muscles differed in both collagen concentration (1.72 +/- 0.5 and 2.53 +/- 0.7%, respectively) and crosslinking (0.24 +/- 0.02 and 0.27 +/- 0.03 moles HP/mole collagen, respectively). At six years of age, both the longissimus dorsi and biceps femoris exhibited slightly elevated collagen concentrations (2.49 and 3.05%, respectively) while crosslinking values were decreased relative to values at six-months of age (0.11 +/- 0.01 and 0.18 +/- 0.01 moles HP/mole of collagen, respectively). The results from this study indicate that skeletal muscle proteoglycans and collagen show developmental changes, which suggests that they are subject to developmental regulation.