title: Specific secondary structures in the capsid-coding region of giardiavirus transcript are required for its translation in Giardia lamblia.
abstract: Enhanced translation of giardiavirus (GLV)-luciferase chimeric mRNA in Giardia lamblia requires the presence of the initial 264 nucleotides of the viral capsid-coding region. A 13 nt downstream box (DB) sequence within this region, complementary to a 15 nt sequence near the 3' end of G. lamblia 16 S-like ribosomal RNA (rRNA), was found to be essential for the enhanced translation. However, DB is located 64-78 nt downstream of the initiation codon, whereas an exponential increase of translation efficiency depends on a further increment of the coding region from nucleotides 111 to 264. Thus, there could be additional structural requirements for translation enhancement in the region downstream from DB. Four major stem-loop structures, designated I to IV, were identified in the MFOLD-predicted secondary structure of the 264 nt capsid-coding region with an estimated minimum free energy (DeltaG degrees ) of -77.16 kcal x mol(-1). Our chemical probing analysis of the free 264 nt RNA molecule in solution supports the predicted presence of stem-loops I, II and III, but casts doubts on stem-loop IV. It suggests, instead, the presence of a stem-loop IVA at a nearby location in the molecule. Site-directed mutagenesis designed to disrupt stem-loop structures I, II, III or IVA resulted in drastic reduction of translation efficiency, which was restored by compensatory sequence changes to regenerate individual stem-loop structures. Mutations disrupting the originally designated stem-loop IV did not exert any detectable effect on translation. However, alterations of the sequence UCUCC between nucleotides 216 and 220 in the flexible loop region of the revised secondary structure led to a precipitous drop in translation. Another stem-loop predicted by MFOLD that consists of a major portion of the DB sequence was examined by chemical probing but found little experimental support. Changes of the DB sequence without affecting the postulated stem structure led to drastic losses of translation efficiency. Thus, a simple structural basis for the enhanced translation could be that stem-loops I, II, III and IVA and the UCUCC sequence may facilitate the interaction between DB and the anti-DB in 16 S-like rRNA in initiating translation of GLV mRNA in G. lamblia.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, USA.
authors.forename: S
authors.initials: S
authors.lastname: Garlapati
authors.forename: J
authors.initials: J
authors.lastname: Chou
authors.forename: C C
authors.initials: CC
authors.lastname: Wang
mesh_terms: D000447:Aldehydes; D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D002074:Butanones; D003028:CME-Carbodiimide / Q000031:analogs & derivatives; D002213:Capsid / Q000235:genetics*; D015967:Gene Expression Regulation, Viral; D016829:Giardia lamblia / Q000235:genetics / Q000821:virology*; D019198:Giardiavirus / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis / Q000235:genetics*; D020871:RNA Stability; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software; D013329:Structure-Activity Relationship; D013463:Sulfuric Acid Esters; D013816:Thermodynamics; D014162:Transfection
chemical_list: D000447:Aldehydes; D002074:Butanones; D012333:RNA, Messenger; D012367:RNA, Viral; D013463:Sulfuric Acid Esters; C060331:1-cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide; D003028:CME-Carbodiimide; C005135:kethoxal; C007482:dimethyl sulfate