ABSTRACT
We have sequenced the complete genome of an isolate of Banana streak virus from banana cv. 'Mysore' and show that it is sufficiently different from a previously characterised isolate from cv. 'Obino l'Ewai' to warrant recognition as a distinct species, for which the name Banana streak Mysore virus (BSMysV) is proposed. The structure of the BSMysV genome was typical of badnaviruses in general, although ORF I had a non-conventional start codon. Evidence that at least part of the BSMysV genome is integrated in the B genome of cultivated Musa is presented and transmissibility by the mealybug Planococcus citri also demonstrated.
Subject(s)
Badnavirus/classification , Badnavirus/genetics , DNA, Viral/genetics , Genome, Plant , Musa/virology , Virus Integration , Base Sequence , DNA Primers , Models, Molecular , Molecular Sequence Data , Musa/genetics , Nucleic Acid Conformation , Open Reading Frames , Phylogeny , Polymerase Chain ReactionABSTRACT
Cauliflower mosaic virus (CaMV) is a DNA-containing pararetrovirus replicating by means of reverse transcription of a terminally redundant pregenomic 35S RNA that is also used as a polycistronic mRNA. The leader of 35S RNA is long, highly structured, and contains multiple short ORFs (sORFs), which strongly interfere with the ribosome scanning process. Translation of this RNA is initiated by a ribosome shunt mechanism, in which ribosomes translate the most 5'-proximal short ORF (sORF A), then skip a large region of the leader containing a putative RNA encapsidation signal and reinitiate translation at the first long viral ORF. Here, we demonstrate that the efficiency of the sORF A-mediated ribosome shunt is an important determinant of viral infectivity. Point mutations in sORF A, which reduced the basal level of shunt-dependent expression and the degree of shunt enhancement by a CaMV-encoded translation transactivator (TAV), consequently reduced infectivity of the virus in turnip plants. First- or second-site reversions appeared in the viral progeny. The second-site reversions restored shuntdependent expression to an extent correlating with their relative abundance in the progeny. Mutations that abolished both the basal and TAV-activated components of shunting proved to be lethal. Finally, by using an artificial stem structure that blocks scanning, we obtained direct evidence that ribosome shunt operates during CaMV infection.
Subject(s)
Brassica/virology , Caulimovirus/genetics , Caulimovirus/pathogenicity , DNA, Viral/chemistry , DNA, Viral/genetics , Ribosomes/physiology , Amino Acid Sequence , Base Sequence , Molecular Sequence Data , Mutagenesis, Site-Directed , Nucleic Acid Conformation , Open Reading Frames , Point Mutation , Polymerase Chain Reaction , RNA, Messenger/genetics , RNA, Ribosomal/genetics , RNA, Viral/genetics , Transfection , Virulence/geneticsABSTRACT
The pathways of scanning ribosome migration controlled by the cauliflower mosaic virus 35 S RNA leader were investigated in vitro and in vivo. This long (600 nucleotides) leader contains several short open reading frames (sORFs) and folds into an extended hairpin structure with three main stable stem sections. Translation initiation downstream of the leader is cap-dependent and occurs via ribosomal shunt under the control of two cis elements, a short open reading frame A (sORF A) followed by stem section 1. Here we show that a second similar configuration comprising sORF B followed by stem section 2 also allows shunting. The efficiency of the secondary shunt was greatly increased when stem section 1 was destabilized. In addition, we present evidence that a significant fraction of reinitiation-competent ribosomes that escape both shunt events migrate linearly via the structured central region but are intercepted by internal AUG start codons. Thus, expression downstream of the 35 S RNA leader is largely controlled by its multiple sORFs.
Subject(s)
5' Untranslated Regions/genetics , Caulimovirus/genetics , Open Reading Frames , Ribosomes/genetics , Base Sequence , Codon, Initiator , Molecular Sequence Data , Nucleic Acid Conformation , RNA, Viral/geneticsABSTRACT
The pregenomic 35 S RNA of cauliflower mosaic virus (CaMV) belongs to the growing number of mRNAs known to have a complex leader sequence. The 612-nucleotide leader contains several short open reading frames (sORFs) and forms an extended hairpin structure. Downstream translation of 35 S RNA is nevertheless possible due to the ribosome shunt mechanism, by which ribosomes are directly transferred from a take-off site near the capped 5' end of the leader to a landing site near its 3' end. There they resume scanning and reach the first long open reading frame. We investigated in detail how the multiple sORFs influence ribosome migration either via shunting or linear scanning along the CaMV leader. The sORFs together constituted a major barrier for the linear ribosome migration, whereas the most 5'-proximal sORF, sORF A, in combination with sORFs B and C, played a positive role in translation downstream of the leader by diverting scanning ribosomes to the shunt route. A simplified, shunt-competent leader was constructed with the most part of the hairpin including all the sORFs except sORF A replaced by a scanning-inhibiting structure. In this leader as well as in the wild type leader, proper translation and termination of sORF A was required for efficient shunt and also for the level of shunt enhancement by a CaMV-encoded translation transactivator. sORF A could be replaced by heterologous sORFs, but a one-codon (start/stop) sORF was not functional. The results implicate that in CaMV, shunt-mediated translation requires reinitiation. The efficiency of the shunt process is influenced by translational properties of the sORF.
Subject(s)
5' Untranslated Regions/genetics , Caulimovirus/genetics , Open Reading Frames , RNA, Messenger/genetics , RNA, Viral/genetics , 5' Untranslated Regions/chemistry , Base Sequence , Genes, Reporter , Molecular Sequence Data , Nucleic Acid Conformation , Protein Biosynthesis , Protoplasts/physiology , RNA, Viral/chemistry , Restriction Mapping , Ribosomes/genetics , Ribosomes/metabolism , TransfectionABSTRACT
Cauliflower mosaic virus pregenomic 35S RNA begins with a long leader sequence containing an extensive secondary structure and up to nine short open reading frames (sORFs), 2 to 35 codons in length. To test whether any of these sORFs are required for virus viability, their start codons were mutated either individually or in various combinations. The resulting viral mutants were tested for infectivity on mechanically inoculated turnip plants. Viable mutants were passaged several times, and the stability of the introduced mutations was analyzed by PCR amplification and sequencing. Mutations at the 5'-proximal sORF A and in the center of the leader resulted in delayed symptom development and in the appearance of revertants. In the central leader region, the predicted secondary structure, rather than the sORF organization, was restored, while true reversions or second-site substitutions in response to mutations of sORF A restored this sORF. Involvement of sORF A and secondary structure of the leader in the virus replication cycle, and especially in translation of the 35S RNA via ribosome shunting, is discussed.
Subject(s)
Caulimovirus/genetics , Nucleic Acid Conformation , Open Reading Frames , RNA, Messenger , RNA, Viral/chemistry , Base Sequence , Caulimovirus/physiology , Directed Molecular Evolution , Genetic Variation , Molecular Sequence Data , Mutagenesis , Phylogeny , Protein BiosynthesisABSTRACT
A wheat germ cell-free system was used to study details of ribosome shunting promoted by the cauliflower mosaic virus 35 S RNA leader. By testing a dicistronic construct with the leader placed between two coding regions, we confirmed that the 35 S RNA leader does not include an internal ribosome entry site of the type observed with picornavirus RNAs. A reporter gene fused to the leader was shown to be expressed by ribosomes that had followed the bypass route (shunted) and, with lower efficiency, by ribosomes that had scanned through the whole region. Stem section 1, the most stable of the three stem sections of the leader, was shown to be an important structural element for shunting. Mutations that abolished formation of this stem section drastically reduced reporter gene expression, whereas complementary mutations that restored stem section 1 also restored shunting. A micro-leader capable of shunting consisting of stem section 1 and flanking sequences could be defined. A small open reading frame preceding stem section 1 enhances shunting.
Subject(s)
Caulimovirus/genetics , Ribosomes/metabolism , Base Composition , Base Sequence , Cell-Free System , Chloramphenicol O-Acetyltransferase/genetics , Molecular Sequence Data , Nucleic Acid Conformation , Oligodeoxyribonucleotides , Open Reading Frames , RNA, Messenger/chemistry , RNA, Messenger/genetics , RNA, Viral/chemistry , RNA, Viral/geneticsABSTRACT
The 5' untranslated leader of potato virus X (PVX) RNA is shown when contiguous to the coding sequence, to enhance the expression of the neomycin phosphotransferase II gene (NPTII) in Nicotiana tabacum protoplasts in vivo. The level of transient expression of the NPTII gene in protoplasts provided by a plasmid containing the coding sequence of the NPTII gene under the control of 35S cauliflower mosaic virus (CaMV) promoter and terminator elements served as the baseline control. Insertion of the viral 5' untranslated leader sequence upstream of the NPTII ATG codon increased the level of expression 4-fold. An 83 nucleotide (nt) leader sequence (lacking only one nucleotide of the complete PVX leader) and a truncated version with a 28 deletion at the 3' end both had similar enhancing abilities. The 28 nt CA region of the PVX leader alone had no enhancement properties.
