ABSTRACT
Pre-mRNA splicing or the removal of introns from precursor messenger RNAs depends on the accurate recognition of intron sequences by the plant splicing machinery. The major components of this machinery are small nuclear ribonucleoprotein protein particles (snRNPs) which consist of snRNAs and snRNP proteins. We have analysed various aspects of intron sequence and structure in relation to splice site selection and splicing efficiency and we have cloned snRNA genes and a gene encoding the snRNP protein, U2B". In the absence of an in vitro splicing system for plants, transient expression in protoplasts and stable plant transformations have been used to analyse splicing of intron constructs. We aim to address the function of the UsnRNP-specific protein, U2B", via the production of transgenic plants expressing antisense U2B" transcripts and epitope-tagged U2B" protein. In addition, we have cloned genes encoding other proteins which potentially interact with RNA, such as RNA helicases, and strategies involving transgenic plants are being developed to analyse their function.
Subject(s)
Plants/genetics , Plants/metabolism , RNA Precursors/genetics , RNA Precursors/metabolism , RNA Splicing/genetics , Base Sequence , DNA/genetics , Genetic Vectors , Introns , Molecular Sequence Data , Plant Proteins/genetics , Plants, Genetically Modified/genetics , Plants, Genetically Modified/metabolism , Plants, Toxic , Ribonucleoproteins, Small Nuclear/genetics , Solanum tuberosum/genetics , Solanum tuberosum/metabolism , Spliceosomes/metabolism , Nicotiana/genetics , Nicotiana/metabolismABSTRACT
The 9.9 kb monopartite ssRNA genome of parsnip yellow fleck virus (PYFV) encodes a polyprotein from which the functional proteins are assumed to arise by proteolytic cleavage. The 22.5K, 26K and 31K particle proteins were mapped in the polyprotein by determining their N-terminal amino acid sequences, and were found to begin at amino acid positions 395, 589 and 811, respectively. There could be polypeptide(s) of up to 43K on the N-terminal side of the particle protein sequences. A region within the 26K particle protein has sequence similarity to the VP3 particle protein of picornaviruses. Three other regions in the PYFV polyprotein have sequence similarity to regions thought to have RNA polymerase, NTP-binding and protease functions in the polyproteins of picornaviruses, comoviruses and nepoviruses. Despite these similarities in sequence and in genome organization to viruses in the picorna-like supergroup, PYFV is distinct from all other plant and animal viruses described. This justifies placing it in a separate plant virus genus for which the name 'sequivirus' has been proposed.
Subject(s)
Plant Viruses/genetics , Proteins/genetics , Amino Acid Sequence , Binding Sites , Endopeptidases/genetics , Genes, Viral , Molecular Sequence Data , Nucleotides/metabolism , Phylogeny , Picornaviridae/genetics , RNA-Dependent RNA Polymerase/genetics , Sequence Alignment , Vegetables , Viral Structural Proteins/geneticsABSTRACT
Parsnip yellow fleck and rice tungro spherical viruses, with monopartite ss RNA genomes, resemble picornaviruses in the polymerase and NTP-binding domains of their encoded polyproteins. Though in separate genera, they may comprise a new family.
Subject(s)
Capsid/chemistry , Picornaviridae/classification , Plant Viruses/classification , Amino Acid Sequence , Animals , Aphids/microbiology , Cluster Analysis , Insect Vectors/microbiology , Molecular Sequence Data , Oryza/microbiology , Picornaviridae/chemistry , Picornaviridae/genetics , Plant Viruses/chemistry , Plant Viruses/genetics , Sequence Homology, Amino Acid , Vegetables/microbiologyABSTRACT
The complete sequence of 9871 nucleotides (nts) of parsnip yellow fleck virus (PYFV; isolate P-121) was determined from cDNA clones and by direct sequencing of viral RNA. The RNA contains a large open reading frame between nts 279 and 9362 which encodes a polyprotein of 3027 amino acids with a calculated M(r) of 336212 (336K). A PYFV polyclonal antiserum reacted with the proteins expressed from phage carrying cDNA clones from the 5' half of the PYFV genome. Comparison of the polyprotein sequence of PYFV with other viral polyprotein sequences reveals similarities to the putative NTP-binding and RNA polymerase domains of cowpea mosaic comovirus, tomato black ring nepovirus and several animal picornaviruses. The 3' untranslated region of PYFV RNA is 509 nts long and does not have a poly(A) tail. The 3'-terminal 121 nts may form a stem-loop structure which resembles that formed in the genomic RNA of mosquito-borne flaviviruses.
Subject(s)
Plant Viruses/genetics , RNA, Viral/genetics , Amino Acid Sequence , Base Sequence , Genes, Viral , Hydrogen Bonding , Molecular Sequence Data , Nucleic Acid Conformation , Open Reading Frames , Proteins/genetics , RNA, Viral/ultrastructure , Vegetables/microbiology , Viral Proteins/genetics , Viral Structural Proteins/geneticsABSTRACT
Oligonucleotide-limited transcription has been used to prepare a series of transcripts which allowed the positions of termination by T7 RNA polymerase to be characterized. The same technique was used to prepare a set of transcripts from a rabbit beta-globin gene that extend in intervals of two nucleotides from the 3' splice site of IVS-1 into the second exon. Splicing efficiency in a HeLa cell nuclear extract decreased with decreasing length of the 3' exon, although both steps of the splicing reaction could still be detected with as few as four nucleotides in this exon. No evidence was found for a lower limit to the length of the 3' exon below which splicing would not take place. With longer substrates, the rate of the second step of splicing was increased substantially.
