We have developed a method, that we call 'sister-scanning', for assessing phylogenetic and compositional signals in the various patterns of identity that occur between four nucleotide sequences. A Monte Carlo randomization is done for all columns (positions) within a window and Z-scores are obtained for four real sequences or three real sequences with an outlier that is also randomized. The usefulness of the approach is demonstrated using tobamovirus and luteovirus sequences. Contradictory phylogenetic signals were distinguished in both datasets, as were regions of sequence that contained no clear signal or potentially misleading signals related to compositional similarities. In the tobamovirus dataset, contradictory phylogenetic signals were separated by coding sequences up to a kilobase long that contained no clear signal. Our re-analysis of this dataset using sister-scanning also yielded the first evidence known to us of an inter-species recombination site within a viral RNA-dependent RNA polymerase gene together with evidence of an unusual pattern of conservation in the three codon positions.
Positive‐stranded genomic RNA of coronavirus MHV and its six subgenomic mRNAs are synthesized in the cytoplasm of the host cell. The mRNAs are composed of leader and body sequences which are non‐contiguous on the genome and are fused together in the cytoplasm by a mechanism which appears to involve an unusual and specific ‘polymerase jumping’ event.
In the eukaryotic cell, both secreted and plasma membrane proteins are synthesized at the endoplasmic reticulum, then transported, via the Golgi complex, to the cell surface. Each of the compartments of this transport pathway carries out particular metabolic functions, and therefore presumably contains a distinct complement of membrane proteins. Thus, mechanisms must exist for localizing such proteins to their respective destinations. However, a major obstacle to the study of such mechanisms is that the isolation and detailed analysis of such internal membrane proteins pose formidable technical problems. We have therefore used the E1 glycoprotein from coronavirus MHV-A59 as a viral model for this class of protein. Here we present the primary structure of the protein, determined by analysis of cDNA clones prepared from viral mRNA. In combination with a previous study of its assembly into the endoplasmic reticulum membrane, the sequence reveals several unusual features of the protein which may be related to its intracellular localization.
Synthetic RNAs coding for chicken lysozyme, calf preprochymosin and Xenopus globin were transcribed in vitro using Sp6 RNA polymerase. The effects of capping and adding a poly(A) tail on the stability, movement and translation of these RNAs in Xenopus oocytes was examined. Capping and polyadenylation increased stability of the transcripts, with at least 40% remaining intact 48 h after injection into oocytes. Capped poly(A)- transcripts moved more rapidly in oocytes than either capped poly(A)+ transcripts or naturally occurring mRNAs. The translational efficiency of most of the synthetic RNAs in oocytes increased with both capping and polyadenylation. The exception was one Xenopus globin transcript which had an unusual 3' end of 20As and 30Cs, where further polyadenylation decreased translational efficiency. Polyadenylation was essential for detectable expression of the synthetic RNAs in cultured cells, but decreased translation of the synthetic RNAs in vitro.
When gene sequences from the influenza virus that caused the 1918 pandemic were first compared with those of related viruses, they yielded few clues about its origins and virulence. Our reanalysis indicates that the hemagglutinin gene, a key virulence determinant, originated by recombination. The "globular domain" of the 1918 hemagglutinin protein was encoded by a part of a gene derived from a swine-lineage influenza, whereas the "stalk" was encoded by parts derived from a human-lineage influenza. Phylogenetic analyses showed that this recombination, which probably changed the virulence of the virus, occurred at the start of, or immediately before, the pandemic and thus may have triggered it.
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