The classic concept of epistatic fitness interactions between genes has been extended to study interactions within gene regions, especially between nucleotides that are important in maintaining pre-mRNA/mRNA secondary structures. It is shown that the majority of linkage disequilibria found within the Drosophila Adh gene are likely to be caused by epistatic selection operating on RNA secondary structures. A recently proposed method of RNA secondary structure prediction based on DNA sequence comparisons is reviewed and applied to several types of RNAs, including tRNA, rRNA, and mRNA. The patterns of covariation in these RNAs are analyzed based on Kimura's compensatory evolution model. The results suggest that this model describes the substitution process in the pairing regions (helices) of RNA secondary structures well when the helices are evolutionarily conserved and thermodynamically stable, but fails in some other cases. Epistatic selection maintaining pre-mRNA/mRNA secondary structures is compared to weak selective forces that determine features such as base composition and synonymous codon usage. The relationships among these forces and their relative strengths are addressed. Finally, our mutagenesis experiments using the Drosophila Adh locus are reviewed. These experiments analyze long-range compensatory interactions between the 5' and 3' ends of Adh mRNA, the different constraints on secondary structures in introns and exons, and the possible role of secondary structures in RNA splicing.
The flagellar operons of Salmonella are divided into three classes with respect to their transcriptional hierarchy. Expression of the class 2 operons requires the class 1 gene products, FlhD and FlhC, and is increased by mutation in the flgM gene, which encodes a class 3-specific anti-sigma factor. Here we report the identification of two novel regulatory genes for class 2 transcription. Presence of the fliZ and fliT genes on multicopy plasmids enhanced and inhibited, respectively, transcription from a chromosomal class 2 promoter. Disruption of the fliZ and fliT genes on the chromosome decreased and increased, respectively, class 2 expression. These results suggest that the fliZ and fliT genes may encode positive and negative regulatory factors, respectively, for class 2 expression. Enhancement of class 2 expression by the flgM mutation was cancelled by the coexisting fliZ mutation, indicating that FliZ is essential for this enhancement.
Allelic variation at the two prolamin loci (Pro1 and Pro2) and its geographical distribution in 560 local cultivars of foxtail millet (Setaria italica) mainly from Eurasia were studied using SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Genetic analysis of a newly detected polymorphic band, band 6, indicated that it is controlled by an allele at the Pro2 locus, which was designated as Pro2f. Two alleles (Pro1a and Pro1null) at the Pro1 locus and six alleles (Pro2a, Pro2b, Pro2c, Pro2d, Pro2e and Pro2f) at the Pro2 locus were detected among the cultivars examined. Although the frequency of the Pro1a allele varied from 0% in the Nansei islands of Japan and Africa to 66% in Afghanistan, no apparent trend was observed in geographical distribution. In contrast, two common alleles at the Pro2 locus, Pro2b and Pro2f, had clear differential geographical distribution. The Pro2b allele was most frequent in Europe and decreased in frequency eastwards. The Pro2f allele occurred frequently in subtropical and tropical regions including the Nansei islands of Japan, the Philippines, Nepal, India, Pakistan and Africa. All eight alleles at the Pro1 and Pro2 loci occurred in China, suggesting China is a center of diversity. The origin of geographical differentiation of local cultivars into a "tropical group" characterized by the Pro2f allele and other genes was discussed.
PCR was performed with degenerate primers which hybridized to the homologous sequences in the reverse transcriptase (rt) genes of gypsy-type retrotransposons from rice (RIRE3, RIRE8 and RIRE2), using total DNA samples from various plants (monocots, dicots, pine, ginkgo, horsetail, liverwort and algae) as templates. Cloning and sequencing showed that the amplified fragments had various degrees of homology to the rt sequences of rice retrotransposons. Phylogenetic analysis showed that these retrotransposon homologues and some additional gypsy-type retrotransposons previously identified from plants could be classified into two families, A and B. In each family, the retrotransposons were further classifiable into several subfamilies. Interestingly, retrotransposons from a single or related plant species were clustered in each subfamily. This indicates that sequence divergence during vertical transmission has been a major influence on the evolution of gypsy-type retrotransposons in plants. The retrotransposons isolated from one plant species could often be classified into the two families. This indicates that the gypsy-type retrotransposons of a family evolved independently within a species without affecting the evolution of retrotransposons of the other family. Retrotransposons in each subfamily are characterized by the lengths of LTR, by the nucleotide sequences in the terminal regions of LTRs, and by the PBS (primer binding site) sequence complementary to the 3' sequence of a particular tRNA species.
N-terminal amino acid sequences of six prolamins encoded by seven alleles at two loci, Pro1 and Pro2, of foxtail millet (Setaria italica (L.) P. Beauv.) were analyzed and compared with other prolamins of subfamily Panicoideae. Based on the N-terminal amino acid sequences, band 3 (the prolamin purified from band 3) which is controlled by an allele at the Pro1 locus and bands 1, 2, 4, 5 and 6 which are controlled by alleles at the Pro2 locus could be classified into three groups. Band 3 was found to be homologous to the prolamin of pearl millet (Pennisetum americanum) and is designated as the "pennisetin-like prolamin". Bands 2 and 4, and bands 1, 5 and 6 were subdivided into "x-type prolamin" and "y-type prolamin". Both of the x-type and y-type prolamins showed homology with prolamin of Echinochloa crus-galli and α-zein-like prolamins of maize, sorghum and Job's tears. Therefore, these prolamins were designated as "α-zein-like prolamin". These results suggest that alleles at the Pro1 locus and those at the Pro2 locus have not arisen from an identical ancestral gene, and that the Pro2 locus comprise two tightly linked genes, which encode similar prolamins. Hypotheses on the diversification of alleles at the Pro2 locus are discussed based on the N-terminal amino acid sequences of the respective bands, combinations of bands controlled by the alleles, and frequencies of the alleles.