Divergent homoeolog evolution of the anthocyanin regulatory gene R in Oryza allopolyploids

Polyploidization is an important evolutionary force in plant speciation and diversification. Retention and elimination of homoeologs derived by polyploidization are prevalent, whereas the evolutionary details of some duplicated genes in closely related natural polyploids are largely unknown. In the present study, we used an important regulatory gene (R) that encodes a bHLH protein in the anthocyanin metabolism pathway to demonstrate divergent evolutionary fates of homoeologs among four related Oryza allotetraploids. The BBCC genome species O. punctata Kotschy ex Steud. maintained both of its homoeologs, whereas three CCDD genome species (O. alta Swallen, O. grandiglumis (Döll) Prod., and O. latifolia Desv.) lost their C subgenome homoeologous copies. In addition, the evolutionary rates of the homoeologs in the polyploids were equivalent to their corresponding homologs in diploids. We also found a slightly higher level of nucleotide diversity inR for the C subgenome homoeolog than for the B subgenome counterpart in O. punctata. After comparing the two types of polyploids, we conclude that inconsistent evolutionary patterns of R in these polyploids are probably associated with different evolutionary time, asymmetrical subgenome evolutionary dynamics, and unique demographical characteristics of these species.     

Neutral evolution of the sex-determining gene transformer in Drosophila

The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. These changes in amino acid sequence are the result of either natural selection or neutral evolution. To differentiate between selective and neutral causes of this evolutionary change, analyses of both intraspecific and interspecific patterns of molecular evolution of tra gene sequences are presented. Sequences of 31 tra alleles were obtained from Drosophila americana. Many replacement and silent nucleotide variants are present among the alleles; however, the distribution of this sequence variation is consistent with neutral evolution. Sequence evolution was also examined among six species representative of the genus Drosophila. For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. In exon 3 of D. virilis and D. americana we find evidence for an elevated rate of nonsynonymous substitution, but no statistical support for a greater rate of nonsynonymous relative to synonymous substitutions. Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function.     

Overexpression of maize anthocyanin regulatory gene Lc affects rice fertility

Seventeen independent transgenic rice plants with the maize anthocyanin regulatory gene Lc under control of the CaMV 35S promoter were obtained and verified by molecular identification. Ten plants showed red spikelets during early development of florets, and the degenerate florets were still red after heading. Additionally, these plants exhibited intense pigmentation on the surface of the anther and the bottom of the ovary. They were unable to properly bloom and were completely sterile. Following pollination with normal pollen, these plants yielded red caryopses but did not mature normally. QRT-PCR analysis indicated that mRNA accumulation of the CHS-like gene encoding a chalcone synthase-related protein was increased significantly in the sterile plant. This is the first report to suggest that upregulation of the CHS gene expression may result in rice sterility and affect the normal development of rice seeds.     

Comparative analysis of sequence variability in the upstream regulatory region of the HLA-DQB1 gene

The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number X74230-X74239.     

Polymorphism in the upstream regulatory region of the HLA-DQB1 gene in liver graft recipients.

HLA-DQB1*0302 allele frequency is increased in liver graft recipients with acute rejection. We investigated polymorphism in the upstream regulatory regions (URRs) of the DQB1 gene to determine whether polymorphism in the DQB1 promoter region influences liver graft acceptance. A combination of typing protocols based on the polymerase chain reaction were used in 103 first-time liver transplants and 108 healthy Spanish controls. The QBP3.21 allele frequency and QBP3.21-DQB1*0302 haplotype were significantly different in recipients with acute rejection compared to those with good graft acceptance and to controls. Of major interest for acute rejection development are the promoter "splits" of DQB1*0302 (QBP3.21, QBP3.22, and QBP3.3 alleles), which are in linkage disequilibrium with DQB1*0302. The promoter splits were equally distributed in all groups. Thus, although there are significant differences in the frequencies of the QBP alleles and QBP-DQB1 haplotypes between recipients with and without acute rejection and controls, the composition of these haplotypes is essentially the same in all groups. In conclusion, our data show that the polymorphism in the DQB1 promoter region does not clearly influence liver graft acceptance, and, as occurs in other populations, QBP alleles exhibit strong linkage disequilibrium with the DQB1 locus.     

Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution

Class II genes of the human major histocompatibility complex (MHC) are polymorphic. Allelic variation of the coding region of these genes is involved in the antigen presentation and is associated with susceptibility to certain autoimmune diseases. The DR region is unique among human class II regions in that multiple DRB genes are expressed. Differential expression of the different DRB loci has been demonstrated, and we sequenced the proximal promoter region of the HLA-DRB genes, known to be involved in the regulation of nucleotide variations in their regulatory regions and we determined the relationship between the regulatory regions of HLA-DRB genes. This polymorphism found in the regulatory conserved boxes could be involved in the observed differential expression of DRB loci. In addition, we found a polymorphism between the regulatory regions of DRB1 alleles which might be involved in an allele-specific regulation and therefore could be considered as an additional factor in susceptibility to autoimmune diseases.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X64436–X64442, X64544, X64546–X64549, X65558–X65569, and X65585–X65587. Correspondence to: J. F. Eliaou.     

Epigenetic neofunctionalisation and regulatory gene evolution in grasses

During plant evolution, genome duplication and subsequent selection acting on new gene pairs has frequently resulted in partition of gene functions, or acquisition of new functions. This 'sub- and neofunctionalisation' (subF and neoF) is held to have driven the expansion of key gene classes. One such gene class in maize (Zea mays) includes a pair of Polycomb group (PcG) protein genes that, unlike their single Arabidopsis (Arabidopsis thaliana) counterpart, are both parentally imprinted with only the maternal alleles being expressed in the seed endosperm. Surprisingly, this imprinting is regulated by different mechanisms in the two genes, resulting in different phasing of parent-specific expression. In this opinion article we propose that recruitment of different imprinting systems constitutes 'epigenetic neoF', and has enhanced maternal control over seed development, with a potential impact on the evolution of the large and persistent endosperms of cereal grains.     

BLG-e1 - a novel regulatory element in the distal region of the beta-lactoglobulin gene promoter

beta-Lactoglobulin (BLG) is a major ruminant milk protein. A regulatory element, termed BLG-e1, was defined in the distal region of the ovine BLG gene promoter. This 299-bp element lacks the established cis-regulatory sequences that affect milk-protein gene expression. Nevertheless, it alters the binding of downstream BLG sequences to histone H4 and the sensitivity of the histone-DNA complexes to trichostatin A treatment. In mammary cells cultured under favorable lactogenic conditions, BLG-e1 acts as a potent, position-independent silencer of BLG/luciferase expression, and similarly affects the promoter activity of the mouse whey acidic protein gene. Intragenic sequences upstream of BLG exon 2 reverse the silencing effect of BLG-e1 in vitro and in transgenic mice.     

The molecular evolution of terminal ear1, a regulatory gene in the genus Zea.

Nucleotide diversity in the terminal ear1 (te1) gene, a regulatory locus hypothesized to be involved in the morphological evolution of maize (Zea mays ssp. mays), was investigated for evidence of past selection. Nucleotide polymorphism in a 1.4-kb region of te1 was analyzed for a sample of 26 sequences isolated from 12 maize lines, five populations of the maize progenitor, Z. mays ssp. parviglumis, six other Zea populations, and two Tripsacum species. Although nucleotide diversity in te1 in maize is reduced relative to ssp. parviglumis, phylogenetic and statistical analyses of the pattern of polymorphism among these sequences provided no evidence of past selection, indicating that the region of the gene studied was probably not involved in maize evolution. The level of reduction in genetic diversity in te1 in maize relative to its progenitor is comparable to that found in previous reports for isozymes and other neutrally evolving maize genes and is consistent with a genome-wide reduction of genetic diversity resulting from a domestication bottleneck. An estimate of the age (1.2-1.4 million yr) of the maize gene pool based on te1 is roughly consistent with previous estimates based on other neutral genes, but may be biased by the apparently slow synonymous substitution rate at te1.