Structural organization of the human gastrointestinal glutathione peroxidase (GPX2) promoter and 3'-nontranscribed region: transcriptional response to exogenous redox agents

We describe a new family of repetitive elements, named Mimo, from the mosquito Culex pipiens. Structural characteristics of these elements fit well with those of miniature inverted-repeat transposable elements (MITEs), which are ubiquitous and highly abundant in plant genomes. The occurrence of Mimo in C. pipiens provides new evidence that MITEs are not restricted to plant genomes, but may be widespread in arthropods as well. The copy number of Mimo elements in C. pipiens (1000 copies in a 540 Mb genome) supports the hypothesis that there is a positive correlation between genome size and the magnitude of MITE proliferation. In contrast to most MITE families described so far, members of the Mimo family share a high sequence conservation, which may reflect a recent amplification history in this species. In addition, we found that Mimo elements are a frequent nest for other MITE-like elements, suggesting that multiple and successive MITE transposition events have occurred very recently in the C. pipiens genome. Despite evidence for recent mobility of these MITEs, no element has been found to encode a protein; therefore, we do not know how they have transposed and have spread in the genome. However, some sequence similarities in terminal inverted-repeats suggest a possible filiation of some of these mosquito MITEs with pogo-like DNA transposons.     

Organization of an Arabidopsis thaliana gene cluster on chromosome 4 including the RPS2 gene, in the Brassica nigra genome

 Genetic and physical maps, consisting of a large number of DNA markers for Arabidopsis thaliana chromosomes, represent excellent tools to determine the organization of related genomes such as those of Brassica. In this paper we report the chromosomal localization and physical analysis by pulsed-field gel electrophoresis (PFGE) of a well-defined gene complex of A. thaliana in the Brassica nigra genome (B genome n=8). This complex is approximately 30 kb in length in A. thaliana and contains a cluster of six genes including ABI1 (ABA-responsive), RPS2 (resistance against Pseudomonas syringae, a bacterial disease), CK1 (casein kinase I), NAP (nucleosome-assembly protein), X9 and X14 (both of unknown function). The Arabidopsis chromosomal complex was found to be duplicated and conserved in gene number at different levels in the Brassica genome. Linkage group B1 had the most-conserved arrangement carrying all six genes tightly linked. Group B4 had an almost complete complex except for the absence of RPS2. Other partial complexes of fewer members were found on three other chromosomes. Our studies demonstrate that by this approach it is possible to identify ancestrally related chromosome segments in a complex and duplicated genome, such as the genome of B. nigra, permitting one to draw conclusions as to its origin and evolution. Received: 11 July 1997 / Accepted: 9 October 1997     

Conservation in wheat high-molecular-weight glutenin gene promoter sequences: comparisons among loci and among alleles of the GLU-B1-1 locus

 The high-molecular-weight glutenin (HMW) genes and encoded subunits are known to be critical for wheat quality characteristics and are among the best-studied cereal research subjects. Two lines of experiments were undertaken to further understand the structure and high expression levels of the HMW-glutenin gene promoters. Cross hybridizations of clones of the paralogous x-type and y-type HMW-glutenin genes to a complete set of six genes from a single cultivar showed that each type hybridizes best within that type. The extent of hybridization was relatively restricted to the coding and immediate flanking DNA sequences. Additional DNA sequences were determined for four published members of the HMW-glutenin gene family (encoding subunits Ax2^*, Bx7, Dx5, and Dy10) and showed that the flanking DNA of the examined genes diverge at approximately −1200 bp 5′ to the start codon and 200–400 bp 3′ to the stop codon. These divergence sites may indicate the boundaries of sequences important in gene expression. In addition, promoter sequences were determined for alleles of the Bx gene (Glu-B1-1), a gene reported to show higher levels of expression than other HMW-glutenin genes and with variation among cultivars. The sequences of Bx promoters from three cultivars and one wild tetraploid wheat indicated that all Bx alleles had few differences and contained a duplicated portion of the promoter sequence “cereal-box” previously suspected as a factor in higher levels of expression. Thus, the “cereal-box” duplication preceeded the origin of hexaploid wheat, and provides no evidence to explain the variations in Bx subunit synthesis levels. One active Bx allele contained a 185-bp insertion that evidently resulted from a transposition event. Received: 5 August 1997 / Accepted: 6 November 1997     

The Path from the RNA World

We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA → RNP → protein, the first proteins in the ``breakthrough organism' (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the ``introns-first' theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like' genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome → eukaryotic-like DNA genome → prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome → eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA → RNP → protein. A likely molecular mechanism, ``plasmid transfer,' is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history. Received: 14 January 1997 / Accepted: 19 May 1997     

Comparative RFLP mapping of meadow and tall fescue

 Molecular markers based on restriction fragment length polymorphism (RFLP) were used to construct a genetic linkage map in diploid meadow fescue, Festuca pratensis Huds. (2n=2x=14, genomic designation PP), and to compare its genomic relationship with a related species, hexaploid tall fescue (Festuca arundinacea Schreb.; 2n=6x=42, PPG₁G₁G₂G₂). Using a collection of 66 tall-fescue (heterologous) markers, an RFLP linkage map was constructed in F. pratensis. This map, which has a total length of 280.1 cM, includes seven linkage groups. A comparison of 33 markers that were mapped in both F. pratensis and F. arundinacea detected highly conserved linkage groups between these two species. Our data are consistent with the proposal that one of the genomes of F. arundinacea was derived from F. pratensis. However, since significant changes in marker sequences, map distances, and homoeologous linkage groups were also detected between the two species, it appears that the P genome diverged substantially during evolution from the diploid to the hexaploid Festuca. Received: 23 May 1997 / Accepted: 15 January 1998     

野生稻基因组随机扩增多态性DNA(RAPD)分析

用18个随机引物对2份栽培稻、12份包含有六个基因组型的野生稻DNA进行了扩增,共获得147个多态性DNA片断,把这些多态性DNA片断作为遗传位点用UPGMA法计算出各材料间的遗传相似性系数,并作了聚类分析．主要结果如下：1普通野生稻同栽培稻的亲缘关系很近,其中江永普通野生稻更接近于粳稻．2．CCDD组的Oryzalatifolia和EE组的O．australiensis遗传多态性相似。3．B、C、D、E组的遗传多态性相似,组成一个复合体,此复合体与A组的遗传多态性也相似,而F组则相距较远．4．O．mcyeriana和Rhynchofyzasabulata尚未确定组型,RAPD测定结果表明,前者与其它组型的种亲缘关系较远,后者则与AC复合体的种较近．     

Histones and nucleosomes in Archaea and Eukarya: a comparative analysis

Archaeal histones from mesophilic, thermophilic, and hyperthermophilic members of the Euryarchaeota have primary sequences, the histone fold, tertiary structures, and dimer formation in common with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. Archaeal histones form nucleoprotein complexes in vitro and in vivo, designated archaeal nucleosomes, that contain histone tetramers and protect approximately 60 base pairs of DNA from nuclease digestion. Based on the sequence and structural homologies and experimental data reviewed here, archaeal nucleosomes appear similar, and may be homologous in evolutionary terms and function, to the structure at the center of the eukaryal nucleosome formed by the histone (H3+H4)₂ tetramer. Received: January 22, 1998 / Accepted: February 16, 1998     

Analysis of the genome of the gram-negative moderate halophiles Halomonas and Chromohalobacter by using pulsed-field gel electrophoresis

The genomes of 11 moderately halophilic bacteria belonging to the genera Halomonas and Chromohalobacter have been analyzed by restriction endonuclease digestion and pulsed-field gel electrophoresis (PFGE). By using the infrequently cutting restriction endonucleases SpeI and SwaI, highly characteristic fingerprintings were obtained for each of the isolates studied. On the basis of the lengths of the SpeI and SwaI fragments, separated by PFGE, the genome size of the 11 strains studied was estimated. The genome size for 8 Halomonas strains ranged from 1450 to 2830 kb, whereas for the 3 Chromohalobacter strains studied it ranged from 1770 to 2295 kb. Finally, we show that macrorestriction fingerprints could be a useful tool to elucidate the taxonomic position of bacteria belonging to the Halomonas–Deleya complex. Received: October 13, 1997 / Accepted: May 12, 1998     

Estimation of genome sizes of hyperthermophiles

Genomes of various hyperthermophilic and extremely thermophilic prokaryotes were analyzed with respect to size, physical organization, and 16S rDNA copy number. Our results show that all the genomes are circular, and they are in the size range of 1.6–1.8 Mb for Pyrodictium abyssi, Methanococcus igneus, Pyrobaculum aerophilum, Archaeoglobus fulgidus, Archaeoglobus lithotrophicus, and Archaeoglobus profundus (the two bacteria Fervidobacterium islandicum and Thermosipho africanus possess genomes of 1.5-Mb size). A systematic study of all validly described species of the order Sulfolobales revealed the existence of two classes of genome size for these archaea, correlating with phylogenetic analyses. The Metallosphaera–Acidianus group, plus Sulfolobus metallicus, have genomes of ca. 1.9 Mb; the other members of the order Sulfolobales group possess genomes >2.7 Mb. The special case of Stygiolobus azoricus is discussed. Received: August 10, 1997 / Accepted: January 1, 1998