Pathogenesis gene families in the common minimal genome of Staphylococcus aureus are hypervariable

Staphylococcus aureus is a versatile pathogen that shows high levels of inter-strain genetic variability and positive evolution in certain pathogenesis-related genes. Apart from gene content differences, variability in shared genes may affect pathogenicity. Studying such variability requires that the common minimal genome (CMG) be identified. In this study, we have surveyed the CMG of S. aureus with respect to variability amongst orthologous family members, and determined that genes involved in pathogenesis preferentially accumulate variations. A negative correlation between variability of genes and their evolution was found, suggesting a preservation of host-specific function while exhibiting sequence diversity. Variation in key pathogenesis genes in S. aureus might predispose them to functional modulation, thereby playing an important role in evasion of host immunity.     

Position-specific incorporation of dansylated non-natural amino acids into streptavidin by using a four-base codon

Novel non-natural amino acids carrying a dansyl fluorescent group were designed, synthesized, and incorporated into various positions of streptavidin by using a CGGG four-base codon in an Escherichia coli in vitro translation system. 2,6-Dansyl-aminophenylalanine (2,6-dnsAF) was found to be incorporated into the protein more efficiently than 1,5-dansyl-lysine, 2,6-dansyl-lysine, and 1,5-dansyl-aminophenylalanine. Fluorescence measurements indicate that the position-specific incorporation of the 2,6-dnsAF is a useful technique to probe protein structures. These results also indicate that well-designed non-natural amino acids carrying relatively large side chains can be accepted as substrates of the translation system.     

Novel mutation at the initiation codon in the Norrie disease gene in two Japanese families

We have identified a new mutation of Norrie disease (ND) gene in two Japanese males from unrelated families; they showed typical ocular features of ND but no mental retardation or hearing impairment. A mutation was found in both patients at the initation codon of exon 2 of the ND gene (ATG to GTG), with otherwise normal nucleotide sequences. Their mothers had the normal and mutant types of the gene, which was expected for heterozygotes of the disease. The mutation of the initiation codon would cause the failure of ND gene expression or a defect in translation thereby truncating the amino terminus of ND protein. In view of the rarity and marked heterogeneity of mutations in the ND gene, the present apparently unrelated Japanese families who have lived in the same area for over two centuries presumably share the origin of the mutation.     

The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number

Extensive cDNA analysis demonstrated that all human and mouse protocadherin-beta genes are one-exon genes. The protein sequences of these genes are highly conserved, especially the three most membrane-proximal extracellular domains. Phylogenetic analysis suggested that this unique gene family evolved by duplication of one single protocadherin-beta gene to 15 copies. The final difference in the number of protocadherin-beta genes in man (#19) and mouse (#22) is probably caused by duplications later in evolution. The complex relationship between human and mouse genes and the lack of pseudogenes in the mouse protocadherin-beta gene cluster suggest a species-specific evolutionary pressure for maintenance of numerous protocadherin-beta genes.     

Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families

The sequences of the adenylate kinase gene (adk) and the RecA gene (recA) were determined from the same isolates ofNeisseria gonorrhoeae, N. meningitidis, N. lactamica, N. polysaccharea, N. cinerea, N. mucosa, N. pharyngis var.flava, N. flavescens, andN. animalis. The patterns of sequence divergence observed atadk andrecA were very different. Dendrograms constructed from therecA data using two different algorithms were statistically robust and were congruent with each other and with the relationships between the species previously proposed using other data. In contrast, the dendrograms derived from theadk data were noncongruent with each other, and with those from therecA data, and were statistically poorly supported. These results, along with the uniform distribution of pairwise sequence divergences between the species atadk, suggest there has been a history of interspecies recombination within theadk gene of the humanNeisseria species which has obscured the phylogenetic relationships between the species. This view was supported by Sawyer's runs test, and the Index of Association (I_A) between codons, which provided significant evidence for interspecies recombination between theadk genes from the humanNeisseria species, but no evidence of interspecies recombination between therecA sequences.     

Position-specific and non-colinear expression of the planarian posterior (Abdominal-B-like) gene

Hox genes are pivotal molecules in the control of morphogenesis along the anterior-posterior (AP) axis in various bilaterians. Planarians are key animals for understanding the evolution of the bilaterian body plan. Furthermore, they are also known for their strong regeneration ability and are thought to use the Hox genes in the process of reconstruction of the AP axis. In the present paper, the identification and analysis of expression of two posterior (Abdominal-B-like) genes, DjAbd-Ba and DjAbd-Bb, is reported in the planarian Dugesia japonica. DjAbd-Ba is expressed in the entire tail region and its anterior boundary is the posterior pharyngeal region. In contrast, DjAbd-Bb is expressed in several types of cells throughout the body. During regeneration, the expression of DjAbd-Ba rapidly recovers a pattern similar to that in the normal worm. These findings suggest the possibility that DjAbd-Ba is involved in the specification of the tail region. The anterior boundary of the expression domain of the posterior gene DjAbd-Ba is anterior to the domains of the central genes Plox4-Dj and Plox5-Dj. These expression patterns of planarian Hox genes seem out of the rule of spatial colinearity and may reflect an ancestral feature of bilaterian Hox genes.     

A comparative study of mutations in Escherichia coli and Salmonella typhimurium shows that codon conservation is strongly correlated with codon usage

Escherichia coli and Salmonella typhimurium are closely related species of enteric bacteria, having diverged from 120 to 160 million years ago, according to the estimate of Ochman & Wilson (1987. J. Mol. Evol.26, 74-86). In order to study base substitution mutations in the genomes of these bacteria, we have compared pairs of genes for the same product in the two species, and have selected a sample in which the protein length is the same in both E. coli and S. typhimurium. From the alignment of these gene pairs, we observe that frequently used codons are more conserved than infrequently used codons, i.e., the apparent mutation rate is higher for rare codons than for popular codons.     

How gene families evolve

Theories and facts of gene family evolution are reviewed. Concerted evolution is commonly observed for gene families which originated a long time ago, however there are many different types of multigene families, from uniform to diverse. The rate of homogenization by unequal crossing-over, gene conversion, etc. has been evolutionarily adjusted for each gene family. When new functions are needed by organisms, gene families may evolve into superfamilies, in which no further concerted evolution takes place, and each member of the family may acquire an indispensable function. The homeobox-containing gene family is a most exciting example of such superfamily.     

Concerted gene duplications in the two keratin gene families

Summary Evolutionary trees were derived from the keratin protein sequences using the Phylogeny Analysis Using Parsimony (PAUP) set of programs. Three major unexpected conclusions were derived from the analysis: The smallest keratin protein subunit, K#19 (Moll et al. 1982), is not the most primitive one, but has evolved to fulfill a highly specialized function, presumably to redress the unbalanced synthesis of keratin subunits. Second, the ancestors of keratins expressed in the early embryonic stages, K#8 and K#18, were the first to diverge from the ancestors of all the other keratins. The branches leading to these two keratins are relatively short, indicating a comparatively strong selection against changes in the sequences of these two proteins. Third, the two keratin families show extraodinary parallelism in their patterns of gene duplications. In both families the genes expressed in embryos diverged first, later bursts of gene duplications created the subfamilies expressed in various differentiated cells, and relatively recent gene duplications gave rise to the hair keratin genes and separated the basal cell-specific keratin from those expressed under hyperproliferative conditions. The parallelism of gene duplications in the two keratin gene families implies a mechanism in which duplications in one family influence duplication events in the other family.     

Predicting gene expression level from codon usage bias

The "expression measure" of a gene, E(g), is a statistic devised to predict the level of gene expression from codon usage bias. E(g) has been used extensively to analyze prokaryotic genome sequences. We discuss 2 problems with this approach. First, the formulation of E(g) is such that genes with the strongest selected codon usage bias are not likely to have the highest predicted expression levels; indeed the correlation between E(g) and expression level is weak among moderate to highly expressed genes. Second, in some species, highly expressed genes do not have unusual codon usage, and so codon usage cannot be used to predict expression levels. We outline a simple approach, first to check whether a genome shows evidence of selected codon usage bias and then to assess the strength of bias in genes as a guide to their likely expression level; we illustrate this with an analysis of Shewanella oneidensis.     

A new hypervariable marker for the human alpha-globin gene cluster.

We have located a highly polymorphic region of DNA approximately 100 kb upstream of the human alpha-globin genes (the alpha-globin 5' hypervariable region; 5'HVR). The element responsible is a minisatellite sequence comprising a variable copy number tandem repeat array of a G/C-rich 57-bp sequence. This increases the number of minisatellite elements in the vicinity of the alpha-globin genes to five, all of which share a region of sequence identity, thus raising questions concerning the distribution and origins of such tandem repeat sequences. The 5'HVR is highly polymorphic and, together with other hypervariable regions at this locus, provides a valuable genetic marker on the short arm of chromosome 16.     

Evolutionary patterns of codon usage in the chloroplast gene rbcL

In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chloroplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure uses maximum likelihood-ratio tests to compare the performance of two models, one in which a single codon is overrepresented and one in which two codons are overrepresented. The measure allowed us to analyze both the extent of bias in each lineage and the evolution of codon choice across the phylogeny. Despite predictions based primarily on the low G + C content of the chloroplast and the high functional importance of rbcL, we found large differences in the extent of bias, suggesting differential molecular selection that is clade specific. The seed plants and simple leafy liverworts each independently derived a low level of bias in rbcL, perhaps indicating relaxed selectional constraint on molecular changes in the gene. Overrepresentation of a single codon was typically plesiomorphic, and transitions to overrepresentation of two codons occurred commonly across the phylogeny, possibly indicating biochemical selection. The total codon bias in each taxon, when regressed against the total bias of each amino acid, suggested that twofold amino acids play a strong role in inflating the level of codon usage bias in rbcL, despite the fact that twofolds compose a minority of residues in this gene. Those amino acids that contributed most to the total codon usage bias of each taxon are known through amino acid knockout and replacement to be of high functional importance. This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness.     

High-resolution analysis of a hypervariable region in the human apolipoprotein B gene.

A hypervariable region occurs immediately 3' of the human apolipoprotein B gene. Several allelic variants of this tandemly repeated sequence can be resolved by genomic blotting. Higher resolution among size variants may be obtained by polymerase-chain-reaction amplification of this region followed by electrophoresis in a denaturing acrylamide gel. Fourteen different alleles containing 25-52 repeats of the basic 15-bp unit were distinguished in a population study of 318 unrelated individuals. This approach should be applicable to pedigree and linkage analysis with the apolipoprotein B gene or other tandemly repeated sequence elements.