Genetic location of the gene (ush) specifying periplasmic uridine 5'-diphosphate glucose hydrolase (5'-nucleotidase) in Escherichia coli K-12.

Further genetic mapping to two- and three-factor crosses show that the ush gene is closely linked to two other genes hemG and pisA, and that the probable gene order is proC-hemG-plsA-ush-gal.     

Evidence for “Deleted” or “Silent” gene homozygous at the locus coding for the constant region of the γ3 chain

Three uncommon stable Gm haplotypes, Gm3;23;--, Gm1,2,17;..;-- and Gm1,17;..;-- have been transmitted through 3 generations of two related Lebanese and Syrian families. No pathological consequence was noted in seven individuals, aged 14--65, whose sera were deficient for all the allotypes carried by the IgG3 chains. Among the different genetic events which could have produced these haplotypes (alteration of a regulatory gene, point mutation, gene hybridization, gene deletion), it appears that a structural deletion is the most probable explanation. The observed data can be explained by either a partial or a total deletion of the constant portion of the IgG3 heavy chain.     

Rooted triple consensus and anomalous gene trees

Background  

Anomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs.     

SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2)

The sequencing of the entire genetic complement of Streptomyces coelicolor A3(2) has been completed with the determination of the 365,023 bp sequence of the linear plasmid SCP1. Remarkably, the functional distribution of SCP1 genes somewhat resembles that of the chromosome: predicted gene products/functions include ECF sigma factors, antibiotic biosynthesis, a gamma-butyrolactone signalling system, members of the actinomycete-specific Wbl class of regulatory proteins and 14 secreted proteins. Some of these genes are among the 18 that contain a TTA codon, making them targets for the developmentally important tRNA encoded by the bldA gene. RNA analysis and gene fusions showed that one of the TTA-containing genes is part of a large bldA-dependent operon, the gene products of which include three proteins isolated from the spore surface by detergent washing (SapC, D and E), and several probable metabolic enzymes. SCP1 shows much evidence of recombinational interactions with other replicons and transposable elements during its history. For example, it has two sets of partitioning genes (which may explain why an integrated copy of SCP1 partially suppressed the defective partitioning of a parAB-deleted chromosome during sporulation). SCP1 carries a cluster of probable transfer determinants and genes encoding likely DNA polymerase III subunits, but it lacks an obvious candidate gene for the terminal protein associated with its ends. This may be related to atypical features of its end sequences.     

Evolutionary trends in the hemoglobins of murine animals

The evolutionary origin of murine line based on a phylogenetic tree made on sequence data of ∞-and β-hemoglobin chains, followed by the diversity spectrum of hemoglobin genes in two wild species of murine rodents:Rattus rattus rufescens (house rat) andBandicota indica (bandicoot rat) has been reported. Each house rat contains six hemoglobin types involving two ∞-and three β-chains, which suggests a probable gene duplication at the oc chain locus and a gene triplication at the β-chain locus. Each bandicoot rat contains one ∞-and two β-chains suggesting a probable gene duplication at the β-chain locus. Peptide pattern analysis of the polypeptide chains of these murine hemoglobins further indicates that intraspecies differences among duplicated chains of the same kind are less than interspecies differences among corresponding ∞-and β-chains.     

Comparative mapping of the human 9q34 region in Fugu rubripes

Twenty-seven genes have been cloned and mapped in Fugu which have orthologues within the human chromosome 9q34 region. The genes are arranged into five cosmid and BAC contigs which physically map to two different Fugu chromosomes. Considering the gene content of these contigs, it is more probable that a translocation event took place early in the Fugu lineage to split the ancestral 9q34 region onto two chromosomes rather than the alternative hypothesis of a large-scale duplication of the region into two chromosomes with subsequent rapid and dramatic gene loss. There are considerable differences in gene order between the two species, which would appear to be the result of a series of complex chromosome inversions; thus suggesting that there have been no positional constraints on this particular gene set.     

Subdivision in an ancestral species creates asymmetry in gene trees

We consider gene trees in three species for which the species tree is known. We show that population subdivision in ancestral species can lead to asymmetry in the frequencies of the two gene trees not concordant with the species tree and, if subdivision is extreme, cause the one of the nonconcordant gene trees to be more probable than the concordant gene tree. Although published data for the human-chimp-gorilla clade and for three species of Drosophila show asymmetry consistent with our model, sequencing error could also account for observed patterns. We show that substantial levels of persistent ancestral subdivision are needed to account for the observed levels of asymmetry found in these two studies.     

Cloning a putative self-incompatibility gene from the pollen of the grass Phalaris coerulescens.

In Phalaris coerulescens, gametophytic self-incompatibility is controlled by two unlinked genes: S and Z. A probable S gene has now been isolated and sequenced. This represents a novel self-incompatibility gene isolated from pollen in the multilocus system of a monocotyledonous plant. The gene is approximately 3 kb long, split by five introns, and exclusively expressed in the mature pollen. The deduced amino acid sequences from the S1, S2, and part of the S4 alleles showed that the protein has a variable N terminus and a conserved C terminus. The sequence of a complete mutant at the S locus indicated that mutations in the conserved C terminus, a thioredoxin-like region, led to loss of function. We propose that the gene has two distinct sections, a variable N terminus determining allele specificity and a conserved C terminus with the catalytic function. The gene structure and its deduced protein sequences strongly suggest that this monocotyledon has developed a self-incompatibility system entirely different from those operating in the dicotyledons. The possible interactions between S and Z genes in both pollen and stigma are discussed.     

Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

Background  

We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric.     

A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment

A rigorous Bayesian analysis is presented that unifies protein sequence-structure alignment and recognition. Given a sequence, explicit formulae are derived to select (1) its globally most probable core structure from a structure library; (2) its globally most probable alignment to a given core structure; (3) its most probable joint core structure and alignment chosen globally across the entire library; and (4) its most probable individual segments, secondary structure, and super-secondary structures across the entire library. The computations involved are NP-hard in the general case (3D-3D). Fast exact recursions for the restricted sequence singleton-only (1D-3D) case are given. Conclusions include: (a) the most probable joint core structure and alignment is not necessarily the most probable alignment of the most probable core structure, but rather maximizes the product of core and alignment probabilities; (b) use of a sequence-independent linear or affine gap penalty may result in the highest-probability threading not having the lowest score; (c) selecting the most probable core structure from the library (core structure selection or fold recognition only) involves comparing probabilities summed over all possible alignments of the sequence to the core, and not comparing individual optimal (or near-optimal) sequence-structure alignments; and (d) assuming uninformative priors, core structure selection is equivalent to comparing the ratio of two global means.     

Primary structure of the full-size DNA copy of the NP gene of influenza virus A/Kiev/59/79 (H1N1)

The complete nucleotide sequence of the cloned full-length DNA copy of A/Kiev/59/79 (H1N1) influenza virus nucleoprotein gene has been determined. This strain is shown to be the natural recombinant that inherited its nucleoprotein gene from contemporary H3N2-influenza strains. The comparison with other NP-genes reveals the probable localization of antigenic determinants and phosphorylation site of the NP-protein.     

Classification and nomenclature of all human homeobox genes

Background

The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.

Results

We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.

Conclusion

We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.