Gene fusion in <Emphasis Type="Italic">Helicobacter pylori</Emphasis>: making the ends meet

Fusion genes have been reported as a means of enabling the development of novel or enhanced functions. In this report, we analyzed fusion genes in the genomes of two Helicobacter pylori strains (26695 and J99) and identified 32 fusion genes that are present as neighbours in one strain (components) and are fused in the second (composite), and vice-versa. The mechanism for each case of gene fusion is explored. 28 out of 32 genes identified as fusion products in this analysis were reported as essential genes in the previously documented transposon mutagenesis of H. pylori strain G27. This observation suggests the potential of the products of fusion genes as putative microbial drug targets. These results underscore the utility of bacterial genomic sequence comparisons for understanding gene evolution and for in silico drug target identification in the post-genomic era. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Resurrection of an ancestral gene: functional and evolutionary analyses of the Ng<Emphasis Type="Italic">rol</Emphasis> genes transferred from<Emphasis Type="Italic"> Agrobacterium</Emphasis> to<Emphasis Type="Italic"> Nicotiana</Emphasis>

The Ngrol genes, which have high similarity in sequence to the rol genes of Agrobacterium rhizogenes, are present in the genome of untransformed plants of Nicotiana glauca. It is thought that bacterial infection resulted in the transfer of the Ngrol genes to plants early in the evolution of the genus Nicotiana, since several species in this genus contain rol-like sequences but others do not. Plants transformed with the bacterial rol genes exhibit various developmental and morphological changes. The presence of rol-like sequences in plant genomes is therefore thought to have contributed to the evolution of Nicotiana species. This paper focuses on studies of the Ngrol genes in present-day plants and during the evolution of the genus Nicotiana. The functional sequences of several Ngrol genes may have been conserved after their ancient introduction from a bacterium to the plant. Resurrection of an ancestral function of one of the Ngrol genes, as examined by physiological and evolutionary analyses, is also described. The origin of the Ngrol genes is then considered, based on results of molecular phylogenetic analyses. The effects of the horizontal transfer of the Ngrol genes and mutations in the genes are discussed on the plants of the genus Nicotiana during evolution.Seishiro Aoki is the recipient of the Botanical Society Award for Young Scientist, 2002.     

Scapharca inaequivalvis tetrameric hemoglobin A and B chains: cDNA sequencing and genomic organization

A and B globin cDNAs from the tetrameric hemoglobin of the bivalve molluscScapharca inaequivalvis were isolated by RT-PCR and sequenced. When compared with the biochemical data, the deduced protein sequences revealed only one amino acid substitution in the B chain. In order to investigate the genomic structure of these invertebrate globin genes, their intronic regions were amplified by PCR. The two genes showed the typical two-intron/three-exon organization found in vertebrates and seemed to reflect the ancestral gene structure, in accordance with the new globin gene evolution theory proposed by Dixon and Pohajadak (Trends Biochem. Sci. 17:486–488, 1992). The alternative hypothesis suggested by Go (Nature 291:90–92, 1981), that the central intron was lost during evolution, is also considered. In contrast to the related clamAnadara trapezia, S. inaequivalvis A and B globin genes were found to be present in multiple copies differing in intron size. In this study we report the complete sequences of the A (1,471 bp) and B (2,221 bp) globin genes, giving a detailed analysis of their intron features.     

A biometric study of theOrnithogalum umbellatum (Hyacinthaceae) complex in France

Macromorphological variation within theOrnithogalum umbellatum L. (Hyacinthaceae) complex in France was studied. The resulting data were treated by numerical taxonomy methods. Three morphs can be identified: one corresponding to diploid plants, another made up of triploids and a third which encompasses plants having ploidy level above 3x (4x, 5x, and 6x). A systematic interpretation of the complex is proposed wherein only one species,O. umbellatum, is retained. This species corresponds to a polyploid complex undergoing evolution.     

Synthesis and assembly of the cytochrome b-f complex in higher plants

The cytochrome b-f complex is composed of four polypeptide subunits, three of which, cytochrome f, cytochrome b-563 and subunit IV, are encoded in chloroplast DNA and synthesised within the chloroplast, and the fourth, the Rieske FeS protein, is encoded in nuclear DNA and synthesised in the cytoplasm. The assembly of the cytochrome b-f complex therefore requires the interaction of subunits encoded by different genomes. A key role for the nuclear-encoded Rieske FeS protein in the assembly of the complex is suggested by a study of cytochrome b-f complex mutants. The assembly of individual subunits of the complex may be regulated by the availability of prosthetic groups. The genes for the chloroplast-encoded subunits and cDNA clones for the Rieske FeS protein have been isolated and characterised. Cytochrome f and the Rieske FeS protein are synthesised initially with N-terminal presequences required for their correct assembly within the chloroplast. The deduced amino acid sequences of the four subunits have been used to suggest models for the arrangement of the polypeptides in the thylakoid membrane.     

Regulation and structure of aspartokinase in the genusBacillus

The aspartate pathway of amino acid biosynthesis in bacteria serves as paradigm for the evolution of patterns of enzyme regulation in response to specific physiological requirements. InBacillus species, the first step in the pathway is catalyzed by multiple forms of aspartokinase, which differ in their structure and feedback regulation. One form of aspartokinase (V-type) functions primarily during cell growth, another form (S-type) during sporulation. The V-type aspartokinase fromBacillus subtilis andBacillus polymyxa is discussed in some detail on account of its complex pattern of regulation by the pathway endproducts lysine and threonine and its unusual subunit structure. The enzyme is composed of two dissimilar subunits, the smaller of which corresponds to the carboxyl-terminal domain of the larger subunit. The coding sequence for the subunits ofBacillus subtilis aspartokinase has recently been cloned inEscherichia coli. The study of its structure and mode of expression has revealed that the two aspartokinase subunits are encoded by in-phase overlapping genes. These unusual features of aspartokinase suggest that important aspects of the regulation of the aspartate pathway are yet to be discovered.     

Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions

We mapped two loci for ADP-ribosylation factor homologues (ARF1, ARF2) and two loci for cysteine proteinase inhibitors (oryzacystatin-I and -II: OCI, OCII) by linkage analysis of restriction fragment length polymorphism loci in rice (Oryza sativa L.) genomic DNAs using their cDNAs as probes.Oc-1 andArf-2 were found to be closely located to each other on chromosome 1, whileOc-2 andArf-1,both found on chromosome 5, were also located close to each other. The map distances are about 2 cM in both pairs. In each chromosome, theArf locus was located about 27 cM from that of the aldolase gene (Ald-2 in chromosome 1 andAld-1 in chromosome 5). These three genes are in the same order,Ald-Arf-Oc, but in opposite orientations relative to the distal ends of the linkage group. The presence of two sets of three linked genes on chromosomes 1 and 5 strongly suggests a structural similarity of the blocks of the two chromosomes, which probably reflects duplication of the segment. A recent investigation by other workers has shown that these rice blocks correspond to two regions in maize chromosomes 8 and 6, that have previously been shown to share many duplicated nucleotide sequences. It is therefore very likely that the duplication of the region occurred before the divergence of rice and maize during the evolution of the subfamilies of the grasses (Gramineae). In view of a recently discovered possible structural similarity between the small GTP-binding protein superfamily, which includesArf andras proteins, and the cystatin family, the close linkage ofOc andArf loci found in the present study suggests a possible cluster of genes related to the small GTP-binding proteins.     

High frequency of hemolytic and cytotoxic activity in Aeromonas spp. isolated from clinical, food and environmental in Rio de Janeiro, Brazil

Molecular study of aerolysin and cytotonic enterotoxin genes by PCR and colony blot hybridization was performed in 117 strains of Aeromonas spp. isolated from different sources. Homogeneous distribution of these genes in A. hydrophila complex strains was observed. For A. caviae and A. sobria complex strains, aerolysin genes were more frequent than cytotonic enterotoxins genes. Of 64 A. caviae complex strains, only one (1.5%) amplified the 451 bp product for the aer gene, however, the same primers detected a 400 bp product in 50 (78%) strains. This product was sequenced and had two short regions with homology to several hemolysin genes. The genotype aer ⁺/aerA⁺/hly ⁺/ast ⁺/alt ⁺ was detected in six A. hydrophila strains from food and environmental source. The most common genotype found in A. hydrophila strains was hly ⁺ (85%) and aerA⁺ (78.7%), while in A. caviae complex strains was aerA⁺ (32.8%). All A. veronii complex sobria strains were aer ⁺/aerA⁺. All A. caviae and A. hydrophila were positive when tested with aer probe using the colony blot test. Thirty-seven percent of A. hydrophila and 53% of A. caviae tested were positive for ast probe. Eighty-nine percent of samples were cytotoxic in Vero cells. Our data demonstrated that Aeromonas spp. can harbor and express virulence genes and reinforce the potential of Aeromonas as a human pathogen.     

The genetics of adaptation in Drosophila sechellia

Drosophila sechellia is an island endemic of the Seychelles. After its geographic isolation on these islands, D. sechellia evolved into a host specialist on the fruit of Morinda citrifolia – a fruit often noxious and repulsive to Drosophila. Specialization on M. citrifolia required the evolution of a suite of adaptations, including resistance to and preference for some of the toxins found in this fruit. Several of these adaptive traits have been studied genetically. Here, I summarize what is known about the genetics of these traits and briefly describe the ecological and geographical context that shaped the evolution of these characters. The data from D. sechellia suggest that adaptations are not as genetically complex as historically thought, although almost all of the adaptations of D. sechellia involve several genes.     

Hox and ParaHox genes: A review on molluscs

Hox and ParaHox genes are involved in patterning the anterior‐posterior body axis in metazoans during embryo development. Body plan evolution and diversification are affected by variations in the number and sequence of Hox and ParaHox genes, as well as by their expression patterns. For this reason Hox and ParaHox gene investigation in the phylum Mollusca is of great interest, as this is one of the most important taxa of protostomes, characterized by a high morphological diversity. The comparison of the works reviewed here indicates that species of molluscs, belonging to different classes, share a similar composition of Hox and ParaHox genes. Therefore evidence suggests that the wide morphological diversity of this taxon could be ascribed to differences in Hox gene interactions and expressions and changes in the Hox downstream genes rather than to Hox cluster composition. Moreover the data available on Hox and ParaHox genes in molluscs compared with those of other Lophotrochozoa shed light on the complex and controversial evolutionary histories that these genes have undergone within protostomes. genesis 52:935–945, 2014. © 2014 Wiley Periodicals, Inc.     

An Inception Report on the TOM Complex of the Amoeba <Emphasis Type="Italic">Acanthamoeba castellanii</Emphasis>, a Simple Model Protozoan in Mitochondria Studies

It is suggested that in the course of the TOM complex evolution at least two lineages have appeared: the animal–fungal and green plant ones. The latter involves also the TOM complexes of algae and protozoans. The amoeba Acanthamoeba castellanii is a free-living nonphotosynthetic soil protozoan, whose mitochondria share many bioenergetic properties with mitochondria of plants, animals and fungi. Here, we report that a protein complex, identified electrophysiologically as the A. castellanii TOM complex, contains a homologue of yeast/animal Tom70. Further, molecular weight of the complex (about 500 kDa) also points to A. castellanii evolutionary relation with fungi and animal. Thus, the data indicates that the TOM complex of A. castellanii is not a typical example of the protozoan TOM complex.     

Asymmetrical Evolution of Cytochrome bd Subunits

Functionally linked genes generally evolve at similar rates and the knowledge of this particular feature of genomic evolution has been used as the basis for the phylogenetic profiling method. We illustrate here an exception to this rule in the evolution of the cytochrome bd complex. This is a two-component oxidase complex, with the subunits I and II known to be widely present in bacteria. The subunits within the cytochrome bd complex are under the same evolutionary pressure and most likely behave in the same evolutionary manner. However, the sequence similarity of genes encoding subunit II varies considerably across species. Genes encoding subunit II evolve 1.2 times faster on most of the branches of their phylogeny than subunit I genes. Furthermore, the genes encoding subunit II in Oceanobacillus iheyensis, Bacillus halodurans, and Staphylococcus species do not have detectable homologues within E. coli due to their large divergence. Together, the two subunits of cytochrome bd reveal an interesting example of an asymmetric pattern of evolutionary change. [Reviewing Editor: Dr. Brian Morton]     

Karyotype evolution in South American species of Hypochaeris (Asteraceae, Lactuceae)

The genus Hypochaeris (Asteraceae, Lactuceae) contains ten species in Europe, three in Asia, and approximately 50 in South America. Previous cytotaxonomic studies have shown two groups of taxa: (1) European species with different basic chromosome numbers and differentiated karyotypes, and (2) South American species with x=4 and uniform asymmetric and bimodal karyotypes. Karyotypic data are synthesized for South American species of Hypochaeris with new information for six Chilean species: H. acaulis, H. apargioides, H. palustris, H. spathulata, H. tenuifolia and H. thrincioides. Four main groups can be distinguished based on presence and localization of secondary constrictions – SCs (bearing Nucleolar Organizer Regions – NORs) on chromosomes 2 and 3, and 18S–25S and 5S rDNA loci number, localization, and activity. We propose karyotypic evolution of South American Hypochaeris (x=4) from H. maculata-like (x=5) European ancestors. The original South American karyotype would have possessed two SCs, one on the long arm of chromosome 2, and the other on the short arm of chromosome 3 (in terminal position). Further evolution would have involved inversion within the short arm of chromosome 3 and inactivation/loss of the SC on chromosome 2.     

Maternal expression increases the rate of <Emphasis Type="Italic">bicoid</Emphasis> evolution by relaxing selective constraint

Population genetic theory predicts that maternal effect genes will evolve differently than genes expressed in both sexes because selection is only half as effective on autosomal genes expressed in one sex but not the other. Here, we use sequences of the tandem gene duplicates, bicoid (bcd) and zerknüllt (zen), to test the prediction that, with similar coefficients of purifying selection, a maternal effect gene evolves more rapidly than a zygotic gene because of this reduction in selective constraint. We find that the maternal effect gene, bcd, is evolving more rapidly than zygotically expressed, zen, providing the first direct confirmation of this prediction of maternal effect theory from molecular evidence. Our results extend current explanations for the accelerated rate of bcd evolution by providing an evolutionary mechanism, relaxed selective constraint, that allows bcd the evolutionary flexibility to escape the typical functional constraints of early developmental genes. We discuss general implications of our findings for the role of maternal effect genes in early developmental patterning.     

Production of H<Subscript>2</Subscript> from sucrose by <Emphasis Type="Italic">Escherichia coli</Emphasis> strains carrying the pUR400 plasmid,which encodes invertase activity

Escherichia coli HD701, a hydrogenase-upregulated strain, has the potential for industrial-scale H₂ production but is unable to metabolise sucrose, which is a major constituent of many waste materials that could be used as feedstocks for H₂ production processes. A 70 kb plasmid (pUR400), which carries the genes necessary for sucrose transport into the cell and its metabolism, was conjugated into E. coli strains HD701 and FTD701 [a derivative of HD701 which has a deletion of the tatC gene of the twin arginine transport (Tat) protein system] from an E. coli K12 strain. Comparative studies on H₂ evolution by FTD701 and HD701, with and without the pUR400 plasmid, were made using sucrose as substrate. The parental strains did not evolve H₂, although HD701/pUR400 and FTD701/pUR400 evolved 1.27 ± 0.09 and 1.38 ± 0.05 ml H₂ mg dry wt^–1 l culture^–1, respectively over 10 h. This work provides the choice for using a recombinant E. coli strain, which produces H₂ from sucrose, as an alternative to coupling-in an upstream invertase, and hence this provides a simpler method for the bioproduction of H₂ from sucrose.Revisions requested 24 August 204; Revisions received 21 October 2004     

Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae)

The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene (∼4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory gene function correlate with petal colors differences that characterize the divergence between two diploid species and the tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions about the evolution of the dwarf dogwood complex.     

Seven Hox gene sequences from the asterinid starfish Patiriella exigua (Echinodermata: Asteroidea)

Partial homeobox gene fragments were amplified from Patiriella exigua genomic DNA by PCR using degenerate primers. The primers spanned a region of 82 nucleotides within the homeobox, encompassing amino acids 21–47 of the homeodomain. The deduced amino acid sequences of the seven Hox gene sequences plus one Xlox-type gene sequence from P. exigua are presented and compared with similar sequences from other organisms. This work is a preliminary step in the analysis of the evolution of development in the Patiriella species group and the roles of Hox gene expression therein.     

Structural evolution of the Drosophila 5S ribosomal genes

We compare the 5S gene structure from nine Drosophila species. New sequence data (5S genes of D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii) and already-published data (5S genes of D. melanogaster, D. simulans, and D. teissieri) are used in these comparisons. We show that four regions within the Drosophila 5S genes display distinct rates of evolution: the coding region (120 bp), the 5-flanking region (54–55 bp), the 3-flanking region (21–22 bp), and the internal spacer (149–206 bp). Intra- and interspecific heterogeneity is due mainly to insertions and deletions of 6–17-bp oligomers. These small rearrangements could be generated by fork slippages during replication and could produce rapid sequence divergence in a limited number of steps. Correspondence to: M. Wegnez     

Cytochrome bc 1 and b 6 f complexes of photosynthetic membranes

All photosynthetic membranes contain a cytochrome bc ₁ or b ₆ f complex that catalyzes the oxidation of quinols and the reduction of a high-potential electron carrier, such as cytochrome c ₂ or plastocyanin. The cytochrome complex also functions in the translocation of protons across the membrane and as a consequence, establishes the proton motive force that is used for the synthesis of ATP. The structure and function of the cytochrome complexes are first reviewed in this chapter. Amino acid sequence information for almost all of the protein subunits of these complexes is now available, and these allow for a detailed consideration of functional domains in the protein subunits and for a further discussion of the evolution of the cytochrome complex in photosynthetic organisms.