Rhodobacter capsulatus genes involved in early steps of the bacteriochlorophyll biosynthetic pathway.

Three open reading frames in the Rhodobacter capsulatus photosynthesis gene cluster, designated F0, F108, and F1025, were disrupted by site-directed mutagenesis. Mutants bearing insertions in these reading frames were defective in converting protoporphyrin IX to magnesium-protoporphyrin monomethyl ester, protochlorophyllide to chlorophyllide a, and magnesium-protoporphyrin monomethyl ester to protochlorophyllide, respectively. These results demonstrate that the genes examined most likely encode enzyme subunits that catalyze steps common to plant and bacterial tetrapyrrole photopigment biosynthetic pathways. The open reading frames were found to be part of a large 11-kilobase operon that encodes numerous genes involved in early steps of the bacteriochlorophyll a biosynthetic pathway.     

The organization of ribosomal genes in vertebrates

The organization of the repeat unit of the ribosomal genes has been determined in 15 different species of vertebrates. The EcoRI and BamHI restriction maps of the rDNA from single individuals of different species of fishes, amphibians, and reptiles have been analysed. Two rDNA clones from Xenopus laevis (representing one complete repeat unit) were used as probes in Southern blots to detect restriction fragments containing ribosomal genes. The results obtained indicate that the transcribed regions are highly conserved in length and sequence inside the same zoological class. These regions are less conserved when species from different classes are compared but a general trend has been observed. In contrast, the length and sequence of the spacer regions are very variable, even within the same zoological class. Different types of heterogeneity have been observed; examples range from a single type of ribosomal repeat unit within a species to the absence of any detectable regular tandem array of units.     

Evolution of genes involved in gamete interaction: evidence for positive selection, duplications and losses in vertebrates

Genes encoding proteins involved in sperm-egg interaction and fertilization exhibit a particularly fast evolution and may participate in prezygotic species isolation [1], [2]. Some of them (ZP3, ADAM1, ADAM2, ACR and CD9) have individually been shown to evolve under positive selection [3], [4], suggesting a role of positive Darwinian selection on sperm-egg interaction. However, the genes involved in this biological function have not been systematically and exhaustively studied with an evolutionary perspective, in particular across vertebrates with internal and external fertilization. Here we show that 33 genes among the 69 that have been experimentally shown to be involved in fertilization in at least one taxon in vertebrates are under positive selection. Moreover, we identified 17 pseudogenes and 39 genes that have at least one duplicate in one species. For 15 genes, we found neither positive selection, nor gene copies or pseudogenes. Genes of teleosts, especially genes involved in sperm-oolemma fusion, appear to be more frequently under positive selection than genes of birds and eutherians. In contrast, pseudogenization, gene loss and gene gain are more frequent in eutherians. Thus, each of the 19 studied vertebrate species exhibits a unique signature characterized by gene gain and loss, as well as position of amino acids under positive selection. Reflecting these clade-specific signatures, teleosts and eutherian mammals are recovered as clades in a parsimony analysis. Interestingly the same analysis places Xenopus apart from teleosts, with which it shares the primitive external fertilization, and locates it along with amniotes (which share internal fertilization), suggesting that external or internal environmental conditions of germ cell interaction may not be the unique factors that drive the evolution of fertilization genes. Our work should improve our understanding of the fertilization process and on the establishment of reproductive barriers, for example by offering new leads for experiments on genes identified as positively selected.     

Evolution of the 5 S RNA genes in vertebrates

Summary We have built the phylogenetic tree of Vertebrate 5S RNA using the sequence data of thirteen species belonging to six groups. Evolution of the 5S genes has been very slow in Vertebrates since 90 residues are identical in all 5S RNAs which are presently sequenced.In Amphibians and Teleosts different 5S genes are active in oocytes and in somatic cells. This dual gene system has probably been acquired independently by Amphibians and Teleosts. In Amphibians, the oocyte-type 5S genes have evolved much faster than the somatic-type genes. This is not true in all species since the oocyte-type genes of one Teleost (Tinca tinca) have evolved more slowly than the somatic-type genes.There are in all Vertebrate 5S RNAs five complementary regions which can be base-paired. The sequence data are compatible with the three secondary-structure models that have been proposed for 5S RNA.     

Molecular mechanisms of early neurogenesis in vertebrates

Recent studies revealed a great variety of genes which control the early development of the central nervous system in vertebrates, including neural induction and differentiation of primary neurons. Most of these genes were first identified inDrosophila melanogaster, then their structural and functional homologs were found in vertebrates. Modern data on the molecular-genetic mechanisms of vertebrate neurogenesis are reviewed. The neurogenetic mechanisms are compared for vertebrates and invertebrates. Widely discussed hypotheses are considered along with the commonly accepted mechanisms.     

Evolution and development of the synarcual in early vertebrates

The synarcual is a structure incorporating the anterior vertebrae of the axial skeleton and occurs in vertebrate taxa such as the fossil group Placodermi and the Chondrichthyes (Holocephali, Batoidea). Although the synarcual varies morphologically in these groups, it represents the first indication, phylogenetically, of a differentiation of the vertebral column into separate regions. Among the placoderms, the synarcual of Cowralepis mclachlani Ritchie, 2005 (Arthrodira) shows substantial changes during ontogeny to produce an elongate, spool-shaped structure with a well-developed dorsal keel. Because the placoderm synarcual is covered in perichondral bone, the ontogenetic history of this Cowralepis specimen is preserved as it developed anteroposteriorly, dorsally and ventrally. As well, in the placoderm Materpiscis attenboroughi Long et al., 2008 (Ptyctodontida), incomplete fusion at the posterior synarcual margin indicates that both neural and haemal arch vertebral elements are added to the synarcual. A survey of placoderm synarcuals shows that taxa such as Materpiscis and Cowralepis are particularly informative because perichondral ossification occurs prior to synarcual fusion such that individual vertebral elements can be identified. In other placoderm synarcuals (e.g. Nefudina qalibahensis Lelièvre et al., 1995; Rhenanida), cartilaginous vertebral elements fuse prior to perichondral ossification so that individual elements are more difficult to recognize. This ontogenetic development in placoderms can be compared to synarcual development in Recent chondrichthyans; the incorporation of neural and haemal elements is more similar to the holocephalans, but differs from the batoid chondrichthyans.     

Bendable genes of warm-blooded vertebrates.

It is shown that in the genomes of warm-blooded vertebrates the elevation of genic GC-content is associated with an increase in the bendability of the DNA helix, which is both absolute and relative as compared with random sequences. This trend takes place both in exons and introns, being more pronounced in the latter. At the same time, the free energy of melting (delta G) of exons and introns increases only absolutely with elevation of GC-content, whereas it decreases as compared with random sequences (again, this trend is stronger in the introns). In genes of cold-blooded animals, plants, and unicellular organisms, these regularities are weaker and often not consistent. Generally, there is a negative correlation between bendability and melting energy at any fixed GC-content value. This effect is stronger in the introns. These findings suggest that GC-enrichment of genes in the homeotherm vertebrates can be caused by selection for increased bendability of DNA.     

Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes

Extant vertebrates are divided into three major groups: hagfishes (Hyperotreti, myxinoids), lampreys (Hyperoartia, petromyzontids), and jawed vertebrates (Gnathostomata). The phylogenetic relationships among the groups and within the jawed vertebrates are controversial, for both morphological and molecular studies have rendered themselves to conflicting interpretations. Here, we use the sequences of 35 nuclear protein-encoding genes to provide definitive evidence for the monophyly of the Agnatha (jawless vertebrates, a group encompassing the hagfishes and lampreys). Our analyses also give a strong support for the separation of Chondrichthyes (cartilaginous fishes) before the divergence of Osteichthyes (bony fishes) from the other gnathostomes.     

Classification of the genes involved in the two-component system of the moss Physcomitrella patens

Physcomitrella patens, belonging to bryopsida, is a basal lineage of land plants. To gain insight into the diversification of the two-component system (TCS), which is widely conserved from prokaryotes to eukaryotes, we compiled TCS-associated genes by employing P. patens genome databases. The moss has a set of His-kinases (HKs), including homologs of the cytokinin- and ethylene-receptors in seed plants. In addition, it has a number of coding-sequences specifying unique HKs. We found evidence that a putative cytokinin-receptor HK in P. patans serves as a sensor for this hormone, and that the HK activity of a putative ethylene-receptor homolog is regulated by ethylene, as observed for Arabidopsis thaliana.     

Evolutionary history of the Rh blood group-related genes in vertebrates

Rh and its homologous Rh50 gene products are considered to form heterotetramers on erythrocyte membranes. Rh protein has Rh blood group antigen sites, while Rh50 protein does not, and is more conserved than Rh protein. We previously determined both Rh and Rh50 gene cDNA coding regions from mouse and rat, and carried out phylogenetic analyses. In this study, we determined Rh50 gene cDNA coding regions from African clawed frog and Japanese medaka fish, and examined the long-term evolution of the Rh blood group and related genes. We constructed the phylogenetic tree from amino acid sequences. Rh50 genes of African clawed frog and Japanese medaka fish formed a cluster with mammalian Rh50 genes. The gene duplication time between Rh and Rh50 genes was estimated to be about 510 million years ago based on this tree. This period roughly corresponds to the Cambrian, before the divergence between jawless fish and jawed vertebrates. We also BLAST-searched an amino acid sequence database, and the Rh blood group and related genes were found to have homology with ammonium transporter genes of many organisms. Ammonium transporter genes can be classified into two major groups (amt alpha and amt beta). Both groups contain genes from three domains (bacteria, archaea, and eukaryota). The Rh blood group and related genes are separated from both amt alpha and beta groups.     

Vestibulospinal system organization in vertebrates

The data on the vestibular nuclear complex and vestibulospinal systems in vertebrates are reviewed. Literature data on the topography, structure, and fiber connections of vestibular cell groups forming descending projections and the effects on the spinal cord and skeletal muscles are summarized. Current conceptions of the structural and functional specificity of different vestibulospinal systems are discussed.O. O. Bogomolets Institute of Physiology, Ukrainian Academy of Sciences, Kiev. Translated from Neirofiziologiya, Vol. 24, No. 2, pp. 215–238, March–April, 1992.     

Gene duplication and divergence in the early evolution of vertebrates

The duplication-degeneration-complementation model of duplicate gene preservation by subfunctionalisation is currently the best explanation for the high level of retention of duplicate genes in early vertebrate evolution. But a direct test of the applicability of this model to such ancient evolutionary events may be difficult. More likely, recent duplications in other lineages will allow us to establish general principles concerning the fate of genes of different types that are duplicated in different ways. These principles may be then extrapolated to understanding the early evolution of the vertebrates.     

Retention of cryptic genes in microbial populations

Cryptic genes are silenced genes that can still be reactivated by mutation.Since they can make no positive contribution to the fitness of theircarriers, it is not clear why many cryptic genes in microbial populationshave not degenerated into useless DNA sequences. Hall et al. (1983) havesuggested that cryptic genes have persisted because of occasional strongenvironmental selection for reactivated genes. The present mathematicalstudy supports their suggestion. It shows that a cryptic gene can beretained without having any selective advantage over a useless DNAsequence, if selection for the reactivated gene occasionally occurs for asubstantially long time.     

Small nucleolar RNAs and their genes in vertebrates

Genes of box C/D small nucleolar RNAs (snoRNAs) were searched for in the genomes of members of all classes of vertebrates that do not belong to placental mammals. A tendency for an increase in the number of copies of snoRNA genes was observed in such vertebrates. This trend was most pronounced in anamnia (amphibians and fish). Box C mutations were found in 14 snoRNAs in all gene copies among all species studied. The role of the described events is discussed.     

CpG islands, genes and isochores in the genomes of vertebrates

We have shown that human genes associated with CpG islands increase in number as they increase in % of guanine + cytosine (GC) levels, and that most genes associated with CpG islands are located in the GC-richest compartment of the human genome. This is an independent confirmation of the concentration gradient of CpG islands (detected as HpaII tiny fragments, or HTF) which was demonstrated in the genome of warm-blooded vertebrates [A?ssani and Bernardi, Gene 106 (1991) 173-183]. We then reassessed the location of CpG islands using the data currently available and confirmed that CpG islands are most frequently located in the 5'-flanking sequences of genes and that they overlap genes to variable extents. We have shown that such extents increase with the increasing GC levels of genes, the GC-richest genes being completely included in CpG islands. Under such circumstances, we have investigated the properties of the 'extragenic' CpG islands located in the 5'-flanking segments of homologous genes from both warm- and cold-blooded vertebrates. We have confirmed that, in cold-blooded vertebrates, CpG islands are often absent; when present, they have lower GC and CpG levels; the latter attain, however, statistically expected values. Finally, we have shown that CpG doublets increase with the increasing GC of exons, introns and intergenic sequences (including 'extragenic' CpG islands) in the genomes from both warm- and cold-blooded vertebrates. The correlations found are the same for both classes of vertebrates, and are similar for exons, introns and intergenic sequences (including 'extragenic' CpG islands). The findings just outlined indicate that the origin and evolution of CpG islands in the vertebrate genome are associated with compositional transitions (GC increases) in genes and isochores.     

Dynamic evolution of bitter taste receptor genes in vertebrates

Background  

Sensing bitter tastes is crucial for many animals because it can prevent them from ingesting harmful foods. This process is mainly mediated by the bitter taste receptors (T2R), which are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires, and marked variation in repertoire size has been noted among species. However, the mechanisms underlying the evolution of vertebrate T2R genes remain poorly understood.