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Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling > 5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome. comparative genomics | genome sequencing | genome analysis | phylogenetics | mammalian evolution

Research has been conducted on Deinococcus radiodurans, an extremely radioresistant bacterium encoding genes which are homologous to those involved in bacterial lysine biosynthesis. Results indicate that this bacterium carries lysine biosynthesis in a unique way.

Research has been conducted on the microbial population evolution. The authors discuss the Monod model explaining the clock-like behaviour of the selection-driven evolution.

The authors review the publications on Escherichia coli elongation and initiation factors. The topics of interest include the initiation and elongation reaction analysis and the structure and function of these factors.

Research has been conducted on the polychlorophenol-degrading sphingomonads. The role of the horizontal pcpB gene transfer in the sphingomonads' evolution and the distribution of this gene have been studied and discussed.

Research has been conducted on Bacillus sphaericos strains. The resistance evolution to these strains in Culex quinquefaciatus populations collected from China and Brazil has been investigated and the details are reported.

Results demonstrate that genetic recombination played a role in the evolution of Legionella pneumophila as shown by the population structure analysis using RNA polymerase gene and DotA gene sequences. Data indicate a horizontal gene transfer or recombination within L. pneumophilia populations.

Research findings suggest that within the Microcystis, the distribution of tRNA(sup)Leu(UAA) group I introns is governed by both intron transfer and recombination in tRNA and intron-containing region. Data suggest a nested evolution of the intron, in which the intron is transferred horizontally to tRNA(sup)Leu(UAA) gene.

Intimin is a 35-kilodalton protein encoded by the locus of enterocyte effacement (LEE) gene, present in multiple forms in Escherichia coli of O111 clonal lineage. Data indicate that amino acid substitutions occur more frequently than normal in the extracellular domains of intimin, leading to divergence in this protein.

The flagellin genes of Natrialba magadii present a mosaic structure and their sequence analyses indicate that horizontal transmissions may have occurred at different regions of the genes in the course of their evolution.

Researchers designed a plasmid that can increase the mutation frequency of a bacterium by 20- to 4,000-fold. Once the desired trait is achieved, the plasmid can be removed, returning the bacterium to its normal mutation rate. This technique could be used to develop bacteria that can biodegrade high concentrations of metabolites and solvents.

Phylogenetic reconstructions of about 400 homologues are discussed for the origin of mitochondrial proteome from genomes of alpha-proteobacterium and an eukaryotic nucleus. While the core respiratory fuction and proteins are primarily derived from the former, the proteins of the functional complexes are derived from the latter source.

Phylogenetic analysis show that clones of Synechococcus are polyphyletic and their differences in thermotolerance correlated with the differences in the 16S rRNA gene sequences suggesting that more thermotolerant species evolved from less thermotolerant ancestors.

The pathway for degradation of the xenobiotic pesticide pentachlorophenol in Sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. The first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. The second enzyme, a reductive dehalogenase, may have evolved from a maleylacetoacetate isomerase normally involved in degradation of tyrosine. This apparently recently assembled pathway does not function very well: pentachiorophenol hydroxylase is quite slow, and tetrachlorohydroquinone dehalogenase is subject to severe substrate inhibition.

Results indicate that the two psychrophilic Moritella strains investigated possess acetylornithinase and exhibit an organizational structure of the arginine genes that is ancestral to different variations seen among Enterobacteriaceae and Vibrionaceae bacteria.

Research was conducted to examine distribution and evolutionary relationship among protein kinases in prokaryotes and eukaryotes. Results show that originally eukaryotic-type protein kinases were the only type in both classes of organisms but prokaryotes lost them during their evolutionary process. Nucleotide sequence data for four genes encoding the enzyme in Streptomyces coelicolor A3(2) is presented.

This review discusses retrotransfer in a bacterial gene exchange process in which the donor bacterium inherits the genetic traits from the mating partner. This phenomenon is seen in IncP and BHR plasmids and its evolutionary and ecological significance are presented.

Research was conducted to characterize the chromosomal insertion sequence IS1626 from a bacterial species. Results show that IS1626 is a 1418 base pair long with 65 mol% of G+C content and without terminal inverted or flanking direct repeats.

Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coil evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is. from an evolutionary perspective, very brief.

Models of evolutionary processes postulate that new alleles appear in populations through random spontaneous mutation. Alleles that confer a competitive advantage in particular environments are selected and populations can be taken over by individuals expressing these advantageous mutations. We have studied the evolutionary process by using Escherichia coil cultures incubated for prolonged periods of time in stationary phase. The populations of surviving cells were shown to be highly dynamic, even after many months of incubation. Evolution proceeded along different paths even when the initial conditions were identical. As cultures aged, the takeovers by fitter mutants were incomplete, resulting in the coexistence of multiple mutant forms and increased microbial diversity. Thus, the study of bacterial populations in stationary phase provides a model system for understanding the evolution of diversity in natural populations.

The evolutionary relationship of archaebacteria with the gram-positive bacteria was explained to prove that the primary division within prokaryotes was not solely dependent on archaebacteria and eubacteria but was between organisms possessing either a monoderm or a diderm cell structure. Phylogenetic analysis was conducted based on either nucleic acid or protein sequences. It was concluded that archaebacteria and gram-positive bacteria were ancestral in nature based on the sequence signature supported by a reference point and provided by the rooting of the prokaryotic tree.

Research was conducted to prove that parallel speciation patterns occur among several partners of the sepiolid squid-luminous bacterial symbioses. Phylogenetic trees for various species of sepiolids were generated using the sequences of one nuclear locus and one mitochondrial locus. Phylogenetic relationships of their symbiotic bacteria were also determined. Results indicate that competitive dominance among strains of luminous bacteria provides an unusual form of evidence for the existence of parallel speciation among a set of animal-bacterial associations.

The nucleotide sequencing of pSK41, a multiresistance plasmid from Staphylococcus aureus, was undertaken to determine the evolution and other functions encoded by these types of plasmid. These plasmids have multiple copies of the insertion element, IS257, acting as catalysts for adaptation. It was revealed that the sequence contained 42 open reading frames representing functional translated genes and three truncated fragments of genes were identified. The transfer systems of these plasmids had a common evolutionary ancestry with that of the pIP501 broad-host-range plasmid.

A study was undertaken to observe the genetic modifications occurring after experimental evolution of bacterial populations from the Ralstonia strain, TFD41. Bacterial experimental evolution is a helpful method used in the study of basic mechanisms involved in adaptive evolution. Genomic alterations were observed through degenerate primers based on repetitive extragenic palindromic sequences and polymerase chain reactions. Results revealed parallel genotypic alterations were generated from genetic recombination resulting in duplications and deletions of DNA sequences.

Nodulation and nitrogen fixation genes of Mesorhizobium loti are encoded on the chromosome of the bacterium. Nevertheless, there is strong evidence that these genes can be transferred from an inoculant strain to nonsymbiotic mesorhizobia in the field environment. Here we report that the chromosomal symbiotic element of M. loti strain ICMP3153 is transmissible in laboratory matings to at least three genomic species of nonsymbiotic mesorhizobia. The element is 500 kb in size, integrates into a phe-tRNA gene, and encodes an integrase of the phage P4 family just within its left end. The entire phe-tRNA gene is reconstructed at the left end of the element upon integration, whereas the 3[prime] 17 nucleotides of the tRNA gene are present as a direct repeat at the right end. We termed the element a symbiosis island on the basis of its many similarities to pathogenicity islands. It may represent a class of genetic element that contributes to microbial evolution by acquisition.

An analysis of the entire yeast genome shows a pattern of gene duplication compatible with the concept that the whole sequence experienced duplication some 100 million years ago. The findings are consistent with Ohno's theory that polyploidy (whole-genome duplication) is an important mechanism for evolutionary novelty. The yeast genome of Saccharomyces cervisiae is thought to be a degenerate tetraplid, different from other unduplicated yeasts because of its capacity to anaerobically ferment sugars to produce ethanol.

The ortholog of a gene for a third family B DNA polymerase was detected from Sulfolobus solfataricus P2. Cloning and sequence analysis of the ortholog of the gene designated as B3 in Sulfolobus shibatae indicated the presence of a multiple family of B DNA polymerases in crenarchaeotes. However, the nucleotide sequences of orthologous Sulfolobus shibatae B3 and Sulfolobus solfataricus P2 B3 exhibited several amino acid differences despite their close evolutionary relationship.

Seventy-three group one and group two sigma70-type sigma factors were analyzed to determine the phylogenetic relationship of different species of eubacteria. Analysis and characterization of the products of sigma factor genes from cyanobacterium, gram-positive photosynthetic bacterium and proteobacterium indicated the high degree of conservation of the sigma factors in eubacteria. Furthermore, the phylogenetic tree that was constructed based on group 1 sigma70 factors was similar to that of SS-ribosomal RNA sequences.

The several strains of Salmonella enterica and Escherichia coli subspecies were analyzed to determine the occurrence, distribution and genetic diversity of the microbes and the evolutionary significance of F plasmid transfer. Analysis of 71 natural isolates of Salmonella enterica indicated the presence of F-like plasmids that exhibited a recent common ancestor with the Escherichia coli F plasmids. The presence of F-like plasmids in several subspecies of Salmonella enterica was also caused by frequent conjugational transfer with Escherichia coli.

The distribution of fimbrial operons among two Salmonella serotypes with distant phylogenetic relationships was analyzed to determine the role of horizontal gene transfer and deletion in the development of the fimbrial operons. Genetic analysis of Salmonella enterica serotypes indicated the limited phylogenetic expression of the sef and lbf operons which were characterized as recent acquisitions by the two distantly related serotypes. Furthermore, the acquisition of specific fimbrial operons served as one of the mechanisms that enabled Salmonella serotypes to expand their host range.

Systematic surveying of sequence similarities among amino acid sequences encoded by Escherichia coli K-12 genes obtained from SwissProt database using FASTA algorithm helps understand the evolutionary origins of E. coli genes. Evolution of E. coli genes involves significant duplication and divergence of ancestral genes. Absence of coherent pattern of favored separations in map distances between genes of sequence-related proteins suggests the absence of genome doubling in the past.

Affinity chromatography on DEAE-cellulose helps purify CspA, the major secreted protein of Clostridium acetobutylicum NCIB 8052, a choline-containing strain. An oligonucleotide probe helps clone the CspA gene encoding a protein with 590 amino acids. A comparative study of CspA with other proteins in the EMBL database indicates the homology of the C-terminal half of CspA with the pneumococcal antigen PspA, the choline-binding domains of the major pneumococcal autolysin and other cell wall-lytic enzymes of pneumococcal phages.

Phylogenetic analysis of the nucleomorph and nuclear 18S rRNA genes of Chilomonas paramecium, a nonphotosynthetic cryptomonad, indicates that nucleomorphs of cryptomonad and chlorarachniophyte may be interrelated, suggesting a common ancestral chimeric cell evolved by a single endosymbiosis of a red algae ancestor for the two phyla. Chromatophyte algae-containing phyla are related to Chlorarachniophyta but the photosynthetic taxa of these phyla radiate from each other following the radiation of the phyla themselves.

DNA sequence analysis and Southern hybridization analysis of Lactococcus lactis subsp. cremoris reveal that their chromosomes exhibit significant levels of divergence in certain regions. Less than 20% divergence exists in the conserved regions, while variable regions exhibit more than 60% divergence. Horizontal gene transfer from distantly related bacteria is responsible for the mosaic structure of the operon with alternating divergent and conserved regions. The gene transfer is significant in the bacterial evolution.

Examination of the evolution of Fusarium graminearum A3/5 grown in a glucose-limited chemostat culture, at a dilution rate of 0.05/h, reveals the absence of the formation of highly branched mutants. Determination of the levels of cycloheximide-resistant macroconidia in the culture helps evaluate the periodic selection of advantageous mutants. Mutants formed at slow dilution rates exhibit higher selection coefficient than those formed at an increased dilution rate. The mutant A28-S formed at a dilution rate of 0.05/h exhibits improved glucose uptake.

A study was conducted to evaluate DNA repair hypothesis. Earlier studies assume that bacteria integrate DNA from similar or closely related species under certain environmental limits. These past results suggest that transformation evolved from DNA repair of damaged chomosomes. The current study tested the hypothesis on Haemophilus influenzae. Results of the experiment support the hypothesis but do not account for higher survival of transformed cultures.

Microorganisms from various areas of the planet had been found to have developed evolutionary changes in the catabolism of manmade compounds. The influence of the amount of xenobiotic compounds introduced by man into the environment on the evolutionary process remains unanswered. However, it was known that gene transfer, mutational drift, and genetic recombination and transposition were the mechanisms that spurred the enviromental adaption.

The fibronectin type III (Fn3) domain is a characteristic of a number of extracellular, intracellular and membrane-receptor proteins of animal origin. However, recent studies have reported the detection of Fn3 domains in proteins of bacterial origin. An investigation was conducted to determine the occurence of Fn3 in a wide range of organisms. The results showed that Fn3 is not present in plant or fungal proteins. However, sequence comparisons between the animal and bacterial Fn3 showed highly similar sequences, indicating that the bacterial sequence originated from an animal source transferred long after the divergence of prokaryotes and eukaryotes.

The Y' element is a highly conserved repeat sequence found at some but not all chromosome ends. The function and origin of this repeat sequence is as yet, unknown. To help elucidate these questions, eight Y's from two strains of Saccharomyces cerevisiae were cloned and sequenced. The results showed that the Y' sequence consists of two overlapping open reading frames with no homologies to other known protein sequences, except for the RNA helicases. Further analyses revealed that the Y' elements probably arose from mobile elements, but now translocate via recombination mechanisms.

The DNA of plasmid p15B and bacteriophage P1 are 82% identical, but differ in their site-specific inversion systems, Min and Cin, respectively. Sequence analyses of these regions showed that they had aquired or lost various sequences giving rise to mosaics of partially related repeated elements. However, homology searches revealed the presence of homologous DNA inversion regions as well as sequences corresponding to phage tail fiber genes. Complementation analysis confirmed the presence of a tail fiber operon in Min.

The 23S rRNA genes of various representatives of the Gram-positive bacteria with high G+C content were analyzed for the presence of a previously characterized structural insertion. The results showed that the insertion is present in all the Gram-positive bacteria with high G+C content and is absent in similar bacteria with low G+C content. Amplified 23S rRNA gene products among the different representatives containing this sequence showed 44% similarity. This insertion can thus act as a phylogenetic marker for Gram-positive bacteria with high G+C content.

A genus Oenothera-pathogenic Mycoplasmalike organism (MLO) was cloned using heterologous DNA probes and its DNA sequence compared with that of analogous genes of Acholeplasma laidlawii. The rpl22 of the MLO and A. laidlawii are 62% identical while their rps3 genes are 67% identical. The amino acid sequences encoded by the rpl22 and rps3 genes of the MLO were deduced and compared with four other organisms including A. laidlawii. Construction of a phylogenetic tree based on these sequences showed close evolutionary relationships of MLO and Acholeplasma laidlawii.

Balansia epichloe is an endophytic fungus that colonizes grass leaves without utilizing seed transmission as its means ofproliferation. Growth studies show the important role sucrose plays in its stromatal development. This sugar exerts its inhibitory effect after it is converted by fungal enzymes into its monomers, glucose and fructose, which affect the fungus differently. The former serves as nutrient while the latter serves as inhibitor. Sufficient intercepted nutrient means stromatal development that proceeds to the development of perithecia when conidia are produced from stromata of opposite mating types. Inhibition is attributed to the presence of high sugar concentration surrounding the inflorescence that prevents seed transmission in this fungus.