Comparative Evolutionary Analysis Research Articles

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms

BackgroundHSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms.ResultsTwelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in vertebrates. Diplomonadida was identified as the most basal organism in the eukaryote lineage.ConclusionThe present study presents the first comparative genomic study and evolutionary analysis of the HSP90 family of genes across all kingdoms of organisms. HSP90 family members underwent multiple duplications and also subsequent losses during their evolution. This study established an overall framework of information for the family of genes, which may facilitate and stimulate the study of this gene family across all organisms.

The α-Globin Gene Family of an Australian Marsupial, Macropus eugenii: The Long Evolutionary History of the θ-Globin Gene and Its Functional Status in Mammals

Comparative evolutionary analyses of gene families among divergent lineages can provide information on the order and timing of major gene duplication events and evolution of gene function. Here we investigate the evolutionary history of the alpha-globin gene family in mammals by isolating and characterizing alpha-like globin genes from an Australian marsupial, the tammar wallaby, Macropus eugenii. Sequence and phylogenetic analyses indicate that the tammar alpha-globin family consists of at least four genes including a single adult-expressed gene (alpha), two embryonic/neonatally expressed genes (zeta and zeta'), and theta-globin, each orthologous to the respective alpha-, zeta-, and theta-globin genes of eutherian mammals. The results suggest that the theta-globin lineage arose by duplication of an ancestral adult alpha-globin gene and had already evolved an unusual promoter region, atypical of all known alpha-globin gene promoters, prior to the divergence of the marsupial and eutherian lineages. Evolutionary analyses, using a maximum likelihood approach, indicate that theta-globin, has evolved under strong selective constraints in both marsupials and the lineage leading to human theta-globin, suggesting a long-term functional status. Overall, our results indicate that at least a four-gene cluster consisting of three alpha-like and one beta-like globin genes linked in the order 5'-zeta-alpha-theta-omega-3' existed in the common ancestor of marsupials and eutherians. However, results are inconclusive as to whether the two tammar zeta-globin genes arose by duplication prior to the radiation of the marsupial and eutherian lineages, with maintenance of exon sequences by gene conversion, or more recently within marsupials.

Comparative evolutionary analysis of VPS33 homologues: genetic and functional insights

VPS33B protein is a homologue of the yeast class C vacuolar protein sorting protein Vps33p that is involved in the biogenesis and function of vacuoles. Vps33p homologues contain a Sec1 domain and belong to the family of Sec1/Munc18 (SM) proteins that regulate fusion of membrane-bound organelles and interact with other vps proteins and also SNARE proteins that execute membrane fusion in all cells. We demonstrated recently that mutations in VPS33B cause ARC syndrome (MIM 208085), a lethal multisystem disease. In contrast, mutations in other Vps33p homologues result in different phenotypes, e.g. a mutation in Drosophila melanogaster car gene causes the carnation eye colour mutant and inactivation of mouse Vps33a causes buff hypopigmentation phenotype. In mammals two Vps33p homologues (e.g. VPS33A and VPS33B in humans) have been identified. As comparative genome analysis can provide novel insights into gene evolution and function, we performed nucleotide and protein sequence comparisons of Vps33 homologues in different species to define their inter-relationships and evolution. In silico analysis (a) identified two homologues of yeast Vps33p in the worm, fly, zebrafish, rodent and human genomes, (b) suggested that Carnation is an orthologue of VPS33A rather than VPS33B and (c) identified conserved candidate functional domains within VPS33B. We have shown previously that wild-type VPS33B induced perinuclear clustering of late endosomes and lysosomes in human renal cells. Consistent with the predictions of comparative analysis: (a) VPS33B induced significantly more clustering than VPS33A in a renal cell line, (b) a putative fly VPS33B homologue but not Carnation protein also induced clustering and (c) the ability to induce clustering in renal cells was linked to two evolutionary conserved domains within VPS33B. One domain was present in VPS33B but not VPS33A homologues and the other was one of three regions predicted to form a t-SNARE binding site in VPS33B. In contrast, VPS33A induced significantly more clustering of melanosomes in melanoma cells than VPS33B. These investigations are consistent with the hypothesis that there are two functional classes of Vps33p homologues in all multicellular organisms and that the two classes reflect the evolution of organelle/tissue-specific functions.

Functional analysis of TMLH variants and definition of domains required for catalytic activity and mitochondrial targeting

epsilon-N-Trimethyllysine hydroxylase (TMLH) (EC 1.14.11.8) is a non-heme-ferrous iron hydroxylase, Fe(++) and 2-oxoglutarate (2OG) dependent, catalyzing the first of four enzymatic reactions of the highly conserved carnitine biosynthetic pathway. Otherwise from all the other enzymes of carnitine biosynthesis, TMLH was found to be associated to the mitochondrial fraction. We here report molecular cloning of two alternative spliced forms of TMLH, which appear ubiquitously expressed in human adult and fetal tissues. The deduced proteins are designated TMLH-a and TMLH-b, and contain 421 and 399 amino acids, respectively. They share the first N-terminal 332 amino acids, including a mitochondrial targeting signal, but diverge at the C-terminal end. TMLH-a and TMLH-b exogenous expression in COS-1 cells shows that the first 15 amino acids are necessary and sufficient for mitochondrial import. Furthermore, comparative evolutionary analysis of the C-terminal portion of TMLH-a identifies a conserved domain characterized by a key triad of residues, His242-Glu244-His389 predicted to bind 2OG end. This sequence is conserved in the TMLH enzyme from all species but is partially substituted by a unique sequence in the TMLH-b variant. Indeed, TMLH-b is not functional by itself as well as a TMLH-H389L mutant produced by site directed mutagenesis. As great interest, we found that TMLH-b and TMLH-H389L, individually co-expressed with TMLH-a in COS-1 cells, negatively affect TMLH activity. Therefore, our studies on the TMLH alternative form provide relevant novel information, first that the C-terminal region of TMLH contains the main determinants for its enzymatic activity including a key H389 residue, and second that TMLH-b could act as a crucial physiological negative regulator of TMLH.

Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice

Olfactory receptor (OR) genes form the largest multigene family in mammalian genomes. Humans have ∼800 OR genes, but >50% of them are pseudogenes. By contrast, mice have ∼1400 OR genes and pseudogenes are ∼25%. To understand the evolutionary processes that shaped the difference of OR gene families between humans and mice, we studied the genomic locations of all human and mouse OR genes and conducted a detailed phylogenetic analysis using functional genes and pseudogenes. We identified 40 phylogenetic clades with high bootstrap supports, most of which contain both human and mouse genes. Interestingly, a particular clade contains ∼100 pseudogenes in humans, whereas the numbers of pseudogenes are <20 for most of the mouse clades. We also found that the organization of OR genomic clusters is well conserved between humans and mice in many chromosomal locations. Despite the difference in the numbers of genes, the numbers of large genomic clusters are nearly the same for humans and mice. These observations suggest that the greater OR gene repertoire in mice has been generated mainly by tandem gene duplication within each genomic cluster.

Transforming Industrial Districts: Large Firms and Small Business Networks in the Italian Eyewear Industry

This study is an evolutionary comparative analysis of how large, vertically integrated firms and networks of small firms perform, in response to the challenges posed by globalization. It focuses on the Italian eyewear industry which represents an ideal laboratory for studying the establishment and transformation of such diverse production models under ceteris paribus conditions (same industry, same challenges, same product, and same geographical location). Looking at longitudinal statistical data for the Belluno eyewear district and case studies of the four leading companies in the industry, this study demonstrates that, locally embedded networks of small firms no longer represent an organizational structure as robust and stable as in the past. Globalization challenges such networks and demands adjustments that transform the nature of the Belluno eyewear district, away from the traditional stereotype so widespread in the literature, towards a configuration characterized by the presence of leading firms and moderate hierarchy.

Gene family phylogenetics: tracing protein evolution on trees.

How have proteins taken on the remarkable diversity of biochemical and physiological functions necessary to create and maintain complex organisms? The majority of proteins are organized hierarchically into families and superfamilies, reflecting an ancient and continuing process of gene duplication and divergence. The techniques of molecular phylogenetics, developed to recover the nested hierarchy of taxa from character information in their gene sequences, can also reconstruct the evolutionary relationships among genes and provide a conceptual foundation for comparative evolutionary analysis of proteins and their functions. In this review, I outline the application of phylogenetic approaches to issues in gene family studies, beginning with the inference of phylogeny and the assessment of the two types of homology by which genes in a family can be related: orthology (common descent from a cladogenetic event) and paralogy (common descent from a gene duplication event). I show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of exon shuffling, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious sequence data being generated by molecular biology and genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analyses

BackgroundIn fungi, aminoadipate reductase converts 2-aminoadipate to 2-aminoadipate 6-semialdehyde. However, other organisms have no homologue to the aminoadipate reductase gene and this pathway appears to be restricted to fungi. In this study, we designed degenerate primers for polymerase chain reaction (PCR) amplification of a large fragment of the aminoadipate reductase gene for divergent fungi.ResultsUsing these primers, we amplified DNA fragments from the archiascomycetous yeast Saitoella complicata and the black-koji mold Aspergillus awamori. Based on an alignment of the deduced amino acid sequences, we constructed phylogenetic trees. These trees are consistent with current ascomycete systematics and demonstrate the potential utility of the aminoadipete reductase gene for phylogenetic analyses of fungi.ConclusionsWe believe that the comparison of aminoadipate reductase among species will be useful for molecular ecological and evolutionary studies of fungi, because this enzyme-encoding gene is a fungal-specific gene and generally appears to be single copy.

MACROALGAL CANDIDATES FOR GENOMICS

Waaland, J. R.1 &amp; Stiller, J. W.2 1Department of Botany, University of Washington, Seattle, WA 98195 USA; 2Department of Biology, East Carolina University, Greenville, NC 27858 USAMacroalgae are important components of aquatic ecosystems. Some are harvested or cultivated for economic uses while others are of interest for their phylogenetic or systematic positions. Although most genes known from macroalgae have been isolated for comparative evolutionary analysis, some have been the subject of more detailed molecular investigations. We examine the current state of knowledge for several macroalgae as candidates for genomic study. Selection criteria for target taxa include features such as a well known sexual life history, availability of established laboratory cultures, mutant strains, basic genetic studies, fossil records, and ecological and economic importance. Among the algae to be considered are: Porphyra, Gracilaria, Ectocarpus, Macrocystis, Laminaria, Fucus, Ulva, Chara and Nitella. A strong case can be made for each of these taxa; however, we will emphasize Porphyra yezoensis because of its importance as a food source, its well‐characterized and easily manipulated reproductive biology, its relatively small genome size, and recent technical advances in genetic manipulation that should lead to fruitful exploitation of genomic information as it becomes available. Further, the genome of a red alga is an attractive target for comparison with those of other multicellular eukaryotes that have been the object of sequencing projects thus far.

Evolutionary Relationships of the Anolis bimaculatus Group from the Northern Lesser Antilles

Lizards in the Anolis bimaculatus group from the northern Lesser Antilles have played an important role in theoretical and empirical developments in ecology, behavior, and evolution over the last four decades. Despite intense interest, the lack of a formal phylogenetic analysis for the bimaculatus group has limited comparative and historical evolutionary analyses. Here we present a phylogenetic analysis of species relationships within the bimaculatus group based on separate and combined analyses of mitochon- drial DNA and previously published allozyme data. These analyses indicate that (1) the wattsi group of small anoles is a basal, well-supported monophyletic group; (2) the large anoles A. bimaculatus and A. leachi are not sister species-rather, there is a well-supported sister relationship between A. bimaculatus and A. gingivinus; (3) the A. marmoratus complex from the Guadeloupean archipelago is deeply differentiated and paraphyletic, with A. sabanus, A. lividus, and possibly A. oculatus nested within it; (4) the phylogenetic position of A. leachi is not well resolved, but a combined analysis of mtDNA and allozyme data favor placing A. leachi as the sister taxon to the (A. marmoratus, A. lividus, A. sabanus, A. oculatus) group; and (5) the phylogenetic position of A. nubilus remains uncertain pending additional data. The proposed phylogeny elucidates the evolutionary history and biogeography of the bimaculatus group and allows a reassessment of the character displacement and taxon cycle/loop hypotheses.

A Genetic Linkage Map of the Baboon (Papio hamadryas) Genome Based on Human Microsatellite Polymorphisms

A first-generation genetic linkage map of the baboon (Papio hamadryas) genome was developed for use in biomedical and evolutionary genetics. Pedigreed baboons (n = 694) were selected from the breeding colony maintained by the Southwest Foundation for Biomedical Research. To facilitate comparison with the human genome, the baboon linkage map consists primarily of human microsatellite loci amplified using published human PCR primers. Genotypes for 325 human microsatellites and 6 novel baboon microsatellites were used in linkage analyses performed with the MultiMap expert system. The resulting sex-averaged meiotic recombination map covers all 20 baboon autosomes, with average spacing among loci of 7.2 cM. Direct comparison among homologous (orthologous) loci reveals that, for 7 human autosomes, locus order is conserved between humans and baboons. For the other 15 autosomes, one or more rearrangements distinguish the two genomes. The total centimorgan distances among homologous markers are 28.0% longer in the human genome than in the baboon, suggesting that rates of recombination may be higher in humans. This baboon linkage map is the first reported for any nonhuman primate species and creates opportunities for mapping quantitative trait loci in baboons, as well as for comparative evolutionary analyses of genome structure.

Primate Evolution of an Olfactory Receptor Cluster: Diversification by Gene Conversion and Recent Emergence of Pseudogenes

The olfactory receptor (OR) subgenome harbors the largest known gene family in mammals, disposed in clusters on numerous chromosomes. We have carried out a comparative evolutionary analysis of the best characterized genomic OR gene cluster, on human chromosome 17p13. Fifteen orthologs from chimpanzee (localized to chromosome 19p15), as well as key OR counterparts from other primates, have been identified and sequenced. Comparison among orthologs and paralogs revealed a multiplicity of gene conversion events, which occurred exclusively within OR subfamilies. These appear to lead to segment shuffling in the odorant binding site, an evolutionary process reminiscent of somatic combinatorial diversification in the immune system. We also demonstrate that the functional mammalian OR repertoire has undergone a rapid decline in the past 10 million years: while for the common ancestor of all great apes an intact OR cluster is inferred, in present-day humans and great apes the cluster includes nearly 40% pseudogenes.

Evolutionary comparative analyses of the relationship between leaf structure and function

summaryWe have applied evolutionary comparative methods to control for phylogenetic relationships between species in order to determine if three recently proposed relationships between leaf structure and function are upheld, using a large database comprising a wide range of species from tropical and temperate ecosystems. The three hypotheses tested were: (i) leaf thickness is positively correlated with total stomatal density (adaxial and abaxial values summed); (ii) amphistomatous leaves (stomata present on the upper and lower surfaces) have a higher maximum stomatal conductance than hypostomatous (stomata on the lower surface only) leaves, and (iii) changes in the stomatal density on upper and lower leaf surfaces are regulated in a compensatory manner. The results showed that, contrary to several mathematical modelling studies, thicker leaves were not associated with more stomata either in species from lowland tropical rain forests or from central Europe. Amphistomatous leaves had a higher maximum stomatal conductance, indicating that one aspect of previous modelling work is correctly underpinned after accounting for relatedness. Finally, we found no evidence that the stomatal densities on upper and tower leaf surfaces are closely regulated. These three physiological traits are discussed with reference both to the modelling of leaf gas exchange and to plant function in relation to microclimate.

Comparative Analysis of Human DNA Variations by Fluorescence-Based Sequencing of PCR Products

Automated, direct cycle sequencing of purified double-stranded PCR products using Taq polymerase and fluorescently labeled dideoxynucleotide terminators provides a robust and highly reproducible method for identifying DNA sequence variations in sequence-tagged sites. We describe a simple and sensitive strategy that reliably detects the presence of DNA variations when sequencing traces from several different individuals are compared. We also demonstrate the use of this strategy to estimate allele frequencies of single nucleotide substitutions in a population. Taken together, this approach provides an automated method for conducting rapid population studies of candidate gene regions that are in linkage or association with a specific disease and for comparative evolutionary analysis of selected regions of the human genome.

Comparative Evolutionary Analysis of Metabolism in Nine Drosophila Species

Comparative Evolutionary Analysis of Metabolism in Nine Drosophila Species

The origin of lysyl oxidase

Lysyl oxidase initiates crosslink formation of the collagen and elastin extracellular matrix, thereby delimiting its expansive properties. Recently lysyl oxidase has been cloned from several species enabling the computation of the relative order of appearance of the various components of this enzyme system. Comparative evolutionary computer-assisted sequence analysis of the enzyme and its various substrates was undertaken to address this issue. These results support the ordered genesis of the collagen substrate → lysyl oxidase enzyme → elastin substrate.

Relations between song repertoire size and the volume of brain nuclei related to song: comparative evolutionary analyses amongst oscine birds

Song and brain structure are compared amongst 41 species of oscine birds by using the method of independent evolutionary contrasts. We find a significant correlation between the relative volume of the song control centre, the high vocal centre (HVC), and the number of song types typically found in the repertoire. Relative HVC volume is not correlated with the number of different syllable types per song bout. The relative volume of a second song nucleus, area X, is not significantly correlated with either measure. Relative HVC volume is uncorrelated with relative volume of the hippocampus, a brain area involved in other forms of memory. This is the first evidence for repeated independent evolution of an association between complexity of learned song and the relative volume of one of the song control nuclei though to be involved in song learning.

Isolation and molecular evolutionary analysis of a cytochrome c gene from Oryza sativa (rice)

A cytochrome c gene, OsCc-1, from rice (Oryza sativa) has been isolated and analyzed. The OsCc-1 gene encodes a cytochrome c protein that is typical of higher-plant cytochrome c proteins. OsCc-1 consists of three exons separated by two introns that are 817 and 747 bp in length, respectively. From genomic DNA hybridization analysis, OsCc-1 appears to be one of possibly two cytochrome c genes in several Asian, American, and Indian rice species and varieties surveyed. A single, unique cytochrome c gene appears to be present in one African cultivated rice species. We performed comparative molecular evolutionary analyses of OsCc-1 and other cytochrome c genes. We calculated a unit evolutionary period of 19.4 Myr for cytochrome c DNA sequences, which agrees closely with previous estimates based on protein sequence comparisons.