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PubMed2002

The evolutionary history of kinetoplastids and their kinetoplasts.

Despite extensive phylogenetic analysis of small subunit ribosomal RNA (SSUrRNA) genes, the deep-level relationships among kinetoplastids remain poorly understood, limiting our grasp of their evolutionary history, especially the origins of their bizarre mitochondrial genome organizations. In this study we examine the SSUrRNA data in the light of a new marker--cytoplasmic heat shock protein 90 (hsp90) sequences. Our phylogenetic analyses divide kinetoplastids into four main clades. Clades 1-3 include the various bodonid kinetoplastids. Trypanosomatids comprise the fourth clade. SSUrRNA analyses give vastly different and poorly supported positions for the root of the kinetoplastid tree, depending on the out-group and analysis method. This is probably due to the extraordinary length of the branch between kinetoplastids and any out-group. In contrast, almost all hsp90 analyses place the root between clade 1 (including Dimastigella, Rhynchomonas, several Bodo spp., and probably Rhynchobodo) and all other kinetoplastids. Maximum likelihood and maximum likelihood distance analyses of hsp90 protein and second codon-position nucleotides place trypanosomatids adjacent to Bodo saltans and Bodo cf. uncinatus (clade 3), as (weakly) do SSUrRNA analyses. Hsp90 first codon- plus second codon-position nucleotide analyses return a slightly different topology. We show that this may be an artifact caused, in part, by the different evolutionary behavior of first- and second-codon positions. This study provides the most robust evidence to date that trypanosomatids are descended from within bodonids and that B. saltans is a close relative of trypanosomatids. A total reevaluation of the high-level systematics within kinetoplastids is needed. We confirm that the interlocking network organization of kinetoplast DNA seen in trypanosomatids is a derived condition within kinetoplastids but suggest that open-conformation minicircles may have arisen early in kinetoplastid evolution. Further understanding of the evolution of kinetoplast structure and RNA editing is hampered by a paucity of data from basal (i.e., clade 1) bodonids.

Animals↗
PubMed2006

Molecular cloning of myostatin gene and characterization of tissue-specific and developmental stage-specific expression of the gene in orange spotted grouper, Epinephelus coioides.

In this article we report the molecular cloning and characterization of a nonmammalian myostatin (growth and differentiation factor-8, MSTN) homolog from the orange spotted grouper (Epinephelus coioides) by polymerase chain reaction (PCR) cloning. The grouper MSTN gene consists of two introns [Intron I (363 bp) and Intron II (811 bp)] flanked by three exons [Exon I (379 bp), Exon II (371 bp) and Exon III (381 bp)]. A full-length cDNA clone (2608 bp) of the MSTN gene (GenBank DQ493889, nucleotide sequence in the coding region identical to GeneBank AY856860) was also isolated. This cDNA encodes a polypeptide of 376 amino acid residues that showed 25% to 96% homology with MSTNs of molluscan, teleostean, avian, and mammalian species. Phylogenetic analysis of the grouper MSTN polypeptide confirmed the evolutionary relationships of this MSTN with other known MSTNs. Results of reverse transcription (RT)-PCR analysis of the total RNA extracted from different tissues revealed that MSTN gene is expressed not only in the skeletal muscle, but also in other tissues. MSTN mRNA was also detected in different embryonic developmental and larval stages. Because the tissue-specific expression of MSTN gene in grouper is different from that in mammals, it might suggest that MSTN gene may possess additional functions other than regulating muscle growth in fish.

Amino Acid Sequence↗
PubMed2000

Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution.

Attempts to estimate the time of origin of human immunodeficiency virus (HIV)-1 by using phylogenetic analysis are seriously flawed because of the unequal evolutionary rates among different viral lineages. Here, we report a new method of molecular clock analysis, called Site Stripping for Clock Detection (SSCD), which allows selection of nucleotide sites evolving at an equal rate in different lineages. The method was validated on a dataset of patients all infected with hepatitis C virus in 1977 by the same donor, and it was able to date exactly the known origin of the infection. Using the same method, we calculated that the origin of HIV-1 group M radiation was in the 1930s. In addition, we show that the coalescence time of the simian ancestor of HIV-1 group M and its closest related cpz strains occurred around the end of the XVII century, a date that could be considered the upper limit to the time of simian-to-human transmission of HIV-1 group M. The results show also that SSCD is an easy-to-use method of general applicability in molecular evolution to calibrate clock-like phylogenetic trees.

Animals↗
PubMed2003

The Arabidopsis basic/helix-loop-helix transcription factor family.

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.

Amino Acid Sequence↗
PubMed1991

Segmentation gene expression in the housefly Musca domestica.

Drosophila and Musca both belong to the group of higher dipteran flies and show morphologically a very similar early development. However, these two species are evolutionary separated by at least 100 million years. This presents the opportunity for a comparative analysis of segmentation gene expression across a large evolutionary distance in a very similar embryonic background. We have analysed in detail the early expression of the maternal gene bicoid, the gap genes hunchback, Krüppel, knirps and tailless, the pair-rule gene hairy, the segment-polarity gene engrailed and the homoeotic gene Ultrabithorax. We show that the primary expression domains of these genes are conserved, while some secondary expression aspects have diverged. Most notable is the finding of hunchback expression in 11-13 stripes shortly before gastrulation, as well as a delayed expression of terminal domains of various genes. We conclude that the early developmental gene hierarchy, as it has been defined in Drosophila, is evolutionary conserved in Musca domestica.

Animals↗
PubMed1999

Chloroplast small heat shock proteins: evidence for atypical evolution of an organelle-localized protein.

Knowledge of the origin and evolution of gene families is critical to our understanding of the evolution of protein function. To gain a detailed understanding of the evolution of the small heat shock proteins (sHSPs) in plants, we have examined the evolutionary history of the chloroplast (CP)-localized sHSPs. Previously, these nuclear-encoded CP proteins had been identified only from angiosperms. This study reveals the presence of the CP sHSPs in a moss, Funaria hygrometrica. Two clones for CP sHSPs were isolated from a F. hygrometrica heat shock cDNA library that represent two distinct CP sHSP genes. Our analysis of the CP sHSPs reveals unexpected evolutionary relationships and patterns of sequence conservation. Phylogenetic analysis of the CP sHSPs with other plant CP sHSPs and eukaryotic, archaeal, and bacterial sHSPs shows that the CP sHSPs are not closely related to the cyanobacterial sHSPs. Thus, they most likely evolved via gene duplication from a nuclear-encoded cytosolic sHSP and not via gene transfer from the CP endosymbiont. Previous sequence analysis had shown that all angiosperm CP sHSPs possess a methionine-rich region in the N-terminal domain. The primary sequence of this region is not highly conserved in the F. hygrometrica CP sHSPs. This lack of sequence conservation indicates that sometime in land plant evolution, after the divergence of mosses from the common ancestor of angiosperms but before the monocot-dicot divergence, there was a change in the selective constraints acting on the CP sHSPs.

Amino Acid Sequence↗
PubMed2004

A family of evolution-entropy hybrid methods for ranking protein residues by importance.

In order to identify the amino acids that determine protein structure and function it is useful to rank them by their relative importance. Previous approaches belong to two groups; those that rely on statistical inference, and those that focus on phylogenetic analysis. Here, we introduce a class of hybrid methods that combine evolutionary and entropic information from multiple sequence alignments. A detailed analysis in insulin receptor kinase domain and tests on proteins that are well-characterized experimentally show the hybrids' greater robustness with respect to the input choice of sequences, as well as improved sensitivity and specificity of prediction. This is a further step toward proteome scale analysis of protein structure and function.

Amino Acid Sequence↗
PubMed1993

Ancestors and homology (the origin of the tetrapod limb).

Current issues concerning the nature of ancestry and homology are discussed with reference to the evolutionary origin of the tetrapod limb. Homologies are argued to be complex conjectural inferences dependent upon a pre-existing phylogenetic analysis and a theoretical model of the evolutionary development of ontogenetic information. Ancestral conditions are inferred primarily from character (synapomorphy/homology) distributions within phylogeny, because of the deficiencies of palaeontological data. Recent analyses of tetrapod limb ontogeny, and the diverse, earliest morphologies known from the fossil record, are inconsistent with typological concepts such as fixed ancestral patterns or bauplans, emphasising the incompatibility of these with evolutionary continuity. The evolutionary origin of the tetrapod limb is also examined in the light of its recent discussion in developmental genetics. While this field promises to reveal more of the fundamental ontogenetic content of homology (identity), at present it is concerned mostly with the abstraction of a new set of types, rather than investigating diversity and change.

Animals↗
PubMed1991

Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants.

Likelihood methods and methods using invariants are procedures for inferring the evolutionary relationships among species through statistical analysis of nucleic acid sequences. A likelihood-ratio test may be used to determine the feasibility of any tree for which the maximum likelihood can be computed. The method of linear invariants described by Cavender, which includes Lake's method of evolutionary parsimony as a special case, is essentially a form of the likelihood-ratio method. In the case of a small number of species (four or five), these methods may be used to find a confidence set for the correct tree. An exact version of Lake's asymptotic chi 2 test has been mentioned by Holmquist et al. Under very general assumptions, a one-sided exact test is appropriate, which greatly increases power.

Animals↗
PubMed1998

ZOO-FISH analysis in insectivores: "Evolution extols the virtue of the status quo".

In evolutionary terms, insectivores are thought to be close to primates. Through ZOO-FISH analysis using human chromosome-specific painting probes, the syntenic relationship between the human and common shrew, Sorex araneus, karyotypes was studied. The human karyotype was found to be conserved in the shrew, with 32 autosomal segments of common synteny. Special arrangements, already known from similar studies on other species, were noted: fusions of HSA 16 and 19, HSA 3 and 21, and HSA 14 and 15. Only 10 breaks are necessary to transform the human karyotype into the karyotype of the common shrew. Together with known ZOO-FISH data from species belonging to other orders, this puts the human karyotype arrangement near the basis of all mammalian karyotypes. Human chromosome 2 was found to be conserved in its entirety as a single chromosome arm in the shrew. Evidence is presented that the same fusion of two original chromosomal segments formed the shrew chromosome ortholog of HSA 2 as the fusion that occurred during primate evolution to form human chromosome 2. This is a remarkable example of chromosomal coevolution.

Animals↗
PubMed1998

A natural view of microbial biodiversity within hot spring cyanobacterial mat communities.

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

Bacteria↗
PubMed1993

Sequence analysis of the beta-N-acetylhexosaminidase gene of Vibrio vulnificus: evidence for a common evolutionary origin of hexosaminidases.

DNA cloned from the marine bacterium Vibrio vulnificus into Escherichia coli HB101 can hydrolyze chitin oligomer analogs in the recipient. The nucleotide sequence of the cloned DNA was determined and a single long open reading frame of 2541 base pairs (initiation codon through termination codon) was found. The nucleotide sequence predicts a gene product of 847 amino acids and a molecular mass of 94.3 kDa. In vitro transcription and translation analyses indicated a single protein of 94 kDa encoded by the cloned DNA. The gene product hydrolyzes methylumbelliferyl beta-D conjugates of chitotriose, chitobiose, N-acetylglucosamine, and N-acetylgalactosamine and has, therefore, been termed a beta-N-acetylhexosaminidase. The predicted protein shares a high degree of sequence similarity with the chitobiase of Vibrio harveyi and limited similarity with the alpha chain of human beta-hexosaminidase. Cluster analyses suggest a common evolutionary ancestor for all known hexosaminidase enzymes, with no detectable relationship to known chitinases.

Amino Acid Sequence↗
PubMedDate not supplied

Microspectroscopy of the photosynthetic compartment of algae.

We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of algae belonging to different taxonomic divisions and higher plants. The feasibility of microspectroscopy for discriminating among species and/or phylogenetic groups was tested on laboratory cultures. Gaussian bands decompositions and a fitting algorithm, together with fourth-derivative transformation of absorbance spectra, provided a reliable discrimination among chlorophylls a, b and c, phycobiliproteins and carotenoids. Comparative analysis of absorption spectra highlighted the evolutionary grouping of the algae into three main lineages in accordance with the most recent endosymbiotic theories.

Eukaryota↗
PubMed1997

Cladistic analysis of disease association with tyrosine hydroxylase: application to manic-depressive disease and alcoholism.

We evaluated the involvement of tyrosine hydroxylase (TH) mutations in susceptibility to manic-depressive disease (MDD) and alcoholism (ALC) with a cladistics-based association analysis. Eighty-one probands with MDD, 113 probands with alcoholism, and 80 normal controls were tested for differences in frequency of nine haplotypes at the TH locus. The haplotypes were comprised of four restriction fragment length polymorphisms spanning the TH gene. A cladogram constructed from the haplotypes provided the evolutionary context for a nested statistical analysis. Statistically significant evidence was found for association of a subgroup of the sample for each of the disorders with different branches of the gene tree, but the findings were sensitive to minor changes in estimated haplotype frequencies.

Alcoholism↗
PubMed2002

Virologic risk factors for vertical transmission of HIV type 1 in Puerto Rico.

HIV-1 vertical transmission in Puerto Rico has decreased significantly due to the implementation of antiviral therapy. Several studies have shown that the phenotype of the HIV-1 isolates initially recovered from infected infants has generally been one that replicates rapidly, infects macrophages, and preferentially use the CCR5 coreceptor. Our hypothesis is that viral genotypic and phenotypic differences exist between HIV-1 nontransmitter and transmitter mothers. Viral DNA samples and virus isolates were analyzed from a Puerto Rican perinatal population. Heteroduplex tracking assay (HTA) was performed on DNA samples to detect env V3 evolutionary variants and the extent of heterogeneity within each sample. HIV-1 C2-V3 variants were cloned from each patient to study sequence variation among the groups. Differences in replication kinetics of viral isolates in macrophage and GHOST CCR5 cells were analyzed by use of repeated measures linear regression analysis. HTA analysis showed that only two nontransmitter patient samples showed the presence of evolutionary variants. Phylogenetic analysis between maternal-infant pairs showed that transmission of a single maternal variant occurred, with the exception of one sample pair. When evaluating amino acid sequences from cloned PCR products, nontransmitting mothers appear to have a higher number of distinct sequences than both the transmitting mothers (p = 0.0410) and the infected infants (p = 0.0315). Analysis of replication kinetics indicated that transmitters showed faster replication kinetics in GHOST CCR5 cell cultures at 12 days postinfection (p = 0.0434) and 15 days postinfection (p = 0.0181). In conclusion, viral homogeneity and rapid replication kinetics were correlated with vertical transmission.

Acquired Immunodeficiency Syndrome↗
PubMed1992

Is the bacteriophage lambda lysozyme an evolutionary link or a hybrid between the C and V-type lysozymes? Homology analysis and detection of the catalytic amino acid residues.

The relationship between the bacteriophage lambda lysozyme (lambda L) and the C and V-type lysozymes has been investigated by sequence alignment, secondary structure prediction and pattern recognition methods. The alignment of the amino terminal part of lambda L with that of V-type lysozymes suggests that Glu19 is a residue essential for catalysis. Its mutation to Gln leads to a completely inactive enzyme. In the alignment of the sequence of lambda L with those of the C-type lysozymes a strongly homologous fragment of about 30 amino acid residues is detected. Taking into consideration this observation and the published structural alignments between C and V-type lysozymes, a repetition of the beta-sheet motif in lambda L is proposed. The multiple alignment draws the attention to a possible catalytic role for Asp34 that would be positioned in the middle of the second strand of the beta-sheet as in the C-type lysozymes. This role is confirmed by mutagenesis. The implications of these observations in terms of the evolutionary relationship between lambda L and the other lysozymes is discussed.

Amino Acid Sequence↗
PubMed1996

Evolutionary dynamics of predator-prey systems: an ecological perspective.

Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals--the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator-prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator-prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamic; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species.

Animals↗
PubMed2001

Molecular evolution of receptor-like kinase genes in hexaploid wheat. Independent evolution of orthologs after polyploidization and mechanisms of local rearrangements at paralogous loci.

Hexaploid wheat is a young polyploid species and represents a good model to study mechanisms of gene evolution after polyploidization. Recent studies at the scale of the whole genome have suggested rapid genomic changes after polyploidization but so far the rearrangements that have occurred in terms of gene content and organization have not been analyzed at the microlevel in wheat. Here, we have isolated members of a receptor kinase (Lrk) gene family in hexaploid and diploid wheat, Aegilops tauschii, and barley (Hordeum vulgare). Phylogenetic analysis has allowed us to establish evolutionary relationships (orthology versus paralogy) between the different members of this gene family in wheat as well as with Lrk genes from barley. It also demonstrated that the sequences of the homoeologous Lrk genes evolved independently after polyploidization. In addition, we found evidence for gene loss during the evolution of wheat and barley. Analysis of large genomic fragments isolated from nonorthologous Lrk loci showed a high conservation of the gene content and gene organization at these loci on the homoeologous group 1 chromosomes of wheat and barley. Finally, sequence comparison of two paralogous fragments of chromosome 1B showed a large number of local events (sequence duplications, deletions, and insertions), which reveal rearrangements and mechanisms for genome enlargement at the microlevel.

Base Sequence↗