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PubMed1998

[Diminution of chromatin, accompanying reorganization of genomic molecular structure: evolutionary aspects].

Chromatin diminution (CD) accompanied by the reorganization of the molecular genomic structure of macronuclei in ciliates and somatic cells in Cyclops and Ascaris is considered. A conclusion is drawn that the physical elimination of most (sometimes 94-98%) genetic material from somatic nuclei directly indicates that, in these species, eliminated sequences possess neither the coding nor the regulatory functions that are required for differentiation. Apparently, the actual functions of eliminated sequences are associated only with germline chromosomes where these sequences act as a factor of genetic isolation. A CD is supposed to be underlain by the coordinated operation of many genes. Consequently, this phenomenon cannot result from stochastic mutagenesis and the random coincidence of required mutations in several genes. For CD formation, canalized mutagenesis is required, which simultaneously generates a set of genes that code the consecutive stages of CD.

Animals↗

PubMed1998

Mutational analysis of human DNase I at the DNA binding interface: implications for DNA recognition, catalysis, and metal ion dependence.

Human deoxyribonuclease I (DNase I), an enzyme used to treat cystic fibrosis patients, has been systematically analyzed by site-directed mutagenesis of residues at the DNA binding interface. Crystal structures of bovine DNase I complexed with two different oligonucleotides have implicated the participation of over 20 amino acids in catalysis or DNA recognition. These residues have been classified into four groups based on the characterization of over 80 human DNase I variants. Mutations at any of the four catalytic amino acids His 134, His 252, Glu 78, and Asp 212 drastically reduced the hydrolytic activity of DNase I. Replacing the three putative divalent metal ion-coordinating residues Glu 39, Asp 168, or Asp 251 led to inactive variants. Amino acids Gln 9, Arg 41, Tyr 76, Arg 111, Asn 170, Tyr 175, and Tyr 211 were also critical for activity, presumably because of their close proximity to the active site, while more peripheral DNA interactions stemming from 13 other positions were of minimal significance. The relative importance of these 27 positions is consistent with evolutionary relationships among DNase I across different species, DNase I-like proteins, and bacterial sphingomyelinases, suggesting a fingerprint for a family of DNase I-like proteins. Furthermore, we found no evidence for a second active site that had been previously implicated in Mn2+-dependent DNA degradation. Finally, we correlated our mutational analysis of human DNase I to that of bovine DNase I with respect to their specific activity and dependence on divalent metal ions.

Animals↗

PubMed2006

A question of timing: emerging links between transcription and replication.

The coordination of transcription and timing of DNA replication during the S phase of the cell cycle has recently been studied chromosome-wide in high resolution. This revealed that in the complex genome of higher eukaryotes actively transcribed genes are more likely to replicate early in S phase. Dynamic changes in chromatin structure and nuclear organization appear to provide the underlying mechanism to link transcription and replication. A possible evolutionary benefit for this connection might result from differential replication fidelity during S phase, and comparisons of the human and chimpanzee genomes are compatible with this hypothesis.

Animals↗

PubMed2006

D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.

The "ribulose phosphate binding" superfamily defined by the Structural Classification of Proteins (SCOP) database is considered the result of divergent evolution from a common (beta/alpha)(8)-barrel ancestor. The superfamily includes d-ribulose 5-phosphate 3-epimerase (RPE), orotidine 5'-monophosphate decarboxylase (OMPDC), and 3-keto-l-gulonate 6-phosphate decarboxylase (KGPDC), members of the OMPDC suprafamily, as well as enzymes involved in histidine and tryptophan biosynthesis that utilize phosphorylated metabolites as substrates. We now report studies of the functional and structural relationships of RPE to the members of the superfamily. As suggested by the results of crystallographic studies of the RPEs from rice [Jelakovic, S., Kopriva, S., Suss, K. H., and Schulz, G. E. (2003) J. Mol. Biol. 326, 127-35] and Plasmodium falciparum [Caruthers, J., Bosch, J., Bucker, F., Van Voorhis, W., Myler, P., Worthey, E., Mehlin, C., Boni, E., De Titta, G., Luft, J., Kalyuzhniy, O., Anderson, L., Zucker, F., Soltis, M., and Hol, W. G. J. (2006) Proteins 62, 338-42], the RPE from Streptococcus pyogenes is activated by Zn(2+) which binds with a stoichiometry of one ion per polypeptide. Although wild type RPE has a high affinity for Zn(2+) and inactive apoenzyme cannot be prepared, the affinity for Zn(2+) is decreased by alanine substitutions for the two histidine residues that coordinate the Zn(2+) ion (H34A and H67A); these mutant proteins can be prepared in an inactive, metal-free form and activated by exogenous Zn(2+). The crystal structure of the RPE was solved at 1.8 A resolution in the presence of d-xylitol 5-phosphate, an inert analogue of the d-xylulose 5-phosphate substrate. This structure suggests that the 2,3-enediolate intermediate in the 1,1-proton transfer reaction is stabilized by bidentate coordination to the Zn(2+) that also is liganded to His 34, Asp 36, His 67, and Asp 176; the carboxylate groups of the Asp residues are positioned also to function as the acid/base catalysts. Although the conformation of the bound analogue resembles those of ligands bound in the active sites of OMPDC and KGPDC, the identities of the active site residues that coordinate the essential Zn(2+) and participate as acid/base catalysts are not conserved. We conclude that only the phosphate binding motif located at the ends of the seventh and eighth beta-strands of the (beta/alpha)(8)-barrel is functionally conserved among RPE, OMPDC, and KGPDC, consistent with the hypothesis that the members of the "ribulose phosphate binding" (beta/alpha)(8)-barrel "superfamily" as defined by SCOP have not evolved by evolutionary processes involving the intact (beta/alpha)(8)-barrel. Instead, this "superfamily" may result from assembly from smaller modules, including the conserved phosphate binding motif associated with the C-terminal (beta/alpha)(2)-quarter barrel.

Amino Acid Motifs↗

PubMed1995

Patterns of genetic variability at individual minisatellite loci in minke whale Balaenoptera acutorostrata populations from three different oceans.

The genetic variability at six cloned minisatellite loci was analyzed in minke whale populations from the North Atlantic, North Pacific, and Antarctic Oceans. Three loci displayed only a few different alleles in each of the three populations, with heterozygosity ranging from 0.00 to 0.47, and three loci revealed many different alleles in at least two fo the three populations, with heterozygosity ranging up to 0.98. Using small sample sizes, samples from two adjacent Antarctic Management Areas were not found to differ significantly in allele frequencies at any of the six loci. The use of principal coordinate analysis to detect multilocus disequilibria was explored. No significant evidence was found of intrapopulation heterogeneity within the pooled Antarctic sample. Pronounced interoceanic differences were observed at every locus, confirming the existence of genetic isolation found earlier using more conventional marker systems. The populations from the three oceans appear to have diverged to such a degree that the hypervariable loci have had time to evolve independently and arrive at different evolutionary stages in different populations. The frequency of undetected "null" alleles is remarkably high in minke whale populations compared to human populations and is probably a result of the cloning protocol used. Minisatellite loci are shown to provide a powerful population genetic tool, supplying levels of resolution appropriate to different degrees of evolutionary divergence.

Alleles↗

PubMed2001

Developmental modularity and the evolutionary diversification of arthropod limbs.

Segmentation is one of the most salient characteristics of arthropods, and differentiation of segments along the body axis is the basis of arthropod diversification. This article evaluates whether the evolution of segmentation involves the differentiation of already independent units, i.e., do segments evolve as modules? Because arthropod segmental differentiation is commonly equated with differential character of appendages, we analyze appendages by comparing similarities and differences in their development. The comparison of arthropod limbs, even between species, is a comparison of serially repeated structures. Arthropod limbs are not only reiterated along the body axis, but limbs themselves can be viewed as being composed of reiterated parts. The interpretation of such reiterated structures from an evolutionary viewpoint is far from obvious. One common view is that serial repetition is evidence of a modular organization, i.e., repeated structures with a common fundamental identity that develop semi-autonomously and are free to diversify independently. In this article, we evaluate arthropod limbs from a developmental perspective and ask: are all arthropod limbs patterned using a similar set of mechanisms which would reflect that they all share a generic coordinate patterning system? Using Drosophila as a basis for comparison, we find that appendage primordia, positioned along the body using segmental patterning coordinates, do indeed have elements of common identity. However, we do not find evidence of a single coordinate system shared either between limbs or among limb branches. Data concerning the other diagnostic of developmental modularity--semi-autonomy of development--are not currently available for sufficient taxa. Nonetheless, some data comparing patterns of morphogenesis provide evidence that limbs cannot always be temporally or spatially decoupled from the development of their neighbors, suggesting that segment modularity is a derived character.

Adaptation, Physiological↗

PubMed2006

Resolving the genetic basis of invasiveness and predicting invasions.

Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, "invasiveness genes" common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.

Arabidopsis↗

PubMed2002

The Eps15 homology (EH) domain.

The Eps15 homology (EH) domain was originally identified as a motif present in three copies at the NH2-termini of Eps15 and of the related molecule Eps15R. Both of these molecules are substrates for the tyrosine kinase activity of the epidermal growth factor receptor and hence the name 'Eps15 homology' or EH domain [Wong et al. (1994) Oncogene 9, 1591-1597; Wong et al. (1995) Proc. Natl. Acad. Sci. USA 92, 9530-9534; Fazioli et al. (1993) Mol. Cell. Biol. 13, 5814-5828] was derived. The motif was subsequently found in several proteins from yeast to nematode, thus establishing its evolutionary conservation. Initial studies with filter-binding assays and phage-displayed libraries demonstrated its protein:protein interaction abilities and identified specific ligands. Subsequently, structural analyses established the molecular bases of recognition between EH domains and cognate peptides. To date, several EH-containing and EH-binding proteins have been identified, which establish in the cell a network of protein:protein interactions, defined as the EH network. This network coordinates cellular functions connected with endocytosis, actin remodeling and intracellular transduction of signals.

Amino Acid Sequence↗

PubMed2006

Roles of DNA polymerases in replication, repair, and recombination in eukaryotes.

The functioning of the eukaryotic genome depends on efficient and accurate DNA replication and repair. The process of replication is complicated by the ongoing decomposition of DNA and damage of the genome by endogenous and exogenous factors. DNA damage can alter base coding potential resulting in mutations, or block DNA replication, which can lead to double-strand breaks (DSB) and to subsequent chromosome loss. Replication is coordinated with DNA repair systems that operate in cells to remove or tolerate DNA lesions. DNA polymerases can serve as sensors in the cell cycle checkpoint pathways that delay cell division until damaged DNA is repaired and replication is completed. Eukaryotic DNA template-dependent DNA polymerases have different properties adapted to perform an amazingly wide spectrum of DNA transactions. In this review, we discuss the structure, the mechanism, and the evolutionary relationships of DNA polymerases and their possible functions in the replication of intact and damaged chromosomes, DNA damage repair, and recombination.

Amino Acid Sequence↗

PubMed1999

AOP2 (antioxidant protein 2): structure and function of a unique thiol-specific antioxidant.

The accumulation of reactive oxygen species (ROS) in response to extracellular signals or intracellular biochemical processes can be regulated by the coordinate action of many antioxidant proteins. Because moderate levels of ROS can act as intracellular messengers in many of these processes, this modulation is critical for the transduction of specific signals. The thiol-specific antioxidant (TSA) family is a highly conserved group of enzymes that can reduce hydroperoxides in the presence of a thiol-containing electron donor. AOP2 (antioxidant protein 2) is a newly described member that shows significant evolutionary conservation between many different organisms. The protein contains three motifs that are highly conserved within the TSA family, including a cysteine residue that is the active site of oxidation for this class of proteins. Although AOP2 possesses TSA activity, it has several unique characteristics, including the absence of a second cysteine residue that is conserved in all other TSA proteins, the presence of a unique carboxy-terminal domain, and a demonstrated phospholipase activity. Furthermore, AOP2 shows conservation of several amino acids important in dimer formation and active site configuration that are not found in the other family members. Together, these data strongly suggest that AOP2 is a novel thiol-dependent antioxidant that functions to scavenge particular hydroperoxides in the cell and mediate specific signals. There is also evidence supporting a role for AOP2 in certain disease processes including atherosclerosis. Further evaluation of this protein and its substrate specificity will likely shed light on its precise role in cellular oxidant defense, signal transduction and pathogenesis.

Amino Acid Motifs↗

PubMed1999

Brain size is not correlated with forelimb dexterity in fissiped carnivores (Carnivora): A comparative test of the principle of proper mass.

To test the hypothesis that brain size and forelimb dexterity are positively correlated, the relative brain size of 41 species of fissiped (terrestrial) carnivores (Order: Carnivora) was examined with respect to their forelimb use during feeding. With the use of a newly derived dexterity index, the forelimb dexterity executed by each of the species was calculated as a single, continuous variable which was then regressed against the residuals of brain size. To account for confounding effects of phylogenetic inertia, the analysis was performed with independent contrasts analysis using a speciational model of evolutionary change (i.e. equal branch lengths). The results suggest that relative brain size and isocortex size are not correlated with the dexterity of the proximal or distal segments or a combination of the two (total forelimb dexterity). The presence of species with widely different brain sizes and similar dexterities, and vice versa, suggests that an increase in the amount of neural substrate might not be necessary for the production of finely coordinated forelimb movements. It is suggested that this outcome is representative of the plasticity of both mammalian brain size and behavior and that variations in brain size and forelimb dexterity could be linked to disparate ecological and phylogenetic factors which act in concert to promote or constrain neural development and behavior in different species.

Animals↗

PubMed2006

Hominin lower second premolar morphology: evolutionary inferences through geometric morphometric analysis.

Mandibular premolars are increasingly used in taxon-specific diagnostic analyses of hominins. Among the principal difficulties in these evaluations is the absence of discrete, discernible, and comparable anatomical structures for rigorous quantitative assessment. Previous research has addressed either internal crown surface features (such as cusps and fossae) or the morphology of the crown outline. In the present paper, we integrate both types of information in the examination of morphological variation of lower P4s (n = 96) among various fossil hominin species with an emphasis on genus Homo. We use a set of 34 2D landmarks combining coordinate data from four classical dental landmarks on the occlusal surface and 30 sliding semilandmarks of the crown outline. Our results indicate that external shape variation is closely related to the configuration of the occlusal morphological features and influenced by dental size. The external and internal shapes of P4 are polymorphic but still useful in depicting a primitive-derived gradient. The primitive pattern seems to have been an asymmetrical contour with a mesially displaced metaconid, development of a bulging talonid, and a broad occlusal polygon. The trend toward dental reduction during the Pleistocene produced different morphological variants with a reduced occlusal polygon and decreased lingual occlusal surface in later Homo species. Homo heidelbergensis/neanderthalensis have fixed plesiomorphic traits in high percentages, whereas in modern humans a symmetrical outline with a centered metaconid and talonid reduction evolved.

Animals↗

PubMed1991

The primary structure of the thymidine kinase gene of fish lymphocystis disease virus.

The DNA nucleotide sequence of the thymidine kinase (TK) gene of fish lymphocystis disease virus (FLDV) which has been localized between the coordinates 0.678 to 0.688 of the viral genome was determined. The analysis of the DNA nucleotide sequence located between the recognition sites of HindIII (0.669 map unit; nucleotide position 1) and AccI (nucleotide position 2032) revealed the presence of an open reading frame of 954 bp on the lower strand of this region between nucleotide positions 1868 (ATG) and 915 (TAA). It encodes for a protein of 318 amino acid residues. The evolutionary relationships of the TK gene of FLDV to the other known TK genes was investigated using the method of progressive sequence alignment. These analyses revealed a high degree of diversity between the protein sequence of FLDV TK gene and the amino acid composition of other TKs tested. However, significant conservations were detected at several regions of amino acid residues of the FLDV TK protein when compared to the amino acid sequence of TKs of African swine fever virus, fowlpox virus, shope fibroma virus, and vaccinia virus and to the amino acid sequences of the cellular cytoplasmic TK of chicken, mouse, and man.

Amino Acid Sequence↗

PubMed2003

A biomechanical model for analysis of muscle force, power output and lower jaw motion in fishes.

Fish skulls are complex kinetic systems with movable components that are powered by muscles. Cranial muscles for jaw closing pull the mandible around a point of rotation at the jaw joint using a third-order lever mechanism. The present study develops a lever model for the jaw of fishes that uses muscle design and the Hill equation for nonlinear length-tension properties of muscle to calculate dynamic power output. The model uses morphometric data on skeletal dimensions and muscle proportions in order to predict behavior and force transmission mediated by lever action. The computer model calculates a range of dynamic parameters of jaw function including muscle force, torque, effective mechanical advantage, jaw velocity, bite duration, bite force, work and power. A complete list of required morphometrics is presented and a software program (MandibLever 2.0) is available for implementing lever analysis. Results show that simulations yield kinematics and timing profiles similar to actual fish feeding events. Simulation of muscle properties shows that mandibles reach their peak velocity near the start of jaw closing, peak force at the end of jaw closing, and peak power output at about 25% of the closing cycle time. Adductor jaw muscles with different mechanical designs must have different contractile properties and/or different muscle activity patterns to coordinate jaw closing. The effective mechanical advantage calculated by the model is considerably lower than the mechanical advantage estimated from morphological lever ratios, suggesting that previous studies of morphological lever ratios have overestimated force and underestimated velocity transmission to the mandible. A biomechanical model of jaw closing can be used to interpret the mechanics of a wide range of jaw mechanisms and will enable studies of the functional results of developmental and evolutionary changes in skull morphology and physiology.

Animals↗

PubMed2026

The factory enters the fray: how mitochondrial protein trafficking shapes the host response to infection.

Beyond textbook functions in homeostatic metabolism, mitochondria are now recognized as central coordinators of cell-intrinsic and cell-extrinsic immune responses to infection. Directed trafficking of proteins and other molecules between mitochondria and the rest of the cell underlies a growing catalog of these activities. Some are pro-host; others are antagonized by viral effectors or co-opted by viruses entirely. How host and viral factors rewire the mitochondrial proteome during infection to shape these outcomes remains incompletely understood. The evolutionary history of this system adds another dimension: mitochondria retain biochemical signatures of their α-proteobacterial endosymbiotic origin, and ongoing co-evolution between viral, host, and mitochondrial genomes continues to shape the proteins that traffic to and from the organelle. Using published examples, we highlight general principles, mechanisms, and consequences of host and viral protein localization to and from the mitochondria. To support discovery, we present integrated gene lists identifying host mitochondrial factors with evidence for type I interferon stimulation, interactions with viral proteins, and signatures of positive selection. Together, these resources and the principles within offer a framework for understanding mitochondria not as passive metabolic machinery but as actively contested cellular territory whose protein composition is continuously negotiated between the host and the pathogen.

adaptation↗

PubMed1991

Characterization and evolutionary aspects of a transcript encoding a neuropeptide precursor of Lymnaea neurons, VD1 and RPD2.

We isolated and characterized a cDNA clone encoding the major prohormone of VD1 and RPD2, two electrotonically coupled identified neurons in the central nervous system of the freshwater snail, Lymnaea stagnalis. The VD1/RPD2 prohormone may be cleaved to generate a set of 4 different neuropeptides, called epsilon, delta, alpha 1 and beta peptides, as well as a single aspartate. Since VD1 and RPD2 probably are involved in O2 perception and modulation of cardio-respiratory functions, it is thought that the neuropeptides synthesized and released by these neurons coordinate the adaptive physiological and behavioural processes that occur in response to changes in O2 availability. Comparison of the Lymnaea VD1/RPD2 precursor with two related precursors, prohormones R15-1 and R15-2, identified from neuron R15 in the marine mollusc Aplysia californica revealed a similar pattern of organization of the preprohormones. The overall homology is rather low, however, detailed comparisons show a highly differential pattern of conservation of peptide regions on the precursors.

Amino Acid Sequence↗

PubMed2004

A protein interaction framework for human mRNA degradation.

The degradation of mRNA is an important regulatory step in the control of gene expression. However, mammalian RNA decay pathways remain poorly characterized. To provide a framework for studying mammalian RNA decay, a two-hybrid protein interaction map was generated using 54 constructs from 38 human proteins predicted to function in mRNA decay. The results provide evidence for interactions between many different proteins required for mRNA decay. Of particular interest are interactions between the poly(A) ribonuclease and the exosome and between the Lsm complex, decapping factors, and 5'-->3' exonucleases. Moreover, multiple interactions connect 5'-->3' and 3'-->5' decay proteins to each other and to nonsense-mediated decay factors, providing the opportunity for coordination between decay pathways. The interaction network also predicts the internal organization of the exosome and Lsm complexes. Additional interactions connect mRNA decay factors to many novel proteins and to proteins required for other steps in gene expression. These results provide an experimental insight into the organization of proteins required for mRNA decay and their coupling to other cellular processes, and the physiological relevance of many of these interactions are supported by their evolutionary conservation. The interactions also provide a wealth of hypotheses to guide future research on mRNA degradation and demonstrate the power of exhaustive protein interaction mapping in aiding understanding of uncharacterized protein complexes and pathways.

Carrier Proteins↗

PubMed2000

Cheap talk when interests conflict.

Most evolutionary analyses of animal communication suggest that low-cost signals can evolve only when both the signaller and the recipient rank outcomes in the same order. When there is a conflict of interest between sender and receiver, honest signals must be costly. However, recent work suggests that low-cost signals can be evolutionarily stable, even when the sender and the receiver rank outcomes in different orders, as long as the interest in achieving coordination is sufficiently great. In this paper, we extend this body of work by analysing a game theory model that shows that low-cost signals can evolve when there are conflicts of interest and no interest in coordination, as long as individuals interact repeatedly. We also present an empirical example indicating that female rhesus macaques, Macaca mulatta, use honest, low-cost, vocal signals to facilitate interactions when conflicts of interest exist. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗