Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Evolutionary coordination”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed2026

Insights into Genome Ejection by a Therapeutic phiKMV-like Bacteriophage.

Ar-KM is a phiKMV-like therapeutic bacteriophage used in clinical candidate phage therapy cocktails to treat lung infections caused by P. aeruginosa. Here, we present an integrative structural atlas of Ar-KM proteins using cryo-EM, proteomics, and bioinformatics. From a single purified Ar-KM preparation, we identified three distinct populations: mature DNA-filled virions, open-nozzle particles with ejection proteins extending from the tail, and closed-nozzle empty particles. Near-atomic-resolution reconstructions of all three states enabled us to build atomic models for eleven structural proteins. The mature virion revealed the pre-ejection conformation of three ejection proteins, gp41, gp42, and gp43, homologous to coliphage T7's gp14, gp15, and gp16, respectively. Unlike T7, peptidoglycan hydrolase activity associated with the ejectosome resides in the gp15-like periplasmic tunnel protein gp42, whereas in T7 the lysozyme-like domain is located at the N-terminus of gp16, underscoring the structural plasticity and evolutionary mosaicity of ejection proteins. We further identified a short α-helical factor, gp34, present in eight copies at the mismatched interface between the portal barrel and gp41. Gp34 forms a cage within the nozzle, acting as a molecular wedge that stabilizes the open conformation and permits gp41 to assemble into a hexameric channel during ejection. Evolutionarily, gp34 appears to be an ortholog of the essential gene gp7.3 in phage T7 and is conserved across sequenced phiKMV-like phages. We propose that this protein functions as an ejection protein assembly factor, stabilizing the open nozzle during infection and allowing the coordinated exit of ejection proteins and their assembly into a DNA-ejectosome.

Pseudomonas phages↗
PubMed2001

Identified nerve cells and insect behavior.

Studies of insect identified neurons over the past 25 years have provided some of the very best data on sensorimotor integration; tracing information flow from sensory to motor networks. General principles have emerged that have increased the sophistication with which we now understand both sensory processing and motor control. Two overarching themes have emerged from studies of identified sensory interneurons. First, within a species, there are profound differences in neuronal organization associated with both the sex and the social experience of the individual. Second, single neurons exhibit some surprisingly rich examples of computational sophistication in terms of (a) temporal dynamics (coding superimposed upon circadian and shorter-term rhythms), and also (b) what Kenneth Roeder called "neural parsimony": that optimal information can be encoded, and complex acts of sensorimotor coordination can be mediated, by small ensembles of cells. Insect motor systems have proven to be relatively complex, and so studies of their organization typically have not yielded completely defined circuits as are known from some other invertebrates. However, several important findings have emerged. Analysis of neuronal oscillators for rhythmic behavior have delineated a profound influence of sensory feedback on interneuronal circuits: they are not only modulated by feedback, but may be substantially reconfigured. Additionally, insect motor circuits provide potent examples of neuronal restructuring during an organism's lifetime, as well as insights on how circuits have been modified across evolutionary time. Several areas where future advances seem likely to occur include: molecular genetic analyses, neuroecological syntheses, and neuroinformatics--the use of digital resources to organize databases with information on identified nerve cells and behavior.

Animals↗
PubMed1998

Molecular characterization of a broad selectivity neutral solute channel.

In all living cells, coordination of solute and water movement across cell membranes is of critical importance for osmotic balance. The current concept is that these processes are of distinct biophysical nature. Here we report the expression cloning of a liver cDNA encoding a unique promiscuous solute channel (AQP9) that confers high permeability for both solutes and water. AQP9 mediates passage of a wide variety of non-charged solutes including carbamides, polyols, purines, and pyrimidines in a phloretin- and mercury-sensitive manner, whereas amino acids, cyclic sugars, Na+, K+, Cl-, and deprotonated monocarboxylates are excluded. The properties of AQP9 define a new evolutionary branch of the major intrinsic protein family of aquaporin proteins and describe a previously unknown mechanism by which a large variety of solutes and water can pass through a single pore, enabling rapid cellular uptake or exit of metabolites with minimal osmotic perturbation.

Amino Acid Sequence↗
PubMedDate not supplied

Developmental plasticity and disparity in early dipnoan (lungfish) dentitions.

Although the lungfish (Dipnoi) belong within the Osteichthyes, their dentitions are radically different from other osteichthyans. Lungfish dentitions also show a uniquely high structural disparity during the early evolution of the group, partly owing to the independent variation of odontogenic and odontoclastic processes that are tightly and stereotypically coordinated in other osteichthyans. We present a phylogenetic analysis of early lungfishes incorporating a novel approach to coding these process characters in preference to the resultant adult dental morphology. The results only partially resolve the interrelationships of Devonian dipnoans, but show that the widely discussed hypothesis of separate tooth-plated, dentine-plated, and denticulated lineages is unlikely to be true. The dipnoan status of Diabolepis is corroborated. Lungfish dentitions seem to have undergone extensive and nonparsimonious evolution during the early history of the group, but much of the resulting disparity can be explained by a modest number of evolutionary steps in the underlying developmental processes, those for dental formation (odontogenic) and those for the remodeling of dentine tissue (odontoclastic). Later in lungfish evolution, this disparity was lost as the group settled to a pattern of dental development that is just as stereotypic as, but completely different from, that of other osteichthyans.

Animals↗
PubMed1997

High coordination lattice models of protein structure, dynamics and thermodynamics.

A high coordination lattice discretization of protein conformational space is described. The model allows discrete representation of polypeptide chains of globular proteins and small macromolecular assemblies with an accuracy comparable to the accuracy of crystallographic structures. Knowledge based force field, that consists of sequence specific short range interactions, cooperative model of hydrogen bond network and tertiary one body, two body and multibody interactions, is outlined and discussed. A model of stochastic dynamics for these protein models is also described. The proposed method enables moderate resolution tertiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when evolutionary information is exploited or/and when sparse experimental data are available. The model responds correctly to sequence mutations and could be used at early stages of a computer aided protein design and protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of polypeptides and proteins and quite detailed theoretical studies of thermodynamics of nontrivial protein models.

Amino Acid Sequence↗
PubMed1980

1H-NMR studies of the coordination geometry at the heme iron and the electronic structure of the heme group in cytochrome c-552 from Euglena gracilis.

The 1H-NMR lines of heme c in reduced and oxidized cytochrome c-552 from Euglena gracilis were individually assigned and the coordination geometry of the axial ligands was investigated. The electronic structure of the heme and the chirality of the axially bound methionine were found to be of the same type as in mammalian cytochrome c, but different from cytochrome c-551 from Pseudomonas aeruginosa. These results provide additional support for a previously proposed correlation between the chirality of attachment of the axial methionine and the electronic wave functions in oxidized cytochromes of the c type. Comparison of mammalian cytochrome c, cytochrome c-551 and cytochrome c-552 indicates that the chirality of the axially bound methionine is not linked with the evolutionary increase of the polypeptide chain length.

Animals↗
PubMed1999

Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway.

The anthocyanin biosynthetic pathway is responsible for the production of anthocyanin pigments in plant tissues and shares a number of enzymes with other biochemical pathways. The six core structural genes of this pathway have been cloned and characterized in two taxonomically diverse plant species (maize and snapdragon). We have recently cloned these genes for a third species, the common morning glory, Ipomoea purpurea. This additional information provides an opportunity to examine patterns of evolution among genes within a single biochemical pathway. We report here that upstream genes in the anthocyanin pathway have evolved substantially more slowly than downstream genes and suggest that this difference in evolutionary rates may be explained by upstream genes being more constrained because they participate in several different biochemical pathways. In addition, regulatory genes associated with the anthocyanin pathway tend to evolve more rapidly than the structural genes they regulate, suggesting that adaptive evolution of flower color may be mediated more by regulatory than by structural genes. Finally, for individual anthocyanin genes, we found an absence of rate heterogeneity among three major angiosperm lineages. This rate constancy contrasts with an accelerated rate of evolution of three CHS-like genes in the Ipomoea lineage, indicating that these three genes have diverged without coordinated adjustment by other pathway genes.

Acyltransferases↗
PubMed2003

Modelling primary and secondary growth processes in plants: a summary of the methodology and new data from an early lignophyte.

A mathematical method, based on polar coordinates that allow modelling of primary and secondary growth processes in stems of extant and fossil plants, is summarized and its potential is discussed in comparison with numerical methods using digitizing tablets or electronic image analysing systems. As an example, the modelling of tissue distribution in the internode of an extant sphenopsid (Equisetum hyemale) is presented. In the second half of the paper we present new data of a functional analysis of stem structure and biomechanics of the early lignophyte Tetraxylopteris schmidtii (Middle Devonian) using the polar coordinate method for modelling the tissue distribution in stems of different ontogenetic age. Calculations of the mechanical properties of the stems, based on the modelling of the tissue arrangement, indicate that there is no increase in structural bending modulus throughout the entire development of the plant. The oldest ontogenetic stage has a significantly smaller bending elastic modulus than the intermediate ontogenetic stage, a 'mechanical signal', which is not consistent with a self-supporting growth form. These results, and the ontogenetic variations of the contributions of different stem tissues to the flexural stiffness of the entire stem, are discussed in the evolutionary context of cambial secondary growth.

Biological Evolution↗
PubMed1992

Penicillin and cephalosporin biosynthetic genes: structure, organization, regulation, and evolution.

Penicillins and cephalosporins are produced by a wide variety of microorganisms, including some filamentous fungi, many gram-positive streptomycetes, and a few gram-negative unicellular bacteria. All produce these beta-lactam antibiotics by essentially the same biosynthetic pathway. Recently, most of the penicillin and cephalosporin biosynthetic genes have been cloned, sequenced, and expressed. The biosynthetic genes code for enzymes that possess multifunctional peptide synthetase, cyclase, epimerase, expandase, hydroxylase, lysine aminotransferase, and acetyltransferase activities and are organized in chromosomal gene clusters and coordinately expressed. DNA hybridization screens of streptomycetes demonstrate that beta-lactam biosynthetic genes may be more widespread in nature than is indicated by conventional antibiotic screens. They offer the possibility of expanding the search for organisms with potential to make new beta-lactam antibiotics. Attempts to improve current yields of beta-lactams in production strains by introducing into them additional copies of biosynthetic genes have been partially successful. Comparative sequence analysis of bacterial and fungal beta-lactam biosynthetic genes show they share very high sequence identity. A model that explains the similarity of biosynthetic genes from an evolutionary standpoint assumes horizontal gene-transfer between the two groups of organisms. Indirect evidence suggests the transfer occurred from the bacteria to the fungi.

Amino Acid Sequence↗
PubMed2004

Structural basis of human cytoglobin for ligand binding.

Cytoglobin (Cgb), a newly discovered member of the vertebrate globin family, binds O(2) reversibly via its heme, as is the case for other mammalian globins (hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb)). While Cgb is expressed in various tissues, its physiological role is not clearly understood. Here, the X-ray crystal structure of wild type human Cgb in the ferric state at 2.4A resolution is reported. In the crystal structure, ferric Cgb is dimerized through two intermolecular disulfide bonds between Cys38(B2) and Cys83(E9), and the dimerization interface is similar to that of lamprey Hb and Ngb. The overall backbone structure of the Cgb monomer exhibits a traditional globin fold with a three-over-three alpha-helical sandwich, in which the arrangement of helices is basically the same among all globins studied to date. A detailed comparison reveals that the backbone structure of the CD corner to D helix region, the N terminus of the E-helix and the F-helix of Cgb resembles more closely those of pentacoordinated globins (Mb, lamprey Hb), rather than hexacoordinated globins (Ngb, rice Hb). However, the His81(E7) imidazole group coordinates directly to the heme iron as a sixth axial ligand to form a hexcoordinated heme, like Ngb and rice Hb. The position and orientation of the highly conserved residues in the heme pocket (Phe(CD1), Val(E11), distal His(E7) and proximal His(F8)) are similar to those of other globin proteins. Two alternative conformations of the Arg84(E10) guanidium group were observed, suggesting that it participates in ligand binding to Cgb, as is the case for Arg(E10) of Aplysia Mb and Lys(E10) of Ngb. The structural diversities and similarities among globin proteins are discussed with relevance to molecular evolutionary relationships.

Amino Acid Sequence↗
PubMed2001

Ligand variation in the transferrin family: the crystal structure of the H249Q mutant of the human transferrin N-lobe as a model for iron binding in insect transferrins.

Proteins of the transferrin (Tf) family play a central role in iron homeostasis in vertebrates. In vertebrate Tfs, the four iron-binding ligands, 1 Asp, 2 Tyr, and 1 His, are invariant in both lobes of these bilobal proteins. In contrast, there are striking variations in the Tfs that have been characterized from insect species; in three of them, sequence changes in the C-lobe binding site render it nonfunctional, and in all of them the His ligand in the N-lobe site is changed to Gln. Surprisingly, mutagenesis of the histidine ligand, His249, to glutamine in the N-lobe half-molecule of human Tf (hTf/2N) shows that iron binding is destabilized and suggests that Gln249 does not bind to iron. We have determined the crystal structure of the H249Q mutant of hTf/2N and refined it at 1.85 A resolution (R = 0.221, R(free) = 0.246). The structure reveals that Gln249 does coordinate to iron, albeit with a lengthened Fe-Oepsilon1 bond of 2.34 A. In every other respect, the protein structure is unchanged from wild-type. Examination of insect Tf sequences shows that the K206.K296 dilysine pair, which aids iron release from the N-lobes of vertebrate Tfs, is not present in the insect proteins. We conclude that substitution of Gln for His does destabilize iron binding, but in the insect Tfs this is compensated by the loss of the dilysine interaction. The combination of a His ligand with the dilysine pair in vertebrate Tfs may have been a later evolutionary development that gives more sophisticated pH-mediated control of iron release from the N-lobe of transferrins.

Amino Acid Sequence↗
PubMed2003

New genes encoding subunits of a cytochrome bc1-analogous complex in the respiratory chain of the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius.

The soxL gene from Sulfolobus acidocaldarius (DSM 639) encodes a Rieske iron-sulfur protein. In this study we report the identification of two open reading frames in its downstream region. The first one, named soxN, codes for a membrane protein bearing a resemblance to the b-type cytochromes of the cytochrome bc1 and b6f complexes. The protein is predicted to contain at least 10 transmembrane helices and features the two conserved histidine pairs coordinating the heme groups of these cytochromes. The second open reading frame, named odsN, encodes a soluble protein of unknown function. The genomic region displays a complex transcription pattern. Northern blot and RT-PCR analyses revealed the presence of mono- and bi-cistronic transcripts as well as a tri-cistronic transcript of soxL and cbsAB, encoding the mono-heme cytochrome b558/566. Phylogenetic analyses of the genes of the soxLN pair and of other archaeal gene pairs encoding Rieske iron-sulfur proteins and b-type cytochromes revealed an identical branching patterns for both protein families, suggesting an evolutionary link of these genes provided by the functional interaction of the proteins. On the basis of the findings of this study and the previously studied properties of the soxL and cbsA proteins, we propose the occurrence of a novel cytochrome bc1-analogous complex in the membranes of Sulfolobus, consisting of the cytochrome b homolog soxN, the Rieske protein soxL, the high potential cytochrome cbsA, as well as the non-redox-active subunits cbsB and odsN.

Amino Acid Sequence↗
PubMed2004

Evolutionary optimization for robust hierarchical computation of the rotation centres of kinematic chains from reduced ranges of motion the lower spine case.

A novel technique based on evolutionary optimization is proposed here to compute the average rotation centres (RCs) of ball joints linked into kinematic chains using 3D trajectories of the markers attached to the external surface of the corresponding articulated structures. The chain is hierarchically solved by iteratively minimizing the variance of the marker distances from the actual RC through an evolutional strategy method (ESM) from proximal to distal joints. In particular, the technique is compared to the non-rigid sphere-fitting method, recently proposed in literature and implemented through a closed-form solution (CFS), in conditions of random and systematic noise superimposed to the marker coordinates. Results from simulated motions showed that, in case of small range of motion (5 degrees , 10 degrees ) the performance of CFS is really unreliable whereas ESM provided satisfactory accuracy. Error propagation along the kinematic chain was found to be negligible. Also in the case of systematic errors, ESM provides an accuracy that is sensibly better than that of the CFS. As a case study, ESM was applied to the in vivo computation of the RCs of the vertebrae in the lower spine region using a specific marker protocol. A set of spine movements by a normal adult male, recorded by an optoelectronic motion capture system, were processed with the developed method. The variability of the estimated average RCs was small (few millimeters) in agreement with the literature data from cadaveric studies and X-ray imaging.

Algorithms↗
PubMed1989

Urate oxidase: primary structure and evolutionary implications.

Urate oxidase, or uricase (EC 1.7.3.3), is a peroxisomal enzyme that catalyzes the oxidation of uric acid to allantoin in most mammals. In humans and certain other primates, however, the enzyme has been lost by some unknown mechanism. To identify the molecular basis for this loss, urate oxidase cDNA clones were isolated from pig, mouse, and baboon, and their DNA sequences were determined. The mouse urate oxidase open reading frame encodes a 303-amino acid polypeptide, while the pig and baboon urate oxidase cDNAs encode a 304-amino acid polypeptide due to a single codon deletion/insertion event. The authenticity of this single additional codon was confirmed by sequencing the mouse and pig genomic copies of the gene. The urate oxidase sequence contains a domain similar to the type 2 copper binding motif found in other copper binding proteins, suggesting that the copper ion in urate oxidase is coordinated as a type 2 structure. Based upon a comparison of the NH2-terminal peptide and deduced sequences, we propose that the maturation of pig urate oxidase involves the posttranslational cleavage of a six-amino acid peptide. Two nonsense mutations were found in the human urate oxidase gene, which confirms, at the molecular level, that the urate oxidase gene in humans is nonfunctional. The sequence comparisons favor the hypothesis that the loss of urate oxidase in humans is due to a sudden mutational event rather than a progressive mutational process.

Amino Acid Sequence↗
PubMed2026

Identification of rice DUF1719 gene family and analysis of alkaline tolerance function of OsDUF1719.8.

Alkaline stress severely constrains the physiological metabolism and growth and development of rice through high pH and ionic toxicity. Domains of unknown function (DUF) play significant roles in plant stress responses. However, the function of the DUF1719 family (PF08224) in rice has not been reported and further research is needed. This study systematically identified the OsDUF1719 gene family in rice and investigated the function of OsDUF1719.8 under alkaline stress. The results demonstrate that the rice DUF1719 family comprises 13 protein members, all containing the PF08224 domain. It is predicted that this domain may play a role in ATPase activation. Evolutionary analysis divided DUF1719 proteins from eight grass species into six subgroups, with highly conserved gene structures, motifs, and tertiary architectures within each subgroup. Promoter analysis indicated enrichment of stress- and hormone-responsive elements, implying broad involvement in stress regulation. Expression analysis revealed that several genes, including OsDUF1719.5 and OsDUF1719.8, were upregulated under multiple abiotic stresses. Notably, OsDUF1719.8 was strongly induced during early alkaline stress. Consequently, we further analyzed the function of OsDUF1719.8 in the rice alkaline stress response. The results demonstrate that overexpression of OsDUF1719.8 enhanced rice alkaline tolerance, whereas knockout mutants exhibited stress sensitivity. OsDUF1719.8 enhances rice tolerance to alkaline stress by coordinately regulating reactive oxygen species metabolism, promoting the accumulation of osmotic adjustment compounds, and modulating ion homeostasis. This study provides the first systematic identification of the DUF1719 family and elucidates the function of OsDUF1719.8 in positively regulating rice alkaline tolerance, offering a novel gene for alkali-tolerant molecular breeding of rice.

Oryza↗
PubMed1992

The evolution of neural circuits controlling feeding behavior in frogs.

Our approach to understanding motor systems is a phylogenetic, 'outside-in' approach, the goal of which is to identify behavioral transitions during phylogenesis and elucidate their neurological basis. In this paper, we review the results of recent behavioral, biomechanical and neurological studies on frog feeding behavior. These studies show that highly protrusible tongues have evolved numerous times independently among frogs, and that the biomechanics and neuromuscular control of feeding behavior have been transformed repeatedly during frog evolution. Many of the independent lineages possess unique biomechanical mechanisms for protracting their tongues and unique neural mechanisms for coordinating feeding behavior. In frogs, there has been considerable evolution at the interface between reticular central pattern generators (CPGs) associated with feeding and sensory feedback circuits that modulate feeding motor output. In particular, the roles of hypoglossal and glossopharyngeal sensory feedback appear to have been relatively plastic in their evolution. Prey-type dependence of hypoglossal sensory feedback in Rana suggests that the interaction between descending visual control and sensory feedback also may be evolutionarily plastic. Comparative studies have found that motor systems sometimes evolve conservatively across morphological and behavioral transitions (i.e., the shoulder in birds) or, alternatively, they may be subject to considerably more evolutionary change than is reflected in morphological characteristics (i.e., feeding in cichlids). We hypothesize that the CPG circuits for feeding behavior in the reticular formation may evolve conservatively because they are highly integrated, multifunctional networks which cannot be optimized for one function without compromising others. In contrast, the interfaces between the CPG, sensory feedback and descending control should be less constrained. When changes in motor patterns occur during evolution, it is likely that sensory feedback or descending control may be involved.

Animals↗
PubMed1998

Evolution, partnerships and cooperation.

In an evolutionary game theoretic setting, players are allowed to choose not only their strategies for a particular interaction, but also to some extent with whom they will play. A stability concept is presented and examined which allows agents to endogenously construct fixed partnerships. A strategy-matching type is said to be recoverable if a population in which it is used by all players is both internally and externally stable to random mutations. Such a strategy-matching type always exists and maximises social efficiency in the population. Some examples are considered in the light of this concept. The ability to form fixed partnerships enables players to coordinate on efficient outcomes. In particular, cooperation is achieved in the Prisoners' Dilemma without recourse to repetition or rigid spatial restriction.

Animals↗
PubMed1997

Is schizophrenia the price that Homo sapiens pays for language?

The dichotomy between schizophrenia and manic-depressive illness is, as E. Kraepelin suspected, flawed; no unequivocal separation can be achieved. There are no categories of psychosis, but only continua of variation. However, the definition of nuclear symptoms by K. Schneider reveals the fundamental characteristics of the core syndrome--it is independent of the environment and constant in incidence across populations that have been separated for thousands of years. The associated genetic variation must be as old as Homo sapiens and represent a component of diversity that crosses the population as a whole. The fecundity disadvantage that accompanies the syndrome requires a balance in a substantial and universal advantage; this advantage, it is proposed, is the speciation characteristic of language; language and psychosis have a common evolutionary origin. Language, it is suggested, originated in a critical change on the sex chromosomes (the 'speciation event'--the genetic change that defined the species) occurring in East Africa between 100 and 250 thousand years ago that allowed the two hemispheres to develop with a degree of independence. Language can be understood as bi-hemispheric with one component function--a linear output sequence--confined to the dominant hemisphere--and a second--parallel distributed sampling occurring mainly in the non-dominant hemisphere. This mechanism provides an account of the generativity of language. The significance of nuclear symptoms is that these reflect a breakdown of bi-hemispheric coordination of language, perhaps specifically of the process of 'indexicalisation' (the distinction between 'I' and 'you') of self- versus other-generated references. Nuclear symptoms can be described as 'language at the end of its tether'; the phenomena and population characteristics of the nuclear syndrome of schizophrenia thus yield clues to the origin of the species.

Biological Evolution↗