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The evolution of function in enzymes.

The evolution of function appears to have proceeded from a primordial catalyst with little specificity to a highly specific one. As specificity increased, the need to exclude water created a need for flexibility, and flexibility in time led to regulation through induced conformational changes. Induced conformational changes in multisubunit proteins then produced cooperativity. Each of these properties is subject ot fine tuning by modification of the protein structure. The function of the enzyme is itself tuned to high efficiency by the evolution of these interrelated functions.

Allosteric Regulation↗

Cloning and sequence analysis of a pituitary prolactin cDNA from the brushtail possum (Trichosurus vulpecula).

Overlapping cDNA partial clones of pituitary prolactin from the marsupial brushtail possum (Trichosurus vulpecula) were isolated and sequenced. The nucleotide and deduced amino acid sequences showed high sequence identity with pig prolactin (84.3 and 92.5%, respectively) and all of the expected structural features of a quadruped prolactin. A prolactin gene tree was constructed and rates of evolution calculated for possum along with several mammalian and nonmammalian prolactins. Possum prolactin was most closely linked to the prolactins of eutherian mammals but branched from the main mammalian line well before the eutherian prolactins. The prolactin/GH family shows variable rates of evolution ranging from 0.3 substitutions/amino acid site/year x 10(9) for pig prolactin to 7.0 substitutions/ amino acid site/year x 10(9) for the mouse. Since divergence from the eutherian mammals, possum prolactin has shown a slow rate of evolution (0.2 substitutions/ amino acid site/year x 10(9)). As expected, the prolactin gene was expressed in the possum pituitary gland but not in the liver, lung, kidney, heart, or mammary gland.

Amino Acid Sequence↗

Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective.

The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. Likewise, the origin of the endemic South American genus Hippidion is unresolved, as is the phylogenetic position of the "stilt-legged" horses of North America. Using ancient DNA sequences, we show that, in contrast to current models based on morphology and a recent genetic study, Hippidion was phylogenetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of c. 10 Ma. Furthermore, we show that stilt-legged horses, commonly regarded as Old World migrants related to the hemionid asses of Asia, were in fact an endemic North American lineage. Finally, our data suggest that there were fewer horse species in late Pleistocene North America than have been named on morphological grounds. Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species.

Animals↗

Associative recognition and storage in a model network of physiological neurons.

We consider a neural network model in which the single neurons are chosen to closely resemble known physiological properties. The neurons are assumed to be linked by synapses which change their strength according to Hebbian rules on a short time scale (100 ms). The dynamics of the network--the time evolution of the cell potentials and the synapses--is investigated by computer simulation. As in more abstract network models (Cooper 1973; Hopfield 1982; Kohonen 1984) it is found that the local dynamics of the cell potentials and the synaptic strengths result in global cooperative properties of the network and enable the network to process an incoming flux of information and to learn and store patterns associatively. A trained net can associate missing details of a pattern, can correct wrong details and can suppress noise in a pattern. The network can further abstract the prototype from a series of patterns with variations. A suitable coupling constant connecting the dynamics of the cell potentials with the synaptic strengths is derived by a mean field approximation. This coupling constant controls the neural sensitivity and thereby avoids both extremes of the network state, the state of permanent inactivity and the state of epileptic hyperactivity.

Animals↗

Damage to the oxygen-evolving complex by superoxide anion, hydrogen peroxide, and hydroxyl radical in photoinhibition of photosystem II.

Under strong illumination of a photosystem II (PSII) membrane, endogenous superoxide anion, hydrogen peroxide, and hydroxyl radical were successively produced. These compounds then cooperatively resulted in a release of manganese from the oxygen-evolving complex (OEC) and an inhibition of oxygen evolution activity. The OEC inactivation was initiated by an acceptor-side generated superoxide anion, and hydrogen peroxide was most probably responsible for the transportation of reactive oxygen species (ROS) across the PSII membrane from the acceptor-side to the donor-side. Besides ROS being generated in the acceptor-side induced manganese loss; there may also be a ROS-independent manganese loss in the OEC of PSII. Both superoxide anion and hydroxyl radical located inside the PSII membrane were directly identified by a spin trapping-electron spin resonance (ESR) method in combination with a lipophilic spin trap, 5-(diethoxyphosphoryl)-5-phenethyl-1-pyrroline N-oxide (DEPPEPO). The endogenous hydrogen peroxide production was examined by oxidation of thiobenzamide.

Electron Spin Resonance Spectroscopy↗

Purification and properties of soluble hydrogenase from Alcaligenes eutrophus H 16.

The soluble hydrogenase (hydrogen: NAD+ oxidoreductase, EC 1.12.1.2) from Alcaligenes eutrophus H 16 was purified 68-fold with a yield of 20% and a final specific activity (NAD reduction) of about 54 mumol H2 oxidized/min per mg protein. The enzyme was shown to be homogenous by polyacrylamide gel electrophoresis. Its molecular weight and isoelectric point were determined to be 205 000 and 4.85 respectively. The oxidized hydrogenase, as purified under aerobic conditions, was of high stability but not reactive. Reductive activation of the enzyme by H2, in the presence of catalytic amounts of NADH, or by reducing agents caused the hydrogenase to become unstable. The purified enzyme, in its active state, was able to reduce NAD, FMN, FAD, menaquinone, ubiquinone, cytochrome c, methylene blue, methyl viologen, benzyl viologen, phenazine methosulfate, janus green, 2,6-dichlorophenoloindophenol, ferricyanide and even oxygen. In addition to hydrogenase activitiy, the enzyme exhibited also diaphorase and NAD(P)H oxidase activity. The reversibility of hydrogenase function (i.e. H2 evolution from NADH, methyl viologen and benzyl viologen) was demonstrated. With respect to H2 as substrate, hydrogenase showed negative cooperativity; the Hill coefficient was n = 0.4. The apparent Km value for H2 was found to be 0.037 mM. The absorption spectrum of hydrogenase was typical for non-heme iron proteins, showing maxima (shoulders) at 380 and 420 nm. A flavin component could be extracted from native hydrogenase characterized by its absorption bands at 375 and 447 nm and a strong fluorescense at 526 nm.

Alcaligenes↗

Region-specific rates of molecular evolution: a fourfold reduction in the rate of accumulation of "silent" mutations in transcribed versus nontranscribed regions of homologous DNA fragments derived from two closely related mouse species.

We have sequenced homologous DNA fragments of 2.7 and 2.8 kbp derived from the closely related mouse species Mus musculus domesticus (M. domesticus) and Mus musculus musculus (M. musculus), respectively. These two species diverged approximately 1 million years ago. Each DNA fragment contains 1.35 kbp of the 3' end of the constitutively expressed 2.2-kbp aprt (adenine phosphoribosyltransferase) gene and a similarly sized nontranscribed region downstream of the aprt gene. The aprt gene region contains protein coding sequences (0.35 kbp), intronic sequences (0.75 kbp), and a 3' nontranslated sequence (0.25 kbp). Both the M. domesticus and M. musculus downstream regions share three partial copies of the B1 repetitive element with the M. musculus downstream region containing an additional complete copy of this element. A comparison of the 2.7- and 2.8-kbp DNA fragments revealed a total of 63 molecular alterations (i.e., mutations) that were approximately fourfold more abundant in the nontranscribed downstream region than in the transcribed aprt gene. Of the 11 mutations observed in the transcribed region, 7 were found in introns, 3 in the 3' untranslated sequence, and 1 was a synonymous change in an exon. A comparison of the human and M. domesticus aprt genes has previously revealed no homology in either the intronic or 3' nontranslated regions with the exception of a 26-bp sequence in intron 3 and sequences at the exon/intron boundaries necessary for correct mRNA splicing (Broderick et al., Proc. Natl. Acad. Sci. USA, 84:3349, 1987). Therefore, there does not appear to be selective pressure for sequences within these regions. We conclude that there is a lower rate of accumulation of "silent" mutations in the transcribed mouse aprt gene than in a contiguous nontranscribed downstream region. A possible molecular mechanism involving preferential DNA repair for the transcribed region is discussed.

Adenine Phosphoribosyltransferase↗

T4 phage evolution data in terms of a time-dependent Topal-Fresco mechanism.

A physical interpretation of the Topal-Fresco [Nature 263, 285 (1976)] model for spontaneous base substitutions suggests that hydrogen-bonded DNA protons satisfy the criteria for a classical noninteracting isolated system. Accessible states for duplex G-C protons include the keto-amino state and the six complementary enol-imine isomers. Hydrogen-bonded enol and imine protons occupy symmetric double-minima created by the two sets of indistinguishable electron lone pairs and a single proton belonging to each enol-imine end group. These protons will consequently participate in coupled quantum mechanical flip-flop, tunneling back and forth between symmetric energy wells. This results in a quantum mixing of proton energy states where the lowest energy state will be a linear combination of available G-C isomers. The resulting conclusion is that metastable keto-amino G-C protons will populate accessible enol-imine stationary states at rates governed by quantum laws of statistical equilibrium, consistent with achieving the lowest energy condition for duplex G-C protons. Enol-imine G-C stationary states are bound more tightly, of the order of 3 to 12 kcal/mol, which requires a modified mode of Topal-Fresco replication that will inhibit reequilibration of enol and imine G and C template isomers and, thus, promote the formation of complementary mispairs. The model is demonstrated on time-dependent base substitutions expressed by T4 phage DNA systems where data are consistent with model explanations, including the prediction that time-dependent evolutionary transversion sites will exhibit both G-C-to-T-A and G-C-to-C-G transversions at replication, due to proton flip-flop alteration of G template genetic specificity. The observation that A-T sites are resistant to time-dependent evolutionary base substitutions, expressed exclusively at G-C sites, allows codons to be classified as either evolutionary sensitive (16 codons) or evolutionary resistant (8 codons). These criteria provide possible explanations for expansion properties of the CGG fragile X sequences. Enol-imine G-C stationary states appear to have been misdiagnosed as deamination of cytosine and oxidation of guanine to 8-hydroxy-guanine.

Amino Acids↗

Evolution of the haem-haem interaction in vertebrate haemoglobins - a hypothesis.

A hypothesis about the evolution of the haem-haem interaction in haemoglobins has been formulated on the basis of available functional and structural data. It emerges that this cooperative muchanism is not necessarily due solely to the higher levels of protomer aggregation, because it occurs only in haemoglobins having the distal histidine. It is thus proposed that this amino acid residue might have had a significant role for the development of low-oxygen-affinity haemoglobins in vertebrates.

Animals↗

Variable lymphocyte receptors in hagfish.

A previously uncharacterized type of variable lymphocyte receptors (VLR) was identified recently in the Sea lamprey. This jawless vertebrate generates an extensive VLR repertoire through differential insertion of neighboring diverse leucine-rich repeat (LRR) cassettes into an incomplete germ-line VLR gene. We report here VLR homologs from two additional lamprey species and the presence of two types of VLR genes in hagfish, the only other order of contemporary jawless vertebrates. As in the Sea lamprey, the incomplete hagfish germ-line VLR-A and -B genes are modified in lymphocyte-like cells to generate highly diverse repertoires of VLR-A and -B proteins via a presently undetermined mechanism. This jawless-fish mode of VLR diversification starkly contrasts with the rearrangement of Ig V(D)J gene segments used by all jawed vertebrates to produce diverse repertoires of T and B lymphocyte antigen receptors. The development of two very different strategies for receptor diversification at the dawn of vertebrate evolution approximately 500 million years ago attests to the fitness value of a lymphocyte-based system of anticipatory immunity.

Amino Acid Motifs↗

The case for selection at CCR5-Delta32.

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Delta32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Delta32 arose within the past 1,000 y and rose to its present high frequency (5%-14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit of much denser genetic maps and extensive control data. We find that the pattern of genetic variation at CCR5-Delta32 does not stand out as exceptional relative to other loci across the genome. Moreover using newer genetic maps, we estimated that the CCR5-Delta32 allele is likely to have arisen more than 5,000 y ago. While such results can not rule out the possibility that some selection may have occurred at C-C chemokine receptor 5 (CCR5), they imply that the pattern of genetic variation seen at CCR5-Delta32 is consistent with neutral evolution. More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome.

Alleles↗

MYC and p53 Alterations Cooperate through VEGF Signaling to Repress Cytotoxic T-cell and Immunotherapy Responses in Prostate Cancer.

UNLABELLED: Patients with castration-resistant prostate cancer (CRPC) are generally unresponsive to tumor-targeted treatments and immunotherapies. Genetic alterations acquired during the evolution of CRPC may affect antitumor immunity and immunotherapy responses, which could inform personalized therapeutic strategies. Using our innovative electroporation-based mouse models, we generated distinct genetic subtypes of CRPC found in patients and uncovered unique immune microenvironments. Specifically, mouse and human prostate tumors with MYC amplification and p53 disruption had weak cytotoxic lymphocyte infiltration and an overall dismal prognosis. MYC and p53 cooperated to induce tumor-intrinsic secretion of VEGF, which signaled through VEGFR2 expressed on CD8+ T cells to directly inhibit T-cell migration and effector functions. Targeting VEGF-VEGFR2 signaling in vivo remodeled the immunosuppressive prostate tumor microenvironment, leading to CD8+ T-cell-mediated primary tumor and metastasis growth suppression and significantly increased overall survival in MYC- and p53-altered CRPC. VEGFR2 blockade also led to the induction of PD-L1 in tumors and produced antitumor efficacy in combination with PD-L1 immune checkpoint blockade in multiple preclinical CRPC mouse models. Thus, these results identify a genetic mechanism of immunosuppression through VEGF signaling in prostate cancer that can be targeted to reactivate immune and immunotherapy responses in an aggressive subtype of CRPC. SIGNIFICANCE: VEGFR2 blockade inhibits VEGF-mediated T-cell suppression and potentiates the effects of PD-L1 immune checkpoint blockade to treat castration-resistant prostate cancer driven by MYC and p53 alterations.

Male↗

A simple classification of the volvocine algae by formal languages.

There are several explanations of why certain primitive multicellular organisms aggregate in particular forms and why their constituent cells cooperate with one another to a particular degree. Utilizing the framework of formal language theory, we have derived one possible simple classification of the volvocine algae-one of the primitive multicells-for some forms of aggregation and some degrees of cooperation among cells. The volvocine algae range from the unicellular Chlamydomonas to the multicellular Volvox globator, which has thousands of cells. The classification we use in this paper is based on the complexity of Parikh sets of families on Chomsky hierarchy in formal language theory. We show that an alga with almost no space closed to the environment, e.g., Gonium pectorale, can be characterized by PsFIN, one with a closed space and no cooperation, e.g., Eudorina elegans, by PsCF, and one with a closed space and cooperation, e.g., Volvox globator, by PslambdauSC. This classification should provide new insights into the necessity for specific forms and degrees of cooperation in the volvocine algae.

Animals↗

Invertebrate cytokines: tunicate cell proliferation stimulated by an interleukin 1-like molecule.

Tunicate pharyngeal cells include lymphocyte-like cells and granular amoebocytes. They are involved in the specific allogeneic and phagocytic reactions of tunicates. Little is known about their regulation or control. A tunicate interleukin 1 (IL-1)-like fraction is shown to stimulate the proliferation of these cells in vitro. This fraction, designated tunicate IL-1 beta, was isolated from tunicate hemolymph by gel filtration and chromatofocusing chromatography. Mitogenic responses to tunicate IL-1 beta were dose dependent and could be eliminated rapidly by removing tunicate IL-1 beta from culture medium. A second tunicate hemolymph fraction had no effect on tunicate cell proliferation even though it exhibited IL-1-like activity in a mouse thymocyte proliferation assay. Phytohemagglutin did not act synergistically with either fraction. These data are discussed in terms of the function and evolution of IL-1-like molecules in invertebrates.

Animals↗

Evidence for perforin-like activity associated with earthworm leukocytes.

Earthworm (Eisenia fetida) coelomic fluid contains several leukocytes (coelomocytes): basophils, acidophils and neutrophils as well as chloragocytes. Small coelomocytes and coelomocyte lysate are cytotoxic for the tumor cell target K562. The expression of a lytic factor was investigated by immunocytochemistry using light and transmission electron microscopy. A rat-anti-mouse-perforin-mAb labeled mainly small coelomocytes (nearly 20%) as visualized by light microscopy. TEM analysis using immunogold showed a homogenous labeling in the cytoplasm of small coelomocytes. The highest number of immunogold particles was estimated in coelomocytes with many small cytoplasmic granules. Coelomocytes with large lysosomal granules were also labeled but less intensely. No antibody binding was observed for chloragocytes either in light or electron microscopy. This suggests that the perforin-like activity is associated with only one cell type and that chloragocytes are responsible for other lytic activities. MALDI-MS revealed calreticulin usually associated with perforin in mammalian cells that mediate lysis (e.g. NK, CTL). Together, results strongly suggest the presence of putative perforin in earthworms. This in turn supports the hypothesis that perforin is a conserved component important in immune defense during evolution.

Journal Article↗