Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions

Organismic evolution requires that variation at distinct hierarchical levels and attributes be coherently integrated, often in the face of disparate environmental and genetic pressures. A central part of the evolutionary analysis of biological systems remains to decipher the causal connections between organism-wide (or genome-wide) attributes (e.g., mRNA abundance, protein length, codon bias, recombination rate, genomic position, mutation rate, etc) as well as their role-together with mutation, selection, and genetic drift-in shaping patterns of evolutionary variation in any of the attributes themselves. Here we combine genome-wide evolutionary analysis of protein and gene expression data to highlight fundamental relationships among genomic attributes and their associations with the evolution of both protein sequences and gene expression levels. Our results show that protein divergence is positively coupled with both gene expression polymorphism and divergence. We show moreover that although the number of protein-protein interactions in Drosophila is negatively associated with protein divergence as well as gene expression polymorphism and divergence, protein-protein interactions cannot account for the observed coupling between regulatory and structural evolution. Furthermore, we show that proteins with higher rates of amino acid substitutions tend to have larger sizes and tend to be expressed at lower mRNA abundances, whereas genes with higher levels of gene expression divergence and polymorphism tend to have shorter sizes and tend to be expressed at higher mRNA abundances. Finally, we show that protein length is negatively associated with both number of protein-protein interactions and mRNA abundance and that interacting proteins in Drosophila show similar amounts of divergence. We suggest that protein sequences and gene expression are subjected to similar evolutionary dynamics, possibly because of similarity in the fitness effect (i.e., strength of stabilizing selection) of disruptions in a gene's protein sequence or its mRNA expression. We conclude that, as more and better data accumulate, understanding the causal connections among biological traits and how they are integrated over time to constrain or promote structural and regulatory evolution may finally become possible.     

Evidence for a single heptahelical domain being turned on upon activation of a dimeric GPCR

G-protein-coupled receptors (GPCRs) have been shown to form dimers, but the relevance of this phenomenon in G-protein activation is not known. Among the large GPCR family, metabotropic glutamate (mGlu) receptors are constitutive dimers. Here we examined whether both heptahelical domains (HDs) are turned on upon full receptor activation. To that aim, we measured G-protein coupling efficacy of dimeric mGlu receptors in which one subunit bears specific mutations. We show that a mutation in the third intracellular loop (i3 loop) known to prevent G-protein activation in a single subunit decreases coupling efficacy. However, when a single HD is blocked in its inactive state using an inverse agonist, 2-methyl-6-(phenylethynyl)pyridine (MPEP), no decrease in receptor activity is observed. Interestingly, in a receptor dimer in which the subunit that binds MPEP is mutated in its i3 loop, MPEP enhances agonist-induced activity, reflecting a 'better' activation of the adjacent HD. These data are consistent with a model in which a single HD is turned on upon activation of such homodimeric receptors and raise important issues in deciphering the functional role of GPCR dimer formation for G-protein activation.     

Diverse patterns of poly(A) tail elongation and shortening of murine maternal mRNAs from fully grown oocyte to 2-cell embryo stages

We previously succeeded in constructing a cDNA library, CPF7, enriched with cDNA derived from maternal RNAs with the extended poly(A) tail in mouse fertilized eggs. In this study, we performed RNA blot analysis to examine the elongation in maternal RNAs using 20 representative clones isolated from CPF7 as probes. Various patterns of elongation, shortening, and/or degradation of maternal RNAs were observed from fully grown oocytes to early 2-cell embryos and could be roughly classified into three types and seven subtypes. These findings indicate that poly(A) elongation and shortening of maternal RNAs are not restricted to certain types of maternal RNAs but occur in many of them, and suggest a complex mechanism governing modification of the 3' end of maternal RNAs during the oocyte-to-embryo transition.     

PKCepsilon-PKD1 signaling complex at Z-discs plays a pivotal role in the cardiac hypertrophy induced by G-protein coupling receptor agonists

Cardiac hypertrophy is triggered in response to mechanical stress and various neurohumoral factors, such as G-protein coupling receptor (GPCR) and gp130 cytokine receptor agonists. Recent studies have suggested cardiac Z-disc plays a pivotal role to regulate these cellular responses. Here, we demonstrate stimulations with GPCR agonists (norepinephrine, angiotensin II, and endothelin 1) and phorbol ester activated and translocated protein kinase D1 (PKD1) to the Z-discs in neonatal rat cardiomyocytes in a protein kinase C (PKC)-dependent manner, whereas gp130 agonist did not. Especially, upon the alpha-adrenergic receptor agonist stimulations, following the PKCepsilon-PKD1 complex formation, PKCepsilon-dependent activation of PKD1 was essential to induce hypertrophic responses. Constitutively active mutant of either PKD1 or PKCepsilon also induced cardiac hypertrophy ex vivo. Taken together, the PKCepsilon-PKD1 complex at Z-discs could play a pivotal role in the cardiac hypertrophy induced by GPCR agonists, at least alpha-adrenergic receptor agonist.     

A new ferromagnetically coupled μ-alkoxo-μ-acetato copper(II) trinuclear complex: [Cu3(H2tea)(Htea)(CH3COO)2](ClO4) (H3tea = triethanolamine)

A μ-alkoxo-μ-acetato trinuclear copper(II) complex, [Cu₃(H₂tea)(Htea)(CH₃COO)₂](ClO₄) 1, has been synthesized by reacting copper(II) perchlorate, triethanolamine and sodium acetate. The unit cell contains two centrosymmetric, crystallographically independent trinuclear Cu(II) complexes and two ions. The crystallographically independent trinuclear Cu(II) complexes differ mainly in some of their geometry parameters. The coordination environment of the central copper atom is square-planar, in one trinuclear entity, and elongated octahedral in the other one (in this last case, the coordination number of the central copper atom increases through the semicoordination of an oxygen atom arising from the aminoalcohol). The acetato groups exhibit the classical syn-syn bridging mode. The distances between the copper(II) ions in the two entities are, respectively: 3.043(3) and 3.034(4) Å. The cryomagnetic investigation of 1 reveals a ferromagnetic interaction between the copper(II) ions (J = +84 cm⁻¹), which is due to a countercomplementary effect of the acetato and alkoxo bridges.     

Syntheses of di-hydrocarbyl derivatives of carbonyl phosphine complexes of iron

Complexes cis,trans-Fe(CO)₂(PMe₃)₂RR′ (R = CH₃, R′ = Ph (2); R = CH₃, R′ = CHCH₂ (3); R = CHCH₂, R′ = Ph (4); R = R′ = CHCH₂ (5); R = R′ = CH₃ (6)) were prepared by reaction of cis,trans-Fe(CO)₂(PMe₃)₂RCl (1) with organolithium reagents LiR′. All complexes were characterized in solution by IR and ¹H, ³¹P and, in a few cases, ¹³C NMR mono- and bi-dimensional spectroscopies. Complexes 5 and 6 were structurally characterized by X-ray diffractometric methods. In solution complexes 2, 3 and 4 undergo slowly coupling of the σ-hydrocarbyl substituents leading to Fe(CO)₃(PMe₃)₂ and other decomposition products. Complex 6 was very stable in solution in the absence of nucleophiles and in the solid state. Complex 5 transformed through intramolecular coupling of the vinyl groups into Fe(CO)(PMe₃)₂(η⁴-butadiene) (7), which was characterized in solution by IR and NMR spectroscopies.     

Synthesis of iron thienyl complexes

Dimetallation of thiophene (TH₂), bithiophene (BTH₂) and 3,6-dimethyl[3,2-b]thienothiophene (TTH₂) using a slight excess of butyl lithium, followed by the addition of [FeCp(CO)₂I], resulted in the formation of [2,5-{FeCp(CO)₂}₂T], 1 and [2-{FeCp(CO)₂}T]. The analogous reaction with bithiophene as precursor afforded similar products [2,2′-{FeCp(CO)₂}₂BT] 2 and [2-{FeCp(CO)₂}BTH] 3. In addition to the expected mono- ([2-{FeCp(CO)₂}-TTH] 4) and binuclear ([2,2′-{FeCp(CO)₂}₂-TT] 5) products, dimetallation of 3,6-dimethyl[3,2-b]thienothiophene and the subsequent reaction with [FeCp(CO)₂I] yielded carbonyl inserted mono-([2-{FeCp(CO)₂}C(O)-{TT}₂H] 6) and binuclear ([2-{FeCp(CO)₂}C(O)-{TT}₂-2′-{FeCp(CO)₂}] 7) carbon-carbon coupled products. The precursor [2,7-{SnMe₃}₂-TT] (8) was prepared and reacted with [FeCp(CO)(PEt₃)I] in the presence of a palladium catalyst to afford [2-{FeCp(CO)(PEt₃)}C(O)-{TT}₂-2′-{SnMe₃}] 10.     

Altered Ca2+ sparks and gating properties of ryanodine receptors in aging cardiomyocytes

To investigate the cellular mechanisms for altered cardiac function in senescence, we measured Ca(2+) transients and Ca(2+) sparks in ventricular cardiomyocytes from 6- to 24-month-old Fisher 344 (F344) rat hearts. The single channel properties of ryanodine receptors from adult and senescent hearts were also studied. In senescent myocytes, we observed a decreased peak [Ca(2+)](i) amplitude and an increased time constant for decay (tau), both of which correlated with a reduced Ca(2+) content of the sarcoplasmic reticulum (SR). Our studies also revealed that senescent cardiomyocytes had an increased frequency of Ca(2+) sparks and a slight but statistically significant decrease in average amplitude, full-width-at-half-maximum (FWHM) and full-duration-at-half-maximum (FDHM). Single channel recordings of ryanodine receptors (RyR2) demonstrated that in aging hearts, the open probability (P(o)) of RyR2 was increased but the mean open time was shorter, providing a molecular correlate for the increased frequency of Ca(2+) sparks and decreased size of sparks, respectively. Thus, modifications of normal RyR2 gating properties may play a role in the altered Ca(2+) homeostasis observed in senescent myocytes.     

Functional Coupling between Nucleoside Diphosphate Kinase of the Outer Mitochondrial Compartment and Oxidative Phosphorylation

In rat liver mitochondria all nucleoside diphosphate kinase of the outer compartment is associated with the outer surface of the outer membrane (Lipskaya, T. Yu., and Plakida, K. N. (2003) Biochemistry (Moscow), 68, 1136-1144). In the present study, three systems operating as ADP donors for oxidative phosphorylation have been investigated. The outer membrane bound nucleoside diphosphate kinase was the first system tested. Two others employed yeast hexokinase and yeast nucleoside diphosphate kinase. The two enzymes exhibited the same activity but could not bind to mitochondrial membranes. In all three systems, muscle creatine phosphokinase was the external agent competing with the oxidative phosphorylation system for ADP. Determination of mitochondrial respiration rate in the presence of increasing quantities of creatine phosphokinase revealed that at large excess of creatine phosphokinase activity over other kinase activities (of the three systems tested) and oxidative phosphorylation the creatine phosphokinase reaction reached a quasi-equilibrium state. Under these conditions equilibrium concentrations of all creatine phosphokinase substrates were determined and K(eq)app of this reaction was calculated for the system with yeast hexokinase. In samples containing active mitochondrial nucleoside diphosphate kinase the concentrations of ATP, creatine, and phosphocreatine were determined and the quasi-equilibrium concentration of ADP was calculated using the K(eq)app value. At balance of quasi-equilibrium concentrations of ADP and ATP/ADP ratio the mitochondrial respiration rate in the system containing nucleoside diphosphate kinase was 21% of the respiration rate assayed in the absence of creatine phosphokinase; in the system containing yeast hexokinase this parameter was only 7% of the respiration rate assayed in the absence of creatine phosphokinase. Substitution of mitochondrial nucleoside diphosphate kinase with yeast nucleoside diphosphate kinase abolished this difference. It is concluded that oxidative phosphorylation is accompanied by appearance of functional coupling between mitochondrial nucleoside diphosphate kinase and the oxidative phosphorylation system. Possible mechanisms of this coupling are discussed.     

Role of cooperative H(+)/e(-) linkage (redox bohr effect) at heme a/Cu(A) and heme a(3)/Cu(B) in the proton pump of cytochrome c oxidase

It is a pleasure to contribute to the special issue published in honor of Vladimir Skulachev, a distinguished scientist who greatly contributes to maintain a high standard of biochemical research in Russia. A more particular reason can be found in his work (Artzabanov, V. Y., Konstantinov, A. A., and Skulachev, V. P. (1978) FEBS Lett., 87, 180–185), where observations anticipating some ideas presented in my article were reported. Cytochrome c oxidase exhibits protonmotive, redox linked allosteric cooperativity. Experimental observations on soluble bovine cytochrome c oxidase are presented showing that oxido-reduction of heme a/Cu_A and heme a ₃/Cu_B is linked to deprotonation/protonation of two clusters of protolytic groups, A₁ and A₂, respectively. This cooperative linkage (redox Bohr effect) results in the translocation of 1 H⁺/oxidase molecule upon oxido-reduction of heme a/Cu_A and heme a ₃/Cu_B, respectively. Results on liposome-reconstituted oxidase show that upon oxidation of heme a/Cu_A and heme a ₃/Cu_B protons from A₁ and A₂ are released in the outer aqueous phase. A₁ but not A₂ appears to take up protons from the inner aqueous space upon reduction of the respective redox center. A cooperative model is presented in which the A₁ and A₂ clusters, operating in close sequence, constitute together the gate of the proton pump in cytochrome c oxidase.Translated from Biokhimiya, Vol. 70, No. 2, 2005, pp. 220–230.Original Russian Text Copyright © 2005 by Papa.This revised version was published online in April 2005 with corrections to the post codes.