Critical Function of γH2A in S-Phase

Phosphorylation of histone H2AX by ATM and ATR establishes a chromatin recruitment platform for DNA damage response proteins. Phospho-H2AX (γH2AX) has been most intensively studied in the context of DNA double-strand breaks caused by exogenous clastogens, but recent studies suggest that DNA replication stress also triggers formation of γH2A (ortholog of γH2AX) in Schizosaccharomyces pombe. Here, a focused genetic screen in fission yeast reveals that γH2A is critical when there are defects in Replication Factor C (RFC), which loads proliferating cell nuclear antigen (PCNA) clamp onto duplex DNA. Surprisingly Chk1, Cds1/Chk2 and the Rad9-Hus1-Rad1 checkpoint clamp, which are crucial for surviving many genotoxins, are fully dispensable in RFC-defective cells. Immunoblot analysis confirms that Rad9-Hus1-Rad1 is not required for formation of γH2A by Rad3/ATR in S-phase. Defects in DNA polymerase epsilon, which binds PCNA in the replisome, also create an acute need for γH2A. These requirements for γH2A were traced to its role in docking with Brc1, which is a 6-BRCT-domain protein that is structurally related to budding yeast Rtt107 and mammalian PTIP. Brc1, which localizes at stalled replication forks by binding γH2A, prevents aberrant formation of Replication Protein A (RPA) foci in RFC-impaired cells, suggesting that Brc1-coated chromatin stabilizes replisomes when PCNA or DNA polymerase availability limits DNA synthesis.     

O2 sensitivity and H2 production activity of hydrogenases—A review

Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron–sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H₂ production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O₂ sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O₂ but proficient in H₂ production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O₂ tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O₂ sensitivity of the enzyme while it catalyzes H₂ production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H₂ production and other industrial processes, as well as our own perspective on future applications.     

基于组蛋白甲基化信息的H2A.Z和H2A核小体识别

组蛋白H2A的变体H2A.Z在基因的表达过程中发挥着重要的作用。根据H2A.Z和H2A核小体中组蛋白甲基化修饰方式的不同,作者应用多样性增量二次判别方法(increment of diversity with quadratic discriminant,IDQD)成功地对H2A.Z和H2A核小体进行了识别,说明了以组蛋白甲基化信息作为特征参数的IDQD模型对H2A.Z和H2A核小体识别的有效性。通过计算DNA序列的柔性,发现H2A.Z核小体对应的DNA序列的平均柔性比常规H2A核小体对应的DNA序列的平均柔性弱。     

γH2A is a component of yeast heterochromatin required for telomere elongation

Histones of heterochromatin are deacetylated in yeast and methylated in more complex eukaryotes to regulate heterochromatin structure and gene silencing. Here, we report that histone H2A phosphorylated at serine 129 (γH2A) in Saccharomyces cerevisiae is a conceptually new type of heterochromatin modification that functions downstream of silent chromatin assembly. We show that γH2A is enriched throughout yeast telomeric and silent mating locus (HM) heterochromatin where γH2A results from the action of kinases Tel1 and Mec1. Interestingly, mutation of γH2A has no apparent effect on the binding of Sir (silent information regulator) complex or on gene silencing. In contrast, deletion of SIR3 abolishes the formation of γH2A at heterochromatin. To address the function of γH2A, we used a Δrif1 mutant strain in which telomeres are excessively elongated to show that γH2A is required for the optimal recruitment of Cdc13, a regulator of telomere elongation, and for telomere elongation itself. Thus, a histone modification that parallels Sir3 protein binding is shown here to be dispensable for the formation of a silent structure but is important for a crucial heterochromatin-specific downstream function in telomere homeostasis.Key words: γH2A, H2AS129 phosphorylation, heterochromatin, telomere, Sir complex, Tel1/Mec1, Rif1/2, Cdc13, yKu proteins     

A density functional theory study of phenyl formation initiated by ethynyl radical (C2H•) and ethyne (C2H2)

An ab initio computational density functional theory (DFT) was used to study the formation of the first cyclic molecule (phenyl) initiated by the ethynyl radical (C₂H•). The study covers a competition reaction between the addition reactions of C₂H• with ethyne (C₂H₂) and some molecular re-arrangement schemes. The minimum energy paths of the preferred cyclic formation route were characterized. A thorough thermochemical analysis was performed by evaluating the differences in the energy of activation (ΔE), enthalpy (ΔH), and Gibb's free energy (ΔG) of the optimized stable and transition state (TS) molecules. The reaction temperatures were set to normal (T = 298 K) and combustion (T = 1,200 K) conditions.

Quantitative and time-course analysis of microbial degradation of 1H,1H,2H,2H,8H,8H–perfluorododecanol in activated sludge

A methylene group in the fluorinated carbon backbone of 1H,1H,2H,2H,8H,8H–perfluorododecanol (degradable telomer fluoroalcohol, DTFA) renders the molecule cleavable by microbial degradation into two fluorinated carboxylic acids. Several biodegradation products of DTFA are known, but their rates of conversion and fates in the environment have not been determined. We used liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) to quantitatively investigate DTFA biodegradation by the microbial community in activated sludge in polyethylene terephthalate (PET) flasks, which we also determined here showed least adsorption of DTFA. A reduction in DTFA concentration in the medium was accompanied by rapid increases in the concentrations of 2H,2H,8H,8H–perfluorododecanoic acid (2H,2H,8H,8H–PFDoA), 2H,8H,8H-2-perfluorododecenoic acid (2H,8H,8H-2-PFUDoA), and 2H,2H,8H-7-perfluorododecenoic acid and 2H,2H,8H-8-perfluorododecenoic acid (2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA), which were in turn followed by an increase in 6H,6H–perfluorodecanoic acid (6H,6H–PFDeA) concentration, and decreases in 2H,2H,8H,8H–PFDoA, 2H,8H,8H-2-PFUDoA, and 2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA concentrations. Accumulation of perfluorobutanoic acid (PFBA), a presumed end product of DTFA degradation, was also detected. Our quantitative and time-course study of the concentrations of these compounds reveals main routes of DTFA biodegradation, and the presence of new biodegradation pathways.

     

Specific features of the kinetics of H2-O2-O2(a 1Δ g ) mixtures: I. formation and quenching of electronically and vibrationally excited (A′) molecules in H2-O2-O2(A 1Δ g ) mixtures at a temperature of 300 K

Available data on the kinetic processes in H₂-O₂-O₂(a ¹Δ _g ) mixtures are analyzed theoretically, and the ranges in which the rate constants of these processes can vary are determined. The processes of energy transformation in an O₂(a ¹Δ _g )-H₂-H-HO₂ system in the approximations of the fast and slow (in comparison with the vibrational relaxation time of the HO₂ radical) quenching of the electronically excited state are considered. The experiments on the quenching of singlet delta oxygen (SDO) molecules O₂(a ¹Δ _g ) excited in a microwave discharge at a temperature of 300 K and pressure of 6 Torr in a lean hydrogen-oxygen mixture are simulated (by a lean fuel mixture is meant a mixture in which the ratio of the fuel to the oxidizer mass fraction is less than the stoichiometric ratio, which is 2: 1 for a hydrogen-oxygen mixture). It is shown that, over the experimental observation times, the SDO quenching frequency depends on the concentration of molecular hydrogen, the residual odd oxygen fraction in the gas flow, and the ratio between the rate constants of kinetic processes involving HO₂ and HO₂* radicals. Simulations of the microwave discharge and the transport of excited oxygen along the drift tube make it possible to determine the residual odd oxygen concentration in the gas flow. Recommendations on the choice of the rate constants for the O₂(a ¹Δ _g ) + HO₂)A″, v₃″ = 0) ? O₂ + HO₂*(A′, v₃′ = 1), HO₂*(A′v₃′ ≤ 1) + O₂(a ¹Δ _g ) → HO₂*(A′,v₃′ ≥ 6) + O₂, and HO₂*(A′,v₃′ ≤ 1) + O₂(a ¹Δ _g ) → H + O₂ + O₂ processes are given. It is shown that, in the case of slow quenching in a H₂-O₂-O₂(a ¹Δ _g ) mixture at a low temperature, the intensity of hydrogen oxidation is enhanced due to the reaction + HO₂*(A′,v₃′ ≤ 1) + O₂(¹Δ) → H + O₂ + O₂.     

On the existence of a possible A2A-D2-β-Arrestin2 complex: A2A agonist modulation of D2 agonist-induced β-arrestin2 recruitment

Given that coactivation of adenosine A(2A) (A(2A)R) and dopamine D(2) (D(2)R) receptors results in the coaggregation, cointernalization, and codesensitization of the A(2A)R and D(2)R and the role of scaffolding protein β-arrestin2 in the desensitization, internalization, and signaling of G-protein-coupled receptors, in this study we explored the ability of the A(2A)R agonist CGS21680 in A(2A)R-D(2)R-coexpressing cells to modulate the D(2)R agonist-induced recruitment of β-arrestin2 to the D(2)R by means of proximity-based bioluminescence resonance energy transfer (BRET(2)) and co-trafficking analysis. We found evidence that CGS21680 can increase the maximal BRET(2) signal between β-arrestin2(RLuc) and D(2L)R(GFP2) upon D(2)R activation, by increasing the potency of the D(2)R agonist to exert this action. In addition, this change was associated with an increased formation of cytoplasmic clusters containing β-arrestin2(GFP2) and D(2L)R(YFP) as seen from the co-trafficking analysis. Furthermore, the A(2A)R agonist advanced the time for the increase in Akt phosphorylation obtained with the D(2)R agonist. Finally, using a novel bioinformatics approach to predict the protein-protein interface, we have also found that amino acid pro-triplets TNY, LLS, RAF, and VSR may be crucial for the -induced β-arrestin2 recruitment by A(2A)R-D(2)R heteromers. Taken together, the results indicate that the antagonistic A(2A)R-D(2)R allosteric receptor-receptor interaction in A(2A)R-D(2)R heteromers favors β-arrestin2 recruitment to the D(2L)R protomer with subsequent cointernalization associated with a reduced time onset of Akt phosphorylation followed by a rapid dephosphorylation. Thus, β-arrestin2 action becomes more rapid and short-lasting and, in this way, mimics G-protein-mediated signaling.     

Early Evolution of Histone Genes: Prevalence of an ‘Orphon’ H1 Lineage in Protostomes and Birth-and-Death Process in the H2A Family

The study of histone evolution has experienced a rebirth, for two main reasons: the identification of new essential histone variants responsible for regulating chromatin dynamics and the subsequent contradictions posed by this variability as it pertains to their long-term evolution process. Although different evolutionary models (e.g., birth-and-death evolution, concerted evolution) may account for the observed divergence of histone genes, conclusive evidence is lacking (e.g., histone H1) or totally nonexistent (e.g., histone H2A). While most of the published work has focused on deuterostomes, very little is known about the diversification and functional differentiation mechanisms followed by histone protein subtypes in protostomes, for which histone variants have only been recently described. In this study, we identify linker and core histone genes in three clam species. Our results demonstrate the prevalence of an 'orphon' H1 lineage in molluscs, a group in which the protostome H1 and sperm nuclear basic proteins are on the verge of diversification. They share an early monophyletic origin with vertebrate-specific variants prior to the differentiation between protostomes and deuterostomes. Given the intringuing evolutionary features of the histone H1 family, we have evaluated the relative importance of gene conversion, point mutation, and selection in maintaining the diversity found among H2A subtypes in eukaryotes. We show evidence for the first time that the long-term evolution of this family is not subject to concerted evolution but, rather, to a gradual evolution following a birth-and-death model under a strong purifying selection at the protein level.