Modulation of coupling in the Escherichia coli ATP synthase by ADP and Pi: Role of the ε subunit C-terminal domain

The ε-subunit of ATP-synthase is an endogenous inhibitor of the hydrolysis activity of the complex and its α-helical C-terminal domain (εCTD) undergoes drastic changes among at least two different conformations. Even though this domain is not essential for ATP synthesis activity, there is evidence for its involvement in the coupling mechanism of the pump. Recently, it was proposed that coupling of the ATP synthase can vary as a function of ADP and P_i concentration. In the present work, we have explored the possible role of the εCTD in this ADP- and P_i-dependent coupling, by examining an εCTD-lacking mutant of Escherichia coli. We show that the loss of P_i-dependent coupling can be observed also in the εCTD-less mutant, but the effects of P_i on both proton pumping and ATP hydrolysis were much weaker in the mutant than in the wild-type. We also show that the εCTD strongly influences the binding of ADP to a very tight binding site (half-maximal effect ≈ 1 nM); binding at this site induces higher coupling in EF_OF₁ and increases responses to P_i. It is proposed that one physiological role of the εCTD is to regulate the kinetics and affinity of ADP/P_i binding, promoting ADP/P_i-dependent coupling.     

Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies

Cohesins are conserved and essential Structural Maintenance of Chromosomes (SMC) protein-containing complexes that physically interact with chromatin and modulate higher-order chromatin organization. Cohesins mediate sister chromatid cohesion and cellular long-distance chromatin interactions affecting genome maintenance and gene expression. Discoveries of mutations in cohesin's subunits and its regulator proteins in human developmental disorders, so-called “cohesinopathies,” reveal crucial roles for cohesins in development and cellular growth and differentiation. In this review, we discuss the latest findings concerning cohesin's functions in higher-order chromatin architecture organization and gene regulation and new insight gained from studies of cohesinopathies. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.     

Magnification of the therapeutic uses of pomegranate fruits and peel in rats injected with carbon tetrachloride (Ccl4)

The liver is more prone to infections that cause fibrosis, such as steatosis, non-alcoholic steatohepatitis, hepatotoxicity, cirrhosis, and hepatocellular carcinoma. Also, Viral hepatitis is a common condition worldwide it worsens into chronic inflammation of the liver. One of the healthiest fruits is the pomegranate for the body and health, as it contains a high nutritional value of minerals, vitamins, antioxidants, so we worked on this investigation to magnify the therapeutic applications of pomegranate fruits (POF) and peel (POP) in carbon tetrachloride-injected rats (Ccl4). The experiment was carried out in a caged animal. All rats were fed a basal diet for one week before the study, and they were divided into seven groups, each with six rats. As a control negative group (C–ve), the first group sample was fed only the basal diet for 28 days. The remaining rats (n = 36) were injected with carbon tetrachloride (Ccl4). Five groups were fed varying concentrations of (5 %, 10 %, 15 % POF, 5 %, and 10 % pomegranate peel (POP)), whereas one group was diagnosed with the illness and disease, and didn't even feed the experimental diet. The results revealed significant increases in T.BIL, D.BIL, and BIL in the serum of rats injected by CC14 to induce hepatopathy compared to the healthy group (normal rats). Also, the best treatment considering the serum D.BIL was recorded for the 5 % POF.     

9-Hydroxydodecanoic acid,an acid from Blepharis sindica seed oil

A hitherto unknown hydroxy acid has been isolated from Blepharis sindica seed oil has been characterized as 9-hydroxydodecanoic acid by IR, NMR and mass spectral studies. The structure of this acid was further supported by its chemical transformations.     

CRISPR-Cas9介导的基因组编辑技术的研究进展

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins)系统为细菌与古生菌中抵御外源病毒或质粒DNA入侵的获得性免疫系统。该系统在crRNA的指导下,使核酸酶Cas识别并降解外源DNA。其中,Ⅱ型CRISPR-Cas系统最为简单,仅包括一个核酸酶Cas9与tracrRNA：crRNA二聚体便可完成其生物功能。基于CRISPR-Cas9的基因组编辑技术的核心为将tracrRNA:crRNA设计为引导RNA,在引导RNA的指导下Cas9定位于特定DNA序列上,进行DNA双链切割,实现基因组的定向编辑。CRISPR-Cas9系统以设计操纵简便、编辑高效与通用性广等优势成为新一代基因组编辑技术,为基因组定向改造调控与应用等带来突破性革命。从CRISPR-Cas9介导的基因组编辑技术的发展与应用等方面综述其最新研究进展,并着重介绍该技术的关键影响因素,为相关研究者提供参考。     

The cellular trafficking of the secretory proprotein convertase PCSK9 and its dependence on the LDLR

Mutations in the proprotein convertase PCSK9 gene are associated with autosomal dominant familial hyper- or hypocholesterolemia. These phenotypes are caused by a gain or loss of function of proprotein convertase subtilisin kexin 9 (PCSK9) to elicit the degradation of the low-density lipoprotein receptor (LDLR) protein. Herein, we asked whether the subcellular localization of wild-type PCSK9 or mutants of PCSK9 and the LDLR would provide insight into the mechanism of PCSK9-dependent LDLR degradation. We show that the LDLR is the dominant partner in regulating the cellular trafficking of PCSK9. In cells lacking the LDLR, PCSK9 localized in the endoplasmic reticulum (ER). In cells expressing the LDLR, PCSK9 sorted to post-ER compartments (i.e. endosomes in cell lines and Golgi apparatus in primary hepatocytes), where it colocalized with the LDLR. In cell lines, PCSK9 also colocalized with the LDLR at the cell surface, requiring the presence of the C-terminal Cys/His-rich domain of PCSK9. We provide evidence that PCSK9 promotes the degradation of the LDLR by an endocytic mechanism, as small interfering RNA-mediated knockdown of the clathrin heavy chain reduced the functional activity of PCSK9. We also compared the subcellular localization of natural mutants of PCSK9 with that of the wild-type enzyme in human hepatic (HuH7) cells. Whereas the mutants associated with hypercholesterolemia (S127R, F216L and R218S) localized to endosomes/lysosomes, those associated with hypocholesterolemia did not reach this compartment. We conclude that the sorting of PCSK9 to the cell surface and endosomes is required for PCSK9 to fully promote LDLR degradation and that retention in the ER prevents this activity. Mutations that affect this transport can lead to hyper- or hypocholesterolemia.     

Crystal structures of MMP-9 complexes with five inhibitors: contribution of the flexible Arg424 side-chain to selectivity

Human matrix metalloproteinase 9 (MMP-9), also called gelatinase B, is particularly involved in inflammatory processes, bone remodelling and wound healing, but is also implicated in pathological processes such as rheumatoid arthritis, atherosclerosis, tumour growth, and metastasis. We have prepared the inactive E402Q mutant of the truncated catalytic domain of human MMP-9 and co-crystallized it with active site-directed synthetic inhibitors of different binding types. Here, we present the X-ray structures of five MMP-9 complexes with gelatinase-specific, tight binding inhibitors: a phosphinic acid (AM-409), a pyrimidine-2,4,6-trione (RO-206-0222), two carboxylate (An-1 and MJ-24), and a trifluoromethyl hydroxamic acid inhibitor (MS-560). These compounds bind by making a compromise between optimal coordination of the catalytic zinc, favourable hydrogen bond formation in the active-site cleft, and accommodation of their large hydrophobic P1' groups in the slightly flexible S1' cavity, which exhibits distinct rotational conformations of the Pro421 carbonyl group in each complex. In all these structures, the side-chain of Arg424 located at the bottom of the S1' cavity is not defined in the electron density beyond C(gamma), indicating its mobility. However, we suggest that the mobile Arg424 side-chain partially blocks the S1' cavity, which might explain the weaker binding of most inhibitors with a long P1' side-chain for MMP-9 compared with the closely related MMP-2 (gelatinase A), which exhibits a short threonine side-chain at the equivalent position. These novel structural details should facilitate the design of more selective MMP-9 inhibitors.     

The crystal structure of Arabidopsis thaliana RAC7/ROP9: the first RAS superfamily GTPase from the plant kingdom

Arabidopsis thaliana RAC/ROP GTPases constitute a plant specific Rho GTPase family in the RAS superfamily, which has been implicated in numerous pivotal signalling cascades in plants. Research has shown that plants in some cases have evolved different modes of regulating Rho GTPase activity as compared to the equivalent systems in animals and yeast. In order to gain structural insight into plant signaling at the molecular level, we have determined the first crystal structure of a RAC-like GTPase belonging to the RAS superfamily from the plant kingdom. The structure of AtRAC7/ROP9 bound to GDP was solved at a resolution of 1.78 A. We have found that the structure of plant Rho GTPases is based upon a conserved G-domain architecture, but structural differences were found concerning the insert region and switch II region of the protein.     

Migrating swans profit from favourable changes in wind conditions at low altitude

Because energy reserves limit flight range, wind assistance may be of crucial importance for migratory birds. We tracked eight Bewicks swans Cygnus columbianus bewickii, using 95-g satellite transmitters with altimeters and activity sensors, during their spring migration from Denmark to northern Russia in 1996. During the 82 occasions where a swans location was recorded in flight, average flight altitude was 165 m a.s.l. with a maximum of 759 m a.s.l., despite winds often being more favourable at higher altitudes. We also counted Bewicks swans departing from the Gulf of Finland and subsequently passing an observatory in the next major stop-over area 800 km further north in the White Sea, northern Russia, during the springs of 1994, 1995 and 1996. A comparison of these counts with wind data provided evidence for Bewicks swans using favourable changes in wind conditions to embark on migration. Changes in the numbers of birds arriving in the White Sea correlated best with favourable changes in winds in the Gulf of Finland 1 day earlier. Again, migratory volume showed a correlation with winds at low altitudes only, despite wind conditions for the swans being more favourable at high altitudes. We conclude that the relatively large Bewicks swan tends to gear its migration to wind conditions at low altitude only. We argue that Bewicks swans do not climb to high altitudes because of mechanical and physiological limitations with respect to the generation of power for flight and to avoid rapid dehydration.Communicated by F. Bairlein