Systems biology of antibiotic production by microorganisms

The synthesis of secondary metabolites by microorganisms, specifically antibiotics, is of great scientific and economic importance. The onset (control and regulation) of secondary metabolite formation has and still is intriguing scientists both in industry and academia. Despite many studies, there is little known about the molecular mechanisms underlying the regulation of secondary metabolism. With the recent developments in genomics and further development of advanced post-genomic techniques, it will be possible to apply a more holistic analysis to the regulation of antibiotic production in microorganisms. Here we review current knowledge about the control and regulation of secondary metabolites, with a focus on antibiotics. We will also review developments in the genomics of antibiotic-producing microorganisms, and discuss the use of systems biology for gaining a better understanding of the networks involved in regulation of antibiotic production.     

Comprehensive analysis of microRNA-mRNA co-expression in circadian rhythm

To investigate the potential role of microRNA (miRNA) in the regulation of circadian rhythm, we performed microarray-based expression profiling study of both miRNA and mRNA in mouse liver for 48 h at 4-hour intervals. Circadian miRNA-mRNA target pair is defined as the pair both elements of which show circadian expression patterns and the sequence-based target relationship of which can be predicted. Circadian initiators, Clock and Bmal1, showed inversely correlated circadian expression patterns against their corresponding miRNAs, miR-181d and miR-191, targeting them. In contrast, circadian suppressors, Per, Cry, CKIe and Rev-erba, exhibited positively correlated circadian expression patterns to their corresponding miRNAs. Genomic location analysis revealed that intronic region showed higher abundance of cyclic than non-cyclic miRNAs targeting circadian genes while other (i.e., 3''-UTR, exon and intergenic) regions showed no difference. It is suggested that miRNAs are involved in the regulation of peripheral circadian rhythm in mouse liver by modulating Clock:Bmal1 complex. Identifying specific miRNAs and their targets that are critically involved in circadian rhythm will provide a better understanding of the regulation of circadian-clock system.     

Akt is involved in the inhibition of cell proliferation by EGF

Axin is a negative regulator of the Wnt/beta-catenin pathway and is involved in the regulation of axis formation and proliferation. Involvement of Axin in the regulation of other signaling pathways is poorly understood. In this study, we investigated the involvement of Akt in growth regulation by Axin in L929 fibroblasts stimulated by EGF. Akt activity was increased by EGF treatment and Ras activation, respectively. Both the EGF- and Ras-induced Akt activations were abolished by Axin induction, as revealed by both Western blot and immunocytochemical analyses. The proliferation and Akt activation induced by EGF were decreased by Axin induction, and the effects of EGF were abolished by treatment of an Akt-specific inhibitor. Therefore, Axin inhibits EGF-induced proliferation of L929 fibroblasts by blocking Akt activation.     

Proteomic and redox‐proteomic study on the role of glutathione reductase in human lung cancer cells

Glutathione reductase (GR), a cytosolic protein, plays a vital role in maintaining a correct redox status in cells. However, comprehensive investigations of GR‐modulated cellular responses, including protein level alteration and redox regulation, have yet to be performed. In this study, we cultured a human lung adenocarcinoma line transfected with empty pLKO.1 vector as a control, CL1‐0shControl, and its GR‐knockdown derivative, CL1‐0shΔGR, to evaluate differential protein level alteration and redox regulation of these two cell lines. We identified 34 spots that exhibited marked changes in intensities, and 13 proteins showing significant changes in thiol reactivity, in response to GR depletion. Several proteins involved in redox regulation, calcium signaling, cytoskeleton regulation, and protein folding showed significant changes in expression, whereas proteins involved in redox regulation, protein folding, and glycolysis displayed changes in thiol reactivity. Interestingly, GR knockdown induces peroxiredoxin‐1 overexpression in the air‐exposed tissue and high oxygen consuming tissue such as cornea and liver, but not in the low oxygen consuming tissues such as breast and uterine. In summary, we used a comprehensive lung adenocarcinoma based proteomic approach for identifying GR‐modulated protein expression alteration and redox modification. Based on our research, this is the first comprehensive proteomic and redox‐proteomic analysis used to investigate the role of GR in a mammalian cell model.     

Using Peptide Arrays to Profile Phosphatase Activity in Cell Lysates

Phosphorylation is an important post-translational modification on proteins involved in many cellular processes; however, understanding of the regulation and mechanisms of global phosphorylation remains limited. Herein, we utilize self-assembled monolayers on gold for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) with three phosphorylated peptide arrays to profile global phosphatase activity in cell lysates derived from five mammalian cell lines. Our results reveal significant differences in the activities of protein phosphatases on phospho- serine, threonine, and tyrosine substrates and suggest that phosphatases play a much larger role in the regulation of global phosphorylation on proteins than previously understood.     

Potentiometric measurement of cell volume changes and intracellular ion concentrations under voltage-clamp conditions in invertebrate nerve cells

Because changes in cell volume might disturb the normal function of animal cells, most cells are endowed with volume-regulating mechanisms. Experimentally induced changes in cell volume are often paralleled by changes in the membrane potential, which might affect a variety of transport processes across the cell membrane and, in turn, volume regulation [1, 2]. We have shown previously that multi-barrelled ion-selective microelectrodes are useful tools for measurement of cell volume and the intracellular concentrations of ions that might be relevant to volume regulation [1]. To investigate whether voltage-dependent transport processes are involved in cell-volume regulation we combined the potentiometric technique of ion-selective microelectrodes with the voltage-clamp technique. This combination enables simultaneous recording of cell volume, relevant intracellular ion concentrations, and ion currents across the cell membrane at a fixed membrane potential.     

The roles of cysteines in the heme domain of human soluble guanylate cyclase

Soluble guanylate cyclase(sGC) is a critical heme-containing enzyme involved in NO signaling.The dimerization of sGC subunits is necessary for its bioactivity and its mechanism is a striking and an indistinct issue.The roles of heme domain cysteines of the sGC on the dimerization and heme binding were investigated herein.The site-directed mutations of three conserved cysteines(C78A,C122A and C174S) were studied systematically and the three mutants were characterized by gel filtration analysis,UV-vis spectroscopy and heme transfer examination.Cys78 was involved in heme binding but not referred to the dimerization,while Cys174 was demonstrated to be involved in the homodimerization.These results provide new insights into the cysteine-related dimerization regulation of sGC.     

Endometriosis,the Silent Disease: Molecular Targets,Active Principles,and Drug Delivery Systems

In this perspective, we provide a broad overview of pathophysiological processes involved in endometriosis, including the role of inflammation, fibrosis, angiogenesis, hormonal regulation, and genetic factors. For each of the functional changes involved with the etiology of the disease, we showcase a selection of active principles in various stages of preclinical and clinical development. Finally, we highlight the role of drug delivery for endometriosis, particularly oral vs. vaginal administration. In doing so, we wish to draw the community's attention to this debilitating disease and highlight the need for interdisciplinary approaches to endometriosis treatment development.     

RNAi: running interference for the cell

RNA interference or RNAi is a recently characterized mechanism of eukaryotic gene regulation in which a short sequence of double-stranded RNA (dsRNA) specifically down-regulates expression of the associated gene. Preliminary characterization of this phenomenon has revealed a set of inter-related cellular pathways which appear to represent both a response to foreign RNA and a mechanism of endogenous gene regulation. Introduction of dsRNA into cells by a variety of means, including transfection of synthetic RNA duplexes, triggers the RNAi response resulting in specific suppression of target gene expression. Recent efforts on a genome wide scale have involved application of RNAi as an important new tool in cell biology to elucidate gene function in living cells.     

Interactions of tetrathionate with sulphite and sulphide

Tetrathionate is converted into thiosulphate in the presence of sulphite, sulphide and their mixtures. These reactions can be applied to analysis for any of these sulphur compounds by determination of the amount of thiosulphate formed. The chemical interactions may also be involved in the regulation of the oxidative sulphur pathways in micro-organisms and be employed to prepare colloidal sulphur particles.     

Association of DNA-dependent protein kinase with hypoxia inducible factor-1 and its implication in resistance to anticancer drugs in hypoxic tumor cells

Tumor hypoxia contributes to the progression of a malignant phenotype and resistance to ionizing radiation and anticancer drug therapy. Many of these effects in hypoxic tumor cells are mediated by expression of specific set of genes whose relation to therapy resistance is poorly understood. In this study, we revealed that DNA-dependent protein kinase (DNA-PK), which plays a crucial role in DNA double strand break repair, would be involved in regulation of hypoxia inducible factor-1 (HIF-1). HIF-1beta-deficient cells showed constitutively reduced expression and DNA-binding activity of Ku, the regulatory subunit of DNA-PK. Under hypoxic condition, the expression and activity of DNA- PK were markedly induced with a concurrent increase in HIF-1alpha expression. Our result also demonstrated that DNA-PK could directly interact with HIF-1, and especially DNA-PKcs, the catalytic subunit of DNA-PK, could be involved in phosphorylation of HIF-1alpha, suggesting the possibility that the enhanced expression of DNA- PK under hypoxic condition might attribute to modulate HIF-1alpha stabilization. Thus, the correlated regulation of DNA-PK with HIF-1 could contribute to therapy resistance in hypoxic tumor cells, and it provides new evidence for developing therapeutic strategies enhancing the efficacy of cancer therapy in hypoxic tumor cells.     

磷酸化蛋白质组学中的分离富集方法研究进展

蛋白质的磷酸化是一种可逆性的翻译后修饰,在细胞的增值、分化、信号转导以及转录与翻译调控、蛋白质复合体的形成、蛋白质降解等方面发挥着极为重要的作用.因此磷酸化蛋白的鉴定成为翻译后修饰研究的重要内容.但由于磷酸化蛋白的丰度较低, 难以用质谱直接检测.为了解决这个问题,改善质谱对磷酸肽的信号响应, 需要对磷酸化蛋白质或磷酸肽进行富集.本文系统地介绍了磷酸化蛋白组学研究中应用较为广泛和最新建立的各种分离富集方法的原理、特点、应用研究进展,包括抗体富集法、激酶特异富集法、亲和富集法、化学修饰法、多种色谱分离富集方法以及MALDI靶盘富集法.     

组氨酸激酶HK853酸碱调控机制的NMR研究

双组分信号转导系统是细菌应对外界刺激和调控自身生理活动的重要系统。组氨酸激酶是双组分信号转导系统的重要组成部分,大多数组氨酸激酶具有多功能性,不仅能自身磷酸化并能把磷酸基团传递给应激调节蛋白(Response regulator,RR)使之磷酸化,还能催化RR的去磷酸化。研究发现组氨酸激酶HK853的功能受pH值调控,该文利用选择性同位素标记方法,通过NMR技术研究了参与HK853与RR468相互作用的关键氨基酸位点。发现DHp结构域His260侧链的pKa值与HK853的磷酸酶活性有很好的对应关系,HK853与底物形成复合物后其pKa值降低,使His260侧链更易于去质子化,有助于HK853磷酸酶活性的提高。阐明了HK853行使磷酸酶功能时的酸碱调控机制。     

硒蛋白S的生物学功能

硒蛋白S是一种新发现的内质网和细胞膜驻留硒蛋白。以往的研究结果揭示硒蛋白S可以保护细胞拮抗氧化损伤及内质网应激诱导的细胞凋亡;参与脂蛋白代谢、精子发育过程、炎症反应及将错误折叠蛋白从内质网腔逆向转移到细胞质中然后降解的过程(即内质网相关蛋白降解)。硒蛋白S基因多态性与糖尿病、冠状动脉心脏病或先兆子痫等疾病密切相关。本文结合本课题组的工作对硒蛋白S的最新研究进展,尤其是硒蛋白S功能的研究成果作了较为详细的介绍,并对未来的研究方向作了展望。     

Selective Monitoring of the Enzymatic Activity of the Tumor Suppressor Fhit

Cancer is a leading cause of death worldwide. Functional inactivation of tumor suppressor proteins, mainly by mutations in the corresponding genes, is a key event in cancer development. The fragile histidine triade protein (Fhit) is a tumor suppressor that is frequently affected in different cancer types. Fhit possesses diadenosine triphosphate hydrolase activity, but although reduction of its enzymatic activity appears to be important for exerting its tumor suppressor function, the regulation of Fhit activity is poorly understood. Here, we introduce a novel fluorogenic probe that is suited to selectively analyze the enzymatic activity of Fhit in extracts derived from human cells. This novel method will allow in‐depth insight into the mechanisms involved in Fhit regulation in biologically relevant setups and, thus, into its role in the development of cancer.