Structure and function of the RedJ protein, a thioesterase from the prodiginine biosynthetic pathway in Streptomyces coelicolor

Prodiginines are a class of red-pigmented natural products with immunosuppressant, anticancer, and antimalarial activities. Recent studies on prodiginine biosynthesis in Streptomyces coelicolor have elucidated the function of many enzymes within the pathway. However, the function of RedJ, which was predicted to be an editing thioesterase based on sequence similarity, is unknown. We report here the genetic, biochemical, and structural characterization of the redJ gene product. Deletion of redJ in S. coelicolor leads to a 75% decrease in prodiginine production, demonstrating its importance for prodiginine biosynthesis. RedJ exhibits thioesterase activity with selectivity for substrates having long acyl chains and lacking a β-carboxyl substituent. The thioesterase has 1000-fold greater catalytic efficiency with substrates linked to an acyl carrier protein (ACP) than with the corresponding CoA thioester substrates. Also, RedJ strongly discriminates against the streptomycete ACP of fatty acid biosynthesis in preference to RedQ, an ACP of the prodiginine pathway. The 2.12 Å resolution crystal structure of RedJ provides insights into the molecular basis for the observed substrate selectivity. A hydrophobic pocket in the active site chamber is positioned to bind long acyl chains, as suggested by a long-chain ligand from the crystallization solution bound in this pocket. The accessibility of the active site is controlled by the position of a highly flexible entrance flap. These data combined with previous studies of prodiginine biosynthesis in S. coelicolor support a novel role for RedJ in facilitating transfer of a dodecanoyl chain from one acyl carrier protein to another en route to the key biosynthetic intermediate 2-undecylpyrrole.     

Multicopy proC in Streptomyces coelicolor A3(2) elicits a transient production of prodiginines, while proC deletion does not yield a proline auxotroph

The last step of proline biosynthesis is typically catalysed by the enzyme Δ(1)-pyrroline-5-carboxylate reductase, encoded by the proC gene. Complete genome sequencing of Streptomyces coelicolor, a soil-dwelling Gram-positive bacterium that uses proline as a precursor for synthesis of prodiginine, revealed a single copy of this gene. Unexpectedly, disruption of this proC homologue (Sco3337) in S. coelicolor M145 yielded a prototrophic strain, yet the reductase activity of Sco3337 was confirmed by complementation of an Escherichia coli proC mutant. Multicopy proC within different genetic contexts elicited a transient production of prodiginines, which showed differential production kinetics of the two most common forms of this natural product produced by S. coelicolor, i.e. streptorubin B (cyclic) and undecylprodigiosin (linear). The metabolic and evolutionary implications of these observations are discussed.     

Endocytic recycling

After endocytosis, most membrane proteins and lipids return to the cell surface, but some membrane components are delivered to late endosomes or the Golgi. We now understand that the pathways taken by internalized molecules that eventually recycle to the cell surface can be surprisingly complex and can involve a series of sorting events that occur in several organelles. The molecular basis for many of these sorting processes is only partly understood.     

综述: 人体体液中细胞外microRNA的起源、功能及潜在诊疗价值

最近大量的研究表明micro RNAs(miRNAs)是一类重要的调控因子．曾经被认为是非常不稳定的RNA分子——miRNA,却可以稳定存在于血液和其他体液中．更加重要的是,细胞外miRNAs被发现和多种疾病密切相关,它们可以作为诸如肿瘤等各种疾病的非侵入性生物标志物．然而,目前关于细胞外miRNA的来源以及生物学功能还不甚清楚．本文将总结最近细胞外miRNA的研究进展,并将重点介绍细胞外miRNA在疾病诊断及治疗中的作用．     

Centralspindlin and α-catenin regulate Rho signalling at the epithelial zonula adherens

The biological impact of Rho depends critically on the precise subcellular localization of its active, GTP-loaded form. This can potentially be determined by the balance between molecules that promote nucleotide exchange or GTP hydrolysis. However, how these activities may be coordinated is poorly understood. We now report a molecular pathway that achieves exactly this coordination at the epithelial zonula adherens. We identify an extramitotic activity of the centralspindlin complex, better understood as a cytokinetic regulator, which localizes to the interphase zonula adherens by interacting with the cadherin-associated protein, α-catenin. Centralspindlin recruits the RhoGEF, ECT2, to activate Rho and support junctional integrity through myosin IIA. Centralspindlin also inhibits the junctional localization of p190 B RhoGAP, which can inactivate Rho. Thus, a conserved molecular ensemble that governs Rho activation during cytokinesis is used in interphase cells to control the Rho GTPase cycle at the zonula adherens.     

Glycobiology in the cytosol: the bitter side of a sweet world

Progress in glycobiology has undergone explosive growth over the past decade with more of the researchers now realizing the importance of glycan chains in various inter- and intracellular processes. However, there is still an area of glycobiology awaiting exploration. This is especially the case for the field of "glycobiology in the cytosol" which remains rather poorly understood. Yet evidence is accumulating to demonstrate that the glycoconjugates and their recognition molecules (i.e. lectins) are often present in this subcellular compartment.     

Glucocorticoid effects on the production and actions of immune cytokines

The immunosuppressive actions of glucocorticoids form the basis for their use in treatment of autoimmune diseases and prevention of allograft rejection. However, the mechanisms responsible for glucocorticoid-induced immunosuppression are still poorly understood. It is now clear that glucocorticoids do not inhibit all aspects of the immune response and, in some cases, may enhance certain functions of immune effector cells. One example is that of the dramatic increase induced by IFN-gamma in the number of IgG Fc receptors on human mononuclear phagocytes, which is enhanced rather than inhibited by glucocorticoids. An aspect of the immune response which appears to be consistently suppressed by glucocorticoids is the production of immune cytokines. Since these hormones appear to be essential mediators for a vigorous immune response, inhibition of their production may be an effective way for glucocorticoids to block the immune response.     

Molecular mechanisms of membrane polarity in renal epithelial cells

Exciting discoveries in the last decade have cast light onto the fundamental mechanisms that underlie polarized trafficking in epithelial cells. It is now clear that epithelial cell membrane asymmetry is achieved by a combination of intracellular sorting operations, vectorial delivery mechanisms and plasmalemma-specific fusion and retention processes. Several well-defined signals that specify polarized segregation, sorting, or retention processes have, now, been described in a number of proteins. The intracellular machineries that decode and act on these signals are beginning to be described. In addition, the nature of the molecules that associate with intracellular trafficking vesicles to coordinate polarized delivery, tethering, docking, and fusion are also becoming understood. Combined with direct visualization of polarized sorting processes with new technologies in live-cell fluorescent microscopy, new and surprising insights into these once-elusive trafficking processes are emerging. Here we provide a review of these recent advances within an historically relevant context.     

Chromosome and protein folding: In search for unified principles

Structural biology has traditionally focused on the structures of proteins, short nucleic acids, small molecules, and their complexes. However, it is now widely recognized that the 3D organization of chromosomes should also be included in this list, despite significant differences in scale and complexity of organization. Here we highlight some notable similarities between the folding processes that shape proteins and chromosomes. Both biomolecules are folded by two types of processes: the affinity-mediated interactions, and by active (ATP-dependent) processes. Both chromosome and proteins in vivo can have partially unstructured and non-equilibrium ensembles with yet to be understood functional roles. By analyzing these biological systems in parallel, we can uncover universal principles of biomolecular organization that transcend specific biopolymers.     

Chemosensory-induced motor behaviors in fish

Chemical sensory signals play a crucial role in eliciting motor behaviors. We now review the different motor behaviors induced by chemosensory stimuli in fish as well as their neural substrate. A great deal of research has focused on migratory, reproductive, foraging, and escape behaviors but it is only recently that the molecules mediating these chemotactic responses have become well-characterized. Chemotactic responses are mediated by three sensory systems: olfactory, gustatory, and diffuse chemosensory. The olfactory sensory neuron responses to chemicals are now better understood. In addition, the olfactory projections to the central nervous system were recently shown to display an odotopic organization in the forebrain. Moreover, a specific downward projection underlying motor responses to olfactory inputs was recently described.     

Induction of chromosomal aberrations by phenolic compounds: possible role of reactive oxygen species

Phenolic molecules are widely present in the environment and some of them are well known carcinogens. Some phenolic molecules are also genotoxic but the mechanisms involved in this process are not fully understood. We have studied the induction of chromosomal aberrations by phenol, catechol and pyrogallol in V79 cells at different pH values (6.0, 7.4 and 8.0). At the same pH values, the production of hydroxyl radicals was assessed by measuring the degradation of deoxyribose. Apart from phenol, which only induces a non-significant increase in chromosomal aberration in this experimental system, catechol and pyrogallol showed clear clastogenic effect in a pH-dependent way. Experiments carried out at pH 7.4 in the presence of S9 Mix, SOD, catalase and catalase + SOD suggest that the formation of reactive oxygen species is not the main mechanism involved in the genotoxicity of catechol. However, concerning pyrogallol, our results suggest that its genotoxicity is almost exclusively mediated by reactive oxygen species. Taken together, these results suggest that, in spite of the structural similarity between the different molecules studied, the mechanisms of genotoxicity of these molecules could be considerably different. The existence of several mechanisms of genotoxicity, partially shared by this class of compounds, could explain the synergistic effects observed between these compounds in several genotoxicity test systems. Accurate knowledge of their mechanisms of genotoxicity could improve considerably the assessment of their relevance to human health, since these compounds, once absorbed, are subject to a wide range of pH values in vivo.     

Inhibitory effects of catechins on neutrophil-dependent gastric inflammation

The inhibitory effects of tea against carcinogenesis have been attributed to the biological activity of the polyphenol fraction of tea. However, the molecular mechanisms of these effects are not completely understood. Chronic inflammation induced by Helicobacterpylori has been proposed to be a causative pathway in the carcinogenesis of stomach cancer. Therefore, an agent possessing anti-inflammatory properties may be chemopreventative against stomach cancer. In the present study, we have investigated the anti-inflammatory effects of tea catechins. After addition of IL-1beta to MKN45 cells, a gastric cancer cell line, or human umbilical vein endothelial cells (HUVECs), IL-8 production was detected in supernatants. This IL-8 production was inhibited by catechins. Incubation of HUVECs or polymorphonuclear leukocytes (PMNs) with IL-1beta or IL-8, respectively, resulted in an increased surface expression of adhesion molecules. Catechins also inhibited this expression of adhesion molecules on HUVECs and PMNs. Of these major effects, the strongest effect of catechins was to reduce expression of the adhesion molecules CD1lb and CD18 on PMNs. These results suggest that tea may inhibit carcinogenesis partly through the anti-inflammatory effects of tea catechins on PMN-dependent gastric mucosal inflammation.     

More than just synaptic building blocks: scaffolding proteins of the post-synaptic density regulate dendritic patterning

The dendritic arbor is responsible for receiving and consolidating neuronal input. Outgrowth and morphogenesis of the arbor are complex stages of development that are poorly understood. However, recent findings have identified synaptic scaffolding proteins as novel regulators of these important events. Scaffolding proteins are enriched in the post-synaptic density where they bind and bring into close proximity neurotransmitter receptors, signaling molecules, and regulators of the actin cytoskeleton. This property is important for dendritic spine morphogenesis and maintenance in the mature neuron. Scaffolding proteins are now being described as key regulators of neurite outgrowth, dendritic development, and pattern formation in immature neurons. These proteins, which include post-synaptic-95, Shank and Densin-180, as well as many of their interacting partners, appear to regulate both the microtubule and actin cytoskeleton to influence dendrite morphology. Through a large array of protein-protein interaction domains, scaffolding proteins are able to form large macromolecular complexes that include cytoskeletal motor proteins as well as microtubule and actin regulatory molecules. Together, the new findings form a persuasive argument that scaffolding proteins deliver critical regulatory elements to sites of dendritic outgrowth and branching to modulate the formation and maintenance of the dendritic arbor.     

14-3-3ε couples protein kinase A to semaphorin signaling and silences plexin RasGAP-mediated axonal repulsion

The biochemical means through which multiple signaling pathways are integrated in navigating axons is poorly understood. Semaphorins are among the largest families of axon guidance cues and utilize Plexin (Plex) receptors to exert repulsive effects on axon extension. However, Semaphorin repulsion can be silenced by other distinct cues and signaling cascades, raising questions of the logic underlying these events. We now uncover a simple biochemical switch that controls Semaphorin/Plexin repulsive guidance. Plexins are Ras/Rap family GTPase activating proteins (GAPs) and we find that the PlexA GAP domain is phosphorylated by the cAMP-dependent protein kinase (PKA). This PlexA phosphorylation generates a specific binding site for 14-3-3ε,?a phospho-binding protein that we find to be necessary for axon guidance. These PKA-mediated Plexin-14-3-3ε interactions prevent PlexA from interacting with its Ras family GTPase substrate and antagonize Semaphorin repulsion. Our results indicate that these?interactions switch repulsion to adhesion and identify a point of convergence for multiple guidance molecules.     

Microbial superantigens: from structure to function

Superantigens are highly potent immune stimulators with a unique ability to interact simultaneously with MHC class II molecules and T cell receptors, forming a trimolecular complex that induces profound T-cell proliferation and massive cytokine production. Recent structural studies have provided a wealth of information regarding these complex interactions, and it is now emerging that, despite their common 3-D architecture, superantigens are able to crosslink MHC class II molecules and T cell receptors in a variety of ways.     

Structure, function and dynamics in the mur family of bacterial cell wall ligases

For bacteria, the structural integrity of its cell wall is of utmost importance for survival, and to this end, a rigid scaffold called peptidoglycan, comprised of sugar molecules and peptides, is synthesized and located outside the cytoplasmic membrane of the cell. Disruption of this peptidoglycan layer has for many years been a prime target for effective antibiotics, namely the penicillins and cephalosporins. Because this rigid layer is synthesized by a multi-step pathway numerous additional targets also exist that have no counterpart in the animal cell. Central to this pathway are four similar ligase enzymes, which add peptide groups to the sugar molecules, and interrupting these steps would ultimately prove fatal to the bacterial cell. The mechanisms of these ligases are well understood and the structures of all four of these ligases are now known. A detailed comparison of these four enzymes shows that considerable conformational changes are possible and that these changes, along with the recruitment of two different N-terminal binding domains, allows these enzymes to bind a substrate which at one end is identical and at the other has the growing polypeptide tail. Some insights into the structure-function relationships in these enzymes is presented.     

Analysis of G-protein-coupled receptor dimerization following chemokine signaling

An abundance of information has been generated in recent decades on the signaling events triggered through G-protein-coupled receptors (GPCRs). Nonetheless, the structural changes at the cell surface that provoke receptor activation are only now beginning to be understood. It is becoming clear that receptors are not isolated entities that are activated following ligand binding, but that they interact with other molecules already present or recruited to the vicinity, which results in a wide variety of new signaling possibilities. Understanding receptor interactions with relatives and/or friends on the cell surface is thus critical. The most important point is to determine which of these interactions are "casual" and which give rise to functional consequences.     

Microbial interventions are an easier alternative to engineer higher organisms

Advances in synthetic biology have made microbes easier to engineer than ever before. However, synthetic biology in animals and plants has lagged behind. Since it is now known that the phenotype of higher organisms depends largely on their microbiota, we propose that this is an easier route to achieving synthetic biology applications in these organisms.

A transition from reading to writing biology has blurred the lines between basic science and engineering creating the field of synthetic biology. With an ever‐expanding genetic toolbox, we now manipulate natural biological systems to optimize our anthropocentric activities. From the synthesis of complex aromatic compounds, to the production of safer vaccines, a problem identified may find its solution lying in the metabolism of a single cell. Initially, synthetic biology was largely focused on the production of such commodities at the industrial scale, not only to maximize profitability, but also to minimize energy and resource consumption. Consequently, this paradigm shift has come to alter the notion of a factory by many orders of magnitude and to create a new bridge between the built and natural world, as we employ nature’s evolutionary machinery to address our modern endeavours.Growth of the genetic toolbox and maturation of synthetic biology as a field has led to speculation about increasingly ambitious applications of writing biology with implications beyond biosynthesis. To date, most applications have been developed using microbes because they are less complex, more well understood and easier to manipulate. Single‐celled organisms can be optimized for production of complicated organic molecules; however, other exploits of genetic engineering will target more ambitious feats and thus require engineering of more than a large monoculture of microbes. Applications of synthetic biology outside of the bioreactor can address such issues as health and longevity, challenges in industrial agriculture and farming, the degradation of natural habitats and the reclamation of limited natural resources.Scope and scale of these applications provide obvious obstacles to the development of effective biotechnologies, but a more immediate limitation to realizing these technologies is the relative lack of genetic tools and insights which would allow the tinkering and rewiring of more complex organisms such as animals and plants. However, because of the natural intimate interactions between higher eukaryotes and microbes and the effect of these on phenotype, it is our vision that a faster, more tractable route to the engineering animal and plant phenotypes is via engineering their microbiomes.