Regulation of ROCKII membrane localization through its C-terminus

RhoA activated kinases (ROCKs) are potent effectors of RhoA signaling for regulation of the cytoskeleton. ROCKs have been shown to be localized to several different subcellular locations, suggesting that its localization is context specific and regulated. However, the signaling mechanisms that control ROCK localization have not been clearly described. In this study we measured ROCKII localization following stimulation with the chemokine CXCL12 or adhesion to collagen 1. Strikingly, each of these extracellular signals targeted ROCKII to membrane protrusions. We further determined that both RhoA and PI3-kinase signaling are required for these stimuli to induce efficient membrane localization. Furthermore, we used a mutational approach to show that two separate domains predicted to respond to these localization signals, the Rho Binding Domain (RBD) and the Pleckstrin Homology domain (PH). Unexpectedly, we found that these two domains work synergistically to lead to membrane localization. This suggests a novel mechanism for controlling ROCKII localization at the membrane, in which the ROCKII C-terminus acts as a coincidence detector for spatial regulatory signals. In other words, efficient membrane targeting requires the ROCKII RBD to receive the RhoA signal and the PH domain to receive the phospholipid signal.     

Quantifying lipid changes in various membrane compartments using lipid binding protein domains

One of the largest challenges in cell biology is to map the lipid composition of the membranes of various organelles and define the exact location of processes that control the synthesis and distribution of lipids between cellular compartments. The critical role of phosphoinositides, low-abundant lipids with rapid metabolism and exceptional regulatory importance in the control of almost all aspects of cellular functions created the need for tools to visualize their localizations and dynamics at the single cell level. However, there is also an increasing need for methods to determine the cellular distribution of other lipids regulatory or structural, such as diacylglycerol, phosphatidic acid, or other phospholipids and cholesterol. This review will summarize recent advances in this research field focusing on the means by which changes can be described in more quantitative terms.     

N-terminal PH domain and C-terminal auto-inhibitory region of CKIP-1 coordinate to determine its nucleus-plasma membrane shuttling

The pleckstrin homology (PH) domain-containing protein casein kinase 2 interacting protein-1 (CKIP-1) plays an important role in regulation of bone formation and muscle differentiation. How CKIP-1 localization is determined remains largely unclear. We observed that isolated CKIP-1-PH domain was predominantly localized in the nucleus and the C-terminus of CKIP-1 counteracted its nuclear localization. The net charge of basic residues and a serine-rich motif within the PH domain plays a pivotal role in the localization switch of both full-length CKIP-1 and the isolated PH domain. We propose that the N-terminal PH domain and C-terminal auto-inhibitory region of CKIP-1 coordinate to determine its subcellular localization and the nucleus-plasma membrane shuttling.     

Plant membrane proteomics

Plant membrane proteins are involved in many different functions according to their location in the cell. For instance, the chloroplast has two membrane systems, thylakoids and envelope, with specialized membrane proteins for photosynthesis and metabolite and ion transporters, respectively. Although recent advances in sample preparation and analytical techniques have been achieved for the study of membrane proteins, the characterization of these proteins, especially the hydrophobic ones, is still challenging. The present review highlights recent advances in methodologies for identification of plant membrane proteins from purified subcellular structures. The interest of combining several complementary extraction procedures to take into account specific features of membrane proteins is discussed in the light of recent proteomics data, notably for chloroplast envelope, mitochondrial membranes and plasma membrane from Arabidopsis. These examples also illustrate how, on one hand, proteomics can feed bioinformatics for a better definition of prediction tools and, on the other hand, although prediction tools are not 100% reliable, they can give valuable information for biological investigations. In particular, membrane proteomics brings new insights over plant membrane systems, on both the membrane compartment where proteins are working and their putative cellular function.     

On vesicles and membrane compartments

Summary Two different mechanisms have been proposed to explain transport along the endocytic and biosynthetic transport routes in cells. The first involves stable compartments connected by vesicular traffic while the second argues that the key organelles (early endosomes or the cis Golgi) form de novo by fusion of vesicles and subsequently mature into later forms. In the first part of this article, I propose a classification that distinguishes between stable, preexisting membrane compartments and vesicles that are, by definition, transient organelles. In this scheme, compartments, but not vesicles, are capable of homotypic fusion while vesicles, but not compartments, are able to mature, a process defined as an irreversible set of biochemical events which lead to a physiologically distinct end-state of the vesicle prior to its vectorial fusion with a target compartment. In the second part, I summarize my current ideas about the ultrastructural organization of the ER-Golgi region. Finally, I review the cell biology of selected examples of different vesicle types in order to exemplify the fascinating diversity of functions that this class of membrane organelles has evolved.Abbreviations COP coatomer - ECV endosome carrier vesicle - ER endoplasmic reticulum - HRP horseradish peroxidase - IC intermediate compartment between ER and Golgi - MVB multivesicular body - NSF N-ethyl maleimide sensitive factor - SNAPS soluble NSF associated proteins - TGN trans Golgi network Dedicated to Professor Eldon H. Newcomb in recognition of his contributions to cell biology     

The subcellular localization of 3-phosphoinositide-dependent protein kinase is controlled by caveolin-1 binding

3-Phosphoinositide-dependent protein kinase 1 (PDK1), a member of the serine/threonine kinase family, has been demonstrated to be crucial for cellular survival, differentiation, and metabolism. Here, we present evidence that PDK1 is associated with caveolin-1, a 22-kDa integral membrane protein, which is the principal structural and regulatory component of the caveolae membranes in COS-1. First, we noted the presence of two potential caveolin-1 binding motifs (¹⁴¹FFVKLYFTF¹⁴⁹ and ²⁹⁹YDFPEKFF³⁰⁶) in the PDK1 catalytic domain. Using a pull-down approach, we observed that PDK1 interacts physically with caveolin-1 both in vivo and in vitro. Second, we detected the co-localization of PDK1 and caveolin-1 via confocal microscopy. The localization of PDK1 to the plasma membrane was disrupted by caveolin binding. Third, in transient transfection assays, interaction with caveolin-1 induced a substantial reduction in the in vivo serine/threonine phosphorylation of PDK1, whereas the caveolin-1 binding site mutant (¹⁴¹FFVKLYFTF¹⁴⁹ and ²⁹⁹YDFPEKFF³⁰⁶ change to ¹⁴¹AFVKLAFTA¹⁴⁹ and ²⁹⁹ADAPEFLA³⁰⁶) did not. Furthermore, a caveolin-1 scaffolding peptide (amino acids 82-101) functionally suppressed the self-phosphorylation and kinase activities of purified recombinant PDK1 protein. Thus, our observations indicated that PDK1 binds to caveolin-1 through its caveolin-binding motifs, and also that the protein-protein interaction between PDK1 and caveolin-1 regulates PDK1 self-phosphorylation, kinase activity, and subcellular localization.     

Subcellular localization of prostaglandin E2 binding sites in bovine adrenal medulla

Prostaglandins E₁ and E₂ are specifically bound by particulate fractions from bovine adrenal medulla. The subcellular localization of these binding sites has been investigated by comparing their distribution in subcellular fractions obtained by differential and gradient centrifugation to those of marker enzymes for various organelles. Prostaglandin E₂ binding sites were purified about 16-fold with respect to the homogenate in a fraction which was highly enriched in plasma membranes on the basis of the activities of the marker enzymes acetylcholinesterase and calcium-dependent ATPase, which were both purified by about 12-fold in this fraction. The plasma membrane fraction contained relatively low activities of marker enzymes for mitochondria (monoamine oxidase), lysosomes (acid phosphatase), endoplasmic reticulum (glucose-6-phosphatase), Golgi (galactosyl transferase) and chromaffin granule membranes (dopamine β-hydroxylase). The only other fractions enriched in prostaglandin E₂ binding sites were those for the endoplasmic reticulum and the Golgi, in which the binding sites were purified about 4-fold and 7-fold, respectively. This is probably due mainly to contamination with plasma membranes, since calcium-dependent ATPase and acetylcholinesterase were each purified to a similar extent in these two fractions. These data suggest that the high-affinity prostaglandin E₂ binding sites of the adrenal medulla are localized primarily on the plasma membranes of the medullary cells.     

Identification of the subcellular localization of mycobacterial proteins using localization motifs

Mycobacterium, the most common disease-causing genus, infects billions of people and is notoriously difficult to treat. Understanding the subcellular localization of mycobacterial proteins can provide essential clues for protein function and drug discovery. In this article, we present a novel approach that focuses on local sequence information to identify localization motifs that are generated by a merging algorithm and are selected based on a binomially distributed model. These localization motifs are employed as features for identifying the subcellular localization of mycobacterial proteins. Our approach provides more accurate results than previous methods and was tested on an independent dataset recently obtained from an experimental study to provide a first and reasonably accurate prediction of subcellular localization. Our approach can also be used for large-scale prediction of new protein entries in the UniportKB database and of protein sequences obtained experimentally. In addition, our approach identified many local motifs involved with the subcellular localization that also interact with the environment. Thus, our method may have widespread applications both in the study of the functions of mycobacterial proteins and in the search for a potential vaccine target for designing drugs.     

Subcellular localization determines the delicate balance between the anti- and pro-apoptotic activity of Livin

Livin is a member of the Inhibitor of Apoptosis Protein family which inhibits apoptosis induced by a variety of stimuli. We previously identified Livin and demonstrated that following apoptotic stimuli, Livin is cleaved by effector caspases to produce a truncated form with paradoxical pro-apoptotic activity. In the present study, we reveal that while full-length Livin shows diffuse cytoplasmic localization, truncated Livin (tLivin) is found in a peri-nuclear distribution with marked localization to the Golgi apparatus. Using mutation analysis, we identified two domains that are crucial for the pro-apoptotic activity of tLivin: the N-terminal region of tLivin which is exposed by cleavage, and the RING domain. We demonstrate that, of the N-terminal sequence, only the first N-terminal glycine residue dictates the peri-nuclear distribution of tLivin. However, while the perinuclear localization of tLivin is essential, it is not sufficient for tLivin to exert its pro-apoptotic function. Once tLivin is properly localized, an intact RING domain enables its pro-apoptotic function. Electronic Supplementary Material Supplementary material is available in the online version of this article at .     

Nuclear localization signal of ING4 plays a key role in its binding to p53

ING4, a novel member of ING family, is recently reported to interact with tumor suppressor p53 and negatively regulate the cell growth with significant G2/M arrest of cell cycle in HepG2 cells through upregulation of p53-inducible gene p21. However, which region of ING4 could have contributed to the binding to p53 remains largely unclear. Herein, the GST-pulldown experiments revealed that the middle region of ING4, a potential bipartite nuclear localization signal (NLS), could be involved in the binding to p53. Furthermore, the interaction of ING4 to p53 was abrogated in vitro and in vivo when certain mutations or the entire deletion of the NLS domain occurred. More interestingly, the mutations of the NLS domain could alter the ING4 nuclear localization, disrupt the interaction of ING4 with p53, and even, deregulate the p53-inducible gene p21 in MCF-7 cells. All data indicated that the NLS domain of ING4 is essential for the binding of ING4 to p53 and the function of ING4 associated with p53.     

Mutual effects of MinD-membrane interaction: I. Changes in the membrane properties induced by MinD binding

In Escherichia coli and other bacteria, MinD, along with MinE and MinC, rapidly oscillates from one pole of the cell to the other controlling the correct placement of the division septum. MinD binds to the membrane through its amphipathic C-terminal α-helix. This binding, promoted by ATP-induced dimerization, may be further enhanced by a consequent attraction of acidic phospholipids and formation of a stable proteolipid domain. In the context of this hypothesis we studied changes in dynamics of a model membrane caused by MinD binding using membrane-embedded fluorescent probes as reporters. A remarkable increase in membrane viscosity and order upon MinD binding to acidic phospholipids was evident from the pyrene and DPH fluorescence changes. This viscosity increase is cooperative with regards to the concentration of MinD-ATP, but not of the ADP form, indicative of dimerization. Moreover, similar changes in the membrane dynamics were demonstrated in the native inverted cytoplasmic membranes of E. coli, with a different depth effect. The mobility of pyrene-labeled phosphatidylglycerol indicated formation of acidic phospholipid-enriched domains in a mixed acidic-zwitterionic membrane at specific MinD/phospholipid ratios. A comparison between MinD from E. coli and Neisseria gonorrhea is also presented.     

Subcellular localization and dynamics of MysPDZ (Myo18A) in live mammalian cells

MysPDZ is an unconventional myosin belonging to the class XVIII myosin containing a KE (lysine and glutamine)-rich domain and a PDZ domain, which codistributes with actin fibers partially without any canonical actin binding sequence in its myosin head domain. Recently, we reported the identification of a novel isoform of MysPDZ lacking these domains and exhibiting subcellular localization and expression profile different from the original form of MysPDZ. In order to delineate domains directing the subcellular localization of MysPDZ, we performed co-immunoprecipitation experiments and image analyses using mutants of MysPDZ fused with enhanced yellow fluorescent protein. Co-immunoprecipitation analyses showed that MysPDZ can self-associate through its C-terminus coiled-coil domain and the KE-rich domain mediates the interaction with actin. We observed by image analyses that the codistribution with actin fibers and the localization in inner surface of cell membrane of MysPDZ are controlled by the KE-rich domain and the PDZ domain, respectively. Time lapse video microscopy showed that MysPDZ in the cytoplasm moves randomly and rapidly within short range and is allocated to a subcellular compartment without ATP hydrolysis by MysPDZ. This suggests that MysPDZ is a protein which is unlike most unconventional myosins. Our study uncovers a novel role of the KE-rich and PDZ domains in directing subcellular localization and also contributes to a better understanding of functional differences in MysPDZ isoforms.     

Signal-anchor sequences are an essential factor for the Golgi-plasma membrane localization of type II membrane proteins

Despite studies of the mechanism underlying the intracellular localization of membrane proteins, the specific mechanisms by which each membrane protein localizes to the endoplasmic reticulum, Golgi apparatus, and plasma membrane in the secretory pathway are unclear. In this study, a discriminant analysis of endoplasmic reticulum, Golgi apparatus and plasma membrane-localized type II membrane proteins was performed using a position-specific scoring matrix derived from the amino acid propensity of the sequences around signal-anchors. The possibility that the sequence around the signal-anchor is a factor for identifying each localization group was evaluated. The discrimination accuracy between the Golgi apparatus and plasma membrane-localized type II membrane proteins was as high as 90%, indicating that, in addition to other factors, the sequence around signal-anchor is an essential component of the selection mechanism for the Golgi and plasma membrane localization. These results may improve the use of membrane proteins for drug delivery and therapeutic applications.     

Unconventional roles for membrane traffic proteins in response to muscle membrane stress

In skeletal muscle fibers, ubiquitous membrane trafficking pathways responsible for transporting newly synthesized proteins, recycling cell surface receptors, and organizing membrane compartmentation have adapted to the high needs of an extremely specialized cell under constant mechanical stress. Membrane remodeling proteins involved in ubiquitous mechanisms such as clathrin-mediated endocytosis, caveolae formation, and membrane fusion have evolved to produce new pathways with sometimes completely different functions such as adhesion and mechanoprotection. In this review, I discuss recent advances in understanding the specialized features of skeletal muscle clathrin-coated plaques, caveolae, and dysferlin-mediated membrane repair. A special emphasis is given on recent findings suggesting that membrane trafficking pathways have evolved to participate into the mechanisms responsible for sarcolemma resistance to mechanical stress and discuss how defects in these pathways result in muscle disease.     

Subcellular localization of talin is regulated by inter-domain interactions

Talin, which is composed of head (THD) and rod domains, plays an important role in cell adhesion events in diverse species including most metazoans and Dictyostelium discoideum. Talin is abundant in the cytosol; however, it mediates adhesion by associating with integrins in the plasma membrane where it forms a primary link between integrins and the actin cytoskeleton. Cells modulate the partitioning of talin between the plasma membrane and the cytosol to control cell adhesion. Here, we combine nuclear magnetic resonance spectroscopy (NMR) with subcellular fractionation to characterize two distinct THD-rod domain interactions that control the interaction of talin with the actin cytoskeleton or its localization to the plasma membrane. An interaction between a discrete vinculin-binding region of the rod (VBS1/2a; Tln1(482-787)), and the THD restrains talin from interacting with the plasma membrane. Furthermore, we show that vinculin binding to VBS1/2a results in talin recruitment to the plasma membrane. Thus, we have structurally defined specific inter-domain interactions between THD and the talin rod domain that regulate the subcellular localization of talin.     

植物蛋白质亚细胞定位相关研究概述

蛋白质在植物细胞内的定位是了解蛋白质功能、 基因调控和蛋白质-蛋白质相互作用的关键.近年来随着各种蛋白质亚细胞定位方法的快速发展和技术的不断提升,蛋白质亚细胞定位实现了高通量、活体动态研究.本文总结了植物蛋白质亚细胞定位的常用技术,以及常用细胞器特异性标记的研究进展,并对此领域研究的发展前景做出了展望.     

衣原体蛋白的亚细胞定位

沙眼衣原体(Chlamydia trachomatis,CT)是一种严格细胞内寄生、有独特发育周期的原核细胞型微生物.CT在宿主细胞浆内增殖,形成光镜可见的典型细胞内包涵体,包涵体为CT在宿主细胞内的生长繁殖提供屏障保护,同时也是CT与宿主细胞进行物质交换和信息传递的门户,CT不仅可从宿主细胞摄取营养物质,还可分泌效应蛋白进入宿主细胞质调节宿主细胞功能.CT基因组DNA序列和功能注释完成后,衣原体蛋白的亚细胞定位、结构和功能的研究已成为衣原体研究领域的热点之一[1-3].在CT与宿主细胞相互作用过程中,Inc蛋白、分泌蛋白等衣原体蛋白可能发挥着重要作用,鉴于蛋白质的亚细胞定位情况往往与其功能密切相关,衣原体蛋白在感染细胞中的定位认识成为其功能研究中的重要环节.     

Analytical subcellular fractionation of rat pituitary homogenates with special reference to the subcellular localization and properties of alkaline phosphatases

Alkaline phosphatase activities of the virgin rat anterior pituitary were studied with a highly sensitive fluorometric assay. Tissue whole homogenates were fractionated on sucrose density gradients in a Beaufay automatic zonal rotor and the gradient fractions assayed for alkaline phosphatase, prolactin and various organelle marker enzymes. Alkaline phosphatase was distributed between two peaks on the gradient. The low-density (1.10–1.15 g·cm^?3) alkaline phosphatase component co-sedimented with the plasma membrane marker, 5′-nucleotidase, had an apparent K_m for 4-methylumbelliferyl phosphate of approx. 59 μM, and was inhibited by levamisole. The high-density (1.20–1.25 g·cm^?3) peak was resistant to levamisole-inhibition, had an apparent K_m of approx. 30 μM and its distribution was distinct from plasma membrane, Golgi, lysosome, endoplasmic reticulum, mitochondria and prolactin granule markers on the isopycnic gradients.     

A novel plastid localization of chalcone synthase in developing grape berry

Chalcone synthase (CHS, E.C. 2.3.1.74) is an entrance enzyme of flavonoid metabolism and a critical point to regulation of biosynthesis of different flavonoid compounds that directly contribute to color and monthfeel of grape and wine. In the present experiment, subcellular localization of CHS in developing grape berry was performed via immunogold electron microscopy technique. The result showed that CHS was localized in rough endoplasmic reticulum (ER) and cytoplasm of the skin cells, while few gold particles representing CHS were found on the cell wall. Besides, two novel localized sites of CHS were observed within a cell of developing grape berry, one being the plastid-distributed throughout developmental stages and the other being vacuole-distributed at late developmental stage. It is speculated that these novel localized patterns may relate to abundant and multi-branch flavonoid metabolism in grape berry. This work will provide new insight for the regulation of different branch pathways leading to diverse flavonoid compounds.     

Subcellular localization of phosphatidylinositol synthesis

It is well-established that the endoplasmic reticulum is the major site of phosphatidylinositol (PtdIns) synthesis. The PtdIns synthetic ability of other organelles, such as plasma membrane and nucleus, remains controversial. In the present study, we re-examine this question by comparing PtdIns synthesis in isolated cytoplasts (enucleated cells) with that in corresponding karyoplasts (nuclei surrounded by plasma membrane but lacking most cytoplasmic components). We report that cytoplasts are competent to carry out both basal and stimulated PtdIns synthesis as well as polyphosphoinositide hydrolysis, while karyoplasts can neither synthesize PtdIns nor hydrolyze phosphoinositides in response to agonists. The karyoplasts are, however, capable of synthesizing phosphatidylcholine (PtdCho), as previously reported. From these data, we conclude that PtdIns synthesis is limited to cytoplasmic components, and cannot be sustained by either plasma membrane or nucleus under conditions that permit robust PtdCho synthesis.