Three pure chaperone proteins of Escherichia coli--SecB, trigger factor and GroEL--form soluble complexes with precursor proteins in vitro.

Diverse studies of three cytoplasmic proteins of Escherichia coli--SecB, trigger factor and GroEL--have suggested that they can maintain precursor proteins in a conformation which is competent for membrane translocation. These proteins have been termed 'chaperones'. Using purified chaperone proteins and precursor protein substrates, we find that each of these chaperones can stabilize proOmpA for translocation and for the translocation-ATPase. These chaperones bind to proOmpA to form isolable complexes. SecB and GroEL will also form complexes with another exported protein, prePhoE. In contrast, these chaperones do not form stable complexes with a variety of soluble proteins such as SecA protein, bovine serum albumin, ovalbumin or ribonuclease A. While chaperones may transiently interact with soluble proteins to catalyze their folding, the stable interaction between chaperones and presecretory proteins, maintaining an open conformation which is essential for translocation, may commit these proteins to the secretion pathway.     

Standard conformations of beta-arches in beta-solenoid proteins

Strand-turn-strand motifs found in beta-helical (more generally, beta-solenoid) proteins differ fundamentally from those found in globular proteins. The latter are primarily beta-hairpins in which the two strands form an antiparallel beta-sheet. In the former, the two strands are relatively rotated by approximately 90 degrees around the strand axes so that they interact via the side-chains, not via the polypeptide backbones. We call the latter structures, beta-arches, and their turns, beta-arcs. In beta-solenoid proteins, beta-arches stack in-register to form beta-arcades in which parallel beta-sheets are assembled from corresponding strands in successive layers. The number of beta-solenoids whose three-dimensional structures have been determined is now large enough to support a detailed analysis and classification of beta-arc conformations. Here, we present a systematic account of beta-arcs distinguished by the number of residues, their conformations, and their propensity to stack into arcades with other like or unlike arches. The trends to emerge from this analysis have implications for sequence-based detection and structural prediction of other beta-solenoid proteins as well as for identification of amyloidogenic sequences and elucidation of amyloid fibril structures.     

Fungal rhodopsins and opsin-related proteins: eukaryotic homologues of bacteriorhodopsin with unknown functions.

In the last decade, several genome sequencing projects revealed the existence of previously unknown photoreceptors. Among those are eukaryotic rhodopsins of haloarchaeal type, mostly represented by fungal sequences. We have classified and analyzed seventy-seven of these fungal proteins, which show a high similarity of their putative transmembrane regions to those of bacteriorhodopsin. Those sequences can be divided into the two subgroups, fungal rhodopsins (RDs) and opsin-related proteins (ORPs), the latter lacking the lysine residue necessary for retinal binding. We have analyzed the conservation pattern of the residues known to have functional or structural importance in bacteriorhodopsin and discussed dramatic differences in the conservation between RDs and ORPs. We found many cases of multiple forms of RDs and/or ORPs and examined possible reasons for such multiplicity. For some species the reason may lie in functional photobiological diversification, while for the others it follows the pattern of evolutionary recent genome duplication and possible functional redundancy.     

Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential

The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. Infection is associated with secretion of proteins surrounded by proliferating cells. Many parasites are known to secrete effectors that interfere with plant innate immunity, enabling infection to occur; they can also release pathogen-associated molecular patterns (PAMPs, e.g., flagellin) that trigger basal immunity through the nematode stylet into the plant cell. This leads to suppression of innate immunity and reprogramming of plant cells to form a feeding structure containing multinucleate giant cells. Effectors have generally been discovered using genetics or bioinformatics, but M. incognita is non-sexual and its genome sequence has not yet been reported. To partially overcome these limitations, we have used mass spectrometry to directly identify 486 proteins secreted by M. incognita. These proteins contain at least segmental sequence identity to those found in our 3 reference databases (published nematode proteins; unpublished M. incognita ESTs; published plant proteins). Several secreted proteins are homologous to plant proteins, which they may mimic, and they contain domains that suggest known effector functions (e.g., regulating the plant cell cycle or growth). Others have regulatory domains that could reprogram cells. Using in situ hybridization we observed that most secreted proteins were produced by the subventral glands, but we found that phasmids also secreted proteins. We annotated the functions of the secreted proteins and classified them according to roles they may play in the development of root knot disease. Our results show that parasite secretomes can be partially characterized without cognate genomic DNA sequence. We observed that the M. incognita secretome overlaps the reported secretome of mammalian parasitic nematodes (e.g., Brugia malayi), suggesting a common parasitic behavior and a possible conservation of function between metazoan parasites of plants and animals.     

A glycosynapse in myelin?

Myelin, the multilayered membrane which surrounds nerve axons, is the only example of a membranous structure where contact between extracellular surfaces of membrane from the same cell occurs. The two major glycosphingolipids (GSLs) of myelin, galactosylceramide (GalC) and its sulfated form, galactosylceramide I(3)-sulfate (SGC), can interact with each other by trans carbohydrate-carbohydrate interactions across apposed membranes. They occur in detergent-insoluble lipid rafts containing kinases and thus may be located in membrane signaling domains. These signaling domains may contact each other across apposed extracellular membranes, thus forming glycosynapses in myelin. Multivalent forms of these carbohydrates, GalC/SGC-containing liposomes, or galactose conjugated to albumin, have been added to cultured oligodendrocytes (OLs) to mimic interactions which might occur between these signaling domains when OL membranes or the extracellular surfaces of myelin come into contact. These interactions between multivalent carbohydrate and the OL membrane cause co-clustering or redistribution of myelin GSLs, GPI-linked proteins, several transmembrane proteins, and signaling proteins to the same membrane domains. They also cause depolymerization of the cytoskeleton, indicating that they cause transmission of a signal across the membrane. Their effects have similarities to those of anti-GSL antibodies on OLs, shown by others, suggesting that the multivalent carbohydrate interacts with GalC/SGC in the OL membrane. Communication between the myelin sheath and the axon regulates both axonal and myelin function and is necessary to prevent neurodegeneration. Participation of transient GalC and SGC interactions in glycosynapses between the apposed extracellular surfaces of mature compact internodal myelin might allow transmission of signals throughout the myelin sheath and thus facilitate myelin-axonal communication.     

Internal proteins of bacteriophage T4D: Their characterization and relation to head structure and assembly

Three basic proteins of low molecular weight (about 8000, 10,000 and 18,000) were isolated from the T4D phage particle. Many molecules of each protein are located within the phage head, possibly in association with the DNA, and together with the proteins which form the head membrane comprise most of the head structural protein. The purified internal proteins were characterized by physicochemical and immunological techniques; a radio-immunoassay allowed measurement of their synthesis in phage infected bacteria. Each internal protein is synthesized at both early and late times after infection. Their structural genes are present in the phage genome, but do not appear to be among the known amber mutant-containing genes of T4D. No evidence was found to suggest that the internal proteins are formed from a common precursor molecule, nor are their origins related to those of the internal peptides; however, one of the internal proteins may be altered before its incorporation into the phage. Pulse-chase experiments with two of these proteins show that they are incorporated into certain defective T4D heads. Whether or not they are incorporated appears to depend on the degree of completion of these heads, perhaps with respect to DNA packaging.     

The Arabidopsis thaliana ATP-binding cassette proteins: an emerging superfamily

Solute transport systems are one of the major ways in which organisms interact with their environment. Typically, transport is catalysed by integral membrane proteins, of which one of the largest groups is the ATP‐binding cassette (ABC) proteins. On the basis of sequence similarities, a large family of ABC proteins has been identified in Arabidopsis. A total of 60 open reading frames (ORFs) encoding ABC proteins were identified by BLAST homology searching of the nuclear genome. These 60 putative proteins include 89 ABC domains. Based on the assignment of transmembrane domains (TMDs), at least 49 of the 60 proteins identified are ABC transporters. Of these 49 proteins, 28 are full‐length ABC transporters (eight of which have been described previously), and 21 are uncharacterized half‐transporters. Three of the remaining proteins identified appear to be soluble, lacking identifiable TMDs, and most likely have non‐transport functions. The eight other ORFs have homology to the nucleotide‐binding and transmembrane components of multi‐subunit permeases. The majority of ABC proteins found in Arabidopsis can, on the basis of sequence homology, be assigned to subfamilies equivalent to those found in the yeast genome. This assignment of the Arabidopsis ABC proteins into easily recognizable subfamilies (with distinguishable subclusters) is an important first step in the elucidation of their functional role in higher plants.     

Interactions between folding factors and bacterial outer membrane proteins

The outer membrane is the first line of contact between Gram-negative bacteria and their external environment. Embedded in the outer membrane are integral outer membrane proteins (OMPs) that perform a diverse range of tasks. OMPs are synthesized in the cytoplasm and are translocated across the inner membrane and probably diffuse through the periplasm before they are inserted into the outer membrane in a folded and biologically active form. Passage through the periplasm presents a number of challenges, due to the hydrophobic nature of the OMPs and the choice of membranes into which they can insert. Recently, a number of periplasmic proteins and one OMP have been shown to play a role in OMP biogenesis. In this review, we describe what is known about these folding factors and how they function in a biological context. In particular, we focus on how they interact with the OMPs at the molecular level and present a comprehensive overview of data relating to a possible effect on OMP folding yield and kinetics. Furthermore, we discuss the role of lipo-chaperones, i.e. lipopolysaccharide and phospholipids, in OMP folding. Important advances have clearly been made in the field, but much work remains to be done, particularly in terms of describing the biophysical basis for the chaperone-OMP interactions which so intricately regulate OMP biogenesis.     

昆虫中肠围食膜蛋白研究进展

围食膜是大多数昆虫中肠内壁附着的一层起润滑和保护作用的半透性粘膜, 按其形成方式不同分为Ⅰ型围食膜和Ⅱ型围食膜。围食膜主要由几丁质和蛋白质构成, 其中蛋白质对于维持围食膜的致密结构至关重要, 对围食膜蛋白的破坏可能会对昆虫的正常生长发育造成干扰, 甚至会导致低龄幼虫的死亡。本文介绍了围食膜的组成与结构, 阐述了昆虫围食膜蛋白研究的新发现、并依据结构特征对它们进行了分类, 总结了以围食膜蛋白为新靶标的害虫防治的可能途径, 讨论了当前围食膜蛋白研究的不足, 最后展望了今后围食膜蛋白研究的发展方向。     

Drivers and passengers wanted! the role of kinesin-associated proteins

Members of the kinesin superfamily of proteins participate in a wide variety of cellular processes. Although much attention has been devoted to the structural and biophysical properties of the force-generating motor domain of kinesins, the factors controlling the functional specificity of each kinesin have only recently been examined. Genetic and biochemical approaches have identified two classes of proteins that associate physically with the diverse non-motor domains of kinesins. These proteins can be divided into two general classes: first, those that form tight complexes with the kinesin and are instrumental in directing the distinct function of the motor (i.e. drivers) and, second, those proteins that might transiently interact with the motor or be an integral part of the motor's cargo (i.e. passengers). Here, we discuss known kinesin-binding proteins, and how they might participate in the activity of their motor partners.     

Self organization of membrane proteins via dimerization

Protein-protein dimerization is ubiquitous in biology, but its role in self-organization remains unexplored. Here we use Monte Carlo simulations to demonstrate that under diffusion-limited conditions, reversible dimerization alone can cause membrane proteins to cluster into oligomer-like structures. When multiple distinct protein species are able to form dimers, then heterodimerization and homodimerization can organize proteins into structured clusters that can affect cellular physiology. As an example, we demonstrate how receptor dimerization could provide a physical mechanism for regulating information flow by controlling receptor-receptor cross talk. These results are physically realistic for some membrane proteins, including members of the G-protein coupled receptor family, and may provide a physiological reason as to why many proteins dimerize.     

Structures of yeast vesicle trafficking proteins

In protein transport between organelles, interactions of v- and t-SNARE proteins are required for fusion of protein-containing vesicles with appropriate target compartments. Mammalian SNARE proteins have been observed to interact with NSF and SNAP, and yeast SNAREs with yeast homologues of NSF and SNAP proteins. This observation led to the hypothesis that, despite low sequence homology, SNARE proteins are structurally similar among eukaryotes. SNARE proteins can be classified into two groups depending on whether they interact with SNARE binding partners via conserved glutamine (Q-SNAREs) or arginine (R-SNAREs). Much of the published structural data available is for SNAREs involved in exocytosis (either in yeast or synaptic vesicles). This paper describes circular dichroism, Fourier transform infrared spectroscopy, and dynamic light scattering data for a set of yeast v- and t-SNARE proteins, Vti1p and Pep12p, that are Q-SNAREs involved in intracellular trafficking. Our results suggest that the secondary structure of Vti1p is highly alpha-helical and that Vti1p forms multimers under a variety of solution conditions. In these respects, Vti1p appears to be distinct from R-SNARE proteins characterized previously. The alpha-helicity of Vti1p is similar to that of Q-SNARE proteins characterized previously. Pep12p, a Q-SNARE, is highly alpha-helical. It is distinct from other Q-SNAREs in that it forms dimers under many of the solution conditions tested in our experiments. The results presented in this paper are among the first to suggest heterogeneity in the functioning of SNARE complexes.     

Review: nuclear lamins--structural proteins with fundamental functions

The nuclear lamina is located between the inner nuclear membrane and the peripheral chromatin. It is composed of both peripheral and integral membrane proteins, including lamins and lamina-associated proteins. Lamins can interact with one another, with lamina-associated proteins, with nuclear scaffold proteins, and with chromatin. Likewise, most of the lamina-associated proteins are likely to interact directly with chromatin. The nuclear lamina is required for proper cell cycle regulation, chromatin organization, DNA replication, cell differentiation, and apoptosis. Mutations in proteins of the nuclear lamina can disrupt these activities and cause genetic diseases. The structure and assembly of the nuclear lamina proteins and their roles in chromatin organization and cell cycle regulation were recently reviewed. In this review, we discuss the roles of the nuclear lamina in DNA replication and apoptosis and analyze how mutations in nuclear lamina proteins might cause genetic diseases.     

Membrane interactions of G proteins and other related proteins

Guanine nucleotide-binding proteins, G proteins, propagate incoming messages from receptors to effector proteins. They switch from an inactive to active state by exchanging a GDP molecule for GTP, and they return to the inactive form by hydrolyzing GTP to GDP. Small monomeric G proteins, such as Ras, are involved in controlling cell proliferation, differentiation and apoptosis, and they interact with membranes through isoprenyl moieties, fatty acyl moieties, and electrostatic interactions. This protein-lipid binding facilitates productive encounters of Ras and Raf proteins in defined membrane regions, so that signals can subsequently proceed through MEK and ERK kinases, which constitute the canonical MAP kinase signaling cassette. On the other hand, heterotrimeric G proteins undergo co/post-translational modifications in the alpha (myristic and/or palmitic acid) and the gamma (farnesol or geranylgeraniol) subunits. These modifications not only assist the G protein to localize to the membrane but they also help distribute the heterotrimer (Galphabetagamma) and the subunits generated upon activation (Galpha and Gbetagamma) to appropriate membrane microdomains. These proteins transduce messages from ubiquitous serpentine receptors, which control important functions such as taste, vision, blood pressure, body weight, cell proliferation, mood, etc. Moreover, the exchange of GDP by GTP is triggered by nucleotide exchange factors. Membrane receptors that activate G proteins can be considered as such, but other cytosolic, membranal or amphitropic proteins can accelerate the rate of G protein exchange or even activate this process in the absence of receptor-mediated activation. These and other protein-protein interactions of G proteins with other signaling proteins are regulated by their lipid preferences. Thus, G protein-lipid interactions control the features of messages and cell physiology.     

Fractionation of membrane proteins by temperature-induced phase separation in Triton X-114. Application to subcellular fractions of the adrenal medulla.

After solubilization with the detergent Triton X-114, membrane proteins may be separated into three groups: if the membrane is sufficiently lipid-rich, one family of hydrophobic constituents separates spontaneously at low temperature; warming at 30 degrees C leads to separation of a detergent-rich phase and an aqueous phase. Using the chromaffin-granule membrane as a model, we found that many intrinsic membrane glycoproteins are found in the latter phase, probably maintained in solution by adherent detergent. They precipitate, however, when this is removed by dialysis, leaving in solution those truly hydrophilic proteins that were originally adhering to the membranes. We have used this method with mitochondria, and with Golgi- and rough-endoplasmic-reticulum-enriched microsomal fractions: it has proved to be a rapid and convenient method for effecting a partial separation of proteins from a variety of different membranes.     

The ulcerative colitis marker protein WAFL interacts with accessory proteins in endocytosis

Ulcerative colitis (UC) is one of the major forms of inflammatory bowel disease with unknown cause. A molecular marker, WAFL, has recently been found to be up-regulated in the inflamed colonic mucosa of UC patients. Towards understanding biological function of WAFL, we analyzed proteins interacting with WAFL in HEK-293 cells by immunoprecipitation and mass spectrometry. Among four proteins found to specifically interact with WAFL, both KIAA0196 and KIAA1033 bind to α-appendage of the adaptor protein complex 2 (AP2), which acts as an interaction hub for accessory proteins in endocytosis mediated by clathrin-coated vesicle (CCV). The specific interaction between WAFL and KIAA0196 was also confirmed in human colorectal carcinoma HCT-116 cells by co-immunoprecipitation with specific antibodies. Meta-analyses of the databases of expressed genes suggest that the three genes are co-expressed in many tissues and cell types, and that their molecular function may be classified in the category of ''membrane traffic protein''. Therefore, these results suggest that WAFL may play an important role in endocytosis and subsequent membrane trafficking by interacting with AP2 through KIAA0196 and KIAA1033.     

Interactions between GPI-anchored proteins and membrane lipids

Proteins anchored in membranes by glycosylphosphatidylinositol (GPI) are widely distributed, but the function of this unusual anchor is a puzzle. Recent evidence shows that these proteins can associate with membrane lipids in special ways. One function of GPI anchorage may be to allow proteins to interact with specialized membrane domains.     

Ankyrin repeat-containing proteins in Arabidopsis: characterization of a novel and abundant group of genes coding ankyrin-transmembrane proteins

Ankyrin repeats are present in a great variety of proteins of eukaryotes, prokaryotes and some viruses and they function as protein-protein interaction domains. We have search for all the ankyrin repeats present in Arabidopsis proteins and determined their consensus sequence. We identified a total of 509 ankyrin repeats present in 105 proteins. Ankyrin repeat containing proteins can be classified in 16 groups of structurally similar proteins. The most abundant group contains proteins with ankyrin repeats and transmembrane domains (AtANKTM). Sequence similarity analysis indicates that these proteins are divided in six families. Some of the AtAnkTm genes are organized in tandem arrays and others are present in duplicated parts of the Arabidopsis genome. The expression of several AtAnkTm genes was analyzed resulting in a wide variety of expression patterns even within the same family. The likely functions of these proteins are discussed in comparison with the known functions of proteins with similar organization in other species.     

Interaction with a lipid membrane: a key step in bacterial toxins virulence

Bacterial toxins are secreted as soluble proteins. However, they have to interact with a cell lipid membrane either to permeabilize the cells (pore forming toxins) or to enter into the cytosol to express their enzymatic activity (translocation toxins). The aim of this review is to suggest that the strategies developed by toxins to insert in a lipid membrane is mediated by their structure. Two categories, which contains both pore forming and translocation toxins, are emerging: alpha helical proteins containing hydrophobic domains and beta sheets proteins in which no hydrophobicity can be clearly detected. The first category would rather interact with the membrane through multi-spanning helical domains whereas the second category would form a beta barrel in the membrane.