Receptins: a novel term for an expanding spectrum of natural and engineered microbial proteins with binding properties for mammalian proteins

A new term ‘receptin’, derived from recipere (lat.), is proposed to denote microbial binding proteins that interact with mammalian target proteins. An example of such a ‘receptin’ is staphyloccocal protein A which binds to the Fc part of many mammalian immunoglobulins. Several other types of ‘receptins’ are listed. This term may easily be distinguished from the similar term ‘receptor’, describing a binding site on a cell surface, mostly eukaryotic, where a secondary effect is induced inside the cell upon binding to a ligand. A receptin, however, does not necessarily have to induce a secondary event. Receptins include so called MSCRAMMs, adhesins, and also engineered receptins, affibodies, and engineered ligands. It denotes any protein of microbial origin, cell‐bound or soluble, which can bind to a mammalian protein. It fulfills the need for an umbrella terminology for a large group of binding structures. In contrast, the term ‘lectin’ represents a group of proteins with affinity for carbohydrate structures. The new term ‘receptin’ includes a number of key microbial proteins involved in host–parasite interactions and in virulence. Some receptins are promising vaccine candidates. Copyright © 1999 John Wiley & Sons, Ltd.     

Y-box结合蛋白功能及对肿瘤发生的影响

Y-box结合蛋白家族成员是一类高度保守的顺式作用元件, 广泛存在于原核及真核生物细胞中。它是一种多功能蛋白, 与转录调节、翻译调控、mRNA选择性剪接、DNA的修复、细胞增殖和再生等有关。Y-box结合蛋白的氨基酸序列包含3个结构域: 氨基酸N末端, 亲水结构域C末端, 冷休克结构域(cold shock domain CSD), 保守的冷休克结构域决定了Y-box结合蛋白的大部分功能。最近研究发现, 定位于细胞核中的YB-1蛋白在局部晚期非小细胞肺癌的预防上可作为新的靶位点, YB-1蛋白还可通过对抑癌基因p53启动子抑制起负调控作用, 此外, YB-1蛋白在PI3K/Akt信号通路中也起到重要的作用, 这些研究都为肿瘤的治疗提供了新的线索和启示。文章就Y-box结合蛋白功能及其对肿瘤发生的影响等方面进行概述。     

Protein cell surface display in Gram-positive bacteria: from single protein to macromolecular protein structure

In the course of evolution, Gram-positive bacteria, defined here as prokaryotes from the domain Bacteria with a cell envelope composed of one biological membrane (monodermita) and a cell wall composed at least of peptidoglycan and covalently linked teichoic acids, have developed several mechanisms permitting to a cytoplasmic synthesized protein to be present on the bacterial cell surface. Four major types of cell surface displayed proteins are currently recognized: (i) transmembrane proteins, (ii) lipoproteins, (iii) LPXTG-like proteins and (iv) cell wall binding proteins. The subset of proteins exposed on the bacterial cell surface, and thus interacting with extracellular milieu, constitutes the surfaceome. Here, we review exhaustively the current molecular mechanisms involved in protein attachment within the cell envelope of Gram-positive bacteria, from single protein to macromolecular protein structure.     

Xenopus embryonic poly(A) binding protein 2 (ePABP2) defines a new family of cytoplasmic poly(A) binding proteins expressed during the early stages of vertebrate development

We describe a new RNA binding protein from Xenopus we have named ePABP2 (embryonic poly(A) binding protein type II). Based on amino acid similarity, ePABP2 is closely related to the ubiquitously expressed nuclear PABP2 protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. However, in contrast to known PABP2 proteins, Xenopus ePABP2 is a cytoplasmic protein that is predominantly expressed during the early stages of Xenopus development and in adult ovarian tissue. Biochemical experiments indicate ePABP2 binds poly(A) with specificity and that this binding requires the RRM domain. Mouse and human ePABP2 proteins were also identified and mouse ePABP2 expression is also confined to the earliest stages of mouse development and adult ovarian tissue. We propose that Xenopus ePABP2 is the founding member of a new class of poly(A) binding proteins expressed in vertebrate embryos. Possible roles for this protein in regulating mRNA function in early vertebrate development are discussed.     

The mysterious RAMP proteins and their roles in small RNA-based immunity

A new class of prokaryotic RNA binding proteins called Repeat Associated Mysterious Proteins (RAMPs), has recently been identified. These proteins play key roles in a novel type immunity in which the DNA of the host organism (e.g. a prokaryote) has sequence segments corresponding to the sequences of potential viral invaders. The sequences embedded in the host DNA confer immunity by directing selective destruction of the nucleic acid of the virus using an RNA-based strategy. In this viral defense mechanism, RAMP proteins have multiple functional roles including endoribonucleotic cleavage and ribonucleoprotein particle assembly. RAMPs contain the classical RNA recognition motif (RRM), often in tandem, and a conserved glycine-rich segment (G-loop) near the carboxyl terminus. However, unlike RRMs that bind single-stranded RNA using their β-sheet surface, RAMPs make use of both sides of the RRM fold and interact with both single-stranded and structured RNA. The unique spatial arrangement of the two RRM folds, facilitated by a hallmark G-loop, is crucial to formation of a composite surface for recognition of specific RNA. Evidence for RNA-dependent oligomerization is also observed in some RAMP proteins that may serve as an important strategy to increase specificity.     

Haemophore functions revisited

Haem is the major iron source for bacteria that develop in higher organisms. In these hosts, bacteria have to cope with nutritional immunity imposed by the host, since haem and iron are tightly bound to carrier and storage proteins. Siderophores were the first recognized fighters in the battle for iron between bacteria and host. They are non-proteinaceus organic molecules having an extremely high affinity for Fe(3+) and able to extract it from host proteins. Haemophores, that display functional analogy with siderophores, were more recently discovered. They are a class of secreted proteins with a high affinity for haem; they are able to extract haem from host haemoproteins and deliver it to specific receptors that internalize haem. In the past few years, a wealth of data has accumulated on haem acquisition systems that are dependent on surface exposed/secreted bacterial proteins. They promote haem transfer from its initial source (in most cases, a eukaryotic haem binding protein) to the transporter that carries out the membrane crossing step. Here we review recent discoveries in this field, with particular emphasis on similar and dissimilar mechanisms in haemophores and siderophores, from the initial host source to the binding protein/receptor at the cell surface.     

c-di-AMP——细菌中第二信使的研究进展

环二腺苷酸(cyclic diadenylate monophosphate,c-di-AMP)是新发现的在细菌中广泛存在的一类重要的第二信使。c-di-AMP不仅与细菌的生长、细胞壁的代谢平衡、生物被膜的形成等密切相关,还在真核宿主细胞抗感染的固有免疫中发挥重要作用。主要从c-di-AMP的合成酶与降解酶、c-di-AMP在病原菌中的结合蛋白以及c-di-AMP与宿主细胞互作过程中的相关受体蛋白等几方面进行综述。     

A structural overview of mycobacterial adhesins: Key biomarkers for diagnostics and therapeutics

Adherence, colonization, and survival of mycobacteria in host cells require surface adhesins, which are attractive pharmacotherapeutic targets. A large arsenal of pilus and non‐pilus adhesins have been identified in mycobacteria. These adhesins are capable of interacting with host cells, including macrophages and epithelial cells and are essential to microbial pathogenesis. In the last decade, several structures of mycobacterial adhesins responsible for adhesion to either macrophages or extra cellular matrix proteins have been elucidated. In addition, key structural and functional information have emerged for the process of mycobacterial adhesion to epithelial cells, mediated by the Heparin‐binding hemagglutinin (HBHA). In this review, we provide an overview of the structural and functional features of mycobacterial adhesins and discuss their role as important biomarkers for diagnostics and therapeutics. Based on the reported data, it appears clear that adhesins are endowed with a variety of different structures and functions. Most adhesins play important roles in the cell life of mycobacteria and are key virulence factors. However, they have adapted to an extracellular life to exert a role in host‐pathogen interaction. The type of interactions they form with the host and the adhesin regions involved in binding is partly known and is described in this review.     

Identification and characterization of a cell surface protein of Prevotella intermedia 17 with broad-spectrum binding activity for extracellular matrix proteins

Prevotella intermedia binds and invades a variety of host cells. This binding is most probably mediated through cell surface proteins termed adhesins. To identify proteins binding to the host extracellular matrix (ECM) component, fibronectin, and study the molecular mechanism underlying bacterial colonization, we applied proteomic approaches to perform a global investigation of P. intermedia strain 17 outer membrane proteins. 2-DE followed by Far Western Blot analysis using fibronectin as a probe revealed a 29-kDa fibronectin-binding protein, designated here AdpB. The molecular identity of the protein was determined using PMF followed by a search of the P. intermedia 17 protein database. Database searches revealed the similarity of AdpB to multiple bacterial outer membrane proteins including the fibronectin-binding protein from Campylobacter jejuni. A recombinant AdpB protein bound fibronectin as well as other host ECM components, including fibrinogen and laminin, in a saturable, dose-dependent manner. Binding of AdpB to immobilized fibronectin was also inhibited by soluble fibronectin, laminin, and fibrinogen, indicating the binding was specific. Finally, immunoelectron microscopy with anti-AdpB demonstrated the cell surface location of the protein. This is the first cell surface protein with a broad-spectrum ECM-binding abilities identified and characterized in P. intermedia 17.     

Vaccination with Staphylococcus aureus fibrinogen binding proteins (FgBPs) reduces colonisation of S. aureus in a mouse mastitis model

Abstract A mouse mastitis model was used to study the effect of vaccination with fibrinogen binding proteins and collagen binding protein from Staphylococcus aureus against challenge infection with S. aureus . The mice vaccinated with fibrinogen binding proteins showed reduced rates of mastitis compared with controls. Gross examination of challenged mammary glands of mice showed that the glands of mice immunized with fibronogen binding proteins developed mild intramammary infection or had no pathological changes compared with glands from control mice. Histopathological examination of tissue sections from challenged glands showed that most glands from mice vaccinated with fibrinogen binding protein developed disseminated necrosis or had no pathological changes. A significantly reduced number of bacteria could be recovered in the glands from mice immunized with fibrinogen binding proteins as compared with controls. In a similar study, immunization of mice with collagen binding protein did not induce protection against challenge infection with S. aureus .     

Binding of a pleurotolysin ortholog from Pleurotus eryngii to sphingomyelin and cholesterol-rich membrane domains

A mixture of sphingomyelin (SM) and cholesterol (Chol) exhibits a characteristic lipid raft domain of the cell membranes that provides a platform to which various signal molecules as well as virus and bacterial proteins are recruited. Several proteins capable of specifically binding either SM or Chol have been reported. However, proteins that selectively bind to SM/Chol mixtures are less well characterized. In our screening for proteins specifically binding to SM/Chol liposomes, we identified a novel ortholog of Pleurotus ostreatus, pleurotolysin (Ply)A, from the extract of edible mushroom Pleurotus eryngii, named PlyA2. Enhanced green fluorescent protein (EGFP)-conjugated PlyA2 bound to SM/Chol but not to phosphatidylcholine/Chol liposomes. Cell surface labeling of PlyA2-EGFP was abolished after sphingomyelinase as well as methyl-β-cyclodextrin treatment, removing SM and Chol, respectively, indicating that PlyA2-EGFP specifically binds cell surface SM/Chol rafts. Tryptophan to alanine point mutation of PlyA2 revealed the importance of C-terminal tryptophan residues for SM/Chol binding. Our results indicate that PlyA2-EGFP is a novel protein probe to label SM/Chol lipid domains both in cell and model membranes.     

An atomic resolution model for assembly, architecture, and function of the Dr adhesins

Pathogenic bacteria possess adhesion protein complexes that play essential roles in targeting host cells and in propagating infection. Although each family of adhesion proteins is generally associated with a specific human disease, the Dr family from Escherichia coli is a notable exception, as its members are associated with both diarrheal and urinary tract infections. These proteins are reported to form both fimbrial and afimbrial structures at the bacterial cell surface and target a common host cell receptor, the decay-accelerating factor (DAF or CD55). Using the newly solved three-dimensional structure of AfaE, we have constructed a robust atomic resolution model that reveals the structural basis for assembly by donor strand complementation and for the architecture of capped surface fibers.     

GST pull-down联合质谱筛选（肌）营养不良短小蛋白结合蛋白1在小鼠睾丸组织中的相互作用蛋白质

（肌）营养不良短小蛋白结合蛋白1（dystrobrevin binding protein 1,dysbindin-1）是溶酶体相关细胞器生物发生复合体-1(biogenesis of lysosome related organelles complex 1, BLOC-1)的1个亚基,在多种组织细胞中广泛表达;然而,其在睾丸组织中的作用至今尚不明确。为寻找（肌）营养不良短小蛋白结合蛋白1在睾丸组织中的相互作用蛋白质,以进一步研究（肌）营养不良短小蛋白结合蛋白1在睾丸中的作用,本研究首先在Rosetta(DE3)菌种中表达可溶性GST-dysbindin-1融合蛋白,经谷胱甘肽 琼脂糖珠亲和纯化后,与小鼠的睾丸组织蛋白质孵育进行GST pull-down实验,并通过液相色谱串联质谱（LC MS/MS）分析筛选（肌）营养不良短小蛋白结合蛋白1在睾丸组织中的相互作用蛋白质。利用BioGPS数据库聚类在睾丸组织中高表达和特异性表达的互作蛋白质,运用DAVID6.8在线分析工具从细胞组分、分子功能、生物学过程和KEGG通路等方面对筛选出的互作蛋白质进行GO（gene ontology）富集分析。本实验共筛选出108个（肌）营养不良短小蛋白结合蛋白1在睾丸组织中的潜在互作蛋白质,其中98个为尚未报道的（肌）营养不良短小蛋白结合蛋白1相互作用蛋白质,7个为睾丸高表达蛋白质,5个为睾丸特异性表达的蛋白质。这些候选蛋白质主要分布在细胞质、细胞核、细胞膜、细胞外泌体等细胞组分中,通过与蛋白质、核酸等分子结合参与蛋白质翻译和转运、囊泡运输及凋亡等生物学过程以及氨基酸生物合成、溶酶体及蛋白酶体等生物学通路。我们推测,在睾丸组织中（肌）营养不良短小蛋白结合蛋白1可能通过与多种蛋白质相互作用参与精子的发生和受精等过程。     

Multiple binding of type 3 streptococcal M protein to human fibrinogen, albumin and fibronectin

Abstract M proteins are major virulence factors of group A streptococci which enable the bacteria to resist phagocytic attack. Their binding capacity for different plasma proteins seems to be one reason for the antiphagocytic activity of M protein. In the present study we demonstrate that M3 protein, isolated from the streptococcal culture supernatant of strain 4/55, and the recombinant form (rM3), purified from an E. coli lysate after cloning in phage γ-EMBL3, show a multiple binding to fibrinogen, albumin and fibronectin in Western blot and dot binding assays. Binding of M3 protein to the multifunctional extracellular matrix and plasma protein fibronectin may not only influence phagocytosis but may also contribute to the adherence of these bacteria to endothelial and epithelial cells.     

RNA结合蛋白在多能干细胞命运转变中的研究进展

RNA结合蛋白(RNA binding proteins,RBPs)是一类通过其RNA结合结构域与RNA相互作用的蛋白质,在细胞内发挥着非常重要的作用。RBPs参与从RNA代谢(包括RNA的可变剪接、稳定性、翻译)到表观遗传修饰等多种调控途径。已有大量文献报道转录因子、表观遗传修饰和细胞外信号通路参与调控干细胞的多能性维持、分化和体细胞重编程,但对于RBPs在细胞命运转变中作用的研究报道甚少。该文主要综述了RBPs通过调控RNA的可变剪接、mRNA稳定性、翻译水平、microRNA代谢及组蛋白修饰进而调控干细胞多能性维持和体细胞重编程。     

Surface proteins of gram-positive bacteria and mechanisms of their targeting to the cell wall envelope.

The cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialized binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections. In this review we describe the mechanisms for both sorting and targeting of proteins to the envelope of gram-positive bacteria and review the functions of known surface proteins.     

Surface Proteins of Gram-Positive Bacteria and Mechanisms of Their Targeting to the Cell Wall Envelope

The cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialized binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections. In this review we describe the mechanisms for both sorting and targeting of proteins to the envelope of gram-positive bacteria and review the functions of known surface proteins.     

Modeling of the structure of the Haemophilus influenzae heme-binding protein suggests a mode of heme interaction.

The structure and function of the periplasmic heme-binding protein HbpA of Haemophilus influenzae were investigated. This protein is involved in the import of heme into the bacteria through the inner membrane, and thus is a key element of the organism's ability to survive in blood. A high degree of sequence similarity between HbpA and the dipeptide-binding protein of Escherichia coli is suggested to be the result of a functional relationship. An HbpA model built using the dipeptide-binding protein suggests a mode of heme binding that is distinct from those known in proteins of the human host. These results provide a starting point for rational drug design.     

Two distinct oxysterol binding protein-related proteins in the parasitic protist Cryptosporidium parvum (Apicomplexa)

Two distinct oxysterol binding protein (OSBP)-related proteins (ORPs) have been identified from the parasitic protist Cryptosporidium parvum (CpORP1 and CpORP2). The short-type CpOPR1 contains only a ligand binding (LB) domain, while the long-type CpORP2 contains Pleckstrin homology (PH) and LB domains. Lipid-protein overlay assays using recombinant proteins revealed that CpORP1 and CpORP2 could specifically bind to phosphatidic acid (PA), various phosphatidylinositol phosphates (PIPs), and sulfatide, but not to other types of lipids with simple heads. Cholesterol was not a ligand for these two proteins. CpOPR1 was found mainly on the parasitophorous vacuole membrane (PVM), suggesting that CpORP1 is probably involved in the lipid transport across this unique membrane barrier between parasites and host intestinal lumen. Although Cryptosporidium has two ORPs, other apicomplexans including Plasmodium, Toxoplasma, and Eimeria possess only a single long-type ORP, suggesting that this family of proteins may play different roles among apicomplexans.     

Identification and functional characterization of the bile acid transport proteins in non-mammalian ileum and mammalian liver

It has been proposed that intracellular carrier proteins mediate active transport of the bile acids within hepatocytes and ileocytes, during the enterohepatic circulation. In mammalian species only ileal bile acid binding proteins have been so far identified, while liver cytosolic carriers have never been found. On the contrary, in non-mammalian vertebrates, only liver, and not ileal, bile acid binding proteins were reported. The aim of the present work is to find the missing cytosolic transport proteins. A bioinformatic search allowed us to identify a non-mammalian putative bile acid binding protein in the chicken ileum (cI-BABP), which we recombinantly expressed and purified. The protein exhibits the capability, tested by in vitro NMR experiments, of binding bile acids. Furthermore, strong NMR evidence reported that the human liver fatty acid binding protein (hL-FABP) can also bind bile acids. Taken together, these data strongly suggest that both cI-BABP and hL-FABP have a bile acid binding function in the two organisms, and support a previous hypothesis on the role of hL-FABP in regulating bile acid metabolism and determining bile acid pool size.