Comparative genomic and phylogenetic analysis of vitellogenin and other large lipid transfer proteins in metazoans

Vitellogenins and other large lipid transfer proteins (LLTP) are well known to play significant roles in the development, metabolism and reproduction of animals. Comparative genomics and phylogenetic analyses of LLTPs using the most comprehensive dataset in metazoans to date are carried out. Our analyses demonstrate that LLTP genes arose significantly earlier, and are more widespread than previously proposed - being present in numerous additional bilaterian and non-bilaterian lineages. A hypothesis is advanced that the most ancestral animal LLTP gene is Vtg, while loss of domains occurred at the bilaterians stem giving rise to apolipoprotein and microsomal triglyceride transfer proteins genes.     

Circulatory lipid transport: lipoprotein assembly and function from an evolutionary perspective

Circulatory transport of neutral lipids (fat) in animals relies on members of the large lipid transfer protein (LLTP) superfamily, including mammalian apolipoprotein B (apoB) and insect apolipophorin II/I (apoLp-II/I). Latter proteins, which constitute the structural basis for the assembly of various lipoproteins, acquire lipids through microsomal triglyceride transfer protein (MTP)—another LLTP family member—and bind them by means of amphipathic structures. Comparative research reveals that LLTPs have evolved from the earliest animals and additionally highlights the structural and functional adaptations in these lipid carriers. For instance, in contrast to mammalian apoB, the insect apoB homologue, apoLp-II/I, is post-translationally cleaved by a furin, resulting in their appearance of two non-exchangeable apolipoproteins in the insect low-density lipoprotein (LDL) homologue, high-density lipophorin (HDLp). An important difference between mammalian and insect lipoproteins relates to the mechanism of lipid delivery. Whereas in mammals, endocytic uptake of lipoprotein particles, mediated via members of the LDL receptor (LDLR) family, results in their degradation in lysosomes, the insect HDLp was shown to act as a reusable lipid shuttle which is capable of reloading lipid. Although the recent identification of a lipophorin receptor (LpR), a homologue of LDLR, reveals that endocytic uptake of HDLp may constitute an additional mechanism of lipid delivery, the endocytosed lipoprotein appears to be recycled in a transferrin-like manner. Binding studies indicate that the HDLp–LpR complex, in contrast to the LDL–LDLR complex, is resistant to dissociation at endosomal pH as well as by treatment with EDTA mimicking the drop in Ca²⁺ concentration in the endosome. This remarkable stability of the ligand–receptor complex may provide a crucial key to the recycling mechanism. Based on the binding and dissociation capacities of mutant and hybrid receptors, the specific binding interaction of the ligand-binding domain of the receptor with HDLp was characterized. These structural similarities and functional adaptations of the lipid transport systems operative in mammals and insects are discussed from an evolutionary perspective.     

Apolipophorin II/I, Apolipoprotein B, Vitellogenin, and Microsomal Triglyceride Transfer Protein Genes Are Derived from a Common Ancestor

Large lipid transfer proteins (LLTP) are nonexchangeable apolipoproteins and intracellular lipid-exchange proteins involved in the assembly, secretion, and metabolism of lipoproteins. We have identified contiguous conserved sequence motifs in alignments of insect apolipophorin II/I precursor (apoLp-II/I), human apolipoprotein B (apoB), invertebrate and vertebrate vitellogenins (VTG), and the large subunit of mammalian microsomal triglyceride transfer protein (MTP). Conserved motifs present in the N-terminal part of nonexchangeable apolipoproteins encompass almost completely the large subunit of MTP, suggesting a derivation from a common ancestral functional unit, termed large lipid transfer (LLT) module. Divergence of LLTP from a common ancestor is supported by (1) the statistical significance of the combined match scores obtained after motif-based database searches, (2) the presence of several identical amino acid residues in all LLTP sequences currently available, (3) the conservation of hydrophobic clusters in an α-helical domain, (4) the phylogenetic analysis of the conserved sequences related to the von Willebrand factor D (VWD) module identified in nonexchangeable apolipoproteins, and (5) the presence of four and one ancestral exon boundaries in the LLT and VWD modules, respectively. Our data indicate that the genes coding for apoLp-II/I, apoB, VTG, and the MTP large subunit are members of the same multigene superfamily. LLTP have emerged from an ancestral molecule designed to ensure a pivotal event in the intracellular and extracellular transfer of lipids and liposoluble substances. Received: 8 June 1998 / Accepted: 15 February 1999     

Microsomal triglyceride transfer protein promotes the secretion of Xenopus laevis vitellogenin A1

Vitellogenins (Vtg) are ancient lipid transport and storage proteins and members of the large lipid transfer protein (LLTP) gene family, which includes insect apolipophorin II/I, apolipoprotein B (apoB), and the microsomal triglyceride transfer protein (MTP). Lipidation of Vtg occurs at its site of synthesis in vertebrate liver, insect fat body, and nematode intestine; however, the mechanism of Vtg lipid acquisition is unknown. To explore whether Vtg biogenesis requires the apoB cofactor and LLTP family member, MTP, Vtg was expressed in COS cells with and without coexpression of the 97-kDa subunit of human MTP. Expression of Vtg alone gave rise to a approximately 220-kDa apoprotein, which was predominantly confined to an intracellular location. Coexpression of Vtg with human MTP enhanced Vtg secretion by 5-fold, without dramatically affecting its intracellular stability. A comparison of wild type and a triglyceride transfer-defective form of MTP revealed that both were capable of promoting Vtg secretion, whereas only wild type MTP could promote the secretion of apoB41 (amino-terminal 41% of apoB). These studies demonstrate that the biogenesis of Vtg is MTP-dependent and that MTP is the likely ancestral member of the LLTP gene family.     

Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering

The protein universe can be organized in families that group proteins sharing common ancestry. Such families display variable levels of structural and functional divergence, from homogenous families, where all members have the same function and very similar structure, to very divergent families, where large variations in function and structure are observed. For practical purposes of structure and function prediction, it would be beneficial to identify sub-groups of proteins with highly similar structures (iso-structural) and/or functions (iso-functional) within divergent protein families. We compared three algorithms in their ability to cluster large protein families and discuss whether any of these methods could reliably identify such iso-structural or iso-functional groups. We show that clustering using profile-sequence and profile-profile comparison methods closely reproduces clusters based on similarities between 3D structures or clusters of proteins with similar biological functions. In contrast, the still commonly used sequence-based methods with fixed thresholds result in vast overestimates of structural and functional diversity in protein families. As a result, these methods also overestimate the number of protein structures that have to be determined to fully characterize structural space of such families. The fact that one can build reliable models based on apparently distantly related templates is crucial for extracting maximal amount of information from new sequencing projects.     

Apolipophorin III: role model apolipoprotein

It has been one-quarter century since the identification of apolipophorin III (apoLp-III) as an important component of insect hemolymph lipid transport processes. Original studies of flight-related lipid transport that led to the discovery of apoLp-III have been followed by detailed studies of its structure and function relations, species distribution as well as its physiological roles beyond lipid transport. The non-exchangeable apoLp-I and -II, which are derived from a common precursor, are structural protein components of the multifunctional lipophorin particle. ApoLp-I/II have been identified as members of a broad lipid-binding protein family based on sequence similarities with their vertebrate counterparts. By contrast, apoLp-III can be found as a lipid-free hemolymph protein that associates with lipophorin during hormone-induced lipid mobilization. Based on structural characterization, apoLp-III belongs to a large family of exchangeable apolipoproteins characterized by segments of amphipathic alpha-helix. The remarkable structural adaptability of apoLp-III can be ascribed to its globular amphipathic alpha-helix bundle conformation wherein hydrophobic lipid-binding regions are stabilized in the absence of lipid by helix-helix interactions. Upon exposure to potential lipid surface-binding sites, the globular helix bundle opens to expose its hydrophobic interior permitting substitution of helix-helix contact in the bundle for helix-lipid interactions. Novel functions of apoLp-III beyond lipid transport have been identified recently. The expanding role of apoLp-III in innate immunity promises to offer exciting research opportunities in the future.     

Fatty Acid- and Retinoid-binding Proteins Have Distinct Binding Pockets for the Two Types of Cargo

Parasitic nematodes cause serious diseases in humans, animals, and plants. They have limited lipid metabolism and are reliant on lipid-binding proteins to acquire these metabolites from their hosts. Several structurally novel families of lipid-binding proteins in nematodes have been described, including the fatty acid- and retinoid-binding protein family (FAR). In Caenorhabditis elegans, used as a model for studying parasitic nematodes, eight C. elegans FAR proteins have been described. The crystal structure of C. elegans FAR-7 is the first structure of a FAR protein, and it exhibits a novel fold. It differs radically from the mammalian fatty acid-binding proteins and has two ligand binding pockets joined by a surface groove. The first can accommodate the aliphatic chain of fatty acids, whereas the second can accommodate the bulkier retinoids. In addition to demonstrating lipid binding by fluorescence spectroscopy, we present evidence that retinol binding is positively regulated by casein kinase II phosphorylation at a conserved site near the bottom of the second pocket. far-7::GFP (green fluorescent protein) expression shows that it is localized in the head hypodermal syncytia and the excretory cell but that this localization changes under starvation conditions. In conclusion, our study provides the basic structural and functional information for investigation of inhibitors of lipid binding by FAR proteins.     

OsLTP47 may function in a lipid transfer relay essential for pollen wall development in rice

In plants, lipid transfer proteins(LTPs) transport pollen wall constituents from the tapetum to the exine, a process essential for pollen wall development. However, the functional cooperation of different LTPs in pollen wall development is not well understood. In this study, we have identified and characterized a grassspecific LTP gene, Os LTP47, an important regulator of pollen wall formation in rice(Oryza sativa). Os LTP47 encodes a membrane-localized LTP and in vitro lipid-binding assays conf...     

Apolipocrustacein,formerly vitellogenin,is the major egg yolk precursor protein in decapod crustaceans and is homologous to insect apolipophorin II/I and vertebrate apolipoprotein B

Background  

In animals, the biogenesis of some lipoprotein classes requires members of the ancient large lipid transfer protein (LLTP) superfamily, including the cytosolic large subunit of microsomal triglyceride transfer protein (MTP), vertebrate apolipoprotein B (apoB), vitellogenin (Vtg), and insect apolipophorin II/I precursor (apoLp-II/I). In most oviparous species, Vtg, a large glycolipoprotein, is the main egg yolk precursor protein.     

Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis

A classification scheme for membrane proteins is proposed that clusters families of proteins into structural classes based on hydropathy profile analysis. The averaged hydropathy profiles of protein families are taken as fingerprints of the 3D structure of the proteins and, therefore, are able to detect more distant evolutionary relationships than amino acid sequences. A procedure was developed in which hydropathy profile analysis is used initially as a filter in a BLAST search of the NCBI protein database. The strength of the procedure is demonstrated by the classification of 29 families of secondary transporters into a single structural class, termed ST[3]. An exhaustive search of the database revealed that the 29 families contain 568 unique sequences. The proteins are predominantly from prokaryotic origin and most of the characterized transporters in ST[3] transport organic and inorganic anions and a smaller number are Na(+)/H(+) antiporters. All modes of energy coupling (symport, antiport, uniport) are found in structural class ST[3]. The relevance of the classification for structure/function prediction of uncharacterised transporters in the class is discussed.     

Crystal structure of the 30 K protein from the silkworm Bombyx mori reveals a new member of the β-trefoil superfamily

The hemolymph of the fifth instar larvae of the silkworm Bombyx mori contains a group of homologous proteins with a molecular weight of approximately 30 kDa, termed B. mori low molecular weight lipoproteins (Bmlps), which account for about 5% of the total plasma proteins. These so-called "30 K proteins" have been reported to be involved in the innate immune response and transportation of lipid and/or sugar. To elucidate their molecular functions, we determined the crystal structure of a 30 K protein, Bmlp7, at 1.91?. It has two distinct domains: an all-α N-terminal domain (NTD) and an all-β C-terminal domain (CTD) of the β-trefoil fold. Comparative structural analysis indicates that Bmlp7 represents a new family, adding to the 14 families currently identified, of the β-trefoil superfamily. Structural comparison and simulation suggest that the NTD has a putative lipid-binding cavity, whereas the CTD has a potential sugar-binding site. However, we were unable to detect the binding of either lipid or sugar. Therefore, further investigations are needed to characterize the molecular function of this protein.     

Electrostatically driven lipid–protein interaction: Answers from FRET

Electrostatics govern the association of a large number of proteins with cellular membranes. In some cases, these proteins present specialized lipid-binding modules or membrane targeting domains while in other cases association is achieved through nonspecific interaction of unstructured clusters of basic residues with negatively charged lipids. Given its spatial resolution in the nanometer range, Förster resonance energy transfer (FRET) is a powerful tool to give insight into protein–lipid interactions and provide molecular level information which is difficult to retrieve with other spectroscopic techniques.In this review we present and discuss the basic formalisms of both hetero- and homo-FRET pertinent to the most commonly encountered problems in lipid–protein interaction studies and highlight some examples of implementations of different FRET methodologies to characterize lipid/protein systems in which electrostatic interactions play a crucial role. This article is part of a Special Issue entitled: Lipid–protein interactions.     

SURF’s UP! — Protein classification by surface comparisons

Large-scale genome sequencing and structural genomics projects generate numerous sequences and structures for 'hypothetical' proteins without functional characterizations. Detection of homology to experimentally characterized proteins can provide functional clues, but the accuracy of homology-based predictions is limited by the paucity of tools for quantitative comparison of diverging residues responsible for the functional divergence. SURF'S UP! is a web server for analysis of functional relationships in protein families, as inferred from protein surface maps comparison according to the algorithm. It assigns a numerical score to the similarity between patterns of physicochemical features(charge, hydrophobicity) on compared protein surfaces. It allows recognizing clusters of proteins that have similar surfaces, hence presumably similar functions. The server takes as an input a set of protein coordinates and returns files with "spherical coordinates" of proteins in a PDB format and their graphical presentation, a matrix with values of mutual similarities between the surfaces, and the unrooted tree that represents the clustering of similar surfaces, calculated by the neighbor-joining method. SURF'S UP! facilitates the comparative analysis of physicochemical features of the surface, which are the key determinants of the protein function. By concentrating on coarse surface features, SURF'S UP! can work with models obtained from comparative modelling. Although it is designed to analyse the conservation among homologs, it can also be used to compare surfaces of non-homologous proteins with different three-dimensional folds, as long as a functionally meaningful structural superposition is supplied by the user. Another valuable characteristic of our method is the lack of initial assumptions about the functional features to be compared. SURF'S UP! is freely available for academic researchers at http://asia.genesilico.pl/surfs_up/.     

Glycolipid transfer proteins

Glycolipid transfer proteins (GLTPs) are small (24 kDa), soluble, ubiquitous proteins characterized by their ability to accelerate the intermembrane transfer of glycolipids in vitro. GLTP specificity encompasses both sphingoid- and glycerol-based glycolipids, but with a strict requirement that the initial sugar residue be beta-linked to the hydrophobic lipid backbone. The 3D architecture of GLTP reveals liganded structures with unique lipid-binding modes. The biochemical properties of GLTP action at the membrane surface have been studied rather comprehensively, but the biological role of GLTP remains enigmatic. What is clear is that GLTP differs distinctly from other known glycolipid-binding proteins, such as nonspecific lipid transfer proteins, lysosomal sphingolipid activator proteins, lectins, lung surfactant proteins as well as other lipid-binding/transfer proteins. Based on the unique conformational architecture that targets GLTP to membranes and enables glycolipid binding, GLTP is now considered the prototypical and founding member of a new protein superfamily in eukaryotes.     

Evolution of the family of intracellular lipid binding proteins in vertebrates

Members of the family of intracellular lipid binding proteins (iLBPs) have been implicated in cytoplasmic transport of lipophilic ligands, such as long-chain fatty acids and retinoids. iLBPs are low molecular mass proteins (14–16 kDa) sharing a common structural fold. The iLBP family likely arose through duplication and diversification of an ancestral iLBP gene. Phylogenetic analysis undertaken in the present study indicates that the ancestral iLBP gene arose after divergence of animals from fungi and plants. The first gene duplication was dated around 930 millions of years ago, and subsequent duplications in the succeeding 550 millions of years gave rise to the 16 iLBP types currently recognized in vertebrates. Four clusters of proteins, each binding a characteristic range of ligands, are evident from the phylogenetic tree. Evolution of different binding properties probably allowed cytoplasmic trafficking of distinct ligands. It is speculated that recruitment of an iLBP during evolution of animals enabled the mitochondrial oxidation of long-chain fatty acids.     

A mechanism of membrane neutral lipid acquisition by the microsomal triglyceride transfer protein

The microsomal triglyceride transfer protein (MTP) and apolipoprotein B (apoB) belong to the vitellogenin (VTG) family of lipid transfer proteins. MTP is essential for the intracellular assembly and secretion of apoB-containing lipoproteins, the key intravascular lipid transport proteins in vertebrates. We report the predicted three-dimensional structure of the C-terminal lipid binding cavity of MTP, modeled on the crystal structure of the lamprey VTG gene product, lipovitellin. The cavity in MTP resembles those found in the intracellular lipid-binding proteins and bactericidal/permeability-increasing protein. Two conserved helices, designated A and B, at the entrance to the MTP cavity mediate lipid acquisition and binding. Helix A (amino acids 725-736) interacts with membranes in a manner similar to viral fusion peptides. Mutation of helix A blocks the interaction of MTP with phospholipid vesicles containing triglyceride and impairs triglyceride binding. Mutations of helix B (amino acids 781-786) and of N780Y, which causes abetalipoproteinemia, have no impact on the interaction of MTP with phospholipid vesicles but impair triglyceride binding. We propose that insertion of helix A into lipid membranes is necessary for the acquisition of neutral lipids and that helix B is required for their transfer to the lipid binding cavity of MTP.     

Functional assignment to JEV proteins using SVM

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).     

A vertebrate model for the study of lipid binding/transfer protein function: Conservation of OSBP-related proteins between zebrafish and human

Oxysterol-binding protein (OSBP) and OSBP-related (ORP) or OSBP-like (OSBPL) proteins constitute a family of lipid-binding/transfer proteins (LTPs) present in eukaryotes from yeast to man. The mechanisms of ORP function have remained incompletely understood. However, several ORPs are present at membrane contact sites and act as either lipid transporters or sensors that control lipid metabolism, cell signaling, and vesicle transport. Zebrafish, Danio rerio, has gained increasing popularity as a model organism in developmental biology, human disease, toxicology, and drug discovery. However, LTPs in the fish are thus far unexplored. In this article we report a series of bioinformatic analyses showing that the OSBPL gene family is highly conserved between the fish and human. The OSBPL subfamily structure is markedly similar between the two organisms, and all 12 human genes have orthologs, designated osbpl and located on 11 chromosomes in D. rerio. Interestingly, osbpl2 and osbpl3 are present as two closely related homologs (a and b), due to gene duplication events in the teleost lineage. Moreover, the domain structures of the distinct ORP proteins are almost identical between zebrafish and man, and molecular modeling in the present study suggests that ORD liganding by phosphatidylinositol-4-phosphate (PI4P) is a feature conserved between yeast Osh3p, human ORP3, and zebrafish Osbpl3. The present analysis identifies D. rerio as an attractive model to study the functions of ORPs in vertebrate development and metabolism.     

Nonvesicular sterol movement from plasma membrane to ER requires oxysterol-binding protein-related proteins and phosphoinositides

Sterols are moved between cellular membranes by nonvesicular pathways whose functions are poorly understood. In yeast, one such pathway transfers sterols from the plasma membrane (PM) to the endoplasmic reticulum (ER). We show that this transport requires oxysterol-binding protein (OSBP)-related proteins (ORPs), which are a large family of conserved lipid-binding proteins. We demonstrate that a representative member of this family, Osh4p/Kes1p, specifically facilitates the nonvesicular transfer of cholesterol and ergosterol between membranes in vitro. In addition, Osh4p transfers sterols more rapidly between membranes containing phosphoinositides (PIPs), suggesting that PIPs regulate sterol transport by ORPs. We confirmed this by showing that PM to ER sterol transport slows dramatically in mutants with conditional defects in PIP biosynthesis. Our findings argue that ORPs move sterols among cellular compartments and that sterol transport and intracellular distribution are regulated by PIPs.     

Scavenging of superoxide anion radical by chaparral

Plant cells contain lipid-transfer proteins (LTPs) able to transfer phospholipids between membranes in vitro. Plant LTPs share in common structural and functional features. Recent structural studies carried out by NMR and X-ray crystallography on an LTP isolated from maize seeds have showed that this protein involves four helices packed against a C-terminal region and stabilized by four disulfide bridges. A most striking feature of this structure is the existence of an internal hydrophobic cavity running through the whole molecule and able to accomodate acyl chains. It was thus of interest to study the ability of maize LTP to bind hydrophobic ligands such as acyl chains or lysophosphatidylcholine and to determine the effect of this binding on phospholipid transfer. The binding abilities of maize LTP, presented in this paper, are discussed and compared to those of lipid-binding proteins from animal tissues.