Complete cDNA sequence of chicken vigilin, a novel protein with amplified and evolutionary conserved domains

The high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease

The high-density lipoprotein binding protein (HDLBP) is the human member of an evolutionarily conserved family of RNA-binding proteins, the vigilin protein family. These proteins are characterized by 14 or 15 RNA-interacting KH (heterologous nuclear ribonucleoprotein K homology) domains. While mainly present at the cytoplasmic face of the endoplasmic reticulum, HDLBP and its homologs are also found in the cytosol and nucleus. HDLBP is involved in various processes, including translation, chromosome segregation, cholesterol transport and carcinogenesis. Especially, its association with the latter two has attracted specific interest in the HDLBP's molecular role. In this review, we give an overview of some of the functions of the protein as well as introduce its impact on different kinds of cancer, its connection to lipid metabolism and its role in viral infection. We also aim at addressing the possible use of HDLBP as a drug target or biomarker and discuss its future implications.

A jack of all trades: the RNA-binding protein vigilin

The vigilin family of proteins is evolutionarily conserved from yeast to humans and characterized by the proteins' 14 or 15 hnRNP K homology (KH) domains, typically associated with RNA-binding. Vigilin is the largest RNA-binding protein (RBP) in the KH domain-containing family and one of the largest RBP known to date. Since its identification 30 years ago, vigilin has been shown to bind over 700 mRNAs and has been associated with cancer progression and cardiovascular disease. We provide a brief historic overview of vigilin research and outline the proteins' different functions, focusing on maintenance of genome ploidy, heterochromatin formation, RNA export, as well as regulation of translation, mRNA transport, and mRNA stability. The multitude of associated functions is reflected by the large number of identified interaction partners, ranging from tRNAs, mRNAs, ribosomes and ribosome-associated proteins, to histone methyltransferases and DNA-dependent protein kinases. Most of these partners bind to vigilin's carboxyterminus, and the two most C-terminal KH domains of the protein, KH13 and KH14, represent the main mRNA-binding interface. Since the nuclear functions of vigilins in particular are not conserved, we outline a model for the basal functions of vigilins, as well as those which were acquired during the transition from unicellular organisms to metazoa. WIREs RNA 2017, 8:e1448. doi: 10.1002/wrna.1448 For further resources related to this article, please visit the WIREs website.

Vigilin Regulates the Expression of the Stress-Induced Ligand MICB by Interacting with Its 5' Untranslated Region

NK cells are part of the innate immune system, and are able to identify and kill hazardous cells. The discrimination between normal and hazardous cells is possible due to an array of inhibitory and activating receptors. NKG2D is one of the prominent activating receptors expressed by all human NK cells. This receptor binds stress-induced ligands, including human MICA, MICB, and UL16-binding proteins 1-6. The interaction between NKG2D and its ligands facilitates the elimination of cells under cellular stress, such as tumor transformation. However, the mechanisms regulating the expression of these ligands are still not well understood. Under normal conditions, the NKG2D ligands were shown to be posttranscriptionally regulated by cellular microRNAs and RNA-binding proteins (RBPs). Thus far, only the 3' untranslated regions (UTRs) of MICA, MICB, and UL16-binding protein 2 were shown to be regulated by RBPs and microRNAs, usually resulting in their downregulation. In this study we investigated whether MICB expression is controlled by RBPs through its 5'UTR. We used an RNA pull-down assay followed by mass spectrometry and identified vigilin, a ubiquitously expressed multifunctional RNA-binding protein. We demonstrated that vigilin binds and negatively regulates MICB expression through its 5'UTR. Additionally, vigilin downregulation in target cells led to a significant increase in NK cell activation against said target cells. Taken together, we have discovered a novel mode of MICB regulation.

The RNA-binding protein vigilin regulates VLDL secretion through modulation of Apob mRNA translation

The liver is essential for the synthesis of plasma proteins and integration of lipid metabolism. While the role of transcriptional networks in these processes is increasingly understood, less is known about post-transcriptional control of gene expression by RNA-binding proteins (RBPs). Here, we show that the RBP vigilin is upregulated in livers of obese mice and in patients with fatty liver disease. By using in vivo, biochemical and genomic approaches, we demonstrate that vigilin controls very-low-density lipoprotein (VLDL) secretion through the modulation of apolipoproteinB/Apob mRNA translation. Crosslinking studies reveal that vigilin binds to CU-rich regions in the mRNA coding sequence of Apob and other proatherogenic secreted proteins, including apolipoproteinC-III/Apoc3 and fibronectin/Fn1. Consequently, hepatic vigilin knockdown decreases VLDL/low-density lipoprotein (LDL) levels and formation of atherosclerotic plaques in Ldlr^−/− mice. These studies uncover a role for vigilin as a key regulator of hepatic Apob translation and demonstrate the therapeutic potential of inhibiting vigilin for cardiovascular diseases.

RNA-binding proteins (RBP) are an emerging group of post-translational regulators. Here the authors show that the RBP vigilin regulates translation of mRNA encoding for proatherogenic proteins—apoB, apoC-III and fibronectin—representing a potential therapeutic target in cardiovascular diseases.

Investigation of effect of 17α-ethinylestradiol on vigilin expression using an isolated recombinant antibody

Vigilin, a highly conserved protein from yeast to mammals, is a multifunctional protein in eukaryotic organisms. One biological function of vigilin is to stabilize the expression level of vitellogenin (VTG). This study aimed to develop vigilin as a new estrogen-inducible biomarker that correlates with the widely applied estrogen-inducible biomarker VTG and expand the ability to detect it in various species. Here, a recombinant monoclonal antibody with high specificity against the conserved C-terminal region of vigilin from zebrafish (Danio rerio) was successfully isolated from a phage display antibody library and found to recognize vigilin proteins from multiple vertebrate species. The effect of 17α-ethinylestradiol (EE2) on vigilin expression in the liver of zebrafish and juvenile crucian carp (Carassius auratus) was investigated. Although vigilin mRNA was expressed in all tissues analyzed from male zebrafish, vigilin protein was detected exclusively in the testis of male zebrafish, as well as the liver of female zebrafish and juvenile crucian carp at a lower level without exposure to EE2. Significant induction of vigilin mRNA by exposure to EE2 was observed in the liver and testis of male zebrafish, even at a low dose of 6.25 ng/L (21.09 pmol/L). In Hela cells, the expression of vigilin coincided with high protein synthesis activity but not dose-dependently by EE2 exposure. Therefore, the recombinant antibody may be used as a detection tool to screen for mammalian cell lines or organs with estrogen-inducible expression of vigilin.

The N-terminus of FILIA forms an atypical KH domain with a unique extension involved in interaction with RNA

FILIA is a member of the recently identified oocyte/embryo expressed gene family in eutherian mammals, which is characterized by containing an N-terminal atypical KH domain. Here we report the structure of the N-terminal fragment of FILIA (FILIA-N), which represents the first reported three-dimensional structure of a KH domain in the oocyte/embryo expressed gene family of proteins. The structure of FILIA-N revealed a unique N-terminal extension beyond the canonical KH region, which plays important roles in interaction with RNA. By co-incubation with the lysates of mice ovaries, FILIA and FILIA-N could sequester specific RNA components, supporting the critical roles of FILIA in regulation of RNA transcripts during mouse oogenesis and early embryogenesis.

Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles

Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins. The complexity and diversity associated with the hnRNPs render them multifunctional, involved not only in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs, but also acting as trans-factors in regulating gene expression. Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1), a subgroup of hnRNPs, is a KH-triple repeat containing RNA-binding protein. It is encoded by an intronless gene arising from hnRNP E2 through a retrotransposition event. hnRNP E1 is ubiquitously expressed and functions in regulating major steps of gene expression, including pre-mRNA processing, mRNA stability, and translation. Given its wide-ranging functions in the nucleus and cytoplasm and interaction with multiple proteins, we propose a post-transcriptional regulon model that explains hnRNP E1's widespread functional diversity.

Vgl1, a multi-KH domain protein, is a novel component of the fission yeast stress granules required for cell survival under thermal stress

Multiple KH-domain proteins, collectively known as vigilins, are evolutionarily highly conserved proteins that are present in eukaryotic organisms from yeast to metazoa. Proposed roles for vigilins include chromosome segregation, messenger RNA (mRNA) metabolism, translation and tRNA transport. As a step toward understanding its biological function, we have identified the fission yeast vigilin, designated Vgl1, and have investigated its role in cellular response to environmental stress. Unlike its counterpart in Saccharomyces cerevisiae, we found no indication that Vgl1 is required for the maintenance of cell ploidy in Schizosaccharomyces pombe. Instead, Vgl1 is required for cell survival under thermal stress, and vgl1Δ mutants lose their viability more rapidly than wild-type cells when incubated at high temperature. As for Scp160 in S. cerevisiae, Vgl1 bound polysomes accumulated at endoplasmic reticulum (ER) but in a microtubule-independent manner. Under thermal stress, Vgl1 is rapidly relocalized from the ER to cytoplasmic foci that are distinct from P-bodies but contain stress granule markers such as poly(A)-binding protein and components of the translation initiation factor eIF3. Together, these observations demonstrated in S. pombe the presence of RNA granules with similar composition as mammalian stress granules and identified Vgl1 as a novel component that required for cell survival under thermal stress.

K homology domains of the mouse polycystic kidney disease-related protein, Bicaudal-C (Bicc1), mediate RNA binding in vitro

BACKGROUND/AIMS

The mouse Bicc1(mBicc1) gene is the orthologue of the DrosophilaBicaudal-C(Bic-C) gene. While the role of Bicc1 in the mouse is unknown, mutations in the mouse Bicc1 gene are associated with polycystic kidney disease (PKD). The mBicc1 protein contains three K homology (KH) domains. Evidence from other KH domain-containing proteins as well as studies involving both Drosophila and Xenopus Bic-C, suggest that this motif is important in interactions with RNA.

METHODS

RNA-binding assays were used to test whether mouse Bicc1 binds homoribopolymers in vitro. A series of constructs coding for different regions of the mBicc1 protein were used to determine which regions of the mBicc1 protein were important for in vitro RNA binding.

RESULTS

Mouse Bicc1 binds homoribopolymers in vitro and the third KH domain is necessary and sufficient for in vitro RNA binding. The mutation responsible for PKD in the jcpk mouse model results in a protein that is incapable of binding RNA in vitro.

CONCLUSIONS

This study demonstrates that mouse Bicc1, a protein associated with PKD, has the ability to bind RNA in vitro. Disruption of this binding capability may be responsible for cyst formation in animals carrying mutations in the mBicc1 gene.

Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160

The K homology (KH) domain is a remarkably versatile and highly conserved RNA-binding motif. Classical KH domains include a characteristic pattern of hydrophobic residues, a Gly-X-X-Gly (GXXG) segment, and a variable loop. KH domains typically occur in clusters, with some retaining their GXXG sequence (conserved), while others do not (diverged). As a first step towards addressing whether GXXG is essential for KH-domain function, we explored the roles of conserved and diverged KH domains in Scp160p, a multiple-KH-domain-containing protein in Saccharomyces cerevisiae. We specifically wanted to know (1) whether diverged KH domains were essential for Scp160p function, and (2) whether diverged KH domains could functionally replace conserved KH domains. To address these questions, we deleted and/or interchanged conserved and diverged KH domains of Scp160p and expressed the mutated alleles in yeast. Our results demonstrated that the answer to each question was yes. Both conserved and diverged KH domains are essential for Scp160p function, and diverged KH domains can function in place of conserved KH domains. These findings challenge the prevailing notions about the requisite features of a KH domain and raise the possibility that there may be more functional KH domains in the proteome than previously appreciated.

The multi-KH domain protein of Saccharomyces cerevisiae Scp160p contributes to the regulation of telomeric silencing

Multi-KH domain proteins are highly evolutionarily conserved proteins that associate to polyribosomes and participate in RNA metabolism. Recent evidence indicates that multi-KH domain proteins also contribute to the structural organization of heterochromatin both in mammals and Drosophila. Here, we show that the multi-KH domain protein of Saccharomyces cerevisiae, Scp160p, contributes to silencing at telomeres and at the mating-type locus, but not to ribosomal silencing. The contribution of Scp160p to silencing is independent of its binding to the ribosome as deletion of the last two KH domains, which mediate ribosomal binding, has no effect on silencing. Disruption of SCP160 increases cell ploidy but this effect is also independent of the contribution of Scp160p to telomeric silencing as strong relief of silencing is observed in Deltascp160 cells with normal ploidy and, vice versa, Deltascp160 cells with highly increased ploidy show no significant silencing defects. The TPE phenotype of Deltascp160 cells associates to a decreased Sir3p deposition at telomeres and, in good agreement, silencing is rescued by SIR3 overexpression and in a Deltarif1Deltarif2 mutant. Scp160p shows a distinct perinuclear localization that is independent of its ability to bind ribosomes. Moreover, telomere clustering at the nuclear envelope is perturbed in Deltascp160 cells and disruption of the histone deacetylase RPD3, which is known to improve telomere clustering, rescues telomeric silencing in Deltascp160 cells. These results are discussed in the context of a model in which Scp160p contributes to silencing by helping telomere clustering.

Drosophila DDP1, a multi-KH-domain protein, contributes to centromeric silencing and chromosome segregation

BACKGROUND

The Drosophila melanogaster DDP1 protein is a highly evolutionarily conserved protein that is characterised by the presence of 15 tandemly organized KH domains, known for mediating high-affinity binding to single-stranded nucleic acids (RNA and ssDNA). Consistent with its molecular organization, DDP1 binds single-stranded nucleic acids with high affinity, in vitro. It was shown earlier that, in polytene chromosomes, DDP1 is found in association with chromocenter heterochromatin, suggesting a contribution to heterochromatin formation and/or maintenance.

RESULTS

In this paper, the actual contribution of DDP1 to the structural and functional properties of heterochromatin was determined through the analysis of the phenotypes associated with the hypomorphic ddp1(15.1) mutation that was generated through the mobilization of a P element inserted in the second intron of ddp1. ddp1(15.1) behaves as a dominant suppressor of PEV in the variegated rearrangement In(1)w(m4) as well as in several transgenic lines showing variegated expression of a hsp70-white(+) transgene. In polytene chromosomes from homozygous ddp1(15.1) larvae, histone H3-K9 methylation and HP1 deposition at chromocentre heterochromatin are strongly reduced. Our results also show that, when the maternal contribution of DDP1 is reduced, chromosome condensation and segregation are compromised. Moreover, in a ddp1(15.1) mutant background, transmission of the nonessential Dp1187 minichromosome is reduced.

CONCLUSIONS

We conclude that DDP1 contributes to the structural and functional properties of heterochromatin. These results are discussed in the context of current models for the formation and maintenance of heterochromatin; in these models, HP1 deposition depends on H3-K9 methylation that, in turn, requires the contribution of the RNAi pathway.

Vigilin is co-localized with 80S ribosomes and binds to the ribosomal complex through its C-terminal domain

The biological relevance of vigilin a ubiquitous multi (KH)-domain protein is still barely understood. Investigations over the last years, however, provided evidence for a possible involvement of vigilin in the nucleo-cytoplasmic transport of tRNA and in the subsequent association of tRNA with ribosomes. We therefore investigated the potential association of vigilin with 80S ribosomes. Immunostaining, gel filtration, westernblot analysis of polyribosomes and high salt treatment of 80S ribosomes isolated from fresh human placenta were applied to analyze the possible association of vigilin with ribosomes. Overlay assays were performed to examine whether vigilin is capable of binding to ribosomal proteins. Immunostaining of HEp-2 cells, gel filtration of a cytoplasmic extract of HEp-2 cells and westernblot analysis of isolated 80S ribosomes clearly demonstrate that vigilin is bond to the ribosomal complex. Vigilin detaches from the ribosomal complex under the influence of high salt concentrations. We present data that radioactively labeled human vigilin interacts directly with a subset of ribosomal proteins from both subunits. We were able to narrow down the putative binding region to the C-terminal domain by using vigilin mutant constructs. Therefore our results provide strong evidence that vigilin is bond to the ribosomal complex and underline the hypothesis that vigilin might be involved in the link between tRNA-export and the channeled tRNA-cycle on ribosomes.

Both KH and non-KH domain sequences are required for polyribosome association of Scp160p in yeast

Scp160p is a 160 kDa RNA-binding protein in yeast previously demonstrated to associate with specific messages as an mRNP component of both soluble and membrane-bound polyribosomes. Although the vast majority of Scp160p sequence consists of 14 closely spaced KH domains, comparative sequence analyses also demonstrate the presence of a potential nuclear localization sequence located between KH domains 3 and 4, as well as a 110 amino acid non-KH N-terminal region that includes a potential nuclear export sequence (NES). As a step toward investigating the structure/function relationships of Scp160p, we generated two truncated alleles, FLAG.SCP160DeltaN1, encoding a protein product that lacks the first 74 amino acids, including the potential NES, and FLAG.SCP160DeltaC1, encoding a protein product that lacks the final KH domain (KH14). We report here that the N-truncated protein, expressed as a green fluorescent protein fusion in yeast, remains cytoplasmic, with no apparent nuclear accumulation. Biochemical studies further demonstrate that although the N-truncated protein remains competent to form RNPs, the C-truncated protein does not. Furthermore, polyribosome association is severely compromised for both truncated proteins. Perhaps most important, both truncated alleles appear only marginally functional in vivo, as demonstrated by the inability of each to complement scp160/eap1 synthetic lethality in a tester strain. Together, these data challenge the notion that Scp160p normally shuttles between the nucleus and cytoplasm, and further implicate polyribosome association as an essential component of Scp160p function in vivo. Finally, these data underscore the vital roles of both KH and non-KH domain sequences in Scp160p.

Atorvastatin reduces CD68, FABP4, and HBP expression in oxLDL-treated human macrophages

With the aim of identifying new target genes that could contribute to limit foam cell formation, we analyzed changes in the pattern of gene expression in human THP-1 macrophages treated with atorvastatin and oxidized-LDL (oxLDL). To this end, we used a human cDNA array containing 588 cardiovascular-related cDNAs. Exposure to oxLDL resulted in differential expression of 26 genes, while coincubation with atorvastatin modified the expression of 29 genes, compared to treatment with oxLDL alone. Changes in the expression of candidate genes, potentially connected to the atherosclerotic process, were confirmed by quantitative RT-PCR and Western blot. We show that atorvastatin prevents the increase in the expression of scavenger receptor CD68 and that of fatty acid binding protein 4 caused by oxLDL. In addition, atorvastatin reduces the expression of HDL-binding protein, apolipoprotein E, and matrix metalloproteinase 9. These findings are relevant to understand the direct antiatherogenic effects of statins on macrophages.

A subtractive approach to characterize genes with regionalized expression in the gliogenic ventral neuroepithelium: identification of chick Sulfatase 1 as a new oligodendrocyte lineage gene

To address the question of the origin of glial cells and the mechanisms leading to their specification, we have sought to identify novel genes expressed in glial progenitors. We adopted suppression subtractive hybridization (SSH) to establish a chick cDNA library enriched for genes specifically expressed at 6 days of incubation (E6) in the ventral neuroepithelium, a tissue previously shown to contain glial progenitors. Screens were then undertaken to select differentially expressed cDNAs, and out of 82 unique SSH clones, 21 were confirmed to display a regionalized expression along the dorsoventral axis of the E6 ventral neuroepithelium. Among these, we identified a transcript coding for the chick orthologue of Sulf1, a recently identified cell surface sulfatase, as a new, early marker of oligodendrocyte (OL) precursors in the chick embryonic spinal cord. This study provides groundwork for the further identification of genes involved in glial specification.

Genetic and biochemical interactions between SCP160 and EAP1 in yeast

Scp160p is a multiple KH-domain RNA-binding protein in yeast known to associate with polyribosomes as an mRNP component, although its biological role remains unclear. As a genetic approach to examine Scp160p function, we applied an ethyl methanesulfonate (EMS) screen for loci synthetically lethal with scp160 loss, and identified a single candidate gene, EAP1, whose protein product functions in translation as an eIF4E-binding protein, with additional uncharacterized spindle pole body functions. To reconfirm scp160/eap1 synthetic lethality, we constructed a strain null for both genes, supported by an SCP160 maintenance plasmid. We used this strain to establish a quantitative assay for both Scp160p and Eap1p functions in vivo, and applied this assay to demonstrate that Y109A EAP1, a previously described allele of EAP1 that cannot bind eIF4E, is markedly impaired with regard to its SCP160-related activity. In addition, we explored the possibility of physical interaction between Eap1p and Scp160p, and discovered that Eap1p associates with Scp160p-containing complexes in an RNA-dependent manner. Finally, we probed the impact of EAP1 loss on Scp160p, and vice versa, and found that loss of each gene resulted in a significant change in either the complex associations or subcellular distribution of the other protein. These results clearly support the hypothesis that Scp160p plays a role in translation, demonstrate that the interaction of SCP160 and EAP1 is biologically significant, and provide important tools for future studies of the in vivo functions of both genes.

Molecular cloning and functional analysis of zebrafish high-density lipoprotein-binding protein

High-density lipoprotein-binding protein (HBP) plays a pivotal role in the endocrine regulation of both lipids and cholesterol. This first study of the zebrafish (Danio rerio) HBP gene in a piscine provides information on the complex molecular events that regulates lipid and cholesterol functions in fish, and allows a comparison with starvation and hormonal regulation. One identical zebrafish HBP cDNA clone was obtained from a 24-h-old zebrafish cDNA library. Zebrafish HBP is composed of 1273 amino acids as residues. The 1273-aa of HBP has 87.8% and 87.0% similarities to human and chicken HBP, respectively. Real-time reverse transcription polymerase chain reaction (RT-PCR) analysis showed that HBP is highly expressed in the 36 h of the developmental stage after fertilization as compared to other stages. As to tissue-specific expression, the HBP is highly expressed in the fin, liver and ovary. In the starvation experiment, results show significant differences between the control group and the group after 3-week starvation. After injecting GH, IGF-I, IGF-II or insulin, no significant differences were shown between the control and the experimental groups. These results suggest that in vivo HBP expression is not regulated by the insulin family or by growth hormone, but other factors present during the starvation may down- or up-regulate the HBP. Although the exact function of the HBP is unknown, its high expression in the liver and ovary suggests a role for this molecule in the cumulative efficiency of fish intake of food or lipid transfer; these results can possibly be applied to aquaculture in the near future.

Scp160p associates with specific mRNAs in yeast

Scp160p is a multiple KH-domain RNA-binding protein in yeast that has been demonstrated previously to associate with both soluble and membrane-bound polyribosomes as an mRNP component. One key question that has remained unanswered, however, is whether the mRNAs in these mRNP complexes are random or specific. We have addressed this question using microarray analyses of RNAs released from affinity isolated Scp160p-containing complexes, compared with total RNA controls from the same lysates. Our results, confirmed by quantitative RT-PCR analysis, clearly demonstrate that Scp160p associates with specific rather than with random messages, and that among the enriched targets are DHH1, YOR338W, BIK1, YOL155C and NAM8. Furthermore, loss of Scp160p resulted in a significant change in both the abundance and distribution between soluble and membrane-associated fractions for at least one of these messages (YOR338W), and in a subtle yet significant shift from soluble polyribosomes to soluble mRNPs for at least two of these target messages (DHH1 and YOR338W). Together, these data not only identify specific mRNA targets associated with Scp160p in vivo, they demonstrate that the association of Scp160p with these messages is biologically relevant.

Regulation of pathways of mRNA destabilization and stabilization

The level of an mRNA in the cytoplasm represents a balance between the rate at which the mRNA precursor is synthesized in the nucleus and the rates of nuclear RNA processing and export and cytoplasmic mRNA degradation. Although most studies of gene expression have focused on gene transcription and in the area of eukaryotic mRNA degradation, but to provide a short general discussion of the importance of mRNA degradation and its regulation and a brief overview of recent findings and present knowledge. The overview is followed by a more in-depth discussion of one of the several pathways for mRNA degradation. We concentrate on the pathway for regulated mRNA degradation mediated by mRNA-binding proteins and endonucleases that cleave within the body of mRNAs. As a potential example of this type of control, we focus on the regulated degradation of the egg yolk precursor protein vitellogenin on the mRNA-binding protein vigilin and the mRNA endonuclease polysomal ribonuclease 1 (PMR-1).

SnapDRAGON: a method to delineate protein structural domains from sequence data

We describe a method to identify protein domain boundaries from sequence information alone based on the assumption that hydrophobic residues cluster together in space. SnapDRAGON is a suite of programs developed to predict domain boundaries based on the consistency observed in a set of alternative ab initio three-dimensional (3D) models generated for a given protein multiple sequence alignment. This is achieved by running a distance geometry-based folding technique in conjunction with a 3D-domain assignment algorithm. The overall accuracy of our method in predicting the number of domains for a non-redundant data set of 414 multiple alignments, representing 185 single and 231 multiple-domain proteins, is 72.4 %. Using domain linker regions observed in the tertiary structures associated with each query alignment as the standard of truth, inter-domain boundary positions are delineated with an accuracy of 63.9 % for proteins comprising continuous domains only, and 35.4 % for proteins with discontinuous domains. Overall, domain boundaries are delineated with an accuracy of 51.8 %. The prediction accuracy values are independent of the pair-wise sequence similarities within each of the alignments. These results demonstrate the capability of our method to delineate domains in protein sequences associated with a wide variety of structural domain organisation.

The brefeldin A resistance protein Bfr1p is a component of polyribosome-associated mRNP complexes in yeast

The yeast gene BFR1 was originally isolated from a genetic screen for high-copy suppressors of brefeldin A-induced lethality in Saccharomyces cerevisiae. While this result suggested a possible role for the encoded protein, Bfr1p, in the secretory pathway, subsequent data have not fully supported this conclusion. Alternatively, Bfr1p has also been found by yeast two-hybrid analysis to interact with Bbp1p, a component of the spindle pole body. Finally, we have reported that Bfr1p associates with cytoplasmic mRNP complexes containing Scp160p, raising the possibility that Bfr1p may function in mRNA metabolism. Here, we have explored this possibility further. We report that Bfr1p associates with yeast polyribosomes and mRNP complexes even in the absence of Scp160p, and that its interaction with Scp160p-containing mRNP complexes is RNA-dependent. Furthermore, we have determined by fluorescence microscopy and subcellular fractionation that Bfr1p and Scp160p demonstrate similar cytoplasmic localization with enrichment around the nuclear envelope/endoplasmic reticulum. Finally, we report that loss of Bfr1p disrupts the interaction of Scp160p with polyribosomes, thereby demonstrating that the relationship between these two proteins is functional as well as physical. Considered together, these data raise the intriguing possibility that Bfr1p may provide a link between mRNA metabolism, the chromosomal segregation machinery and perhaps secretion in yeast.

Scp160p, an RNA-binding, polysome-associated protein, localizes to the endoplasmic reticulum of Saccharomyces cerevisiae in a microtubule-dependent manner

Scp160p is an RNA-binding protein containing 14 tandemly repeated heterogenous nuclear ribonucleoprotein K-homology domains, which are implicated in RNA binding. Scp160p interacts with free and membrane-bound polysomes that are dependent upon the presence of mRNA. Despite its presence on cytosolic polysomes, Scp160p is predominantly localized to the endoplasmic reticulum (ER). Accumulation of Scp160p-ribosome complexes at the ER requires the function of microtubules but is independent of the actin cytoskeleton. We propose that the multi-K-homology-domain protein Scp160p functions as an RNA binding platform, interacting with polysomes that are transported to the ER.

DDP1, a heterochromatin-associated multi-KH-domain protein of Drosophila melanogaster, interacts specifically with centromeric satellite DNA sequences

DDP1 is a single-stranded nucleic acid binding protein of Drosophila melanogaster that associates with pericentric heterochromatin. DDP1 contains 15 consecutive KH domains and is homologous to the highly conserved vigilin proteins that, in Saccharomyces cerevisiae, are involved in the control of cell ploidy. DDP1 was identified and purified on the basis of its binding to the pyrimidine-rich C strand of the centromeric Drosophila dodeca-satellite. Here, the interaction of DDP1 with the dodeca-satellite C strand was analyzed in detail. This interaction is sequence specific. In particular, a guanine residue which is highly conserved in natural dodeca-satellite sequences was found to be essential for the efficient binding of DDP1. DDP1 binding was also found to be strongly influenced by the length and extent of secondary structure of the DNA substrate. Efficient DDP1 binding required a minimal length of about 75 to 100 nucleotides and was facilitated by the lack of secondary structure of the substrate. DDP1 also showed a significant affinity for the unstructured pyrimidine-rich strand of the most abundant centromeric Drosophila AAGAG satellite. The stoichiometry of the complexes formed with the dodeca-satellite C strand suggests that, in DDP1, the 15 consecutive KH domains are organized such that they define two nucleic acid binding surfaces. These results are discussed in the context of the possible contribution of DDP1 to heterochromatin organization and function.

Novel RNA-binding motif: the KH module

The KH motif has recently been identified in single or multiple copies in a number of RNA associated proteins. Here we review the current knowledge accumulated about the sequence, structure, and functions of the KH. The multidomain architecture of most of the KH-containing proteins inspired an approach based on the production of peptides spanning the sequence of an isolated KH motif. Correct identification of the minimal length necessary for producing a folded peptide has had a number of important consequences for interpreting functional data. The presence of the KH motifs in fmr1, the protein responsible for the fragile X syndrome, and their possible role in the fmr1 functions are also discussed.

Assembly of the alpha-globin mRNA stability complex reflects binary interaction between the pyrimidine-rich 3' untranslated region determinant and poly(C) binding protein alphaCP

Globin mRNAs accumulate to 95% of total cellular mRNA during terminal erythroid differentiation, reflecting their extraordinary stability. The stability of human alpha-globin mRNA is paralleled by formation of a sequence-specific RNA-protein (RNP) complex at a pyrimidine-rich site within its 3' untranslated region (3'UTR), the alpha-complex. The proteins of the alpha-complex are widely expressed. The alpha-complex or a closely related complex also assembles at pyrimidine-rich 3'UTR segments of other stable mRNAs. These data suggest that the alpha-complex may constitute a general determinant of mRNA stability. One or more alphaCPs, members of a family of hnRNP K-homology domain poly(C) binding proteins, are essential constituents of the alpha-complex. The ability of alphaCPs to homodimerize and their reported association with additional RNA binding proteins such as AU-rich binding factor 1 (AUF1) and hnRNP K have suggested that the alpha-complex is a multisubunit structure. In the present study, we have addressed the composition of the alpha-complex. An RNA titration recruitment assay revealed that alphaCPs were quantitatively incorporated into the alpha-complex in the absence of associated AUF1 and hnRNP K. A high-affinity direct interaction between each of the three major alphaCP isoforms and the alpha-globin 3'UTR was detected, suggesting that each of these proteins might be sufficient for alpha-complex assembly. This sufficiency was further supported by the sequence-specific binding of recombinant alphaCPs to a spectrum of RNA targets. Finally, density sedimentation analysis demonstrated that the alpha-complex could accommodate only a single alphaCP. These data established that a single alphaCP molecule binds directly to the alpha-globin 3'UTR, resulting in a simple binary structure for the alpha-complex.

The mub gene encodes a protein containing three KH domains and is expressed in the mushroom bodies of Drosophila melanogaster

The ring gland function of Drosophila melanogaster is controlled by the CNS. To identify genes that are active in brain cells and are involved in the ring gland control, we analysed enhancer trap lines with respect to CNS- and/or ring gland-specific lacZ expression in third-instar larvae. From one of the enhancer trap lines, which shows specific lacZ expression in the CNS and prothoracic part of the ring gland, the mub gene was cloned. The gene is strongly expressed in the mushroom bodies throughout development. Nucleotide sequence analysis of cDNA clones revealed a high degree of similarity to vertebrate RNA binding KH domain proteins, suggesting a function of the MUB protein in binding and stabilizing of specific mRNAs in the mushroom bodies. Null mutants of the mub gene do not exhibit a visible mutant phenotype. We speculate, therefore, that the mub gene is involved in learning and memory processes.

In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein

The function(s) and RNA binding properties of vigilin, a ubiquitous protein with 14 KH domains, remain largely obscure. We recently showed that vigilin is the estrogen-inducible protein in polysome extracts which binds specifically to a segment of the 3' untranslated region (UTR) of estrogen-stabilized vitellogenin mRNA. In order to identify consensus mRNA sequences and structures important in binding of vigilin to RNA, before vigilin was purified, we developed a modified in vitro genetic selection protocol. We subsequently validated our selection procedure, which employed crude polysome extracts, by testing natural and in vitro-selected RNAs with purified recombinant vigilin. Most of the selected up-binding mutants exhibited hypermutation of G residues leading to a largely unstructured, single-stranded region containing multiple conserved (A)nCU and UC(A)n motifs. All eight of the selected down-binding mutants contained a mutation in the sequence (A)nCU. Deletion analysis indicated that approximately 75 nucleotides are required for maximal binding. Using this information, we predicted and subsequently identified a strong vigilin binding site near the 3' end of human dystrophin mRNA. RNA sequences from the 3' UTRs of transferrin receptor and estrogen receptor, which lack strong homology to the selected sequences, did not bind vigilin. These studies describe an aproach to identifying long RNA binding sites and describe sequence and structural requirements for interaction of vigilin with RNAs.

Cloning of cell-specific secreted and surface proteins by subtractive antibody screening

To identify and clone genes that encode cell- or tissue-specific secreted and surface proteins, a polyclonal antiserum was raised against a complex mixture of surface or secreted proteins from the target cell, followed by immunodepletion of antibodies that recognize proteins from a nontarget cell or tissue. The depleted antiserum is used to screen bacteriophage cDNA expression libraries. Because of our interest in how adipocytes communicate with other cells, we have used this method to clone cDNAs encoding secreted and plasma membrane proteins that are induced during adipocyte differentiation. We describe several of these, including a novel plasma membrane-associated protein, S3-12.

Production of trypsin by cells of the exocrine pancreas is paralleled by the expression of the KH protein vigilin

Vigilin, a protein with a continuous series of 14 KH motifs, forms part of a multiprotein complex containing tRNA. Several lines of evidence have suggested that vigilin expression is enhanced in those cells which were actively engaged in protein synthesis. Accordingly, we show here by immunoelectronmicroscopy a close association of vigilin with the rough endoplasmic reticulum in rat pancreatic cells. Histological examination of these cells furthermore demonstrates the highest intensity of vigilin staining in the perinuclear, intranuclear, and basolateral regions where the endoplasmic reticulum is mainly amassed. In vivo challenge of starving rats fed prior to sacrifice raised in parallel the protein levels of both trypsin and vigilin when compared to unchallenged animals and was associated with enhanced expression of the vigilin gene. In contrast, in human and rat cell lines of pancreatic tumors with a constitutively high expression of vigilin no further stimulation by cholecystokinin treatment could be achieved. Our data provide circumstantial evidence that vigilin may play a crucial role in the ability of an organ, e.g., pancreas, to cope with the physiological demand to upregulate protein synthesis.

Genetic variability in white leghorns revealed by chicken liver expressed sequence tags

A total of 92 expressed sequence tags from chicken liver (CLEST) were searched for homology with known genes. Among the CLEST, 29% had no sequence similarities with known genes, 34% showed sequence similarity to rRNA, 9% to mitochondrial genes, 23% to known nuclear genes, and 5% to human expressed sequence tags. Among the nuclear CLEST (excluding rRNA), clones with sequence similarity to aldolase B were represented four times, whereas all the other clones represented unique genes. The presence of MspI and TaqI restriction fragment length polymorphisms (RFLP) associated with CLEST were analyzed by bulk Southern blotting in 16 strains of White Leghorn chickens derived from five different genetic bases. No RFLP were observed with rRNA CLEST and a single MspI RFLP was observed with mitochondrial CLEST. The nuclear CLEST with sequence similarity to known nuclear genes were grouped into two classes on the basis of their involvement in intermediary metabolism. Among the nine genes coding for metabolic enzymes, all but one were polymorphic at MspI and/or TaqI sites in at least one of the strains, whereas among the other genes six of nine were polymorphic. The average frequency of clones revealing RFLP per cDNA clone and restriction enzyme for the two classes were 0.7 and 0.3, respectively. The analysis indicated that in White Leghorns, RFLP markers in the vicinity of nuclear CLEST are relatively frequent. Further, RFLP in the vicinity of genes coding for metabolic enzymes were significantly more frequent than near genes coding for other proteins.

High-density lipoprotein-binding protein (HBP)/vigilin is expressed in human atherosclerotic lesions and colocalizes with apolipoprotein E

Accumulation of cholesteryl esters within cells of the arterial intima is a hallmark of atherosclerosis. A small number of proteins have been shown in vitro to be upregulated by cellular cholesterol loading, including apolipoprotein E (apoE) and the recently cloned HDL-binding protein (HBP), but only apoE has been shown to be upregulated in cholesterol-loaded cells in atherosclerosis. To determine whether HBP (also called vigilin) might be expressed in human atherosclerosis, immunohistochemistry and in situ hybridization were performed on coronary arteries of 18 patients. HBP/vigilin was detected on all endothelial cells. HBP/vigilin mRNA and protein also were detected on a subset of macrophages and occasionally on smooth muscle cells (SMC) in atherosclerotic plaques but were not detected on these cell types in nondiseased coronary intima. The majority of HBP/vigilin-expressing macrophages were foam cells, but HBP/vigilin expression also was detected rarely in nonfoam cell macrophages. Foam cell macrophage HBP/vigilin expression was present in 100% of atherosclerotic quadrants, and nonfoam cell macrophage HBP/vigilin expression was present in 6% of atherosclerotic quadrants. HBP/vigilin-expressing human plaque cells also expressed apoE. However, HBP/vigilin was detected in cardiac myocyte foam cells of an apoE-deficient mouse, demonstrating that HBP/vigilin expression can occur independently of apoE. These results suggest that in vivo HBP/vigilin expression is upregulated by intracellular cholesterol loading but also that other factors present in atherosclerotic plaques may upregulate HBP/vigilin. Although the exact function of HBP/vigilin is unknown, its expression in plaque macrophages suggests a role for this molecule in atherogenesis.

Purification and nucleic-acid-binding properties of a Saccharomyces cerevisiae protein involved in the control of ploidy

Scp160p (Saccharomyces cerevisiae protein involved in the control of ploidy), a polypeptide with a molecular mass of around 160 kDa, is associated with the nuclear envelope and the endoplasmic reticulum. The most noteworthy phenotype of SCP160 deletion mutants is a decrease in viability and an increased number of chromosomes in the surviving cells [Wintersberger, U., Kühne, C. & Karwan, A. (1995) Yeast 11, 929-944]. Scp160p contains 14 KH domains, conserved motifs that have lately been identified in a variety of RNA-binding proteins. In this report, we demonstrate that the Scp160p sequence shows nearly perfect colinearity with the putative gene product of C08H9.2 from the nematode Caenorhabditis elegans as well as with the vigilins, vertebrate RNA-binding proteins with a cellular location similar to that of Scp160p. Moreover, we found that Scp160p contains a potential nuclear-export signal (NES) near its N-terminus and a potential nuclear-localization signal (NLS) between KH domains 3 and 4. To determine whether the protein is able to bind to RNA, we purified Scp160p from yeast cell extract by DNA-cellulose and anti-Scp160p affinity chromatography. In northwestern blotting experiments, the electrophoretically homogeneous protein bound to ribohomopolymers and ribosomal RNA as well as to single-stranded and double-stranded DNA. Subcellular fractionation studies revealed that the major part of Scp160p is membrane associated via ionic interactions and can be released from the membrane fraction under conditions that lead to a dissociation of ribosomes. Together, our findings suggest that Scp160p is the yeast homologue of the vigilins, and point to a role for Scp160p in nuclear RNA export or in RNA transport within the cytoplasm.

Chicken vigilin gene: a distinctive pattern of hypersensitive sites is characteristic for its transcriptional activity

Vigilin, a multidomain hn-ribonucleo-K-homologous protein, is part of a ribonucleoprotein complex with cognate tRNA and is found in both the nucleus and the cytoplasm. In an approach to identify genomic regions involved in regulation of the chicken vigilin gene, we carried out transfection studies with a reporter gene in suitable chicken cells. After including a distantly positioned 5'-sequence in the construct, we observed a 10.5-fold increase in luciferase (EC 1. 13.12.7) expression compared with basal promoter activity. Accordingly, chromatin analysis of freshly isolated embryonic tendon fibroblasts with high levels of vigilin mRNA expression shows a DNase-I-hypersensitive site (DHS1) localized 2.2 kb upstream of the transcriptional start site. Similarly, phytohaemagglutinin-stimulated lymphocytes with a 4-fold elevated expression of vigilin mRNA compared with resting lymphocytes also exhibited this unique DHS, having switched from that found at 3.3 kb (DHS2) in resting lymphocytes. Furthermore, using gel-retardation experiments with DNA representing either DHS1 or DHS2, a specific interaction with chicken nuclear extracts was seen.

Vigilin, a ubiquitous protein with 14 K homology domains, is the estrogen-inducible vitellogenin mRNA 3'-untranslated region-binding protein

RNA-binding proteins containing KH domains are widely distributed. One KH domain protein of unknown function, vigilin (also known as the high density lipoprotein-binding protein), contains 14 KH domains and is ubiquitous in vertebrate cells. We previously used RNA gel mobility shift assays to describe an estrogen-inducible protein which binds specifically to a segment of the 3'-untranslated region (3'-UTR) of vitellogenin mRNA, an area which has been implicated in the estrogen-mediated stabilization of vitellogenin mRNA. Here we show that the vitellogenin mRNA-binding protein (VitRNABP) is vigilin. The VitRNABP was isolated as a 150-155-kDa protein on a vitellogenin mRNA 3'-UTR affinity column. Peptide microsequencing revealed that the purified protein was vigilin, a conclusion confirmed in Western blot analysis with antibodies to vigilin. Direct confirmation that vigilin is the VitRNABP was obtained from RNA gel mobility shift assays which demonstrated that antibodies to chicken vigilin supershifted the Xenopus VitRNABP band. Xenopus liver vigilin mRNA and the VitRNABP exhibited similar induction by estrogen, providing additional confirmation that vigilin is the estrogen-inducible protein which binds to the 3'-UTR of estrogen-stabilized vitellogenin mRNA. These data support a role for vigilin in the hormonal control of mRNA metabolism.

Evidence for a novel cytoplasmic tRNA-protein complex containing the KH-multidomain protein vigilin

Vigilin, a protein found predominantly in cells and tissues with a high biosynthetic capacity, was isolated in its native form from human HEp-2 cells (A.T.C.C. CCL23) by immunoaffinity chromatography. Vigilin forms part of a novel ribonucleoprotein complex that also contains additional, as yet uncharacterized, proteins. Experimental evidence suggests that the nucleic acids entrapped in this complex are protected from RNase and belong to the tRNA family. Using either a pool of total human RNA or radioactively labelled tRNA (tRNA (Asp**)) in rebinding experiments, we could show that tRNA is selectively recaptured by the RNA-depleted vigilin-containing complex.

Characterisation of the nucleic-acid-binding activity of KH domains. Different properties of different domains

The KH module is a sequence motif recently identified in a number of diversified RNA-binding proteins and suggested to be the functional element responsible for RNA binding. So far, however, this hypothesis has not received direct experimental support. We have expressed the three KH-domains from heterogeneous nuclear ribonucleoprotein K (hnRNP-K), the poly(C)-binding proteins PCBP-1 and PCBP-2, the first three to four domains from the high-density binding protein HBP, the one and a half domain from the archaeon Halobacterium halobium ORF139 and one and a half domain of the fragile-X protein FMR1 in Escherichia coli and analysed their nucleic-acid-binding properties in vitro. The results showed that the in vitro poly(rC)-binding activity of hnRNP-K can be assigned to KH-domain 3, whereas both domains 1 and 3 in the PCBPs bind poly(rC). In addition, all these domains exhibit binding activity towards other nucleic acids, albeit at a significantly lower level. The first KH domain from the FMR1 protein binds poly(rG) and single-stranded and double-stranded DNA. The N-terminal three or four domains from HBP bind poly(rG) and, at a much lower level, single-stranded and double-stranded DNA. Thus, single KH domains are discrete and independent nucleic-acid-binding units. Moreover, different KH domains bind different nucleic acids, suggesting that KH domains are composed of a conserved, weakly nucleic-acid-binding, structure that is fine tuned, by sequence variation, resulting in sequence-specific nucleic-acid-binding entities.

Two additional 5' exons in the human Vigilin gene distinguish it from the chicken gene and provide the structural basis for differential routes of gene expression

Vigilin, a 150-kDa protein, contains 14 tandemly arranged domains, each consisting of a KH RNA-binding motif and a spacer region. Here, we report on the physical structure of the human Vigilin gene with 29 exons, thereby outnumbering the chicken gene by two additional 5' exons. These additional exons, 1A and 1B, are alternatively though concurrently spliced to exon 1C which is homologous to the first exon in the chicken gene. None of the additional human exons code for an amino-terminal extension of Vigilin, due to in-frame stop codons. Structural features of exon 1A, however, would allow the translation of a 13-amino-acid peptide from an upstream open reading frame preceding the vigilin open reading frame. We suggest that exons 1A and 1B have been gained during evolution, allowing alternative routes of expression control of the human Vigilin gene.

Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome

The KH module is a sequence motif found in a number of proteins that are known to be in close association with RNA. Experimental evidence suggests a direct involvement of KH in RNA binding. The human FMR1 protein, which has two KH domains, is associated with fragile X syndrome, the most common inherited cause of mental retardation. Here we present the three-dimensional solution structure of the KH module. The domain consists of a stable beta alpha alpha beta beta alpha fold. On the basis of our results, we suggest a potential surface for RNA binding centered on the loop between the first two helices. Substitution of a well-conserved hydrophobic residue located on the second helix destroys the KH fold; a mutation of this position in FMR1 leads to an aggravated fragile X phenotype.

Vigilin contains a functional nuclear localisation sequence and is present in both the cytoplasm and the nucleus

Vigilin is a member of the KH protein family and contains 14 tandemly arranged potential RNA-binding domains. Between KH domains 2 and 3 we have identified a nuclear localization sequence by cloning this sequence into the NH2-terminal region of phage T7 RNA polymerase as a reporter protein and by showing its transfer into the nucleus. Furthermore we provide experimental evidence that Vigilin is present both in the nucleus and in the cytoplasm in similar concentrations. These observations support the notion that Vigilin may shuttle between nucleus and cytoplasm presumably in contact with RNA molecules.

Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing

PSI is an RNA-binding protein involved in repressing splicing of the P element third intron in Drosophila somatic cell extracts. PSI produced in bacteria restores splicing inhibition to an extract relieved of inhibitory activity, indicating that PSI plays a direct role in somatic inhibition. Sequence analysis of cDNAs encoding PSI reveals three KH RNA-binding domains, a conserved motif also found in the yeast splicing regulator MER1. Notably, PSI is expressed highly in somatic embryonic nuclei but is undetectable in germ-line cells. In contrast, hrp48, another protein implicated in somatic inhibition, is found in the nucleus and cytoplasm of both tissues. The splicing inhibitory properties and soma-specific expression of PSI may be sufficient to explain the germ-line-specific transposition of P elements.

The KH module has an alpha beta fold

The KH module has recently been identified in a number of RNA associated proteins including vigilin and FMR1, a protein implicated in the fragile X syndrome. In this work, NMR spectroscopy was used to determine the secondary structure in solution of a KH domain (repeat 5 from vigilin). Almost complete assignments were obtained for the 1H and 15N resonances using uniform 15N-labeling of the protein combined with homo-nuclear 2D 1HNMR and 3D 15N correlated 1H NMR. On the basis of NOE patterns, secondary chemical shifts and amide solvent exposure, the secondary structure consists of an antiparallel three stranded beta sheet connected by two helical regions. This domain may also be stabilized by an appended C-terminal helix which is common to many but not all members of the KH family.

The human vigilin gene: identification, chromosomal localization and expression pattern

Chick vigilin cRNA clones were used to isolate the cognate human gene, by screening a pWE15 genomic library. Three independent cosmid clones were isolated and characterized by restriction mapping. The gene was identified by sequencing an internal EcoRI fragment containing two exons homologous to exon 24 and 25 of the chicken vigilin gene and corresponding to nucleotides 1973-2104 of the human HBP-cDNA. The homology between the chicken and human sequences was 77% and 82% at the cDNA level, and 91% and 100% at the amino acid level. In addition, the analyzed intron/exon boundaries were invariantly conserved. The 5' and 3' regions of the human gene were mapped by Southern analysis of the respective clones with synthetic oligonucleotides. The entire vigilin gene spans a region of about 50 kb and has been assigned to chromosome 2q36-q37.2 (FL-pter value of 0.96 +/- 0.03) by fluorescence in situ hybridization to metaphase spreads from normal peripheral blood lymphocytes. The vigilin gene is localized in a chromosomal region comprising a cluster of collagen genes (COLIVA3, COLVIA3) and the locus of the Waardenburg syndrome I. Only one mRNA species of 4.4 kb is transcribed from the human vigilin gene. In accordance with previous observations on chicken mRNA, the expression of the human vigilin mRNA depends on the stage of cytodifferentiation both in vitro and in situ.

Essential role for KH domains in RNA binding: impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome

The KH domain is an evolutionarily conserved sequence motif present in many RNA-binding proteins, including the pre-mRNA-binding (hnRNP) K protein and the fragile X mental retardation gene product (FMR1). We assessed the role of KH domains in RNA binding by mutagenesis of KH domains in hnRNP K and FMR1. Conserved residues of all three hnRNP K KH domains are required for its wild-type RNA binding. Interestingly, while fragile X syndrome is usually caused by lack of FMR1 expression, a previously reported mutation in a highly conserved residue of one of its two KH domains (Ile-304-->Asn) also results in mental retardation. We found that the binding of this mutant protein to RNA is severely impaired. These results demonstrate an essential role for KH domains in RNA binding. Furthermore, they strengthen the connection between fragile X syndrome and loss of the RNA binding activity of FMR1.

FMR1 protein: conserved RNP family domains and selective RNA binding

Fragile X syndrome is the result of transcriptional suppression of the gene FMR1 as a result of a trinucleotide repeat expansion mutation. The normal function of the FMR1 protein (FMRP) and the mechanism by which its absence leads to mental retardation are unknown. Ribonucleoprotein particle (RNP) domains were identified within FMRP, and RNA was shown to bind in stoichiometric ratios, which suggests that there are two RNA binding sites per FMRP molecule. FMRP was able to bind to its own message with high affinity (dissociation constant = 5.7 nM) and interacted with approximately 4 percent of human fetal brain messages. The absence of the normal interaction of FMRP with a subset of RNA molecules might result in the pleiotropic phenotype associated with fragile X syndrome.