beta-Scruin, a homologue of the actin crosslinking protein scruin, is localized to the acrosomal vesicle of Limulus sperm

A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum

Background

According to the World Health organization, half the world's population is at risk of contracting malaria. They estimated that in 2010 there were 219 million cases of malaria, resulting in 660,000 deaths and an enormous economic burden on the countries where malaria is endemic. The adoption of various high-throughput genomics-based techniques by malaria researchers has meant that new avenues to the study of this disease are being explored and new targets for controlling the disease are being developed. Here, we apply a novel neighborhood subnetwork alignment approach to identify the interacting elements that help regulate the cell cycle of the malaria parasite Plasmodium falciparum.

Results

Our novel subnetwork alignment approach was used to compare networks in Escherichia coli and P. falciparum. Some 574 P. falciparum proteins were revealed as functional orthologs of known cell cycle proteins in E. coli. Over one third of these predicted functional orthologs were annotated as "conserved Plasmodium proteins" or "putative uncharacterized proteins" of unknown function. The predicted functionalities included cyclins, kinases, surface antigens, transcriptional regulators and various functions related to DNA replication, repair and cell division.

Conclusions

The results of our analysis demonstrate the power of our subnetwork alignment approach to assign functionality to previously unannotated proteins. Here, the focus was on proteins involved in cell cycle regulation. These proteins are involved in the control of diverse aspects of the parasite lifecycle and of important aspects of pathogenesis.

Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis

Fungi and oomycetes are the causal agents of many of the most serious diseases of plants. Here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. The predicted translational products of each genome have been clustered into groups of potential orthologues using Markov Chain Clustering and the data integrated into the e-Fungi object-oriented data warehouse (http://www.e-fungi.org.uk/). Analysis of the species distribution of members of these clusters has identified proteins that are specific to filamentous fungal species and a group of proteins found only in plant pathogens. By comparing the gene inventories of filamentous, ascomycetous phytopathogenic and free-living species of fungi, we have identified a set of gene families that appear to have expanded during the evolution of phytopathogens and may therefore serve important roles in plant disease. We have also characterised the predicted set of secreted proteins encoded by each genome and identified a set of protein families which are significantly over-represented in the secretomes of plant pathogenic fungi, including putative effector proteins that might perturb host cell biology during plant infection. The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis.

Selected BTB/POZ-kelch proteins bind ATP

Proteins with a bric-à-brac, tramtrack, broad-complex/Poxvirus zinc fingers (BTB/POZ) domain are implicated in a broad variety of biological processes, including DNA binding, regulation of gene transcription and organization of macromolecular structures. Kelch domain containing BTB/POZ proteins like Mayven and Keap1 display limited sequence similarity with the actin-fragmin kinase from Physarum, a protein kinase with a kelch domain. We show that mouse Keap1, a Caenorhabditis elegans protein that we named CKR, and human Mayven bind 5'-p-fluorosulfonyl-benzoyl-adenosine (FSBA), a covalently modifying ATP analogue. Binding with 2-azido-ATP or ATP-Sepharose is also demonstrated. In contrast to Mayven, FSBA binding by CKR and Keap1 was specifically inhibited by excess ATP. The ATP binding pocket is located in the N-terminal half of Keap1. Our findings indicate that several, but not all, BTB/POZ-kelch domain proteins possess an inconspicuous ATP binding cassette.

Identification and characterization of KLHL4, a novel human homologue of the Drosophila Kelch gene that maps within the X-linked cleft palate and Ankyloglossia (CPX) critical region

X-linked cleft palate (CPX) is a rare nonsyndromic form of orofacial clefting that is, unlike more common forms, inherited as a highly penetrant Mendelian trait. Linkage studies using a large Icelandic kindred localized the gene to Xq21.3, and a physical map defining a 2.0-Mb candidate region was subsequently constructed. Genomic sequence is now available for much of the critical region and has been surveyed for potential transcriptional units. Through this analysis, we have identified a novel human homologue of Kelch, KLHL4. The transcript represents a mRNA of approximately 3.6 kb and encodes a protein of 718 amino acids. Protein domain analysis reveals six tandem repeats (Kelch repeats) at the C-terminus and a POZ/BTB protein-binding domain toward the N-terminus, characteristic of Drosophila Kelch and other family members. KLHL4 consists of 11 exons spanning a genomic interval of approximately 150 kb. From EST sequences and RT-PCR analysis, there is evidence for the use of alternative 3' UTRs. The mRNA is expressed in a range of fetal tissues including tongue, palate, and mandible. Mutational analysis in affected CPX patients revealed one sequence alteration that was most likely to be a silent polymorphism.

Genomic organization, chromosomal localization and regulation of expression of the neuronal nuclear matrix protein NRP/B in human brain tumors

The nuclear matrix and its role in cell physiology are largely unknown, and the discovery of any matrix constituent whose expression is tissue- and/or cell-specific offers a new avenue of exploration. Studies of the novel neuronal nuclear matrix protein, NRP/B, reveal that it is an early and highly specific marker of neuronal induction and development in vertebrates, since its expression is restricted mainly to the developing and mature nervous system. These studies also show that NRP/B is involved in neuronal differentiation. To further examine the structure-function of NRP/B, we have cloned and characterized the murine Nrp/b gene. The murine gene consists of four exons interrupted by three introns that span 7.6kb of DNA. The complete open reading frame is localized in exon 3, suggesting that NRP/B is highly conserved during evolution. Chromosomal analysis shows that NRP/B is localized to chromosome 13 in mouse and chromosome 5q12-13 in human. Since our previous studies demonstrated that NRP/B is expressed in primary hippocampal neurons but not in primary astrocytes, we have characterized NRP/B mRNA and protein expression in various brain cell lines and in human brain tumors. Abundant expression of NRP/B mRNA and protein was observed in human neuroblastoma cell lines (IMR32, SKN-MC, SKN-SH), in glioblastoma cell lines (A172, T98G, U87-MG, U118-MG, U138-MG, and U373-MG), in neuroglioma (H4) and astrocytoma cell lines (CCF-STTG1 and SW1088). Confocal analysis of NRP/B in U87-MG glioblastoma cells indicated nuclear localization of NRP/B. NRP/B expression was also observed in human primary brain tumors including glioblastoma multiformae and astrocytomas (total of five cases). These results suggest that NRP/B expression is upregulated in human brain tumors including glioblastomas and astrocytomas, while under normal conditions NRP/B expression is restricted to neurons. This study implicates a role for NRP/B in brain tumor development.

Definition of minimal domains of interaction within the recombination-activating genes 1 and 2 recombinase complex

During V(D)J recombination, recognition and cleavage of the recombination signal sequences (RSSs) requires the coordinated action of the recombination-activating genes 1 and 2 (RAG1/RAG2) recombinase complex. In this report, we use deletion mapping and site-directed mutagenesis to determine the minimal domains critical for interaction between RAG1 and RAG2. We define the active core of RAG2 required for RSS cleavage as aa 1-371 and demonstrate that the C-terminal 57 aa of this core provide a dominant surface for RAG1 interaction. This region corresponds to the last of six predicted kelch repeat motifs that have been proposed by sequence analysis to fold RAG2 into a six-bladed beta-propeller structure. Residue W317 within this sixth repeat is shown to be critical for mediating contact with RAG1 and concurrently for stabilizing binding and directing cleavage of the RSS. We also show that zinc finger B (aa 727-750) of RAG1 provides a dominant interaction domain for recruiting RAG2. In all, the data support a model of RAG2 as a multimodular protein that utilizes one of its six faces for establishing productive contacts with RAG1.

Molecular characterization of KLHL3, a human homologue of the Drosophila kelch gene

The Drosophila kelch protein is a structural component of ring canals and is required for oocyte maturation. Here, we report the cloning and genomic structure of a new human homologue of kelch, KLHL3. At the amino acid level, KLHL3 shares 77% similarity with Drosophila kelch and 89% similarity with Mayven (KLHL2), another human kelch homolog. The approximately 6.5-kb mRNA has a single open reading frame encoding a protein of 587 amino acids with a predicted molecular mass of 650 kDa. Like kelch and KLHL2, the KLHL3 protein contains a poxvirus and zinc finger domain at the N-terminus and six tandem repeats (kelch repeats) at the C-terminus. At least three isoforms, which differ in the length of the N-terminus, are produced and may be the result of alternative promoter usage. We also identified alternative polyadenylation sites and alternative splicing; thus, as many as 12 mRNA variants and six putative protein isoforms could be produced. The KLHL3 gene is mapped to human chromosome 5, band q31, contains 17 exons, and spans approximately 120 kb of genomic DNA. KLHL3 maps within the smallest commonly deleted segment in myeloid leukemias characterized by a deletion of 5q; however, we detected no inactivating mutations of KLHL3 in malignant myeloid disorders with loss of 5q.

Krp1, a novel kelch related protein that is involved in pseudopod elongation in transformed cells

We have previously shown that the transcription factor AP-1 regulates the expression of genes which allow neoplastically transformed rat fibroblasts to become invasive. Searches for further AP-1 target genes led to the identification of a gene encoding a novel rat kelch family member, named kelch related protein 1 (Krp1). Kelch family members are characterized by a series of repeats at their carboxyl terminus and a BTB/POZ domain near their amino terminus. Rat Krp1 has a primarily cytoplasmic localization, and a small fraction appears to accumulate and co-localize with F-actin at membrane ruffle-like structures in the tips of pseudopodia. Overexpression of Krp1 in transformed rat fibroblasts led to the formation of dramatically elongated pseudopodia, while expression of truncated Krp1 polypeptides resulted in a reduction in the length of pseudopodia. We propose that the transformation-specific expression of Krp1 is required for pseudopod elongation, which are structures that are required for cell motility and invasion.

The kelch repeat superfamily of proteins: propellers of cell function

The kelch motif was discovered as a sixfold tandem element in the sequence of the Drosophila kelch ORF1 protein. The repeated kelch motifs predict a conserved tertiary structure, a beta-propeller. This module appears in many different polypeptide contexts and contains multiple potential protein-protein contact sites. Members of this growing superfamily are present throughout the cell and extracellularly and have diverse activities. In this review, we discuss current information concerning the structural organization of kelch repeat proteins, their biological roles and the molecular basis of their action.

kel-1, a novel Kelch-related gene in Caenorhabditis elegans, is expressed in pharyngeal gland cells and is required for the feeding process

BACKGROUND

Kelch-related proteins constitute an expanding family, members of which carry two conserved motifs named the BTB/POZ and the kelch repeat domains. The best-characterized member, Drosophila Kelch, constitutes the ring canals in the egg chamber in association with actin. However, physiological and biochemical functions of the members of this family remain largely uncharacterized.

RESULTS

We identified the kel-1 gene encoding a Kelch-related protein in the nematode Caenorhabditis elegans. The deduced KEL-1 protein had 618 amino acid residues and was most similar to Drosophila Kelch. Loss of kel-1 function caused growth arrest at an early larval stage, most likely at the beginning of L2. The kel-1 deletion mutant appeared normal in morphology, movement and pumping action for the initial two to three days after hatching, but it failed to convey foods effectively to intestine and could hardly increase in body size. Analyses using immunostaining and reporter gene expression indicated that kel-1 was expressed almost exclusively in the g1 pharyngeal gland cells during late embryogenesis and at all developmental stages thereafter.

CONCLUSIONS

C. elegans KEL-1 protein is essential for the larval development, probably performing a function required for feeding in the pharyngeal g1 gland cells, which are supposed to secrete materials aiding digestion.

Isolation and characterization of IPP, a novel human gene encoding an actin-binding, kelch-like protein

The kelch family of proteins is defined by a 50 amino-acid repeat that has been shown to associate with actin. Here we describe the cloning and initial characterization of IPP, a novel human gene that predicts a kelch family protein homologous to the mouse Ipp gene, a previously described kelch family member. A 3kb IPP cDNA clone was isolated from a human placenta library using a probe derived from Ipp. Restriction mapping and Southern blot analysis show that IPP comprises eight exons spanning more than 47kb of genomic DNA. Fluorescence in situ hybridization maps the gene to chromosome 1p32-1p34. Northern blot analysis reveals transcripts of 1.4, 2.2, 5. 0, and 7.3kb. The 1.4 and 2.2kb messages are found exclusively in testis, while the 5.0 and 7.3kb messages are expressed at varying levels in ovary, placenta, small intestine, spleen, testis, and thymus. The IPP cDNA clone contains a 1752bp open reading frame that predicts a 584 amino-acid, 66kDa protein. Sequence analysis indicates an N-terminal POZ protein-protein interaction domain and a C-terminal kelch repeat domain consisting of six tandemly arranged repeats. Cosedimentation assays performed with these domains expressed as glutathione S-transferase fusion proteins demonstrate an actin-binding activity mediated specifically by the kelch repeat domain of IPP.

Myxoma virus encodes an alpha2,3-sialyltransferase that enhances virulence

A 4.7-kb region of DNA sequence contained at the right end of the myxoma virus EcoRI-G2 fragment located 24 kb from the right end of the 163-kb genome has been determined. This region of the myxoma virus genome encodes homologs of the vaccinia virus genes A51R, A52R, A55R, A56R, and B1R; the myxoma virus gene equivalents have been given the prefix M. The MA55 gene encodes a protein belonging to the kelch family of actin-binding proteins, while the MA56 gene encodes a member of the immunoglobulin superfamily related to a variety of cellular receptors and adhesion molecules. A novel myxoma virus early gene, MST3N, is a member of the eukaryotic sialyltransferase gene family located between genes MA51 and MA52. Detergent lysates prepared from myxoma virus-infected cell cultures contained a virally encoded sialyltransferase activity that catalyzed the transfer of sialic acid (Sia) from CMP-Sia to an asialofetuin glycoprotein acceptor. Analysis of the in vitro-sialylated glycoprotein acceptor by digestion with N-glycosidase F and by lectin binding suggested that the MST3N gene encodes an enzyme with Galbeta1,3(4)GlcNAc alpha2,3-sialyltransferase specificity for the N-linked oligosaccharide of glycoprotein. Lectin binding assays demonstrated that alpha2,3-sialyltransferase activity is expressed by several known leporipoxviruses that naturally infect Sylvilagus rabbits. The sialyltransferase is nonessential for myxoma virus replication in cell culture; however, disruption of the MST3N gene caused attenuation in vivo. The possible implications of the myxoma virus-expressed sialyltransferase in terms of the host's defenses against infection are discussed.

Identification of Kel1p, a kelch domain-containing protein involved in cell fusion and morphology in Saccharomyces cerevisiae

We showed previously that protein kinase C, which is required to maintain cell integrity, negatively regulates cell fusion (Philips, J., and I. Herskowitz. 1997. J. Cell Biol. 138:961-974). To identify additional genes involved in cell fusion, we looked for genes whose overexpression relieved the defect caused by activated alleles of Pkc1p. This strategy led to the identification of a novel gene, KEL1, which encodes a protein composed of two domains, one containing six kelch repeats, a motif initially described in the Drosophila protein Kelch (Xue, F., and L. Cooley. 1993. Cell. 72:681- 693), and another domain predicted to form coiled coils. Overexpression of KEL1 also suppressed the defect in cell fusion of spa2Delta and fps1Delta mutants. KEL2, which corresponds to ORF YGR238c, encodes a protein highly similar to Kel1p. Its overexpression also suppressed the mating defect associated with activated Pkc1p. Mutants lacking KEL1 exhibited a moderate defect in cell fusion that was exacerbated by activated alleles of Pkc1p or loss of FUS1, FUS2, or FPS1, but not by loss of SPA2. kel1Delta mutants form cells that are elongated and heterogeneous in shape, indicating that Kel1p is also required for proper morphology during vegetative growth. In contrast, kel2Delta mutants were not impaired in cell fusion or morphology. Both Kel1p and Kel2p localized to the site where cell fusion occurs during mating and to regions of polarized growth during vegetative growth. Coimmunoprecipitation and two-hybrid analyses indicated that Kel1p and Kel2p physically interact. We conclude that Kel1p has a role in cell morphogenesis and cell fusion and may antagonize the Pkc1p pathway.

NS1-Binding protein (NS1-BP): a novel human protein that interacts with the influenza A virus nonstructural NS1 protein is relocalized in the nuclei of infected cells

We used the yeast interaction trap system to identify a novel human 70-kDa protein, termed NS1-binding protein (NS1-BP), which interacts with the nonstructural NS1 protein of the influenza A virus. The genetic interaction was confirmed by the specific coprecipitation of the NS1 protein from solution by a glutathione S-transferase-NS1-BP fusion protein and glutathione-Sepharose. NS1-BP contains an N-terminal BTB/POZ domain and five kelch-like tandem repeat elements of approximately 50 amino acids. In noninfected cells, affinity-purified antibodies localized NS1-BP in nuclear regions enriched with the spliceosome assembly factor SC35, suggesting an association of NS1-BP with the cellular splicing apparatus. In influenza A virus-infected cells, NS1-BP relocalized throughout the nucleoplasm and appeared distinct from the SC35 domains, which suggests that NS1-BP function may be disturbed or altered. The addition of a truncated NS1-BP mutant protein to a HeLa cell nuclear extract efficiently inhibited pre-mRNA splicing but not spliceosome assembly. This result could be explained by a possible dominant-negative effect of the NS1-BP mutant protein and suggests a role of the wild-type NS1-BP in promoting pre-mRNA splicing. These data suggest that the inhibition of splicing by the NS1 protein may be mediated by binding to NS1-BP.

The complete genomic sequence of the modified vaccinia Ankara strain: comparison with other orthopoxviruses

The complete genomic DNA sequence of the highly attenuated vaccinia strain modified vaccinia Ankara (MVA) was determined. The genome of MVA is 178 kb in length, significantly smaller than that of the vaccinia Copenhagen genome, which is 192 kb. The 193 open reading frames (ORFs) mapped in the MVA genome probably correspond to 177 genes, 25 of which are split and/or have suffered mutations resulting in truncated proteins. The left terminal genomic region of MVA contains four large deletions and one large insertion relative to the Copenhagen strain. In addition, many ORFs in this region are fragmented, leaving only eight genes structurally intact and therefore presumably functional. The inserted DNA codes for a cluster of genes that is also found in the vaccinia WR strain and in cowpox virus and includes a highly fragmented gene homologous to the cowpox virus host range gene, providing further evidence that a cowpox-like virus was the ancestor of vaccinia. Surprisingly, the central conserved region of the genome also contains some fragmented genes, including ORF F5L, encoding a major membrane protein, and ORFs F11L and O1L, encoding proteins of 39.7 and 77.6 kDa, respectively. The right terminal genomic region carries three large deletions all classical poxviral immune evasion genes and all ankyrin-like genes located in this region are fragmented except for those encoding the interleukin-1 beta receptor and the 68-kDa ankyrin-like protein B18R. Thus, the attenuated phenotype of MVA is the result of numerous mutations, particularly affecting the host interactive proteins, including the ankyrin-like genes, but also involving some structural proteins.

Genetic analysis of the actin cytoskeleton in the Drosophila ovary

The Drosophila ovary provides a favorable model system in which to study cellular morphogenesis. The development of a mature egg involves a syncytium of 16 germline cells and over 1000 somatically derived follicle cells. Intercellular transport, stable intercellular bridges, cell migrations, cell shape changes, and specific subcellular localization of many embryonic patterning determinants contribute to egg development and require a dynamic cytoskeleton. We discuss many of the recent genetic and cell biological studies that have led to insights into how the actin cytoskeleton is assembled and regulated during the morphogenesis of the Drosophila egg.

Drosophila kelch is an oligomeric ring canal actin organizer

Drosophila kelch has four protein domains, two of which are found in kelch-family proteins and in numerous nonkelch proteins. In Drosophila, kelch is required to maintain ring canal organization during oogenesis. We have performed a structure-function analysis to study the function of Drosophila kelch. The amino-terminal region (NTR) regulates the timing of kelch localization to the ring canals. Without the NTR, the protein localizes precociously and destabilizes the ring canals and the germ cell membranes, leading to dominant sterility. The amino half of the protein including the BTB domain mediates dimerization. Oligomerization through the amino half of kelch might allow cross-linking of ring canal actin filaments, organizing the inner rim cytoskeleton. The kelch repeat domain is necessary and sufficient for ring canal localization and likely mediates an additional interaction, possibly with actin.

Examination of the function of two kelch proteins generated by stop codon suppression

The Drosophila kelch gene produces a single transcript with a UGA stop codon separating two open reading frames (ORF1 and ORF2). From the transcript, 76 kDa ORF1 and 160 kDa full-length (ORF1 + ORF2) proteins are made. The expression of these two proteins is regulated in a tissue-specific manner causing the ratio of full-length to ORF1 protein to vary in different tissues. The only detected defect for kelch mutants is female sterility, and kelch protein is localized to the ovarian ring canals. kelch mutant ring canals are disorganized and have partly occluded lumens, causing a failure to transport cytoplasm. ORF1 and full-length kelch proteins co-sediment with ring canals suggesting that both proteins are found in the ring canals. Transgenetic analysis reveals that ORF1 kelch protein is sufficient to rescue ring canal morphology and fertility. In addition, we have mutated the UGA stop codon to a UAA stop codon and to three sense codons that allow constitutive readthrough. Analysis of these mutants reveals that a full-length kelch protein can partially compensate for the loss of endogenous kelch, but the residue included at the stop codon is critical for function. Finally, these studies suggest that the mechanism of stop codon suppression of kelch is by tRNA suppression.

Characterization of the actin cross-linking properties of the scruin-calmodulin complex from the acrosomal process of Limulus sperm

During activation of the Limulus sperm acrosomal process, actin filaments undergo a change in twist that is linked with the conversion from a coiled to a straight scruin-actin bundle. Since scruin had not been purified, its identity as an actin-binding protein has not been demonstrated. Using HECAMEG (methyl-6-O-(N-heptyl-carbamoyl)-alpha-D-glucopyranoside) detergent extraction in concert with high calcium, we purified native scruin and identified it as an equimolar complex with calmodulin. 125I-Calmodulin overlays and calmodulin-Sepharose indicate that scruin binds calmodulin in calcium but not in EGTA. Overlay experiments also map the calmodulin binding site between the putative N- and C-terminal beta-propeller domains within residues 425-446. Immunofluorescence microscopy reveals that calmodulin colocalizes with scruin and actin in the coiled bundle. Although scruin binds calmodulin, pelleting assays and electron microscopy show that the scruin cross-links F-actin into bundles independently of calcium. Based on our biochemical and structural studies, we suggest a model to explain how scruin controls a change in twist of actin filaments during the acrosome reaction. We predict that calcium subtly alters scruin conformation through its calmodulin subunit and the conformation change in scruin causes a shift in the relative positions of the scruin-bound actin subunits.

M-caveolin, a muscle-specific caveolin-related protein

Caveolae, small invaginations of the plasma membrane, are a characteristic feature of many mammalian cells. The best-characterised caveolar protein is the integral membrane protein, VIP21-caveolin. We now describe a novel homologue of VIP21-caveolin, M-caveolin, which is expressed exclusively in muscle. M-caveolin was shown to be expressed in differentiated myotubes but not myoblasts. Epitope-tagged M-caveolin expressed in non-muscle cells was targetted to surface caveolae where it colocalized with endogenous VIP21-caveolin. M-caveolin may play a specialised role in the caveolae of muscle cells.

M-caveolin, a muscle-specific caveolin-related protein

Caveolae, small invaginations of the plasma membrane, are a characteristic feature of many mammalian cells. The best-characterised caveolar protein is the integral membrane protein, VIP21-caveolin. We now describe a novel homologue of VIP21-caveolin, M-caveolin, which is expressed exclusively in muscle. M-caveolin was shown to be expressed in differentiated myotubes but not myoblasts. Epitope-tagged M-caveolin expressed in non-muscle cells was targetted to surface caveolae where it colocalized with endogenous VIP21-caveolin. M-caveolin may play a specialised role in the caveolae of muscle cells.