N-and C-terminal Domains Research Articles

YpeB dimerization may be required to stabilize SleB for effective germination of Bacillus anthracis spores

BackgroundBacillus cells faced with unfavorable environmental conditions undergo an asymmetric division process ultimately leading to the formation of the bacterial spore. In some instances the spore serves as an infectious agent; such is the case with the spore of Bacillus anthracis and the disease anthrax. Spores are resistant to a variety of environment conditions including traditional decontamination techniques due to the formation of specialized cellular structures. One such structure, the spore cortex, is a thick layer of modified peptidoglycan that contributes to spore dormancy through maintenance of the dehydrated state of the spore core. During spore germination, degradation of the cortex is required to facilitate complete hydration of the core and a return to vegetative growth. Degradation of the cortex is accomplished through the action of germination-specific lytic enzymes. One of these enzymes, SleB, has been previously shown to require the presence of the YpeB protein for its stable incorporation and subsequent function in spores of B. anthracis. The focus of the present study is to identify protein interactions of YpeB through in vivo chemical cross-linking and two-hybrid analysis.ResultsConserved residues within YpeB PepSY domains were altered to facilitate implementation of a site-specific chemical cross-linker, 4-Azidophenacyl bromide. Analyses of crosslinked-spore extracts suggests that YpeB exists as a dimer or larger multimer within the spore, potentially mediated through interactions of the C-terminal domains. Spores expressing stable truncated forms of YpeB were crosslinked and corresponding truncated dimers were detected. Further characterization of individual YpeB domains using bacterial two-hybrid analysis indicated a possible role for both N-and C-terminal domains in YpeB oligomerization.ConclusionsThe YpeB protein likely exists as dimer or higher-order multimer in the dormant spore. Both the N- and C-terminal YpeB domains contribute to multimerization. SleB likely also exists as an oligomer, and SleB and YpeB may be found together within a protein complex. Disassembly of this complex during spore germination likely allows SleB to become active in spore cortex degradation. Further study of this protein complex may contribute to the development of methods to inhibit or stimulate germination, allowing more effective spore decontamination.

Effect of the additional cysteine 503 of vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) and the mechanism of AhpF and subunit C assembling

The vancomycin-resistant Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) is of paramount importance to restore redox homeostasis. Therefore, knowledge about this defense system is essential to understand its antibiotic-resistance and survival in hosts. Recently, we described the crystallographic structures of EfAhpC, the two-fold thioredoxin-like domain of EfAhpF, the novel phenomenon of swapping of the catalytic domains of EfAhpF as well as the unique linker length, connecting the catalytically active N-and C-terminal domains of EfAhpF. Here, using mutagenesis and enzymatic studies, we reveal the effect of an additional third cysteine (C503) in EfAhpF, which might optimize the functional adaptation of the E. faecalis enzyme under various physiological conditions. The crystal structure and solution NMR data of the engineered C503A mutant of the thioredoxin-like domain of EfAhpF were used to describe alterations in the environment of the additional cysteine residue during modulation of the redox-state. To glean insight into the epitope and mechanism of EfAhpF and -AhpC interaction as well as the electron transfer from the thioredoxin-like domain of EfAhpF to AhpC, NMR-titration experiments were performed, showing a coordinated disappearance of peaks in the thioredoxin-like domain of EfAhpF in the presence of full length EfAhpC, and indicating a stable EfAhpF-AhpC-complex. Combined with docking studies, the interacting residues of EfAhpF were identified and a mechanism of electron transfer of the EfAhpF donor to the electron acceptor EfAhpC is described.

Backbone 1H, 13C and 15N chemical shift assignment of full-length human uracil DNA glycosylase UNG2.

Human uracil N-glycosylase isoform 2-UNG2 consists of an N-terminal intrinsically disordered regulatory domain (UNG2 residues 1-92, 9.3kDa) and a C-terminal structured catalytic domain (UNG2 residues 93-313, 25.1kDa). Here, we report the backbone 1H, 13C, and 15N chemical shift assignment as well as secondary structure analysis of the N-and C-terminal domains of UNG2 representing the full-length UNG2 protein.

Lipid Transfer Mechanism of CETP between HDL and LDL: A Coarse-Grained Simulation Study

Cholesteryl ester transfer protein (CETP) mediates the bidirectional exchange of cholesteryl esters (CEs) and triglycerides between HDL and LDL (1)⁠. Animal models along with early clinical studies have demonstrated that the impairment of CETP's functionality is important for the efficient treatment of cardiovascular diseases. Despite the pharmacological interest, CETP's lipid transfer mechanism is poorly understood. Recent cryo-electron microscopy studies suggested that CETP penetrates its N-and C-terminal β-barrel domains into HDL and LDL respectively to form a ternary complex (2)⁠. Further it was proposed that the hydrophobic tunnel of CETP can simultaneously interact with the core of HDL and LDL for continuous lipid exchange. However, the detailed lipid transfer process is still inconclusive. In this study, we employed coarse-grained molecular dynamics simulations to illuminate the lipid transfer mechanism of CETP in HDL-CETP-LDL ternary complex. The extent of penetration of CETP into HDL and LDL in our ternary complex model corroborated well with the experimental findings. Further, the results demonstrated that the ejection of C-terminal plug-in phospholipid (PLC) and subsequently the diffusion of CETP-bound CEs into LDL droplet through PLC opening. A detailed analysis on interactions of PLC pocket lining residues with the discharged lipids revealed residues with significant role in CE transfer. The detailed mechanism of lipid transfer by CETP as explored in this study might help designing future CETP research and subsequent CETP therapeutics.

The Anti-HIV-1 Cytidine Deaminase APOBEC3G Is a Cellular Site-Specific RNA Editing Enzyme

Background:The APOBEC3 (A3) family of cytidine deaminases in primates is comprised of seven homologous enzymes that are structurally related to the RNA editing enzyme APOBEC1. APOBEC3G (A3G) is a restriction factor for HIV-1 and endogenous retroviruses, and is highly expressed in T lymphocytes. Encapsidation of A3G into HIV-1 particles is essential for its antiviral activity which leads to hypermutation of its cDNA in target cells, and requires RNA binding by A3G to form a ribonucleoprotein complex with viral proteins. A3G can also reduce HIV-1 production in producer cells independently of its DNA deaminating activity. A3G has homologous N-and C-terminal catalytic domains (NTD and CTD) but only the CTD is active for deamination of ssDNAs. The zinc-coordinating catalytic residues as well as non-catalytic residues in A3G-NTD are known to bind RNA and this interaction is required for A3G's binding to the HIV-1 nucleocapsid for recruitment into nascent virions as well as for A3G dimerization. A3G binds to DNA and RNA substrates with similar affinity. Thus far, studies have demonstrated DNA deamination by A3G whereas deamination has not been observed in HIV-1 RNA or synthetic RNA oligonucleotides, thereby, ruling out the RNA editing function of A3G. We recently described that the structurally related enzyme A3A induces widespread site-specific C-to-U RNA editing of cellular transcripts in pro-inflammatory macrophages and in monocytes exposed to hypoxia and/or interferons. We hypothesized that A3G may also have RNA editing function, which may play a role in HIV-1 restriction.Methods:To determine if A3G is capable of RNA editing, we transiently overexpressed the protein in 293T cells, a model routinely used by various labs to study A3G function and its mode of HIV-1 restriction, and then performed transcriptome-wide RNA sequencing (RNA-Seq), Sanger sequencing and site-directed mutagenesis.Results: RNA sequencing analysis showed site-specific RNA editing in hundreds of genes' transcripts, including approximately 200 genes that acquire protein recoding. The transcripts edited by A3G are largely distinct from those edited by A3A. We find that several host genes including NMT1, CHMP4B, MAPK1, ACIN1, MED1, NFAT5, RBM14 which areinvolved in HIV-1 infection acquire pathogenic recoding RNA mutations by A3G-mediated RNA editing. By performing Sanger sequencing of PCR-amplified cDNA, we validated site-specific, non-synonymous C-to-U RNA editing for 21 of 21 (100%) tested sites in 20 genes that we had selected for experimental confirmation. As expected no genomic mutations were seen in the DNA sequences corresponding to the RNA-edited sites in 11 tested genes. The discovery of A3G's RNA editing function prompted us to study the role of the N-terminal domain in RNA editing. We made mutations in the zinc-coordinating and non-catalytic residues in both N-terminal and C-terminal domains of A3G. We demonstrate that mutating zinc-coordinating residues in either N- and C-terminal domains of A3G in 293T cells greatly reduce or abolish editing in its target transcripts.Conclusions: We demonstrate a novel RNA editing function for the A3G cytidine deaminase. Our study shows that the RNAs of genes involved in HIV-1 replication, assembly, transcription and infectivity are targets of A3G-mediated RNA editing. This result raises the possibility that the editing of host transcripts may be a novel mechanism by which HIV-1 infection is inhibited by A3G. Our findings suggest a previously unrecognized role for the N-terminal domain of A3G in RNA editing. A3G is the second of the seven members of the APOBEC3 family of cytidine deaminases and the first two-domain cytidine deaminase for which a previously unrecognized RNA editing activity has been discovered. It suggests that other APOBEC3 proteins may also possess hitherto unknown RNA editing activity that may underpin some of their biological roles. Our findings have the potential to significantly expand on the role of C-to-U RNA editing in epitranscriptomic regulation in T lymphocytes, define specific gene targets of A3G-mediated RNA editing and open new avenues of inquiry on the functions of APOBEC3 genes in HIV-1 restriction. DisclosuresNo relevant conflicts of interest to declare.

Distinct functional domains of PNMA5 mediate protein-protein interaction, nuclear localization, and apoptosis signaling in human cancer cells.

Members of paraneoplastic Ma (PNMA) family have been identified as onconeuronal antigens, which aberrant expressions in cancer cells of patients with paraneoplastic disorder (PND) are closely linked to manifestation of auto-immunity, neuro-degeneration, and cancer. The purpose of present study was to determine the role of PNMA5 and its functional relationship to MOAP-1 (PNMA4) in human cancer cells. PNMA5 mutants were generated through deletion or site-directed mutagenesis and transiently expressed in human cancer cell lines to investigate their role in apoptosis, subcellular localization, and potential interaction with MOAP-1 through apoptosis assays, fluorescence microscopy, and co-immunoprecipitation studies, respectively. Over-expressed human PNMA5 exhibited nuclear localization pattern in both MCF-7 and HeLa cells. Deletion mapping and mutagenesis studies showed that C-terminus of PNMA5 is responsible for nuclear localization, while the amino acid residues (391KRRR) within the C-terminus of PNMA5 are required for nuclear targeting. Deletion mapping and co-immunoprecipitation studies showed that PNMA5 interacts with MOAP-1 and N-terminal domain of PNMA5 is required for interaction with MOAP-1. Furthermore, co-expression of PNMA5 and MOAP-1 in MCF-7 cells significantly enhanced chemo-sensitivity of MCF-7 to Etoposide treatment, indicating that PNMA5 and MOAP-1 interact synergistically to promote apoptotic signaling in MCF-7 cells. Our results show that PNMA5 promotes apoptosis signaling in HeLa and MCF-7 cells and interacts synergistically with MOAP-1 through its N-terminal domain to promote apoptosis and chemo-sensitivity in human cancer cells. The C-terminal domain of PNMA5 is required for nuclear localization; however, both N-and C-terminal domains of PNMA5 appear to be required for pro-apoptotic function.

Role of SIRT7 in hepatic lipid metabolism

Sirtuins are evolutionarily conserved enzymes that regulate a wide variety of biological processes, such as aging, genomic stability, tumorigenesis, and metabolism [1]. To date, seven sirtuins have been identified in mammals (SIRT1–SIRT7), which share a highly conserved NADbinding and catalytic core domain, but have distinct flanking Nand C-terminal domains. The divergent Nand C-termini of sirtuins are responsible for the different functions and subcellular localizations of these enzymes. Although sirtuins were originally described as NAD-dependent histone deacetylases, these enzymes are now known to act not only on histones, but also on numerous transcription factors and enzymes. SIRT1 controls the acetylation of proliferator-activated receptor-c co-activator 1a (PGC1a), p53, and forkhead box O, among other targets, whereas SIRT3 is a major deacetylase in mitochondria [2, 3]. In addition, a few sirtuins have either weak or undetectable deacetylase activity. For example, SIRT4 is reported to act as an ADP-ribosyltransferase [4], and SIRT5 has both demalonylase and desuccinylase activities [5]. SIRT6 has been shown to deacetylate acetylated lysine 9 of histone H3 (H3K9Ac) and was also recently reported to preferentially hydrolyze long-chain fatty acyl groups on acylated protein targets [6]. SIRT7 mRNA is ubiquitously expressed in all tissues examined to date, with the exception of skeletal muscle [7]. Human (NP_057622.1), mouse (NP_694696.2), and rat (NP_001100543.1) SIRT7 proteins consist of 400, 402, and 402 amino acids, respectively. Human SIRT7 contains a conserved NAD-binding and catalytic core domain (amino acids 90–331) as well as flanking N-terminal (amino acids 1–89) and C-terminal (332–400) regions (Fig. 1a). The histidine residue at position 187 (H187) (corresponding to mouse H188) is highly conserved among sirtuins and is reported to be important for binding with NAD [8]. The N-terminal region of SIRT7 contains a nuclear localization signal (NLS) (LQGRSRRREGLKRRQE, amino acids 61–76), and the C-terminal region contains a nucleolar localization signal (NoLS) (KRTKRKKVT, amino acids 392–400) [9]. SIRT7 is enriched in the nucleolus, but is also present in the nucleoplasm (Fig. 1b). In contrast to SIRT1 to SIRT6, the enzymatic activity and physiological functions of SIRT7 were poorly defined until recently. SIRT7 was first reported to promote ribosomal RNA transcription by interacting with RNA polymerase I (Pol I) and the transcription factor UBF [7, 10]. PAF53, a subunit of Pol I that is required for rDNA transcription, was recently identified as a target of SIRT7 [11]. SIRT7 was also shown to function as NAD-dependent deacetylase with high selectivity for acetylated lysine 18 of histone H3 (H3K18Ac) [12]. This deacetylase activity plays a role in the gene-specific transcriptional repression of a select subset of H3K18Ac-containing promoters, such as RPS20 and NME1 [12]. H3K18Ac-specific deacetylation by SIRT7 is important for maintaining the phenotype and stabilizing the tumorigenicity of human cancer cells [12]. Our group also demonstrated that Myb-binding protein 1a (Mybbp1a) binds to SIRT7, thereby inhibiting the deacetylation of H3K18 [13]. & Kazuya Yamagata k-yamaga@kumamoto-u.ac.jp

Recombinant production and characterization of full-length and truncated β-1,3-glucanase PglA from Paenibacillussp. S09

Backgroundβ-1,3-Glucanases catalyze the hydrolysis of glucan polymers containing β-1,3-linkages. These enzymes are of great biotechnological, agricultural and industrial interest. The applications of β-1,3-glucanases is well established in fungal disease biocontrol, yeast extract production and wine extract clarification. Thus, the identification and characterization of novel β-1,3-glucanases with high catalytic efficiency and stability is of particular interest.ResultsA β-1,3-glucanase gene designated PglA was cloned from a newly isolated strain Paenibacillus sp. S09. The gene PglA contained a 2631-bp open reading frame encoding a polypeptide of 876 amino acids which shows 76% identity with the β-1,3-glucanase (BglH) from Bacillus circulans IAM1165. The encoded protein PglA is composed of a signal peptide, an N-terminal leader region, a glycoside hydrolase family 16 (GH16) catalytic domain and a C-terminal immunoglobulin like (Ig-like) domain. The Escherichia coli expression system of PglA and five truncated derivatives containing one or two modules was constructed to investigate the role of catalytic and non-catalytic modules. The pH for optimal activity of the enzymes was slightly affected (pH 5.5-6.5) by the presence of different modules. However, the temperature for optimal activity was strongly influenced by the C-terminal domain and ranged from 50 to 60°C. Deletion of C-terminal domain resulted in obviously enhancing enzymatic thermostability. Specific activity assay indicated that PglA specifically hydrolyzes β-1,3-glucan. Insoluble β-1,3-glucan binding and hydrolysis were boosted by the presence of N-and C-terminal domains. Kinetic analysis showed that the presence of N-and C-terminus enhances the substrate affinity and catalytic efficiency of the catalytic domain toward laminarin. Carbohydrate-binding assay directly confirmed the binding capabilities of the N-and C-terminal domains.ConclusionsThis study provides new insight into the impacts of non-catalytic modules on enzymatic properties of β-1,3-glucanase. Activity comparison of full-length PglA and truncated forms revealed the negative effect of C-terminal region on thermal stability of the enzyme. Both the N-and C-terminal domains exerted strong binding activity toward insoluble β-1,3-glucan, and could be classified into CBM families.

A new β-glucosidase gene from the zygomycete fungus Rhizomucor miehei

In this study, a beta-glucosidase coding gene (bgl) of the zygomycete fungus Rhizomucor miehei has been cloned and characterized. The gene comprises a total of 2,826 bp including the coding sequence of a 717 amino acids length putative protein and 10 introns dispersed in the whole coding region. The putative N-and C-terminal catalytic domains (aa 68 to aa 274 and aa 358-601, respectively) were identified; the two domains are connected with a 84-amino-acids linker. The catalytic region showed an extensive sequence homology with other fungal beta-glucosidases classified as family 3 glycoside hydrolases. The isolated Rhizomucor gene was expressed in the related fungus Mucor circinelloides. Transformant Mucor strains maintained the introduced plasmid in an autoreplicative manner and showed significantly higher cellobiase activity than the recipient strain.

SNASP, a Histone H1-Specific Eukaryotic Chaperone Dimer that Facilitates Chromatin Assembly

NASP has been described as a histone H1 chaperone in mammals. However, the molecular mechanisms involved have not yet been characterized. Here, we show that this protein is not only present in mammals but is widely distributed throughout eukaryotes both in its somatic and testicular forms. The secondary structure of the human somatic version consists mainly of clusters of α-helices and exists as a homodimer in solution. The protein binds nonspecifically to core histone H2A-H2B dimers and H3-H4 tetramers but only forms specific complexes with histone H1. The formation of the NASP-H1 complexes is mediated by the N-and C-terminal domains of histone H1 and does not involve the winged helix domain that is characteristic of linker histones. In vitro chromatin reconstitution experiments show that this protein facilitates the incorporation of linker histones onto nucleosome arrays and hence is a bona fide linker histone chaperone.

An Arthropod Cuticular Chitin-binding Protein Endows Injured Sites with Transglutaminase-dependent Mesh

In mammals, the cornified cell envelope forms beneath the plasma membrane in epithelia and provides a vital physical barrier consisting of insoluble proteins cross-linked by transglutaminase (TGase). In the horseshoe crab Tachypleus tridentatus, TGase is stored in hemocytes and secreted in response to the simulation of bacterial lipopolysaccharides. Here we characterized a TGase substrate designated as caraxin that was identified in horseshoe crab cuticle. One of the homologs, caraxin-1, possessed a unique domain structure consisting of N-and C-terminal heptad repeats and a central domain with a tandem-repeated structure of a pentapeptide. Western blotting showed the specific localization of caraxin-1 in sub-cuticular epidermis. Moreover, we identified the pentapeptide motif to be a chitin-binding unit. Analytical ultracentrifugation revealed that caraxin-1 exists as an oligomer with 310-350 kDa, which is approximately 20-mer based on the molecular mass of the monomer. The oligomers were cross-linked by TGase to form an elaborate mesh with honeycomb structures, which was electron-microscopically found to be different from the clotting mesh triggered by lipopolysaccharide-induced hemocyte exocytosis. We determined several cross-linking sites in the N-and C-terminal domains of caraxin-1. The replacements of Leu to Pro at positions 36 and 118 in caraxin-1 reduced the alpha-helix content, which destroyed the TGase-dependent mesh, thus indicating the importance of the N-and C-terminal domains for the proper mesh formation. In arthropods, TGase-dependent protein cross-linking may be involved in the initial stage of host defense at the sub-cuticular epidermis, as in the case of mammalian skin.

On a roll for new TRF targets: Figure 1.

In the early 1990s, one of us wrote in these pages a review entitled “TBP, a universal transcription factor?” (Hernandez 1993). At the time, it had become clear that the TATA-box-binding protein TBP was not a transcription factor exclusively involved in transcription from RNA polymerase II (pol II) promoters as had been thought before, but rather a factor involved in transcription by all three main types of eukaryotic nuclear RNA polymerases. In retrospect, however, the question mark at the end of the title was a wise touch! Indeed, shortly thereafter, the first TBP-related factor, TRF1, was described (Crowley et al. 1993). Since then, two more TRFs have been discovered (for review, see Berk 2000; Davidson 2003; Hochheimer and Tjian 2003), and it was found that some genes dispense with TBP and TRFs altogether (Wieczorek et al. 1998). This “expansion” of TBP into a TBP family of proteins begs the question of which promoters are targeted by which TBP family member. In this issue of Genes & Development, Isogai et al. (2007a) report that the TATA-less histone H1 promoter is regulated by TRF2. This provides a possible mechanism for earlier observations linking TRF2 with chromatin structure (Martianov et al. 2002; Kopytova et al. 2006). Furthermore, the identification by Isogai et al. (2007a) of a large number of TRF2-bound sites in the Drosophila genome helps to establish Drosophila TRF2 as a broadly used core-promoter factor. Among the three classes of TBP-related factors described so far, TRF2—also called TBP-like protein (TLP) or TBP-like factor (TLF)—is the only one to be widely present in metazoans (Ohbayashi et al. 1999; Kaltenbach et al. 2000; Veenstra et al. 2000). TRF1 has been found only in Drosophila and Anopheles (Crowley et al. 1993; Isogai et al. 2007b), and TRF3 is restricted to vertebrates (Persengiev et al. 2003). All three proteins contain a core domain related to the TBP C-terminal core domain, and some also contain variable Nand C-terminal domains.

The Intersubunit Interaction Interface in the Kir 1.1 (ROMK) Channel Controls pH‐Dependent Gating

Our previous studies on Bartter’s disease mutations in Kir 1.1 suggested a cytoplasmic C-terminal tail domain, involving residues 331–361, folds onto the cytoplasmic N-terminus of an adjacent subunit to maintain the local structure around the pH-trigger, K80, in an open state. Here, we critically test this hypothesis. A series of strategic mutations in the cytoplasmic N-and C-terminal domains were created and pH-dependent channel gating was examined. Alanine scanning mutagensis in the relevant C-terminal region pinpointed the pH-gating determinant to short track of amino-acids (335–343). This region precisely encompasses the beta-M stand, a structure predicted to form the chief C-terminal intersubunit interaction site. Point mutations in the beta-M strand (V339A, D340A, F341A) uniquely altered pH-dependent channel gating and these effects were specifically rescued with a suppressor mutation in the pH trigger (K80M). Channels bearing N-terminal mutations in the parallel beta-A strand exhibited identical gating phenotypes as channels bearing the C-terminal mutations. In summary, the beta-A/ beta-M intersubunit interaction interface in Kir 1.1 controls pH-dependent gating. Such an interaction may provide a mechanism to translate physiological relevant chemical modification of cytoplasmic COOH, such as phosphorylation or PIP2-binding, to the pH-dependent gating process.

Functional characterization of cadmium-responsive garlic gene AsMT2b: A new member of metallothionein family

A new gene of metallothionein (MT) family was cloned from garlic (Allium sativum) seedlings using RACE method and designated AsMT2b. The full length of AsMT2b cDNA was 520 bp encoding 80 amino acids. The deduced amino acids of AsMT2b showed that AsMT2b contained the characteristic structure of type 2 MT proteins, but the number and arrangement of the cysteine residues in the N-and C-terminal domains was different from other type 2 MT proteins. Semi-quantitative reverse transcriptase-PCR showed that transcript levels of AsMT2b were enhanced only in response to higher concentrations or longer incubation time of Cd. Such an expression pattern of AsMT2b greatly differed from that of other type 2 MT genes. Yeast cells transformed with this gene had improved resistance to Cd. AsMT2b overexpressing Arabidopsis showed stronger Cd tolerance and higher Cd accumulation compared with wild-type plants. These results suggest that AsMT2b should be useful in phytoremediation of Cd-polluted soil in the future.

Structure and Properties of the C-terminal Domain of Insulin-like Growth Factor-binding Protein-1 Isolated from Human Amniotic Fluid

Insulin-like growth factor (IGF)-binding protein-1 (IGFBP-1) regulates the activity of the insulin-like growth factors in early pregnancy and is, thus, thought to play a key role at the fetal-maternal interface. The C-terminal domain of IGFBP-1 and three isoforms of the intact protein were isolated from human amniotic fluid, and sequencing of the four N-terminal polypeptide chains showed them to be highly pure. The addition of both intact IGFBP-1 and its C-terminal fragment to cultured fibroblasts has a similar stimulating effect on cell migration, and therefore, the domain has a biological activity on its own. The three-dimensional structure of the C-terminal domain was determined by x-ray crystallography to 1.8 Angstroms resolution. The fragment folds as a thyroglobulin type I domain and was found to bind the Fe(2+) ion in the crystals through the only histidine residue present in the polypeptide chain. Iron (II) decreases the binding of intact IGFBP-1 and the C-terminal domain to IGF-II, suggesting that the metal binding site is close to or part of the surface of interaction of the two molecules.

Phosphorylation of Smad signaling proteins by receptor serine/threonine kinases.

Transforming growth factor-β (TGF-β) family members, which include TGF-βs, activins, and bone morphogenetic proteins (BMPs), elicit their multifunctional effects by binding to and complex formation of type I and type II serine/threonine kinase receptors (see Fig. 1). Each family member signals via distinct combinations of type I and type II receptors, both of which are required for signaling. Upon formation of the heteromeric receptor complex, the type I receptor is phosphorylated by the type II receptor kinase. Phosphorylation occurs predominantly in a region rich in glycine and serine residues (GS domain) in the juxtamembrane domain of the type I receptor, which possibly leads to a conformational change and thereby activates the type I receptor kinase (see Fig. 1) (, , ). The activated type I receptor propagates the signal downstream through transient interaction with, and phosphorylation of, particular Smoeand mad related protein (Smad) molecules (, , ). Certain Smads are phosphorylated directly by activated type I receptors in a differential manner; they are therefore termed pathway-restricted Smads. Whereas Smad2 and Smad3 act in TGF-β and activin pathways, Smad1, Smad5, and Smad8 are thought to act in BMP pathways. Phosphorylation occurs at the two most C-terminal serine residues in a conserved C-terminal Ser-Ser-X-Ser motif (see Fig. 2). Pathway-restricted Smads oligomerize with Smad4, which acts as a common mediator in TGF-β, activin, and BMP signaling. After translocation to the nucleus, the oligomers interact with DNA directly, or in complex with other DNA-binding proteins, and control transcription of target genes (see Figs. 1 and 2). Recently, inhibitory Smads, Smad6, and Smad7, have been identified that antagonize TGF-β family signaling (). Open image in new window Fig. 1. TGF-β signaling through Smad proteins. A hypothetical signal transduction pathway for TGF-β family members through their serine/threonine kinase receptors and downstream effector molecules of the Smad family, is depicted. Open image in new window Fig. 2. Functional domains in Smad proteins. Type I receptor-induced phosphorylation of pathway-restricted Smads may induce an unfolding of the N-and C-terminal domains (shown on left side), allowing heteromeric complex formation and transcriptional activation mediated by C-terminal domain and direct DNA-binding via N-terminal domain (shown on right side). The phospho-acceptor site of type I receptor kinase is indicated. The conserved regions in the N-terminal domain (MH1 domain) and C-terminal domain (MH2 domain), are indicated by black and hatched boxes, respectively.

Amino acids within the extracellular matrix (ECM) binding region (201-218) of rat insulin-like growth factor binding protein (IGFBP)-5 are important determinants in binding IGF-I.

The highly conserved N-and C-terminal domains of IGFBPs are believed to participate in IGF binding, but only recently have some of the critical residues in the IGFBP sequence involved in ligand binding been identified. Here we describe two highly conserved amino acids in the C-terminal domain of rat IGFBP-5 that are involved in binding IGF-I. Site-directed mutagenesis was used to produce two mutants, G203K and Q209A, of rIGFBP-5. Relative to wild-type rIGFBP-5, an 8-fold reduction in affinity for human IGF-I was found for recombinant G203K protein in both IGF-I ligand blots and solution phase ligand binding assays, and a 7-and 6-fold reduction for Q209A respectively. This shows that Gly203 and Gln209 in IGFBP-5 are important determinants in binding IGF-I, and due to their complete conservation in all IGFBP sequences, we suggest that they are likely to be involved in binding IGF-I in all six binding proteins. In addition, these two non-basic residues lie within the ECM binding region (201-218) of IGFBP-5, demonstrating that the C-terminus contains partially overlapping IGF-I and ECM binding sites. We therefore propose that heparin binding to basic amino acids in IGFBP-5 between 201-218 may physically occlude subsequent interaction between IGF-I and Gly203/Gln209, and that this may explain previous work of others showing reduced affinity of ECM bound IGFBP-5 for IGF-I.

Human mRNA Capping Enzyme (RNGTT) and Cap Methyltransferase (RNMT) Map to 6q16 and 18p11.22–p11.23, Respectively

Eukaryotic cellular and viral mRNAs contain a 59-terminal mGpppN cap structure, which has important consequences at multiple levels of gene expression including RNA splicing, 39 end formation, transcript stability, nuclear export, and translation initiation (6, 12, 15, 16). Recent studies have demonstrated that capping enzyme selectively binds to the phosphorylated, elongating form of RNA polymerase II (pol II) (23). This finding accounts for the specific capping of pol II transcripts. It may also provide new insights into how HIV tat protein promotes pol II phosphorylation by tat-activated kinase (TAK) to enhance polymerase processivity (5). Caps are formed on nascent pre-mRNAs by the sequential action of RNA 59-triphosphatase, which removes the g-phosphate of the initiating nucleotide, RNA guanylyltransferase, which transfers GMP from GTP to the resulting diphosphate end, and RNA (guanine-7) methyltransferase, which methylates the guanine N7 position of the newly formed GpppN termini (4, 12, 15). These three enzymatic activities are present as separate polypeptides in yeasts, and strains null for the triphosphatase (18), guanylyltransferase (14), or methyltransferase (7) are nonviable. Metazoans including humans contain a separate cap methyltransferase (RNA guanine-7-methyltransferase, RNMT), but the RNA 59-triphosphatase and guanylyltransferase activities are contained as Nand C-terminal domains in a bifunctional capping enzyme (RNGTT) encoded by a single gene (23). Despite this difference in genomic organization between uniand multicellular organisms, capping enzyme is functionally conserved, and Saccharomyces cerevisiae strains null for guanylyltransferase or RNA 59-triphosphatase are complemented for growth by the mammalian counterpart (21, 23). In light of the importance of mRNA capping for gene expression, we determined the chromosomal location of the human capping enzyme gene (RNGTT) by PCR using as template the NIGMS human/rodent somatic cell hybrid panel 2, version 3 (Coriell Institute for Medical Research Cell Repositories, Camden, NJ). This panel consists of DNA isolated from 24 human/rodent somatic cell hybrid lines that each retained one intact human chromosome. Primers 1, 59-CAGTGTGTCCATTCTGGCAGTGGTTTTG-39, and 2, 59GTGGGAGAGCATTTTCTGGTGACAGC-39, from the 39-UTR of the human capping enzyme cDNA sequence (Accession No. AF025654) were designed to give a human-specific 318-bp PCR product. PCR results demonstrated that the human capping enzyme gene RNGTT is located on chromosome 6 (data not shown). Fine-mapping was performed by PCR analysis of the GeneBridge 4 radiation hybrid panel (Research Genetics, Inc., Huntsville, AL) with 25 ng template genomic DNA and primers 1 and 2 in a 12.5-ml reaction. After an initial denaturation step at 94°C for 5 min, 35 cycles of amplification consisting of denaturation at 94°C for 30 s, annealing at 55°C for 30 s, and extension at 72°C for 30 s were performed, followed by a final extension of 5 min at 72°C. Amplification products were analyzed by agarose gel electrophoresis. Data were submitted to the Whitehead Institute/MIT Center for Genome Research STS mapping server for statistical analysis with the RHMAPPER software package (http://www-genome.wi.mit.edu/cgi-bin/contig/rhmapper.pl). The data vector for RNGTT was 00100 01101 02101 0011

The zebrafish Fgf-3 gene: cDNA sequence, transcript structure and genomic organization

We report the isolation and characterization of genomic and cDNA clones encoding zebrafish fibroblast growth factor 3 (FGF3). An initial cDNA clone was generated by PCR amplification using degenerate oligo primers corresponding to a conserved region of protein found in the mouse and human homologues. Screening a cDNA library made from 30–33-h-old zebrafish embryos with this PCR product led to the isolation of two cDNA clones. Sequence analysis of the longest cDNA insert (1810 bp) revealed a 256-amino-acid (aa) orf. The central region, composed of approx. 155 aa, shares 78% identity with the analogous region of Xenopus laevis FGF3 and 72% identity with the product of the more distantly related human gene. However, the N-and C-terminal domains of zebrafish FGF3 are very different from those of other known homologues. The cDNA was used as a probe on genomic DNA to create a physical map of the locus and to isolate a genomic clone encompassing the entire coding region and 5′ sequences. DNA sequencing and RNase protection analyses indicate that zebrafish Fgf-3 (ZFgf-3) is structurally analogous to the mouse gene and regulated through two different promoters. The transcription start point of the proximal promoter aligns to that of mouse promoter P3 and lies within a conserved region of sequence.

Two domains of superfamily I helicases may exist as separate proteins.

DNA and RNA helicases of superfamily I are characterized by seven conserved motifs. The five N-terminal motifs are separated from the two C-terminal ones by a spacer that is highly variable in both sequence and length, suggesting the existence of two distinct domains. Using computer methods for protein sequence analysis, we show that PhoH, an ATP-binding protein that is conserved in Escherichia coli and Mycobacterium leprae, is homologous to the putative N-terminal domain of the helicases, whereas the putative E. coli protein YjhR is homologous to the C-terminal domain. These findings suggest that the N-and C-terminal domains of superfamily I helicases have distinct activities, with only the N-terminal domain having the ATPase activity. It is speculated that PhoH and YjhR have evolved from helicases through deletion of the portions of the helicase genes coding for the C- and N-terminal domain, respectively.