Functional characterization of domains in AtTRB1, a putative telomere-binding protein in Arabidopsis thaliana

Telomeres are nucleoprotein structures ensuring the stability of eukaryotic chromosome ends. Two protein families, TRFL (TFL-Like) and SMH (Single-Myb-Histone), containing a specific telobox motif in their Myb domain, have been identified as potential candidates involved in a functional nucleoprotein structure analogous to human "shelterin" at plant telomeres. We analyze the DNA-protein interaction of the full-length and truncated variants of AtTRB1, a SMH-family member with a typical structure: N-terminal Myb domain, central H1/5 domain and C-terminal coiled-coil. We show that preferential interaction of AtTRB1 with double-stranded telomeric DNA is mediated by the Myb domain, while the H1/5 domain is involved in non-specific DNA-protein interaction and in the multimerization of AtTRB1.     

Interactions of putative telomere-binding proteins in Arabidopsis thaliana: identification of functional TRF2 homolog in plants

Telomere-binding proteins are required for forming the functional structure of chromosome ends and regulating telomerase action. Although a number of candidate proteins have been identified by homology searches to plant genome databases and tested for their affinity to telomeric DNA sequences in vitro, there are minimal data relevant to their telomeric function. To address this problem, we made a collection of cDNAs of putative telomere-binding proteins of Arabidopsis thaliana to analyse their protein-protein interactions with the yeast two-hybrid system. Our results show that one myb-like protein, AtTRP1, interacts specifically with AtKu70, the latter protein having a previously described role in plant telomere metabolism. In analogy to the interaction between human Ku70 and TRF2 proteins, our results suggest that AtTRP1 is a likely homolog of TRF2. The AtTRP1 domain responsible for AtKu70 interaction occurs between amino acid sequence positions 80 and 269. The protein AtTRB1, a member of the single myb histone (Smh) family, shows self-interaction and interactions to the Smh family proteins AtTRB2 and AtTRB3. Protein AtTRB1 also interacts with AtPot1, the Arabidopsis homolog of oligonucleotide-binding-fold-containing proteins which bind G-rich telomeric DNA. In humans, the TRF1-complex recruits hPot1 to telomeres by protein-protein interactions where it is involved in telomere length regulation. Possibly, AtTRB1 has a similar role in recruiting AtPot1.     

The GCN2 homologue in Arabidopsis thaliana interacts with uncharged tRNA and uses Arabidopsis eIF2α molecules as direct substrates

Phosphorylation of eIF2α is an important strategy for living organisms to adapt to metabolic and physiological changes that are often associated with external stimuli. GCN2 is one of the well‐studied eIF2α kinases in yeast and mammals, which is responsible for the survival of the organism under amino acid starvation. Despite the downstream reactions being quite divergent, AtGCN2 exhibits a high primary sequence similarity to its yeast and animal counterparts. In this study, we provide experimental evidence to show that AtGCN2 shares similar biochemical properties to the yeast and animal homologues. Our in vitro assays demonstrate the binding of the C‐terminus of AtGCN2 to uncharged tRNA molecules and the enzymatic activities of AtGCN2 on both eIF2α homologues in A. thaliana, thus providing essential information for further understanding the functions of plant general control non‐repressible (GCN) homologues.     

Folding type-specific secondary structure propensities of amino acids,derived from α-helical, β-sheet, α/β, and α+β proteins of known structures

Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35–49, 1998     

Mapping of interaction domains mediating binding between BACE1 and RTN/Nogo proteins

BACE1 is a membrane-bound aspartyl protease that specifically cleaves amyloid precursor protein (APP) at the beta-secretase site. Membrane bound reticulon (RTN) family proteins interact with BACE1 and negatively modulate BACE1 activity through preventing access of BACE1 to its cellular APP substrate. Here, we focused our study on RTN3 and further show that a C-terminal QID triplet conserved among mammalian RTN members is required for the binding of RTN to BACE1. Although RTN3 can form homo- or heterodimers in cells, BACE1 mainly binds to the RTN monomer and disruption of the QID triplet does not interfere with the dimerization. Correspondingly, the C-terminal region of BACE1 is required for the binding of BACE1 to RTNs. Furthermore, we show that the negative modulation of BACE1 by RTN3 relies on the binding of RTN3 to BACE1. The knowledge from this study may potentially guide discovery of small molecules that can mimic the effect of RTN3 on the inhibition of BACE1 activity.     

Perfluoroarene-based peptide macrocycles that inhibit the Nrf2/Keap1 interaction

The Nrf2/Keap1 interaction is a target in the development of new therapeutic agents, where inhibition of the interaction activates Nrf2 and leads to the generation of downstream anti-inflammatory effects. Peptides that mimic the β-turn in the Keap1 active site and are constrained by a disulfide bridge have high affinity for Keap1 but no intracellular activity. The introduction of a perfluoroalkyl-bridging group to constrain the peptides, coupled with a glutamic acid to proline replacement leads to a new peptide with a K_i of 6.1?nM for the Nrf2/Keap1 binding interaction, although this does not translate into intracellular activity.     

Interaction of iodinated vinculin, metavinculin and α-actinin with cytoskeletal proteins

Iodinated vinculin, metavinculin and α-actinin were used to probe the interaction of these proteins with electrophoretically separated cytoskeletal proteins. Using the gel overlay technique, we detected strong binding of ¹²⁵I-vinculin and ¹²⁵I-metavinculin to α-actinin, 175 kDa polypeptide, talin, vinculin and metavinculin themselves, and moderate binding to actin.¹²⁵I-α-actinin was capable of interacting with vinculin and metavinculin. The specific binding of ¹²⁵-I-α-actinin to vinculin and metavinculin immobilized on a polysterene surface was also demonstrated. We suggest that the ability of vinculin and α-actinin to form a complex may be realized in microfilament-membrane linkages.     

α-Helical coiled-coil oligomerization domains in extracellular proteins

Subunit oligomerization of many proteins is mediated by α-helical coiled-coil domains. 3,4-Hydrophobic heptad repeat sequences, the characteristic feature of the coiled-coil protein folding motif, have been found in a wide variety of gene products including cytoskeletal, nuclear, muscle, cell surface, extracellular, plasma, bacterial, and viral proteins. Whereas the majority of coiled-coil structures is represented by intracellular α-helical bundles that contain two polypeptide chains, examples of extracellular coiled-coil proteins are fewer in number. Most proteins located in the extracellular space form three-stranded α-helical assemblies. Recently, five-stranded coiled coils have been identified in thrombospondins 3 and 4 in cartilage oligomeric matrix protein, and the formation of a heterotetramer has been observed in in vitro studies with the recombinant asialoglycoprotein receptor oligomerization domain. Coiled-coil domains in laminins and probably also in tenascins and thrombospondins are responsible for the formation of tissue-specific isoforms by selective oligomerization of different polypeptide chains.     

The expression of α2β1 integrin and α smooth muscle actin in fibroblasts grown on collagen

The maturation of connective tissue involves the organization of collagen fibres by resident fibroblasts. Fibroblast attachment to collagen has been demonstrated to involve cell surface receptors, integrins of the β₁ family. Integrins are associated with cytoplasmic actin of microfilaments either directly or through focal adhesions. The major actin isoform of fibroblast microfilaments is β actin and to a lesser extent α smooth muscle (α SM) actin. Cultured human dermal fibroblasts derived from adult dermis, newborn foreskin or keloid scar were grown on either uncoated or collagen-coated surfaces. The expression and synthesis of both α₂β₁ integrin and α SM actin were followed by immunohistology and immunoprecipitation. Fibroblasts on uncoated surfaces expressed little α₂β₁ integrin on their surface, while 20 per cent of them demonstrated α SM actin within microfilaments. Fibroblasts grown on a collagen-coated surface minimally expressed α SM actin in microfilament structures and a majority of the cells were positive for α₂β₁ integrin on their membranes. Using [³⁵S]-methionine incorporation and immunoprecipitation, it was shown that fibroblasts grown in uncoated dishes synthesized more α SM actin than fibroblasts grown on collagen-coated dishes. In contrast, fibroblasts grown on collagen coated dishes synthesized more α₂β₁ integrin compared to the same cells grown on uncoated dishes. Fibroblasts maintained on a type I collagen upregulate the expression and synthesis of α₂β₁ integrin, and downregulate the expression and synthesis of α SM actin. © 1998 John Wiley & Sons, Ltd.     

Characterization of the interaction between Oidium heveae and Arabidopsis thaliana

Oidium heveae, an obligate biotrophic pathogen of rubber trees (Hevea brasiliensis), causes significant yield losses of rubber worldwide. However, the molecular mechanisms underlying the interplay between O. heveae and rubber trees remain largely unknown. In this study, we isolated an O. heveae strain, named HN1106, from cultivated H. brasiliensis in Hainan, China. We found that O. heveae HN1106 triggers the hypersensitive response in a manner that depends on the effector‐triggered immunity proteins EDS1 (Enhanced Disease Susceptibility 1) and PAD4 (Phytoalexin Deficient 4) and on salicylic acid (SA) in the model plant Arabidopsis thaliana. However, SA‐independent resistance also appears to limit O. heveae infection of Arabidopsis, because the pathogen does not produce conidiospores on npr1 (nonexpressor of pr1), sid2 (SA induction deficient 2) and NahG plants, which show disruptions in SA signalling. Furthermore, we found that the callose synthase PMR4 (Powdery Mildew Resistant 4) prevents O. heveae HN1106 penetration into leaves in the early stages of infection. To elucidate the potential mechanism of resistance of Arabidopsis to O. heveae HN1106, we inoculated 47 different Arabidopsis accessions with the pathogen, and analysed the plant disease symptoms and O. heveae HN1106 hyphal growth and conidiospore formation on the leaves. We found that the accession Lag2‐2 showed significant susceptibility to O. heveae HN1106. Overall, this study provides a basis for future research aimed at combatting powdery mildew caused by O. heveae in rubber trees.     

Targeting of the protein interaction site between FAK and IGF-1R

The interaction of focal adhesion kinase (FAK) and insulin-like growth factor-1 receptor (IGF-1R) plays an important role in cancer cell survival. Targeting this interaction with small molecule drugs could be a novel strategy in cancer therapy. By a series of pull-down assays using GST-tagged FAK fragments and His-tagged IGF-1R intracellular fragments, we showed that the FAK-NT2 (a.a. 127-243) domain directly interacts with the N-terminal part of the IGF-1R intracellular domain. Overexpressed FAK-NT2 domain was also shown to co-localize with IGF-1R in pancreatic cells. Computational modeling was used to predict the binding configuration of these two domains and to screen for small molecules binding to the interaction site. This strategy successfully identified a lead compound that disrupts FAK/IGF-1R interaction.     

Peroxidase activity of annexin 1 from Arabidopsis thaliana

On the basis of earlier reports suggesting that annexin A1 from Arabidopsis thaliana (AnnAt1) participates in limiting the excessive levels of reactive oxygen species during oxidative burst in plants, we examined the sensitivity of recombinant AnnAt1 to hydrogen peroxide and its peroxidase activity. Purified recombinant protein remains mostly alpha-helical and binds to lipids in a calcium-dependent manner. Upon oxidation recombinant AnnAt1 exhibits a tendency to form dimers in vitro. AnnAt1 is also sensitive to the presence of reducing agents, suggesting that AnnAt1 is a redox sensor in plant cells. Moreover, using two independent methods we found that AnnAt1 displayed peroxidase activity which is probably related to the presence of a heme-binding domain within AnnAt1, as present in other peroxidases. Indeed, site-directed mutagenesis within this domain resulted in a complete abrogation of the activity of AnnAt1. Furthermore, this activity was found to be sensitive to the phosphorylation state of the protein.     

The EGF-like proteins DLK1 and DLK2 function as inhibitory non-canonical ligands of NOTCH1 receptor that modulate each other's activities

The protein DLK2, highly homologous to DLK1, belongs to the EGF-like family of membrane proteins, which includes NOTCH receptors and their DSL-ligands. The molecular mechanisms by which DLK proteins regulate cell differentiation and proliferation processes are not fully established yet. In previous reports, we demonstrated that DLK1 interacts with itself and with specific EGF-like repeats of the NOTCH1 extracellular region involved in the binding to NOTCH1 canonical ligands. Moreover, the interaction of DLK1 with NOTCH1 caused an inhibition of basal NOTCH signaling in preadipocytes and mesenchymal multipotent cells. In this work, we demonstrate, for the first time, that DLK2 interacts with itself, with DLK1, and with the same NOTCH1 receptor region as DLK1 does. We demonstrate also that the interaction of DLK2 with NOTCH1 similarly results in an inhibition of NOTCH signaling in preadipocytes and Mouse Embryo fibloblasts. In addition, we demonstrate that a membrane DLK1 variant, lacking the sequence recognized by the protease TACE, also inhibits NOTCH signaling. Furthermore, both DLK1 and DLK2 are able to decrease NOTCH activity also when triggered by specific NOTCH ligands. However, the decrease in NOTCH signaling induced by overexpression of Dlk2 is reversed by the overexpression of Dlk1, and viceversa. We conclude that DLK1 and DLK2 act as inhibitory non-canonical protein ligands for the NOTCH1 receptor that modulate NOTCH signaling.     

Small molecule scaffolds that disrupt the Rev1-CT/RIR protein-protein interaction

Translesion synthesis (TLS) is a DNA damage tolerance mechanism that allows replicative bypass of DNA lesions, including DNA adducts formed by cancer chemotherapeutics. Previous studies demonstrated that suppression of TLS can increase sensitivity of cancer cells to first-line chemotherapeutics and decrease mutagenesis linked to the onset of chemoresistance, marking the TLS pathway as an emerging therapeutic target. TLS is mediated by a heteroprotein complex consisting of specialized DNA polymerases, including the Y-family DNA polymerase Rev1. Previously, we developed a screening assay to identify the first small molecules that disrupt the protein–protein interaction between the C-terminal domain of Rev1 (Rev1-CT) and the Rev1-interacting region (RIR) present in multiple DNA polymerases involved in TLS. Herein we report additional hit scaffolds that inhibit this key TLS PPI. In addition, through a series of biochemical, computational, and cellular studies we have identified preliminary structure–activity relationships and determined initial pharmacokinetic parameters for our original hits.     

Altered glycosylation of α(s)β1 integrins from rat colon carcinoma cells decreases their interaction with fibronectin

Malignant cell transformation is generally accompanied by changes in their interactions with environing matrix proteins in a way to facilitate their migration and generate invasion. Our results show the binding of rat colon adenocarcinoma PROb cells to fibronectin strongly reduced when compared to normal rat intestine epithelial cells. This decrease was not due to the level of α(s)β1 integrins expressed at the surface of the cell line. However, β₁- and α_(s)-associated subunits appeared to be structurally altered as shown by immunoprecipitation followed by electrophoresis. Pulse chase experiments using ³⁵S methionine evidenced differences in the biosynthesis of β1- and α (s) associated integrins: normal epithelial IEC18 cells required 16 h for maximal biosynthesis of the completely mature β1 subunit, while PROb cells did it within 4-6 h. Studies using endoglycosidases O, H, D, and N glycanase confirmed that the molecular weight alterations were due to abnormal glycosylation and suggested that α(s)β1 integrins of PROb cells could bear both mature complex and immature high mannose types while IEC18 cells borne only mature complex type oligosaccharidic chains. Treatment of both cell types with castanospermine, an inhibitor of N-glycosylation, reduced the differences observed in their adhesion to the fibronectin without significantly affecting β1 receptors expression at the cell surface. These results strongly suggest a role of the glycosylation of β1 receptors in the adhesion of rat colon adenocarcinoma PROb cells to fibronectin substrata. © 1996 Wiley-Liss, Inc.     

Ligand interaction of human α2-macroglobulin-α2-macroglobulin receptor studied by partitioning in aqueous two-phase systems

Alpha 2-macroglobulin (α2-M) is a major proteinase inhibitor in human blood and tissue. Besides its antiproteolytic potential, α2-M was found to modulate antigen- and mitogen-driven immune responses and cell growth by binding and transporting distinct cytokines, growth factors and hormones. The inhibitor is cleared from circulation by binding to a multifunctional cellular receptor present on different cell types. α2-M, as well as its receptor, are capable of binding a variety of ligands. In the present study we have applied aqueous two-phase systems to analyze the interaction of IL-1β and α2-M receptor to different forms of α2-M. The partition of IL-1β was changed by addition of transformed α2-M to the two-phase systems rather than by the native inhibitor. The interaction between IL-1β and α2-M was enhanced by divalent cations. In addition, the complex formation between ¹²⁵I-labelled receptor and α2-M could clearly be demonstrated by partitioning. In the presence of divalent cations, transformed α2-M, in contrast to the native inhibitor, effectively changed the partition of the receptor. However, the observed alteration of the partition coefficient was found to be less compared with the values obtained by partitioning of the receptor in the presence of whole plasma containing the inhibitor in equivalent concentrations. The results indicate that other components of the plasma exist which competitively bind to the receptor but independent of Ca²⁺-ions.     

17α-Ethyl-5β-estrane-3α,17β-diol, a biological marker for the abuse of norethandrolone and ethylestrenol in slaughter cattle

The metabolism of the illegal growth promoter ethylestrenol (EES) was evaluated in bovine liver cells and subcellular fractions of bovine liver preparations. Incubations with bovine microsomal preparations revealed that EES is extensively biotransformed into norethandrolone (NE), another illegal growth promoter. Furthermore, incubations of monolayer cultures of hepatocytes with NE indicated that NE itself is rapidly reduced to 17α-ethyl-5β-estrane-3α,17β-diol (EED). In vivo tests confirmed that, after administration of either EES or NE, EED is excreted as a major metabolite. Therefore, it was concluded that, both in urine and faeces samples, EED can be used as a biological marker for the illegal use of EES and/or NE. Moreover, by monitoring EED in urine or faeces samples, the detection period after NE administration is significantly prolonged. These findings were further confirmed by three cases of norethandrolone abuse in a routine screening program for forbidden growth promoters.