Synthesis and FTIR Conformational Studies of Peptides From the Basic Region of c-Jun: a Critical Analysis on the Basis of CD and NMR Data

Abstract

The peptide (35 residues) corresponding to the basic subdomain (bSD) of c-Jun (residues 252–281) and its fragments NP (N-terminal peptide, 1–19) and CP (C-terminal peptide, 1635) were synthesized in stepwise solid-phase using the tert-butyloxycarbonyl/benzyl strategy. In a previous paper, we have shown that during its binding to the DNA site CRE (cAMP- responsive element) the bSD structure was converted into α-helix from an initial random coil conformation [Krebs, D., Dahmani, B., El Antri, S., Monnot, M., Convert, O., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 231, 370–380 (1995)]. Our results suggested both a high flexibility and a helical potential in bSD, these two properties seeming crucial for the accommodation of the basic subdomain of c-Jun to its specific DNA targets. In this work, we assessed the conformational variability of bSD through the study of the secondary structures of its NP and CP fragments in trifluoroethanol (TFE)/²H₂O mixtures, using Fourier transform infrared (FTIR) spectroscopy. The IR results were critically analyzed in light of our previously reported circular dichroism (CD) and NMR data [Krebs, D., Dahmani, B., Monnot, M., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 235, 699–712 (1996)]. Upon addition of TFE, the relative areas of the seven components of the amide I band (1700–1620 cm^?1) reflected the conversion of a large amount of random coil conformation into α-helix for the two fragments and bSD. This effect was accompanied by more subtle variations of the less populated structures, in agreement with the results of CD and NMR experiments. The IR results stipulated the conservation of the parent bSD secondary structures in both fragments; however, NP and CP peptides did not display similar random-to-α-helix stabilization pattern upon additions of TFE to aqueous solutions. The profile from CD signal at 222 nm was found sigmoidal for NP and almost linear for CP, while that corresponding to the parent peptide bSD was just in between those of its fragments. Thus, the present study confirms the high flexibility and helix propensity of the c-Jun basic subdomain and suggests that the N- and C-terminal parts of the peptide do not follow the same random-to-helix conversion profile during their complexation with DNA.     

Isolation of DNA markers informative in purebred dog families by genomic representational difference analysis (gRDA)

Genomic Representational Difference Analysis (gRDA) is a subtractive DNA method to clone the differences between two related genomes, called tester and driver. We have evaluated this method to obtain polymorphic DNA markers for pedigree dogs. Amplified size-selected genomic restriction fragments (amplicons) of two dog littermates were repeatedly hybridized to each other in order to remove (subtract) those restriction fragments common to both sibs. Already after two rounds of subtractive hybridization, a clear enrichment of presumably tester-specific restriction fragments was observed, which was even more pronounced after the third round of subtraction. A plasmid library of 3000 recombinant clones was constructed of the second round and of the third round difference product. DNA sequence determination of randomly chosen clones of each difference product showed that approximately 1000 unique clones were obtained in the second-round difference product and approximately 500 in the third-round difference product. About half of the clones identified in the second-round difference product were also present in the third-round difference product. Of the second-round difference product, 39 different gRDA fragments could be identified, of which 21 were tester specific. In the third-round difference product, 22 different gRDA fragments were identified, of which 18 were tester specific. There were 13 fragments in common, resulting in a total of 48 different fragments. In order to establish the localization of these markers, we performed mapping using the dog radiation hybrid panel RHDF5000. Of 39 mapped clones, 29 were mapped to 20 existing RH groups, and 10 remained unlinked. It is concluded that gRDA is suitable to generate DNA markers to track disease genes within lines of pedigree dogs. Received: 26 April 2000 / Accepted: 11 May 2000     

Analysis of SRC Oncogenic Signaling in Colorectal Cancer by Stable Isotope Labeling with Heavy Amino Acids in Mouse Xenografts

The non-receptor tyrosine kinase SRC is frequently deregulated in human colorectal cancer (CRC), and SRC increased activity has been associated with poor clinical outcomes. In nude mice engrafted with human CRC cells, SRC over-expression favors tumor growth and is accompanied by a robust increase in tyrosine phosphorylation in tumor cells. How SRC contributes to this tumorigenic process is largely unknown. We analyzed SRC oncogenic signaling in these tumors by means of a novel quantitative proteomic analysis. This method is based on stable isotope labeling with amino acids of xenograft tumors by the addition of [¹³C₆]-lysine into mouse food. An incorporation level greater than 88% was obtained in xenograft tumors after 30 days of the heavy lysine diet. Quantitative phosphoproteomic analysis of these tumors allowed the identification of 61 proteins that exhibited a significant increase in tyrosine phosphorylation and/or association with tyrosine phosphorylated proteins upon SRC expression. These mainly included molecules implicated in vesicular trafficking and signaling and RNA binding proteins. Most of these proteins were specific targets of SRC signaling in vivo, as they were not identified by analysis via stable isotope labeling by amino acids in cell culture (SILAC) of the same CRC cells in culture. This suggests that oncogenic signaling induced by SRC in tumors significantly differs from that induced by SRC in cell culture. We next confirmed this notion experimentally with the example of the vesicular trafficking protein and SRC substrate TOM1L1. We found that whereas TOM1L1 depletion only slightly affected SRC-induced proliferation of CRC cells in vitro, it drastically decreased tumor growth in xenografted nude mice. We thus concluded that this vesicular trafficking protein plays an important role in SRC-induced tumor growth. Overall, these data show that SILAC analysis in mouse xenografts is a valuable approach for deciphering tyrosine kinase oncogenic signaling in vivo.The non-receptor tyrosine kinase (TK)¹ SRC mediates cellular signaling induced by growth factors and integrins (1) leading to cell growth, survival, and migration. It also has oncogenic activity when deregulated, a role originally described for the constitutively active v-SRC (2) that has since been observed in a large variety of human cancers (3). Remarkably, elevated SRC kinase activity has been found in more than 80% of colorectal cancers (CRCs) to levels (5- to 10-fold) consistent with oncogenic properties (4). Moreover, SRC deregulation has been associated with poor clinical outcomes (3), suggesting an additional function of SRC during late tumorigenesis. SRC deregulation largely occurs in the absence of mutations in the SRC gene. Instead, it primarily involves protein over-expression (2) and inhibition of SRC negative regulators, such as the transmembrane protein Cbp/PAG (5, 6). A large body of evidence indicates that SRC deregulation is an important event in colon tumorigenesis (3, 6). Indeed, SRC controls growth, survival, and invasion of some CRC cell lines in vitro (4). Moreover, it contributes to tumor growth, angiogenesis, and metastasis formation in mouse colon tumor xenograft models (7–11). However, our knowledge of the SRC-dependent oncogenic signaling pathway in CRC is largely incomplete, mostly because the majority of data have been obtained in two-dimensional cell culture models. Moreover, the standard culture conditions of CRC cells do not allow the recapitulation of all the SRC-dependent signaling cascades that are activated during tumorigenesis to promote tumor growth, angiogenesis, and interactions with the microenvironment.MS-based quantitative phosphoproteomic technology has been a valuable tool for deciphering signaling pathways initiated by a given TK (12). Particularly, the method of stable isotope labeling with amino acids in cell culture (SILAC) has been employed for the characterization of oncogenic TK signaling pathways in cell culture, including HER2 (13) and BCR-ABL (14). We recently used this powerful approach to investigate SRC-dependent oncogenic signaling in CRC cells (15) and identified the first SRC-dependent tyrosine “phosphoproteome” in these cells. Additionally, we found that SRC phosphorylated a small cluster of TKs that mediate its oncogenic activity, thus uncovering a TK network that is important for the induction of CRC cell growth (15). Whether these signaling processes also operate in vivo is, however, currently unknown.SRC oncogenic signaling could be investigated in vivo using similar MS-based quantitative phosphoproteomic approaches in animal models or tumor biopsies. However, the application of the SILAC method in vivo has been challenging until recently because it requires efficient protein labeling in different tissues, which is conditioned by the rate of de novo protein synthesis. Recently, Mann et al. described the successful development of a SILAC approach for labeling mice that is based on the addition of [¹³C₆]-lysine to their food (16). They reported complete labeling from the F2 generation. Similar SILAC approaches were then described for additional multicellular organisms, such as worms (17), flies (18), and zebrafish (19). Here, we report a similar SILAC approach in which we labeled tumors in nude mice xenografted with human CRC cells. We reasoned that the high rate of de novo protein synthesis occurring in tumors should allow efficient tumor labeling in a short period of time. Indeed, we obtained consistent (>88%) labeling of the tumor proteome by feeding xenografted mice with the SILAC mouse diet for only 30 days. We then used this approach to compare the tyrosine phosphoproteome of SRC over-expressing tumors (labeled with heavy amino acids) and of control tumors (labeled with light amino acids) and report the first SRC-dependent tyrosine phosphoproteome of CRC in vivo. Finally, comparison of the in vivo and in vitro SRC-dependent tyrosine phosphoproteomes showed that some of the SRC substrates were specifically activated only in CRC xenograft tumors, and not in cultured CRC cells.     

Colonization of Pacific islands by parasites of low dispersal ability: phylogeography of two monogenean species parasitizing butterflyfishes in the South Pacific Ocean

Aim To investigate the phylogeographical patterns of two poorly dispersing but widely distributed monogenean species, Haliotrema aurigae and Euryhaliotrematoides grandis, gill parasites of coral reef fishes from the family Chaetodontidae. Location South Pacific Ocean (SPO). Methods Sequence data from the mitochondrial cytochrome oxidase subunit I (COI) gene were obtained from samples from five localities of the SPO (Heron Island, Lizard Island, Moorea, Palau and Wallis) for the two parasite species. Phylogenetic and genetic diversity analyses were used to reconstruct phylogeographical patterns, and dates of cladogenetic events were estimated. Results Overall, 50 individuals of 17 Haliotrema aurigae and 33 of Euryhaliotrematoides grandis were sequenced from five localities of the SPO for COI mtDNA (798 bp). Our results revealed a deep phylogeographical structure in the species Euryhaliotrematoides grandis. The molecular divergence between individuals from Moorea and individuals from the remaining localities (7.7%) may be related to Pleistocene sea‐level fluctuations. In contrast, Haliotrema aurigae shows no phylogeographical patterns with the presence of most of the mitochondrial haplotypes in every locality sampled. Main conclusions Our study shows contrasting phylogeographical patterns of the two monogenean parasite species studied, despite many shared characteristics. Both parasites are found on the same host family, share the same geographical range and ecology, and are phylogenetically close. We propose two hypotheses that may help explain the diparity: the hypotheses involve differences in the evolutionary age of the parasite species and their dispersal capabilities. Additionally, the lack of phylogeographical structure in Haliotrema aurigae contrasts with its apparently restricted dispersion, which is likely to occur during the egg stage of the life cycle, inducing a passive dispersal mechanism in butterflyfish monogeneans.     

Zoledronate Effects on Systemic and Jaw Osteopenias in Ovariectomized Periostin-Deficient Mice

Osteoporosis and periodontal disease (PD) are frequently associated in the elderly, both concurring to the loss of jaw alveolar bone and finally of teeth. Bisphosphonates improve alveolar bone loss but have also been associated with osteonecrosis of the jaw (ONJ), particularly using oncological doses of zoledronate. The effects and therapeutic margin of zoledronate on jaw bone therefore remain uncertain. We reappraised the efficacy and safety of Zoledronate (Zol) in ovariectomized (OVX) periostin (Postn)-deficient mice, a unique genetic model of systemic and jaw osteopenia. Compared to vehicle, Zol 1M (100 µg/kg/month) and Zol 1W (100 µg/kg/week) for 3 months both significantly improved femur BMD, trabecular bone volume on tissue volume (BV/TV) and cortical bone volume in both OVX Postn^+/+ and Postn^−/− (all p<0.01). Zol 1M and Zol 1W also improved jaw alveolar and basal BV/TV, although the highest dose (Zol 1W) was less efficient, particularly in Postn^−/−. Zol decreased osteoclast number and bone formation indices, i.e. MAR, MPm/BPm and BFR, independently in Postn^−/− and Postn^+/+, both in the long bones and in deep jaw alveolar bone, without differences between Zol doses. Zol 1M and Zol 1W did not reactivate inflammation nor increase fibrous tissue in the bone marrow of the jaw, whereas the distance between the root and the enamel of the incisor (DRI) remained high in Postn^−/− vs Postn^+/+ confirming latent inflammation and lack of crestal alveolar bone. Zol 1W and Zol 1M decreased osteocyte numbers in Postn^−/− and Postn^+/+ mandible, and Zol 1W increased the number of empty lacunae in Postn^−/−, however no areas of necrotic bone were observed. These results demonstrate that zoledronate improves jaw osteopenia and suggest that in Postn^−/− mice, zoledronate is not sufficient to induce bone necrosis.     

Carbocyclic phosphonate analogs of 2′,3′-dideoxyadenosine-5′-monophosphate as substrates of 5-phosphoribosyl-1-pyrophosphate (PRPP) synthetate

Several carbocyclic phosphonate analogs of 2′,3′-dideoxyadenosine-5′-monophosphate (ddAMP) were pyrophosphorylated by E. coli 5-phosphoribosyl-1-pyrophosphate (PRPP) synthetase in the presence of PRPP. Structure-activity relationships are discussed.     

Molecular modelling of theDolichos biflorus seed lectin and its specific interactions with carbohydrates: α-D-N-acetyl-galactosamine,Forssman disaccharide and blood group A trisaccharide

The three-dimensional structure ofDolichos biflorus seed lectin has been constructed using five legume lectins for which high resolution crystal structures were available. The validity of the resulting model has been thoroughly investigated. Final structure optimization was conducted for the lectin complexed with GalNAc, providing thereby the first three-dimensional structure of lectin/GalNAc complex. The role of theN-acetyl group was clearly evidenced by the occurrence of a strong hydrogen bond between the protein and the carbonyl oxygen of the carbohydrate and by hydrophobic interaction between the methyl group and aromatic amino acids. Since the lectin specificity is maximum for the Forssman disaccharide GalNAc(1–3)GalNAc-O-Me and the blood group A trisaccharide GalNAc(1–3)[Fuc(1–2)]Gal-O-Me, the complexes with these oligosaccharides have been also modelled.