Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques.

Although the characterization of proteins cannot solely rely upon sequence similarity, it has been widely proved that all-vs-all massive sequence comparisons may be an effective approach and a good basis for the prediction of biochemical functions or for the delineation of common shared properties. The program Cluster-C presented here enables a stand-alone and efficient construction of protein families within whole proteomes. The algorithm, which is based on the detection of cliques, ensures a high level of connectivity within the clusters. As opposed to the single transitive linkage method, Cluster-C allows a large number of sequences to be classified in such a way that the multidomain proteins do not produce a chain-grouping effect resulting in meaningless clusters. Moreover, some proteins can be present in several different but relevant clusters, which is of help in the determination of their functional domains. In the present analysis we used the Z-value, an evaluation of the significance of the similarity score, as the criterion for connecting sequences (the user can freely define the threshold of the similarity criterion). The clusters built with a rather low threshold (Z= 14) include more than 97% of the sequences and are consistent with known protein families and PROSITE patterns.

PHYTOPROT: a database of clusters of plant proteins.

All the protein sequences from plants (including Arabidopsis thaliana) available from SwissProt/TrEMBL have been the subject of an all-by-all systematic comparison and grouped into clusters of related proteins. Within each cluster, the sequences have been submitted to pyramidal classification; in the case where two or several subfamilies have been grouped together, the pyramidal tree helps in finding which sequences make the links between subfamilies. In addition, the 'domains' that are common to two or more sequences within a cluster were determined and displayed à la ProDom. The resulting graphical representations proved to be quite efficient in pinpointing those protein sequences suffering from a probable error in the annotation of their genes. The clusters can be searched through various criteria and their pyramidal classifications and their domain representations can be displayed by querying http://genoplante-info. infobiogen.fr/phytoprot. The user can also launch a BLAST search of a query sequence against all the clusters.

N-myc regulation of type I insulin-like growth factor receptor in a human neuroblastoma cell line.

Insulin-like growth factors I and II (IGF-I and IGF-II) stimulate proliferation and differentiation in many cell types, including cell lines derived from human neuroblastomas. Their effects are mediated via the IGF-I receptor (IGF-IR) that is essential for growth in these cells. Amplification of the N-myc oncogene is a marker for poor prognosis in neuroblastoma development, and it therefore seemed of interest to analyze the relationships that may exist between IGF-IR and N-myc. N-myc-deficient SK-N-SH neuroblastoma cells were used as an experimental model. After stable transfection with N-myc cDNA, Northern blotting revealed a marked increased in IGF-IR, IGF-II, IGF-binding protein (IGFBP)-2, and IGFBP-4 mRNA levels, whereas IGFBP-6 mRNA levels were clearly diminished. Western immunoblot analysis also demonstrated increased intact IGFBP-2 but decreased IGFBP-6 in the presence of N-myc oncogene. Parallel binding experiments using IGF-I missing the first 3 amino acids revealed a 47% increase in binding sites for IGF-I and an increase of at least 335% in DNA synthesis, as measured by labeled thymidine incorporation into DNA. s.c. injection of these cells into nude mice provoked xenograft development in 50-100% of cases (depending on the series of experiments). Control cells, in contrast, were not tumorigenic. In cells transfected with bp -420/+60 of the human IGF-IR promoter controlling expression of the luciferase reporter gene, promoter activity was stimulated by a factor of 3.8 +/- 0.6 (n = 6) in the presence of N-myc oncogene. This suggests transcriptional regulation of IGF-IR expression by N-myc. IGF-IR activity and N-myc amplification are two events that to date have been identified as independently instrumental in the etiology of human neuroblastoma. Our results provide the first evidence of a direct link between them and demonstrate the effects of the oncogene on components of the IGF system in neuroblastoma cell growth in vitro and in vivo.

Insulin-like growth factor (IGF) binding protein-3 interacts with the type 1 IGF receptor, reducing the affinity of the receptor for its ligand: an alternative mechanism in the regulation of IGF action.

With a view to determining the mechanisms by which insulin-like growth factor binding protein-3 (IGFBP-3) and its proteolytic fragments modulate IGF action, we used a fibroblast cell line to investigate the possibility of an interaction with the type 1 IGF receptor (IGFR-1). In competitive binding experiments, IGFBP-3 was as potent as unlabelled IGF-I in displacing its truncated analogue, 125I-des(1-3)IGF-I, which has weak affinity for IGFBPs, from its binding to the cell surface. None of the proteolytic fragments of IGFBP-3 tested affected this binding. IGFBP-3 had no effect on insulin binding to its receptor. At 10 nM, IGFBP-1 was ineffective where IGFBP-3 provoked 90% displacement of 125I-des(1-3)IGF-I, but it was equally potent in displacing 125I-IGF-I. At the same concentration, binding of 125I-des(1-3)IGF-I to free IGFBP-3 in the supernatant was only 2%. After pre-incubation of the cells with 125I-des(1-3)IGF-I, low concentrations of IGFBP-3 were as potent as IGF-I in dissociating IGFR-1-bound ligand. After pre-incubation of cells with IGFBP-3, washing and then incubation with 125I-des(1-3)IGF-I, inhibition by low IGFBP-3 concentrations was suppressed, but some degree of inhibition by high concentrations persisted. At these high concentrations, addition of IGF-I restored binding owing to uptake of cell-associated IGFBP-3. The present results provide the first evidence that IGFBP-3 may inhibit IGF binding to IGFR-1, and hence limit IGF action via a cellular mechanism that is different from the extracellular mechanism of sequestration.