Lydie Bougueleret

The candidate gene for the X-linked Kallmann syndrome encodes a protein related to adhesion molecules.

Kallmann syndrome associates hypogonadotropic hypogonadism and anosmia and is probably due to a defect in the embryonic migration of olfactory and GnRH-synthesizing neurons. The Kallmann gene had been localized to Xp22.3. In this study 67 kb of genomic DNA, corresponding to a deletion interval containing at least part of the Kallmann gene, were sequenced. Two candidate exons, identified by multiparameter computer programs, were found in a cDNA encoding a protein of 679 amino acids. This candidate gene (ADMLX) is interrupted in its 3 coding region in the Kallmann patient, in which the proximal end of the KAL deletion interval was previously defined. A 5 end deletion was detected in another Kallmann patient. The predicted protein sequence shows homologies with the fibronectin type III repeat. ADMLX thus encodes a putative adhesion molecule, consistent with the defect of embryonic neuronal migration.

Implications of a Fab-like structure for the T-cell receptor.

The antigen-specific receptor of T lymphocytes (TCR) and the Fab moiety of immunoglobulins are expected to fold into similar three-dimensional structures because of their identical protein domain organization, the conservation of key residues and their overall sequence homology. However, T cells mostly appear to recognize short peptide antigens bound to MHC class I or class II presenting molecules. A complete model of the human leucocyte antigen molecule (HLA-A2) reconstructed from the alpha-carbon coordinates was used to investigate the putative organization of a TCR/peptide/HLA-A2 complex. In this article, Jean-Michel Claverie and co-workers show that the respective geometries of a Fab-like TCR structure and of the HLA-A2 antigen binding site suggest a model where the third variable regions of both chains of the TCR mainly interact with the peptide antigen, while the first and/or second less variable regions are in position for making contact with residues pointing up from the alpha 1 and alpha 2 helical regions of the HLA-A2 molecule.

Heuristic informational analysis of sequences

Nucleotide or amino-acid sequences are interpreted as successions of words of length k (k-tuples) the frequencies of which are highly variable in different statistical populations of genes or proteins. After building k-tuple reference tables from coherent subsets or entire data banks, the local information content profile of individual sequences is drawn. Anomalous regions (peaks or depressions) of such a profile can lead to the discovery and identification of specific sequence patterns. Along the same principle, the simultaneous use of two reference statistical populations and the computation of an index combining the two information profiles lead to a general and powerful discriminant analysis methods. The identification of a signal associated with gene conversion, the introns/exons discrimination and the location of function specific patterns in proteins are given as examples of successful applications of this heuristic informational approach.

K-TUPLE FREQUENCY ANALYSIS : FROM INTRON/EXON DISCRIMINATION TO T-CELL EPITOPE MAPPING

Publisher Summary This chapter presents methods that take advantage of the frequencies of occurrence of all subsequences of length k (k-tuples) as computed from the sequence of interest, ranging from introdexon discrimination to T-cell epitope mapping. A set of FORTRAN 77 programs has been designed to perform all the tasks involved in the general methodology described here. This includes the computation of k-tuple frequency catalogs from data bank subsets or private sequence collections, software tools for the consultation, editing, and manipulation of these catalogs as well as for the manipulation of k-tuple coded sequences, and interactive programs for the computation and display of the sequence frequency profiles. At the very first level, the k-tuple reference catalog can be constituted from the test sequence itself. The method then provides clear graphical information about the repeated versus unique regions of the molecule. The profiles computed from any type of k-tuple frequency catalog can always be used as a graphical tool to represent very large sequences (several kilobases) in a way allowing one to pick up at a glance some characteristic features.

Conjugative R plasmids in Streptococcus agalactiae (group B)

Abstract Twenty-one drug-resistant clinical isolates of group B streptococci were investigated for drug-resistance transfer by conjugation. Six strains were resistant to tetracycline, two to chloramphenicol, one to both drugs, and twelve to macrolide antibiotics (erythromycin, oleandomycin and spiramycin), lincomycin, pristinamycin I, and/or chloramphenicol and tetracycline. Ten strains carried R plasmids which were transferable to group B and/or group D recipients by a conjugation-like phenomenon. Six plasmids were transferred at a high frequency (9 × 10−2 to 4 × 10−4) and four, at low frequency (5 × 10−6 to 7 × 10−8). The molecular weight of one plasmid (pIP501) was investigated after transfer into the new hosts and was found to be similar to that carried by the wild strain (19.8 × 106).

Conjugative transfer of multiple-antibiotic resistance markers in beta-hemolytic group A, B, F, and G streptococci in the absence of extrachromosomal deoxyribonucleic acid.

Abstract Nine clinical isolates of group A, B, F, and G streptococci resistant to tetracycline, macrolides, lincosamides, and streptogramin B (MLS resistance) and to chloramphenicol were investigated for the conjugative transfer of the antibiotic-resistance markers into streptococcal recipients (groups B and D). The wild donors transferred the resistance markers en bloc , at a low frequency (10 −6 to 10 −8 ) and only into one of the two recipients tested. In addition, one of the strains transferred only the MLS resistance at a high frequency (10 −3 ). All attempts to detect extrachromosomal DNA in wild donors or in transconjugants were unsuccessful, except in one transconjugant. This plasmid DNA, designated pIP659, had a molecular weight of 17.5 × 10 6 and a restriction fingerprint similar to other plasmids determining MLS resistance.

Rare sequence motifs are common constituents of hypervariable antibody regions.

An analysis of the amino acid sequences of variable regions of human and mouse antibody molecules was performed. It involved comparison of their constituent tetrapeptides with those found in a reference set (the somatic self) built with non-immunological proteins found in a protein data base. It appeared that hypervariable regions, particularly CDR1 and CDR3, are often made up of rare tetrapeptides not present in the reference set. As assessed by simple statistical tests, this bias was significant. We discuss its possible connection with the problem of antibody immunogenicity. This result provides indirect support for the existence of idiopeptides predicted by the peptidic self model.

Computer generation and statistical analysis of a data bank of protein sequences translated from GenBank

We describe PGtrans, a new and freely available protein sequence databank (2625 sequences, 554198 amino-acids). This data bank is routinely produced by automatic computer translation of the nucleotide sequence library GenBank. The information needed for the translation process (transcriptional orientation, location of coding regions, splice sites and pertinent genetic code) is gathered by the translation program through an intelligent scanning of the documentary field of each GenBank entry. Inconsistencies resulting in unexpected termination codons are detected and reported thus allowing the correction of data bank errors. PGtrans is intended as a tool for protein similarity searches. Its reasonable overall size (2 Moctets) makes it suitable for micro-computer environments. Up to date amino-acid composition data and relative abundances of di-, tri-, and tetra-peptides in proteins of known sequences are presented and discussed.