Biomedical subjects

G Labesse

Publications and source records attributed to G Labesse.

24 records · Page 2Linked to original sources

PubMed1996

MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis.

The protein sequence similarity search has become a major tool for biologists. Various efficient and rapid programs and comparison matrices have been designed and refined in order to perform the scanning task (BLAST, FASTA, Automat, etc.). However, the final step of the search, the analysis of the results, is still tedious and time consuming. In order to optimize true-positive hit screening, we have developed a program which makes a multiple alignment from the BLAST search output. Conserved sequence segments are pointed out. It makes the recognition of already known as well as new sequence patterns easier. It allows at a glance a rapid identification of significant similarities, protein family signature and new sequence motifs. This alignment is written in a compatible format for the GCG programs LineUp and ProfileMake.

Algorithms↗

PubMed1995

Automat and BLAST: comparison of two protein sequence similarity search programs.

Since the early 1980s, protein/DNA sequence similarity search has become of major importance to biologists, and the need for fast and efficient tools grows with the size of databanks. Two programs use the strategy of finite state deterministic automatons to accomplish these searches. One of these two is BLAST, which is now widely used, and the other Automat, which has just been published. The differences and similarities in their basic principles, their use and their performances are analysed in this paper in order to allow optimal use of these important softwares.

Algorithms↗

PubMed1995

Flavohaemoglobin HmpX: a new pathogenicity determinant in Erwinia chrysanthemi strain 3937.

Unlike wild-type Erwinia chrysanthemi strain 3937, which fully macerates inoculated Saintpaulia plants, HmpX- mutants produce necrotic lesions or no symptoms. The hmpX gene was sequenced and the corresponding protein sequence analysed. We show that HmpX belongs to a family of flavohaemoproteins (HMP), previously identified in two yeasts and in Escherichia coli. Comparisons of protein sequences at the secondary structure level by hydrophobic cluster analysis have shown that HmpX possesses two functional regions, a haemoglobin domain in its N-terminal part and a flavin reductase domain in its C-terminal part. In an HmpX- strain, the synthesis of pectate lyases, which are pathogenicity determinants in E. chrysanthemi, was reduced in conditions of low oxygen tension. Using gus fusion in hmpX, it was shown that hmpX transcription was induced in coculture with tobacco cells. A putative function for HmpX is discussed.

Amino Acid Sequence↗

PubMed1994

Structural comparisons lead to the definition of a new superfamily of NAD(P)(H)-accepting oxidoreductases: the single-domain reductases/epimerases/dehydrogenases (the 'RED' family).

Using both primary- and tertiary-structure comparisons, we have established new structural similarities shared by reductases, epimerases and dehydrogenases not previously known to be related. Despite the low sequence identity (down to 10%), short consensus segments are identified. We show that the sequence, the active site and the supersecondary structure are well conserved in these proteins. New homologues (the protochlorophyllide reductases) are detected, and we define a new superfamily composed of single-domain dinucleotide-binding enzymes. Rules for the cofactor-binding specificity are deduced from our sequence alignment. The involvement of some amino acids in catalysis is discussed. Comparison with two-domain dehydrogenases allows us to distinguish two general mechanisms of divergent evolution.

Amino Acid Sequence↗

PubMed1994

Polyhydroxynaphthalene reductase involved in melanin biosynthesis in Magnaporthe grisea. Purification, cDNA cloning and sequencing.

During the biosynthesis of fungal melanin, tetrahydroxynaphthalene reductase catalyzes the NADPH-dependent reduction of 1,3,6,8-tetrahydroxynaphthalene (T4HN) into (+)-scytalone and 1,3,8-trihydroxynaphthalene into (-)-vermelone. The enzyme from Magnaporthe grisea, the fungus responsible for rice blast disease, has been purified to homogeneity. It is a tetramer of four identical 30-kDa subunits. A full-length cDNA clone of about 1 kb encoding T4HN reductase has been isolated from a cDNA library constructed in the lambda ZAP II vector and characterized. The clone contains a 846-bp open reading frame. Translation of the DNA sequence gave a 282-residue amino acid sequence with a calculated molecular mass of 29.9 kDa. Sequences corresponding to the amino-terminal part and three internal proteolytic peptides were present in the translated sequence. T4HN reductase exhibits characteristics of the short-chain alcohol dehydrogenase family. The reductase shares 56% identity with a putative ketoreductase involved in aflatoxin biosynthesis in Aspergillus parasiticus.

Amino Acid Sequence↗

PubMed1993

Characterization and overexpression of the pem gene encoding pectin methylesterase of Erwinia chrysanthemi strain 3937.

The pem gene encoding the pectin methylesterase (PME) of Erwinia chrysanthemi strain 3937 was subcloned and its nucleotide sequence determined. The gene contains an open reading frame of 1098 bp and codes for a protein of 366 amino acids (aa). The mature 37-kDa form of the protein is 342 aa long and has a calculated isoelectric point of 9.64. A plasmid was constructed to overproduce PME: a DNA fragment carrying pem was amplified by the polymerase chain reaction and cloned downstream from the pL promoter of the lambda phage, in a high-copy-number plasmid. In an Escherichia coli strain transformed with this plasmid, an increase in PME production of more than 60-fold was obtained, compared with the wild-type Er. chrysanthemi strain. PME represents about 5% of the total protein content of the cells. Comparison of this PME sequence with six PMEs from prokaryotic or eukaryotic organisms showed six highly conserved segments whose possible role in enzyme activity are discussed.

Amino Acid Sequence↗