Biomedical subjects

B Billoud

Publications and source records attributed to B Billoud.

8 recordsLinked to original sources

PubMed2001

Classification and phylogeny of hydrogenases.

Hydrogenases (H2ases) catalyze the reversible oxidation of molecular hydrogen and play a central role in microbial energy metabolism. Most of these enzymes are found in Archaea and Bacteria, but a few are present in Eucarya as well. They can be distributed into three classes: the [Fe]-H2ases, the [NiFe]-H2ases, and the metal-free H2ases. The vast majority of known H2ases belong to the first two classes, and over 100 of these enzymes have been characterized genetically and/or biochemically. Compelling evidence from sequences and structures indicates that the [NiFe]- and [Fe]-H2ases are phylogenetically distinct classes of proteins. The catalytic core of the [NiFe]-H2ases is a heterodimeric protein, although additional subunits are present in many of these enzymes. Functional classes of [NiFe]-H2ases have been defined, and they are consistent with categories defined by sequence similarity of the catalytic subunits. The catalytic core of the [Fe]-H2ases is a ca. 350-residue domain that accommodates the active site (H-cluster). A few monomeric [Fe]-H2ases are barely larger than the H-cluster domain. Many others are monomeric as well, but possess additional domains that contain redox centers, mostly iron-sulfur. Some [Fe]-H2ases are oligomeric. The modular structure of H2ases is strikingly illustrated in recently unveiled sequences and structures. It is also remarkable that most of the accessory domains and subunits of H2ases have counterparts in other redox complexes, in particular NADH-ubiquinone oxidoreductase (Complex I) of respiratory chains. Microbial genome sequences are bringing forth a significant body of additional H2ase sequence data and contribute to the understanding of H2ase distribution and evolution. Altogether, the available data suggest that [Fe]-H2ases are restricted to Bacteria and Eucarya, while [NiFe]-H2ases, with one possible exception, seem to be present only in Archaea and Bacteria. H2ase processing and maturation involve the products of several genes which have been identified and are currently being characterized in the case of the [NiFe]-H2ases. In contrast, near to nothing is known regarding the maturation of the [Fe]-H2ases. Inspection of the currently available genome sequences suggests that the [NiFe]-H2ase maturation proteins have no similar counterparts in the genomes of organisms possessing [Fe]-H2ases only. This observation, if confirmed, would be consistent with the phylogenetic distinctiveness of the two classes of H2ases. Sequence alignments of catalytic subunits of H2ases have been implemented to construct phylogenetic trees that were found to be consistent, in the main, with trees derived from other data. On the basis of the comparisons performed and discussed here, proposals are made to simplify and rationalize the nomenclature of H2ase-encoding genes.

Amino Acid Sequence↗

PubMed2000

Cirripede phylogeny using a novel approach: molecular morphometrics.

We present a new method using nucleic acid secondary structure to assess phylogenetic relationships among species. In this method, which we term "molecular morphometrics," the measurable structural parameters of the molecules (geometrical features, bond energies, base composition, etc.) are used as specific characters to construct a phylogenetic tree. This method relies both on traditional morphological comparison and on molecular sequence comparison. Applied to the phylogenetic analysis of Cirripedia, molecular morphometrics supports the most recent morphological analyses arguing for the monophyly of Cirripedia sensu stricto (Thoracica + Rhizocephala + Acrothoracica). As a proof, a classical multiple alignment was also performed, either using or not using the structural information to realign the sequence segments considered in the molecular morphometrics analysis. These methods yielded the same tree topology as the direct use of structural characters as a phylogenetic signal. By taking into account the secondary structure of nucleic acids, the new method allows investigators to use the regions in which multiple alignments are barely reliable because of a large number of insertions and deletions. It thus appears to be complementary to classical primary sequence analysis in phylogenetic studies.

Animals↗

PubMed1996

Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified.

Base Sequence↗

PubMed1996

What role might lampbrush chromosomes play in maternal gene expression?

The biological significance of lampbrush chromosomes from urodelan amphibians is far from being elucidated. Their particularly well developed lateral loops are the site of intense transcriptional activity, which can be visualized in electron microscopy using the Miller spreading procedure. All transcription units functioning in lampbrush loops synthesize RNA at a maximum rate. In situ hybridization has provided evidence for transcription of both unique coding sequences and highly repetitive sequences. The role of lampbrush transcripts in the production of maternal information remains unclear. RNAs transcribed from unique coding sequences are exported to the cytoplasm; there, they contribute either to maintaining the required level of maternal messenger RNA in a basal state during late oogenesis, or to increasing the store of these maternal RNAs throughout oocyte growth, i.e., until stage VI. For repetitive sequences, their intense transcription appears to be non-productive, in that RNAs are not translatable and might be useless products of readthrough transcription. The non-productive transcription of repetitive sequences, the expression of which is directly related to hyperdevelopment of lateral loops, raises the issue of the role of lampbrush chromosome transcription.

Animals↗

PubMed1995

Evidence for a 90 kDa heat-shock protein gene expression in the amphibian oocyte.

In order to study expression of a 90-kDa heat-shock protein during amphibian oogenesis at physiological temperature, we isolated a Pleurodeles waltl hsc90 cDNA by screening an ovarian cDNA library with a chicken hsp90 cDNA probe. The cDNA thus obtained--named Pw90--shows a high homology level with the hsp90 gene in other species. RNase protection analysis led us to conclude that this sequence is part of the cognate gene hsc90 and is constitutively expressed in oocytes. Furthermore, results of quantitative Northern blot analysis, as well as in situ hybridizations on oocyte sections or lampbrush chromosome spreads, provide evidence for expression of hsc90 transcripts at every stage of oogenesis. Moreover, they point to the fact that an accumulation of transcripts occurs very early in oogenesis. Simultaneously, the expression of HSC90-related protein was analyzed on Western blots using a monoclonal antibody (AC88) and a polyclonal antibody (AP90Ct) raised against the Pleurodeles C-terminal part of HSC90. We provide evidence for a net accumulation of HSC90-related protein in oocytes. Immunolocalization shows that a nuclear transfer occurs in the course of oogenesis and leads to a concentration equilibrium between cytoplasm and nucleus in stage VI oocytes.

Amino Acid Sequence↗

PubMed1994

Transcription of amphibian lampbrush chromosomes is disturbed by microinjection of HSP70 monoclonal antibodies.

To investigate the possible involvement of HSP70 in nuclear transport of proteins associated with the transcription process in amphibian oocyte lampbrush chromosomes, we examined the effect of anti-HSP70 mouse monoclonal antibodies on the transcriptional activity of lampbrush chromosomes. When injected into the oocyte cytoplasm, anti-HSP70 induced disorganization followed by retraction of chromosomal lateral loops. This retraction reflected inhibition of transcription, which was confirmed by our electron microscopic observations. At the same time, while nucleoli were morphologically disorganized, nucleolar transcription persisted. These modifications were completely reversible. In contrast, no modifications were observed when antibodies were directly microinjected into nuclei. Similar observations were registered at the level of lampbrush chromosomes when wheat germ agglutinin was injected into oocyte cytoplasm. All of these results suggest that HSP70 mediates the nuclear transport of proteins involved in the lampbrush chromosome transcriptional process.

Animals↗

PubMed1993

Constitutive expression of a somatic heat-inducible hsp70 gene during amphibian oogenesis.

We isolated and characterized a sequence coding for heat-shock protein 70 (HSP70) of the amphibian Pleurodeles waltl. Results from S1 nuclease protection assays led us to conclude that an hsp70 gene, strictly inducible in somatic cells during heat shock, is constitutively active during oogenesis. By quantitative northern and western blot analysis, we showed that both hsp70 mRNA and HSP70-related protein levels increased in oocytes from stage II to stage VI under physiological conditions. Furthermore, by in situ hybridization to the nascent transcripts of lampbrush chromosome loops, we provided evidence for a clear-cut relationship between this increase in hsp70 mRNA and transcriptional activity during the lampbrush stage of oogenesis. These results strongly suggest that hsp70 genes are actively transcribed throughout oogenesis. HSP70-related proteins localized in the cytoplasm of young oocytes are progressively transferred to the nucleus in the course of oogenesis and preferentially accumulated in the nuclei of some stage VI oocytes.

Amino Acid Sequence↗

PubMedDate not supplied

Identification of new small non-coding RNAs from tobacco and Arabidopsis.

Small non-coding RNAs (ncRNAs) have typically been searched in fully sequenced genomes using one of two approaches-experimental or computational. We developed a mixed method, using both types of information, which has the advantage of applying bio-computing methods to actually expressed sequences. Our method allowed the identification of new small ncRNAs in Arabidopsis thaliana and in the unfinished genome of Nicotiana tabacum. We constructed a N. tabacum cDNA library from small RNAs ranging from 20 to 30 nucleotides (nt). The sequences from 73 unique clones were compared to the A. thaliana genome and to all plant sequences using a pattern-matching approach (program Patbank). Thus, we selected 15 clones from the library corresponding mostly to A. thaliana or N. tabacum non-coding sequences. By Northern blot analyses, we confirmed the presence of most RNA candidates in Arabidopsis and in Nicotiana sylvestris with a size range of 21-100 nt. To gain more insight into the possible genesis of 21-24 nt sequences, stable folding of sRNAs with their flanking regions were predicted with the software MIRFOLD dedicated to the folding of microRNAs (miRNA). Stable hairpins structures were observed for some putative miRNAs.

Arabidopsis↗