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H Philippe

Publications and source records attributed to H Philippe.

At least 55 records · Page 3Linked to original sources
PubMed1997

Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae.

In molecular phylogenies based on ribosomal RNA, three amitochondriate protist lineages, Microsporidia, Metamonada (including diplomonads) and Parabasala (including trichomonads), are the earliest offshoots of the eukaryotic tree. As an explantation for the lack of mitochondria in these organisms, the hypothesis that they have diverged before the mitochondrial endosymbiosis is preferred to the less parsimonious hypothesis of several independent losses of the organelle. Nevertheless, if they had descended from mitochondrion-containing ancestors, it may be possible to find in their nuclear DNA genes that derive from the endosymbiont which gave rise to mitochondria. Based on similar evidence, secondary losses of mitochondria have recently been suggested for Entamoeba histolytica and for Trichomonas vaginalis. In this study, we have isolated a gene encoding a chaperone protein (HSP70, 70 kDa heat shock protein) from the microspordian Nosema locustae. In phylogenetic trees, this HSP70 was located within a group of sequences that in other lineages is targetted to the mitochondrial compartment, itself included in the proteobacterial clade. In addition, the N. locustae protein contained the GDAW(V) motif shared by mitochondrial and proteobacterial sequences, with only one conservative substitution. Moreover, microsporidia, a phylum which was assumed to emerge close to the base of the eukaryotic tree, appears as the sister-group of fungi in the HSP70 phylogeny, in agreement with some ultrastructural characters and phylogenies based on alpha- and beta-tubulins. Loss of mitochondria, now demonstrated for several amitochondriate groups, indicates that the common ancestor of all the extant eukaryotic species could have been a mitochondriate eukaryote.

Amino Acid Sequence↗
PubMed1996

Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes.

Molecular phylogenetic analyses, based mainly on ribosomal RNA, show that three amitochondriate protist lineages, diplomonads, microsporidia, and trichomonads, emerge consistently at the base of the eukaryotic tree before groups having mitochondria. This suggests that these groups could have diverged before the mitochondrial endosymbiosis. Nevertheless, since all these organisms live in anaerobic environments, the absence of mitochondria might be due to secondary loss, as demonstrated for the later emerging eukaryote Entamoeba histolytica. We have now isolated from Trichomonas vaginalis a gene encoding a chaperone protein (HSP70) that in other lineages is addressed to the mitochondrial compartment. The phylogenetic reconstruction unambiguously located this HSP70 within a large set of mitochondrial sequences, itself a sister-group of alpha-purple bacteria. In addition, the T. vaginalis protein exhibits the GDAWV sequence signature, so far exclusively found in mitochondrial HSP70 and in proteobacterial dnaK. Thus mitochondrial endosymbiosis could have occurred earlier than previously assumed. The trichomonad double membrane-bounded organelles, the hydrogenosomes, could have evolved from mitochondria.

Amino Acid Sequence↗
PubMed1996

Innate immunity. Isolation of several cysteine-rich antimicrobial peptides from the blood of a mollusc, Mytilus edulis.

We have isolated from the blood of immune-challenged and untreated mussels (Mytilus edulis) antibacterial and antifungal peptides. We have characterized two isoforms of a novel 34-residue, cysteine-rich, peptide with potent bactericidal activity and partially characterized a novel 6.2-kDa antifungal peptide containing 12 cysteines. We report the presence of two members of the insect defensin family of antibacterial peptides and provide a phylogenetic analysis that indicates that mollusc and arthropod defensins have a common ancestry. Our data argue that circulating antimicrobial peptides represent an ancient host defense mechanism that predated the separation between molluscs and arthropods at the root of the Cambrian, about 545 million years ago.

Amino Acid Sequence↗
PubMed1996

Human myosin VIIA responsible for the Usher 1B syndrome: a predicted membrane-associated motor protein expressed in developing sensory epithelia.

The gene encoding human myosin VIIA is responsible for Usher syndrome type III (USH1B), a disease which associates profound congenital sensorineural deafness, vestibular dysfunction, and retinitis pigmentosa. The reconstituted cDNA sequence presented here predicts a 2215 amino acid protein with a typical unconventional myosin structure. This protein is expected to dimerize into a two-headed molecule. The C terminus of its tail shares homology with the membrane-binding domain of the band 4.1 protein superfamily. The gene consists of 48 coding exons. It encodes several alternatively spliced forms. In situ hybridization analysis in human embryos demonstrates that the myosin VIIA gene is expressed in the pigment epithelium and the photoreceptor cells of the retina, thus indicating that both cell types may be involved in the USH1B retinal degenerative process. In addition, the gene is expressed in the human embryonic cochlear and vestibular neuroepithelia. We suggest that deafness and vestibular dysfunction in USH1B patients result from a defect in the morphogenesis of the inner ear sensory cell stereocilia.

Alternative Splicing↗
PubMed1996

16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny.

In the last few years many attempts have been made to differentiate more than 20 Bifidobacterium species. It has been recognized that identification of bifidobacterial species is problematic because of phenetic and genetic heterogeneities. In order to contribute to our understanding of Bifidobacterium taxonomy, we studied Bifidobacterium phylogeny by performing both 16S rRNA and 16S to 23S (16S-23S) internally transcribed spacer (ITS) sequence analyses. In this study, we determined 16S rRNA sequences of five Bifidobacterium strains representing four species, and compared them with the sequences available in the GenBank database, and used them to construct a distance tree and for a bootstrap analysis. Moreover, we determined the ITS sequences of 29 bifidobacterial strains representing 18 species and compared these sequences with each other. We constructed a phylogenetic tree based on these sequence data and compared this tree with the tree based on 16S rRNA sequence data. We found that the two trees were similar topologically, suggesting that the two types of molecules provided the same kind of phylogenetic information. However, while 16S rRNA sequences are a good tool to infer interspecific links, the 16S-23S rDNA spacer data allowed us to determine intraspecific relationships. Each of the strains was characterized by its own ITS sequence; hence, 16S-23S rRNA sequences are a good tool for strain identification. Moreover, a comparison of the ITS sequences allowed us to estimate that the maximum level of ITS divergence between strains belonging to the same species was 13%. Our data allowed us to confirm the validity of most of the Bifidobacterium species which we studied and to identify some classification errors. Finally, our results showed that Bifidobacterium strains have no tRNA genes in the 16S-23S spacer region.

Base Sequence↗
PubMed1995

Characterization and detection of plant trypanosomatids by sequence analysis of the small subunit ribosomal RNA gene.

The complete sequences of the genomic small subunit ribosomal RNA gene from two Phytomonas isolates: one associated with palm pathologies (P. cocos FGuiana) and one found in lactiferous plants with no apparent pathology (P. Euphorbe Senegal), were analyzed. Partial sequences from a number of other Phytomonas isolates were also determined. The sequences obtained were used to determine the phylogenetic relationships between Phytomonas and other trypanosomatids as well as within the genus Phytomonas. The analysis showed that the intraphloemic isolates associated with pathologies in palm trees formed a homogeneous group that diverged from the more heterogeneous group of non-pathogenic isolates found in latex plant. Sequence comparisons of the full and partial SSU rRNA gene, identified sequences which are specific to the genus Phytomonas and an EcoRI restriction nuclease site which specifically identifies the Phytomonas isolates associated with diseases in palm trees.

Animals↗
PubMed1995

An evolutionary view of drug-receptor interaction: the bioamine receptor family.

The large molecular diversity of receptors and their subtypes means that the pharmacologist is faced with many puzzling characterization questions. First, the molecular diversity of the receptors is deciphered only in part by a pharmacological approach, which precludes a satisfactory receptor classification based solely on pharmacological characteristics. Second, the physiological counterpart of the numerous subtypes of receptors specifically activated by single endogenous ligands remains unclear. Here, Philippe Vernier and colleagues use the example of the bioamine G protein-coupled receptors to show that many of the apparent inconsistencies that emerge from pharmacological and molecular characterizations of receptors can be better understood if the evolutionary history of the receptors is taken into account.

Amines↗
PubMed1994

How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences.

The evolution of bootstrap proportions (BP) with sequence length was studied using a 28S ribosomal RNA data set. For different sequence lengths, informative sites were jackknifed several times. Bootstrapping was subsequently performed on each of these subsamples. For each node, BPs so obtained were plotted against sequence length, showing the evolution of the robustness with increasing number of informative sites. For robust nodes (BP of 100%), the pattern of BPs is unvarying and is described by a simple function BP = 100 (1-e-b(x-x')), where x is the number of informative sites and b and x' are two parameters estimated using a nonlinear regression procedure. When a node has a BP < 100% and the pattern of BPs fits this function, it is possible to estimate the number of informative sites required to obtain a given average BP. The method also identifies nonrobust nodes (nonascending clusters of BP dots), for which it seems to be more cost effective and fruitful to turn to other species and/or genes rather than to continue sequencing longer gene lengths from the same species to reach a BP of 95%.

Animals↗
PubMed1994

The phylogenetic position of Dimastigella trypaniformis within the parasitic kinetoplastids.

The nuclear 16S-like rRNA coding regions of two strains of the kinetoplastid flagellate Dimastigella trypaniformis Sandon (strain Ulm and strain Glasgow) were sequenced and phylogenetically analyzed. Strain Ulm was isolated from the hindgut contents of the Australian termite Mastotermes darwiniensis Frogatt, whereas strain Glasgow originates from a soil sample in Scotland. After preparation of genomic DNA the 16S-like rRNA coding regions were amplified using polymerase chain reaction (PCR) technology. The amplification products were cloned in a plasmid vector and sequenced according to standard methods. The sequence of the 16S-like rRNA coding region of strain Ulm differs less than 2% from the sequence of strain Glasgow, indicating that the two strains are most probably members of one species. Phylogenetic analysis of the sequence data positioned D. trypaniformis Sandon as a deep branching lineage near the root of the kinetoplastid group of flagellates.

Animals↗
PubMed1994

Phylogeny of dermatophytes and dimorphic fungi based on large subunit ribosomal RNA sequence comparisons.

The phylogeny of dermatophytes and dimorphic fungi was considered using the large-subunit of ribosomal RNA (25S rRNA). Aligned sequences of 595 nucleotides covering the two most divergent domains D1 and D2, permitted a comparison of phylogenetic relationships at different levels. The dimorphic species (Onygenaceae) were significantly separated from dermatophytes (Arthrodermataceae) and from a third group including geophilic or very weakly pathogenic species (Onygenaceae and Gymnoascaceae). On a species level, the varietal status of Histoplasma duboisii and Histoplasma farciminosum, as close relations of Histoplasma capsulatum, was confirmed. The dimorphic fungus Emmonsia parva, in spite of a completely different parasitic form (adiaspores instead of yeast-like cells), clustered with Blastomyces dermatitidis which has a perfect form resembling that of H. capsulatum. From our data, teleomorphs of E. parva, Paracoccidioides brasiliensis and H. farciminosum, three dimorphic fungi known only under their anamorphic states, should belong to the family of Onygenaceae and the genus Ajellomyces. Among Arthrodermataceae, and family containing the most keratinophilic species, it was not possible to establish a clear hierarchy of species. Only Ctenomyces serratus, the species adapted to degrade keratin of feathers, Trichophyton ajelloi and Trichophyton terrestre were significantly separated. The speciation of true dermatophytes resulted most likely from a very recent evolution by adaptation to parasitism. Among species used as outgroups, the two emerging pathogens Pseudallescheria boydii (Scedosporium apiospermum) and Scedosporium prolificans (Scedosporium inflatum) were shown to be closely related to each other.

Arthrodermataceae↗
PubMed1993

MUST, a computer package of Management Utilities for Sequences and Trees.

The MUST package is a phylogenetically oriented set of programs for data management and display, allowing one to handle both raw data (sequences) and results (trees, number of steps, bootstrap proportions). It is complementary to the main available software for phylogenetic analysis (PHYLIP, PAUP, HENNING86, CLUSTAL) with which it is fully compatible. The first part of MUST consists of the acquisition of new sequences, their storage, modification, and checking of sequence integrity in files of aligned sequences. In order to improve alignment, an editor function for aligned sequences offers numerous options, such as selection of subsets of sequences, display of consensus sequences, and search for similarities over small sequence fragments. For phylogenetic reconstruction, the choice of species and portions of sequences to be analyzed is easy and very rapid, permitting fast testing of numerous combinations of sequences and taxa. The resulting files can be formatted for most programs of tree construction. An interactive tree-display program recovers the output of all these programs. Finally, various modules allow an in-depth analysis of results, such as comparison of distance matrices, variation of bootstrap proportions with respect to various parameters or comparison of the number of steps per position. All presently available complete sequences of 28S rRNA are furnished aligned in the package. MUST therefore allows the management of all the operations required for phylogenetic reconstructions.

Amino Acid Sequence↗
PubMed1993

Species sampling has a major impact on phylogenetic inference.

Representative properties of gnathostome species of a rich 28S rRNA data base were studied through the analysis of the fluctuations they provoked in bootstrap proportions (BPs) of nodes of parsimonious trees. Using original programs which permit BP comparison between different trees, it is empirically demonstrated that 4- to 24-species-trees are highly sensitive to species sampling: the inferences obtained from subsets of 4, 8, 16, or 24 species are not congruent with the whole set of 31 species. Study of trees obtained from exhaustively sampling all combinations of single species taken from each presumed monophyletic group shows precisely the impact of each species on the BP of each node. This procedure also shows that the impact of species changes within a given group on tree BPs is localized to its two or three neighboring nodes. The observation of differing impacts of species emphasizes the importance of sampling several species per presumed monophyletic group. It is also concluded that it is necessary to sample several successive outgroups and that the impact of a species on BPs depends mainly on the sampling context. Before undertaking extensive sequencing, the impact of species should be more often considered, since its effect on BPs is stronger than previously thought.

Animals↗
PubMed1993

Analysis of variability among endogenous ecotropic MuLV loci in laboratory mice.

We have isolated a molecular clone of an ecotropic murine leukemia virus from the ovaries of an SWR/J x RF/J hybrid female. The molecularly cloned virus, named pSR3, was demonstrated to induce virus production upon transfection into SWR/J immortalized fibroblasts and to promote germ line integration of proviruses in a fraction of the offspring germline when inoculated to neonate SWR/J females. Sequence analysis reveals that pSR3 is closely related to p623, a plasmid derived from Emv-11 (also referred to as AKV-1). Alignment of the pSR3 sequence with the partial nucleotide sequence of Emv-11 (an endogenous virus carried by BALB/c and C3H/He mice) together with p623 then allows a comparison between three viral sequences. Analysis of these data gives (a) an estimation of the natural divergence rate of MuLV genomes in the course of viral replication (1-5 x 10(-5) mutations per cycle and per nucleotide) and (b) molecular evidence for a recent origin through germ line infection of endogenous loci. From additional clues, Emv-11 appears to be the probable ancestor of at least some of these loci.

Alleles↗
PubMed1993

Bioamine receptors: evolutionary and functional variations of a structural leitmotiv.

Bioamines act as neurohormonal messengers through their binding to receptors which belong to the largest membrane protein family known so far: the seven spanning membrane receptors. This class of receptors transmits the effect of agonist binding to intracellular effectors by interacting with an intermediary G-protein. The diversity of receptor subtypes inside the protein family, observed in many animal species, is the result of a long evolutionary process. The tendency to protein diversification depends upon gene duplications and upon the continuous accumulation of mutations. The maintenance of vital functions in organisms, however, strictly requires enough structural conservation to ensure the functionality of the corresponding proteins. Both forces cooperate to ensure the adaptation of organisms to a changing environment. We have reviewed here the main conformational and functional constraints exerted on the structure of the bioamine receptors. They are mainly the transmembrane conformation of the receptors, their ability to bind ligands, to interact with G-proteins and to desensitize. The molecular basis of the biochemical and pharmacological differences used to classify the members of the receptor family have also been examined. Interestingly, this classification is very close to that obtained by the molecular phylogeny methods, used to elucidate the evolutionary relationships between bioamine receptors. However, this latter classification allows to accurately distinguish between different receptor subtypes (paralogous genes) and species homologous (orthologous genes). In addition, the calculation of phylogenetical distances reveals two main periods of diversification: the first one occurred before the separation of arthropods from vertebrates, in the Precambrian, and corresponds to the appearance of the main subtypes of the bioamine receptors. The second one, which occurred about 400 million years ago, might accompany the cephalization of the CNS in vertebrates.

Animals↗
PubMed1993

Sorghum phosphoenolpyruvate carboxylase gene family: structure, function and molecular evolution.

Although housekeeping functions have been shown for the phosphoenolpyruvate carboxylase (EC 4.1.1.31, PEPC) in plants and in prokaryotes, PEPC is mainly known for its specific role in the primary photosynthetic CO2 fixation in C4 and CAM plants. We have shown that in Sorghum, a monocotyledonous C4 plant, the enzyme is encoded in the nucleus by a small multigene family. Here we report the entire nucleotide sequence (7.5 kb) of the third member (CP21) that completes the structure of the Sorghum PEPC gene family. Nucleotide composition, CpG islands and GC content of the three Sorghum PEPC genes are analysed with respect to their possible implications in the regulation of expression. A study of structure/function and phylogenetic relationships based on the compilation of all PEPC sequences known so far is presented. Data demonstrated that: (1) the different forms of plant PEPC have very similar primary structures, functional and regulatory properties, (2) neither apparent amino acid sequences nor phylogenetic relationships are specific for the C4 and CAM PEPCs and (3) expression of the different genes coding for the Sorghum PEPC isoenzymes is differently regulated (i.e. by light, nitrogen source) in a spatial and temporal manner. These results suggest that the main distinguishing feature between plant PEPCs is to be found at the level of genes expression rather than in their primary structure.

Amino Acid Sequence↗
PubMed1993

The gene encoding the nucleocapsid protein: sequence analysis in murine hepatitis virus type 3 and evolution in Coronaviridae.

The nucleoprotein-encoding gene (N) of murine hepatitis virus type 3 (MHV 3), from the Mill Hill strain, was cloned and sequenced. It was compared to gene N from other murine coronaviruses and was found to share more similarities with N sequences from MHV 1 and MHV JHM strains than with the published MHV 3 N sequence which is almost identical to MHV A59. We suggest that the evolution of some MHV N sequences resulted from a double recombination phenomenon between two ancestors. Furthermore, comparison of protein N from avian and mammalian coronaviruses leads to the hypothesis that horizontal transfer events of the virus from one host species to another have occurred.

Amino Acid Sequence↗