Biomedical subjects

Guillaume Lecointre

Publications and source records attributed to Guillaume Lecointre.

7 recordsLinked to original sources

PubMed2003

Evolution of amino acid metabolism inferred through cladistic analysis.

Because free amino acids were most probably available in primitive abiotic environments, their metabolism is likely to have provided some of the very first metabolic pathways of life. What were the first enzymatic reactions to emerge? A cladistic analysis of metabolic pathways of the 16 aliphatic amino acids and 2 portions of the Krebs cycle was performed using four criteria of homology. The analysis is not based on sequence comparisons but, rather, on coding similarities in enzyme properties. The properties used are shared specific enzymatic activity, shared enzymatic function without substrate specificity, shared coenzymes, and shared functional family. The tree shows that the earliest pathways to emerge are not portions of the Krebs cycle but metabolisms of aspartate, asparagine, glutamate, and glutamine. The views of Horowitz (Horowitz, N. H. (1945) Proc. Natl. Acad. Sci. U. S. A. 31, 153-157) and Cordón (Cordón, F. (1990) Tratado Evolucionista de Biologia, Aguilar, Madrid, Spain), according to which the upstream reactions in the catabolic pathways and the downstream reactions in the anabolic pathways are the earliest in evolution, are globally corroborated; however, with some exceptions. These are due to later opportunistic connections of pathways (actually already suggested by these authors). Earliest enzymatic functions are mostly catabolic; they were deaminations, transaminations, and decarboxylations. From the consensus tree we extracted four time spans for amino acid metabolism development. For some amino acids catabolism and biosynthesis occurred at the same time (Asp, Glu, Lys, Leu, Ala, Val, Ile, Pro, Arg). For others ultimate reactions that use amino acids as a substrate or as a product are distinct in time, with catabolism preceding anabolism for Asn, Gln, and Cys and anabolism preceding catabolism for Ser, Met, and Thr. Cladistic analysis of the structure of biochemical pathways makes hypotheses in biochemical evolution explicit and parsimonious.

Amino Acids↗

PubMed2003

Polymorphism of genes encoding SOS polymerases in natural populations of Escherichia coli.

High fidelity replicative DNA polymerases can be blocked during DNA replication by various base damages, which represents a potentially lethal event. Escherichia coli possesses three DNA polymerases, PolII, PolIV and PolV, that can continue replication over such lesions in template DNA, thus allowing for cell survival. Genes coding for these enzymes, polB, dinB, and umuCD respectively, belong to the stress-inducible SOS regulon. We have analyzed the patterns of nucleotide sequence variability of genes encoding for three SOS polymerases from E. coli natural isolates in order to identify the nature of selective forces that determine their evolution. The frequency of inferred inter-strain recombination events, and the frequency of synonymous and non-synonymous base substitutions within these genes do not deviate significantly from those observed for the control group composed of 2 genes coding for DNA polymerases PolI and PolIII and 10 metabolic genes. This suggests that the loci coding for SOS polymerases are subject to selective pressure for the maintenance of their function and specificity. The fact that genes coding for translesion-synthesis (TLS) polymerases, particularly dinB and umuC homologs, have been conserved during evolution and the present analysis suggest that their activity is essential for the cellular survival and fitness.

Bacterial Proteins↗

PubMed2003

Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa.

Although much progress has been made recently in teleostean phylogeny, relationships among the main lineages of the higher teleosts (Acanthomorpha), containing more than 60% of all fish species, remain poorly defined. This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes. We compiled and analyzed three independent data sets, including: (i) mitochondrial ribosomal fragments from 12S and 16s (814bp for 97 taxa); (ii) nuclear ribosomal 28S sequences (847bp for 74 taxa); and (iii) a nuclear protein-coding gene, rhodopsin (759bp for 86 taxa). Detailed analyses were conducted on each data set separately and the principle of taxonomic congruence without consensus trees was used to assess confidence in the results as follows. Repeatability of clades from separate analyses was considered the primary criterion to establish reliability, rather than bootstrap proportions from a single combined (total evidence) data matrix. The new and reliable clades emerging from this study of the acanthomorph radiation were: Gadiformes (cods) with Zeioids (dories); Beloniformes (needlefishes) with Atheriniformes (silversides); blenioids (blennies) with Gobiesocoidei (clingfishes); Channoidei (snakeheads) with Anabantoidei (climbing gouramies); Mastacembeloidei (spiny eels) with Synbranchioidei (swamp-eels); the last two pairs of taxa grouping together, Syngnathoidei (aulostomids, macroramphosids) with Dactylopteridae (flying gurnards); Scombroidei (mackerels) plus Stromatoidei plus Chiasmodontidae; Ammodytidae (sand lances) with Cheimarrhichthyidae (torrentfish); Zoarcoidei (eelpouts) with Cottoidei; Percidae (perches) with Notothenioidei (Antarctic fishes); and a clade grouping Carangidae (jacks), Echeneidae (remoras), Sphyraenidae (barracudas), Menidae (moonfish), Polynemidae (threadfins), Centropomidae (snooks), and Pleuronectiformes (flatfishes).

Animals↗

PubMed2002

Phylogeny of Antarctic dragonfishes (Bathydraconidae, Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes.

Although Antarctic teleosts of the suborder Notothenioidei are well studied, the status of some families remains unclear because of limited taxonomic sampling and sometimes poor statistical support from molecular phylogenies. It is true for the Bathydraconidae, the sister-family of the famous haemoglobin-less icefishes, the Channichthyidae. The present study is aimed at clarifying bathydraconid phylogeny and the interrelationships of higher notothenioid families, taking nototheniids as the outgroup. For this purpose, about 300 positions in the mitochondrial control region, 750 positions in the cytochrome b, and a matrix of morphological characters were employed for separate and simultaneous phylogenetic analyses. We conclude that (1) molecular data strongly support the split of bathydraconids into three clades, here called the Bathydraconinae (Bathydraco, Prionodraco, Racovitzia), the Gymnodraconinae (Gymnodraco, Psilodraco, Acanthodraco), and the Cygnodraconinae (Cygnodraco, Gerlachea, Parachaenichthys). Interrelationships between these three and the Channichthyidae remain unclear. Molecular data support neither paraphyly nor monophyly of the bathydraconids, while morphology leads to the monophyly of the family based on the synapomorphic loss of the spinous dorsal fin; (2) The Channichthyidae, the Harpagiferidae, and the Artedidraconidae are monophyletic families; (3) the phylogeny of the haemoglobin-less channichthyids is completely resolved and congruent with the conclusions of based on anatomical characters; (4) The present molecular results as well as other molecular studies favour the hypothesis that harpagiferids are the sister-group of artedidraconids, though our morphological matrix puts harpagiferids as the sister-group of all other families on the basis of a single character. With regard to harpagiferid relationships, it is interesting to notice that, when analysed simultaneously, morphological characters are not automatically "swamped" within molecular ones: in the tree based on the simultaneous analysis of all available data, morphological characters impose their topology on molecules.

Animals↗

PubMed2002

Early steps of metabolism evolution inferred by cladistic analysis of amino acid catabolic pathways.

Among abiotic molecules available in primitive environments, free amino acids are good candidates as the first source of energy and molecules for early protocells. Amino acid catabolic pathways are likely to be one of the very first metabolic pathways of life. Among them, which ones were the first to emerge? A cladistic analysis of catabolic pathways of the sixteen aliphatic amino acids and two portions of the Krebs cycle is performed using four criteria of homology. The cladogram shows that the earliest pathways to emerge are not portions of the Krebs cycle but catabolisms of aspartate, asparagine, glutamate, glutamine, proline, arginine. Earliest enzymatic catabolic functions were deaminations and transaminations. Later on appeared enzymatic decarboxylations. The consensus tree allows to propose four time spans for catabolism development and corroborates the views of Cordón in 1990 about the evolution of catabolism.

Amino Acids↗

PubMed2002

Assessment of otocephalan and protacanthopterygian concepts in the light of multiple molecular phylogenies.

The rise of cladistics in ichthyology has dramatically improved our knowledge of teleostean basal interrelationships. However, some questions have remained open, among them the reliability of the Otocephala, a clade grouping clupeomorphs and ostariophysans, and the relationships of the Esocoidei. These two questions have been investigated in the light of new DNA sequences (from 28S and rhodopsin genes) and sequences from data banks (cytochrome b, 12-16S, 18S, MLL and RAG1). The ability of each of these markers to resolve basal teleostean interrelationships is assessed, and the cytochrome b was not found appropriate. Practical (i.e. different taxonomic samplings) and epistemological grounds led us to perform multiple separated phylogenetic analyses, in order to estimate the reliability of the above clades from their repeatability among trees from independent sequence data. The Otocephala are found monophyletic from most of the datasets; otherwise, they are not significantly contradicted from the others, which exhibit unresolved relationships. We conclude that the evidence provided here favours the sister-group relationship of clupeomorphs and ostariophysans. Morphological evidence including fossils is discussed, concluding that morphological works have not yet provided sufficient data to support this group. Salmonids and esocoids are found sister-groups from every molecular dataset in which these groups were sampled. Based on these convincing results, the Protacanthopterygii of Johnson and Patterson [1] are redefined, including the Esocoidei.

Animals↗

PubMed2002

When does the incongruence length difference test fail?

This paper examines the efficiency of the incongruence length difference test (ILD) proposed by Farris et al. (1994) for assessing the incongruence between sets of characters. DNA sequences were simulated under various evolutionary conditions: (1) following symmetric or asymmetric trees, (2) with various mutation rates, (3) with constant or variable evolutionary rates along the branches, and (4) with different among-site substitution rates. We first compared two sets of sequences generated along the same tree and under the same evolutionary conditions. The probability of a Type-I error (wrongly rejecting the true hypothesis of congruence) was substantially below the standard 5% level of significance given by the ILD test; this finding indicates that the choice of the 5% level is rather conservative in this case. We then compared two data sets, still generated along the same tree, but under different evolutionary conditions (constant vs. variable evolutionary rate, homogeneity vs. heterogeneity rate of substitution). Under these conditions, the probability of rejecting the true hypothesis of congruence was greater than the 5% given by the ILD test and increased with the number of sites and the degree to which the tree was asymmetric. Finally, the comparison of the two data sets, simulated under contrasting tree structures (symmetric vs. asymmetric) but under the same evolutionary conditions, led us to reject the hypothesis of congruence, albeit weakly, particularly when the number of informative sites was low and among-site substitution rate heterogeneous. We conclude that the ILD test has only limited power to detect incongruence caused by differences in the evolutionary conditions or in the tree topology, except when numerous characters are present and the substitution rate is homogeneous from site to site.

Artifacts↗