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Levasseur, Anthony; Gouret, Philippe; Lesage‐Meessen, Laurence; Asther, Michèle; Asther, Marcel; Record, Éric; Pontarotti, Pierre

doi:10.1186/1471-2148-6-92

Cited by 43 publications

(15 citation statements)

References 42 publications

(38 reference statements)

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“…Comparing these positively-selected sites to the laccase from Ascomycotina could target potential sites for future directed mutagenesis research. Hybrid laccases combining Ascomycotina sequences and positively-selected sites identified in Basidiomycotina could prove useful for testing new physico-chemical properties for biotechnology applications [60,61]. In addition, testing positively-selected sites could be valuable in drawing a parallel between functional and evolutionary shifts in the multi-copper family.…”

Section: Discussionmentioning

confidence: 99%

Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study

et al. 2010

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BackgroundThe diversity and function of ligninolytic genes in soil-inhabiting ascomycetes has not yet been elucidated, despite their possible role in plant litter decay processes. Among ascomycetes, Trichoderma reesei is a model organism of cellulose and hemicellulose degradation, used for its unique secretion ability especially for cellulase production. T. reesei has only been reported as a cellulolytic and hemicellulolytic organism although genome annotation revealed 6 laccase-like multicopper oxidase (LMCO) genes. The purpose of this work was i) to validate the function of a candidate LMCO gene from T. reesei, and ii) to reconstruct LMCO phylogeny and perform evolutionary analysis testing for positive selection.ResultsAfter homologous overproduction of a candidate LMCO gene, extracellular laccase activity was detected when ABTS or SRG were used as substrates, and the recombinant protein was purified to homogeneity followed by biochemical characterization. The recombinant protein, called TrLAC1, has a molecular mass of 104 kDa. Optimal temperature and pH were respectively 40-45°C and 4, by using ABTS as substrate. TrLAC1 showed broad pH stability range of 3 to 7. Temperature stability revealed that TrLAC1 is not a thermostable enzyme, which was also confirmed by unfolding studies monitored by circular dichroism. Evolutionary studies were performed to shed light on the LMCO family, and the phylogenetic tree was reconstructed using maximum-likelihood method. LMCO and classical laccases were clearly divided into two distinct groups. Finally, Darwinian selection was tested, and the results showed that positive selection drove the evolution of sequences leading to well-known laccases involved in ligninolysis. Positively-selected sites were observed that could be used as targets for mutagenesis and functional studies between classical laccases and LMCO from T. reesei.ConclusionsHomologous production and evolutionary studies of the first LMCO from the biomass-degrading fungus T. reesei gives new insights into the physicochemical parameters and biodiversity in this family.

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Section: Discussionmentioning

confidence: 99%

Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study

et al. 2010

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“…An ω value of < 1 indicates that a gene is undergoing purifying selection, an ω value = 1 is indicative of genetic drift or neutral evolution, while ω > 1 signifies positive selection. The relationship between positive selection and protein functional shift has been validated biochemically through the rational mutagenesis of various fungal, plant and mammal enzymes [ 21 - 24 ]. Whilst positive selection has been reported for between 38% and 62% of protein coding genes in mammals [ 25 ], it is generally held that the majority of codon positions are evolving neutrally or under purifying selection [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Molecular adaptation of telomere associated genes in mammals

et al. 2013

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BackgroundPlacental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these traits, there are exceptions that warrant further investigation. Species such as naked mole rat, human and certain bat species all exhibit extreme longevity with respect to body size. It has long been established that telomeres and telomere maintenance have a clear role in ageing but it has not yet been established whether there is evidence for adaptation in telomere maintenance proteins that could account for increased longevity in these species.ResultsHere we carry out a molecular investigation of selective pressure variation, specifically focusing on telomere associated genes across placental mammals. In general we observe a large number of instances of positive selection acting on telomere genes. Although these signatures of selection overall are not significantly correlated with either longevity or body size we do identify positive selection in the microbat species Myotis lucifugus in functionally important regions of the telomere maintenance genes DKC1 and TERT, and in naked mole rat in the DNA repair gene BRCA1.ConclusionThese results demonstrate the multifarious selective pressures acting across the mammal phylogeny driving lineage-specific adaptations of telomere associated genes. Our results show that regardless of the longevity of a species, these proteins have evolved under positive selection thereby removing increased longevity as the single selective force driving this rapid rate of evolution. However, evidence of molecular adaptations specific to naked mole rat and Myotis lucifugus highlight functionally significant regions in genes that may alter the way in which telomeres are regulated and maintained in these longer-lived species.

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“…In this study we tested for evidence of variation in selective pressure on the SLPs specific to particular RTs. As positive selection has been shown to be synonymous with protein functional shift, we wished to test if this sequence variation, some of which is a result of positive selection on the SLPs, could potentially influence the host response [34, 35]. …”

Section: Discussionmentioning

confidence: 99%

Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

et al. 2017

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Background Clostridium difficile is a nosocomial pathogen prevalent in hospitals worldwide and increasingly common in the community. Sequence differences have been shown to be present in the Surface Layer Proteins (SLPs) from different C. difficile ribotypes (RT) however whether these differences influence severity of infection is still not clear.ResultsWe used a molecular evolutionary approach to analyse SLPs from twenty-six C. difficile RTs representing different slpA sequences. We demonstrate that SLPs from RT 027 and 078 exhibit evidence of positive selection (PS). We compared the effect of these SLPs to those purified from RT 001 and 014, which did not exhibit PS, and demonstrate that the presence of sites under positive selection correlates with ability to activate macrophages. SLPs from RTs 027 and 078 induced a more potent response in macrophages, with increased levels of IL-6, IL-12p40, IL-10, MIP-1α, MIP-2 production relative to RT 001 and 014. Furthermore, RTs 027 and 078 induced higher expression of CD40, CD80 and MHC II on macrophages with decreased ability to phagocytose relative to LPS.ConclusionsThese results tightly link sequence differences in C. difficile SLPs to disease susceptibility and severity, and suggest that positively selected sites in the SLPs may play a role in driving the emergence of hyper-virulent strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0937-8) contains supplementary material, which is available to authorized users.

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Cited by 43 publications

References 42 publications

Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study

Exploring laccase-like multicopper oxidase genes from the ascomycete Trichoderma reesei: a functional, phylogenetic and evolutionary study

Molecular adaptation of telomere associated genes in mammals

Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

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