Diversification and adaptive sequence evolution of Caenorhabditis lysozymes (Nematoda: Rhabditidae)

<p>Abstract</p> <p>Background</p> <p>Lysozymes are important model enzymes in biomedical research with a ubiquitous taxonomic distribution ranging from phages up to plants and animals. Their main function appears to be defence against pathogens, although some of them have also been implicated in digestion. Whereas most organisms have only few lysozyme genes, nematodes of the genus <it>Caenorhabditis </it>possess a surprisingly large repertoire of up to 15 genes.</p> <p>Results</p> <p>We used phylogenetic inference and sequence analysis tools to assess the evolution of lysozymes from three congeneric nematode species, <it>Caenorhabditis elegans</it>, <it>C. briggsae</it>, and <it>C. remanei</it>. Their lysozymes fall into three distinct clades, one belonging to the invertebrate-type and the other two to the protist-type lysozymes. Their diversification is characterised by (i) ancestral gene duplications preceding species separation followed by maintenance of genes, (ii) ancestral duplications followed by gene loss in some of the species, and (iii) recent duplications after divergence of species. Both ancestral and recent gene duplications are associated in several cases with signatures of adaptive sequence evolution, indicating that diversifying selection contributed to lysozyme differentiation. Current data strongly suggests that genetic diversity translates into functional diversity.</p> <p>Conclusion</p> <p>Gene duplications are a major source of evolutionary innovation. Our analysis provides an evolutionary framework for understanding the diversification of lysozymes through gene duplication and subsequent differentiation. This information is expected to be of major value in future analysis of lysozyme function and in studies of the dynamics of evolution by gene duplication.</p

Phenotypic covariance of longevity, immunity and stress resistance in the Caenorhabditis nematodes

Background \ud Ageing, immunity and stresstolerance are inherent characteristics of all organisms. In animals, these traits are regulated, at least in part, by forkhead transcription factors in response to upstream signals from the Insulin/Insulin– like growth factor signalling (IIS) pathway. In the nematode Caenorhabditis elegans, these phenotypes are molecularly linked such that activation of the forkhead transcription factor DAF-16 both extends lifespan and simultaneously increases immunity and stress resistance. It is known that lifespan varies significantly among the Caenorhabditis species but, although DAF-16 signalling is highly conserved, it is unclear whether this phenotypic linkage occurs in other species. Here we investigate this phenotypic covariance by comparing longevity, stress resistance and immunity in four \ud Caenorhabditis species. \ud \ud Methodology/Principal Findings \ud We show using phenotypic analysis of DAF-16 influenced phenotypes that among four closely related Caenorhabditis nematodes, the gonochoristic species (Caenorhabditis remanei and Caenorhabditis brenneri) have diverged \ud significantly with a longer lifespan, improved stress resistance and higher immunity than the hermaphroditic species (C. elegans and Caenorhabditis briggsae). Interestingly, we also observe significant differences in expression levels between the daf-16 homologues in these species using Real-Time PCR, which positively correlate with the observed phenotypes. Finally, we provide additional evidence in support of a role for DAF-16 in regulating phenotypic coupling by using a combination of wildtype isolates, constitutively active daf-16 mutants and bioinformatic analysis. \ud \ud Conclusions \ud The gonochoristic species display a significantly longer lifespan (p < 0.0001)and more robust immune and stress response (p<0.0001, thermal stress; p<0.01, heavy metal stress; p<0.0001, pathogenic stress) than the hermaphroditic species. Our data suggests that divergence in DAF-16 mediated phenotypes may underlie many of the differences observed between these four species of Caenorhabditis nematodes. These findings are further supported by the correlative higher daf-16 expression levels among the gonochoristic species and significantly higher lifespan, immunity and stress tolerance in the constitutively active daf-16 hermaphroditic mutants

Phenotypic covariance of Longevity, Immunity and Stress Resistance in the Caenorhabditis Nematodes

Background: Ageing, immunity and stresstolerance are inherent characteristics of all organisms. In animals, these traits are regulated, at least in part, by forkhead transcription factors in response to upstream signals from the Insulin/Insulin–like growth factor signalling (IIS) pathway. In the nematode Caenorhabditis elegans, these phenotypes are molecularly linked such that activation of the forkhead transcription factor DAF-16 both extends lifespan and simultaneously increases immunity and stress resistance. It is known that lifespan varies significantly among the Caenorhabditis species but, although DAF-16 signalling is highly conserved, it is unclear whether this phenotypic linkage occurs in other species. Here we investigate this phenotypic covariance by comparing longevity, stress resistance and immunity in four Caenorhabditis species. \ud \ud Methodology/Principal Findings: We show using phenotypic analysis of DAF-16 influenced phenotypes that among four closely related Caenorhabditis nematodes, the gonochoristic species (Caenorhabditis remanei and Caenorhabditis brenneri) have diverged significantly with a longer lifespan, improved stress resistance and higher immunity than the hermaphroditic species (C. elegans and Caenorhabditis briggsae). Interestingly, we also observe significant differences in expression levels between the daf-16 homologues in these species using Real-Time PCR, which positively correlate with the observed phenotypes. Finally, we provide additional evidence in support of a role for DAF-16 in regulating phenotypic coupling by using a combination of wildtype isolates, constitutively active daf-16 mutants and bioinformatic analysis. \ud \ud Conclusions: The gonochoristic species display a significantly longer lifespan (p<0.0001) and more robust immune and stress response (p<0.0001, thermal stress; p<0.01, heavy metal stress; p<0.0001, pathogenic stress) than the hermaphroditic species. Our data suggests that divergence in DAF-16 mediated phenotypes may underlie many of the differences observed between these four species of Caenorhabditis nematodes. These findings are further supported by the correlative higher daf-16 expression levels among the gonochoristic species and significantly higher lifespan, immunity and stress tolerance in the constitutively active daf-16 hermaphroditic mutants

Protist-Type Lysozymes of the Nematode Caenorhabditis elegans Contribute to Resistance against Pathogenic Bacillus thuringiensis

Pathogens represent a universal threat to other living organisms. Most organisms express antimicrobial proteins and peptides, such as lysozymes, as a protection against these challenges. The nematode Caenorhabditis elegans harbours 15 phylogenetically diverse lysozyme genes, belonging to two distinct types, the protist- or Entamoeba-type (lys genes) and the invertebrate-type (ilys genes) lysozymes. In the present study we characterized the role of several protist-type lysozyme genes in defence against a nematocidal strain of the Gram-positive bacterium Bacillus thuringiensis. Based on microarray and subsequent qRT-PCR gene expression analysis, we identified protist-type lysozyme genes as one of the differentially transcribed gene classes after infection. A functional genetic analysis was performed for three of these genes, each belonging to a distinct evolutionary lineage within the protist-type lysozymes (lys-2, lys-5, and lys-7). Their knock-out led to decreased pathogen resistance in all three cases, while an increase in resistance was observed when two out of three tested genes were overexpressed in transgenic lines (lys-5, lys-7, but not lys-2). We conclude that the lysozyme genes lys-5, lys-7, and possibly lys-2 contribute to resistance against B. thuringiensis, thus highlighting the particular role of lysozymes in the nematode's defence against pathogens

Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)-2

<p><b>Copyright information:</b></p><p>Taken from "Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)"</p><p>http://www.biomedcentral.com/1471-2148/8/114</p><p>BMC Evolutionary Biology 2008;8():114-114.</p><p>Published online 19 Apr 2008</p><p>PMCID:PMC2383907.</p><p></p

Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)-7

in Fig. 4.<p><b>Copyright information:</b></p><p>Taken from "Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)"</p><p>http://www.biomedcentral.com/1471-2148/8/114</p><p>BMC Evolutionary Biology 2008;8():114-114.</p><p>Published online 19 Apr 2008</p><p>PMCID:PMC2383907.</p><p></p

Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)-4

En in Additional file 1. In both cases, black lines at the beginning of the alignment denote the inferred signal peptides. Alignment 4 (see methods and results) includes all taxa and the entire protein sequences. Vertical black lines with arrows below the alignment indicate the regions used for specific DNA sequence analysis of all protist-type lysozymes (alignment 5). Vertical black lines with arrows above the alignment indicate those regions analyzed for the clade 1 lysozymes (alignments 6 and 7 for protein and DNA sequences, respectively). Clade 2 lysozyme analysis was based on complete sequences (alignments 8 and 9 for protein and DNA sequences, respectively). Note that all alignments are subsets of alignment 4, i.e. the position of indels is identical. The red box and arrow indicate the sequence position, which was inferred to be under positive selection for the clade 1 lysozymes.<p><b>Copyright information:</b></p><p>Taken from "Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)"</p><p>http://www.biomedcentral.com/1471-2148/8/114</p><p>BMC Evolutionary Biology 2008;8():114-114.</p><p>Published online 19 Apr 2008</p><p>PMCID:PMC2383907.</p><p></p

Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)-8

Icated by vertical lines, whereby lines above chromosomes indicate gene transcription from the sense strand and lines below chromosome transcription from the complementary strand.<p><b>Copyright information:</b></p><p>Taken from "Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)"</p><p>http://www.biomedcentral.com/1471-2148/8/114</p><p>BMC Evolutionary Biology 2008;8():114-114.</p><p>Published online 19 Apr 2008</p><p>PMCID:PMC2383907.</p><p></p

Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)-3

Efer to the bootstrap results inferred from protein and DNA sequence analysis, respectively. Only bootstrap values larger than 50 are shown. Branches in are drawn in proportion to the estimated number of substitutions per site, as indicated by the bar in the bottom left corner. Red-coloured branches indicate those inferred to be under positive selection. The unrooted topology is the most appropriate representation of the genealogy since the exact position of the root is unknown. The representation in serves to illustrate branch-names for the analysis of positive selection; the branch-names are identical to those given in Table 3.<p><b>Copyright information:</b></p><p>Taken from "Diversification and adaptive sequence evolution of lysozymes (Nematoda: Rhabditidae)"</p><p>http://www.biomedcentral.com/1471-2148/8/114</p><p>BMC Evolutionary Biology 2008;8():114-114.</p><p>Published online 19 Apr 2008</p><p>PMCID:PMC2383907.</p><p></p