Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover

<p>Abstract</p> <p>Background</p> <p>Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as <it>Brugia</it>, <it>Meloidogyne</it>, <it>Bursaphelenchus </it>and <it>Pristionchus </it>indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes.</p> <p>Results</p> <p>We examine the transfer of cellulase genes to the free-living and beetle-associated nematode <it>Pristionchus pacificus</it>, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven <it>Pristionchus </it>species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of <it>Pristionchus pacificus </it>suggests these high evolutionary dynamics to be associated with copy number variations and positive selection.</p> <p>Conclusion</p> <p>We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.</p

A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain

In barley endosperm arabinoxylan (AX) is the second most abundant cell wall polysaccharide and in wheat it is the most abundant polysaccharide in the starchy endosperm walls of the grain. AX is one of the main contributors to grain dietary fibre content providing several health benefits including cholesterol and glucose lowering effects, and antioxidant activities. Due to its complex structural features, AX might also affect the downstream applications of barley grain in malting and brewing. Using a high pressure liquid chromatography (HPLC) method we quantified AX amounts in mature grain in 128 spring 2-row barley accessions. Amounts ranged from ~ 5.2 μg/g to ~ 9 μg/g. We used this data for a Genome Wide Association Study (GWAS) that revealed three significant quantitative trait loci (QTL) associated with grain AX levels which passed a false discovery threshold (FDR) and are located on two of the seven barley chromosomes. Regions underlying the QTLs were scanned for genes likely to be involved in AX biosynthesis or turnover, and strong candidates, including glycosyltransferases from the GT43 and GT61 families and glycoside hydrolases from the GH10 family, were identified. Phylogenetic trees of selected gene families were built based on protein translations and were used to examine the relationship of the barley candidate genes to those in other species. Our data reaffirms the roles of existing genes thought to contribute to AX content, and identifies novel QTL (and candidate genes associated with them) potentially influencing the AX content of barley grain. One potential outcome of this work is the deployment of highly associated single nucleotide polymorphisms markers in breeding programs to guide the modification of AX abundance in barley grain

Plant Fucosyltransferases and the Emerging Biological Importance of Fucosylated Plant Structures

Plants frequently incorporate the monosaccharide l-fucose (Fuc; 6-deoxy-l-galactose) into glycans and glycopolymers located in diverse cellular locations. The incorporation of Fuc onto these varied glycans is carried out by fucosyltransferases (FUTs), that make up a protein superfamily with equally varied and diverse functions. The structures wherein Fuc is found have numerous proposed and validated functions, ranging from plant growth and development, cell expansion, adhesion, and signaling, to energy metabolism, among others. FUTs from several different plant species have been identified and described; however, very few of them have been extensively characterized biochemically and biologically. In this review, we summarize plant FUTs that have been biochemically characterized and biologically investigated for associated phenotypes, offering greater insight and understanding into the physiological importance of Fuc in plants and in plant cell wall structures, glycans, and proteins

Plant Fucosyltransferases and the Emerging Biological Importance of Fucosylated Plant Structures

Plants frequently incorporate the monosaccharide l-fucose (Fuc; 6-deoxy-l-galactose) into glycans and glycopolymers located in diverse cellular locations. The incorporation of Fuc onto these varied glycans is carried out by fucosyltransferases (FUTs), that make up a protein superfamily with equally varied and diverse functions. The structures wherein Fuc is found have numerous proposed and validated functions, ranging from plant growth and development, cell expansion, adhesion, and signaling, to energy metabolism, among others. FUTs from several different plant species have been identified and described; however, very few of them have been extensively characterized biochemically and biologically. In this review, we summarize plant FUTs that have been biochemically characterized and biologically investigated for associated phenotypes, offering greater insight and understanding into the physiological importance of Fuc in plants and in plant cell wall structures, glycans, and proteins