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When a tree dies, it forms the foundation for new life: In a slow, invisible process, leaves, wood and roots are gradually decomposed \u2013 not by wind or weather but by millions and millions of tiny organisms. Fungi thread their way through the dead wood and degrade cell walls. Tiny animals such as insect larvae and mites gnaw through the tissue. And something very important happens in the process: The carbon stored in the plant is released, ultimately placing it at the disposal of plants again for the purpose of photosynthesis. But what exactly is responsible for performing this task in the global carbon cycle? And which molecular tools do the organisms use for it? To answer these questions, the researchers have developed a new bioinformatics-based method, which they have now presented in Molecular Biology and Evolution<\/em>.<\/p>\n\n\n\n This method, called fDOG (Feature architecture-aware directed ortholog search<\/em>), makes it possible to search in the genetic material of various organisms for genes that have evolved from the same precursor gene. It is assumed that these genes, known as \u201corthologs\u201d, encode proteins with similar functions. For the current study, the scientists searched for the genes of plant cell wall-degrading enzymes (PCDs). Unlike previous methods, fDOG not only searches through masses of genomic information but also analyzes the architecture of the proteins found \u2013 i.e. their structural composition, which reveals a lot about an enzyme\u2019s function.<\/p>\n\n\n\n \u201cWe start with a gene from one species, referred to as the seed, and then trawl through tens of thousands of species in the search for orthologous genes,\u201d explains Ingo Ebersberger, Professor for Applied Bioinformatics at Goethe University Frankfurt. \u201cIn the process, we constantly monitor whether the genes we find perhaps differ from the seed in terms of function and structure \u2013 for example, through the loss or gain of individual areas relevant for function.\u201d<\/p>\n\n\n\n The research team used this method to search for more than 200 potential PCD candidates in over 18,000 species from all three domains of life \u2013 bacteria, archaea and eukaryotes (plants, animals, fungi). The result is a detailed global map \u2013 with unprecedented accuracy \u2013 of enzymes capable of degrading plant cell walls.<\/p>\n\n\n\n The researchers devised special visualization methods to analyze the vast amounts of data and detect patterns. This revealed characteristic changes in the enzyme repertoire of the fungi under study, indicating a change in lifestyle of certain fungal species: From a decomposing lifestyle \u2013 i.e. the degradation of dead plants \u2013 to a parasitic lifestyle in which they infest living animals. Such evolutionary transitions are mirrored in characteristic patterns of enzyme loss.<\/p>\n\n\n\n A special surprise in the animal kingdom was the discovery that some arthropods possess an unexpectedly wide range of plant cell wall-degrading enzymes. These enzymes presumably originated from fungi and bacteria and entered the genome of invertebrates via direct gene transfer between different organisms \u2013 i.e. horizontal gene transfer. This suggests that they might be able to degrade plant material independently and are not reliant on the bacteria in their intestines, as was previously assumed. In another case, however, it emerged that the potential PCD genes in the analyzed sequence could be ascribed to microbial contamination \u2013 an important sign that such data need to be checked very carefully.<\/p>\n\n\n\n18,000 species in the spotlight<\/h2>\n\n\n\n
Surprising discoveries among fungi and animals<\/h2>\n\n\n\n