Evolutionary reconstruction, nomenclature and functional meta-analysis of the Kiwellin protein family

Structural and Functional Analysis of the Lectin-like Protein Llp1 Secreted by Ustilago maydis upon Infection of Maize

The biotrophic fungus Ustilago maydis, which causes smut disease in maize, secretes numerous proteins upon plant colonization. Some of them, termed effectors, help to evade plant defenses and manipulate cellular processes within the host. The function of many proteins specifically secreted during infection remains elusive. In this study, we biochemically characterized one such protein, UMAG_00027, that is highly expressed during plant infection. We show that UMAG_00027 is a secreted protein with a lectin-like fold and therefore term it Llp1 (lectin-like-protein 1). Llp1 decorated the fungal cell wall of cells grown in axenic culture or proliferating in planta, which is in agreement with its potential sugar-binding ability. We were unable to identify the precise sugar moieties that are bound by Llp1. CRISPR/Cas9-mediated deletion of llp1 reveals that the gene is not essential for fungal virulence. A structural search shows the presence of several other lectin-like proteins in U. maydis that might compensate for the function of Llp1 in ∆llp1 mutants. We therefore speculate that Llp1 is part of a family of lectin-like proteins with redundant functions.

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs

Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set of species. It finds application in comparative and functional genomics, phylogenomics, and evolutionary reconstructions. With a rapidly increasing number of available genomes, the demand for large-scale predictions is also growing. In this contribution, we evaluate and implement major algorithmic improvements that significantly enhance the speed of the analysis without reducing precision. Graph-based detection of (co-)orthologs is typically based on a reciprocal best alignment heuristic that requires an all vs. all comparison of proteins from all species under study. The initial identification of similar proteins is accelerated by introducing an alternative search tool along with a revised search strategy-the pseudo-reciprocal best alignment heuristic-that reduces the number of required sequence comparisons by one-half. The clustering algorithm was reworked to efficiently decompose very large clusters and accelerate processing. Proteinortho6 reduces the overall processing time by an order of magnitude compared to its predecessor while maintaining its small memory footprint and good predictive quality.