Two-component signal transduction in Agaricus bisporus: A comparative genomic analysis with other basidiomycetes through the web-based tool BASID2CS

• Published in: Fungal genetics and biology Vol. 55; pp. 77 - 84
• Main Authors: Lavín, José L., García-Yoldi, Alberto, Ramírez, Lucía, Pisabarro, Antonio G., Oguiza, José A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2013
• Subjects: Agaricus - genetics; Agaricus - growth & development; Agaricus - physiology; Agaricus bisporus; Basidiomycetes; Basidiomycota; Comparative genomics; Computational Biology - methods; Conserved Sequence; Fungal Proteins - genetics; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genome, Fungal; Genomics; Histidine kinase; Internet; Response regulator; Signal Transduction; Soil Microbiology; Comparative genomics; Response regulator; Agaricus bisporus; Signal transduction; Basidiomycetes; Histidine kinase
• ISSN: 1087-1845; 1096-0937
• DOI: 10.1016/j.fgb.2012.09.012

►Agaricus bisporus contains eight genes coding for two-component system (TCS) proteins. ► Genomes of basidiomycetes show a conserved core complement of five TCS proteins. ► Dual-histidine kinases are limited to various species of basidiomycetes. ► The A. bisporus Skn7-like response regulator gene is up-regulated on compost. ► BASID2CS is a web server for large-scale TCS protein analyses of basidiomycetes. Two-component systems (TCSs) are signal transduction mechanisms present in many eukaryotes, including fungi that play essential roles in the regulation of several cellular functions and responses. In this study, we carry out a genomic analysis of the TCS proteins in two varieties of the white button mushroom Agaricus bisporus. The genomes of both A. bisporus varieties contain eight genes coding for TCS proteins, which include four hybrid Histidine Kinases (HKs), a single histidine-containing phosphotransfer (HPt) protein and three Response Regulators (RRs). Comparison of the TCS proteins among A. bisporus and the sequenced basidiomycetes showed a conserved core complement of five TCS proteins including the Tco1/Nik1 hybrid HK, HPt protein and Ssk1, Skn7 and Rim15-like RRs. In addition, Dual-HKs, unusual hybrid HKs with 2 HK and 2 RR domains, are absent in A. bisporus and are limited to various species of basidiomycetes. Differential expression analysis showed no significant up- or down-regulation of the Agaricus TCS genes in the conditions/tissue analyzed with the exception of the Skn7-like RR gene (Agabi_varbisH97_2|198669) that is significantly up-regulated on compost compared to cultured mycelia. Furthermore, the pipeline web server BASID2CS (http://bioinformatics.unavarra.es:1000/B2CS/BASID2CS.htm) has been specifically designed for the identification, classification and functional annotation of putative TCS proteins from any predicted proteome of basidiomycetes using a combination of several bioinformatic approaches.