Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

Abstract

cCryptococcus, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648 Cryptococcus gene names have been published. However, these data are scattered throughout the literature and are challenging to find. Furthermore, conflicts in locus identification exist, so that named genes have been subsequently published under new names or names associated with one locus have been used for another locus. To avoid these conflicts and to provide a central source of Cryptococcus gene information, we have collected all published Cryptococcus gene names from the scientific literature and associated them with standard Cryptococcus locus identifiers and have incorporated them into FungiDB (www.fungidb.org). FungiDB is a panfungal genome database that collects gene information and functional data and provides search tools for 61 species of fungi and oomycetes. We applied these published names to a manually curated ortholog set of all Cryptococcus species currently in FungiDB, including Cryptococcus neoformans var. neoformans strains JEC21 and B-3501A, C. neoformans var. grubii strain H99, and Cryptococcus gattii strains R265 and WM276, and have written brief descriptions of their functions. We also compiled a protocol for gene naming that summarizes guidelines proposed by members of the Cryptococcus research community. The centralization of genomic and literature-based information for Cryptococcus at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen.

Systematic functional profiling of transcription factor networks in Cryptococcus neoformans

“…Out of the 155 TFs whose mutants were constructed, 57 TF genes possess names designated in published studies or reserved by other researchers through registration in FungiDB ( www.fungidb.org ). For the remaining 98 TFs, we provided gene names by following the systematic genetic nomenclature flowchart in C. neoformans recently reported by Inglis et al 14 ( Supplementary Data 1 ).…”

“…Phenotype strengths (strong, intermediate and weak) are distinguished in gradients of red or blue, as indicated in the right panel. Genes reported previously or genes whose names are reserved in FungiDB 14 are denoted in black, whereas genes that we newly named in this study are denoted in red. Transcriptional levels for each TF under distinct conditions were retrieved from the RNA sequencing data, which were reported in the previous C. neoformans H99 genome paper 4 .…”

A Single Protein S-acyl Transferase Acts through Diverse Substrates to Determine Cryptococcal Morphology, Stress Tolerance, and Pathogenic Outcome

“…This gene is highly homologous to S . cerevisiae PFA4 , which encodes a palmitoyl acyltransferase (PAT), and was accordingly given the same name (following guidelines in [ 27 ]). PATs are DHHC zinc finger domain-containing enzymes that mediate the reversible addition of palmitate to proteins, thereby regulating their membrane association and biological function [ 11 ].…”

The enigmatic role of fungal annexins: the case of Cryptococcus neoformans

“…This cryptococcal gene is annotated as AnnexinXIV, likely due to homology with the first described fungal annexin in Neurospora crassa (18). Based on the nomenclature conventions of annexins (32), we name the gene product as annexinC1 (AnxC1) and the gene ANXC1 .…”