RNA Sequencing-Based Genome Reannotation of the DermatophyteArthroderma benhamiaeand Characterization of Its Secretome and Whole Gene Expression Profile during Infection.
Dermatophytes are the most common agents of superficial mycoses in humans and animals. The aim of the present investigation was to systematically identify the extracellular, possibly secreted, proteins that are putative virulence factors and antigenic molecules of dermatophytes. A complete gene expression profile ofArthroderma benhamiaewas obtained during infection of its natural host (guinea pig) using RNA sequencing (RNA-seq) technology. This profile was completed with those of the fungus cultivatedin vitroin two media containing either keratin or soy meal protein as the sole source of nitrogen and in Sabouraud medium. More than 60% of transcripts deduced from RNA-seq data differ from those previously deposited forA. benhamiae. Using these RNA-seq data along with an automatic gene annotation procedure, followed by manual curation, we produced a new annotation of theA. benhamiaegenome. This annotation comprised 7,405 coding sequences (CDSs), among which only 2,662 were identical to the currently available annotation, 383 were newly identified, and 15 secreted proteins were manually corrected. The expression profile of genes encoding proteins with a signal peptide in infected guinea pigs was found to be very different from that duringin vitrogrowth when using keratin as the substrate. Especially, the sets of the 12 most highly expressed genes encoding proteases with a signal sequence had only the putative vacuolar aspartic protease genePEP2in common, during infection and in keratin medium. The most upregulated gene encoding a secreted protease during infection was that encoding subtilisin SUB6, which is a known major allergen in the related dermatophyteTrichophyton rubrum.IMPORTANCEDermatophytoses (ringworm, jock itch, athlete's foot, and nail infections) are the most common fungal infections, but their virulence mechanisms are poorly understood. Combining transcriptomic data obtained from growth under various culture conditions with data obtained during infection led to a significantly improved genome annotation. About 65% of the protein-encoding genes predicted with our protocol did not match the existing annotation forA. benhamiae. Comparing gene expression during infection on guinea pigs with keratin degradationin vitro, which is supposed to mimic the host environment, revealed the critical importance of using realin vivoconditions for investigating virulence mechanisms. The analysis of genes expressedin vivo, encoding cell surface and secreted proteins, particularly proteases, led to the identification of new allergen and virulence factor candidates.
Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Van Du T
0000-0003-2074-5029
VD
Tran
Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
Niccolò
N
De Coi
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
Marc
M
Feuermann
Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Emanuel
E
Schmid-Siegert
Fundamental and Applied Research for Animals & Health (FARAH), Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
Elena-Tatiana
ET
Băguţ
Fundamental and Applied Research for Animals & Health (FARAH), Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
Bernard
B
Mignon
Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
Patrice
P
Waridel
Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
Corinne
C
Peter
Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
Sylvain
S
Pradervand
Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Marco
M
Pagni
Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
Michel
M
Monod
Arthroderma benhamiae; RNA-seq; Trichophyton; annotation; dermatophytes; infection; proteases; secreted proteins