Bioinformatic survey of ABC transporters in dermatophytes.

ATP binding cassette (ABC) transporters constitute a very large and ubiquitous superfamily of membrane proteins. They are responsible for ATP hydrolysis driven translocation of countless substrates. Being a very old and diverse group of proteins present in all organisms they share a common feature, which is the presence of an evolutionary conservative nucleotide binding domain (NBD)--the engine that drives the transport. Another common domain is a transmembrane domain (TMD) which consists of several membrane-spanning helices. This part of protein is substrate-specific, thus it is much more variable. ABC transporters are known for driving drug efflux in many pathogens and cancer cells, therefore they are the subject of extensive studies. There are many examples of conferring a drug resistance phenotype in fungal pathogens by ABC transporters, however, little is known about these proteins in dermatophytes--a group of fungi causing superficial mycoses. So far only a single ABC transporter has been extensively studied in this group of pathogens. We analyzed available genomic sequences of seven dermatophyte species in order to provide an insight into dermatophyte ABC protein inventory. Phylogenetic studies of ABC transporter genes and their products were conducted and included ABC transporters of other fungi. Our results show that each dermatophyte genome studied possesses a great variety of ABC transporter genes. Detailed analysis of selected genes and their products indicates that relatively recent duplication of ABC transporter genes could lead to novel substrate specificity.

Application of microsatellite-primed PCR (MSP-PCR) and PCR melting profile (PCR-MP) method for intraspecies differentiation of dermatophytes.

In this study, two PCR-based methods (MSP-PCR and PCR-MP) were compared for their abilities to identify intraspecies variations of 23 isolates of Trichophyton rubrum, 78 isolates of Trichophyton interdigitale and 22 isolates of Microsporum canis, obtained mainly from patients in Lódz city. The results allowed to distinguish four types (containing two subtypes) characteristic for T. interdigitale and three types characteristic for T. rubrum using PCR-MP method. Analysis conducted using MSP-PCR with (GACA)4 primer revealed four types for T. rubrum and three types (containing one subtype) for T. interdigitale and with (GTG), primer showed two types (containing one subtype) for T. rubrum and six types (containing one subtype) for T. interdigitale. No differentiation was observed for the M. canis isolates with either method.

Novel SINEs families in Medicago truncatula and Lotus japonicus: bioinformatic analysis.

Although short interspersed elements (SINEs) were discovered nearly 30 years ago, the studies of these genomic repeats were mostly limited to animal genomes. Very little is known about SINEs in legumes--one of the most important plant families. Here we report identification, genomic distribution and molecular features of six novel SINE elements in Lotus japonicus (named LJ_SINE-1, -2, -3) and Medicago truncatula (MT_SINE-1, -2, -3), model species of legume. They possess all the structural features commonly found in short interspersed elements including RNA polymerase III promoter, polyA tail and flanking repeats. SINEs described here are present in low to moderate copy numbers from 150 to 3000. Bioinformatic analyses were used to searched public databases, we have shown that three of new SINE elements from M. truncatula seem to be characteristic of Medicago and Trifolium genera. Two SINE families have been found in L. japonicus and one is present in both M. truncatula and L. japonicus. In addition, we are discussing potential activities of the described elements.