Comprehensive Analysis of Carbohydrate-Active Enzymes from the Filamentous Fungus Scytalidium candidum 3C.

Complete enzymatic degradation of plant polysaccharides is a result of combined action of various carbohydrate-active enzymes (CAZymes). In this paper, we demonstrate the potential of the filamentous fungus Scytalidium candidum 3C for processing of plant biomass. Structural annotation of the improved assembly of S. candidum 3C genome and functional annotation of CAZymes revealed putative gene sequences encoding such proteins. A total of 190 CAZyme-encoding genes were identified, including 104 glycoside hydrolases, 52 glycosyltransferases, 28 oxidative enzymes, and 6 carbohydrate esterases. In addition, 14 carbohydrate-binding modules were found. Glycoside hydrolases secreted during the growth of S. candidum 3C in three media were analyzed with a variety of substrates. Mass spectrometry analysis of the fungal culture liquid revealed the presence of peptides identical to 36 glycoside hydrolases, three proteins without known enzymatic function belonging to the same group of families, and 11 oxidative enzymes. The activity of endo-hemicellulases was determined using specially synthesized substrates in which the glycosidic bond between monosaccharide residues was replaced by a thio-linkage. During analysis of the CAZyme profile of S. candidum 3C, four ß-xylanases from the GH10 family and two ß-glucanases from the GH7 and GH55 families were detected, partially purified, and identified.

Distinct Mechanisms of Phenotypic Effects of Inactivation and Prionization of Swi1 Protein in Saccharomyces cerevisiae.

Prions are proteins that under the same conditions can exist in two or more conformations, and at least one of the conformations has infectious properties. The prionization of a protein is typically accompanied by its functional inactivation due to sequestration of monomers by the prion aggregates. The most of prions has been identified in the yeast Saccharomyces cerevisiae. One of them is [SWI+], a prion isoform of the Swi1 protein, which is a component of the evolutionarily conserved chromatin remodeling complex SWI/SNF. Earlier, it was shown that the prionization of [SWI+] induces a nonsense suppression, which leads to weak growth of the [SWI+] strains containing mutant variants of the SUP35 gene and the nonsense allele ade1-14UGA on selective medium without adenine. This effect occurs because of [SWI+] induction that causes a decrease in the amount of the SUP45 mRNA. Strains carrying the SWI1 deletion exhibit significantly higher suppression of the ade1-14UGA nonsense mutation than the [SWI+] strains. In the present study, we identified genes whose expression is altered in the background of the SWI1 deletion using RNA sequencing. We found that the ade1-14UGA suppression in the swi1Δ strains is caused by an increase in the expression of this mutant allele of the ADE1 gene. At the same time, the SUP45 expression level in the swi1Δ strains does not significantly differ from the expression level of this gene in the [swi-] strains. Thus, we have shown that the phenotypic effects of Swi1 prionization and deletion are mediated by different molecular mechanisms. Based on these data, we have concluded that the prionization of proteins is not only unequal to their inactivation, but also can lead to the acquisition of novel phenotypic effects and functions.

Study of tumor-specific expression of some evolutionary new genes.

In this paper we have showed that evolutionary new genes DCD1(Dermicidin), LINC00309 (Long intergenic non-protein coding RNA 309) and CLLU1(Chronic lymphocytic leukemia up-regulated 1) have tumor-specific expression profile. Along with our previously published results this confirms the existence of the phenomenon of TSEEN (Tumor-Specifically Expressed, Evolutionarily Novel).

[Hyperplastic skin growth on the head of goldfish--comparative oncology aspects].

Dynamics of development and morphology of hyperplastic skin lesions ("hoods") on the head of goldfish, which were bred using artificial selection for more than thousand years, were studied. During monitoring of hundred fishes, at the age of 6 months "hoods" were found in 39.5%, among 14 months-old fishes in 60,7%. Morphologic examination of "hoods" on various stages of development revealed epithelial hyperplasia with increased clear mucous cells number, dermis thickening and oedema. On later stages developed papillomatous outgrowth and areas of epithelial intrusion. The comparative oncology analysis allow to hypothesize these skin growth to be a genetically determined benign neoplasm. This is the first example of artificially selected neoplasm described in the literature. It supports our hypothesis of the possible evolutionary role of tumors.

[Locus HS.633957 expression in human gastrointestinal tract and tumors].

Human locus HS.633957 corresponds to its namesake cluster in the UniGene database http:/www.ncbi.nlm.nih.gov/unigene. It is located on chromosome 7 and is 3.7 tpn in size. It does not seem to encode proteins nor has its function been identified. According to bioinformation evidence, its expression is tumor-specific. PCR assay on kDNA samples from different intact human tissues detected its slight expression in liver, heart, embryonal brain and kidney as well as in a wide spectrum of tumors. This work features locus Hs.633957 expression in different parts of human gastrointestinal tract and tumors.

[Tumor-specific expression of PBOV1, a new gene in evolution].

We identified mRNA of the newly discovered gene PBOV1 in a multitude of samples from tumors of the brain, lung, liver, gallbladder, colon, small intestine, mammary gland, uterus, ovary, ureter, adrenals, parotid, thymus and spleen. However, out of 29 intact adult and 8 fetal tissues, only pancreas was characterized by weak expression of the gene. Our results demonstrated that the PBOV1 gene expression is tumor-specific and has a potential as tumor marker. It is worth mentioning that we had predicted that property on the basis of available evolutionary data.

[Expression of transcripts related to the cluster HS.633957 in human normal and tumor tissues].

Using computational methods for analysis of electronic databases we identified a number of human nucleotide sequences expressed predominantly in tumors. We experimentally studied one of the sequences, which is related to the UniGene database cluster Hs.633957 and located near the telomere in the chromosome 7p22.3. All the RNA sequences of the cluster Hs.633957 are non-coding and their role was not described yet, but expression pattern of the locus makes it theoretically and practically interesting. Here we studied expression of the sequence Hs.633957 in various normal and tumor tissues using reverse transcription polymerase chain reaction. Of all the normal adult tissues studied weak expression was only identified in heart and liver. It was also identified in embryonic brain and kidney. Locus Hs.633957 is expressed in tumors of various tissue origin including tumors of lung, intestines, breast, stomach, cervix, lymph nodes and others. Thus the Hs.633957 locus is expressed predominantly in tumors and may be considered a prospective tumor marker.

[Investigation of transcription factor Brachyury (T) expression in human normal and tumor tissues].

By using computational differential display approach we identified a number of UniGene clusters which comprised 90% or more of ESTs from tumor cDNA libraries. One of them was cluster Hs.389457 which corresponds to the human gene Brachyury (T). That encodes a T-box gene family member transcription factor which is pivotal in early embryonal development. To experimentally verify our in silico findings of T expression, PCR was conducted using panels of cDNA from various human normal and tumor tissues. According to our results, Brachynry is expressed in tumors of the digestive tract, testis, ovary, breast, kidney, bladder, lung and brain tunic as well as in lymphomas. Weak amplification signals were picked up from normal tissues of small intestine, spleen and testis. Our results support earlier hypothesis on predominant tumor-related expression of Brachyury gene in adults.