dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates.

PULs (polysaccharide utilization loci) are discrete gene clusters of CAZymes (Carbohydrate Active EnZymes) and other genes that work together to digest and utilize carbohydrate substrates. While PULs have been extensively characterized in Bacteroidetes, there exist PULs from other bacterial phyla, as well as archaea and metagenomes, that remain to be catalogued in a database for efficient retrieval. We have developed an online database dbCAN-PUL (http://bcb.unl.edu/dbCAN_PUL/) to display experimentally verified CAZyme-containing PULs from literature with pertinent metadata, sequences, and annotation. Compared to other online CAZyme and PUL resources, dbCAN-PUL has the following new features: (i) Batch download of PUL data by target substrate, species/genome, genus, or experimental characterization method; (ii) Annotation for each PUL that displays associated metadata such as substrate(s), experimental characterization method(s) and protein sequence information, (iii) Links to external annotation pages for CAZymes (CAZy), transporters (UniProt) and other genes, (iv) Display of homologous gene clusters in GenBank sequences via integrated MultiGeneBlast tool and (v) An integrated BLASTX service available for users to query their sequences against PUL proteins in dbCAN-PUL. With these features, dbCAN-PUL will be an important repository for CAZyme and PUL research, complementing our other web servers and databases (dbCAN2, dbCAN-seq).

Draft Genome Sequence of Clostridium perfringens Strain TAMU, Which Causes Necrotic Enteritis in Broiler Chickens.

Clostridium perfringens causes severe gastrointestinal diseases, which include necrotic enteritis (NE) in chickens, a deadly disease worldwide. We report here the draft genome sequence of Clostridium perfringens strain TAMU, which was used in developing an NE chicken challenge model. This C. perfringens TAMU genome sequence will aid in advancing potential intervention strategies to reduce NE pathogenesis.

Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion.

Previous analysis of charophyte green algal (CGA) genomes and transcriptomes for specific protein families revealed that numerous land plant characteristics had already evolved in CGA. In this study, we have sequenced and assembled the transcriptome of Zygnema circumcarinatum UTEX 1559, and combined its predicted protein sequences with those of 13 additional species [five embryophytes (Emb), eight charophytes (Cha), and two chlorophytes (Chl) as the outgroup] for a comprehensive comparative genomics analysis. In total 25,485 orthologous gene clusters (OGCs, equivalent to protein families) of the 14 species were classified into nine OGC groups. For example, the Cha+Emb group contains 4,174 OGCs found in both Cha and Emb but not Chl species, representing protein families that have evolved in the common ancestor of Cha and Emb. Different OGC groups were subjected to a Gene Ontology (GO) enrichment analysis with the Chl+Cha+Emb group (including 5,031 OGCs found in Chl and Cha and Emb) as the control. Interestingly, nine of the 20 top enriched GO terms in the Cha+Emb group are cell wall-related, such as biological processes involving celluloses, pectins, lignins, and xyloglucans. Furthermore, three glycosyltransferase families (GT2, 8, 43) were selected for in-depth phylogenetic analyses, which confirmed their presence in UTEX 1559. More importantly, of different CGA groups, only Zygnematophyceae has land plant cellulose synthase (CesA) orthologs, while other charophyte CesAs form a CGA-specific CesA-like (Csl) subfamily (likely also carries cellulose synthesis activity). Quantitative real-time-PCR experiments were performed on selected GT family genes in UTEX 1559. After osmotic stress treatment, significantly elevated expression was found for GT2 family genes ZcCesA, ZcCslC and ZcCslA-like (possibly mannan and xyloglucan synthases, respectively), as well as for GT8 family genes (possibly pectin synthases). All these suggest that the UTEX 1559 cell wall polysaccharide synthesis-related genes respond to osmotic stress in a manner that is similar to land plants.