PULDB: the expanded database of Polysaccharide Utilization Loci

Abstract

The Polysaccharide Utilization Loci (PUL) database was launched in 2015 to present PUL predictions in ∼70 Bacteroidetes species isolated from the human gastrointestinal tract, as well as PULs derived from the experimental data reported in the literature. In 2018 PULDB offers access to 820 genomes, sampled from various environments and covering a much wider taxonomical range. A Krona dynamic chart was set up to facilitate browsing through taxonomy. Literature surveys now allows the presentation of the most recent (i) PUL repertoires deduced from RNAseq large-scale experiments, (ii) PULs that have been subjected to in-depth biochemical analysis and (iii) new Carbohydrate-Active enzyme (CAZyme) families that contributed to the refinement of PUL predictions. To improve PUL visualization and genome browsing, the previous annotation of genes encoding CAZymes, regulators, integrases and SusCD has now been expanded to include functionally relevant protein families whose genes are significantly found in the vicinity of PULs: sulfatases, proteases, ROK repressors, epimerases and ATP-Binding Cassette and Major Facilitator Superfamily transporters. To cope with cases where susCD may be absent due to incomplete assemblies/split PULs, we present ‘CAZyme cluster’ predictions. Finally, a PUL alignment tool, operating on the tagged families instead of amino-acid sequences, was integrated to retrieve PULs similar to a query of interest. The updated PULDB website is accessible at www.cazy.org/PULDB_new/

Distinct polysaccharide growth profiles of human intestinalPrevotella copriisolates

“…Consistent with this prediction, the V1-V3 16S sequences of select isolates were most closely related to two previously reported non-omnivore-associated P. copri Consistent with the 17 predicted PULs for P. copri DSM 18205, the number of predicted PULs per isolate ranged from 14-28, with a median of 23 (Terrapon et al, 2018). Intestinal Prevotella have been reported to utilize xylan and, as expected, xylan pPULs were ubiquitously represented throughout the isolate genomes (Tan et al, 2018).…”

Open prediction of polysaccharide utilisation loci (PUL) in 5414 publicBacteroidetesgenomes using PULpy

“…A PUL is a genomic locus that encodes all the necessary machinery to bind a particular class of polysaccharide at the cell surface, perform an initial cleavage and import the products inside the cell. Characterised PUL in Bacteroidetes generally consist of a susC-susD pair with a number of CAZymes encoded close by 12,13 . The SusCD proteins are responsible for binding the carbohydrate, and the CAZymes for cleavage.…”

“…CAZy is updated every few weeks and includes both automatic and manual annotation 16 . PULDB is built upon CAZy -initially published as an algorithm to predict PUL in 67 Bacteroidetes genomes 12 , a recent update extended this to 820 genomes 13 . Like CAZy, PULDB consists of automatic predictions and manually curated information.…”

The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics

“…The current version of PULDB 58 , the public database of PUL, contains 30,232 PUL; and recently we released data on over 96,000 PUL from all public Bacteroidetes genomes 56 . The additional 15,629 PUL predicted here ensures that ruminant-microbe-encoded PUL are represented in the public domain, and these loci will be a hugely interesting resource for researchers interested in carbohydrate utilisation in the rumen.…”