UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

MOTIVATION: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. RESULTS: In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. AVAILABILITY AND IMPLEMENTATION: UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.

MOTIVATION: Similarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation. New approaches that overcome the limitations of methods that rely solely upon sequence similarity are attracting increased attention. One of these novel approaches is to use the organization of the structural domains in proteins. RESULTS: We propose a method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and propagating functional annotation. The performance of this method was measured through a cross-validation analysis using the Gene Ontology (GO) annotation of a sub-set of UniProtKB/Swiss-Prot. The results demonstrate the effectiveness of this approach in detecting functional similarity with an average F-score: 0.85. We applied the method on nearly 55.3 million uncharacterized proteins in UniProtKB/TrEMBL resulted in 44 818 178 GO term predictions for 12 172 114 proteins. 22% of these predictions were for 2 812 016 previously non-annotated protein entries indicating the significance of the value added by this approach. AVAILABILITY AND IMPLEMENTATION: The results of the method are available at: ftp://ftp.ebi.ac.uk/pub/contrib/martin/DAAC/ CONTACT: tdogan@ebi.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mycobacterial chaperonins: the tail wags the dog.

Molecular chaperones are defined as proteins that assist the noncovalent assembly of other protein-containing structures in vivo, but which are not components of these structures when they are carrying out their normal biological functions. There are numerous families of protein that fit this definition of molecular chaperones, the most ubiquitous of which are the chaperonins and the Hsp70 families, both of which are required for the correct folding of nascent polypeptide chains and thus essential genes for cell viability. The groE genes of Escherichia coli were the first chaperonin genes to be discovered, within an operon comprising two genes, groEL and groES, that function together in the correct folding of nascent polypeptide chains. The identification of multiple groEL genes in mycobacteria, only one of which is operon-encoded with a groES gene, has led to debate about the functions of their encoded proteins, especially as the essential copies are surprisingly often not the operon-encoded genes. Comparisons of these protein sequences reveals a consistent functional homology and identifies an actinomycete-specific chaperonin family, which may chaperone the folding of enzymes involved in mycolic acid synthesis and thus provide a unique target for the development of a new class of broad-spectrum antimycobacterial drugs.

Extensin network formation in Vitis vinifera callus cells is an essential and causal event in rapid and H(2)O(2)-induced reduction in primary cell wall hydration.

BACKGROUND: Extensin deposition is considered important for the correct assembly and biophysical properties of primary cell walls, with consequences to plant resistance to pathogens, tissue morphology, cell adhesion and extension growth. However, evidence for a direct and causal role for the extensin network formation in changes to cell wall properties has been lacking. RESULTS: Hydrogen peroxide treatment of grapevine (Vitis vinifera cv. Touriga) callus cell walls was seen to induce a marked reduction in their hydration and thickness. An analysis of matrix proteins demonstrated this occurs with the insolubilisation of an abundant protein, GvP1, which displays a primary structure and post-translational modifications typical of dicotyledon extensins. The hydration of callus cell walls free from saline-soluble proteins did not change in response to H(2)O(2), but fully regained this capacity after addition of extensin-rich saline extracts. To assay the specific contribution of GvP1 cross-linking and other wall matrix proteins to the reduction in hydration, GvP1 levels in cell walls were manipulated in vitro by binding selected fractions of extracellular proteins and their effect on wall hydration during H(2)O(2) incubation assayed. CONCLUSIONS: This approach allowed us to conclude that a peroxidase-mediated formation of a covalently linked network of GvP1 is essential and causal in the reduction of grapevine callus wall hydration in response to H(2)O(2). Importantly, this approach also indicated that extensin network effects on hydration was only partially irreversible and remained sensitive to changes in matrix charge. We discuss this mechanism and the importance of these changes to primary wall properties in the light of extensin distribution in dicotyledons.

A new view of pectin structure revealed by acid hydrolysis and atomic force microscopy.

Individual pectin polymers and complexes, isolated from the pericarp of unripe tomato (Lycopersicon esculentum var. Rutgers), were subjected to a mild acid hydrolysis and visualised and characterised by atomic force microscopy (AFM). The AFM images confirm earlier studies showing that individual pectic polysaccharides often possess long branches. The AFM data have been used to construct size and molecular weight distributions for the single molecules and complexes, from which the calculated number-average and weight-average molecular weights can then be compared directly with the published literature data on the rheology of bulk samples. Loss of the neutral sugars arabinose, galactose and rhamnose from the pectin samples does not significantly alter either the size or the branching density of the individual polymers, but is reflected in a breakdown of the complexes. Significant loss of galacturonic acid at long hydrolysis times was found to be accompanied by changes in the size and branching of the single polymers and further breakdown of the complexes. The results suggest that rhamnose, arabinose and galactose are not the major components of the individual polymers but are, instead, confined to the complexes. The polysaccharides represent a previously unrecognised branched homogalacturonan with a minimum mean size some three times larger than that previously reported. The complexes consist of homogalacturonans (HGs) held together by rhamnogalacturonan I (RG-I) regions. Comparison of the rate of depolymerisation of the homogalacturonans and complexes with the published data on changes in the intrinsic viscosity of bulk pectin samples, subjected to similar acid hydrolysis, suggests that the different rates of depolymerisation of RG-I and HG contribute separately to the observed changes in intrinsic viscosity during acid hydrolysis. Thus data obtained using a single molecule microscopy technique provides new insights into the behaviour in the bulk.

Pectin-chitosan interactions and gel formation.

The effect of chitosan concentration on the gelation of pectins differing in charge density and distribution was examined, through the determination of gel stiffness and the binding of chitosan to the gel network. Chitosan acts as a crosslinker of concentrated pectin solutions, with its effectiveness showing a dependency on charge on the pectin. The networks produced are clear even under conditions of charge neutralisation.

Material properties of concentrated pectin networks.

We have examined the mechanical behaviour of different types of pectin at high concentrations (> 30% w/w), relevant to the behaviour of pectin in the plant cell wall, and as a film-forming agent. Mechanical properties were examined as a function of counterion type (K(+), Ca(2+), Mg(2+)), concentration and extent of hydration. Hydration was controlled in an osmotic stress experiment where pectin films were exposed to concentrated polyethylene glycol [PEG] solutions of known osmotic pressure. We investigated the mechanical behaviour under simple extension. The results show that the swelling and stiffness of the films are strongly dependent on pectin source and ionic environment. At a fixed osmotic stress, both Ca(2+) or Mg(2+) counterions reduce swelling and increase the stiffness of the film.

Physicochemical studies of pectin/poly-L-lysine gelation.

The effect of poly-L-lysine concentration and degree of polymerisation on the gelation of pectins differing in charge density and distribution was examined, through the determination of gel stiffness, swelling behaviour and the binding of poly-L-lysine to the gel network. Poly-L-lysine acts as a crosslinker of concentrated pectin solutions, with its effectiveness showing dependencies on pH and charge distribution on the pectin. Neutralisation of the anionic charge on the pectin with the polycationic peptide leads to gel opacity and eventually network collapse.