Improved solubility of replication factor C (RFC) Walker A mutants

Differently Expressed Genes (DEGs) Relevant to Type 2 Diabetes Mellitus Identification and Pathway Analysis via Integrated Bioinformatics Analysis

BACKGROUND The aim of this study was to evaluate the differently expressed genes (DEGs) relevant to type 2 diabetes mellitus (T2DM) and pathway by performing integrated bioinformatics analysis. MATERIAL AND METHODS The gene expression datasets GSE7014 and GSE29221 were downloaded in GEO database, and DEGs from type 2 diabetes mellitus and normal skeletal muscle tissues were identified. Biological function analysis of the DEGs was enriched by GO and KEEG pathway. A PPI network for the identified DEGs was built using the STRING database. RESULTS Thirty top DEGs were identified from 2 datasets: GSE7014 and GSE29221. Of the 30 top DEGs, 20 were up-regulated and 10 were down-regulated. The 20 up-regulated genes were enriched in regulation of mRNA, protein biding, and phospholipase D signaling pathway. The 10 down-regulated genes were enriched in telomere maintenance via semi-conservative replication, AGE-RAGE signaling pathway in diabetic complications, and insulin resistance pathway. In the PPI network of 20 up-regulated DEGs, there were 40 nodes and 84 edges, with an average node degree of 4.2. For the 10 down-regulated DEGs, we found a total of 30 nodes and 105 edges, with an average node degree of 7.0 and local clustering coefficient of 0.812. Among the 30 DEGs, 10 hub genes (CNOT6L, CNOT6, CNOT1, CNOT7, RQCD1, RFC2, PRIM1, RFC4, RFC5, and RFC1) were also identified through Cytoscape. CONCLUSIONS DEGs of T2DM may play an essential role in disease development and may be potential pathogeneses of T2DM.

The interplay of primer-template DNA phosphorylation status and single-stranded DNA binding proteins in directing clamp loaders to the appropriate polarity of DNA

Sliding clamps are loaded onto DNA by clamp loaders to serve the critical role of coordinating various enzymes on DNA. Clamp loaders must quickly and efficiently load clamps at primer/template (p/t) junctions containing a duplex region with a free 3′OH (3′DNA), but it is unclear how clamp loaders target these sites. To measure the Escherichia coli and Saccharomyces cerevisiae clamp loader specificity toward 3′DNA, fluorescent β and PCNA clamps were used to measure clamp closing triggered by DNA substrates of differing polarity, testing the role of both the 5′phosphate (5′P) and the presence of single-stranded binding proteins (SSBs). SSBs inhibit clamp loading by both clamp loaders on the incorrect polarity of DNA (5′DNA). The 5′P groups contribute selectivity to differing degrees for the two clamp loaders, suggesting variations in the mechanism by which clamp loaders target 3′DNA. Interestingly, the χ subunit of the E. coli clamp loader is not required for SSB to inhibit clamp loading on phosphorylated 5′DNA, showing that χ·SSB interactions are dispensable. These studies highlight a common role for SSBs in directing clamp loaders to 3′DNA, as well as uncover nuances in the mechanisms by which SSBs perform this vital role.

A novel function for the conserved glutamate residue in the walker B motif of replication factor C

In all domains of life, sliding clamps tether DNA polymerases to DNA to increase the processivity of synthesis. Clamp loaders load clamps onto DNA in a multi-step process that requires ATP binding and hydrolysis. Like other AAA+ proteins, clamp loaders contain conserved Walker A and Walker B sequence motifs, which participate in ATP binding and hydrolysis, respectively. Mutation of the glutamate residue in Walker B motifs (or DExx-boxes) in AAA+ proteins typically reduces ATP hydrolysis by as much as a couple orders of magnitude, but has no effect on ATP binding. Here, the Walker B Glu in each of the four active ATP sites of the eukaryotic clamp loader, RFC, was mutated to Gln and Ala separately, and ATP binding- and hydrolysis-dependent activities of the quadruple mutant clamp loaders were characterized. Fluorescence-based assays were used to measure individual reaction steps required for clamp loading including clamp binding, clamp opening, DNA binding and ATP hydrolysis. Our results show that the Walker B mutations affect ATP-binding-dependent interactions of RFC with the clamp and DNA in addition to reducing ligand-dependent ATP hydrolysis activity. Here, we show that the Walker B glutamate is required for ATP-dependent ligand binding activity, a previously unknown function for this conserved Glu residue in RFC.

The ATP sites of AAA+ clamp loaders work together as a switch to assemble clamps on DNA

Clamp loaders belong to a family of proteins known as ATPases associated with various cellular activities (AAA+). These proteins utilize the energy from ATP binding and hydrolysis to perform cellular functions. The clamp loader is required to load the clamp onto DNA for use by DNA polymerases to increase processivity. ATP binding and hydrolysis are coordinated by several key residues, including a conserved Lys located within the Walker A motif (or P-loop). This residue is required for each subunit to bind ATP. The specific function of each ATP molecule bound to the Saccharomyces cerevisiae clamp loader is unknown. A series of point mutants, each lacking a single Walker A Lys residue, was generated to study the effects of abolishing ATP binding in individual clamp loader subunits. A variety of biochemical assays were used to analyze the function of ATP binding during discrete steps of the clamp loading reaction. All mutants reduced clamp binding/opening to different degrees. Decreased clamp binding activity was generally correlated with decreases in the population of open clamps, suggesting that differences in the binding affinities of Walker A mutants stem from differences in stabilization of proliferating cell nuclear antigen in an open conformation. Walker A mutations had a smaller effect on DNA binding than clamp binding/opening. Our data do not support a model in which each ATP site functions independently to regulate a different step in the clamp loading cycle to coordinate these steps. Instead, the ATP sites work in unison to promote conformational changes in the clamp loader that drive clamp loading.