Probing the Functional Mechanism of Escherichia coli GroEL Using Circular Permutation

Background: The Escherichia coli chaperonin GroEL subunit consists of three domains linked via two hinge regions, and each domain is responsible for a specific role in the functional mechanism. Here, we have used circular permutation to study the structural and functional characteristics of the GroEL subunit. Methodology/Principal Findings: Three soluble, partially active mutants with polypeptide ends relocated into various positions of the apical domain of GroEL were isolated and studied. The basic functional hallmarks of GroEL (ATPase and chaperoning activities) were retained in all three mutants. Certain functional characteristics, such as basal ATPase activity and ATPase inhibition by the cochaperonin GroES, differed in the mutants while at the same time, the ability to facilitate the refolding of rhodanese was roughly equal. Stopped-flow fluorescence experiments using a fluorescent variant of the circularly permuted GroEL CP376 revealed that a specific kinetic transition that reflects movements of the apical domain was missing in this mutant. This mutant also displayed several characteristics that suggested that the apical domains were behaving in an uncoordinated fashion. Conclusions/Significance: The loss of apical domain coordination and a concomitant decrease in functional ability highlights the importance of certain conformational signals that are relayed through domain interlinks in GroEL. W

Metabolomic approach to the exploration of biomarkers associated with disease activity in rheumatoid arthritis

We aimed to investigate metabolites associated with the 28-joint disease activity score based on erythrocyte sedimentation rate (DAS28-ESR) in patients with rheumatoid arthritis (RA) using capillary electrophoresis quadrupole time-of-flight mass spectrometry. Plasma and urine samples were collected from 32 patients with active RA (DAS28-ESR≥3.2) and 17 with inactive RA (DAS28-ESR<3.2). We found 15 metabolites in plasma and 20 metabolites in urine which showed a significant but weak positive or negative correlation with DAS28-ESR. When metabolites between active and inactive patients were compared, 9 metabolites in plasma and 15 in urine were found to be significantly different. Consequently, we selected 11 metabolites in plasma and urine as biomarker candidates which significantly correlated positively or negatively with DAS28-ESR, and significantly differed between active and inactive patients. When a multiple logistic regression model was built to discriminate active and inactive cohorts, three variables—histidine and guanidoacetic acid from plasma and hypotaurine from urine—generated a high area under the receiver operating characteristic (ROC) curve value (AUC = 0.8934). Thus, this metabolomics approach appeared to be useful for investigating biomarkers of RA. Combination of plasma and urine analysis may lead to more precise and reliable understanding of the disease condition. We also considered the pathophysiological significance of the found biomarker candidates

Stopped-flow fluorescence analysis of GroEL R231W and GroEL CP376-RW.

<p>Experiments were performed at 25°C. Solid traces indicate changes in tryptophan fluorescence for CP376-RW and dotted traces indicate fluorescence changes for GroEL R231W. <i>A.</i> Changes triggered by addition of 1 mM ATP, <i>B.</i> changes triggered by addition of 1 mM ATP and an equimolar concentration of GroES heptamer. In <i>A.</i>, fits to the raw traces are also shown; in white for CP376-RW and in black for R231W. The kinetic constants derived from the fits are as follows: for CP376-RW; <i>k</i>₁ = 145.8±13.2 s⁻¹, Amp₁ = 0.086±0.004, <i>k</i>₂ = 14.2±2.0 s⁻¹, Amp₂ = 0.017±0.002. For R231W; <i>k</i>₁ = 116.4±7.9 s⁻¹, Amp₁ = 0.076±0.003, <i>k</i>₂ = 2.1±0.15 s⁻¹, Amp₂ = −0.037±0.0008. Values are shown as mean ± standard errors. Negative values for amplitude denote phases with increases in fluorescence. <i>C.</i> The changes in the rate constant of Phase B in GroEL CP376-RW as a function of the ATP concentration. Kinetic traces were measured under conditions identical to that for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026462#pone-0026462-g005" target="_blank">Figure 5A</a> and varying the concentration of ATP during measurement. The traces were analyzed to obtain the value of <i>k</i> (± standard error) at each ATP concentration. The results of two separate experimental sessions are shown (<i>blue filled circles</i>). For comparison, results of a previous identical experiment performed on GroEL R231W <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026462#pone.0026462-Taniguchi1" target="_blank">[6]</a> is shown in <i>black circles</i>.</p

N- and C- terminal sequences of the circularly permuted GroEL subunits constructed in this study.

<p><u>Underlines</u> and <>\scale 90%\raster="rg1"<>wavy underlines are added to highlight corresponding sequence elements between each CP mutant and wild type (WT). Sequences in <i>italics</i> denote amino acids that are not from the native sequence of GroEL, added as a consequence of the circular permutation protocol. In addition, we found that in CP376, the N-terminal amino acid sequence had been altered, and apparently insertion of an extra alanine residue had occurred (double underlined). We decided to name this mutant CP376 based on the fact that the native GroEL amino acid sequence continues uninterrupted after Val376. GroEL CP376-RW contains an additional Arg to Trp point mutation at the position corresponding to Arg231 in the wild type sequence.</p

Locations of the N- and C-termini in the three circular permutation mutants of the present study.

<p>An X-ray structural model of a single GroEL/GroES subunit pair taken from PDB structure file 1 AON <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026462#pone.0026462-Xu1" target="_blank">[3]</a>, depicting the three locations where the N- and C-termini were relocated in the three CP mutants. The locations are indicated by colored CPK representation of the first (N-terminal end) amino acid of each CP mutant, excepting the starting methionine and any extraneous amino acids that were added as a consequence of the experimental protocol (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026462#s4" target="_blank">Materials and Methods</a>). The <i>green</i> molecule denotes Glu 209, the <i>yellow</i> molecule Val 254, and the <i>magenta</i> molecule Val 376 in wild type GroEL.</p

Relative stability of the GroEL-ADP-GroES complexes formed at 37°C.

<p>Each GroEL sample was incubated for 2 h at 37°C with an equimolar concentration of GroES. After incubation, samples were partitioned by centrifugal concentration (100 kDa cutoff). Samples denoted "Conc." indicate a 24 µg aliquot of each sample recovered from the upper reservoir concentrate of the filtering apparatus. Samples denoted "Filt." represent proteins that were recovered from a 200 µl aliquot of the lower reservoir filtrate of the apparatus. Experiments were performed in the absence (<i>−ATP, A</i>) and presence (<i>+ATP, B</i>) of 0.2 mM ATP. <i>RW</i> indicates GroEL R231W, and <i>CP</i> indicates GroEL CP376-RW samples. The apparent molecular weights of a commercial marker mixture (Dalton VII molecular weight marker, Sigma) are indicated to the left of the figure.</p

Electron Micrographs of GroEL CP376-RW.

<p>Samples were stained with 1% uranyl acetate. The scale bar in each figure indicates 100 nm. Magnification was x 60,000. <i>Wild Type</i> denotes wild type GroEL, <i>R231W</i> indicates GroEL R231W. <i>CPRW</i> denotes samples of GroEL CP376-RW, and +<i>ATPES</i> indicates samples where 0.2 mM ATP and an equimolar concentration of GroES were added in the course of sample preparation (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026462#s4" target="_blank">Materials and Methods</a>). Below each panel, representative zoomed images of an end-on view (left) and side view (right) particle for each sample are shown.</p