Effects of pressure and temperature on the binding of RecA protein to single-stranded DNA

Merrin, Jack; Kumar, Pradeep; Libchaber, Albert

doi:10.1073/pnas.1112646108

Cited by 21 publications

(17 citation statements)

References 44 publications

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“…These models were then optimized through iterative rounds of refinement and model building. At the end stages of the refinement, TLS was used with TLS-groups determined with the TLSMD server 30 31 and hydrogens were added (except for ligands and solvent molecules). The analysis of these final models ( Table 2 ) showed no residues in disallowed regions of the Ramachandran plot (99.7% and 99.3% in preferred and allowed regions for PyaGRHPR and PfuGRHPR respectively).…”

Section: Methodsmentioning

confidence: 99%

New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

Lassalle¹,

Engilberge²,

Madern³

et al. 2016

Sci Rep

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Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 Å resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 Å resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action.

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Section: Methodsmentioning

confidence: 99%

New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

Lassalle¹,

Engilberge²,

Madern³

et al. 2016

Sci Rep

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“…No detection of the dimer here could be an artifact from the detection limit of the instrument or could be due to slow binding on‐rate of Cdh23 EC1‐2 (WT) toward dimerization . Moreover, it is well documented that the K D obtained from SV or SE varies widely for the same proteins and these variations are mainly attributed to the differences in internal pressure in AUC cell arising from different run‐time .…”

Section: Resultsmentioning

confidence: 97%

Structural basis of the strong cell‐cell junction formed by cadherin‐23

et al. 2019

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Cadherin-23, a giant atypical cadherin, form homophilic interactions at the cell-cell junction of epithelial cells and heterophilic interactions with protocadherin-15 at the tip links of neuroepithelial cells. While the molecular structure of the heterodimer is solved, the homodimer structure is yet to be resolved. The homodimers play an essential role in cell-cell adhesion as the downregulation of cadherin-23 in cancers loosen the intercellular junction resulting in faster migration of cancer cells and a significant drop in patient survival. In vitro studies have measured a stronger aggregation propensity of cadherin-23 compared to typical E-cadherin. Here, we deciphered the unique trans-homodimer structure of cadherin-23 in solution and show that it consists of two electrostatic-based interfaces extended up to two terminal domains. The interface is robust, with a low off-rate of~8 9 10 À4 s À1 that supports its strong aggregation propensity. We identified a point mutation, E78K, that disrupts this binding. Interestingly, a mutation at the interface was reported in skin cancer. Overall, the structural basis of the strong cadherin-23 adhesion may have far-reaching applications in the fields of mechanobiology and cancer.

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“…Microorganisms that sustain metabolic processes at cold temperatures produce cold acclimation and cold shock proteins involved in DNA replication (GyrA, RecA, and DnaA) (77)(78)(79) (79,(85)(86)(87), pyruvate metabolism (AceE and AceF) (88,89), and unsaturated fatty acid metabolism (fatty acid desaturases; DnaJ) (1,(90)(91)(92). Genes encoding such proteins were identified as containing cold adaptation features within the LH metagenome and originated mostly from Proteobacteria, Bacteroidetes, and Cyanobacteria (see Table S6 in the supplemental material).…”

Section: Resultsmentioning

confidence: 99%

Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

Lay

Mykytczuk

Yergeau

et al. 2013

Appl Environ Microbiol

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bThe Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (؊5°C), hypersalinity (salinity, 24%), and reducing (Ϸ؊165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H 2 S/sulfides (up to 25 ppm), ammonia (Ϸ381 M), and methane (11.1 g day ؊1 ). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/ subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments. Cryoenvironments are defined as permanently subzero or frozen environments, such as permafrost, glaciers, ice sheets, multiyear sea ice, high-elevation Antarctic dry valleys, and some cold saline springs (1-6). Microorganisms inhabiting cryoenvironments must face the challenges of subzero temperatures, low water activity, and, often, high solute concentrations to sustain their viability. The cold saline springs on Axel Heiberg Island (AHI) in the Canadian high Arctic discharge through 500 to 600 m of thick permafrost, maintain a liquid state at subzero temperatures, and offer a unique opportunity to assess microbial adaptations to extremes of both high salinity and subzero temperatures (3, 4, 7-9). These springs occur in an area with an average annual air temperature of Ϫ15°C, reaching below Ϫ40°C during the winter months, and probably originate from subpermafrost groundwater flow through carboniferous evaporites in areas of diapiric uplift on AHI (10, 11). Other Arctic cold springs, on Ellesmere Island in the Canadian high Arctic and on the Norwegian highArctic Svalbard archipelago, have been reported (12-14), although t...

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Effects of pressure and temperature on the binding of RecA protein to single-stranded DNA

Cited by 21 publications

References 44 publications

New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

Structural basis of the strong cell‐cell junction formed by cadherin‐23

Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

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