e coli  (ATCC)

Journal: The Journal of Biological Chemistry

Article Title: Molecular basis of collagen triple helix recognition by VWF A-like domain two of collagen VII: Implications for interlaced anchoring fibril formation

doi: 10.1016/j.jbc.2026.113448

Figure Lengend Snippet: Binding of von Willebrand factor A3-like domains to bead-conjugated peptides. A , guest sequences of the peptides used for peptide-conjugated beads. Overlapping α1(III) 578 to 580 sequences of Pep 4 and Pep 5 are underlined. B , Peptide-conjugated beads were incubated with E. coli lysates expressing GST fusion proteins of collagen VII A2, VWF A3, or integrin α2I domains. Beads-bound proteins were separated by 12% SDS-PAGE under a reducing condition and visualized by Coomassie Brilliant Blue (CBB) staining. The molecular sizes of collagen VII A2, VWF A3, and integrin α2I are approximately 48 kDa. GST-accept resin and mock-coupled beads served as positive and negative controls, respectively. Pep 5 and Pep 6 were included as reference peptides for VWF A3 and integrin α2I binding.

Article Snippet: The resulting plasmid was verified by sequencing and transformed into SHuffle T7 Express Competent E. coli cells (New England Biolabs) for protein expression.

Techniques: Binding Assay, Incubation, Expressing, SDS Page, Staining

Journal: Cell

Article Title: Mitochondrial proteome of Acanthamoeba delineates aerobic and anaerobic pathways dynamically regulated by oxygen

doi: 10.1016/j.cell.2026.08.056

Figure Lengend Snippet: (A) Venn diagram of AcMitoCarta and the mitoproteome of Gawryluk et al. Heat maps show Z-scores for our PCP proteomics. (B) Box plots of DeepLoc2.1 mito scores for the sets of proteins depicted in panel A. Center lines, medians; box limits, 25th & 75th percentiles; whiskers, 1.5x interquartile range (IQR); dots, outliers. n = 316, 806, 197. (C) For the protein sets depicted in panel A, box plots of whole cell protein abundance (log 10 normalized MS intensity in PCP proteomics). Center lines, medians; box limits, 25th & 75th percentiles; whiskers, 1.5x IQR; dots, outliers. n = 301, 792, 153 sample points. (D) Comparison of mitochondrial protein homology relationships to those of all proteins from humans, yeast ( S. cerevisiae ), and Acanthamoeba (based on orthogroup membership; lineage indicates Opisthokonta or Amoebozoa). (E) Pie charts indicate shared AcMitoCarta orthogroup memberships with mitochondrial proteins of humans or yeast ( S. cerevisiae ). The fractions of unique mitochondrial proteins without a Pfam or without a bidirectional best hit (BBH) in Dictyostelium are also shown. (F) Pie charts as above, but for only the 316 AcMitoCarta-specific proteins indicated in the Venn diagram in panel A. (G) Presence and absence matrix for AcMitoCarta proteins and their orthologs across 203 eukaryotes, 34 prokaryotic clades, and a small set of archaea (rows indicate orthogroups in AcMitoCarta, columns indicate species, and blue marks indicate shared orthogroup membership). On the right, examples of orthogroups mapping to human MitoPathways, with tick marks indicating pathway members. (H) Human-centric MitoPathways analysis, with bar graphs indicating Acanthamoeba orthogroup mapping (or lack thereof) to mammalian MitoPathway members in the indicated pathways. (I) Fractions of AcMitoCarta proteins arising from prokaryotic HGT at the indicated evolutionary branch. (J) Acanthamoeba HupA protein domain schematic indicating a DNA binding domain shared with E. coli HupA (green). (K) Electromobility shift assay for DNA binding of WT & R66E mutant recombinant purified AcHupA. Yellow marks show baseline migration of DNA, which shifts when bound to HupA. The green triangle marks the lane in which a full shift above the baseline is observed. (L) Confocal microscopy of HupA-3xHA in Acanthamoeba showing co-localization with mtDNA. The signal intensity across one mitochondrion is quantified in the indicated box (yellow) as an example. See also .

Article Snippet: NiCo21(DE3) Competent E. coli , NEB , C2529H.

Techniques: Quantitative Proteomics, Comparison, Yeast, Analysis, Binding Assay, Electromobility Shift Assay, Mutagenesis, Recombinant, Purification, Migration, Confocal, Microscopy

Journal: Cell

Article Title: Mitochondrial proteome of Acanthamoeba delineates aerobic and anaerobic pathways dynamically regulated by oxygen

doi: 10.1016/j.cell.2026.08.056

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: NiCo21(DE3) Competent E. coli , NEB , C2529H.

Techniques: Produced, Cell-Signaling, Recombinant, Purification, Mutagenesis, Blocking Assay, Glass, Staining, Protease Inhibitor, Cation-Exchange Chromatography, Extraction, Sequencing, Modification, Mass Spectrometry, Bicinchoninic Acid Protein Assay, Cell Viability Assay, Profiling, Blue Native PAGE, Immunoprecipitation, Transcriptomics, Confocal, Microscopy, Plasmid Preparation, Software, Isolation, Sample Prep

Journal: Acta Crystallographica Section F: Structural Biology Communications

Article Title: Structure of recombinant Thermoascus aurantiacus xylanase TaXyn10 with an authentic N-terminal pyroglutamate

doi: 10.1107/S2053230X26009155

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: TaXyn10 was recombinantly produced in SHuffle T7 E. coli cells (New England Biolabs) grown in Terrific Broth medium at 30°C.

Techniques: Expressing, Plasmid Preparation, Sequencing, Construct, Produced

Journal: Cell

Article Title: Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS

doi: 10.1016/j.cell.2026.08.057

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: AcMito-MDH was expressed in E. coli NiCo21(DE3) cells (New England BioLabs) in terrific broth (TB) broth at 37 °C and induced by 1mM isopropyl-β- d-thiogalactoside (IPTG) at an optical density (OD600) of around 0.5.

Techniques: Recombinant, Purification, Mutagenesis, Plasmid Preparation, Software, Electron Microscopy, Imaging