Journal: Protein Science : A Publication of the Protein Society

Article Title: Sequence‐encoded dynamics diversify allostery within a conserved protein scaffold

doi: 10.1002/pro.70821

Figure Lengend Snippet: Comparison of structures and C‐helices hinge‐associated hydrogen‐bonding networks between CRP E. coli and CRP MTB . (a, b) Crystal structures of CRP E. coli and CRP MTB highlighting differences within the dimerization C‐helices hinge region. In both CRPs, the N‐terminal cAMP binding domains are in blue (CRP E. coli ) or beige (CRP MTB ), while the C‐terminal DNA binding domains are shown in orange (CRP E. coli ) or light blue (CRP MTB ). The dashed red circles mark the C‐helices hinge region that links the two functional domains. Enlarged views (right panels) show the conformational changes upon binding cAMP (magenta spheres). In apo‐CRP E. coli , the hinge adopts a coiled conformation, whereas in CRP MTB the C‐helices remain helical, forming a pre‐assembled dimer interface. (c, d) Top and side view of CRP E. coli . cAMP (magenta) forms hydrogen bonds (yellow dashes) involving residues T127 and S128 from the adjacent subunit. Specifically, T127 of subunit A (T127 A ) and S128 of subunit B (S128 B ) accept hydrogen bonds from the bound cAMP of subunit A (cAMP A ), and vice versa. These residues, in turn, donate hydrogen bonds to R123 A and L124 B , respectively, drawing the C‐helices closer together to propagate the coil‐to‐helix transition. (e, f) Top and side view of CRP MTB . The homologous residues T134 A and N135 B , also accept hydrogen bonds from the bound cAMP A . However, N135 B is proposed to donate an additional hydrogen bond to cAMP A , rather than to L131 B . See Materials and Methods for Protein Data Bank codes.

Article Snippet: The CRP MTB mutant constructs (Swap 1, Swap 2, and N135S) were obtained from GenScript, and expressed in E. coli T7 Express pLysY cells (NEB).

Techniques: Comparison, Binding Assay, Functional Assay

Journal: Protein Science : A Publication of the Protein Society

Article Title: Sequence‐encoded dynamics diversify allostery within a conserved protein scaffold

doi: 10.1002/pro.70821

Figure Lengend Snippet: Helical propensity and sequence analyses of C‐helix sequence properties in proteobacterial (top row) and actinobacterial (bottom row) cAMP receptor protein (CRP) homologs. (a, b) Residue‐specific helical propensities calculated for proteobacteria (top; CRP E. coli ‐like) and actinobacteria (bottom; CRP MTB ‐like). Individual homologs are shown as gray curves, lineage‐average profiles are shown as red curves with the red error bars representing the standard deviation (SD) at each residue position, and blue curves represent CRP E. coli and CRP MTB within their respective lineages. The dashed vertical gray line marks the boundary of the C‐helix hinge region. (c, d) Sequence logos showing residue conservation across the C‐helix of proteobacterial and actinobacterial CRPs. Letter height corresponds to positional conservation. (e, f) Scatter plots comparing conservation scores with the mean helical propensity at each residue position. No statistically significant relationship was observed in either lineage (proteobacteria, p ‐value = 0.50; actinobacteria, p ‐value = 0.51). (g, h) Scatter plots showing the correlation between positional conservation scores and the SD of helical propensity across each lineage. The green and magenta points represent residues in the pre‐hinge and hinge of the C‐helix, respectively. A negative correlation indicates that highly conserved residues exhibit reduced variability in helical propensity. This relationship is statistically significant in both proteobacteria ( p ‐value = 0.03) and actinobacteria ( p ‐value = 1.17 × 10 −3 ).

Article Snippet: The CRP MTB mutant constructs (Swap 1, Swap 2, and N135S) were obtained from GenScript, and expressed in E. coli T7 Express pLysY cells (NEB).

Techniques: Sequencing, Residue, Standard Deviation

Journal: Nucleic Acids Research

Article Title: An intrinsically disordered domain of transcription terminator Rho governs genome-wide Rho utilization ( Rut ) site selection in Mycobacterium tuberculosis

doi: 10.1093/nar/gkag973

Figure Lengend Snippet: Detection of discrete Rut peaks along the M. tuberculosis genome. ( A ) Representative R 10 /R 0 enrichment profiles obtained with FL Mtb Rho (mean traces; Log 10 scale) along both strands of the H37Rv genome. Positive values are in dark blue while negative values are in red. Blue asterisks mark significant Rut peaks detected with PEAKachu (Benjamini–Hochberg adjusted P -value <.05). Pink symbols locate 3′-end positions identified by Term-seq and attributed to high-confidence RDTT events . ( B ) Venn diagram of significant Rut peaks obtained with FL Mtb Rho or ΔNID- Mtb Rho. ( C ) Motifs enriched in FL- Rut (E-value = 3.5 × 10 −5 and 1.6 × 10 −4 for motifs 1 and 2, respectively) and ΔNID- Rut (E-value = 4.4 × 10 −2 ) peaks as determined by differential MEME analysis (see the Supplementary data). The MEME motif enriched in Rut peaks in E. coli is shown for comparison. This motif reflects RNA binding preferences per Ec Rho subunit while both the length and sequence of inter-subunit RNA linkers are much less constrained [ , ]. Percentages correspond to the number of MEME cases with respect to total number of Rut peaks. The gray boxes locate the position of the 5′YC-binding (Y = U or C) PBS pocket of E. coli ’s Rho. ( D ) Box plots for selected sequence descriptors for FL- Rut , ΔNID- Rut , and Rut -less sequence pools. ΔG Mfold /kB is the Mfold free energy of secondary structure formation normalized for a kilobase. Mann–Withney U -tests for all pairwise comparisons are provided in . Pairwise tests with P -value >.05 are indicated by “ ns ”(not significant) above graphs. Effects sizes (R) between Rut -less and FL (red) or Rut -less and ΔNID (orange) datasets are indicated below graphs.

Article Snippet: Mtb RNAP core was expressed in BL21(DE3) E. coli carrying the pMR4 plasmid [ ] and purified by HisTrap FF (Cytiva) affinity chromatography followed by anion-exchange chromatography on MonoQ 5/50GL (Cytiva), as described [ ].

Techniques: Analysis, Comparison, RNA Binding Assay, Sequencing, Binding Assay

Journal: Nucleic Acids Research

Article Title: An intrinsically disordered domain of transcription terminator Rho governs genome-wide Rho utilization ( Rut ) site selection in Mycobacterium tuberculosis

doi: 10.1093/nar/gkag973

Figure Lengend Snippet: Localization of Rut sites in M. tuberculosis . ( A ) Categories of Rut peaks (blue arrows) and their respective proportions, comparing data from this work (FL- Rut peaks only) to H-SELEX analyses of RDTT in E. coli and B. subtilis . ( B – D ) Examples of Rut peaks found in 5′UTRs and potentially involved in conditional RDTT. ( E ) Probability plot of the shortest distances between transcript 3′-ends determined by Term-seq and the FL- Rut peaks. The reference point (0) corresponds to the downstream edge of the nearest Rut peak, as depicted in the diagram above the graph. Under ideal conditions, the 3′ends of RDTT transcripts are expected to localize downstream (d > 0) of the Rut site. However, in vivo 3′-to-5′ exonucleolytic trimming—sometimes extending beyond the Rut site (d < 0)—can occur until blocked by a sufficiently stable RNA structure (see diagram above graph). The red curve represents the analysis using only the subset of transcript 3′-ends assigned to RDTT with high-confidence in previous work , while the black curve includes all transcript 3′-ends. See also

Article Snippet: Mtb RNAP core was expressed in BL21(DE3) E. coli carrying the pMR4 plasmid [ ] and purified by HisTrap FF (Cytiva) affinity chromatography followed by anion-exchange chromatography on MonoQ 5/50GL (Cytiva), as described [ ].

Techniques: In Vivo, Analysis

Journal: RSC Advances

Article Title: BamA as a next-generation antibacterial target: mechanistic insights, inhibitor landscape, and rational drug design strategies

doi: 10.1039/d6ra06788c

Figure Lengend Snippet: Mechanistic and activity comparison of BamA-targeting and BamA-associated compounds according to binding site, mechanism of action, evidence for BamA engagement, reported minimum inhibitory concentration (MIC/MIC 90 ), and available in vivo efficacy

Article Snippet: Darobactin A , Lateral gate (β1–β16) , β-Strand mimicry , Direct structural and genetic evidence , 2 μg mL −1 ( E. coli ATCC 25922) , Yes; mouse septicemia models .

Techniques: Activity Assay, Comparison, Binding Assay, Concentration Assay, In Vivo, Infection, Inhibition, Disruption, Functional Assay, Membrane

Journal: World Journal of Microbiology & Biotechnology

Article Title: Phenotypic and genotypic assessment of antimicrobial and biocide resistance in enterobacteria from anaerobic digestion of dairy waste: implications for environmental and public health

doi: 10.1007/s11274-026-05319-9

Figure Lengend Snippet: Distribution of the number of screened resistance genes per E. coli -like enterobacterial isolate from anaerobic digester influent and biofertilizer

Article Snippet: All isolates and the E. coli ATCC 25,922 reference strain yielded 6-mm measurements with lactic acid, indicating that the tested LA condition was non-discriminatory.

Techniques:

Journal: World Journal of Microbiology & Biotechnology

Article Title: Phenotypic and genotypic assessment of antimicrobial and biocide resistance in enterobacteria from anaerobic digestion of dairy waste: implications for environmental and public health

doi: 10.1007/s11274-026-05319-9

Figure Lengend Snippet: Absolute frequency of selected resistance-gene detection in E. coli -like enterobacterial isolates from anaerobic digester influent and biofertilizer

Article Snippet: All isolates and the E. coli ATCC 25,922 reference strain yielded 6-mm measurements with lactic acid, indicating that the tested LA condition was non-discriminatory.

Techniques:

Journal: World Journal of Microbiology & Biotechnology

Article Title: Phenotypic and genotypic assessment of antimicrobial and biocide resistance in enterobacteria from anaerobic digestion of dairy waste: implications for environmental and public health

doi: 10.1007/s11274-026-05319-9

Figure Lengend Snippet: Antimicrobial susceptibility profiles of E. coli -like enterobacterial isolates from anaerobic digester influent and biofertilizer. Legend: GEN (Gentamicin), AMC (Amoxicillin-clavulanate), CLO (Chloramphenicol), CAZ (Ceftazidime), MER (Meropenem), LVX (Levofloxacin), TET (Tetracycline). Colors represent CLSI susceptible, intermediate, and resistant classifications

Article Snippet: All isolates and the E. coli ATCC 25,922 reference strain yielded 6-mm measurements with lactic acid, indicating that the tested LA condition was non-discriminatory.

Techniques:

Journal: World Journal of Microbiology & Biotechnology

Article Title: Phenotypic and genotypic assessment of antimicrobial and biocide resistance in enterobacteria from anaerobic digestion of dairy waste: implications for environmental and public health

doi: 10.1007/s11274-026-05319-9

Figure Lengend Snippet: Distribution of the number of tested antimicrobial agents classified as resistant (R) per presumptive E. coli -like enterobacterial isolate from effluent and biofertilizer

Article Snippet: All isolates and the E. coli ATCC 25,922 reference strain yielded 6-mm measurements with lactic acid, indicating that the tested LA condition was non-discriminatory.

Techniques:

Journal: World Journal of Microbiology & Biotechnology

Article Title: Phenotypic and genotypic assessment of antimicrobial and biocide resistance in enterobacteria from anaerobic digestion of dairy waste: implications for environmental and public health

doi: 10.1007/s11274-026-05319-9

Figure Lengend Snippet: Biocide inhibition-zone profiles of E. coli -like enterobacterial isolates from effluent and biofertilizer. Data are presented as mean ± SD. The dashed line indicates the 6-mm disk diameter. H 2 O 2 inhibition zones differed significantly between matrices after Benjamini–Hochberg correction (q = 0.00493). LA 2% (2% Lactic Acid); BAC 0.28% (0.28% Benzalkonium chloride), H 2 O 2 3% (3% hydrogen peroxide); CHX 1% (1% chlorhexidine digluconate)

Article Snippet: All isolates and the E. coli ATCC 25,922 reference strain yielded 6-mm measurements with lactic acid, indicating that the tested LA condition was non-discriminatory.

Techniques: Inhibition