Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: The multi-functional DHAP shunt of E. coli . ( A ) Genomic organization of the DHAP shunt operon and neighboring genes in E. coli ATCC 25922. The operon specifically consists of mtnK , mtnA , ald2 , and an annotated permease of unknown function . The pfs gene, conserved across all E. coli , is encoded in a different region of the E. coli genome. ( B ) Multiple sequence alignment of the DHAP shunt 5′-UTR region from 1,569 E. coli genomes containing the DHAP shunt operon. Positions matching the ATCC 25922 reference are shown in gray, while mismatches are shown in red. ( C and D ) Biochemical reactions catalyzed by the DHAP shunt pathway enzymes, with 5′-deoxyadenosine ( C ) or 5′-methylthioadenosine ( D ) as initial substrate.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Functional Assay, Sequencing

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: Regulation of E. coli ATCC 25922 transcriptome during growth on glucose, 5dR, or carbon starvation. Volcano plots of changes in ATCC 25922 transcript abundance for ( A ) wild-type ATCC 25922 grown with 5dR versus glucose, ( B ) MtnR deletion strain (∆ mtnR ) versus wild-type ATCC 25922 grown with glucose, and ( C ) ATCC 25922 incubated under carbon starvation conditions versus carbon replete (glucose) conditions. Gray lines indicate 2.5 log 2 -fold change thresholds; DHAP shunt genes are highlighted in pink. ( A ) DHAP shunt genes are strongly upregulated (~7.5 log 2 ) in the presence of 5dR. ( B ) Deletion of MtnR (∆ mtnR ) results in ~5 log 2 increased expression of DHAP shunt genes compared to the wild-type strain in the presence of glucose. ( C ) Carbon starvation only moderately upregulated DHAP shunt gene expression. ( D ) Inventory of genes differentially expressed under 5dR growth and carbon starvation relative to growth on glucose. Carbon starvation triggers a large change in the proteome compared to growth on 5dR, indicating the proteome change during growth on 5dR is specific to the substrate and not a general stress response.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Incubation, Expressing, Gene Expression

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: DHAP shunt 5′-UTR regions required for operon expression and repression by MtnR. ( A ) E. coli ATCC 25922 DHAP shunt genomic context and sections of 5′-UTR used for construction of plasmids (pLacZ###) with promoter– lacZ fusions. ( B, D ) LacZ activity assays from cell extracts of wild-type E. coli ATCC 25922 and ( C, E ) LacZ activity assays from cell extracts of MtnR deletion strain (Δ mtnR ) containing the indicated DHAP shunt 5′-UTR– lacZ fusion plasmids when grown with either 5 mM glucose (Glc), 5 mM glucose plus 5 mM 5dR (Glc + 5dR), or 5dR as the carbon source. The pLacZ control is a Lac promoter– lacZ fusion without added IPTG. Average and standard deviation error bars are for n = 3 independent replicates. ** P > 0.05, * P > 0.1; two-tailed t -test. ( F ) Log 2 -fold change in mtnK mRNA expression from transcriptomic analysis ( ; ) and measured by qRT-PCR for wild-type ATCC 25922 (WT), mtnR deletion strain (Δ mtnR ), and mtnR deletion strain complemented with mtnR from a plasmid (Δ mtnR + pmtnR). Tetracycline (10 ng/mL) was added to induce expression of mtnR from pmtnR plasmid. qRT-PCR average and standard deviation error bars are for n = 4 independent biological replicates except for WT Glc + 5dR versus Glc ( n = 8) and Δ mtnR + pmtnR Glc + 5dR versus Glc ( n = 3). ** P > 0.05; two-tailed t -test.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Expressing, Activity Assay, Control, Standard Deviation, Two Tailed Test, Quantitative RT-PCR, Plasmid Preparation

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: DHAP shunt expression is not activated by other alternative growth substrates. LacZ activity assays from cell extracts of E. coli ATCC 25922 containing the DHAP shunt 5′-UTR– lacZ fusion plasmid placZ255 and grown with either 5 mM glucose, NANA, l -fucose, l -arabinose, l -rhamnose, or 5-deoxy- d -ribose (5dR) as the sole carbon source. Average and standard deviation error bars are for n = 3 independent replicates. ** P > 0.05.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Expressing, Activity Assay, Plasmid Preparation, Standard Deviation

Journal: Journal of Bacteriology

Article Title: Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

doi: 10.1128/jb.00280-25

Figure Lengend Snippet: CRP is required for growth of E. coli ATCC 25922 using 5dR as a substrate. ( A and B ) Growth of wild-type ATCC 25922 (diamonds), CRP deletion strain (Δ crp ; triangles), and CRP deletion strain complemented with crp expressed from a plasmid (Δ crp + pCRP; circles) with ( A ) 5dR or ( B ) glucose as the sole carbon source. Average and standard deviation error bars are for n = 4 for growth on 5dR and n = 5 for growth on glucose. ( C ) Diauxic growth observed when wild-type ATCC 25922 is grown on a combination of 1 mM glucose plus 8 mM 5dR (diamonds), as compared to cultures grown with 1 mM glucose (triangles) or 8 mM 5dR (circles) as the sole carbon source. Dotted lines and fit parameters are for exponential regression fit to the growth data. Average and standard deviation error bars are for n = 5 independent biological replicates.

Article Snippet: Regions upstream of the DHAP shunt operon were amplified from E. coli ATCC 25922 genomic DNA as templates for sequencing ladders.

Techniques: Plasmid Preparation, Standard Deviation

Journal: Poultry

Article Title: Virulence and Antimicrobial Resistance of Avian Pathogenic Escherichia coli (APEC) Isolates from Poultry in Brazil

doi: 10.3390/poultry4010010

Figure Lengend Snippet: Figure 1. Map of Brazil demonstrating the different states where the 126 E. coli isolates were obtained. Pie graphs present the frequencies of APEC and AFEC isolates in each state.

Article Snippet: Negative (water) and positive (DNA of E. coli ATCC®25922TM strain) were included in all runs.

Techniques:

Journal: Poultry

Article Title: Virulence and Antimicrobial Resistance of Avian Pathogenic Escherichia coli (APEC) Isolates from Poultry in Brazil

doi: 10.3390/poultry4010010

Figure Lengend Snippet: Figure 2. Relationship between states, APEC, AFEC and virulence genes of the 126 E. coli isolates. The first column indicates the isolate origin state. The second column shows the classification into APEC (blue) or AFEC (green). Columns 3 to 7 classify the strain according to the presence (black) and absence (white) of the five virulence genes iroN, hlyF, iutA, iss, and ompT.

Article Snippet: Negative (water) and positive (DNA of E. coli ATCC®25922TM strain) were included in all runs.

Techniques:

Journal: Poultry

Article Title: Virulence and Antimicrobial Resistance of Avian Pathogenic Escherichia coli (APEC) Isolates from Poultry in Brazil

doi: 10.3390/poultry4010010

Figure Lengend Snippet: Figure 3. Multiple and individual profiles of antimicrobial susceptibility testing in 126 E. coli isolates. The first column indicates the isolate state origin. The second column shows the classification as APEC (blue) or AFEC (green). Columns 3 to 12 represent the antimicrobials tested (AMX = Amoxicillin; CEF = Ceftiofur; CIP = Ciprofloxacin; ENR = Enrofloxacin; NOR = Norfloxacin; GEN = Gentamicin; NEO = Neomycin; FFC = Florfenicol; DOX = Doxycycline; TET = Tetracycline), red is complete resistance, yellow is intermediate resistance, and grey is non-resistant/susceptible. The last column indicates whether the isolate is MDR (black) or non-MDR (white).

Article Snippet: Negative (water) and positive (DNA of E. coli ATCC®25922TM strain) were included in all runs.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: MICs and MBCs of rutin against ten strains of E. coli (mg/mL).

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: FICIs of rutin combined with different antibiotics against E. coli .

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Time–kill curves of rutin and amikacin combined against Escherichia coli . ( A ): Escherichia coli ATCC 25922; ( B ): Escherichia coli T31.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Scanning Electron Microscopy observation of Escherichia coli morphology (10,000×). ( A ): Escherichia coli ATCC 25922; ( B ): Amikacin-treated Escherichia coli ATCC 25922; ( C ): Rutin-treated Escherichia coli ATCC 25922; ( D ): Rutin and Amikacin-treated Escherichia coli ATCC 25922; ( E ): Escherichia coli T31; ( F ): Amikacin-treated Escherichia coli T31; ( G ): Rutin-treated Escherichia coli T31; ( H ): Rutin and Amikacin-treated Escherichia coli T31. The red parts are the representative change of the pictures.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques: Electron Microscopy

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Effect of rutin and amikacin alone or combined on Escherichia coli Alkaline Phosphatase leakage. ( A ): Escherichia coli ATCC 25922; ( B ): Escherichia coli T31. Each value is presented as the mean ± SD ( n = 3). ns p -value > 0.05, *** p -value < 0.001, **** p -value < 0.0001.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Effect of rutin and amikacin alone or combined on Escherichia coli K + leakage. ( A ): Escherichia coli ATCC 25922; ( B ): Escherichia coli T31. Each value is presented as the mean ± SD ( n = 3). ns p -value > 0.05, *** p -value < 0.001, **** p -value < 0.0001.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Effect of rutin and amikacin alone or combined on Escherichia coli protein leakage. ( A ): Escherichia coli ATCC 25922; ( B ): Escherichia coli T31. Each value is presented as the mean ± SD ( n = 3). * p -value < 0.05, *** p -value < 0.001, **** p -value < 0.0001.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Confocal Laser Scanning Microscopy observes changes in Escherichia coli cell membrane integrity. ( A ): Escherichia coli ATCC 25922; ( B ): amikacin-treated Escherichia coli ATCC 25922; ( C ): rutin-treated Escherichia coli ATCC 25922; ( D ): rutin and amikacin-treated Escherichia coli ATCC 25922; ( E ): Escherichia coli T31; ( F ): amikacin-treated Escherichia coli T31; ( G ): rutin-treated Escherichia coli T31; and ( H ): rutin and amikacin-treated Escherichia coli T31. Scale Bar: 50 µm.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques: Confocal Laser Scanning Microscopy, Membrane

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Analysis of the red–green ratio of bacteria in Confocal Laser Scanning Microscopy results. ( A ): Escherichia coli ATCC 25922; ( B ): Escherichia coli T31. Each value is presented as the mean ± SD ( n = 3). ns p -value > 0.05, * p -value < 0.05, **** p -value < 0.0001.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques: Bacteria, Confocal Laser Scanning Microscopy

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: MICs and FICIs of 6 flavonoids against E. coli .

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Synergistic Effects and Mechanisms of Action of Rutin with Conventional Antibiotics Against Escherichia coli

doi: 10.3390/ijms252413684

Figure Lengend Snippet: Diagram of the mechanism of action of rutin and amikacin combined against Escherichia coli. When rutin is combined with amikacin, it destroys the cell wall and cell membrane of E. coli , allowing a large amount of the drug to enter the bacteria. Amikacin inhibits ribosomes from synthesizing proteins. At the same time, AKP, intracellular K + , and proteins are leaked in large quantities, eventually causing the bacteria to lose their vitality.

Article Snippet: However, after the treatment with peptides for 6 h at a concentration of 1/2 MIC rutin + 1/2 MIC amikacin, the shapes of the E. coli ATCC 25922 ( D) and T31 cells ( H) were perturbed and the cells were broken.

Techniques: Membrane, Bacteria