agrobacterium tumefaciens genomic dna  (ATCC)

Journal: eLife

Article Title: Engineering NIR-sighted bacteria

doi: 10.7554/eLife.107069

Figure Lengend Snippet: ( a ) Light-dose response of Ec N harboring Av NIRusk after incubation at varying NIR- (purple circles), red- (red squares), and blue-light (blue pentagons) intensities. Corresponding data for Ac NIRusk are shown in . ( b ) Schematic of the Av NIRlux and Dm REDlux circuits based on Av PCM and Dm PCM. The tricistronic cassette comprising heme oxygenase (HO1), the sensor histidine kinase (chimera of Av / Dm PCM and FixL), and FixJ is controlled by the constitutive PmamDC promoter from Magnetospirillum gryphiswaldense , whereas the FixK2 promoter regulates the expression of the luxABCDE operon. ( c ) A. tumefaciens bacteria bearing Av NIRlux (left) and Dm REDlux (right) were spotted on plates and incubated at different light conditions (darkness, NIR, red, or blue light), followed by luminescence (Lumi.) measurements (see ). ( d ) A. tumefaciens bacteria carrying Av NIRlux and Dm REDlux were incubated in liquid culture for 20 h under different light conditions (gray: darkness, purple: NIR light, red: red light), followed by recording of reporter luminescence (see ). Data in panels a and d represent mean ± s.d. of three biologically independent samples.

Article Snippet: The Dm REDlux and Av NIRlux plasmids were transferred to A. tumefaciens C58 (also known as Agrobacterium fabrum C58, Lab collection, ATCC 33970) by biparental conjugation using E. coli WM3064 as a diaminopimelic acid auxotrophic donor strain (William Metcalf, UIUC, unpublished; thrB1004 pro thi rpsL hsdS lacZ∆ M15 RP4-1360 ∆(araBAD)567 ∆dapA1341::[erm pir (wt)] ).

Techniques: Incubation, Expressing, Bacteria

Journal: eLife

Article Title: Engineering NIR-sighted bacteria

doi: 10.7554/eLife.107069

Figure Lengend Snippet: ( a ) Quantified luminescence from the spotting assay in . Bar colors represent incubation in darkness (gray), NIR (purple), red (red), or blue (blue) light. ( b ) Optical density at 650 nm of A. tumefaciens bacteria bearing Av NIRlux or Dm REDlux grown in liquid culture under different light conditions. ( c ) Normalized reporter luminescence of the bacteria from panel ( b ) harboring Av NIRlux and grown in darkness (gray) or under NIR light (purple). The vertical black line denotes a time point of 20 h on which the data in are based. ( d ) As for ( c ) but for A. tumefaciens bacteria containing Dm REDlux and illumination with red instead of NIR light (red). Data in panels a-d represent mean ± s.d. of at least three biologically independent samples.

Article Snippet: The Dm REDlux and Av NIRlux plasmids were transferred to A. tumefaciens C58 (also known as Agrobacterium fabrum C58, Lab collection, ATCC 33970) by biparental conjugation using E. coli WM3064 as a diaminopimelic acid auxotrophic donor strain (William Metcalf, UIUC, unpublished; thrB1004 pro thi rpsL hsdS lacZ∆ M15 RP4-1360 ∆(araBAD)567 ∆dapA1341::[erm pir (wt)] ).

Techniques: Spotting Assay, Incubation, Bacteria

Journal: eLife

Article Title: Engineering NIR-sighted bacteria

doi: 10.7554/eLife.107069

Figure Lengend Snippet: Biliverdin binding pocket in the photosensory core modules (PCM) of ( a ) Azorhizobium caulinodans bacteriophytochrome (BphP), ( b ) Agrobacterium vitis BphP, ( c ) Pseudomonas aeruginosa BphP, and ( d ) Agrobacterium tumefaciens Agp2 BphP. Whereas experimental structures are available for the PCMs of AgP2 [PDB entry 6g1y ] and Pa BphP [3c2w , for Ac BphP and Av BphP, PCM models were calculated with AlphaFold3 ]. Tyrosine 190 and serine 275 are highlighted in the Pa PCM structure by magenta color. The other three PCMs feature less polar phenylalanine and alanine residues, respectively, in the structurally equivalent positions.

Article Snippet: The Dm REDlux and Av NIRlux plasmids were transferred to A. tumefaciens C58 (also known as Agrobacterium fabrum C58, Lab collection, ATCC 33970) by biparental conjugation using E. coli WM3064 as a diaminopimelic acid auxotrophic donor strain (William Metcalf, UIUC, unpublished; thrB1004 pro thi rpsL hsdS lacZ∆ M15 RP4-1360 ∆(araBAD)567 ∆dapA1341::[erm pir (wt)] ).

Techniques: Binding Assay