t5 caption a7 strains relevant characteristics source  (ATCC)

Journal: Biophysical Journal

Article Title: Collective Motion of Surfactant-Producing Bacteria Imparts Superdiffusivity to Their Upper Surface

doi: 10.1016/j.bpj.2011.07.019

Figure Lengend Snippet: Strains used in this study

Article Snippet: Of the three B. subtilis motility mutants, DS1677 is nonmotile, because it lacks the flagellar filament gene hag ; DS90 is motile and swarming-proficient but its flagellar motors are counterclockwise (CCW)-biased; and DS73 is motile but swarming-defective because its motors are clockwise (CW)-biased ( 18 ). table ft1 table-wrap mode="anchored" t5 caption a7 Strain Relevant characteristic(s) Source Swarming Surfactant ∗ S. marcescens 274 WT S. marcescens + + ATCC † RH1041 Serrawettin mutant of S. marcescens 274 + — ( 31 ) ‡ S. mar A WT S. marcescens + + UT Austin § B. subtilis 3610 WT Bacillus subtilis + + Daniel Kearns ¶ DS1677 B. subtilis 3610 Δ hag — + Daniel Kearns ¶ DS73 B. subtilis 3610 cheA :: tet ‖ — + Daniel Kearns ¶ DS90 B. subtilis 3610 cheB :: tet + + Daniel Kearns ¶ AW405 Motile E. coli K12 + — Julius Adler ∗∗ RP437 Motile E. coli K12 + — John S. Parkinson †† Open in a separate window ∗ The surfactants made by Serratia and Bacillus strains are serrawettin and surfactin, respectively.

Techniques: Mutagenesis

Journal: Molecular oral microbiology

Article Title: Characterization of a novel family of fibronectin-binding proteins with M23 peptidase domains from Treponema denticola

doi: 10.1111/j.2041-1014.2010.00584.x

Figure Lengend Snippet: (A) Predicted identifiable peptide motifs (www.ebi.ac.uk/InterProScan/) of Treponema pallidum fibronectin-binding protein Tp0155 and potential orthologues identified from the Treponema denticola genome using BLAST similarity searches. LysM domains are shown with vertical bars (A) or dots (B). Treponema pallidum and T. denticola M23 peptidase domains (diagonal bars) retain 37% identity. Potential signal sequences (solid black) were identified using http://bioinformatics.leeds.ac.uk/prot_analysis/signal.html. (B) Alignments of LysM(A) and LysM(B) domain sequences from T. pallidum Tp0155 and potential T. denticola orthologues showing high degree of consensus across the different peptide sequences. Degree of identity is shown from highest (e.g. ) to lowest (e.g. H). The LysM motif YxxxxGxx(Hyd) (Turner et al., 2004) is boxed. Asterisk indicates residues that do not fit the specified motif.

Article Snippet: The E. coli was cultured on Luria Bertani (LB) agar ( Sambrook et al ., 1989 ) or in LB broth, containing appropriate antibiotics (ampicillin, 100μg ml −1 ; kanamycin 25μg ml −1 ). table ft1 table-wrap mode="anchored" t5 caption a7 Strain/plasmid Relevant characteristics Source Treponema denticola ATCC 35405 Type strain ( Chan et al ., 1993 ) Escherichia coli XL-1 Blue recA1 endA1 gyrA96 thi hsdR17 supE44 relA1 lac [ F ‘proAB lacl q Z Δ M15 Tn10 (Tet R )] Stratagene M15 (pREP-4 Kn R ) nal s str s rif s thi − lac − ara + gal + mtl − F − recA + uvr + lon + Qiagen Plasmids pQE30 bla ColE1 ori (Ap R ) Qiagen pQE30-TDE2318 bla ColE1 ori This study pQE30-TDE2753 bla ColE1 ori This study pQE30-TDE1738 bla ColE1 ori This study pQE30-TDE0110 bla ColE1 ori This study pQE30-TDE2189 bla ColE1 ori This study pQE30-TDE1136 bla ColE1 ori This study pQE30-TDE1297 bla ColE1 ori This study Open in a separate window Bacterial strains and plasmids used in this study

Techniques: Binding Assay

Journal: Molecular oral microbiology

Article Title: Characterization of a novel family of fibronectin-binding proteins with M23 peptidase domains from Treponema denticola

doi: 10.1111/j.2041-1014.2010.00584.x

Figure Lengend Snippet: Detection of proteins on the surface of Treponema denticola ATCC 35405 using antibodies to the Treponema pallidum protein Tp0155 which had first been pre-adsorbed against Treponema phagedenis (Kazan). (A, C, E, G, I, K and M) Phase-contrast images; (B, D, F, H, J, L and N) corresponding immunofluorescence. (A, B) Preimmune serum for Tp0155-specific antibodies; (C, D), Tp0155-specific antibodies, non-detergent-treated T. denticola; (E, F), Tp0155-specific antibodies, Triton X-114-treated T. denticola; (G, H), preimmune serum for Tp0249-specific antibodies; (I, J), Tp0249-specific antibodies, non-detergent-treated T. denticola (negative control); (K, L), Tp0249-specific antibodies, Triton X-114-treated T. denticola; (M, N), anti-T. denticola antibodies (control) (Edwards et al., 2005).

Article Snippet: The E. coli was cultured on Luria Bertani (LB) agar ( Sambrook et al ., 1989 ) or in LB broth, containing appropriate antibiotics (ampicillin, 100μg ml −1 ; kanamycin 25μg ml −1 ). table ft1 table-wrap mode="anchored" t5 caption a7 Strain/plasmid Relevant characteristics Source Treponema denticola ATCC 35405 Type strain ( Chan et al ., 1993 ) Escherichia coli XL-1 Blue recA1 endA1 gyrA96 thi hsdR17 supE44 relA1 lac [ F ‘proAB lacl q Z Δ M15 Tn10 (Tet R )] Stratagene M15 (pREP-4 Kn R ) nal s str s rif s thi − lac − ara + gal + mtl − F − recA + uvr + lon + Qiagen Plasmids pQE30 bla ColE1 ori (Ap R ) Qiagen pQE30-TDE2318 bla ColE1 ori This study pQE30-TDE2753 bla ColE1 ori This study pQE30-TDE1738 bla ColE1 ori This study pQE30-TDE0110 bla ColE1 ori This study pQE30-TDE2189 bla ColE1 ori This study pQE30-TDE1136 bla ColE1 ori This study pQE30-TDE1297 bla ColE1 ori This study Open in a separate window Bacterial strains and plasmids used in this study

Techniques: Immunofluorescence, Negative Control, Control

Journal: Molecular oral microbiology

Article Title: Characterization of a novel family of fibronectin-binding proteins with M23 peptidase domains from Treponema denticola

doi: 10.1111/j.2041-1014.2010.00584.x

Figure Lengend Snippet: (A) Alignments of M23 peptidase domains from TDE1738 of Treponema denticola and homologous regions of peptidoglycan-degrading enzymes lysostaphin from Staphylococcus simulans biovar staphylolyticus, zoocin A from Streptococcus equi subsp zooepidemicus and ALE-1 from Staphylococcus capitis. The M23 peptidase domain of TDE1738 retains 43% identity to lysostaphin, 43% identity to zoocin A and 40% identity to ALE-1 with conservation across the HxGxD and HLH active sites. (B) Alignments of a 92 amino acid (aa) residue portion regions of TDE1739 of T. denticola and lysostaphin immunity factor from S. simulans biovar staphylolyticus, demonstrating homology (29% identity) between these peptides. Sequence consensus is shown as is degree of identity from highest (e.g. ) to lowest (e.g. A). (C) Diagram depicting genes encoding potential and known peptidoglycan degradation enzymes and adjacent immunity factors which provide protection from autolysis by the peptidoglycanolytic enzyme. (i) The chromosomal gene TDE1738 from T. denticola encodes for a potential peptidoglycan-degrading enzyme, and TDE1739 for a potential immunity factor. (ii) Lysostaphin and adjacent lysostaphin immunity factor (Lif/Epr) are encoded on the plasmid pACK1 of S. simulans biovar staphylolyticus. (iii) The gene encoding zoocin A and corresponding zoocin A immunity factor (Zif) is on the chromosome of Streptococcus equi subsp zooepidemicus, while (iv) ale-1 and adjacent endopeptidase resistance (epr) genes are located on a plasmid in Staphylococcus capitis. (v) Tp0706 from the Treponema pallidum chromosome, with homology to TDE1738 may also be an enzyme with peptidoglycan-degrading activity and the adjacent gene Tp0705 is annotated as a pencillin-binding protein in the same manner as zoocin A immunity factor (Zif).

Article Snippet: The E. coli was cultured on Luria Bertani (LB) agar ( Sambrook et al ., 1989 ) or in LB broth, containing appropriate antibiotics (ampicillin, 100μg ml −1 ; kanamycin 25μg ml −1 ). table ft1 table-wrap mode="anchored" t5 caption a7 Strain/plasmid Relevant characteristics Source Treponema denticola ATCC 35405 Type strain ( Chan et al ., 1993 ) Escherichia coli XL-1 Blue recA1 endA1 gyrA96 thi hsdR17 supE44 relA1 lac [ F ‘proAB lacl q Z Δ M15 Tn10 (Tet R )] Stratagene M15 (pREP-4 Kn R ) nal s str s rif s thi − lac − ara + gal + mtl − F − recA + uvr + lon + Qiagen Plasmids pQE30 bla ColE1 ori (Ap R ) Qiagen pQE30-TDE2318 bla ColE1 ori This study pQE30-TDE2753 bla ColE1 ori This study pQE30-TDE1738 bla ColE1 ori This study pQE30-TDE0110 bla ColE1 ori This study pQE30-TDE2189 bla ColE1 ori This study pQE30-TDE1136 bla ColE1 ori This study pQE30-TDE1297 bla ColE1 ori This study Open in a separate window Bacterial strains and plasmids used in this study

Techniques: Residue, Sequencing, Plasmid Preparation, Activity Assay, Binding Assay

Journal: Applied and Environmental Microbiology

Article Title: Anaerobic Obligatory Xylitol Production in Escherichia coli Strains Devoid of Native Fermentation Pathways ▿

doi: 10.1128/AEM.01890-10

Figure Lengend Snippet: Anaerobic xylitol production in engineered E. coli. Glucose conversion to acetate serves as the source of reducing power for xylose reduction to xylitol by heterologously expressed, NADPH-dependent xylose reductase (CbXR). Reducing equivalents are transferred from NADH to NADP+ in a reaction catalyzed by the native pyridine nucleotide transhydrogenase PntAB. Xylose reduction to xylitol serves as the primary means of NAD(P)H reoxidation and maintenance of intracellular redox balance.

Article Snippet: Subsequent strains were created via phage P1 transductions followed by flippase recombinase-mediated excision of the corresponding antibiotic resistance marker gene ( 8 ). table ft1 table-wrap mode="anchored" t5 caption a7 E. coli strain Relevant characteristics Source or reference W3110 Wild type ATCC 27325 JC11 W3110, Δ xylB ::FRT HK022::( CbXR- FRT) Chin and Cirino, submitted OA126 JC11, Δ ldhA ::FRT Δ adhE ::FRT Δ frdA ::FRT This study YK87 a W3110, Δ ldhA Δ( focA-pflB )::FRT Δ adhE FRT -kan- FRT lpd101 (E354K) 14 OA87 YK87 Δ xylAB ::FRT Δ frdA ::FRT HK022::( CbXR- FRT) This study OA176 b OA87, Δ( zwf - eda )::FRT This study OA163 OA87, Δ sthA ::FRT This study OA120 OA87, Δ pntA ::FRT This study OA207 OA120, Δ sthA ::FRT This study OA205 OA176, Δ pntA ::FRT This study Open in a separate window a Strain YK87 was a gift from K. T. Shanmugam (University of Florida). b The zwf , edd , and eda genes were deleted in strain OA176.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Anaerobic Obligatory Xylitol Production in Escherichia coli Strains Devoid of Native Fermentation Pathways ▿

doi: 10.1128/AEM.01890-10

Figure Lengend Snippet: E. coli central pathways and fermentation products. The Embden-Meyerhof-Parnas (EMP), pentose phosphate (PP), and Entner-Doudoroff (ED) pathways convert glucose-6-phosphate ultimately to pyruvate. The PP and ED pathways branch from glucose-6-phosphate and re-enter glycolysis at different locations. The molar yields of ATP (denoted as n) and NAD(P)H (denoted as m) per glucose depend on the pathway used in glucose oxidation. The EMP pathway generates the most ATP (nEMP = 2 for conversion of 1 mole of glucose to 2 moles of pyruvate), with a corresponding mEMP of 2 (16). Major fermentation products obtained from the central pathways are shown in boxes. Dashed arrows indicate multistep reactions. Abbreviations: glucose-6-P, glucose-6-phosphate; Glc-PTS, glucose phosphotransferase system; PEP, phosphoenolpyruvate; PYR, pyruvate; Zwf, glucose-6-phosphate dehydrogenase; Pgi, phosphoglucoisomerase; Edd, 6-phosphogluconate dehydratase; Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase; FrdA, flavoprotein of the fumarate reductase enzyme complex; LdhA, lactate dehydrogenase; PflB, subunit of the pyruvate-formate lyase; PDHc, pyruvate dehydrogenase enzyme complex; AdhE, alcohol dehydrogenase; CoA, coenzyme A.

Article Snippet: Subsequent strains were created via phage P1 transductions followed by flippase recombinase-mediated excision of the corresponding antibiotic resistance marker gene ( 8 ). table ft1 table-wrap mode="anchored" t5 caption a7 E. coli strain Relevant characteristics Source or reference W3110 Wild type ATCC 27325 JC11 W3110, Δ xylB ::FRT HK022::( CbXR- FRT) Chin and Cirino, submitted OA126 JC11, Δ ldhA ::FRT Δ adhE ::FRT Δ frdA ::FRT This study YK87 a W3110, Δ ldhA Δ( focA-pflB )::FRT Δ adhE FRT -kan- FRT lpd101 (E354K) 14 OA87 YK87 Δ xylAB ::FRT Δ frdA ::FRT HK022::( CbXR- FRT) This study OA176 b OA87, Δ( zwf - eda )::FRT This study OA163 OA87, Δ sthA ::FRT This study OA120 OA87, Δ pntA ::FRT This study OA207 OA120, Δ sthA ::FRT This study OA205 OA176, Δ pntA ::FRT This study Open in a separate window a Strain YK87 was a gift from K. T. Shanmugam (University of Florida). b The zwf , edd , and eda genes were deleted in strain OA176.

Techniques: