Journal:

Article Title: Transcriptional Regulation of the pdt Gene Cluster of Pseudomonas stutzeri KC Involves an AraC/XylS Family Transcriptional Activator (PdtC) and the Cognate Siderophore Pyridine-2,6-Bis(Thiocarboxylic Acid) ▿

doi: 10.1128/AEM.01518-06

Figure Lengend Snippet: Bacterial strains and plasmids

Article Snippet: E. coli cultures were incubated in a rotary shaker. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Description Source or reference E. coli BW20767 Pir + mob + S. Minnoch, University of Idaho JM109 rec A endA Promega, Madison, WI S17.1 Sm r mob + S. Minnoch P. stutzeri KC Wild-type PDTC producer C. Criddle, Stanford University SEMΔ pdtC KC Δ pdt C ::Km This study P. putida KT2440 Wild type Estacion Exp.

Techniques: Plasmid Preparation, Mutagenesis, Cloning, Construct

Journal: The Journal of Biological Chemistry

Article Title: DndEi Exhibits Helicase Activity Essential for DNA Phosphorothioate Modification and ATPase Activity Strongly Stimulated by DNA Substrate with a GAAC/GTTC Motif *

doi: 10.1074/jbc.M115.694018

Figure Lengend Snippet: Genomic organization of the PT-modifying genes in 7 members of bacteria. Strains and GenBankTM accession numbers: S. lividans 66 (CM001889.1); E. coli B7A (CP005998.1); Pseudomonas fluorescens Pf0–1 (CP000094.2); Flavobacterium psychrophilum KU060626-59 (KF241852); R. anatipestifer ATCC 11845 (CP003388.1); Bacteroides faecis MAJ27 (NZ_AGDG01000022.1); Psychroflexus torquis ATCC 700755 (CP003879.1).

Article Snippet: Escherichia coli strains were routinely grown in Luria broth (LB) at 37 °C and R. anatipestifer strains were cultured in tryptic soybean broth (Difco Laboratories, Detroit, MI) at 37 °C under 5% CO 2 . table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Strain or plasmid Characteristics Source or reference E. coli DH5α F − Δlacu169 ( φ80lacZΔM15), recA1, endA1, hsdR17 Biomedal BL21(DE3) hsdS gal, chromosomal insertion of T7 pol Novagen S17-1 lpir hsdR pro thi; chromosomal integrated RP4–2 Tc::Mu Km::Tn7 Biomedal R. anatipestifer ATCC 11845 Wild-type, PT + 15 HXb2 Wild-type, PT − 15 Plasmids pBluescript SK(+) Bla, lacZ, orif1, ColE, Ap r Stratagene pET-28a Expression vector, pBR322 replicon, P T7 , His 6 tag, Km r Novagen pT1 Based on pET-28a, with DNA region coding DndEi inserted at NdeI-SalI sites This study pT2 Based on pET-28a, with DNA region coding DndEih inserted at NdeI-SalI sites This study pT3 Based on pT1, with A (the 599 th nucletide in dndEi gene) mutated to C This study pT4 Based on pT1, with A (the 1232nd nucletide in dndEi gene) mutated to C This study pReS0 ColE1 ori, Ap r , E. coli-R. anatipestifer shuttle plasmid 15 pJ1 Based on pReS0, with dndCD genes and their promoter region inserted at XbaI-XhoI sites This study pJ2 Based on pReS0, with dndCDEie genes and their promoter region inserted at XbaI-XhoI sites This study pJ3 Based on pReS0, with dndCDEi genes and their promoter region inserted at XbaI-XhoI sites This study pJ4 Based on pJ3, with A (the 599th nucletide in dndEi gene) mutated to C This study pJ5 Based on pJ3, with A (the 1232nd nucletide in dndEi gene) mutated to C This study Open in a separate window Strains and plasmids used in this study Gene Cloning and Plasmid Construction E. coli strain DH5α was used for plasmid construction.

Techniques: Bacteria

Journal: The Journal of Biological Chemistry

Article Title: DndEi Exhibits Helicase Activity Essential for DNA Phosphorothioate Modification and ATPase Activity Strongly Stimulated by DNA Substrate with a GAAC/GTTC Motif *

doi: 10.1074/jbc.M115.694018

Figure Lengend Snippet: Strains and plasmids used in this study

Article Snippet: Escherichia coli strains were routinely grown in Luria broth (LB) at 37 °C and R. anatipestifer strains were cultured in tryptic soybean broth (Difco Laboratories, Detroit, MI) at 37 °C under 5% CO 2 . table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Strain or plasmid Characteristics Source or reference E. coli DH5α F − Δlacu169 ( φ80lacZΔM15), recA1, endA1, hsdR17 Biomedal BL21(DE3) hsdS gal, chromosomal insertion of T7 pol Novagen S17-1 lpir hsdR pro thi; chromosomal integrated RP4–2 Tc::Mu Km::Tn7 Biomedal R. anatipestifer ATCC 11845 Wild-type, PT + 15 HXb2 Wild-type, PT − 15 Plasmids pBluescript SK(+) Bla, lacZ, orif1, ColE, Ap r Stratagene pET-28a Expression vector, pBR322 replicon, P T7 , His 6 tag, Km r Novagen pT1 Based on pET-28a, with DNA region coding DndEi inserted at NdeI-SalI sites This study pT2 Based on pET-28a, with DNA region coding DndEih inserted at NdeI-SalI sites This study pT3 Based on pT1, with A (the 599 th nucletide in dndEi gene) mutated to C This study pT4 Based on pT1, with A (the 1232nd nucletide in dndEi gene) mutated to C This study pReS0 ColE1 ori, Ap r , E. coli-R. anatipestifer shuttle plasmid 15 pJ1 Based on pReS0, with dndCD genes and their promoter region inserted at XbaI-XhoI sites This study pJ2 Based on pReS0, with dndCDEie genes and their promoter region inserted at XbaI-XhoI sites This study pJ3 Based on pReS0, with dndCDEi genes and their promoter region inserted at XbaI-XhoI sites This study pJ4 Based on pJ3, with A (the 599th nucletide in dndEi gene) mutated to C This study pJ5 Based on pJ3, with A (the 1232nd nucletide in dndEi gene) mutated to C This study Open in a separate window Strains and plasmids used in this study Gene Cloning and Plasmid Construction E. coli strain DH5α was used for plasmid construction.

Techniques: Plasmid Preparation, Expressing

Journal:

Article Title: Screening of Thermotolerant Gluconobacter Strains for Production of 5-Keto- d -Gluconic Acid and Disruption of Flavin Adenine Dinucleotide-Containing d -Gluconate Dehydrogenase ▿

doi: 10.1128/AEM.00640-09

Figure Lengend Snippet: Bacterial strains, plasmids, and primers used in this study

Article Snippet: The oligonucleotides used in this study were purchased from FASMAC Co. Ltd. (Kanagawa, Japan) and are listed in Table . table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain, plasmid, or primer Relevant trait(s) or sequence Source or reference E. coli DH5α r − m + recA1 lacZYA φ80d lac Δ( lacZ )M15 Bethesda Research Laboratories, Inc. Gluconobacter strains THE42 Parental strain 12 THE42 gndG ::Km Km r , strain THE42 with gndG disrupted This study THF55 Parental strain 12 THF55 gndG ::Km Km r , strain THF55 with gndG disrupted This study THG42 Parental strain 12 THG42 gndG ::Km Km r , strain THG42 with gndG disrupted This study Plasmids pGEM-T Easy Cloning vector Promega pTKm Contains nonpolar Km r cassette 23 pGEM-CA-F 1.9-kb PCR product inserted into pGEM-T Easy This study pGEM-CA-F::Km Km r , used for gndG disruption, Km r cassette inserted at SmaI site This study Primers gndL-F 5′-CCGTCAACTCGCAGCCTTTCTGC-3′ This study gndL-R 5′-GCGGGCAGGATATTCACGTTGGG-3′ This study F-igL-1 5′-TAGGTGACGCCGTAATCCTG-3′ This study R-igL-2 5′-TCGGATACCATCCCTATTCCC-3′ This study F-gnDH-3 5′-TCATGGACTGGGTCAATCAG-3′ This study R-gnDH-2 5′-TGCAAGCAAAGGCCAGGATT-3′ This study Open in a separate window Bacterial strains, plasmids, and primers used in this study

Techniques: Plasmid Preparation, Sequencing, Clone Assay