Journal: FEMS Microbiology Letters

Article Title: Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp.

doi: 10.1016/s0378-1097(03)00328-8

Figure Lengend Snippet: Fig. 1. PCR detection of Rieske center in total genomic DNA extracts, using the mix of primers P1.1.f, P.1.2.f, P2.1.r and P2.2.r [24]. The DNA was separated in 3.5% agarose gel. Lanes 1, 15, DNA molecular mass markers; 2, M. vanbaalenii PYR-1; 3, Mycobacterium sp. PAH2.135; 4, M. £avescens PYR-GCK; 5, M. gilvum BB1; 6, M. fred- eriksbergense FAn9T; 7, Rhodococcus sp. R-22; 8, M. vaccae JOB-5; 9, M. album 7E1B1W; 10, R. rhodochrous 7E1C; 11, M. petroleophilum; 12, M. chlorophenolicum PCP-1; 13, M. austroafricanum; 14, M. aurum.

Article Snippet: FEMSLE 10997 16-6-03 Table 1 Bacterial strains and results of the assaysa Strain Isolation Characteristics Plate spraying testb PCRc Southern hybridizationd Phe Pyr Rieskee nidAf nidBg nidA nidB M. vanbaalenii PYR-1 (DSM 7251) Oil-contaminated sediment, Texas [17] PAH degradation [17,21,22,36,37] + + + + + + + Mycobacterium sp. PAH 2.135 (RJGII-135) Coal gasi¢cation site soil, Illinois [20] PAH degradation [20,38] + + + 3 n + + M. £avescens PYR-GCK (ATCC 700033) Polluted sediment, Indiana [18] PAH degradation [18] + + + + + + + M. gilvum BB1 (DSM 9487) Former coal gasi¢cation site, Germany [19] PAH degradation [19] + + + + + + + M. frederiksbergense FAn9T (DSM 44346) Coal tar-contaminated soil, Denmark [32] PAH degradation [32] + + + + + + + Rhodococcus sp. R-22 (ATCC 29671) Soil Gaseous, long chain and cyclopara⁄nic hydrocarbon degradation [39,40] 3 3 3 n n 3 n M. vaccae JOB-5 (ATCC 29678) Soil Gaseous, long chain, cyclopara⁄nic and monoaromatic hydrocarbon degradation [40^43] 3 3 3 n n 3 n Mycobacterium sp. 7E1B1W (ATCC 29676) Soil Gaseous and long chain hydrocarbon degradation [40,44] 3 3 3 n n n n R. rhodochrous 7E1C (ATCC 19067) Soil Long chain and cyclopara⁄nic hydrocarbon degradation [40] 3 3 3 n n n n M. petroleophilum (ATCC 21497) Drilling well n-Para⁄n utilization, production of single cell protein [45] 3 3 3 n n n n M. chlorophenolicum PCP-1 (ATCC 49826) Paper industry-polluted sediment, Finland Polychlorinated phenol degradation [46] 3 3 3 n n 3 n M. austroafricanum (ATCC 33464) Soil, south Africa Type strain, related to M. vanbaalenii [26,34] 3 3 3 n n 3 n M. aurum (ATCC 23366) Soil Type strain 3 3 3 n n 3 n a+, positive result ; 3, negative result ; n, not performed. bPlate spraying test : positive results in the case of Phe (phenanthrene) and Pyr (pyrene) mean formation of signi¢cant clearing in the PAH layer. cAll primers are listed in Table 2. dDigoxigenin-labeled DNA probes were used. eIdentical results obtained with primer mix P1.1.f, P.1.2.f, P2.1.f, P2.2.f [24] and primer pair DP1, DP2 [25] f Identical results for nidA and nidA1 primer pairs. gIdentical results for nidB and nidB1 primer pairs.

Techniques: Agarose Gel Electrophoresis

Journal: Frontiers in Microbiology

Article Title: Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557

doi: 10.3389/fmicb.2021.670928

Figure Lengend Snippet: Genes encoding oestrogen degradation enzymes found within the genomes of known oestrogen degrading bacteria.

Article Snippet: According to ANI analyses based on BLAST ( ) Rhodococcus sp. Br-6, Rhodococcus hoagii ATCC 33707, R. hoagii 103S, and R. hoagii NBRC 101255 were the genomes most closely related to R. equi ATCC13557, these have been highlighted green ( ).

Techniques: Bacteria

Journal:

Article Title: Cloning and Expression of the Benzoate Dioxygenase Genes from Rhodococcus sp. Strain 19070

doi: 10.1128/AEM.67.6.2507-2514.2001

Figure Lengend Snippet: Phylogenetic trees based on comparisons with homologs of the Rhodococcus sp. strain 19070 Bop proteins. (A) BopX was aligned with alpha components of oxygenase subunits. (B) BopY was aligned with the corresponding beta components of oxygenases from Panel A (C) BopZ was aligned with available reductase components associated with oxygenases from panel A and other reductases or putative reductases. (D) The putative BopL dehydrogenase was aligned with dehydrogenases and putative dehydrogenases associated with the proteins displayed in trees A to C, as well as ORF4 (Ro). (E) BopK, a putative transport protein, was aligned with proteins that may be involved in transporting organic compounds. Gene clusters are associated with metabolism and/or transport of the indicated compounds: BopXYZLK, Rhodococcus sp. ATCC 19070, benzoate-toluate (AF279141), BenABCDK(Pp), P. putida strain PRS200, benzoate (AF218267), BenABCDK(Ac), Acinetobacter sp. strain ADP1, benzoate (AF009224), XylXYZ(pDK1), P. putida sp. plasmid pDK1, toluate (AF134348), XylXYZL(TOL), P. putida sp. TOL plasmid, benzoate (M64747), CbdABC, Burkholderia cepacia, halobenzoate (X79076), AntABC, Acinetobacter sp. strain ADP1, anthranilate (AF071556), TftAB, B. cepacia, 2,4,5-trichlorophenoxyacetic acid (U11420), AtdAB, Acinetobacter sp. plasmid pYA1, aniline (D86080), TdnA1B1, P. putida strain UCC22 (pTDN1) F1, aniline (D85415), CmtAbAcB, P. putida, p-cymene (U24215), NidAB, Rhodococcus sp. strain I24, indene (AF121905), NarAaAbB, Rhodococcus sp. strain NCIMB12038, naphthalene (AF082663), BphA1A2B, Rhodococcus sp. strain RHA1, biphenyl (D32142), NahAcAdAa, P. putida strain G7, napthalene (M83949), BpdC1C2B, Rhodococcus sp. strain M5, biphenyl-chlorobiphenyl (U27591), TodC1C2D, P. putida sp. strain F1, toluene (J04996), ORF6, A. calcoaceticus strain NCIB8250, phenol (Z36909), XylA, P. putida sp. TOL plasmid, xylene (M37480), PheA6, P. putida sp. strain BH, phenol (D28864), PhhP, P. putida sp. strain P35X (NCIB9869), phenol (X79063), TbmF, Pseudomonas sp. strain JS150, toluene-benzene (L40033), PahAB, P. aeruginosa strain PaK1, naphthalene (D84146), ORF4(Ro), Rhodococcus opacus sp. strain 1CP putative short-chain dehydrogenase (AF030176), PcaK(Ac), Acinetobacter sp. strain ADP1, protocatechuate transporter (L05770), ORF4(Sg), Streptomyces griseus, putative tyrosine transporter (AB022095), PcaK(Pp), P. putida sp. strain PRS2000, protocatechuate transporter (U10895), HppK, Rhodococcus globerulus sp. strain PWD1, putative 3-hydrox-yphenyl propionate transporter (U89712), FcbT, Arthrobacter sp. strain TM1, 4-chlorobenzoate transporter (AF042490), MucK, Acinetobacter sp. strain ADP1, cis,cis-muconate transporter (U87258), VanK, Acinetobacter sp. strain ADP1, vanillate transporter (AF009672). Accession numbers are indicated parenthetically. Circles represent branch points that occur with a frequency of 85 to 100%, respectively, as calculated by bootstrap analysis using 100 replicates.

Article Snippet: Rhodococcus sp. strain ATCC 19070 was grown at 37°C in Luria-Bertani broth or M9 minimal medium ( 39 ).

Techniques: Plasmid Preparation