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rhodococcus sp strain rha1 (Takeda)

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Takeda rhodococcus sp strain rha1
Rhodococcus Sp Strain Rha1, supplied by Takeda, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: Microbial Chemical Sensing of Microplastic-Derived Compounds in Insect Gut Ecosystems.
Article Snippet: Microplastic (MP) pollution threatens terrestrial and aquatic ecosystems worldwide.. Insects, essential for pollination, decomposition, and nutrient cycling, ingest MPs through feeding and contact.. Despite growing evidence of MP-caused gut microbe imbalance, how insect gut microbiomes detect and react to MP leachates, mainly organic additives like phthalates and bisphenol A, is still unclear, limiting our understanding of adaptive resilience against toxicity.

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Proposed pathway for aerobic bacterial degradation of biphenyl in Rhodococcus sp. strain RHA1. The gene(s) responsible for each enzyme step is indicated above an arrow and is described in the text.

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: Proposed pathway for aerobic bacterial degradation of biphenyl in Rhodococcus sp. strain RHA1. The gene(s) responsible for each enzyme step is indicated above an arrow and is described in the text.

Article Snippet: The plasmids used in this study are listed in Table . table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Relevant characteristic(s) a Reference or origin Strains Rhodococcus sp. strain RHA1 PCB degrader, BPH + 30 Rhodococcus sp. strain SDR1 bphS mutant of strain RHA1, BPH − This study R. erythropolis IAM1399 (= ATCC 15963) Wild type, BPH − IAM culture collection b Plasmids pBluescript II KS+ Cloning vector, Ap r Stratagene pG1013F pBluescript II KS+ with 8.8-kb HindIII fragment of RHA1 carrying bphST This study pBSL pBluescript II KS+ with new SpeI site in place of KpnI site This study pBAB14 pBSL with 1.4-kb ApaI-BglII fragment of RHA1 carrying bphT This study pBAB62 4.8-kb ApaI fragment carrying bphS inserted into pBAB14 This study pBAB62ΔSacI 1.0-kb SacI fragment carrying bphT deleted from pBAB62, leaving bphS This study pBAS52 SacI site of pBAB62ΔSacI converted to a SpeI site This study pET21(+) Expression vector, Ap r Novagen pETT14 pET21(+) with SpeI fragment of pBAB14 carrying bphT This study pETST62 pET21(+) with SpeI fragment of pBAB62 carrying bphST This study pKLA1 Promoter probe vector containing luciferase structural gene, luxAB from V. harveyi , Km r ( neo ) 38 pKLAF1 pKLA1 with 1.4-kb XhoI-BamHI fragment of RHA1 carrying promoter region of bphA1 This study pKA851 pKLAF1 with 8.8-kb HindIII fragment of RHA1 carrying bphST This study pKAD1-12 pKLAF1 with deletion derivatives of 8.8-kb HindIII fragment of RHA1 This study pKLAS1 pKLAF1 with 5.4-kb SacI fragment of RHA1 carrying bphS This study pKLAST1 pKLAF1 with 6.2-kb ApaI-BglII fragment of RHA1 carrying bphST This study pKLASF pKLA1 with 0.9-kb PstI-ClaI fragment of RHA1 carrying promoter region of bphS ; direction of bphS is identical to that of luxAB reporter gene This study pKLASR pKLA1 with 0.9-kb PstI-ClaI fragment of RHA1 carrying promoter region of bphS ; direction of bphS is opposite that of luxAB reporter gene This study pUC-KmD Gene disruption plasmid, Km r ( aphII ) 29 pUKSD bphS disruption plasmid pUC-KmD with 1.3-kb ClaI fragment carrying bphS internal fragment of RHA1 This study pFAJ2574 Rhodococcus-E. coli shuttle vector, Cm r 5 pFJS1 pFAJ2574 with 5.2-kb SpeI fragment of pBAS52 carring bphS This study Open in a separate window a BPH + , growth on biphenyl; BPH − , no growth on biphenyl. b IAM, Institute of Applied Microbiology.

Techniques:

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: Strains and plasmids used in this study

Techniques: Plasmid Preparation, Mutagenesis, Cloning, Expressing, Luciferase, Disruption

Transcriptional activation of bphA1 promoter. (A) Physical maps of pKLAF1 and pKA851. pKLAF1 was constructed by inserting the 1.4-kb XhoI-BamHI bphA1 promoter fragment into a promoter probe vector, pKLA1. The 8.8-kb HindIII fragment containing the region downstream of bphB was cloned in the KpnI site of pKLAF1 to construct pKA851. The restriction sites in parentheses are the sites that were used to generate fragments and were lost by blunt-end formation prior to ligation. (B) Luciferase activity of Rhodococcus sp. strain RHA1 harboring pKLAF1. Cells were grown in 0.2× LB medium in the absence or presence of the substrates. The chemical structures of the substrates are shown. The data are means ± standard deviations from at least three determinations. The luciferase activities of RHA1 cells harboring a promoter probe vector, pKLA1, were all less than 0.1 × 105 light units (LU) per A600 unit (see Materials and Methods). (C) Luciferase activity of R. erythropolis IAM1399 harboring pKLAF1 or pKA851. Cells were grown in 0.2× LB medium in the absence or presence of substrates. The data are means ± standard deviations from at least three determinations.

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: Transcriptional activation of bphA1 promoter. (A) Physical maps of pKLAF1 and pKA851. pKLAF1 was constructed by inserting the 1.4-kb XhoI-BamHI bphA1 promoter fragment into a promoter probe vector, pKLA1. The 8.8-kb HindIII fragment containing the region downstream of bphB was cloned in the KpnI site of pKLAF1 to construct pKA851. The restriction sites in parentheses are the sites that were used to generate fragments and were lost by blunt-end formation prior to ligation. (B) Luciferase activity of Rhodococcus sp. strain RHA1 harboring pKLAF1. Cells were grown in 0.2× LB medium in the absence or presence of the substrates. The chemical structures of the substrates are shown. The data are means ± standard deviations from at least three determinations. The luciferase activities of RHA1 cells harboring a promoter probe vector, pKLA1, were all less than 0.1 × 105 light units (LU) per A600 unit (see Materials and Methods). (C) Luciferase activity of R. erythropolis IAM1399 harboring pKLAF1 or pKA851. Cells were grown in 0.2× LB medium in the absence or presence of substrates. The data are means ± standard deviations from at least three determinations.

Techniques: Activation Assay, Construct, Plasmid Preparation, Clone Assay, Ligation, Luciferase, Activity Assay

Characterization of the bphA1 promoter. (A) DNA probes used for RNA slot blot hybridization. A 1.1-kb KpnI fragment (probe 1), a 0.9-kb EcoRI-HincII fragment (probe 2), and a 0.7-kb HincII-BamHI fragment (probe 3) of the bphA1 upstream region were used to localize the promoter region of bphA1. The position of the 1.4-kb XhoI-BamHI fragment containing the bphA1 promoter is indicated by a line below the physical map. (B) RNA slot blot hybridization analysis of bphA1 transcripts in Rhodococcus sp. strain RHA1. Two micrograms of total RNA from RHA1 cells grown in LB medium or on a substrate as a sole source of carbon in W minimal medium was blotted onto a nylon membrane and hybridized with digoxigenin-labeled probes 1, 2, and 3.

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: Characterization of the bphA1 promoter. (A) DNA probes used for RNA slot blot hybridization. A 1.1-kb KpnI fragment (probe 1), a 0.9-kb EcoRI-HincII fragment (probe 2), and a 0.7-kb HincII-BamHI fragment (probe 3) of the bphA1 upstream region were used to localize the promoter region of bphA1. The position of the 1.4-kb XhoI-BamHI fragment containing the bphA1 promoter is indicated by a line below the physical map. (B) RNA slot blot hybridization analysis of bphA1 transcripts in Rhodococcus sp. strain RHA1. Two micrograms of total RNA from RHA1 cells grown in LB medium or on a substrate as a sole source of carbon in W minimal medium was blotted onto a nylon membrane and hybridized with digoxigenin-labeled probes 1, 2, and 3.

Techniques: Dot Blot, Hybridization, Membrane, Labeling

In vitro expression of the bphS and bphT genes of Rhodococcus sp. strain RHA1. The bphST and bphT genes in pBAB62 and pBAB14, respectively, were expressed in the E. coli S30 extract system containing [35S]methionine. Labeled polypeptides were separated by SDS-PAGE. The expected bphS and bphT products are indicated by arrowheads. Lane 1, 14C-labeled molecular weight marker (Pharmacia); lanes 2, 3, and 4, gene products of pBSL (vector control), pBAB62, and pBAB14, respectively.

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: In vitro expression of the bphS and bphT genes of Rhodococcus sp. strain RHA1. The bphST and bphT genes in pBAB62 and pBAB14, respectively, were expressed in the E. coli S30 extract system containing [35S]methionine. Labeled polypeptides were separated by SDS-PAGE. The expected bphS and bphT products are indicated by arrowheads. Lane 1, 14C-labeled molecular weight marker (Pharmacia); lanes 2, 3, and 4, gene products of pBSL (vector control), pBAB62, and pBAB14, respectively.

Techniques: In Vitro, Expressing, Labeling, SDS Page, Molecular Weight, Marker, Plasmid Preparation, Control

Transcription of the bphS gene in RHA1. (A) Physical map of the region from bphA1 to bphT. The open box below the map represents the fragment used to construct reporter plasmids pKLASF and pKLASR. The lines below the map indicate intergenic or internal segments of bph genes that were expected to be amplified by RT-PCR. The numbers below the lines indicate the PCR primer sets shown in Table Table2.2. Restriction enzyme site abbreviations: P, PstI; C, ClaI; H, HindIII. (B) bphS and bphT gene transcripts in RHA1. Total RNAs from RHA1 cells grown on LB medium, on biphenyl (BPH), or on ethylbenzene (ETB) were reverse transcribed under the intensive conditions (left and right panels) or the usual conditions (center panel). The reverse transcripts were subjected to PCR amplification by using the primer sets indicated by the numbers above the panels, which correspond to the numbers in panel A and Table Table2.2. RNA samples were concurrently analyzed in PCR mixtures with (+) and without (−) reverse transcriptase (RT) to verify the absence of total DNA. The position and size of each PCR product are indicated by an arrowhead on the right. (C) Intergenic RT-PCR products of the bphA1A2A3A4C1BST genes in RHA1. Total RNAs from RHA1 were reverse transcribed under the usual conditions, amplified, and analyzed as described above. An arrowhead indicates the position and size of each PCR product.

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: Transcription of the bphS gene in RHA1. (A) Physical map of the region from bphA1 to bphT. The open box below the map represents the fragment used to construct reporter plasmids pKLASF and pKLASR. The lines below the map indicate intergenic or internal segments of bph genes that were expected to be amplified by RT-PCR. The numbers below the lines indicate the PCR primer sets shown in Table Table2.2. Restriction enzyme site abbreviations: P, PstI; C, ClaI; H, HindIII. (B) bphS and bphT gene transcripts in RHA1. Total RNAs from RHA1 cells grown on LB medium, on biphenyl (BPH), or on ethylbenzene (ETB) were reverse transcribed under the intensive conditions (left and right panels) or the usual conditions (center panel). The reverse transcripts were subjected to PCR amplification by using the primer sets indicated by the numbers above the panels, which correspond to the numbers in panel A and Table Table2.2. RNA samples were concurrently analyzed in PCR mixtures with (+) and without (−) reverse transcriptase (RT) to verify the absence of total DNA. The position and size of each PCR product are indicated by an arrowhead on the right. (C) Intergenic RT-PCR products of the bphA1A2A3A4C1BST genes in RHA1. Total RNAs from RHA1 were reverse transcribed under the usual conditions, amplified, and analyzed as described above. An arrowhead indicates the position and size of each PCR product.

Techniques: Construct, Amplification, Reverse Transcription Polymerase Chain Reaction, Reverse Transcription

bphS gene disruption in RHA1. (A) Strategy for bphS gene disruption. Disruption was accomplished by a single crossover between the native bphS gene (top) and the 1.3-kb internal fragment of bphS in pUKSD (middle). The possible region of recombination in the disruption derivative (bottom) is shaded diagonally. The positions of the bphS and aphII probes used in Southern hybridization are indicated by thick lines above bphS (top) and aphII (bottom). The sizes of ClaI and HindIII fragments containing the bphS sequence are indicated below the ORF maps (top and bottom). (B) Southern hybridization analysis of bphS disruption mutant strain SDR1 performed with the aphII (upper panel) and bphS (lower panel) probes. Lane 1, 1-kb ladder marker; lane 2, SDR1 total DNA digested with ClaI; lane 3, RHA1 total DNA digested with ClaI; lane 4, SDR1 total DNA digested with HindIII; lane 5, RHA1 total DNA digested with HindIII. The position and size of each signal derived from the bona fide bphS sequence are indicated by an open arrowhead and an arrow on the right, respectively. (C) Growth on biphenyl of SDR1 and bphS gene-containing SDR1. RHA1, SDR1, SDR1 carrying the vector pFAJ2574, and SDR1 carrying the bphS plasmid pFJS1 were grown in W minimal medium containing 0.2% biphenyl. Growth was measured by determining the optical density at 600 nm (OD600). The data are averages based on triplicate experiments.

Journal:

Article Title: Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1

doi: 10.1128/JB.186.7.2134-2146.2004

Figure Lengend Snippet: bphS gene disruption in RHA1. (A) Strategy for bphS gene disruption. Disruption was accomplished by a single crossover between the native bphS gene (top) and the 1.3-kb internal fragment of bphS in pUKSD (middle). The possible region of recombination in the disruption derivative (bottom) is shaded diagonally. The positions of the bphS and aphII probes used in Southern hybridization are indicated by thick lines above bphS (top) and aphII (bottom). The sizes of ClaI and HindIII fragments containing the bphS sequence are indicated below the ORF maps (top and bottom). (B) Southern hybridization analysis of bphS disruption mutant strain SDR1 performed with the aphII (upper panel) and bphS (lower panel) probes. Lane 1, 1-kb ladder marker; lane 2, SDR1 total DNA digested with ClaI; lane 3, RHA1 total DNA digested with ClaI; lane 4, SDR1 total DNA digested with HindIII; lane 5, RHA1 total DNA digested with HindIII. The position and size of each signal derived from the bona fide bphS sequence are indicated by an open arrowhead and an arrow on the right, respectively. (C) Growth on biphenyl of SDR1 and bphS gene-containing SDR1. RHA1, SDR1, SDR1 carrying the vector pFAJ2574, and SDR1 carrying the bphS plasmid pFJS1 were grown in W minimal medium containing 0.2% biphenyl. Growth was measured by determining the optical density at 600 nm (OD600). The data are averages based on triplicate experiments.

Techniques: Disruption, Hybridization, Sequencing, Mutagenesis, Marker, Derivative Assay, Plasmid Preparation

Proteins homologous to ORFs found in pVBC (deduced amino acid sequence)

Journal:

Article Title: Novel 2,4-Dichlorophenoxyacetic Acid Degradation Genes from Oligotrophic Bradyrhizobium sp. Strain HW13 Isolated from a Pristine Environment

doi: 10.1128/JB.184.2.509-518.2002

Figure Lengend Snippet: Proteins homologous to ORFs found in pVBC (deduced amino acid sequence)

Article Snippet: ORF (protein encoded) Homolog (% identity) Origin (plasmid) Function or enzyme Accession no. ORF1 (CadR) NitR (21) Rhodococcus rhodochrous J1 Regulator for nitrilase D67026 FeaR (18) Escherichia coli K-12 Regulator for 2-phenylethylamine catabolism AE000235 ORF2 (CadA) TftA (46) Burkholderia cepacia AC1100 2,4,5-T oxygenase large subunit U11420 BenA (34) Acinetobacter sp. strain ADP1 Benzoate 1,2-dioxygenase terminal oxygenase large subunit AF009224 BenA (34) Rhodococcus sp. strain RHA1 Benzoate 1,2-dioxygenase terminal oxygenase large subunit AB055706 ORF3 (CadB) TftB (44) Burkholderia cepacia AC1100 2,4,5-T oxygenase small subunit U11420 BenB (32) Acinetobacter sp. strain ADP1 Benzoate 1,2-dioxygenase terminal oxygenase small subunit AF009224 BenB (31) Rhodococcus sp. strain RHA1 Benzoate 1,2-dioxygenase terminal oxygenase small subunit AB055706 ORF4 (CadK) TfdK (60) Ralstonia eutropha JMP134(pJP4) 2,4-D transporter U16782 Pcak (28) Acinetobacter sp. strain ADP1 4-Hydroxybenzoate transporter L05770 BenK (27) Acinetobacter sp. strain ADP1 Benzoate transporter AF009224 ORF5 (CadC) ThcC (37) Rhodococcus erythropolis NI86/21 Putative ferredoxin U17130 FdVI (37) Rhodobacter capsulatus B10 Putative ferredoxin Y11304 CamB (35) Pseudomonas putida ATCC 17453 Putidaredoxin for cytochrome P-450cam monooxygenase J05406 Open in a separate window Proteins homologous to ORFs found in pVBC (deduced amino acid sequence). .

Techniques: Sequencing, Plasmid Preparation

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rhodococcus sp strain rha1 (Takeda)

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