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  • 1
    Language: English
    In: Journal of Bacteriology, pp. 6618-6619
    Description: Article discussing the draft genome sequence of the cyanide-utilizing bacterium 'Pseudomonas fluorescens' strain NCIMB 11764.
    Keywords: Pseudomanas Fluorescens ; Genetics ; Cyanide
    ISSN: 00219193
    E-ISSN: 10985530
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  • 2
    Language: English
    In: Applied Microbiology and Biotechnology, 2012, Vol.94(1), pp.131-140
    Description: Cyanide dihydratase is an enzyme in the nitrilase family capable of transforming cyanide to formate and ammonia. This reaction has been exploited for the bioremediation of cyanide in wastewater streams, but extending the pH operating range of the enzyme would improve its utility. In this work, we describe mutants of Bacillus pumilus C1 cyanide dihydratase (CynD pum ) with improved activity at higher pH. Error-prone PCR was used to construct a library of CynD pum mutants, and a high-throughput screening system was developed to screen the library for improved activity at pH 10. Two mutant alleles were identified that allowed cells to degrade cyanide in solutions at pH 10, whereas the wild-type was inactive above pH 9. The mutant alleles each encoded three different amino acid substitutions, but for one of those, a single change, E327G, accounted for the phenotype. The purified proteins containing multiple mutations were five times more active than the wild-type enzyme at pH 9, but all purified enzymes lost activity at pH 10. The mutation Q86R resulted in the formation of significantly longer fibers at low pH, and both E327G and Q86R contributed to the persistence of active oligomeric assemblies at pH 9. In addition, the mutant enzymes proved to be more thermostable than the wild type, suggesting improved physical stability rather than any change in chemistry accounts for their increased pH tolerance.
    Keywords: Nitrilase ; Cyanide ; Bioremediation ; Cyanide dihydratase ; pH tolerance ; Protein stability
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 3
    Language: English
    In: Applied microbiology and biotechnology, April 2017, Vol.101(8), pp.3029-3042
    Description: The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.
    Keywords: Bioremediation ; Cyanide ; Cyanide Dihydratase ; Nitrilase ; Protein Engineering ; Protein Stability ; Biodegradation, Environmental ; Aminohydrolases -- Genetics ; Cyanides -- Metabolism
    ISSN: 01757598
    E-ISSN: 1432-0614
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  • 4
    In: Biotechnology and Bioengineering, March 2015, Vol.112(3), pp.588-600
    Description: A new antibiotic persistence pathway involving the regulatory signals cAMP and indole is identified in . The authors demonstrate that oxygen‐sensing phosphodiesterase DosP increases persistence a thousand fold. The mechanism for this increase is that DosP cleaves cAMP, thus controlling the cAMP‐CRP transcriptional regulatory network and down‐regulating , which encodes tryptophanase. Low amounts of tryptophanase lead to reduced levels of the intercellular signal indole, which is shown here to inversely influence persistence (i.e., low indole yields high persistence).
    Keywords: Dosp ; Persistence ; C‐Di‐Gmp ; Indole ; Tnaa
    ISSN: 0006-3592
    E-ISSN: 1097-0290
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  • 5
    Language: English
    In: Nucleic acids research, June 2014, Vol.42(10), pp.6448-62
    Description: For toxin/antitoxin (TA) systems, no toxin has been identified that functions by cleaving DNA. Here, we demonstrate that RalR and RalA of the cryptic prophage rac form a type I TA pair in which the antitoxin RNA is a trans-encoded small RNA with 16 nucleotides of complementarity to the toxin mRNA. We suggest the newly discovered antitoxin gene be named ralA for RalR antitoxin. Toxin RalR functions as a non-specific endonuclease that cleaves methylated and unmethylated DNA. The RNA chaperone Hfq is required for RalA antitoxin activity and appears to stabilize RalA. Also, RalR/RalA is beneficial to the Escherichia coli host for responding to the antibiotic fosfomycin. Hence, our results indicate that cryptic prophage genes can be functionally divergent from their active phage counterparts after integration into the host genome.
    Keywords: Bacterial Toxins -- Metabolism ; Endodeoxyribonucleases -- Metabolism ; Escherichia Coli -- Enzymology ; Escherichia Coli Proteins -- Metabolism ; RNA, Small Untranslated -- Metabolism ; Transcription Factors -- Metabolism
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    Language: English
    In: Nucleic acids research, March 2012, Vol.40(5), pp.2247-57
    Description: Translation of the TnaC nascent peptide inhibits ribosomal activity in the presence of l-tryptophan, inducing expression of the tnaCAB operon in Escherichia coli. Using chemical methylation, this work reveals how interactions between TnaC and the ribosome are affected by mutations in both molecules. The presence of the TnaC-tRNA(Pro) peptidyl-tRNA within the ribosome protects the 23S rRNA nucleotide U2609 against chemical methylation. Such protection was not observed in mutant ribosomes containing changes in 23S rRNA nucleotides of the A748-A752 region. Nucleotides A752 and U2609 establish a base-pair interaction. Most replacements of either A752 or U2609 affected Trp induction of a TnaC-regulated LacZ reporter. However, the single change A752G, or the dual replacements A752G and U2609C, maintained Trp induction. Replacements at the conserved TnaC residues W12 and D16 also abolished the protection of U2609 by TnaC-tRNA(Pro) against chemical methylation. These data indicate that the TnaC nascent peptide in the ribosome exit tunnel interacts with the U2609 nucleotide when the ribosome is Trp responsive. This interaction is affected by mutational changes in exit tunnel nucleotides of 23S rRNA, as well as in conserved TnaC residues, suggesting that they affect the structure of the exit tunnel and/or the nascent peptide configuration in the tunnel.
    Keywords: Protein Biosynthesis ; Escherichia Coli Proteins -- Biosynthesis ; Ribosomes -- Chemistry ; Tryptophan -- Analogs & Derivatives
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 7
    Language: English
    In: Applied Microbiology and Biotechnology, 2015, Vol.99(7), pp.3093-3102
    Description: The cyanide dihydratases from Bacillus pumilus and Pseudomonas stutzeri share high amino acid sequence similarity throughout except for their highly divergent C-termini. However, deletion or exchange of the C-termini had different effects upon each enzyme. Here we extended previous studies and investigated how the C-terminus affects the activity and stability of three nitrilases, the cyanide dihydratases from B. pumilus (CynD pum ) and P. stutzeri (CynD stut ) and the cyanide hydratase from Neurospora crassa . Enzymes in which the C-terminal residues were deleted decreased in both activity and thermostability with increasing deletion lengths. However, CynD stut was more sensitive to such truncation than the other two enzymes. A domain of the P. stutzeri CynD stut C-terminus not found in the other enzymes, 306GERDST311, was shown to be necessary for functionality and explains the inactivity of the previously described CynD stut - pum hybrid. This suggests that the B. pumilus C-terminus, which lacks this motif, may have specific interactions elsewhere in the protein, preventing it from acting in trans on a heterologous CynD protein. We identify the dimerization interface A-surface region 195–206 (A2) from CynD pum as this interaction site. However, this A2 region did not rescue activity in C-terminally truncated CynD stut Δ302 or enhance the activity of full-length CynD stut and therefore does not act as a general stability motif.
    Keywords: Cyanide dihydratase ; Nitrilase ; Cyanide ; Bioremediation
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 8
    In: Journal of Bacteriology, Feb, 1997, Vol.179(3-4), p.677(7)
    Description: The mechanisms involved in the extracellular secretion of nuclease from the outer membrane of Serratia marcescens were analyzed via sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. SDS-PAGE analysis of nuclease secretion across the outer membrane of Serratia marcescens indicated the presence of a two-step process involving the rapid secretion of nuclease from the cytoplasmic membrane to the periplasm and outer membrane. Secretion from the outer membrane was also dependent on the hydrogen-ion concentration of the growth medium.
    Keywords: Gram-negative Bacteria -- Research ; Active Biological Transport -- Research ; Microbial Enzymes -- Analysis
    ISSN: 0021-9193
    E-ISSN: 10985530
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  • 9
    Language: English
    In: Journal of bacteriology, August 2002, Vol.184(15), pp.4321-5
    Description: Alanine racemases are ubiquitous prokaryotic enzymes providing the essential peptidoglycan precursor D-alanine. We present evidence that the enzymes from Pseudomonas aeruginosa and Escherichia coli function exclusively as homodimers. Moreover, we demonstrate that expression of a K35A Y235A double mutation of dadX in E. coli suppresses bacterial growth in a dominant negative fashion.
    Keywords: Alanine Racemase -- Genetics ; Escherichia Coli -- Enzymology ; Pseudomonas Aeruginosa -- Enzymology
    ISSN: 0021-9193
    E-ISSN: 10985530
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  • 10
    Language: English
    In: Bioengineered Bugs, 01 September 2010, Vol.1(5), pp.337-340
    Description: A simple and efficient method utilizing in vivo recombination to create recombinant libraries incorporating the products of PCR amplification is described. This will be especially useful for generating large pools of randomly mutagenized clones after error-prone PCR mutagenesis. Here we investigate various parameters to optimize this approach and we demonstrate that as little as1 pmole of PCR fragment can generate a library with greater than 10 4 clones in a single transformation without ligation.
    Keywords: Engineering ; Public Health
    ISSN: 1949-1018
    E-ISSN: 1949-1026
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