Amino Acid Substitution in an Amidase Produced by an Acetanilide-utilizing Mutant of Pseudomonas aeruginosa

ABSTRACT A number of transcriptional regulators mediate their effects through direct contact with the ς70 subunit ofEscherichia coli RNA polymerase (RNAP). In particular, several regulators have been shown to contact a C-terminal portion of ς70 that harbors conserved region 4. This region of ς contains a putative helix-turn-helix DNA-binding motif that contacts the −35 element of ς70-dependent promoters directly. Here we report the use of a recently developed bacterial two-hybrid system to study the interaction between the putative anti-ς factor Rsd and the ς70 subunit of E. coli RNAP. Using this system, we found that Rsd can interact with an 86-amino-acid C-terminal fragment of ς70 and also that amino acid substitution R596H, within region 4 of ς70, weakens this interaction. We demonstrated the specificity of this effect by showing that substitution R596H does not weaken the interaction between ς and two other regulators shown previously to contact region 4 of ς70. We also demonstrated that AlgQ, a homolog of Rsd that positively regulates virulence gene expression inPseudomonas aeruginosa, can contact the C-terminal region of the ς70 subunit of RNAP from this organism. We found that amino acid substitution R600H in ς70 fromP. aeruginosa, corresponding to the R596H substitution in E. coli ς70, specifically weakens the interaction between AlgQ and ς70. Taken together, our findings suggest that Rsd and AlgQ contact similar surfaces of RNAP present in region 4 of ς70 and probably regulate gene expression through this contact.

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VIM-15 and VIM-16, Two New VIM-2-Like Metallo-β-Lactamases in Pseudomonas aeruginosa Isolates from Bulgaria and Germany

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00175-08 ◽

2008 ◽

Vol 52 (8) ◽

pp. 2977-2979 ◽

Cited By ~ 16

Author(s):

Ines Schneider ◽

Emma Keuleyan ◽

Rudolf Rasshofer ◽

Rumyana Markovska ◽

Anne Marie Queenan ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Enzyme Activity ◽

Amino Acid ◽

Amino Acid Substitution ◽

Class I ◽

Class I Integrons

ABSTRACT Two Pseudomonas aeruginosa urine isolates from Bulgaria and Germany produced two new VIM-2 variants. VIM-15 had one amino acid substitution (Tyr218Phe) which caused a significant increase in hydrolytic efficiency. The substitution Ser54Leu, characterizing VIM-16, showed no influence on enzyme activity. Both genes were part of class I integrons located in the chromosome.

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Carbapenem Resistance Mechanisms in Pseudomonas aeruginosa Clinical Isolates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.2.480-484.2001 ◽

2001 ◽

Vol 45 (2) ◽

pp. 480-484 ◽

Cited By ~ 123

Author(s):

Hyunjoo Pai ◽

Jong-Won Kim ◽

Jungmin Kim ◽

Ji Hyang Lee ◽

Kang Won Choe ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Amino Acid ◽

Amino Acid Substitution ◽

Carbapenem Resistance ◽

Resistance Mechanisms ◽

Clinical Isolates ◽

Efflux System ◽

Clinical Strains ◽

Carbapenem Resistant

ABSTRACT In order to define the contributions of the mechanisms for carbapenem resistance in clinical strains of Pseudomonas aeruginosa, we investigated the presence of OprD, the expressions of the MexAB-OprM and MexEF-OprN systems, and the production of the β-lactamases for 44 clinical strains. All of the carbapenem-resistant isolates showed the loss of or decreased levels of OprD. Three strains overexpressed the MexAB-OprM efflux system by carrying mutations inmexR. These three strains had the amino acid substitution in MexR protein, Arg (CGG) → Gln (CAG), at the position of amino acid 70. None of the isolates, however, expressed the MexEF-OprN efflux system. For the characterization of β-lactamases, at least 13 isolates were the depressed mutants, and 12 strains produced secondary β-lactamases. Based on the above resistance mechanisms, the MICs of carbapenem for the isolates were analyzed. The MICs of carbapenem were mostly determined by the expression of OprD. The MICs of meropenem were two- to four-fold increased for the isolates which overexpressed MexAB-OprM in the background of OprD loss. However, the elevated MICs of meropenem for some individual isolates could not be explained. These findings suggested that other resistance mechanisms would play a role in meropenem resistance in clinical isolates of P. aeruginosa.

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Integron-Located oxa-32 Gene Cassette Encoding an Extended-Spectrum Variant of OXA-2 β-Lactamase from Pseudomonas aeruginosa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.46.2.566-569.2002 ◽

2002 ◽

Vol 46 (2) ◽

pp. 566-569 ◽

Cited By ~ 30

Author(s):

Laurent Poirel ◽

Patrick Gerome ◽

Christophe De Champs ◽

Jean Stephanazzi ◽

Thierry Naas ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Amino Acid ◽

Clinical Isolate ◽

Amino Acid Substitution ◽

Gene Cassette ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Class 1 Integron ◽

Class D ◽

Class 1

ABSTRACT Pseudomonas aeruginosa clinical isolate CY-1, which was resistant to ceftazidime, harbored a conjugative ca. 250-kb plasmid that contained a class 1 integron with two gene cassettes encoding OXA-32, an OXA-2- type β-lactamase, and the aminoglycoside acetyltransferase AAC(6′)Ib9. OXA-32 differed from OXA-2 by an Leu169Ile amino acid substitution (class D numbering). Site-directed mutagenesis established that Ile169 is responsible for resistance to ceftazidime but not to cefotaxime.

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Development of carbapenem resistance in Pseudomonas aeruginosa is associated with OprD polymorphisms, particularly the amino acid substitution at codon 170

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkx158 ◽

2017 ◽

Vol 72 (9) ◽

pp. 2489-2495 ◽

Cited By ~ 9

Author(s):

Jwu-Ching Shu ◽

An-Jing Kuo ◽

Lin-Hui Su ◽

Tsui-Ping Liu ◽

Ming-Hsun Lee ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Amino Acid ◽

Amino Acid Substitution ◽

Carbapenem Resistance

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Hubsm: A Novel Amino Acid Substitution Matrix for Comparing Hub Proteins

International Journal of Advanced Research in Computer Science and Software Engineering ◽

10.23956/ijarcsse.v7i8.53 ◽

2017 ◽

Vol 7 (8) ◽

pp. 212

Author(s):

Renganayaki G. ◽

Achuthsankar S. Nair

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Low Complexity ◽

Database Search ◽

Substitution Matrix ◽

Compositional Bias ◽

Sequence Alignments ◽

Amino Acid Substitution Matrix ◽

Alignment Algorithms ◽

Hub Proteins

Sequence alignment algorithms and database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid. In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs, the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.

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