Sequence of the hpcC and hpcG genes of the meta-fission homoprotocatechuic acid pathway of Escherichia coli C: nearly 40% amino-acid identity with the analogous enzymes of the catechol pathway

Gene ◽  
1995 ◽  
Vol 156 (1) ◽  
pp. 47-51 ◽  
Author(s):  
David I. Roper ◽  
Joseph M. Stringfellow ◽  
Ronald A. Cooper
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Acid Pathway

scholarly journals PBP5, PBP6 and DacD play different roles in intrinsic β-lactam resistance of Escherichia coli

Microbiology ◽  
2011 ◽  
Vol 157 (9) ◽  
pp. 2702-2707 ◽  
Author(s):  
Sujoy Kumar Sarkar ◽  
Mouparna Dutta ◽  
Chiranjit Chowdhury ◽  
Akash Kumar ◽  
Anindya S. Ghosh
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Parent Strain ◽  
Amino Acid Identity ◽  
Enzymic Activity ◽  
Exponential Phase ◽  
Wild Type ◽  
Acid Identity ◽  
Penicillin Binding Proteins ◽  
E Coli

Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substantial amino acid identity and together constitute ~50 % of the total penicillin-binding proteins of E. coli. PBP5 helps maintain intrinsic β-lactam resistance within the cell. To test if PBP6 and DacD play simlar roles, we deleted dacC and dacD individually, and dacC in combination with dacA, from E. coli 2443 and compared β-lactam sensitivity of the mutants and the parent strain. β-Lactam resistance was complemented by wild-type, but not dd-carboxypeptidase-deficient PBP5, confirming that enzymic activity of PBP5 is essential for β-lactam resistance. Deletion of dacC and expression of PBP6 during exponential or stationary phase did not alter β-lactam resistance of a dacA mutant. Expression of DacD during mid-exponential phase partially restored β-lactam resistance of the dacA mutant. Therefore, PBP5 dd-carboxypeptidase activity is essential for intrinsic β-lactam resistance of E. coli and DacD can partially compensate for PBP5 in this capacity, whereas PBP6 cannot.

scholarly journals Chromosome-Encoded Ambler Class D β-Lactamase of Shewanella oneidensis as a Progenitor of Carbapenem-Hydrolyzing Oxacillinase

2004 ◽  
Vol 48 (1) ◽  
pp. 348-351 ◽  
Author(s):  
Laurent Poirel ◽  
Claire Héritier ◽  
Patrice Nordmann
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Klebsiella Pneumoniae ◽  
Reference Strain ◽  
Shewanella Oneidensis ◽  
Amino Acid Identity ◽  
Gram Negative ◽  
Acid Identity ◽  
Class D ◽  
Lactamase Gene

ABSTRACT A chromosome-encoded β-lactamase gene from a Shewanella oneidensis reference strain was cloned and expressed in Escherichia coli. It encoded a carbapenem-hydrolyzing Ambler class D β-lactamase, OXA-54, that shared 92% amino acid identity with the plasmid-encoded carbapenem-hydrolyzing oxacillinase OXA-48 from Klebsiella pneumoniae. This work suggests that Shewanella spp. may produce the progenitor of oxacillinases compromising the efficacy of imipenem in clinically relevant gram-negative pathogens.

scholarly journals Cloning of a Novel Gene for Quinolone Resistance from a Transferable Plasmid in Shigella flexneri 2b

2005 ◽  
Vol 49 (2) ◽  
pp. 801-803 ◽  
Author(s):  
Mami Hata ◽  
Masahiro Suzuki ◽  
Masakado Matsumoto ◽  
Masao Takahashi ◽  
Katsuhiko Sato ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Clinical Isolate ◽  
Shigella Flexneri ◽  
Amino Acid Identity ◽  
Quinolone Resistance ◽  
Acid Identity ◽  
Low Level ◽  
Novel Gene ◽  
Level Resistance

ABSTRACT A novel gene for quinolone resistance was cloned from a transferable plasmid carried by a clinical isolate of Shigella flexneri 2b that was resistant to fluoroquinolones. The plasmid conferred low-level resistance to quinolones on Escherichia coli HB101. The protein encoded by the gene showed 59% amino acid identity with Qnr.

scholarly journals Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

2016 ◽  
Author(s):  
Michael G. Napolitano ◽  
Matthieu Landon ◽  
Christopher J. Gregg ◽  
Marc J. Lajoie ◽  
Lakshmi N. Govindarajan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Secondary Structure ◽  
Binding Site ◽  
Amino Acid Identity ◽  
Mrna Secondary Structure ◽  
Acid Identity ◽  
Genetic Codes ◽  
Genome Wide ◽  
Ribosomal Binding Site

AbstractThe degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as non-coding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU, but the remaining thirteen “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multi-dimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To further evaluate synonymous and non-synonymous alternatives to essential AGRs, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild type allele, allowing us to exhaustively evaluate the fitness impact of all 64 codon alternatives. Using this method, we confirmed relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes.Significance StatementThis work presents the genome-wide replacement of all rare AGR arginine codons in the essential genes of Escherichia coli with synonymous CGN alternatives. Synonymous codon substitutions can lethally impact non-coding function by disrupting mRNA secondary structure and ribosomal binding site-like motifs. Here we quantitatively define the range of tolerable deviation in these metrics and use this relationship to provide critical insight into codon choice in recoded genomes. This work demonstrates that genome-wide removal of AGR is likely to be possible, and provides a framework for designing genomes with radically altered genetic codes.

scholarly journals Chromosome-Encoded Ambler Class A β-Lactamase of Kluyvera georgiana, a Probable Progenitor of a Subgroup of CTX-M Extended-Spectrum β-Lactamases

2002 ◽  
Vol 46 (12) ◽  
pp. 4038-4040 ◽  
Author(s):  
Laurent Poirel ◽  
Peter Kämpfer ◽  
Patrice Nordmann
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Reference Strain ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Class A ◽  
Extended Spectrum ◽  
Lactamase Gene

ABSTRACT A chromosome-encoded β-lactamase gene, cloned and expressed in Escherichia coli from Kluyvera georgiana reference strain CUETM 4246-74 (DSM 9408), encoded the extended-spectrum β-lactamase KLUG-1, which shared 99% amino acid identity with the plasmid-mediated β-lactamase CTX-M-8. This work provides further evidence that Kluyvera spp. may be the progenitor(s) of CTX-M-type β-lactamases.

Mutations in aarE, the ubiA Homolog of Providencia stuartii, Result in High-Level Aminoglycoside Resistance and Reduced Expression of the Chromosomal Aminoglycoside 2′-N-Acetyltransferase

1998 ◽  
Vol 42 (4) ◽  
pp. 959-962 ◽  
Author(s):  
Michael R. Paradise ◽  
Gregory Cook ◽  
Robert K. Poole ◽  
Philip N. Rather
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Second Step ◽  
Aminoglycoside Resistance ◽  
Acid Identity ◽  
E Coli ◽  
Small Colony ◽  
Providencia Stuartii ◽  
High Level

ABSTRACT The aarE1 allele was identified on the basis of the resulting phenotype of increased aminoglycoside resistance. TheaarE1 mutation also resulted in a small-colony phenotype and decreased levels of aac(2′)-Ia mRNA. The deduced AarE gene product displayed 61% amino acid identity to theEscherichia coli UbiA protein, an octaprenyltransferase required for the second step of ubiquinone biosynthesis. Complementation experiments in both Providencia stuartiiand E. coli demonstrated that aarE andubiA are functionally equivalent.

scholarly journals Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

2016 ◽  
Vol 113 (38) ◽  
pp. E5588-E5597 ◽  
Author(s):  
Michael G. Napolitano ◽  
Matthieu Landon ◽  
Christopher J. Gregg ◽  
Marc J. Lajoie ◽  
Lakshmi Govindarajan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Genome Maintenance ◽  
Acid Identity ◽  
Genetic Codes ◽  
Systematic Strategy ◽  
Identity Based ◽  
Ribosomal Binding Site

The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes.

scholarly journals Identification of a Progenitor of the CTX-M-9 Group of Extended-Spectrum β-Lactamases from Kluyvera georgiana Isolated in Guyana

2005 ◽  
Vol 49 (5) ◽  
pp. 2112-2115 ◽  
Author(s):  
Adam B. Olson ◽  
M. Silverman ◽  
David A. Boyd ◽  
Allison McGeer ◽  
Barbara M. Willey ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Chromosomal Region ◽  
Amino Acid Identity ◽  
Nucleotide Identity ◽  
Acid Identity ◽  
Extended Spectrum ◽  
M 14

ABSTRACT Chromosomal β-lactamase genes (bla KLUY) from six Kluyvera georgiana strains isolated in Guyana were cloned and expressed in Escherichia coli. KLUY-1 exhibited 100% amino acid identity with the extended-spectrum β-lactamase CTX-M-14. We also show that a 2.7-kb Kluyvera chromosomal region exhibits 99% nucleotide identity to a portion of In60 that includes bla CTX-M-9.

scholarly journals The Class A Carbapenemases BKC-1 and GPC-1 Both Originate from the Bacterial Genus Shinella

2020 ◽  
Vol 64 (12) ◽  
Author(s):  
Nicolas Kieffer ◽  
Stefan Ebmeyer ◽  
D. G. Joakim Larsson
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Comparative Genomics ◽  
Amino Acid Identity ◽  
Gene Fragment ◽  
Content Type ◽  
Acid Identity ◽  
Bacterial Genus ◽  
Class A

ABSTRACT Comparative genomics identified the environmental bacterial genus Shinella as the most likely origin of the class A carbapenemases BKC-1 and GPC-1. Available sequences and PCR analyses of additional Shinella species revealed homologous β-lactamases showing up to 85.4% and 93.3% amino acid identity to both enzymes, respectively. The genes conferred resistance to β-lactams once expressed in Escherichia coli. blaBKC-1 likely evolved from a putative ancestral Shinella gene with higher homology through duplication of a gene fragment.

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