Effect of aminoglycoside concentration on reaction rates of aminoglycoside-modifying enzymes

Structuring evolution: biochemical networks and metabolic diversification in birds

Background

Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a “global” carotenoid network – comprising of all known enzymatic reactions among naturally occurring carotenoids – with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds.

Results

We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network – compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution.

Conclusions

The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0731-z) contains supplementary material, which is available to authorized users.

The Landscape of Evolution: Reconciling Structural and Dynamic Properties of Metabolic Networks in Adaptive Diversifications

The network of the interactions among genes, proteins, and metabolites delineates a range of potential phenotypic diversifications in a lineage, and realized phenotypic changes are the result of differences in the dynamics of the expression of the elements and interactions in this deterministic network. Regulatory mechanisms, such as hormones, mediate the relationship between the structural and dynamic properties of networks by determining how and when the elements are expressed and form a functional unit or state. Changes in regulatory mechanisms lead to variable expression of functional states of a network within and among generations. Functional properties of network elements, and the magnitude and direction of evolutionary change they determine, depend on their location within a network. Here, we examine the relationship between network structure and the dynamic mechanisms that regulate flux through a metabolic network. We review the mechanisms that control metabolic flux in enzymatic reactions and examine structural properties of the network locations that are targets of flux control. We aim to establish a predictive framework to test the contributions of structural and dynamic properties of deterministic networks to evolutionary diversifications.

Inhaled antibiotics for Gram-negative respiratory infections

Several disease states create conditions that lead to opportunistic Gram-negative respiratory infections. Inhalation is the most direct and, until recently, underutilized means of antimicrobial drug targeting for respiratory tract infections. All approved antimicrobial agents for administration by inhalation are indicated for Pseudomonas aeruginosa infections in patients with cystic fibrosis. These inhaled therapies have directly contributed to a significant reduction in exacerbations and hospitalizations in this patient population over the last few decades. The relentless adaptation of pathogenic organisms to current treatment options demands that the pharmaceutical industry continue designing next-generation antimicrobial agents over 70 years after they were first introduced. Recent technological advances in inhalation devices and drug formulation techniques have broadened the scope of antimicrobial structural classes that can be investigated by inhalation; however, there is an urgent need to discover novel compounds with improved resistance profiles relative to those drugs that are already marketed.

Aminoglycoside resistance resulting from tight drug binding to an altered aminoglycoside acetyltransferase

The aacA29b gene, which confers an atypical aminoglycoside resistance pattern to Escherichia coli, was identified on a class 1 integron from a multidrug-resistant isolate of Pseudomonas aeruginosa. On the basis of amino acid sequence homology, it was proposed that the gene encoded a 6'-N-acetyltransferase. The resistance gene was cloned into the pET23a(+) vector, and overexpression conferred high-level resistance to the usual substrates of the aminoglycoside N-acetyltransferase AAC(6')-I, except netilmicin. The level of resistance conferred by aacA29b correlated perfectly with the level of expression of the gene. The corresponding C-terminal six-His-tagged AAC(6')-29b protein was purified and found to exist as a dimer in solution. With a spectrophotometric assay, an extremely feeble AAC activity was detected with acetyl coenzyme A (acetyl-CoA) as an acetyl donor. Fluorescence titrations of the protein with aminoglycosides demonstrated the very tight binding of tobramycin, dibekacin, kanamycin A, sisomicin (K(d), </=1 micro M) and a weaker affinity for amikacin (K(d), approximately 60 micro M). The binding of netilmicin and acetyl-CoA could not be detected by either fluorescence spectroscopy or isothermal titration calorimetry. The inability of AAC(6')-29b to efficiently bind acetyl-CoA is supported by an alignment analysis of its amino acid sequence compared with those of other AAC(6')-I family members. AAC(6')-29b lacks a number of residues involved in acetyl-CoA binding. These results lead to the conclusion that AAC(6')-29b is able to confer aminoglycoside resistance by sequestering the drug as a result of tight binding.

Different aminoglycoside-resistant phenotypes in a rabbit Staphylococcus aureus endocarditis infection model

The impact of different types of enzymatic resistance on the in vivo antibacterial activity of aminoglycosides (amikacin, gentamicin, and netilmicin) was studied in the rabbit endocarditis model with four strains of Staphylococcus aureus. Animals were treated in a manner simulating the administration of a single daily human dose. Amikacin had no effect on the three kanamycin-resistant strains despite apparent susceptibility in the disk diffusion test. Gentamicin appears to be the preferable aminoglycoside for treatment of staphylococcal infections.

Aminoglycoside resistance in Mycobacterium kansasii, Mycobacterium avium-M. intracellulare, and Mycobacterium fortuitum: are aminoglycoside-modifying enzymes responsible?

Aminoglycoside acetyltransferase was detected in Mycobacterium kansasii and M. fortuitum but not in M. avium-M. intracellulare when they were screened by a radioassay. Aminoglycoside phosphotransferase and nucleotidyltransferase activities were absent from all three species tested. Acetyltransferases from both M. kansasii and M. fortuitum displayed relatively high K(m)s, all at the millimolar level, for substrates including tobramycin, neomycin, and kanamycin A. The K(m) of each substrate was well above the corresponding maximum achievable level in serum. The low affinities of these enzymes for their substrates suggested that drug modification in vivo was very unlikely. Among the various substrates tested, no apparent positive correlation was found between substrate affinity and resistance level. The presence of aminoglycoside-modifying enzymes in these mycobacterial species was therefore not shown to confer resistance to aminoglycosides.

Aminoglycoside resistance in Haemophilus influenzae

From September 1, 1990 to December 31, 1993 a total of 425 Haemophilus influenzae strains from clinical specimens were isolated in the Microbiology Laboratory of the Zaragoza University Hospital. Of these strains, 16 (33.33%) were resistant to kanamycin, neomycin, paromomycin, lividomycin and streptomycin. Demonstration of APH (3')-I activity by the phosphocellulose paper binding assay, based on the incorporation of radiolabel into lividomycin was sixfold greater than into butirosin. Two DNA probes were prepared to screen for the genes encoding APH(3') activity in kanamycin-resistant H. influenzae. Homology was observed between the aphA1 DNA probe and total cellular DNA from all 16 APH(3')-I producers. On the other hand, streptomycin-resistance was not through metabolic modification of the antibiotic.

Overproduction of 3'-aminoglycoside phosphotransferase type I confers resistance to tobramycin in Escherichia coli

Escherichia coli HM69, isolated from urine, was resistant to high levels of kanamycin (MIC, > 1,000 micrograms/ml) and a low level of tobramycin (MIC, 8 micrograms/ml). Phosphocellulose paper-binding assays and molecular cloning indicated that resistance to both aminoglycosides was due to synthesis of a 3'-aminoglycoside phosphotransferase type I, an enzyme that phosphorylates kanamycin but not tobramycin. The structural gene for the enzyme was borne by an 80-kb conjugative plasmid, pIP1518, and was nearly identical to aphA1 of Tn903. Incubation of extracts of resistant cells with tobramycin or kanamycin led to a decrease (> 80%) of antibiotic activity as determined by a microbiological assay. Heat treatment showed that loss of activity was reversible and dependent upon the native enzyme. In the presence of ATP, only inactivation of kanamycin was reversible. These results suggest that resistance to low levels of tobramycin was due to formation of a complex between the enzyme and the antibiotic.

Molecular cloning and nucleotide sequencing of a novel aminoglycoside 6'-N-acetyltransferase gene from an R-plasmid of Salmonella typhimurium S24 isolated in Taiwan

A conjugative aminoglycoside resistance plasmid pST2 has been isolated from Escherichia coli K-12 14R525, which was mated with a clinical isolate of Salmonella typhimurium S24. A novel resistance gene of aminoglycoside 6'-N-acetyltransferase[AAC(6')] was cloned from plasmid pST2 on a 1,393 kilobase (kb) of SphI-SalI fragment into vector pACYC184 and pUC18. This novel AAC(6') gene in plasmid pST2 acetylated kanamycin, amikacin, dibekacin, tobramycin, gentamicin, netilmicin, and sisomicin. The complete nucleotide sequence of the novel AAC(6') gene and its neighboring sequences were also determined. Minicell experiments detected only one protein of 24.7 kilodaltons (kDa) translated from an open reading frame of the 618 base pairs (bp) gene.

Nucleotide sequence of the aacC3 gene, a gentamicin resistance determinant encoding aminoglycoside-(3)-N-acetyltransferase III expressed in Pseudomonas aeruginosa but not in Escherichia coli

A chromosomal gentamicin resistance determinant from Pseudomonas aeruginosa was cloned on a 2.4-kb fragment in the broad-host-range vector pLAFR3. Substrate profiles for eight aminoglycosides at three concentrations showed that resistance was due to aminoglycoside-(3)-N-acetyltransferase III. This enzyme was produced in Pseudomonas strains but not in an Escherichia coli strain bearing the aacC3 gene. Nucleotide sequencing revealed two contiguous open reading frames (ORFs) preceded by a potential promoter and a ribosome-binding site. ORF-1 was 642 bp in length and encoded a protein of unknown function with a molecular mass of 23.9 kDa. ORF-2 was 813 bp in length and encoded a protein of 29.6 kDa. From deletion mutagenesis, in vitro transcription-translation data, and protein analysis of bacterial lysates, it was inferred that this 29.6-kDa protein represents the aminoglycoside-(3)-N-acetyltransferase III enzyme. A polymerase chain reaction with two specific intragenic 20-mer primers was developed to detect the aacC3 gene. A BstEII restriction site in the amplified DNA region was used to demonstrate the specificity of the reaction. Tests of 23 reference strains, which produced 12 different aminoglycoside-modifying enzymes, confirmed the specificities of the primers. The gene proved to be absent from a collection of 50 gentamicin-resistant P. aeruginosa strains selected at random in The Netherlands.

Nucleotide sequence of the aacC2 gene, a gentamicin resistance determinant involved in a hospital epidemic of multiply resistant members of the family Enterobacteriaceae

A gentamicin resistance determinant of a conjugative plasmid from Enterobacter cloacae was cloned on a 3.2-kilobase fragment in the PstI site of pBR322. Substrate profiles for eight aminoglycosides at three concentrations showed that the resistance was due to aminoglycoside-(3)-N-acetyltransferase isoenzyme II. Insertion mapping by the gamma-delta transposon revealed that the size of the gene was approximately 1 kilobase. Nucleotide sequencing of the aacC2 gene identified an open reading frame of 858 base pairs, preceded by a promoter and a ribosome-binding site. From these data the molecular mass of the protein was calculated to be 30.6 kilodaltons. A comparison of the nucleotide sequence of the aacC2 gene with those published for the aacC3 and aacC4 genes showed complete homology of the aacC2 gene and the presumed aacC3 gene. An internal restriction fragment of the gene used as a probe in colony hybridization demonstrated the presence of the aacC2 gene in 86% of 86 multiply resistant isolates of the family Enterobacteriaceae obtained during an 18-month hospital epidemic. This corroborates our earlier data on the enzyme identification by the susceptibility profiling method.