Analysis of lincomycin resistance mutations in Escherichia coli

The application of antibiotics in broiler production and the resulting antibiotic resistance in Escherichia coli: A global overview

The increase in antibiotic resistance is a global concern for human and animal health. Resistant microorganisms can spread between food-producing animals and humans. The objective of this review was to identify the type and amount of antibiotics used in poultry production and the level of antibiotic resistance in Escherichia coli isolated from broilers. Isolate information was obtained from national monitoring programs and research studies conducted in large poultry-producing regions: US, China, Brazil, and countries of EU-Poland, United Kingdom, Germany, France, and Spain. The survey results clearly display the absence of a harmonized approach in the monitoring of antibiotics per animal species and the evaluation of resistances using the same methodology. There is no public long-term quantitative data available targeting the amount of antibiotics used in poultry, with the exception of France. Data on antibiotic-resistant E. coli are available for most regions but detection of resistance and number of isolates in each study differs among regions; therefore, statistical evaluation was not possible. Data from France indicate that the decreased use of tetracyclines leads to a reduction in the detected resistance rates. The fluoroquinolones, third-generation cephalosporins, macrolides, and polymyxins ("highest priority critically important" antibiotics for human medicine according to WHO) are approved for use in large poultry-producing regions, with the exception of fluoroquinolones in the US and cephalosporins in the EU. The approval of cephalosporins in China could not be evaluated. Tetracyclines, aminoglycosides, sulfonamides, and penicillins are registered for use in poultry in all evaluated countries. The average resistance rates in E. coli to representatives of these antibiotic classes are higher than 40% in all countries, with the exception of ampicillin in the US. The resistance rates to fluoroquinolones and quinolones in the US, where fluoroquinolones are not registered for use, are below 5%, while the average of resistant E. coli is above 40% in Brazil, China, and EU, where use of fluoroquinolones is legalized. However, banning of fluoroquinolones and quinolones has not totally eliminated the occurrence of resistant populations.

Efficiently activated ε-poly-L-lysine production by multiple antibiotic-resistance mutations and acidic pH shock optimization in Streptomyces albulus

ε‐Poly‐L‐lysine (ε‐PL) is a food additive produced by Streptomyces and is widely used in many countries. Working with Streptomyces albulus FEEL‐1, we established a method to activate ε‐PL synthesis by successive introduction of multiple antibiotic‐resistance mutations. Sextuple mutant R6 was finally developed by screening for resistance to six antibiotics and produced 4.41 g/L of ε‐PL in a shake flask, which is 2.75‐fold higher than the level produced by the parent strain. In a previous study, we constructed a double‐resistance mutant, SG‐31, with high ε‐PL production of 3.83 g/L and 59.50 g/L in a shake flask and 5‐L bioreactor, respectively. However, we found that R6 did not show obvious advantages in fed‐batch fermentation when compared with SG‐31. For further activation of ε‐PL synthesis ability, we optimized the fermentation process by using an effective acidic pH shock strategy, by which R6 synthetized 70.3 g/L of ε‐PL, 2.79‐fold and 1.18‐fold greater than that synthetized by FEEL‐1 and SG‐31, respectively. To the best of our knowledge, this is the highest reported ε‐PL production to date. This ε‐PL overproduction may be due to the result of R99P and Q856H mutations in ribosomal protein S12 and RNA polymerase, respectively, which may be responsible for the increased transcription of the ε‐poly‐lysine synthetase gene (pls) and key enzyme activities in the Lys synthesis metabolic pathway. Consequently, ε‐PL synthetase activity, intracellular ATP, and Lys concentrations were improved and directly contributed to ε‐PL overproduction. This study combined ribosome engineering, high‐throughput screening, and targeted strategy optimization to accelerate ε‐PL production and probe the fermentation characteristics of hyperyield mutants. The information presented here may be useful for other natural products produced by Streptomyces.

Dramatic activation of antibiotic production in Streptomyces coelicolor by cumulative drug resistance mutations

We recently described a new method to activate antibiotic production in bacteria by introducing a mutation conferring resistance to a drug such as streptomycin, rifampin, paromomycin, or gentamicin. This method, however, enhanced antibiotic production by only up to an order of magnitude. Working with Streptomyces coelicolor A3(2), we established a method for the dramatic activation of antibiotic production by the sequential introduction of multiple drug resistance mutations. Septuple and octuple mutants, C7 and C8, thus obtained by screening for resistance to seven or eight drugs, produced huge amounts (1.63 g/liter) of the polyketide antibiotic actinorhodin, 180-fold higher than the level produced by the wild type. This dramatic overproduction was due to the acquisition of mutant ribosomes, with aberrant protein and ppGpp synthesis activity, as demonstrated by in vitro protein synthesis assays and by the abolition of antibiotic overproduction with relA disruption. This new approach, called "ribosome engineering," requires less time, cost, and labor than other methods and may be widely utilized for bacterial strain improvement.

The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus

BACKGROUND

Detailed structural information on ribosomal proteins has increased our understanding of the structure, function and evolution of the ribosome. L14 is one of the most conserved ribosomal proteins and appears to have a central role in the ribonucleoprotein complex. Studies have indicated that L14 occupies a central location between the peptidyl transferase and GTPase regions of the large ribosomal subunit.

RESULTS

The crystal structure of L14 from Bacillus stearothermophilus has been solved using a combination of isomorphous replacement and multiwavelength anomalous dispersion (MAD) methods. The structure comprises a five-stranded beta-barrel, a C-terminal loop region that contains two small alpha-helices, and a beta-ribbon that projects from the beta-barrel. An analysis of the structure and the conserved amino acids reveals three surface patches that probably mediate L14-RNA and L14-protein interactions within the ribosome.

CONCLUSIONS

The accepted role of ribosomal proteins is to promote the folding and stabilization of ribosomal RNA. The L14 structure is consistent with this notion, and it suggests that the RNA binds in two sites. One RNA-binding site appears to recognize a distinct region of ribosomal RNA during particle assembly. The second site is smaller and may become occupied during the later compaction of the RNA. The surface hydrophobic patch is a likely site of protein-protein interaction, possibly with L19.

Isolation and analysis of a human cDNA highly homologous to the yeast gene encoding L17A ribosomal protein

A cDNA from human brain poly(A)+RNA with significant similarity to the gene encoding yeast L17A large subunit ribosomal (r) protein (L17A) was isolated using the polymerase chain reaction. The deduced amino acid (aa) sequence of 140 aa (calculated pI of 10.79) exhibits a 78% similarity to that of the yeast L17A r protein (88% when conservative aa replacements are considered as well). This indicates that L17A is one of the best conserved r-proteins and therefore may play a critical role in ribosome function. In contrast to its eubacterial and chloroplast counterparts, human L17A contains an N-terminal extension of 19 aa which may be involved in nuclear targeting of the r-protein. Approximately five to seven genes in mammalian genomes give strong hybridization signals when probed with the human L17A homologue cDNA. Whereas the L17A homologue was found to be expressed at similar levels in several human tissues as a transcript of 600 nucleotides, a several-fold higher transcript level was detected in the rapidly growing neuroblastoma cell line, SK-N-BE.

Affinity labeling of the virginiamycin S binding site on bacterial ribosome

Virginiamycin S (VS, a type B synergimycin) inhibits peptide bond synthesis in vitro and in vivo. The attachment of virginiamycin S to the large ribosomal subunit (50S) is competitively inhibited by erythromycin (Ery, a macrolide) and enhanced by virginiamycin M (VM, a type A synergimycin). We have previously shown, by fluorescence energy transfer measurements, that virginiamycin S binds at the base of the central protuberance of 50S, the putative location of peptidyltransferase domain [Di Giambattista et al. (1986) Biochemistry 25, 3540-3547]. In the present work, the ribosomal protein components at the virginiamycin S binding site were affinity labeled by the N-hydroxysuccinimide ester derivative (HSE) of this antibiotic. Evidence has been provided for (a) the association constant of HSE-ribosome complex formation being similar to that of native virginiamycin S, (b) HSE binding to ribosomes being antagonized by erythromycin and enhanced by virginiamycin M, and (c) a specific linkage of HSE with a single region of 50S, with virtually no fixation to 30S. After dissociation of covalent ribosome-HSE complexes, the resulting ribosomal proteins have been fractionated by electrophoresis and blotted to nitrocellulose, and the HSE-binding proteins have been detected by an immunoenzymometric procedure. More than 80% of label was present within a double spot corresponding to proteins L18 and L22, whose Rfs were modified by the affinity-labeling reagent. It is concluded that these proteins are components of the peptidyltransferase domain of bacterial ribosomes, for which a topographical model, including the available literature data, is proposed.

Novel mechanisms of resistance to lincosamides in Staphylococcus and Arthrobacter spp

Clinical isolates of Staphylococcus and Arthrobacter spp. were screened for lincosamide resistance. Six different patterns of resistance were found. Strains designated SF27 and SF28 showed low-level resistance to lincosamides: one was susceptible to erythromycin (SF27) and the other was resistant (SF28). Analysis of ribosomes from the resistant strains in an in vitro poly(U)-dependent protein-synthesizing system showed that ribosomes of both strains were sensitive to lincomycin and clindamycin. Four patterns of high-level resistance to lincosamides were observed (strains SF4, SF19, SF30, and SF31). All of these except SF30 had ribosomes which were highly resistant in vitro to the antibiotics and showed a close correlation with results of the in vivo experiments. In vivo protein synthesis by strain SF30 was resistant to lincomycin and sensitive to clindamycin, whereas the ribosomes were sensitive when assayed in vitro. Lincosamide-inactivating enzymes were not detected in cell extracts of the six resistant strains. Strains SF19 and SF31 demonstrated two ribosome-mediated lincosamides resistance mechanisms that were not previously reported. Both strains were highly resistant to lincosamides and susceptible to erythromycin, but SF19 was also highly resistant to oleandomycin and partially resistant to various macrolides.

Nucleotide sequence and linkage map position of the genes for ribosomal proteins L14 and S8 in the maize chloroplast genome

The nucleotide sequence of a 1287-base-pair segment of the maize (Zea mays) chloroplast DNA, encoding chloroplast ribosomal proteins L14, S8 and the C-terminal part of L16, has been determined using the dideoxy-chain-termination method. These data from a monocot plant are compared to the corresponding data from a dicot and a lower plant and from two bacteria. The deduced amino acid sequence of maize chloroplast L14 shows 80%, 81%, 51% and 52% and that of S8 shows 75%, 58%, 39% and 38% sequence identity, respectively, to the corresponding sequences of Nicotiana tabacum, Marchantia polymorpha, Bacillus stearothermophilus and Escherichia coli. The starting map coordinates of rpL14 and rpS8 in the physical map of the maize chloroplast DNA [Larrinua, I. M., Muskavitch, K. M. T., Gubbins, E. J. and Bogorad, L. (1983) Plant Mol. Biol. 2, 129-140] are 31.330 and 31.841. The gene order is rpL16-spacer-rpL14-spacer-rpS8. Shine-Dalgarno sequences (GGA and AGGAGG) and computer-derived stem-loop structures of dyad symmetry are present in the spacers and the 3' downstream region of rpS8, respectively, but a chloroplast promoter-like sequence could not be detected suggesting that the latter might be located further upstream in this ribosomal protein gene cluster in maize chloroplast DNA.

Tiamulin resistance mutations in Escherichia coli

Forty "two-step" and 13 "three-step" tiamulin-resistant mutants of Escherichia coli PR11 were isolated and tested for alteration of ribosomal proteins. Mutants with altered ribosomal proteins S10, S19, L3, and L4 were detected. The S19, L3, and L4 mutants were studied in detail. The L3 and L4 mutations did not segregate from the resistance character in transductional crosses and therefore seem to be responsible for the resistance. Extracts of these mutants also exhibited an increased in vitro resistance to tiamulin in the polyuridylic acid and phage R17 RNA-dependent polypeptide synthesis systems, and it was demonstrated that this was a property of the 50S subunit. In the case of the S19 mutant, genetic analysis showed segregation between resistance and the S19 alteration and therefore indicated that mutation of a protein other than S19 was responsible for the resistance phenotype. The isolated ribosomes of the S19, L3, and L4 mutants bound radioactive tiamulin with a considerably reduced strength when compared with those of wild-type cells. The association constants were lower by factors ranging from approximately 20 to 200. When heated in the presence of ammonium chloride, these ribosomes partially regained their avidity for tiamulin.

Photolabile antibiotics as probes of ribosomal structure and function

In summary, our studies have resulted in the development of new reagents and synthetic procedures for the introduction of both radioactivity and photolability into antibiotics; have provided examples of how PAGE analysis can be used to conveniently test various aspects of photoaffinity labeling of complex receptors, such as the ribosome; have revealed examples of unexpected photoreactivity, as in the case of puromycin; and have provided strong evidence regarding the three-dimensional location of the peptidyl transferase center and the site of that interaction of the 3' and of aminoacyl-tRNA with the 30S subunit. Work that is now in progress should provide similar detailed information regarding other functional sites in the ribosome.