Nucleotide sequence of the ribostamycin phosphotransferase gene and of its control region in Streptomyces ribosidificus

Prospects for circumventing aminoglycoside kinase mediated antibiotic resistance

Aminoglycosides are a class of antibiotics with a broad spectrum of antimicrobial activity. Unfortunately, resistance in clinical isolates is pervasive, rendering many aminoglycosides ineffective. The most widely disseminated means of resistance to this class of antibiotics is inactivation of the drug by aminoglycoside-modifying enzymes (AMEs). There are two principal strategies to overcoming the effects of AMEs. The first approach involves the design of novel aminoglycosides that can evade modification. Although this strategy has yielded a number of superior aminoglycoside variants, their efficacy cannot be sustained in the long term. The second approach entails the development of molecules that interfere with the mechanism of AMEs such that the activity of aminoglycosides is preserved. Although such a molecule has yet to enter clinical development, the search for AME inhibitors has been greatly facilitated by the wealth of structural information amassed in recent years. In particular, aminoglycoside phosphotransferases or kinases (APHs) have been studied extensively and crystal structures of a number of APHs with diverse regiospecificity and substrate specificity have been elucidated. In this review, we present a comprehensive overview of the available APH structures and recent progress in APH inhibitor development, with a focus on the structure-guided strategies.

Aminoglycoside modifying enzymes

Aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. Unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. In some cases the levels of resistance reached the point that rendered them virtually useless. Among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. Aminoglycoside modifying enzymes catalyze the modification at different -OH or -NH₂ groups of the 2-deoxystreptamine nucleus or the sugar moieties and can be nucleotidyltransferases, phosphotransferases, or acetyltransferases. The number of aminoglycoside modifying enzymes identified to date as well as the genetic environments where the coding genes are located is impressive and there is virtually no bacteria that is unable to support enzymatic resistance to aminoglycosides. Aside from the development of new aminoglycosides refractory to as many as possible modifying enzymes there are currently two main strategies being pursued to overcome the action of aminoglycoside modifying enzymes. Their successful development would extend the useful life of existing antibiotics that have proven effective in the treatment of infections. These strategies consist of the development of inhibitors of the enzymatic action or of the expression of the modifying enzymes.

Versatility of aminoglycosides and prospects for their future

Aminoglycoside antibiotics have had a major impact on our ability to treat bacterial infections for the past half century. Whereas the interest in these versatile antibiotics continues to be high, their clinical utility has been compromised by widespread instances of resistance. The multitude of mechanisms of resistance is disconcerting but also illuminates how nature can manifest resistance when bacteria are confronted by antibiotics. This article reviews the most recent knowledge about the mechanisms of aminoglycoside action and the mechanisms of resistance to these antibiotics.

Isolation of a gene encoding a novel spectinomycin phosphotransferase from Legionella pneumophila

A gene capable of conferring spectinomycin resistance was isolated from Legionella pneumophila, the agent of Legionnaires' disease. The gene (aph) encoded a 36-kDa protein which has similarity to aminoglycoside phosphotransferases. Biochemical analysis confirmed that aph encodes a phosphotransferase which modifies spectinomycin but not hygromycin, kanamycin, or streptomycin. The strain that was the source of aph demonstrated resistance to spectinomycin, and Southern hybridizations determined that aph also exists in other legionellae.

Active-site labeling of an aminoglycoside antibiotic phosphotransferase (APH(3')-IIIa)

The aminoglycoside antibiotics are inactivated by modifying enzymes that are now widely distributed in many pathogenic bacteria. This situation threatens the continued use of these clinically important drugs. We have undertaken studies to understand the molecular mechanism of aminoglycoside resistance, and we report the affinity labeling of the enterococcal aminoglycoside 3'-phosphotransferase, APH(3')-IIIa, with an electrophilic ATP analogue, 5'-[p-(fluorosulfonyl)benzoyl]adenosine (FSBA). Incubation of purified APH(3')-IIIa with FSBA resulted in time-dependent irreversible inactivation of enzyme activity with a binding constant, Ki, of 0.406 mM and a rate of maximal inactivation, kmax, of 0.086 min-1. Addition of ATP completely protected the enzyme from inactivation, consistent with labeling of the ATP binding site. Reaction of APH(3')-IIIa with [14C]FSBA showed that inactivated APH(3')-IIIa incorporates 1 mol of FSBA/mol of enzyme. Peptide mapping of FSBA-inactivated APH(3')-IIIa resulted in the identification of two peptide peaks with highly increased absorbance at 260 nm, indicative of covalent labeling with FSBA. Analysis by electrospray ionization mass spectrometry and Edman degradation revealed two tryptic peptides, Val31-Lys44 and Leu34-Arg49, which incorporated the FSBA label at Lys33 and Lys44, respectively. This establishes the importance of the N-terminal region of APHs in ATP binding, a region of these enzymes which has heretofore not been considered for involvement in substrate binding.

Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes

The three classes of enzymes which inactivate aminoglycosides and lead to bacterial resistance are reviewed. DNA hybridization studies have shown that different genes can encode aminoglycoside-modifying enzymes with identical resistance profiles. Comparisons of the amino acid sequences of 49 aminoglycoside-modifying enzymes have revealed new insights into the evolution and relatedness of these proteins. A preliminary assessment of the amino acids which may be important in binding aminoglycosides was obtained from these data and from the results of mutational analysis of several of the genes encoding aminoglycoside-modifying enzymes. Recent studies have demonstrated that aminoglycoside resistance can emerge as a result of alterations in the regulation of normally quiescent cellular genes or as a result of acquiring genes which may have originated from aminoglycoside-producing organisms or from other resistant organisms. Dissemination of these genes is aided by a variety of genetic elements including integrons, transposons, and broad-host-range plasmids. As knowledge of the molecular structure of these enzymes increases, progress can be made in our understanding of how resistance to new aminoglycosides emerges.

In vivo translational start site selection on leaderless mRNA transcribed from the Streptomyces fradiae aph gene

The message of the Streptomyces fradiae aph gene lacks a leader sequence and therefore is translated in the absence of a conventional Shine-Dalgarno interaction between mRNA and 30S ribosomal subunits. Insertion mutations generating short leaders of 2 or 4 nucleotides on the 5' end of the aph transcript reduced translational efficiency. A 4-base leader (5'-AUGC-3') placing a potential out-of-frame start codon immediately upstream of the aph coding sequence prevented detectable translation in the aph reading frame. The upstream AUG in this mutant was able to drive the expression of a reporter gene in a translational fusion vector, implying that this start codon was utilized in favor of the downstream AUG. Additional leaders (5'-AUAUGC-3' or 5'-CAUAUGC-3') placing 2 or 3 nucleotides 5' to the upstream AUG relieved this apparent discrimination, permitting translation of the APH protein from the downstream AUG. These results suggest that the position of a start codon with respect to the 5' terminus of aph mRNA is a determinant of translational efficiency and start site selection.

Sequence and transcriptional analysis of the Streptomyces glaucescens tcmAR tetracenomycin C resistance and repressor gene loci

Sequence analysis of the tcmA tetracenomycin C resistance gene from Streptomyces glaucescens GLA.O (ETH 22794) identifies one large open reading frame whose deduced product has sequence similarity to the mmr methylenomycin resistance gene from Streptomyces coelicolor, the Streptomyces rimosus tet347 (otrB) tetracycline resistance gene, and the atr1 aminotriazole resistance gene from Saccharomyces cerevisiae. These genes are thought to encode proteins that act as metabolite export pumps powered by transmembrane electrochemical gradients. A divergently transcribed gene, tcmR, is located in the region upstream of tcmA. The deduced product of tcmR resembles the repressor proteins encoded by tetR regulatory genes from Escherichia coli and the actII-orf1 gene from S. coelicolor. Transcriptional analysis of tcmA and tcmR indicates that these genes have back-to-back and overlapping promoter regions.

Nucleotide sequence and transcriptional analysis of activator-regulator proteins for beta-lactamase in Streptomyces cacaoi

The nucleotide sequence of the 2.7-kb DNA fragment upstream of the structural gene of beta-lactamase in Streptomyces cacaoi was determined. Computer-aided "FRAME" analysis revealed four possible open reading frames (ORFs), three in one direction and one in the opposite direction. One of them (ORF1, BlaA) encoded an activator-regulator protein whose deduced amino acid sequence was similar to that of other activator-regulator proteins in bacteria. Insertion of an 8-bp BamHI linker into the BlaA region decreased the beta-lactamase activity sharply, from 50 U to 1 U/ml. This protein (BlaA) was found to bind to the nucleotide sequence between the bla (beta-lactamase structural gene) and blaA genes. Another ORF (ORF2, BlaB) in the same orientation had a couple of amino acid sequences similar to that of pBR322 beta-lactamase. However, insertion of the 8-bp BamHI linker indicated that this ORF was functional as an activator-regulator but not as a beta-lactamase. Therefore, there were two activator-regulator proteins in the upstream region of the structural gene of the beta-lactamase. Nuclease S1 mapping predicted that transcription for the activator proteins commenced at the translational initiation codon or within a few nucleotides from the translational start site. Transcription was in the opposite direction to that of the beta-lactamase structural gene.

Compilation and analysis of DNA sequences associated with apparent streptomycete promoters

The DNA sequences associated with 139 apparent streptomycete transcriptional start sites are compiled and compared. Of these, 29 promoters appeared to belong to a group which are similar to those recognized by eubacterial RNA polymerases containing sigma 70-like subunits. The other 110 putative promoter regions contain a wide diversity of sequences; several of these promoters have obvious sequence similarities in the -10 and/or -35 regions. The apparent Shine-Dalgarno regions of 44 streptomycete genes are also examined and compared. These were found to have a wide range of degree of complementarity to the 3' end of streptomycete 16S rRNA. Eleven streptomycete genes are described and compared in which transcription and translation are proposed to be initiated from the same or nearby nucleotide. An updated consensus sequence for the E sigma 70-like promoters is proposed and a potential group of promoter sequences containing guanine-rich -35 regions also is identified.

Cloning and sequence of a gene encoding macrotetrolide antibiotic resistance from Streptomyces griseus

A gene (nonR) conferring tetranactin resistance on the macrotetrolide-sensitive strain, Streptomyces lividans TK64, was isolated during a shotgun cloning experiment, in which chromosomal fragments from Streptomyces griseus were ligated into the vector pIJ699 and then introduced by transformation into S. lividans TK64. The sequence (3326 bp) of the cloned DNA revealed three complete open reading frames (ORFs) and one incomplete ORF encoded on one strand of the DNA. The nonR gene (designated here ORFA) encodes a polypeptide of 279 amino acids (Mr 30610) and contains a putative active site motif, GXSXG, characteristic of serine proteases and esterases. A functional role for the nonR gene product may involve the inactivation of the antibiotic through hydrolysis of one or more ester linkages in the macrotetrolide ring. The deduced product of the incomplete ORFX lying adjacent to ORFA showed 27.9% sequence identity with the C-terminal region of rat mitochondrial enoyl-CoA hydratase, and is possibly a macrotetrolide biosynthetic enzyme.

Transcriptional organization and regulation of the nosiheptide resistance gene in Streptomyces actuosus

The nosiheptide resistance gene (nshR) and a putative regulatory gene (nshA) are found together on a 2326 bp BamHI-PstI DNA fragment isolated from Streptomyces actuosus ATCC 25421. The putative regulatory gene, nshA, situated upstream from the nosiheptide resistance gene in the 2326 bp DNA fragment, contains apparent DNA-binding and RNA-binding domains. Interruption of nshA in the chromosome of S. actuosus alters nosiheptide production, suggesting that nshA is involved in regulation of nosiheptide biosynthesis. Two transcription initiation sites were found upstream of nshA as demonstrated by high-resolution S1 nuclease mapping. A weak transcription start site for nshR was found which initiated transcription from the first nucleotide of the open reading frame. Although a stem-loop structure with apparent termination activity was found between nshA and nshR, readthrough of transcription between nshA and nshR was demonstrated by S1 nuclease mapping of the 3' terminus of the nshA transcript. Time-course S1 experiments of the three promoters (nshA-pl, nshA-p2, nshR-p) indicated highly regulated differential expression of the promoters. nshA-p2 is a strong, constitutive promoter whereas 30% of the total nshA-p1/p2 transcript reads through the terminator and into the nshR gene, accounting for more than half of the total steady-state nshR transcript. The implications of the regulation of nshA and nshR gene expression, as well as the expression of two other linked genes, are presented.

Nucleotide sequence and transcriptional analysis of the nosiheptide-resistance gene from Streptomyces actuosus

The nucleotide (nt) sequence of a 2326-bp BamHI-PstI DNA fragment previously isolated from Streptomyces actuosus ATCC25421 that confers resistance to the thiopeptide antibiotics, nosiheptide (Nh) and thiostrepton (Ts) upon Streptomyces lividans 1326 was determined. Two open reading frames (ORFs) were found in this 2326-bp sequence; one containing 699 nt and another of 822 nt, both reading in the same direction. The Nh-resistance gene determinant (nsh) is encoded by orf822, as determined by the 74% identity of the deduced amino acid sequence of its gene product to that of the 23S rRNA methylase encoded by the Ts-resistance gene (tsr) of Streptomyces azureus. (The respective sequences had a 72% homology.) ORF699, encoded by a gene situated upstream from orf822, contained an apparent alpha-helix-beta-turn-alpha-helix configuration which is common to DNA-binding proteins and suggests that ORF699 may be a regulatory protein. Two transcription start points (tsp) were found upstream from orf699 as demonstrated by high-resolution S1 nuclease mapping. There was also a weak tsp for the nsh gene at the first nt of ORF. Moreover, transcription was observed to read through a stem-loop structure separating the orf699 and nsh genes, as demonstrated by S1 nuclease mapping of the 3' terminus of the orf699 gene, suggesting an antitermination mechanism for regulation of nsh transcription.

Evolutionary origin of aminoglycoside phosphotransferase resistance genes

The protein sequences of seven 3'-aminoglycoside phosphotransferases falling into the six identified types and three 6'-aminoglycoside phosphotransferases were analyzed to give a rooted phylogenetic tree. This tree supports the origin of these groups of enzymes in an ancestor closely related to the actinomycetes, and that horizontal transfer of the resistance genes occurred, possibly via transposons. The implications for genetic engineering of a novel antibiotic are discussed.