Characterization and structure determination of prolyl‐tRNA synthetase from Pseudomonas aeruginosa and development as a screening platform

Pseudomonas aeruginosa is an opportunistic multi‐drug resistant pathogen implicated as a causative agent in nosocomial and community acquired bacterial infections. The gene encoding prolyl‐tRNA synthetase (ProRS) from P. aeruginosa was overexpressed in Escherichia coli and the resulting protein was characterized. ProRS was kinetically evaluated and the K_M values for interactions with ATP, proline, and tRNA were 154, 122, and 5.5 μM, respectively. The turn‐over numbers, k_cat^obs, for interactions with these substrates were calculated to be 5.5, 6.3, and 0.2 s^?1, respectively. The crystal structure of the α₂ form of P. aeruginosa ProRS was solved to 2.60 Å resolution. The amino acid sequence and X‐ray crystal structure of P. aeruginosa ProRS was analyzed and compared with homologs in which the crystal structures have been solved. The amino acids that interact with ATP and proline are well conserved in the active site region and overlay of the crystal structure with ProRS homologs conforms to a similar overall three‐dimensional structure. ProRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 890 chemical compounds, resulting in the identification of two inhibitory compounds, BT06A02 and BT07H05. This work confirms the utility of a screening system based on the functionality of ProRS from P. aeruginosa.     

Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase

It has previously been shown that the single mutation E222K in glutaminyl-tRNA synthetase (GlnRS) confers a temperature-sensitive phenotype onEscherichia coli. Here we report the isolation of a pseudorevertant of this mutation, E222K/C171G, which was subsequently employed to investigate the role of these residues in substrate discrimination. The three-dimensional structure of the tRNA^Gln: GlnRS:ATP ternary complex revealed that both E222 and C171 are close to regions of the protein involved in interactions with both the acceptor stem and the 3 end of tRNA^Gln. The potential involvement of E222 and C171 in these interactions was confirmed by the observation that GlnRS-E222K was able to mischargesupF tRNA^Tyr considerably more efficiently than the wild-type enzyme, whereas GlnRS-E222K/C171G could not. These differences in substrate specificity also extended to anticodon recognition, with the double mutant able to distinguishsupE tRNA _CUA ^Gln from tRNA ₂ ^Gln considerably more efficiently than GlnRS E222K. Furthermore, GlnRS-E222K was found to have a 15-fold higher K_m for glutamine than the wild-type enzyme, whereas the double mutant only showed a 7-fold increase. These results indicate that the C171G mutation improves both substrate discrimination and recognition at three domains in GlnRS-E222K, confirming recent proposals that there are extensive interactions between the active site and regions of the enzyme involved in tRNA binding.     

Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNA interaction

This paper focuses on several aspects of the specificity of mutants of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) and tRNA^Gln. Temperature-sensitive mutants located in glnS, the gene for GlnRS, have been described previously. The mutations responsible for the temperature-sensitive phenotype were analyzed, and pseudorevertants of these mutants isolated and characterized. The nature of these mutations is discussed in terms of their location in the three-dimensional structure of the tRNA^Gln: GlnRS complex. In order to characterize the specificity of the aminoacylation reaction, mutant tRNA^Gln species were synthesized with either a 2′-deoxy AMP or 3′-deoxy AMP as their 3′-terminal nucleotide. Subsequent assays for aminoacylation and ATP/PP_i exchange activity established the esterification of glutamine to the 2′-hydroxyl of the terminal adenosine: there is no glutaminylation of the 3′-OH group. This correlates with the classification of GlnRS as a class I aminoacyl-tRNA synthetase. Mutations in tRNA^Gln are discussed which affect the recognition of GlnRS and the current concept of glutamine identity in E coli is reviewed.     

Synthesis of hybrid bisnucleoside 5′, 5‴ — P1, P4 — tetraphosphates by aminoacyl — tRNA synthetases

Aminoacyl tRNA synthetases, by means of a back reaction, are able to synthesize certain 5, 5 - P¹, P⁴ — bisnucleoside tetraphosphates of biological importance, such as ANA. Here it is shown that HisRS and TrpRS (Bacillus stearothermophilus) and AlaRS (E. coli) also synthesize the hybrid compounds Ap₄G, Ap₄C, and Ap₄U. GInRS (E. coli) is unable to synthesize any of the above compounds.AlaRS synthesizes Ap₄U very poorly, and Ap₄C and Ap₄G almost as effectively as Ap₄A. HisRS and TrpRS synthesize Ap₄G, Ap₄U and Ap₃U quite effectively, and Ap₄C very poorly. The fact that hybrid bisnucleoside tetraphosphates can be made by the same enzymes, and at rates comparable to Ap₄A, suggests that these compounds may also occur in vivo.Abbreviations HPLC high pressure liquid chromatography - PEI polyethyleneimine - RS aminoacyl tRNA synthetase     

Crystal structure of human cytosolic aspartyl‐tRNA synthetase,a component of multi‐tRNA synthetase complex

Human cytosolic aspartyl‐tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi‐tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at a resolution of 2.25 Å. DRS is a homodimer with a dimer interface of 3750.5 Ų which comprises 16.6% of the monomeric surface area. Our structure reveals the C‐terminal end of the N‐helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N‐helix for the transfer of tRNA^Asp to elongation factor 1α. From our analyses of the crystal structure and post‐translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions.Proteins 2013; 81:1840–1846. © 2013 Wiley Periodicals, Inc.     

Relationship between the structure and function of Escherichia coli initiator tRNA

Through functional studies of mutant tRNAs, we have identified sequence and/or structural features important for specifying the many distinctive properties of E coli initiator tRNA. Many of the mutant tRNAs contain an anticodon sequence change from CAU→CUA and are now substrates for E coli glutaminyl-tRNA synthetase (GlnRS). We describe here the effect of further mutating the discriminator base 73 and nucleotide 72 at the end of the acceptor stem on: i) recognition of the mutant tRNAs by E coli GlnRS; ii) recognition by E coli methionyl-tRNA transformylase; and iii) activity of the mutant tRNAs in initiation in E coli. For GlnRS recognition, our results are, in general, consistent with interactions found in the crystal structure of the E coli GlnRS-glutamine tRNA complex. The results also support our previous conclusion that formylation of initiator tRNA is important for its function in initiation.     

Idiosyncrasy and identity in the prokaryotic Phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP

The crystal structure of Phenylalanyl‐tRNA synthetase from E. coli (EcPheRS), a class II aminoacyl‐tRNA synthetase, complexed with phenylalanine and AMP was determined at 3.05 Å resolution. EcPheRS is a (αβ)₂ heterotetramer: the αβ heterodimer of EcPheRS consists of 11 structural domains. Three of them: the N‐terminus, A1 and A2 belong to the α‐subunit and B1‐B8 domains to the β subunit. The structure of EcPheRS revealed that architecture of four helix‐bundle interface, characteristic of class IIc heterotetrameric aaRSs, is changed: each of the two long helices belonging to CLM transformed into the coil‐short helix structural fragments. The N‐terminal domain of the α‐subunit in EcPheRS forms compact triple helix domain. This observation is contradictory to the structure of the apo form of TtPheRS, where N‐terminal domain was not detected in the electron density map. Comparison of EcPheRS structure with TtPheRS has uncovered significant rearrangements of the structural domains involved in tRNA^Phe binding/translocation. As it follows from modeling experiments, to achieve a tighter fit with anticodon loop of tRNA, a shift of ～5 Å is required for C‐terminal domain B8, and of ～6 to 7 Å for the whole N terminus. EcPheRSs have emerged as an important target for the incorporation of novel amino acids into genetic code. Further progress in design of novel compounds is anticipated based on the structural data of EcPheRS.     

Discrimination between transfer-RNAs by tyrosyl-tRNA synthetase

We have constructed a model of the complex between tyrosyl-tRNA synthetase (TyrRS) from Bacillus stearothermophilus and tRNA^Tyr by successive cycles of predictions, mutagenesis of TyrRS and molecular modeling. We confront this model with data obtained independently, compare it to the crystal structures of other complexes and review recent data on the discrimination between tRNAs by TyrRS. Comparison of the crystal structures of TyrRs and GlnRS, both of which are class I synthetases, and comparison of the identity elements of tRNA^Tyr and tRNA^Gln indicate that the two synthetases bind their cognate tRNAs differently. The mutagenesis data on tRNA^Tyr confirm the model of the TyrRS:tRNA^Tyr complex on the following points. TyrRS approaches tRNA^Tyr on the side of the variable loop. The bases of the first three pairs of the acceptor stem are not recognized. The presence of the NH₂ group in position C6 and the absence of a bulky group in position C2 are important for the recognition of the discriminator base A73 by TyrRS, which is fully realized only in the transition state for the acyl transfer. The anticodon is the major identity element of tRNA^Tyr. We have set up an in vivo approach to study the effects of synthetase mutations on the discrimination between tRNAs. Using this approach, we have shown that residue Glul52 of TyrRS acts as a purely negative discriminant towards non-cognate tRNAs, by electrostatic and steric repulsions. The overproductions of the wild type TyrRSs from E coli and B stearothermophilus are toxic to E coli, due to the mischarging or the non-productive binding of tRNAs. The construction of a family of hybrids between the TyrRSs from E coli and B stearothermophilus has shown that their sequences and structures have remained locally compatible through evolution, for holding and function, in particular for the specific recognition and charging of tRNA^Tyr.     

Classical molecular dynamics simulation of seryl tRNA synthetase and threonyl tRNA synthetase bound with tRNA and aminoacyl adenylate

Lacunae of understanding exist concerning the active site organization during the charging step of the aminoacylation reaction. We present here a molecular dynamics simulation study of the dynamics of the active site organization during charging step of subclass IIa dimeric SerRS from Thermus thermophilus (^ttSerRS) bound with ^tttRNA^Ser and dimeric ThrRS from Escherichia coli (^ecThrRS) bound with ^ectRNA^Thr. The interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the ^tttRNA^Ser exhibits fast dynamics in free State, which is significantly slowed down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics (a slow diffusive mode of nanosecond time scale and fast librational mode of dynamics in picosecond time scale). The active site residues of the motif 2 loop approach the proximal bases of tRNA and adenylate by slow diffusive motion (in nanosecond time scale) and make conformational changes of the respective side chains via ultrafast librational motion to develop precise hydrogen bond geometry. Presence of bound Mg²⁺ ions around tRNA and dynamically slow bound water are other common features of both aaRSs. The presence of dynamically rigid Zinc ion coordination sphere and bipartite mode of recognition of ^ectRNA^Thr are observed.     

Genetic encoding of non‐natural amino acids in Drosophila melanogaster Schneider 2 cells

Insect cells are useful for the high‐yield production of recombinant proteins including chemokines and membrane proteins. In this study, we developed an insect cell‐based system for incorporating non‐natural amino acids into proteins at specific sites. Three types of promoter systems were constructed, and their efficiencies were compared for the expression of the prokaryotic amber suppressor tRNA^Tyr in Drosophila melanogaster Schneider 2 cells. When paired with a variant of Escherichia coli tyrosyl‐tRNA synthetase specific for 3‐iodo‐L ‐tyrosine, the suppressor tRNA transcribed from the U6 promoter most efficiently incorporated the amino acid into proteins in the cells. The transient and stable introductions of these prokaryotic molecules into the insect cells were then compared in terms of the yield of proteins containing non‐natural amino acids, and the “transient” method generated a sevenfold higher yield. By this method, 4‐azido‐L ‐phenylalanine was incorporated into human interleukin‐8 at a specific site. The yield of the azido‐containing IL‐8 was 1 μg/1 mL cell culture, and the recombinant protein was successfully labeled with a fluorescent probe by the Staudinger–Bertozzi reaction.     

The physiological target for LeuRS translational quality control is norvaline

The fidelity of protein synthesis depends on the capacity of aminoacyl‐tRNA synthetases (AARSs) to couple only cognate amino acid‐tRNA pairs. If amino acid selectivity is compromised, fidelity can be ensured by an inherent AARS editing activity that hydrolyses mischarged tRNAs. Here, we show that the editing activity of Escherichia coli leucyl‐tRNA synthetase (EcLeuRS) is not required to prevent incorrect isoleucine incorporation. Rather, as shown by kinetic, structural and in vivo approaches, the prime biological function of LeuRS editing is to prevent mis‐incorporation of the non‐standard amino acid norvaline. This conclusion follows from a reassessment of the discriminatory power of LeuRS against isoleucine and the demonstration that a LeuRS editing‐deficient E. coli strain grows normally in high concentrations of isoleucine but not under oxygen deprivation conditions when norvaline accumulates to substantial levels. Thus, AARS‐based translational quality control is a key feature for bacterial adaptive response to oxygen deprivation. The non‐essential role for editing under normal bacterial growth has important implications for the development of resistance to antimicrobial agents targeting the LeuRS editing site.     

Transfer RNA Identity Change in Anticodon Variants of E. coli tRNAPhe in Vivo

The anticodon sequence is a major recognition element for most aminoacyl-tRNA synthetases. We investigated the in vivo effects of changing the anticodon on the aminoacylation specificity in the example of E. coli tRNA^Phe. Constructing different anticodon mutants of E. coli tRNA^Phe by site-directed mutagenesis, we isolated 22 anticodon mutant tRNA^Phe; the anticodons corresponded to 16 amino acids and an opal stop codon. To examine whether the mutant tRNAs had changed their amino acid acceptor specificity in vivo, we tested the viability of E. coli strains containing these tRNA^Phe genes in a medium which permitted tRNA induction. Fourteen mutant tRNA genes did not affect host viability. However, eight mutant tRNA genes were toxic to the host and prevented growth, presumably because the anticodon mutants led to translational errors. Many mutant tRNAs which did not affect host viability were not aminoacylated in vivo. Three mutant tRNAs containing anticodon sequences corresponding to lysine (UUU), methionine (CAU) and threonine (UGU) were charged with the amino acid corresponding to their anticodon, but not with phenylalanine. These three tRNAs and tRNA^Phe are located in the same cluster in a sequence similarity dendrogram of total E. coli tRNAs. The results support the idea that such tRNAs arising from in vivo evolution are derived by anticodon change from the same ancestor tRNA.     

Fusarial wilt control and growth promotion of pigeon pea through bioactive metabolites produced by two plant growth promoting rhizobacteria

The bioactive metabolites produced by two plant growth promoting rhizobacteria strains, a Pseudomonas aeruginosa strain RRLJ 04 and a Bacillus cereus strain BS 03, which showed growth promotion and disease control in pigeon pea against Fusarium udum, were isolated and screened for their efficacy to control fusarial wilt of pigeon pea under gnotobiotic and nursery condition. Bioactive metabolites viz., BM 1 and BM 2 from RRLJ 04 and BM 3 from BS 03 also showed in vitro antibiosis against F. udum. Seeds treated with 50 μl seed^?1 of BM 1, 30 μl seed^?1 of BM 2 and 70 μl seed^?1 of BM 3 and grown in pathogen infested soil showed suppression of wilt disease besides growth enhancement. Per cent disease control was 90 % with BM 2 application as compared to 87 and 83 %, respectively in BM 1 and BM 3 after 90 days of growth. BM 2 treated plants were more resistant to the pathogen as compared to the other fractions tested. Mycelial dry weight was found to be reduced on treatment with the bioactive metabolites. Formation of chlamydospore-like structures was observed in the pathogen mycelium treated with BM 3. The analytical studies confirmed that two of these metabolites are phenazine derivatives.     

Construction and performance of heterologous polyketide‐producing K‐12‐ and B‐derived Escherichia coli

Aims: Escherichia coli has emerged as a viable heterologous host for the production of complex, polyketide natural compounds. In this study, polyketide biosynthesis was compared between different E. coli strains for the purpose of better understanding and improving heterologous production. Methods and Results: Both B and K‐12 E. coli strains were genetically modified to support heterologous polyketide biosynthesis [specifically, 6‐deoxyerythronolide B (6dEB)]. Polyketide production was analysed using a helper plasmid designed to overcome rare codon usage within E. coli. Each strain was analysed for recombinant protein production, precursor consumption, by‐product production, and 6dEB biosynthesis. Of the strains tested for biosynthesis, 6dEB production was greatest for E. coli B strains. When comparing biosynthetic improvements as a function of mRNA stability vs codon bias, increased 6dEB titres were observed when additional rare codon tRNA molecules were provided. Conclusions: Escherichia coli B strains and the use of tRNA supplementation led to improved 6dEB polyketide titres. Significance and Impact of the Study: Given the medicinal potential and growing field of polyketide heterologous biosynthesis, the current study provides insight into host‐specific genetic backgrounds and gene expression parameters aiding polyketide production through E. coli.     

Comparative hydrocarbon utilization by hydrophobic and hydrophilic variants of Pseudomonas aeruginosa

Aims: To investigate hydrocarbon degradation by hydrophobic, hydrophilic and parental strains of Pseudomonas aeruginosa. Methods and Results: Partitioning of hydrocarbon‐degrading P. aeruginosa strain in a solvent/aqueous system yielded hydrophobic and hydrophilic fractions. Exhaustive partitioning of aqueous‐phase cells yielded the hydrophilic variants (L), while sequential fractionation of the hydrophobic phase cells yielded successive fractions exhibiting increasing cell‐surface hydrophobicity (CSH). In hydrocarbon adherence assays (bacterial attachment to hydrocarbon), L had a value of 20%, which increased from 61·7% in first hydrophobic fraction (H₁) to 72·2% in the third (H₃). Crude oil degradation by L was 70%, but increased from 82% in H₁ to 93% in H₃. L variant produced most exopolysaccharides and reduced surface tension from about 73 to 49 mN m^?1. Rhamnolipid production was highest in L, but was not detected in all crude oil cultures. Conclusions: Hydrophobic subpopulations of hydrocarbon‐degrading P. aeruginosa exhibited greater hydrocarbon‐utilizing ability than hydrophilic ones, or the parental strain. Significance and Impact of the Study: Results demonstrate that a population of P. aeruginosa consists of cells with different CSH which affect hydrocarbon utilization. This potentially provides the population with the capacity to utilize different hydrophobic substrates found in petroleum. Judicious selection of such hydrophobic subpopulations can enhance hydrocarbon pollution bioremediation.     

Inhibition of Arabidopsis growth by the allelopathic compound azetidine‐2‐carboxylate is due to the low amino acid specificity of cytosolic prolyl‐tRNA synthetase

The toxicity of azetidine‐2‐carboxylic acid (A2C), a structural analogue of L‐proline, results from its incorporation into proteins due to misrecognition by prolyl‐tRNA synthetase (ProRS). The growth of Arabidopsis thaliana seedling roots is more sensitive to inhibition by A2C than is cotyledon growth. Arabidopsis contains two ProRS isozymes. AtProRS‐Org (At5g52520) is localized in chloroplasts/mitochondria, and AtProRS‐Cyt (At3g62120) is cytosolic. AtProRS‐Cyt mRNA is more highly expressed in roots than in cotyledons. Arabidopsis ProRS isoforms were expressed as His‐tagged recombinant proteins in Escherichia coli. Both enzymes were functionally active in ATP‐PPi exchange and aminoacylation assays, and showed similar K_m for L‐proline. A major difference was observed in the substrate specificity of the two enzymes. AtProRS‐Cyt showed nearly identical substrate specificity for L‐proline and A2C, but for AtProRS‐Org the specificity constant was 77.6 times higher for L‐proline than A2C, suggesting that A2C‐sensitivity may result from lower amino acid specificity of AtProRS‐Cyt. Molecular modelling and simulation results indicate that this specificity difference between the AtProRS isoforms may result from altered modes of substrate binding. Similar kinetic results were obtained with the ProRSs from Zea mays, suggesting that the difference in substrate specificity is a conserved feature of ProRS isoforms from plants that do not accumulate A2C and are sensitive to A2C toxicity. The discovery of the mode of action of A2C toxicity could lead to development of biorational weed management strategies.     

The cell wall amidase AmiB is essential for Pseudomonas aeruginosa cell division,drug resistance and viability

The physiological function of cell wall amidases has been investigated in several proteobacterial species. In all cases, they have been implicated in the cleavage of cell wall material synthesized by the cytokinetic ring. Although typically non‐essential, this activity is critical for daughter cell separation and outer membrane invagination during division. In Escherichia coli, proteins with LytM domains also participate in cell separation by stimulating amidase activity. Here, we investigated the function of amidases and LytM proteins in the opportunistic pathogen Pseudomonas aeruginosa. In agreement with studies in other organisms, ^PaAmiB and three LytM proteins were found to play crucial roles in P. aeruginosa cell separation, envelope integrity and antibiotic resistance. Importantly, the phenotype of amidase‐defective P. aeruginosa cells also differed in informative ways from the E. coli paradigm; ^PaAmiB was found to be essential for viability and the successful completion of cell constriction. Our results thus reveal a key role for amidase activity in cytokinetic ring contraction. Furthermore, we show that the essential function of ^PaAmiB can be bypassed in mutants activated for a Cpx‐like envelope stress response, suggesting that this signaling system may elicit the repair of division machinery defects in addition to general envelope damage.     

Comparative bioelectrochemical analysis of Pseudomonas aeruginosa and Escherichia coli with anaerobic consortia as anodic biocatalyst for biofuel cell application

Aims: To study the bioelectrochemical behaviour of Pseudomonas aeruginosa (MTCC 17702) and Escherichia coli (MTCC 10436) and to assess their potential to act as anodic biocatalyst with the function of anaerobic consortia for microbial (bio) fuel cell (BFC) application. Methods and Results: Three BFCs (single chamber; open‐air cathode; noncatalysed electrodes) were operated simultaneously in acidophilic microenvironments. Pseudomonas aeruginosa (BFC_P) showed higher current density (264 mA m^?2) followed by mixed culture (BFC_M; 166 mA m^?2) and E. coli (BFC_E; 147 mA m^?2). However, total operating period and substrate degradation were relatively found to be effective with mixed culture (58%; 72 h) followed by BFC_P (39%; 60 h) and BFC_E (31%; 48 h). Higher electron discharge (ED) was observed with Ps. aeruginosa while mixed culture showed the involvement of redox mediators in the ED process. Conclusions: Mixed culture showed to sustain biopotential for longer periods along with a stable ED. The presence of redox signals and high substrate degradation was also evidencing its performance compared to the pure strains studied. This supports the practical utility of mixed culture over the pure cultures for real‐field BFC applications especially while operating with wastewater. Significance and Impact of the Study: This study revealed the efficiency and viability of mixed consortia in comparison with pure strains for microbial (bio) fuel cell applications.     

Association of tRNA acceptor identity with phosphate-sugar backbone interactions observed in the crystal structure of the Escherichia coli glutaminyl-tRNA synthetase-tRNA complex

We isolated several mutants with nucleotide substitutions in alanine tRNA (tRNA^Ala) that resulted in glutamine tRNA (tRNA^Gli) acceptor identity in Escherichia coli. These substitutions were in three regions of tRNA structure not previously associated with tRNA^Gln acceptor identity. Only the phosphate-sugar backbone moieties of these nucleotides interact with the enzyme in the previously determined X-ray crystal structure of the complex between tRNA^Gln and glutaminyl-tRNA synthetase. We conclude that these sequence-dependent phosphate-sugar backbone interactions contribute to tRNA^Gln identity, and argue that the interactions help communicate enzyme recognition of the anticodon to the acceptor end of the tRNA and the catalytic center of the enzyme.