Comparison of the basic Escherichia coli antizyme 1 and antizyme 2 with the ribosomal proteins S20/L26 and L34

Impact of suppression of the SOS response on protein expression in clinical isolates of Escherichia coli under antimicrobial pressure of ciprofloxacin

Introduction/objective

Suppression of the SOS response in combination with drugs damaging DNA has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of lexA-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy consisting on suppression of the SOS response in combination with quinolones on the proteome profile of Escherichia coli clinical strains.

Materials and methods

Five clinical isolates of E. coli carrying different chromosomally- and/or plasmid-mediated quinolone resistance mechanisms with different phenotypes were selected, with E. coli ATCC 25922 as control strain. In addition, from each clinical isolate and control, a second strain was created, in which the SOS response was suppressed by deletion of the recA gene. Bacterial inocula from all 12 strains were then exposed to 1xMIC ciprofloxacin treatment (relative to the wild-type phenotype for each isogenic pair) for 1 h. Cell pellets were collected, and proteins were digested into peptides using trypsin. Protein identification and label-free quantification were done by liquid chromatography-mass spectrometry (LC-MS) in order to identify proteins that were differentially expressed upon deletion of recA in each strain. Data analysis and statistical analysis were performed using the MaxQuant and Perseus software.

Results

The proteins with the lowest expression levels were: RecA (as control), AphA, CysP, DinG, DinI, GarL, PriS, PsuG, PsuK, RpsQ, UgpB and YebG; those with the highest expression levels were: Hpf, IbpB, TufB and RpmH. Most of these expression alterations were strain-dependent and involved DNA repair processes and nucleotide, protein and carbohydrate metabolism, and transport. In isolates with suppressed SOS response, the number of underexpressed proteins was higher than overexpressed proteins.

Conclusion

High genomic and proteomic variability was observed among clinical isolates and was not associated with a specific resistant phenotype. This study provides an interesting approach to identify new potential targets to combat antimicrobial resistance.

YfiF, an unknown protein, affects initiation timing of chromosome replication in Escherichia coli

The Escherichia coli YfiF protein is functionally unknown, being predicted as a transfer RNA/ribosomal RNA (tRNA/rRNA) methyltransferase. We find that absence of the yfiF gene delays initiation of chromosome replication and the delay is reversed by ectopic expression of YfiF, whereas excess YfiF causes an early initiation. A slight decrease in both cell size and number of origin per mass is observed in ΔyfiF cells. YfiF does not genetically interact with replication proteins such as DnaA, DnaB, and DnaC. Interestingly, YfiF is associated with ribosome modulation factor (RMF), hibernation promotion factor (HPF), and the tRNA methyltransferase TrmL. Defects in replication initiation of Δrmf, Δhpf, and ΔtrmL can be rescued by overexpression of YfiF, indicating that YfiF is functionally identical to RMF, HPF, and TrmL in terms of replication initiation. Also, YfiF interacts with the rRNA methyltransferase RsmC. Moreover, the total amount of proteins and DnaA content per cell decreases or increases in the absence of YfiF or the presence of excess YfiF. These facts suggest that YfiF is a ribosomal dormancy-like factor, affecting ribosome function. Thus, we propose that YfiF is involved in the correct timing of chromosome replication by changing the DnaA content per cell as a result of affecting ribosome function.

Escherichia coli Small Proteome

Escherichia coli was one of the first species to have its genome sequenced and remains one of the best-characterized model organisms. Thus, it is perhaps surprising that recent studies have shown that a substantial number of genes have been overlooked. Genes encoding more than 140 small proteins, defined as those containing 50 or fewer amino acids, have been identified in E. coli in the past 10 years, and there is substantial evidence indicating that many more remain to be discovered. This review covers the methods that have been successful in identifying small proteins and the short open reading frames that encode them. The small proteins that have been functionally characterized to date in this model organism are also discussed. It is hoped that the review, along with the associated databases of known as well as predicted but undetected small proteins, will aid in and provide a roadmap for the continued identification and characterization of these proteins in E. coli as well as other bacteria.

Characterization of a Counterpart to Mammalian Ornithine Decarboxylase Antizyme in Prokaryotes

The degradation of mammalian ornithine decarboxylase (ODC) (EC 4.1.1.17) by 26 S proteasome, is accelerated by the ODC antizyme (AZ), a trigger protein involved in the specific degradation of eukaryotic ODC. In prokaryotes, AZ has not been found. Previously, we found that in Selenomonas ruminantium, a strictly anaerobic and Gram-negative bacterium, a drastic degradation of lysine decarboxylase (LDC; EC 4.1.1.18), which has decarboxylase activities toward both L-lysine and L-ornithine with similar K(m) values, occurs upon entry into the stationary phase of cell growth by protease together with a protein of 22 kDa (P22). Here, we show that P22 is a direct counterpart of eukaryotic AZ by the following evidence. (i) P22 synthesis is induced by putrescine but not cadaverine. (ii) P22 enhances the degradation of both mouse ODC and S. ruminantium LDC by a 26 S proteasome. (iii) S. ruminantium LDC degradation is also enhanced by mouse AZ replacing P22 in a cell-free extract from S. ruminantium. (iv) Both P22 and mouse AZ bind to S. ruminantium LDC but not to the LDC mutated in its binding site for P22 and AZ. In this report, we also show that P22 is a ribosomal protein of S. ruminantium.

Control of ornithine decarboxylase activity by polyamines and absence of antizyme in Tetrahymena

1. In cells of Tetrahymena pyriformis and thermophila, ODC activity was significantly suppressed but ODC decay was not stimulated by putrescine. 2. Free antizyme and ODC-antizyme complex were both not detected in extracts of cells of T. pyriformis treated with putrescine. 3. It was concluded that in Tetrahymena, unlike vertebrate cells, ODC is not subject to polyamine-induced destabilization mediated by antizyme.

Relationship of the expression of the S20 and L34 ribosomal proteins to polyamine biosynthesis in Escherichia coli

Polyamine biosynthesis in Escherichia coli is regulated transcriptionally and post-translationally. Antizyme and ribosomal proteins S20 and L34 participate in post-translational inhibition of the polyamine biosynthetic enzymes ornithine and arginine decarboxylase. The aim of the present study was to investigate the significance of S20 and L34 in polyamine regulation in vivo. In vivo overexpression of S20 and L34 lowered the activities of ornithine and arginine decarboxylases and decreased total polyamine production. The levels of cadaverine, a related diamine whose synthesis is not regulated by S20 and L34, did not decrease but increased. The diminished ornithine and arginine decarboxylase activities are shown to result from reversible post-translational inhibition since the enzymes could be reactivated to normal levels upon titration of the inhibitors. The effects were specific as overexpression of eight other ribosomal proteins had no influence. Overexpression of ornithine decarboxylase results in elevated polyamine production and it increases S20 and L34 levels but not those of other ribosomal proteins. Ornithine depletion decreases S20 and L34 to normal levels in the ornithine decarboxylase overproducing cells. Immunoprecipitation experiments coupled with immunoblots indicated that ornithine and arginine decarboxylases physically interact with S20 and L34. This study shows that ribosomal proteins S20 and L34 can inhibit ornithine and arginine decarboxylases and polyamine biosynthesis in vivo. It is concluded that, unlike other basic ribosomal proteins and polycationic compounds which inhibit the activities of these enzymes only in vitro, S20 and L34 are biologically relevant in the regulation of the polyamine biosynthetic pathway.

Post-translational and transcriptional regulation of polyamine biosynthesis in Escherichia coli

Ornithine and arginine decarboxylases (ODC and ADC) of Escherichia coli are inhibited post-translationally by antizyme and ribosomal proteins S20 and L34. The inhibition of either enzyme is relieved when excess of the other decarboxylase is added. Using this approach, in vitro as well as in vivo, we demonstrate that the extent of the post-translational inhibition of ODC and ADC in E. coli is at least 65 and 50%, respectively. The inhibited enzyme levels increase even further upon exposure of cells to polyamines. The post-translational mode of regulation can counteract a 4-fold increase of ODC protein in the cell. The negative transcriptional regulation of ODC and ADC expression by polyamines is mediated by transcription factors and not by direct polyamine effects on the promoters of their genes. Three proteins interacting with the ODC promoter region were found by southwestern blot analysis.

Modulation of ribonuclease P expression in Escherichia coli by polyamines

1. The presence of polyamines in the growth medium of Escherichia coli can modulate the activity of the RNA-processing enzyme, ribonucleoprotein ribonuclease P (RNase P), by altering the expression of the rnpA and rnpB genes, which encode its C5 protein and M1 RNA subunits, respectively. 2. Following growth in the presence of 1 mM spermidine the levels of C5 protein mRNA and catalytic M1 RNA were significantly elevated in the wild type E. coli K-12 strain MG1655. 3. The rnpA mRNA, together with the ribosomal protein L34 (rpmH) mRNA, was found to constitute a dicistronic rpmH-rnpA message whose half-life did not change upon Escherichia coli growth in the presence of spermidine. 4. This suggests that the spermidine effect is on the transcriptional level. 5. Increased expression of the rnpA and rnpB genes was reflected in the activity of RNase P, which almost doubled. 6. These results identify yet another component of the protein synthetic machinery which is specifically affected by polyamines.

Cyclic AMP inhibits and putrescine represses expression of the speA gene encoding biosynthetic arginine decarboxylase in Escherichia coli

The speA gene of Escherichia coli encodes biosynthetic arginine decarboxylase (ADC), the first of two enzymes in a putrescine biosynthetic pathway. The activity of ADC is negatively regulated by mechanisms requiring cyclic AMP (cAMP) and cAMP receptor protein (CRP) or putrescine. A 2.1-kb BamHI fragment containing the speA-metK intergenic region, speA promoter, and 1,389 bp of the 5' end of the speA coding sequence was used to construct transcriptional and translational speA-lacZ fusion plasmids. A single copy of either type of speA-lacZ fusion was transferred into the chromosomes of Escherichia coli KC14-1, CB806, and MC4100, using bacteriophage lambda. The speA gene in lysogenized strains remained intact and served as a control. Addition of 5 mM cAMP to lysogenic strains resulted in 10 to 37% inhibition of ADC activity, depending on the strain used. In contrast, the addition of 5 or 10 mM cAMP to these strains did not inhibit the activity of beta-galactosidase (i.e., ADC::beta-galactosidase). Addition of 10 mM putrescine to lysogenized strains resulted in 24 to 31% repression of ADC activity and 41 to 47% repression of beta-galactosidase activity. E. coli strains grown in 5 mM cAMP and 10 mM putrescine produced 46 to 61% less ADC activity and 41 to 52% less beta-galactosidase activity. cAMP (0.1 to 10 mM) did not inhibit ADC activity assayed in vitro. The effects of cAMP and putrescine on ADC activity were additive, indicating the use of independent regulatory mechanisms. These results show that cAMP acts indirectly to inhibit ADC activity and that putrescine causes repression of speA transcription.

Presence of ornithine decarboxylase antizyme in primary cultured hepatocytes of the frog Xenopus laevis

Ornithine decarboxylase (ODC; EC 4.1.1.17) could be induced in primary cultured hepatocytes of the frog, Xenopus laevis, by a hypotonic treatment. Addition of 10 mM putrescine caused a rapid decay of preinduced ODC after a lag period of 30 min. The putrescine-induced ODC decay was faster than the ODC decay in the presence of cycloheximide. Simultaneous addition of cycloheximide blocked the putrescine-induced acceleration of ODC decay, indicating an involvement of protein synthesis. Addition of putrescine to normal medium caused complete loss of ODC activity in 2 h and then ODC-inhibitory activity appeared and progressively increased. The inhibitory factor was non-dialysable and temperature-sensitive and showed a time-independent and stoichiometric pattern of ODC inhibition. On the basis of these observations the inhibitory factor was identified as ODC antizyme. These results indicated that in frog hepatocytes, like in mammalian cells and tissues, ODC is under negative feedback regulation mediated by antizyme.

Adjustment of polyamine contents in Escherichia coli

Adjustment of polyamine contents in Escherichia coli was studied with strains of Escherichia coli producing normal (DR112) and excessive amounts of ornithine decarboxylase [DR112(pODC)] or S-adenosylmethionine decarboxylase [DR112(pSAMDC)]. Although DR112(pODC) produced approximately 70 times more ornithine decarboxylase than DR112 did, the amounts of polyamines in the cells of both strains did not change significantly. The amounts of polyamines in DR112(pODC) were adjusted by excretion of excessive amounts of putrescine to the medium. When ornithine was deficient in cells, polyamine contents in DR112(pODC) were much higher than those in DR112, although polyamine contents were low in both strains. This indicates that large amounts of ornithine decarboxylase increased the utilization of ornithine for putrescine synthesis. During ornithine deficiency, strain DR112 produced 3.4 times more ornithine decarboxylase. Strain DR112(pSAMDC) produced seven times more S-adenosylmethionine decarboxylase than DR112 did. In DR112(pSAMDC) an increase (40%) in spermidine content, a decrease (35%) in putrescine content, and no significant excretion of putrescine and spermidine were observed. The amount of ornithine decarboxylase in DR112(pSAMDC) was approximately 30% less than that in DR112. In addition, S-adenosylmethionine decarboxylase activity was strongly inhibited by spermidine. A possible regulatory mechanism to maintain polyamine contents in Escherichia coli is discussed based on the results.

Regulation of ornithine decarboxylase from Mycobacterium smegmatis

The activity of ornithine decarboxylase in Mycobacterium smegmatis is regulated by a novel macromolecular inhibitor--a ribonucleic acid. Addition of polyamines to the growth medium enhances the level of this inhibitor, suggesting that the level of this negative modulator changes in response to the intracellular concentration of polyamines. Thus, while other modes of regulation may be operational, the control by polyamines at the transcriptional level leading to the generation of a specific RNA inhibitor seems to be a key element in the regulation of ornithine decarboxylase in mycobacteria.

Nonspecific inhibition of Escherichia coli ornithine decarboxylase by various ribosomal proteins: detection of a new ribosomal protein possessing strong antizyme activity

Escherichia coli ornithine decarboxylase (L-ornithine carboxy-lyase, EC 4.1.1.17) was found to be inhibited by several basic proteins. When ribosomal proteins were tested, major ribosomal proteins, with the exceptions of S1, S5, S6, S8, S10, L3, L5, L6, L7/L12, L8, L9 and L10 proteins, showed antizyme activity in addition to the recognized antizymes (S20/L26 and L34 proteins). Furthermore, it was found that L20 protein and a new ribosomal protein, tentatively named X1 protein and bound to 50 S ribosomal subunits, showed stronger antizyme activity than S20/L26 and L34 proteins. The antizyme activity of S20/L26 and L34 proteins was at most 10% of the total antizyme activity of ribosomal proteins. Several basic polypeptides also showed antizyme activity in the order polyarginine greater than protamine greater than histone greater than polylysine. Ribosomal proteins and basic polypeptides inhibited ornithine decarboxylase activity competitively. Ribosome-bound antizymes were inactive as antizymes, and antizyme inhibition of ornithine decarboxylase was eliminated by ribosomes. When E. coli extracts were separated into ribosomes and 100,000 X g supernatant fraction, no significant antizyme activity was observed in the supernatant fraction. Results of these in vitro experiments infer that basic antizymes may not function as inhibitors of ornithine decarboxylase in vivo.

Non-competitive inhibition of ornithine decarboxylase by a phosphopeptide and phosphoamino acids

In Tetrahymena pyriformis the cytosolic ornithine decarboxylase (L-ornithine carboxy-lyase, EC 4.1.1.17) activity is considerably inhibited by the presence of polyamines in the growth medium, while the nuclear ornithine decarboxylase is only slightly affected. Experimental evidence suggests that the presence of putrescine and/or spermidine elicits the appearance of non-competitive inhibitors of ornithine decarboxylase. One of the inhibitors has a molecular weight of 25,000 and properties of antizyme. In addition, two other low molecular weight inhibitors are extracted, one which is a phosphoserine oligopeptide, and the other which is phosphotyrosine. All inhibit non-competitively the homologous and heterologous (Escherichia coli and rat liver) ornithine decarboxylases. Similarly, non-competitive inhibition was obtained when the commercially available phosphoamino acids were tested against the already mentioned ornithine decarboxylases.

Effect of N-alkyl and C-alkylputrescines on the activity of ornithine decarboxylase from rat liver and E. coli

N-Methyl-, N-ethyl-, N-propyl-, N-butyl-, N,N-dimethyl- and N,N'-dimethylputrescines were assayed as inhibitors of ornithine decarboxylase (EC 4.1.1.17) from rat liver and from Escherichia coli. They were found to be poor inhibitors, with the exception of N-propylputrescine and N,N-dimethylputrescine, which were inhibitory at 25 mM. A homologous series of 1-alkylputrescines ranging from 1-methylputrescine (1,4-diaminopentane) to 1-heptylputrescine (1,4-diaminoundecane) was assayed for effect on the activity of ornithine decarboxylase from the same sources. 1-Methylputrescine (5 mM) inhibited the mammalian enzyme, while the higher homologues showed significantly less inhibitory activity. When assayed on the bacterial enzyme, 1-methylputrescine (5 mM) was not inhibitory, while the higher homologues showed inhibitory effects. At higher concentrations, 1-methylputrescine and 1-heptylputrescine were the best inhibitors of these series of rat liver ornithine decarboxylase. When 1-methylputrescine, 2-methylputrescine, 1,2-dimethylputrescine, 1,3-dimethylputrescine and 1,4-dimethylputrescine were assayed as inhibitors of the decarboxylase, 2-methylputrescine was found to be the best inhibitor of the rat liver enzyme, while 1,3-dimethylputrescine was the best inhibitor of the bacterial enzyme. 1,4-Dimethylputrescine (2,5-diaminohexane) did not inhibit the enzyme from either source. Both, 2-methylputrescine and 1-methylputrescine, as well as the 1,2- and 1,3-dimethylputrescines were competitive inhibitors of the enzyme, and a Ki of 1 mM was obtained for 2-methylputrescine when the rat liver decarboxylase was used. N-Methyl, 1-methyl and 2-methylputrescines were found to inhibit in vivo the activity of rat liver ornithine decarboxylase which had been previously induced by thioacetamide treatment. 2-Methylputrescine (50 mumol/100 g body weight) was found to be the best in vivo inhibitor (93% inhibition), while putrescine under similar conditions inhibited 56% of the enzymatic activity.

Regulation of polyamine biosynthesis by antizyme and some recent developments relating the induction of polyamine biosynthesis to cell growth. Review

This review considers the role of antizyme, of amino acids and of protein synthesis in the regulation of polyamine biosynthesis. The ornithine decarboxylase of eukaryotic cells and of Escherichia coli can be non-competitively inhibited by proteins, termed antizymes, which are induced by di- and poly- amines. Some antizymes have been purified to homogeneity and have been shown to be structurally unique to the cell of origin. Yet, the E. coli antizyme and the rat liver antizyme cross react and inhibit each other's biosynthetic decarboxylases. These results indicate that aspects of the control of polyamine biosynthesis have been highly conserved throughout evolution. Evidence for the physiological role of the antizyme in mammalian cells rests upon its identification in normal uninduced cells, upon the inverse relationship that exists between antizyme and ornithine decarboxylase as well as upon the existence of the complex of ornithine decarboxylase and antizyme in vivo. Furthermore, the antizyme has been shown to be highly specific; its Keq for ornithine decarboxylase is 1.4 X 10(11) M-1. In addition, mammalian cells contain an anti-antizyme, a protein that specifically binds to the antizyme of an ornithine decarboxylase-antizyme complex and liberates free ornithine decarboxylase from the complex. In E. coli, in which polyamine biosynthesis is mediated both by ornithine decarboxylase and by arginine decarboxylase, three proteins (one acidic and two basic) have been purified, each of which inhibits both these enzymes. They do not inhibit the biodegradative ornithine and arginine decarboxylases nor lysine decarboxylase. The two basic inhibitors have been shown to correspond to the ribosomal proteins S20/L26 and L34, respectively. The relationship of the acidic antizyme to other known E. coli proteins remains to be determined. In mammalian cells, ornithine decarboxylase can be induced by a broad spectrum of compounds. These range from hormones and growth factors to natural amino acids such as asparagine and to non-metabolizable amino acid analogues such as alpha-amino-isobutyric acid. The amino acids that induce ornithine decarboxylase as well as those that promote polyamine uptake utilize the sodium dependent A and N transport systems. Consequently, they act in concert and increase intracellular polyamine levels by both mechanisms. The induction of ornithine decarboxylase by growth factors, such as NGF, EGF, and PDGF as well as by insulin requires the presence of these same amino acids and does not occur in their absence. However, the inducing amino acid need not be incorporated into protein nor covalently modified.(ABSTRACT TRUNCATED AT 400 WORDS)