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Journal of Bacteriology, January 2008, p. 442-446, Vol. 190, No. 1
0021-9193/08/$08.00+0     doi:10.1128/JB.01429-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Two Segments in Bacterial Antizyme P22 Are Essential for Binding and Enhance Degradation of Lysine/Ornithine Decarboxylase in Selenomonas ruminantium

Yoshihiro Yamaguchi,^1, Yumiko Takatsuka,^1, and Yoshiyuki Kamio^2*

Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan,¹ Department of Human Health and Nutrition, Graduate School of Comprehensive Human Sciences, Shokei Gakuin University, Yurigaoka 4-10-1, Natori 981-1295, Japan²

Received 4 September 2007/ Accepted 18 October 2007

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In Selenomonas ruminantium, a strictly anaerobic and gram-negative bacterium, the degradation of lysine/ornithine decarboxylase (LDC/ODC) by ATP-requiring protease(s) is accelerated by the binding of P22, which is a ribosomal protein of this strain. Amino acid sequence alignment of S. ruminantium P22 with the L10 ribosomal proteins of gram-positive and -negative bacteria showed that P22 has a 5-residue K¹⁰¹NKLD¹⁰⁵ segment and an 11-residue G¹⁶⁰VIRNAVYVLD¹⁷⁰ segment, both of which are lacking in L10 in any other gram-positive and gram-negative bacteria reported. To elucidate whether the two segments are involved in P22 function, a series of mutant genes of P22 were constructed and expressed in Escherichia coli. The proteins were isolated and assayed for their function with respect to S. ruminantium LDC/ODC and mouse ODC. The results indicated that the two segments of P22 are crucial for P22 binding to both enzymes and also accelerated degradation of both decarboxylases.

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In Selenomonas ruminantium, a strictly anaerobic and gram-negative bacterium, cadaverine or putrescine covalently links to the -carboxyl group of the D-glutamic acid residue of the peptidoglycan (7-9) as an essential constituent of the peptidoglycan to maintain the integrity of the cell envelope of this strain (10). Cadaverine and putrescine are synthesized from L-lysine or L-ornithine, respectively, by lysine/ornithine decarboxylase (LDC/ODC [EC 4.1.1.18]), which comprises two identical monomeric subunits of 43 kDa (19), and transferred to the -carboxyl group of the D-glutamic acid residue of the lipid intermediate for synthesis of the peptidoglycan by a lipid intermediate:diamine transferase (11). The LDC/ODC gene was cloned, and the following findings were reported (20). (i) The amino acid sequence of LDC/ODC is 35% identical and 53 to 60% similar to those of eukaryotic ODC (EC 4.1.1.17); 26 amino acid residues, all of which are implicated either in contributing to 5'-pyridoxalphosphate- and substrate-binding domains or in formation of the homodimeric forms of eukaryotic ODCs, are conserved in LDC/ODC. (ii) LDC/ODC has a sequence homologous to that of the mouse antizyme (AZ)-binding region in mouse ODC. (iii) LDC/ODC is classified as a fold type III protein similar to eukaryotic ODC but not to bacterial ODC or other LDCs. These findings show that S. ruminantium LDC/ODC and eukaryotic ODC resemble each other in both biochemical and biophysical characteristics, except for the broad substrate specificity of S. ruminantium LDC/ODC. We previously reported that a drastic decrease of LDC activity occurs on entry into the stationary phase of cell growth, which is due to the rapid degradation of LDC/ODC (19). In the previous work, we isolated a new protein of 22 kDa (P22), which is induced in putrescine-grown S. ruminantium cells as a regulatory factor for LDC/ODC degradation by an ATP-requiring protease (21). In the preceding paper, we characterized P22 and demonstrated that P22 is a direct counterpart of eukaryotic AZ for the acceleration of degradation of both S. ruminantium LDC/ODC and mouse ODC (22). We also showed that P22 is a ribosomal protein of S. ruminantium with no similarity to mouse AZ in amino acid sequence (22). We identified a 26-residue segment, G¹⁰¹LKAAADYNVRRFTFDDSEIDKMAK¹²⁶, in LDC/ODC for its binding site to P22 (22). Here, we identify two crucial segments in P22 for its binding to LDC/ODC and mouse ODC, followed by enhanced degradation of both LDC/ODC and mouse ODC in a P22-free cytoplasmic fraction from S. ruminantium.

In the preceding paper, we showed that P22 exhibits 47% identity and 60 to 66% similarity in amino acid sequence compared to those of the bacterial ribosomal L10 proteins. However, the P22 protein could not be replaced by RplJ in enhancing LDC/ODC degradation (22). The purified Escherichia coli ribosomal protein L10 (RplJ) preparation did not bind to LDC/ODC (data not shown). To identify the segment(s) responsible for the P22 functions, a series of mutants of P22 were created as fusion proteins with a glutathione S-transferase (GST) as described below (Fig. 1).

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FIG. 1. Schematic representation of GP22 and its mutants. White and hatched boxes represent P22 and GST, respectively. "Inhibition activity" of GP22 or its mutants to S. ruminantium LDC/ODC or mouse ODC activity indicates the percentage of activity compared to that of the intact P22 preparation.

For expression of GP22, a DNA fragment containing only the p22 structural gene was amplified from pHP22 (22) by PCR using primers P22Fw (5'-TTTGGATCCATGGCAAATATGACGAAG-3') and P22Rv (5'-TTTGAATTCTTATGCGGATTCCTTCTGAGCGCGAACAGCG-3'), which are located upstream and downstream of p22, respectively. In both primers, single- and double-underlined sequences represent the BamHI and EcoRI restriction sites, respectively. The amplified fragment was digested with BamHI and EcoRI and subsequently inserted into similarly digested pGEX-4T-1 (GE Healthcare, Uppsala, Sweden) bearing an N-terminal GST sequence to construct plasmid pGP22, in which the structure gene of the fusion protein is under the control of the tac promoter. Each deletion mutant of P22 was constructed by PCR, using the oligonucleotide primers shown in Table 1 together with either primer P22Fw or P22Rv. The P22 mutant, which affects the internal region (amino acids 101 to 105), was constructed by an overlapping-extension method (4, 6), using two pairs of oligonucleotide primers, DelAFw (5'-AGCTTCATCGAAAACGAAGTGC-3') and DelARv (5'-CGTTTTCGATGAAGCTGCAGATAACC-3') and T7Fw (5'-TAATACGACTCACTGTA-3') and T7Rv (5'-GCTAGTTATTGCTCAGCGG-3'). The PCR products were digested with both BamHI and EcoRI and ligated into the plasmid pGEX-4T-1 to create fusion proteins with various deletions in the P22 portion. For isolation and purification of GP22 and its mutants, E. coli BL21 having an appropriate plasmid was grown in LB (1% Bacto tryptone, 0.5% Bacto yeast extract, 1% NaCl) medium containing ampicillin (100 µg/ml) at 37°C with shaking to an optical density of 0.6 at 660 nm; IPTG9 (isopropyl-β-D-thiogalactopyranoside) was added at a final concentration of 0.4 mM, followed by incubation with shaking for an additional 2 h at 30°C. The cells were collected by centrifugation and resuspended in phosphate-buffered saline (PBS [pH 7.3]) containing 10 mM sodium phosphate, 1.8 mM potassium phosphate, 140 mM sodium chloride, and 2.7 mM potassium chloride. The cells were disrupted in a French pressure cell, and the cell lysate was centrifuged at 200,000 x g for 1 h. The supernatant obtained was applied to a 1-ml GSTrap FF column (GE Healthcare) equilibrated with PBS. After washing the column extensively with PBS, GP22 and its mutant derivatives were eluted from the column with 50 mM Tris-HCl (pH 8.0) containing 10 mM reduced glutathione. Preparations of Gp22 and its mutant derivatives were dialyzed against 10 mM HEPES (pH 7.4) at 4°C for 12 h.

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TABLE 1. Primers used in this study

For the binding assay of GP22 and its mutants to S. ruminantium LDC/ODC or mouse ODC, His-tagged recombinant LDC/ODC and mouse ODC, which were prepared previously (22), were used. The GP22, GP22 mutant, or GST preparations (500 nM each) were mixed together with either 500 nM LDC/ODC or mouse ODC on ice for 1 h in 10 mM HEPES (pH 7.4) containing 150 mM NaCl and 0.05% Triton X-100. The samples were mixed with glutathione-Sepharose beads (20 µl of a 50% slurry) for an additional 1 h at 4°C with rolling, and then the beads were washed extensively in the same buffer. Bound proteins were eluted with PBS containing 10 mM reduced glutathione, then treated with sodium dodecyl sulfate (2%) in the presence of 2-mercaptoethanol (2%) at 100°C for 5 min and analyzed on 12.5% sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The proteins on the gel were transferred to a nitrocellulose membrane (Hybond-ECL) and then incubated with anti-His antibody (GE Healthcare). The antigen-antibody complex was detected with anti-mouse immunoglobulin G (Fc)-horseradish peroxidase conjugate (Promega, Madison, WI). Bands were visualized with ECL reagent system from GE Healthcare. The intensity of the LDC/ODC or ODC bands was quantitated using the NIH Image 1.61 program.

For inhibition assays of GP22 and its mutants to the S. ruminantium LDC activity in vitro, the purified preparations were added to a reaction mixture containing 0.1 M Tris-HCl (pH 7.5), 0.1 mM pyridoxal phosphate, and either the purified S. ruminantium LDC/ODC or purified mouse ODC preparation. The mixture was incubated for 10 min at 0°C, and then the remaining LDC/ODC or ODC activity was measured by the method described previously (7, 20).

The assay for degradation of LDC/ODC and mouse ODC by GP22 or its mutants was carried out at 37°C in a reaction mixture which contained 500 nM GP22 or its mutants, 10 mM MgCl₂, 1 mM ATP, 1 mM dithiothreitol, and S. ruminantium P22-free extract prepared by the method described previously (22). Relative amounts of the remaining LDC/ODC and mouse ODC proteins after 4 h of incubation were expressed as a percentage of the starting amount of the protein preparations. Eight series of GST-fused P22 mutants, GP22 1-140, GP22 1-110, GP22 1-100, GP22 100-179, GP22 67-179, GP22 30-179, GP22 101-105, and GP22 160-170, as well as GP22, were purified from a crude extract of E. coli having an appropriate plasmid (Fig. 1). The purified preparations were assayed for their binding and inhibition activities to S. ruminantium LDC/ODC and mouse ODC, and their accelerating activities for the degradation of both enzymes. GP22 bound to both S. ruminantium LDC/ODC and mouse ODC to the same extent as intact P22 did. Binding was accompanied with the inhibition of activities of both enzymes (Fig. 1, lanes 1 and 11). GP22 also accelerated the degradation of both enzymes in a P22-free cytoplasmic fraction from S. ruminantium to the same extent as intact P22 did. The mutants GP22 1-140, GP22 1-110, and GP22 1-100 lost the binding activity to LDC/ODC and mouse ODC and did not inhibit both enzyme activities (Fig. 1, lanes 2 to 4). In contrast, GP22 100-179, GP22 67-179, and GP22 30-179 maintained the binding activities to LDC/ODC and mouse ODC, accompanied by the inhibition of the enzyme activity and acceleration activity for degradation of the enzymes (Fig. 1, lanes 5 to 7). The data clearly showed that the C-terminal 39 residues of P22 are crucial for its binding to S. ruminantium LDC/ODC or mouse ODC and for acceleration of LDC/ODC and mouse ODC degradation and that the N-terminal 100-residue truncation of P22 does not affect its binding to S. ruminantium LDC/ODC and mouse ODC (Fig. 1, lane 5).

In the amino acid sequence in the C-terminal 79-residue portion of P22, we found two unique segments, K¹⁰¹NKLD¹⁰⁵ (segment A) and G¹⁶⁰VIRNAVYVLD¹⁷⁰ (segment B), both of which are lacking in ribosomal protein L10 from E. coli (1), Pseudomonas aeruginosa (17), Bacillus anthracis (15), Bacillus halodurans (18), Clostridium perfringens (16), and Staphylococcus aureus (5) (Fig. 2). These data suggest that these segments are crucial for binding of P22 to S. ruminantium LDC/ODC or mouse ODC. Accordingly, two mutants of P22, GP22 101-105 and GP22 160-170, were assayed for their binding to LDC/ODC or mouse ODC and the accelerating activity for the degradation of the enzymes. Neither GP22 101-105 nor GP22 160-170 had binding activity to S. ruminantium LDC/ODC and mouse ODC, which resulted in the mutants showing neither inhibition to the enzymes nor accelerating activity for the degradation of the enzymes (Fig. 1, lanes 8 and 9). These results clearly indicate that both segments, A and B, in P22 are crucial for the binding of P22 to S. ruminantium LDC/ODC and mouse ODC, followed by enhanced degradation of both enzymes. The purified recombinant GP22 and its mutants, GP22 160-170 and GP22 101-105, were analyzed by circular dichroism (CD) spectrometry, using a Jasco J-720 spectropolarimeter at room temperature in a 1-mm-path-length cell containing 50 µM protein in 5 mM potassium phosphate buffer (pH 6.5) to determine whether global structural modification were induced by the mutations. The far-UV CD spectra of the mutants were similar to that of the intact P22 preparation (data not shown). These results strongly suggest that no major conformational alterations occurred in GP22 160-170 and GP22 101-105. It is interesting to note a computer analysis of the predicted secondary and ternary structures of the intact P22 and its mutants and E. coli ribosomal protein L10 (RplJ), which was designed by Garnier et al. for secondary structures (3) and Peitsch for ternary structures (14). Intact P22 and RplJ showed similar predicted secondary and ternary structures. All of the mutants of P22 in which the N-terminal region was truncated (GP22 30-179, GP22 60-179, and GP22 100-179) (Fig. 1) showed a predicted secondary structure similar to that of intact P22. In the mutants GP22 160-170 and GP22 101-105, a striking dissimilarity of the predicted secondary structures was not observed compared to that of intact P22. The computer analysis also suggests that no major conformational alterations occurred in mutant versions of P22 that no longer bind to LDC/ODC and accelerate its degradation.

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FIG. 2. Amino acid sequence alignment of S. ruminantium P22 with the L10 ribosomal proteins of gram-negative and gram-positive bacteria and archaea. On the consensus line below the aligned sequences, identical amino acids are indicated by asterisks and conserved residues are indicated by dots. Boxes correspond to segments A and B.

Previously, we reported that the amino acid sequence of the predicted ODCs of Aquifex aeolicus (2) and Thermotoga maritima (12), which have been placed as the deepest and most slowly evolving lineages among the archaea (13), show 35% identity overall with that of S. ruminantium LDC/ODC (20). In T. maritima ODC, 22 of the 26 amino acid residues, which are essential for eukaryotic ODC activity and S. ruminantium LDC/ODC activity, and homologous amino acid sequences to that of AZ-binding region in S. ruminantium LDC/ODC or mouse ODC, are also conserved (20). On the other hand, both segments A and B in S. ruminantium P22 were found in the putative L10s from both A. aeolicus and T. maritima (Fig. 2). The data suggest the occurrence of a bacterial group which has the eukaryotic ODC and the mechanism for the degradation of ODC through L10.

In conclusion, the segments A and B in S. ruminantium P22 are crucial for P22 binding to S. ruminantium LDC/ODC, followed by the acceleration of LDC/ODC degradation by an ATP-requiring protease. Although it is not clear whether both segments directly bind to the binding site G¹⁰¹LKAAADYNVRRFTFDDSEIDKMAK¹²⁶ in LDC/ODC, LDC/ODC may change its conformation by binding to P22 to form a P22-LDC/ODC complex and the complex might be accessible to ATP-dependent protease(s).

 
* Corresponding author. Mailing address: Department of Human Health and Nutrition, Graduate School of Comprehensive Human Sciences, Shokei Gakuin University, Yurigaoka 4-10-1, Natori 981-1295, Japan. Phone and fax: 81-22-381-3347. E-mail: ykamio{at}shokei.ac.jp

Published ahead of print on 26 October 2007.

Present address: Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202.

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Journal of Bacteriology, January 2008, p. 442-446, Vol. 190, No. 1
0021-9193/08/$08.00+0     doi:10.1128/JB.01429-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

This Article Abstract Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Yamaguchi, Y. Articles by Kamio, Y. Search for Related Content PubMed PubMed Citation Articles by Yamaguchi, Y. Articles by Kamio, Y.