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MMPphg from the thermophilic Meiothermus bacteriophage MMP17 as a potential antimicrobial agent against both Gram-negative and Gram-positive bacteria
Virology Journal volume 17, Article number: 130 (2020)
New strategies are urgently needed to deal with the growing problem of multidrug-resistant bacterial pathogens. As the natural viruses against bacteria, recently, bacteriophages have received particular attention. Here, we identified and characterized a novel peptidoglycan hydrolase named MMPphg by decoding the complete genome sequence of Meiothermus bacteriophage MMP17, which was isolated in Tengchong hot spring in China and contains a circular genome of 33,172 bp in size and a GC content of 63.4%.
We cloned the MMPphg gene, overproduced and purified the phage lytic protein, which contains a highly conserved M23 metallopeptidase domain and can be activated by Mg2+ and Zn2+. MMPphg is capable of withstanding temperatures up to 70 °C, and preserved more than 80% of its activity after a 30 min treatment between 35 and 65 °C. More interestingly, by disrupting bacterial cells, MMPphg exhibits surprising antimicrobial activity against both Gram-negative and Gram-positive pathogenic bacteria, especially antibiotic-resistant strains such as Escherichia coli O157, Staphylococcus aureus and Klebsiella pneumonia.
In the current age of mounting antibiotic resistance, these results suggest the great potential of MMPphg, the gene product of bacteriophage MMP17, in combating bacterial infections and shed light on bacteriophage-based strategies to develop alternatives to conventional antibiotics for human or veterinary applications.
With the uncontrolled and inappropriate use of antibiotics, multidrug-resistant bacterial pathogens are becoming increasingly common, which is one of the major concerns in combating serious bacterial infections, presenting great challenge for clinical therapy [1, 2]. To deal with this problem of antibiotic resistance, there is an urgent need to develop alternative therapeutic methods to replace or supplement antibiotics .
Bacteriophages (also known as phages) are natural viruses of microbes that specifically infect only host bacterial cells without affecting other microflora and exist in nearly every environment [4, 5]. They were found to be natural agents against bacteria in the early part of the twentieth century . Recently, phage lytic enzymes that can destroy the cell wall of bacteria and thus cause host cell lysis have also gained new ground as alternative antibacterial agents because of their safety and high efficiency [7, 8].
Meiothermus bacteria belong to the family Thermaceae of the phylum Deinococcus-Thermus, which are moderately thermophilic strains and grow at temperatures of 35–68 °C . Phages infecting Meiothermus bacteria are particularly interesting because they are sources of valuable agents resistant to denaturation at high temperatures. So far, however, studies on Meiothermus phages and their genome are scarce. Previously, we have isolated a Meiothermus phage named MMP17 from Tengchong hot spring in Yunnan Province of China . In this study, we further decoded its complete genome sequence, and present the antimicrobial potential of MMPphg, an interesting gene product of Meiothermus phage MMP17.
The genomic DNA of phage MMP17 was extracted using the phenol-chloroform method as previously described  and sequenced in the majorbio company (Shanghai, China) by Sanger sequencing. As shown in Fig. 1a, MMP17 has a small genome of 33,172 bp in size and a GC content of 63.4%; the high GC content of phage MMP17 is consistent with its growth temperature (63 °C). Based on reads overlapping features in the assembly, MMP17 has a circular genome. To validate this, the restriction enzymes digestion of MMP17 genome DNA was performed. As expected, the NcoI and HindIII (both have a single cutting site in the genome) digestion results were in line with the circular topology of MMP17 genome (Additional file 1: Fig. S1). Similar to many other thermophilic phage genomes such as P23–77 (GenBank accession: NC_013197.1) and IN93 (GenBank accession: NC_004462.2), this circular organization contributes to genome stability and may help the survival of phage MMP17 under extreme environment. This genome project has been deposited in GenBank under the accession number MH939157.
The BLASTn analysis further indicated that, at the nucleotide level, MMP17 exhibits no significant similarity to publicly available phage genomes in the GenBank database, suggesting its novelty. The closest neighbor of MMP17 is Thermus aquaticus Y51MC23 (GenBank accession: NZ_CP010822.1), but with only 1% sequence coverage and 82.9% identity, followed by Meiothermus ruber DSM1279 (GenBank accession: CP005385.1), with 1% sequence coverage and 80.4% identity. Open reading frame (ORF) prediction and annotation of MMP17 genome were performed with ORF finder on NCBI website and further refined with BLASTp program. Through these analyses, we found 86 ORFs in the MMP17 genome but there is no tRNA or rRNA gene in it. Of the 86 protein-encoding genes, only 26.7% (23/86) were assigned predicted functions (Additional file 3: Table S1). Consistent with current taxonomic results [9, 12], whole-genome-based neighbor-joining phylogenetic analysis demonstrated that there is a close evolutionary relationship between Meiothermus phage MMP17 and representatives of Thermus phages (Fig. 1b). In the phylogenetic tree, the most intimate relatives of MMP17 are Thermus phage phiOH16 (GenBank accession: LC210520) and Thermus phage phiOH3 (GenBank accession: LC035386). However, comparisons at the protein level by employing CoreGenes 3.5  showed that only 2/86 (2.3%) proteins of phage MMP17 are homologous to those of both phiOH16 and phiOH3. Together, these results suggest that MMP17 indeed represents a novel phage.
Among all the protein-encoding genes in MMP17 genome, ORF20 with a length of 633 bp is very interesting as it encodes a M23 family metallopeptidase which is composed of 210 aa (GenBank accession: QAY18044.1). The used initiation codon and termination codon of ORF20 are ATG and TAG, respectively. For convenience, we named ORF20 as MMPphg (peptidoglycan hydrolytic gene of MMP17) in this study. Next, we carried out the conserved domain analysis of MMPphg against NCBI Conserved Domain Database (CDD v3.17, last update: 2019-04-03) . The results revealed that it contains a conserved M23 peptidase domain (NCBI domain architecture ID: 10480195) and is highly similar to peptidase of M23 family (accession: pfam01551) (Additional file 2: Fig. S2). Further, multiple sequence alignment of MMPphg and other six representatives of M23 peptidase family was performed by using Clustal Omega (version 1.2.4) with the default settings . As shown in Fig. 2, there are 18 fully conserved residues (P77, H105, G107, D109, A127, G131, V133, G144, H151, Y161, H163, G178, G185, H196, L197, H198, F199 and E200) in the amino acid sequence of MMPphg. Interestingly, we also found a fully conserved motif HLHFE at the C-terminus of MMPphg M23 domain , which might be involved in the peptidoglycan-degrading process of bacterial cell wall and deserves further study.
Next, the DNA sequence of the putative peptidoglycan hydrolase, MMPphg, was cloned by PCR amplification (Fig. 3a). To overproduce MMPphg, E. coli Rosetta cells containing the recombinant expression vector pET28a-MMPphg were cultivated at 37 °C in LB medium supplemented with Kanamycin (50 μg/mL), and lactose (1 g/L) was used for induction of T7 promoter in the vector (Fig. 3b). The purification step was performed using HisTrap affinity column according to the manufacturer’s instructions (GE Healthcare, USA), and the purity of recombinant MMPphg was confirmed by 12% SDS-PAGE (Fig. 3c). The details of PCR primers, regular gene cloning, recombinant protein expression and purification are presented in Additional file 4. Subsequently, the capability of MMPphg to digest cell wall obtained from Meiothermus sp. TG17 (GenBank accession: GU329951), the host bacterium for phage MMP17, was confirmed (Fig. 3d). It is known that members of M23 peptidase family are usually zinc-dependent metallopeptidases , to confirm this, the effects of metal ions (Mn2+, Ca2+, Mg2+, Zn2+, Fe2+ and K+) on the lytic activity of MMPphg against Meiothermus sp. TG17 cells were evaluated. It can be seen from Fig. 3e that both Zn2+ and Mg2+ showed positive effects on MMPphg lytic activity. Especially, with a concentration of 1 mM, Zn2+ can reconstitute MMPphg activity to 363.4% compared with untreated control, possibly because of increased interaction of MMPphg with the peptidoglycan backbone mediated by divalent zinc cations . Together, these results are in line with the function of MMPphg as a peptidoglycan hydrolase belonging to M23 peptidase family.
Furthermore, the thermostability of MMPphg was examined at different temperatures ranging from 10 to 75 °C. It is noteworthy that MMPphg retained more than 80% of its activity after a 30 min heat treatment between 35 and 65 °C, and still preserved more than 50% activity at 70 °C (Fig. 4), suggesting its considerable thermo-resistance to denaturation. Recently, a few lysins from thermophilic phages have been studied [19, 20]. For example, it was reported that an endolysin named PlyGVE2 from the deep-sea thermophilic Geobacillus phage GVE2 was relatively stable and active over a broad range of temperatures from 40 to 80 °C, and maintained 80% of its activity after a 30 min incubation at 55 °C [21, 22], which is similar to MMPphg. Moreover, the engineered chimeolysin of PlyGVE2, PlyGVE2CpCWB, could still preserve 57% activity after a treatment at 55 °C for 30 min . More surprisingly, two endolysins with extremely high thermostability have also been reported [24, 25]. The first one is Ph2119 endolysin from the Thermus scotoductus MAT2119 bacteriophage Ph2119, and it retains approximately 86.7% of its initial activity after 6 h of incubation at 95 °C . The other is Ts2631 endolysin from the Thermus scotoductus phage vB_Tsc2631. The Ts2631 endolysin has been demonstrated to be not only thermoresistant, maintaining 64.8% of its original activity after 2 h at 95 °C, but also highly thermodynamically stable, with a Tm of 99.8 °C . By comparison, PlyC, an antimicrobial endolysin against Streptococcus pyogenes, completely lost its activity after a 50 °C heat treatment for 30 min [20, 26]. Therefore, we strongly believe that studies and development of these thermo-resistant phage proteins would be very helpful for biotechnological applications in humans or livestock.
Next, the bacteriolytic activity of MMPphg was tested at 37 °C in a turbidity reduction assay against Salmonella ser. Paratyphi B (without treatment by permeabilization agents), which is a Gram-negative pathogenic bacterium that can contaminate many food products especially those of animal origin, and cause diseases in poultry and pork farming [27, 28]. As shown in Fig. 5a, the bacteriolytic activity of MMPphg increased proportionally to its concentration, and the curve pattern exhibited rapid kinetics of bacterial cell lysis by MMPphg. For example, with the MMPphg concentration of 7.5 μM, an OD600 reduction of 0.34 could be achieved after a 20 min incubation of MMPphg with the bacteria at 37 °C. For bacterial colony counting of Salmonella ser. Paratyphi B after MMPphg treatment on LB agar plates, the dose-dependent effect was also observed (Fig. 5b). Finally, a log10 reduction by 5.05 ± 0.46 in bacterial counts was reached upon exposure of 107 CFU/mL of Salmonella ser. Paratyphi B cells to MMPphg (7.5 μM) at 37 °C for 1 h.
Considering the potential antimicrobial applications of MMPphg, we further tested its bactericidal activity against various Gram-negative or Gram-positive bacteria (see Additional file 4 for the detailed information of bacterial strains and methods). As shown in Table 1 and Additional file 4: Table S2, MMPphg exhibits antimicrobial activity against both Gram-negative and Gram-positive bacterial pathogens, which is quite rare and very interesting as currently most reported phage lysins only have lytic activity against Gram-negative or Gram-positive strains [3, 18, 29]. Recently, Plotka et al. have demonstrated that the Ts2631 endolysin, a promising antimicrobial agent from the extremophilic Thermus scotoductus bacteriophage vB_Tsc2631 , has a unique 20-residue N-terminus with 7 positively charged amino acids. And this 20-residue N-terminus of Ts2631 endolysin mediates peptidoglycan binding and is crucial for the antibacterial activity of the protein . The same functional features were also highlighted in the case of the lytic enzyme LysC from Clostridium intestinale URNW , and it is noteworthy that the highly positively charged N-terminal tail of LysC is of vital importance for antimicrobial activity of the enzyme, which sheds light on new strategies to develop antimicrobial agents with superb activity. Accordingly, we found that the C-terminal tail of M23 peptidase domain of MMPphg (GRGDPRAPFLAHLHFEIRTR) contains six positively charged residues (underlined) as well as a highly conserved motif HLHFE. We hypothesize that this special 20-residue tail could assist penetration of MMPphg through the outer membrane of Gram-negative bacteria by electrostatic interactions with negatively charged molecules on the bacterial surface [33, 34], and hence be responsible for the observed antibacterial activity of MMPphg. Together, these clues suggest that MMPphg might be a multifunctional phage lytic protein with specific structure that is able to interfere with the outer membrane and hydrolyze bacterial peptidoglycan , which warrants future structure-based studies.
In addition, we found that MMPphg also has broad antimicrobial activity against different multidrug-resistant strains of Klebsiella pneumoniae (Table 1); these Gram-negative strains belong to the ESKAPE group pathogens and are very difficult to treat in clinic care because of their antibiotic resistance and virulence . To further investigate the detailed view of bacterial cell alteration after MMPphg treatment, scanning electron microscope (Quanta 200, FEI, Holland) analysis was performed according to the manufacturer’s instructions. As shown in Fig. 6, exogenous MMPphg treatment (5 μM) at 37 °C for 1 h could severely promote bacteria destruction of both Gram-negative (E. coli O157) and Gram-positive (S. aureus) cells, resulting in release of their intracellular components. These findings are consistent with the aforementioned activity of MMPphg and further confirmed the role of MMPphg as a phage-derived lytic enzyme with surprising antimicrobial activity against both Gram-negative and Gram-positive bacteria.
Summarily, we report here the complete genome sequence of Meiothermus phage MMP17, and by annotating it, we identified and characterized a novel peptidoglycan hydrolase, MMPphg, which has antimicrobial activity against both Gram-negative and Gram-positive bacteria, especially multidrug-resistant pathogenic strains. In the current age of mounting antibiotic resistance, these results suggest the potential applications of MMPphg as an antimicrobial agent to fight against bacterial infections and provide insights into bacteriophage-based technologies to develop novel alternatives to antibiotics for human or veterinary applications. Still, future optimization and structure-based studies are needed to further increase the efficiency of MMPphg and delineate the underlying mechanism more precisely.
Availability of data and materials
The complete genome sequence of Meiothermus bacteriophage MMP17 generated in this study was deposited in GenBank with the accession number MH939157.1 (https://www.ncbi.nlm.nih.gov/nuccore/MH939157.1/). All the other materials are available from the corresponding author on reasonable request.
Peptidoglycan hydrolytic gene of MMP17
Meiothermus Myoviridae Phage 17
Open reading frame
Sodium dodecyl sulfate polyacrylamide gel electrophoresis
Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species
Scanning electron microscope
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We thank Prof. Xueshan Xia and Dr. Yuzhu Song from the Research Center of Molecular Medicine of Yunnan Province, Kunming University of Science and Technology for kindly providing the strains of Klebsiella pneumoniae.
This study was funded by the Natural Science Foundation of China under Grant No. 31760042 to LL and Grant No. 31760338 to FW, and the Start-up Grant from Kunming University of Science and Technology for the Introduction of Talent Research Project under Grant No. KKSY201626003 to FW. These funding sources had no role in the design of the study; the collection, analysis, and interpretation of data; or in writing of this manuscript.
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Additional file 1: Fig. S1.
Patterns of restriction enzymes digestion of phage MMP17 genome DNA. a The positions of two restriction enzymes, NcoI and HindIII. Both have a single cutting site in the genome of phage MMP17. b Restriction enzymes cutting results of MMP17 genome DNA.
Additional file 2: Fig. S2.
The conserved domain analysis of MMPphg at both nucleotide and protein levels.
Additional file 3: Table S1.
Genetic features of open reading frames in the Meiothermus phage MMP17 genome. Protein sequences of the predicted ORFs of Meiothermus phage MMP17 were subjected to BLASTp program to analyze their best known matches on the NCBI website (https://blast.ncbi.nlm.nih.gov). The NCBI non-redundant database (nrdb) was used as the reference database, with the cutoff E-value set at 1E-05.
Additional file 4: Table S2 and additional methods.
Table S2. Detailed antibiotic-resistant information for the bacteria used in this study.
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Wang, F., Xiong, Y., Xiao, Y. et al. MMPphg from the thermophilic Meiothermus bacteriophage MMP17 as a potential antimicrobial agent against both Gram-negative and Gram-positive bacteria. Virol J 17, 130 (2020). https://doi.org/10.1186/s12985-020-01403-0
- Meiothermus bacteriophage
- Genome sequencing
- Antibiotic-resistant bacteria
- Antimicrobial activity