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1.
Microbiol Spectr ; 12(5): e0353423, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38534149

ABSTRACT

To address intracellular mycobacterial infections, we developed a cocktail of four enzymes that catalytically attack three layers of the mycobacterial envelope. This cocktail is delivered to macrophages, through a targeted liposome presented here as ENTX_001. Endolytix Cocktail 1 (EC1) leverages mycobacteriophage lysin enzymes LysA and LysB, while also including α-amylase and isoamylase for degradation of the mycobacterial envelope from outside of the cell. The LysA family of proteins from mycobacteriophages has been shown to cleave the peptidoglycan layer, whereas LysB is an esterase that hydrolyzes the linkage between arabinogalactan and mycolic acids of the mycomembrane. The challenge of gaining access to the substrates of LysA and LysB provided exogenously was addressed by adding amylase enzymes that degrade the extracellular capsule shown to be present in Mycobacterium tuberculosis. This enzybiotic approach avoids antimicrobial resistance, specific receptor-mediated binding, and intracellular DNA surveillance pathways that limit many bacteriophage applications. We show this cocktail of enzymes is bactericidal in vitro against both rapid- and slow-growing nontuberculous mycobacteria (NTM) as well as M. tuberculosis strains. The EC1 cocktail shows superior killing activity when compared to previously characterized LysB alone. EC1 is also powerfully synergistic with standard-of-care antibiotics. In addition to in vitro killing of NTM, ENTX_001 demonstrates the rescue of infected macrophages from necrotic death by Mycobacteroides abscessus and Mycobacterium avium. Here, we demonstrate shredding of mycobacterial cells by EC1 into cellular debris as a mechanism of bactericide.IMPORTANCEThe world needs entirely new forms of antibiotics as resistance to chemical antibiotics is a critical problem facing society. We addressed this need by developing a targeted enzyme therapy for a broad range of species and strains within mycobacteria and highly related genera including nontuberculous mycobacteria such as Mycobacteroides abscessus, Mycobacterium avium, Mycobacterium intracellulare, as well as Mycobacterium tuberculosis. One advantage of this approach is the ability to drive our lytic enzymes through encapsulation into macrophage-targeted liposomes resulting in attack of mycobacteria in the cells that harbor them where they hide from the adaptive immune system and grow. Furthermore, this approach shreds mycobacteria independent of cell physiology as the drug targets the mycobacterial envelope while sidestepping the host range limitations observed with phage therapy and resistance to chemical antibiotics.


Subject(s)
Galactans , Macrophages , Mycobacteriophages , Mycobacterium tuberculosis , Nontuberculous Mycobacteria , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Mycobacteriophages/genetics , Mycobacteriophages/enzymology , Macrophages/microbiology , Macrophages/virology , Humans , Nontuberculous Mycobacteria/drug effects , Liposomes/chemistry , Anti-Bacterial Agents/pharmacology , Peptidoglycan/metabolism , Microbial Sensitivity Tests , Endopeptidases/metabolism , Endopeptidases/pharmacology , Endopeptidases/genetics
2.
Int J Mol Sci ; 21(9)2020 Apr 30.
Article in English | MEDLINE | ID: mdl-32365915

ABSTRACT

Mycobacteriophages possess different sets of lytic enzymes for disruption of the complex cell envelope of the mycobacteria host cells and release of the viral progeny. Lysin B (LysB) enzymes are mycolylarabinogalactan esterases that cleave the ester bond between the arabinogalactan and mycolic acids in the mycolylarabinogalactan-peptidoglycan (mAGP) complex in the cell envelope of mycobacteria. In the present study, four LysB enzymes were produced recombinantly and characterized with respect to their enzymatic and antibacterial activities. Examination of the kinetic parameters for the hydrolysis of para-nitrophenyl ester substrates, shows LysB-His6 enzymes to be active against a range of substrates (C4-C16), with a catalytic preference towards p-nitrophenyl laurate (C12). With p-nitrophenyl butyrate as substrate, LysB-His6 enzymes showed highest activity at 37 °C. LysB-His6 enzymes also hydrolyzed different Tween substrates with highest activity against Tween 20 and 80. Metal ions like Ca2+ and Mn2+ enhanced the enzymatic activity of LysB-His6 enzymes, while transition metal ions like Zn2+ and Cu2+ inhibited the enzymatic activity. The mycolylarabinogalactan esterase activity of LysB-His6 enzymes against mAGP complex was confirmed by LC-MS. LysB-His6 enzymes showed marginal antibacterial activity when tested alone against Mycobacterium smegmatis, however a synergetic activity was noticed when combined with outer membrane permealizers. These results confirm that LysB enzymes are lipolytic enzymes with potential application as antimycobacterials.


Subject(s)
Esterases/metabolism , Mycobacteriophages/enzymology , Viral Proteins/metabolism , Copper/metabolism , Esterases/chemistry , Galactans/metabolism , Manganese/metabolism , Peptidoglycan/metabolism , Viral Proteins/chemistry , Zinc/metabolism
3.
World J Microbiol Biotechnol ; 36(6): 83, 2020 May 28.
Article in English | MEDLINE | ID: mdl-32468233

ABSTRACT

Bacteriophage-derived endolysin enzymes play a critical role in disintegration of the host bacterial cell wall and hence have gained considerable attention as possible therapeutics for the treatment of drug-resistant infections. Endolysins can target both dividing and non-dividing cells and given the vital role peptidoglycan plays in bacterial survival, bacteria are less likely to modify it even if continuously exposed to lysins. Hence, probability of bacteria developing resistance to lysins appear bleak. Endolysins from mycobacteriophages offer great potential as alternative therapeutics for the drug-resistant TB. However, considering that a large number of mycobacteriophages have been discovered so far, the information on endolysins come from only a few mycobacteriophages. In this study, we report the structural and functional characterization of endolysins (LysinA and LysinB) encoded by mycobacteriophage PDRPxv which belongs to B1 sub cluster. On in silico analysis, we found LysinA to be a modular protein having peptidase domain at the N-terminal (104 aa), a central amidase domain (174 aa) and the peptidoglycan binding domain (62 aa) at the C-terminal. Additionally, 'H-X-H', which is a conserved motif and characteristic of peptidase domains, and the conserved residues His-His-Asp, which are characteristic of amidase domain were also observed. In LysinB enzyme, a single α/ß hydrolase domain having a catalytic triad (Ser-Asp-His) and G-X-S-X-G motif, which are characteristic of the serine esterase enzymes were predicted to be present. Both the enzymes were purified as recombinant proteins and their antimycobacterial activity against M. smegmatis was demonstrated through turbidimetric experiments and biochemical assay. Interesting observation in this study is the secretory nature of LysinA evident by its periplasmic expression in E.coli, which might explain the ability of PDRPxv to lyse the bacterial host in the absence of transmembrane Holin protein.


Subject(s)
Endopeptidases , Mycobacteriophages/enzymology , Anti-Bacterial Agents/biosynthesis , Computer Simulation , Endopeptidases/biosynthesis , Endopeptidases/chemistry , Endopeptidases/isolation & purification , Endopeptidases/pharmacology , Escherichia coli/metabolism , Mycobacterium smegmatis/drug effects , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Viral Proteins/biosynthesis , Viral Proteins/chemistry , Viral Proteins/isolation & purification , Viral Proteins/pharmacology
4.
PLoS Negl Trop Dis ; 13(8): e0007113, 2019 08.
Article in English | MEDLINE | ID: mdl-31425525

ABSTRACT

Buruli Ulcer (BU) is a cutaneous disease caused by Mycobacterium ulcerans. The pathogenesis of this disease is closely related to the secretion of the toxin mycolactone that induces extensive destruction of the skin and soft tissues. Currently, there are no effective measures to prevent the disease and, despite availability of antibiotherapy and surgical treatments, these therapeutic options are often associated with severe side effects. Therefore, it is important to develop alternative strategies for the treatment of BU. Endolysins (lysins) are phage encoded enzymes that degrade peptidoglycan of bacterial cell walls. Over the past years, lysins have been emerging as alternative antimicrobial agents against bacterial infections. However, mycobacteria have an unusual outer membrane composed of mycolylarabinogalactan-peptidoglycan. To overcome this complex barrier, some mycobacteriophages encode a lipolytic enzyme, Lysin B (LysB). In this study, we demonstrate for the first time that recombinant LysB displays lytic activity against M. ulcerans isolates. Moreover, using a mouse model of M. ulcerans footpad infection, we show that subcutaneous treatment with LysB prevented further bacterial proliferation, associated with IFN-γ and TNF production in the draining lymph node. These findings highlight the potential use of lysins as a novel therapeutic approach against this neglected tropical disease.


Subject(s)
Buruli Ulcer/drug therapy , Endopeptidases/administration & dosage , Mycobacteriophages/enzymology , Mycobacterium ulcerans/drug effects , Animals , Bacteriolysis , Buruli Ulcer/pathology , Disease Models, Animal , Endopeptidases/pharmacology , Female , Interferon-gamma/analysis , Lymph Nodes/immunology , Mice, Inbred BALB C , Mycobacterium ulcerans/virology , Recombinant Proteins/administration & dosage , Recombinant Proteins/pharmacology , Treatment Outcome , Tumor Necrosis Factor-alpha/analysis
5.
Biomolecules ; 10(1)2019 12 27.
Article in English | MEDLINE | ID: mdl-31892223

ABSTRACT

Mycobacteriophage endolysins have emerged as a potential alternative to the current antimycobacterial agents. This study focuses on mycolylarabinogalactan hydrolase (LysB) enzymes of the α/ß-hydrolase family, which disrupt the unique mycolic acid layer of mycobacterium cell wall. Multiple sequence alignment and structural analysis studies showed LysB-D29, the only enzyme with a solved three-dimensional structure, to share several common features with esterases (lacking lid domain) and lipases (acting on long chain lipids). Sequence and structural comparisons of 30 LysB homology models showed great variation in domain organizations and total protein length with major differences in the loop-5 motif harboring the catalytic histidine residue. Docking of different p-nitrophenyl ligands (C4-C18) to LysB-3D models revealed that the differences in length and residues of loop-5 contributed towards wide diversity of active site conformations (long tunnels, deep and superficial funnels, shallow bowls, and a narrow buried cave) resembling that of lipases, cutinases, and esterases. A set of seven LysB enzymes were recombinantly produced; their activity against p-nitrophenyl esters could be related to their active site conformation and acyl binding site. LysB-D29 (long tunnel) showed the highest activity with long chain p-nitrophenyl palmitate followed by LysB-Omega (shallow bowl) and LysB-Saal (deep funnel).


Subject(s)
Esterases/chemistry , Esterases/metabolism , Galactans/metabolism , Mycobacteriophages/enzymology , Amino Acid Sequence , Esterases/genetics , Models, Molecular , Molecular Docking Simulation , Protein Conformation , Sequence Alignment
6.
Viruses ; 10(8)2018 08 14.
Article in English | MEDLINE | ID: mdl-30110929

ABSTRACT

Mycobacteriophages are viruses that specifically infect mycobacteria, which ultimately culminate in host cell death. Dedicated enzymes targeting the complex mycobacterial cell envelope arrangement have been identified in mycobacteriophage genomes, thus being potential candidates as antibacterial agents. These comprise lipolytic enzymes that target the mycolic acid-containing outer membrane and peptidoglycan hydrolases responsive to the atypical mycobacterial peptidoglycan layer. In the recent years, a remarkable progress has been made, particularly on the comprehension of the mechanisms of bacteriophage lysis proteins activity and regulation. Notwithstanding, information about mycobacteriophages lysis strategies is limited and is mainly represented by the studies performed with mycobacteriophage Ms6. Since mycobacteriophages target a specific group of bacteria, which include Mycobacterium tuberculosis responsible for one of the leading causes of death worldwide, exploitation of the use of these lytic enzymes demands a special attention, as they may be an alternative to tackle multidrug resistant tuberculosis. This review focuses on the current knowledge of the function of lysis proteins encoded by mycobacteriophages and their potential applications, which may contribute to increasing the effectiveness of antimycobacterial therapy.


Subject(s)
Cell Membrane/chemistry , Cell Wall/chemistry , Lysogeny , Mycobacteriophages/genetics , Mycobacterium tuberculosis/virology , Viral Proteins/genetics , Cell Membrane/metabolism , Cell Wall/metabolism , Endopeptidases/chemistry , Endopeptidases/genetics , Endopeptidases/metabolism , Gene Expression , Hydrolysis , Lipase/chemistry , Lipase/genetics , Lipase/metabolism , Mycobacteriophages/enzymology , Mycobacterium tuberculosis/chemistry , Mycobacterium tuberculosis/metabolism , N-Acetylmuramoyl-L-alanine Amidase/chemistry , N-Acetylmuramoyl-L-alanine Amidase/genetics , N-Acetylmuramoyl-L-alanine Amidase/metabolism , Peptidoglycan/chemistry , Peptidoglycan/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism
7.
Acta Crystallogr F Struct Biol Commun ; 74(Pt 3): 161-165, 2018 03 01.
Article in English | MEDLINE | ID: mdl-29497020

ABSTRACT

Tuberculosis (TB) continues to remain a leading cause of death globally. Of particular concern is the emergence and rise in incidence of multidrug-resistant and extremely drug-resistant cases of TB. To counter this threat, it is important to explore alternative therapies, including phage therapy. Phage BTCU-1 specifically infects Mycobacterium spp. and kills the majority of them. Intriguingly, many proteins from the phage do not share high amino-acid sequence identity with proteins from species other than phages. Here, the expression, purification and crystallization of one such protein, a putative phosphoribosyl transferase from phage BTCU-1, is reported. The crystals belonged to space group C2221, with unit-cell parameters a = 59.71, b = 64.42, c = 65.32 Å, α = ß = γ = 90°. The crystals diffracted X-rays to 2.2 Šresolution.


Subject(s)
Mycobacteriophages/enzymology , Pentosyltransferases/chemistry , Pentosyltransferases/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism , Amino Acid Sequence , Catalytic Domain , Crystallization , Crystallography, X-Ray , Models, Molecular , Pentosyltransferases/isolation & purification , Protein Conformation , Sequence Homology , Viral Proteins/isolation & purification
8.
Viruses ; 9(11)2017 11 17.
Article in English | MEDLINE | ID: mdl-29149017

ABSTRACT

All dsDNA phages encode two proteins involved in host lysis, an endolysin and a holin that target the peptidoglycan and cytoplasmic membrane, respectively. Bacteriophages that infect Gram-negative bacteria encode additional proteins, the spanins, involved in disruption of the outer membrane. Recently, a gene located in the lytic cassette was identified in the genomes of mycobacteriophages, which encodes a protein (LysB) with mycolyl-arabinogalactan esterase activity. Taking in consideration the complex mycobacterial cell envelope that mycobacteriophages encounter during their life cycle, it is valuable to evaluate the role of these proteins in lysis. In the present work, we constructed an Ms6 mutant defective on lysB and showed that Ms6 LysB has an important role in lysis. In the absence of LysB, lysis still occurs but the newly synthesized phage particles are deficiently released to the environment. Using cryo-electron microscopy and tomography to register the changes in the lysis phenotype, we show that at 150 min post-adsorption, mycobacteria cells are incompletely lysed and phage particles are retained inside the cell, while cells infected with Ms6wt are completely lysed. Our results confirm that Ms6 LysB is necessary for an efficient lysis of Mycobacterium smegmatis, acting, similarly to spanins, in the third step of the lysis process.


Subject(s)
Esterases/metabolism , Mycobacteriophages/genetics , Mycobacteriophages/physiology , Mycobacterium/virology , Cryoelectron Microscopy , Endopeptidases , Esterases/genetics , Galactans , Hydrolysis , Mycobacteriophages/enzymology , Mycobacteriophages/ultrastructure , Mycobacterium/metabolism , Mycobacterium/ultrastructure , Tomography , Viral Proteins/genetics
9.
J Mol Model ; 22(8): 180, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27411553

ABSTRACT

Mycobacteriophages produce lysins that break down the host cell wall at the end of lytic cycle to release their progenies. The ability to lyse mycobacterial cells makes the lysins significant. Mycobacteriophage Che12 is the first reported temperate phage capable of infecting and lysogenising Mycobacterium tuberculosis. Gp11 of Che12 was found to have Chitinase domain that serves as endolysin (lysin A) for Che12. Structure of gp11 was modeled and evaluated using Ramachandran plot in which 98 % of the residues are in the favored and allowed regions. Che12 lysin A was predicted to act on NAG-NAM-NAG molecules in the peptidoglycan of cell wall. The tautomers of NAG-NAM-NAG molecule were generated and docked with lysin A. The stability and binding affinity of lysin A - NAG-NAM-NAG tautomers were studied using molecular dynamics simulations.


Subject(s)
Molecular Docking Simulation , Molecular Dynamics Simulation , Mycobacteriophages/enzymology , Mycobacterium tuberculosis/virology , Peptidoglycan/chemistry , Viral Proteins/chemistry , Structural Homology, Protein
10.
Appl Microbiol Biotechnol ; 100(18): 8169-77, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27345061

ABSTRACT

The soaring incidences of infection by antimicrobial resistant (AR) pathogens and shortage of effective antibiotics with new mechanisms of action have renewed interest in phage therapy. This scenario is exemplified by resistant tuberculosis (TB), caused by resistant Mycobacterium tuberculosis. Mycobacteriophage SWU1 A321_gp67 encodes a putative GTPase-activating protein. Mycobacterium smegmatis with gp67 overexpression showed changed colony formation and biofilm morphology and supports the efficacy of streptomycin and capreomycin against Mycobacterium. gp67 down-regulated the transcription of genes involved in cell wall and biofilm development. To our knowledge, this is the first report to show that phage protein in addition to lysin or recombination components can synergize with existing antibiotics. Phage components might represent a promising new clue for better antibiotic potentiators.


Subject(s)
Antitubercular Agents/pharmacology , Capreomycin/pharmacology , GTP Phosphohydrolase Activators/metabolism , GTPase-Activating Proteins/metabolism , Mycobacteriophages/enzymology , Mycobacterium smegmatis/drug effects , Streptomycin/pharmacology , GTPase-Activating Proteins/genetics , Mycobacteriophages/genetics , Mycobacterium smegmatis/genetics , Mycobacterium smegmatis/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
11.
J Bacteriol ; 198(2): 352-62, 2016 01 15.
Article in English | MEDLINE | ID: mdl-26527643

ABSTRACT

UNLABELLED: Mycobacterium species such as M. smegmatis and M. tuberculosis encode at least two translesion synthesis (TLS) polymerases, DinB1 and DinB2, respectively. Although predicted to be linked to DNA repair, their role in vivo remains enigmatic. M. smegmatis mc(2)155, a strain commonly used to investigate mycobacterial genetics, has two copies of dinB2, the gene that codes for DinB2, by virtue of a 56-kb chromosomal duplication. Expression of a mycobacteriophage D29 gene (gene 50) encoding a class II ribonucleotide reductase in M. smegmatis ΔDRKIN, a strain derived from mc(2)155 in which one copy of the duplication is lost, resulted in DNA replication defects and growth inhibition. The inhibitory effect could be linked to the deficiency of dTTP that resulted under these circumstances. The selective inhibition observed in the ΔDRKIN strain was found to be due solely to a reduced dosage of dinB2 in this strain. Mycobacterium bovis, which is closely related to M. tuberculosis, the tuberculosis pathogen, was found to be highly susceptible to gene 50 overexpression. Incidentally, these slow-growing pathogens harbor one copy of dinB2. The results indicate that the induction of a dTTP-limiting state can lead to growth inhibition in mycobacteria, with the effect being maximum in cells deficient in DinB2. IMPORTANCE: Mycobacterium species, such as M. tuberculosis, the tuberculosis pathogen, are known to encode several Y family DNA polymerases, one of which is DinB2, an ortholog of the DNA repair-related protein DinP of Escherichia coli. Although this protein has been biochemically characterized previously and found to be capable of translesion synthesis in vitro, its in vivo function remains unknown. Using a novel method to induce dTTP deficiency in mycobacteria, we demonstrate that DinB2 can aid mycobacterial survival under such conditions. Apart from unraveling a specific role for the mycobacterial Y family DNA polymerase DinB2 for the first time, this study also paves the way for the development of drugs that can kill mycobacteria by inducing a dTTP-deficient state.


Subject(s)
Bacterial Proteins/metabolism , Mycobacteriophages/enzymology , Mycobacterium bovis/metabolism , Mycobacterium smegmatis/metabolism , Ribonucleotide Reductases/metabolism , Thymine Nucleotides/metabolism , Bacterial Proteins/genetics , Cloning, Molecular , Gene Expression Regulation, Bacterial/physiology , Mycobacteriophages/genetics , Mycobacterium bovis/genetics , Mycobacterium smegmatis/genetics , Ribonucleotide Reductases/genetics
12.
PLoS One ; 10(8): e0134762, 2015.
Article in English | MEDLINE | ID: mdl-26237048

ABSTRACT

The bacterial replicative helicases known as DnaB are considered to be members of the RecA superfamily. All members of this superfamily, including DnaB, have a conserved C- terminal domain, known as the RecA core. We unearthed a series of mycobacteriophage encoded proteins in which the RecA core domain alone was present. These proteins were phylogenetically related to each other and formed a distinct clade within the RecA superfamily. A mycobacteriophage encoded protein, Wildcat Gp80 that roots deep in the DnaB family, was found to possess a core domain having significant sequence homology (Expect value < 10-5) with members of this novel cluster. This indicated that Wildcat Gp80, and by extrapolation, other members of the DnaB helicase family, may have evolved from a single domain RecA core polypeptide belonging to this novel group. Biochemical investigations confirmed that Wildcat Gp80 was a helicase. Surprisingly, our investigations also revealed that a thioredoxin tagged truncated version of the protein in which the N-terminal sequences were removed was fully capable of supporting helicase activity, although its ATP dependence properties were different. DnaB helicase activity is thus, primarily a function of the RecA core although additional N-terminal sequences may be necessary for fine tuning its activity and stability. Based on sequence comparison and biochemical studies we propose that DnaB helicases may have evolved from single domain RecA core proteins having helicase activities of their own, through the incorporation of additional N-terminal sequences.


Subject(s)
DnaB Helicases/genetics , Evolution, Molecular , Mycobacteriophages/enzymology , Viral Proteins/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphate/metabolism , Cloning, Molecular , DNA, Single-Stranded/metabolism , DnaB Helicases/chemistry , DnaB Helicases/classification , DnaB Helicases/metabolism , Hydrolysis , Mycobacteriophages/genetics , Oligodeoxyribonucleotides/metabolism , Phylogeny , Protein Binding , Protein Structure, Tertiary , Rec A Recombinases/classification , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Structure-Activity Relationship , Substrate Specificity , Thioredoxins , Viral Proteins/chemistry , Viral Proteins/metabolism
13.
FEMS Microbiol Lett ; 361(1): 84-93, 2014 12.
Article in English | MEDLINE | ID: mdl-25307893

ABSTRACT

Mycobacteriophage D29 encodes a protein Gp66 which has been predicted to be a calcineurin family phosphoesterase. Phylogenetically Gp66 and related proteins mostly derived from mycobacteriophages form a distinct clade within this family. Interestingly, the presence of gene 66 orthologs can be traced to bacteria of diverse phylogenetic lineages such as Aquifex aeolicus, a deep branching eubacteria and Methanococcus jannaschii, an archaebacteria. The promiscuous nature of gene 66 suggests that it may have been transferred across genus barriers by horizontal gene transfer mechanisms. The biological function of members of this novel clade comprising mostly the mycobacteriophage phosphoesterases have not been elucidated so far. In this investigation, it has been demonstrated for the first time that Gp66, a member of this novel family, is a 2', 3' cyclic phosphodiesterase. The gene is expressed during phage infection and the net result is negative regulation of bacteriophage as well as bacterial growth.


Subject(s)
Calcineurin/metabolism , Mycobacteriophages/enzymology , Mycobacterium smegmatis/virology , Phosphoric Diester Hydrolases/metabolism , Phosphoric Monoester Hydrolases/metabolism , Amino Acid Sequence , Calcineurin/genetics , Mutation , Mycobacteriophages/genetics , Mycobacteriophages/growth & development , Mycobacterium smegmatis/metabolism , Phosphoric Diester Hydrolases/genetics , Phosphoric Monoester Hydrolases/genetics , Phylogeny , Recombinant Proteins , Sequence Alignment , Viral Proteins/genetics , Viral Proteins/metabolism
14.
J Mol Biol ; 426(2): 412-22, 2014 Jan 23.
Article in English | MEDLINE | ID: mdl-24112940

ABSTRACT

The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis crystals contain five subunits in the asymmetric unit, four of which align into a Xis filament and a fifth that is generated by an unusual domain swap. Extensive intersubunit contacts stabilize a bent filament-like arrangement with Xis monomers aligned head to tail. The structure implies a DNA bend of ~120°, which is in agreement with DNA bending measured in vitro. Formation of attR-containing intasomes requires only Int and Xis, distinguishing Pukovnik from lambda. Therefore, we conclude that, in Pukovnik, Xis-induced DNA bending is sufficient to promote intramolecular Int-mediated bridges during intasome formation.


Subject(s)
DNA Nucleotidyltransferases/chemistry , DNA Nucleotidyltransferases/metabolism , DNA, Viral/chemistry , DNA, Viral/metabolism , Mycobacteriophages/enzymology , Viral Proteins/chemistry , Viral Proteins/metabolism , Attachment Sites, Microbiological , Binding Sites , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization
15.
J Mol Biol ; 426(2): 318-31, 2014 Jan 23.
Article in English | MEDLINE | ID: mdl-24161951

ABSTRACT

Phage-encoded serine integrases are large serine recombinases that mediate integrative and excisive site-specific recombination of temperate phage genomes. They are well suited for use in heterologous systems and for synthetic genetic circuits as the attP and attB attachment sites are small (<50 bp), there are no host factor or DNA supercoiling requirements, and they are strongly directional, doing only excisive recombination in the presence of a recombination directionality factor. Combining different recombinases that function independently and without cross-talk to construct complex synthetic circuits is desirable, and several different serine integrases are available. However, we show here that these functions are not reliably predictable, and we describe a pair of serine integrases encoded by mycobacteriophages Bxz2 and Peaches with unusual and unpredictable specificities. The integrases share only 59% amino acid sequence identity and the attP sites have fewer than 50% shared bases, but they use the same attB site and there is non-reciprocal cross-talk between the two systems. The DNA binding specificities do not result from differences in specific DNA contacts but from the constraints imposed by the configuration of the component half-sites within each of the attachment site DNAs.


Subject(s)
Integrases/metabolism , Mycobacteriophages/enzymology , Recombination, Genetic , Serine/metabolism , Viral Proteins/metabolism , Attachment Sites, Microbiological , Base Sequence , DNA, Bacterial/metabolism , DNA, Viral/metabolism , Electrophoretic Mobility Shift Assay , Integrases/genetics , Molecular Sequence Data , Prophages/enzymology , Protein Binding , Sequence Homology, Amino Acid , Substrate Specificity , Viral Proteins/genetics
16.
Microbiol Spectr ; 2(1): MGM2-0017-2013, 2014 Feb.
Article in English | MEDLINE | ID: mdl-26082104

ABSTRACT

We have been witnessing an increased interest in bacteriophage studies focused on their use as antibacterial agents to fight pathogenic bacteria. This interest is a consequence of the phages' ability to lyse a bacterial host. Until recently, little was known about the mechanisms used by mycobacteriophages to induce lysis of their complex hosts. However, studies on Ms6-induced lysis have changed this scenario and provided new insights into the mechanisms of bacteriophage-induced lysis. Specific lysis protein genes have been identified in mycobacteriophage genomes, reflecting the particular mycobacterial cell envelope composition. These include enzymes that target mycolic acid-containing lipids and proteins that participate in the secretion of the phage endolysin, functioning as chaperone-like proteins. This chapter focuses on the current knowledge of mycobacteriophage-induced lysis, starting with an overview of phage lysis and basic features of the lysis players.


Subject(s)
Bacteriolysis , Endopeptidases/genetics , Mycobacteriophages/enzymology , Mycobacteriophages/physiology , Viral Proteins/genetics , Endopeptidases/metabolism , Viral Proteins/metabolism
17.
Appl Environ Microbiol ; 79(3): 768-73, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23160121

ABSTRACT

Since the peptidoglycan isolated from Mycobacterium spp. is refractory to commercially available murolytic enzymes, possibly due to the presence of various modifications found on this peptidoglycan, the utility of a mycobacteriophage-derived murolytic enzyme was assessed for an analysis of peptidoglycan from mycobacteria. We cloned, expressed, and purified the lysA gene product, a protein with homology to known peptidoglycan-degrading amidases, from bacteriophage Ms6. The recombinant protein was shown to cleave the bond between l-Ala and d-muramic acid of muramyl pentapeptide and to release up to 70% of the diaminopimelic acid present in the isolated mycobacterial cell wall. In contrast to lysozyme, which, in culture, inhibits the growth of both Mycobacterium smegmatis and Mycobacterium tuberculosis, LysA had no effect on the growth of either species. However, the enzyme is useful for solubilizing the peptide chains of isolated mycobacterial peptidoglycan for analysis. The data indicate that the stem peptides from M. smegmatis are heavily amidated, containing few free carboxylic acids, regardless of the cross-linking status.


Subject(s)
Amidohydrolases/metabolism , Cell Wall , Mycobacteriophages/enzymology , Mycobacterium/drug effects , Peptidoglycan/metabolism , Cloning, Molecular , Diaminopimelic Acid/metabolism , Gene Expression , Mycobacteriophages/genetics
18.
PLoS One ; 7(3): e34052, 2012.
Article in English | MEDLINE | ID: mdl-22470512

ABSTRACT

The mycobacterial cell wall presents significant challenges to mycobacteriophages--viruses that infect mycobacterial hosts--because of its unusual structure containing a mycolic acid-rich mycobacterial outer membrane attached to an arabinogalactan layer that is in turn linked to the peptidoglycan. Although little is known about how mycobacteriophages circumvent these barriers during the process of infection, destroying it for lysis at the end of their lytic cycles requires an unusual set of functions. These include Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, chaperones required for endolysin delivery to peptidoglycan, holins that regulate lysis timing, and the endolysins (Lysin As) that hydrolyze peptidoglycan. Because mycobacterial peptidoglycan contains atypical features including 3→3 interpeptide linkages, it is not surprising that the mycobacteriophage endolysins also have non-canonical features. We present here a bioinformatic dissection of these lysins and show that they are highly diverse and extensively modular, with an impressive number of domain organizations. Most contain three domains with a novel N-terminal predicted peptidase, a centrally located amidase, muramidase, or transglycosylase, and a C-terminal putative cell wall binding domain.


Subject(s)
Endopeptidases/metabolism , Mycobacteriophages/enzymology , Peptidoglycan/metabolism , Viral Proteins/metabolism , Amino Acid Sequence , Biocatalysis , Cell Wall/metabolism , Endopeptidases/chemistry , Endopeptidases/genetics , Galactans/metabolism , Molecular Sequence Data , Protein Binding , Protein Structure, Tertiary , Viral Proteins/chemistry , Viral Proteins/genetics
19.
Gene ; 495(1): 42-8, 2012 Mar 01.
Article in English | MEDLINE | ID: mdl-22227494

ABSTRACT

Mycobacteriophage Bxb1 encodes a serine-integrase that catalyzes both integrative and excisive site-specific recombination. However, excision requires a second phage-encoded protein, gp47, which serves as a recombination directionality factor (RDF). The viability of a Bxb1 mutant containing an S153A substitution in gp47 that eliminates the RDF activity of Bxb1 gp47 shows that excision is not required for Bxb1 lytic growth. However, the inability to construct a Δ47 deletion mutant of Bxb1 suggests that gp47 provides a second function that is required for lytic growth, although the possibility of an essential cis-acting site cannot be excluded. Characterization of a mutant prophage of mycobacteriophage L5 in which gene 54 - a homologue of Bxb1 gene 47 - is deleted shows that it also is defective in induced lytic growth, and exhibits a strong defect in DNA replication. Bxb1 gp47 and its relatives are also unusual in containing conserved motifs associated with a phosphoesterase function, although we have not been able to show robust phosphoesterase activity of the proteins, and amino acid substitutions with the conserved motifs do not interfere with RDF activity. We therefore propose that Bxb1 gp47 and its relatives provide an important function in phage DNA replication that has been co-opted by the integration machinery of the serine-integrases to control the directionality of recombination.


Subject(s)
DNA Replication/genetics , Integrases/physiology , Mycobacteriophages/enzymology , Recombination, Genetic , Virus Activation/genetics , Virus Replication/genetics , Amino Acid Sequence , Base Sequence , Integrases/genetics , Molecular Sequence Data , Mycobacteriophages/genetics , Sequence Deletion
20.
PLoS One ; 6(6): e20515, 2011.
Article in English | MEDLINE | ID: mdl-21694774

ABSTRACT

Mycobacteriophages are dsDNA viruses that infect mycobacterial hosts. The mycobacteriophage Ms6 accomplishes lysis by producing two cell wall hydrolytic enzymes, Lysin A (LysA) that possesses a central peptidoglycan recognition protein (PGRP) super-family conserved domain with the amidase catalytic site, that cleaves the amide bond between the N-acetylmuramic acid and L-alanine residues in the oligopeptide crosslinking chains of the peptidoglycan and Lysin B (LysB) a mycolylarabinogalactan esterase that hydrolyzes the mycolic acids from the mycolyl-arabinogalactan-peptidoglycan complex. Examination of the endolysin (lysA) DNA sequence revealed the existence of an embedded gene (lysA(241)) encoded in the same reading frame and preceded by a consensus ribosome-binding site. In the present work we show that, even though lysA is essential for Ms6 viability, phage mutants that express only the longer (Lysin(384)) or the shorter (Lysin(241)) endolysin are viable, but defective in the normal timing, progression and completion of host cell lysis. In addition, both endolysins have peptidoglycan hydrolase activity and demonstrated broad growth inhibition activity against various gram-positive bacteria and mycobacteria.


Subject(s)
Endopeptidases/genetics , Genes, Viral/genetics , Mycobacteriophages/genetics , Anti-Bacterial Agents/pharmacology , Bacteriolysis/drug effects , Cell Wall/drug effects , Cell Wall/metabolism , Endopeptidases/biosynthesis , Escherichia coli , Hydrolysis/drug effects , Microbial Sensitivity Tests , Mutation/genetics , Mycobacteriophages/drug effects , Mycobacteriophages/enzymology , Mycobacterium smegmatis/drug effects , Mycobacterium smegmatis/virology , N-Acetylmuramoyl-L-alanine Amidase/metabolism , Time Factors , Viral Proteins/genetics , Viral Proteins/metabolism
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