The Ms6 Mycolyl-Arabinogalactan Esterase LysB is Essential for an Efficient Mycobacteriophage-Induced Lysis

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.

Cluster J mycobacteriophages: intron splicing in capsid and tail genes

Bacteriophages isolated on Mycobacterium smegmatis mc²155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution.

Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.

Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements

Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41,901 bp, 42,289 bp and 41,441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.

Mycobacteriophages as versatile tools for genetic manipulation of mycobacteria and development of simple methods for diagnosis of mycobacterial diseases

Tuberculosis, caused by Mycobacterium tuberculosis, is responsible for over two million deaths per year worldwide. Due to its long doubling time (18 h), the microbiological detection of M. tuberculosis by conventional methods takes up to one month, unless the number of bacilli in the biological sample is high enough. Thus, drug resistance assessment requires at least one month for obtaining the primary culture and another month to determine its susceptibility to antimycobacterial drugs. Moreover, for a long time, the lack of genetic tools for mycobacteria has been a barrier for undertaking studies aimed at understanding the mechanisms of drug resistance and drug target identification, being all these topics of utmost importance considering the increase in the number of drug-resistant clones and the few therapeutic options available. Mycobacteriophages are promising as a novel source of genetic elements for mycobacteria manipulation, as well as for the development of versatile, simple, fast and cheap methods for drug resistance assessment of M. tuberculosis clinical isolates. We herein describe the background related to the use of mycobacteriophages, with emphasis placed on their utilization for drug resistance analysis in our country.

Non-STEM undergraduates become enthusiastic phage-hunters

To increase science literacy and appreciation among nonscience majors, we offered a course in which 20 non-STEM (science, technology, engineering, math) undergraduates participated in a unique, two-semester research experience. Each student isolated and characterized his or her own bacteriophage from soil samples. One bacteriophage was selected for sequencing and together, the class annotated the genome of the newly sequenced bacteriophage. The class produced a group poster and gave PowerPoint presentations, and one student presented the joint work at a science symposium.

Characterization of temperate phage Che12 and construction of a new tool for diagnosis of tuberculosis

A temperate phage, Che12, able to infect Mycobacterium tuberculosis, was isolated from soil samples taken from tuberculosis sanatorium area in Chennai, India. The plaque morphology of this phage showed varying grades of turbidity on lawns of M. tuberculosis. The temperate nature of Che12 was established by super infection immunity. Phage integration into the host genomic DNA was confirmed by Southern hybridization using Che12 DNA as a probe. PCR amplification and sequencing of a part of the integrated phage genome in a M. tuberculosis lysogen also confirmed the temperate nature of Che12. The morphology of the phage particles was observed by electron microscopy, revealing similarities to other mycobacteriophages like L5, D29 and TM4. A luciferase reporter phage, phAETRC16, was constructed by cloning firefly luciferase gene into Che12. Infection of viable M. tuberculosis cells by phAETRC16 resulted in expression of luciferase leading to sustained light output. Che12, a true temperate phage infecting M. tuberculosis, is thus ideally suited for developing a diagnostic tool facilitating rapid diagnosis of M. tuberculosis.

Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria

Mycobacteriophage Tweety is a newly isolated phage of Mycobacterium smegmatis. It has a viral morphology with an isometric head and a long flexible tail, and forms turbid plaques from which stable lysogens can be isolated. The Tweety genome is 58 692 bp in length, contains 109 protein-coding genes, and shows significant but interrupted nucleotide sequence similarity with the previously described mycobacteriophages Llij, PMC and Che8. However, overall the genome possesses mosaic architecture, with gene products being related to other mycobacteriophages such as Che9d, Omega and Corndog. A gene encoding an integrase of the tyrosine-recombinase family is located close to the centre of the genome, and a putative attP site has been identified within a short intergenic region immediately upstream of int. This Tweety attP–int cassette was used to construct a new set of integration-proficient plasmid vectors that efficiently transform both fast- and slow-growing mycobacteria through plasmid integration at a chromosomal locus containing a tRNA^Lys gene. These vectors are maintained well in the absence of selection and are completely compatible with integration vectors derived from mycobacteriophage L5, enabling the simple construction of complex recombinants with genes integrated simultaneously at different chromosomal positions.

A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells

The predominant morphotype of mycobacteriophage virions has a DNA-containing capsid attached to a long flexible non-contractile tail, features characteristic of the Siphoviridae. Within these phage genomes the tape measure protein (tmp) gene can be readily identified due to the well-established relationship between the length of the gene and the length of the phage tail--because these phages typically have long tails, the tmp gene is usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain small motifs with sequence similarity to host proteins. One of these motifs (motif 1) corresponds to the Rpf proteins that have lysozyme activity and function to stimulate growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of unknown function, although some of the related proteins of the host are predicted to be involved in cell wall catabolism. We show here that motif 3-containing proteins have peptidoglycan-hydrolysing activity and that while this activity is not required for phage viability, it facilitates efficient infection and DNA injection into stationary phase cells. Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a selective disadvantage that results from changes in peptidoglycan in non-growing cells.

Origins of highly mosaic mycobacteriophage genomes

Bacteriophages are the most abundant organisms in the biosphere and play major roles in the ecological balance of microbial life. The genomic sequences of ten newly isolated mycobacteriophages suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere. Genomic comparison of these mycobacteriophages contributes to our understanding of the mechanisms of viral evolution and provides compelling evidence for the role of illegitimate recombination in horizontal genetic exchange. The promiscuity of these recombination events results in the inclusion of many unexpected genes including those implicated in mycobacterial latency, the cellular and immune responses to mycobacterial infections, and autoimmune diseases such as human lupus. While the role of phages as vehicles of toxin genes is well established, these observations suggest a much broader involvement of phages in bacterial virulence and the host response to bacterial infections.

[Properties of MTPN11 mycobacteriophage]

Some characteristics of the poorly studied phage MTPH11, which is used for identification of mycobacteria, are presented. The phage has an isometric head and a long noncontractile tail (B1 morphotype). The attachment apparatus of this phage includes a basal plate composed of two joint disks and a single tail fiber. The constant of phage adsorption on Mycobacterium smegmatis ATCC607 cells is 6.6 x 10(-9) ml/min. The latent infection period in the MTPH11-host strain 607 system in 65 min; phage progeny ranges from 30 to 40 virions per one cell. The constant of phage inactivation with a homologous antiserum is 50 min-1. The buoyant density of intact MTPH11 virion in CsCl amounts to 1.520 g/cm3. The phage is susceptible to chloroform, retains lytic activity within a pH range of 5 to 9, and is resistant to inactivating agents. The G + C content of the phage DNA is 63 mol%.

[Study of the interaction of MTPN11 mycobacteriophage with host cells based on electron microscopy, fluorimetry, and electro-oriented spectroscopy]

According to electron-microscopic data, various cells in the M. smegmatis ATCC607 population interact differently with phage MTPH11. Fluorometric studies of phage-host interactions were performed using a membranotropic fluorescent probe, 8-anilino-1-naphthalene sulfonate (ANS). Changes in the electric characteristics of mycobacterial cells infected with the phage were studied by electro-orientational (EO) spectroscopy. The problem of the employment of fluorometry and EO spectroscopy for rapid phage typing of mycobacteria is discussed.

Genome structure of mycobacteriophage D29: implications for phage evolution

Mycobacteriophage D29 is a lytic phage that infects both fast and slow-growing mycobacterial species. The complete genome sequence of D29 reveals that it is a close relative of the temperate mycobacteriophage L5, whose sequence has been described previously. The overall organization of the D29 genome is similar to that of L5, although a 3.6 kb deletion removing the repressor gene accounts for the inability of D29 to form lysogens. Comparison of the two genomes shows that they are punctuated by a large number of insertions, deletions, and substitutions of genes, consistent with the genetic mosaicism of lambdoid phages.

DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics

Genetic studies of Mycobacterium tuberculosis and other mycobacterial pathogens have suffered from the lack of a sophisticated genetic system. To address this issue we have developed a viral system through a detailed characterization of mycobacteriophage L5, a temperate phage that infects both fast- and slow-growing mycobacteria. We describe here the complete DNA sequence of the L5 genome and initial characterization of L5 virion structure and gene expression. In addition to providing a genetic 'tool-box' for the mycobacteria we find that L5 offers a new paradigm for dsDNA phages, being phenotypically temperate but employing genetic strategies for phage growth usually associated with lytic bacteriophages.

Isolation and characterization of temperature sensitive mutants of the F5 deletion mutant of mycobacteriophage D29

Seven thermosensitive mutants of the F5 deletion mutant of the mycobacteriophage D29 were described. The mutants were obtained using N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) mutagenesis, and were characterized using temperature shift assays, complementation and recombination tests, electron microscopy of infected host bacteria at non-permissive temperature, and serum blocking power. Mutants deficient in tail assembly, and mutants deficient in head and tail assembly were described. Mutants deficient in head assembly but capable of assembling tails were not isolated during this study. From the data, 3 provisional linkage map of the phage F5 was proposed.

Induction of bacteriophage from members of the Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum serocomplex

Bacteriophages have been induced from strains in the Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum serocomplex by exposure of cultures to UV light or treatment with mitomycin C. One-sixth of the strains examined, representing all but one of the 31 authenticated serotypes, were found to possess phages lytic for a Mycobacterium smegmatis indicator strain. Four single-plaque isolated phages, TM4, TM9, TM10 and TM20, were purified and shown to have a similar morphology on electron micrographs. They had an isometric head of diameter 50-58 nm and a flexible non-contractile tail about 170 nm in length with a terminal bulb. All had an identical buoyant density in CsCl of 1.521 g cm-3 and extreme sensitivity to chloroform. The induced phages differed in host range and possessed the unique ability to lyse other members of the serocomplex. Interest in these phages centres on a possible role in mediating genetic interrelationships between members of the serocomplex.

Morphology of bacteriophages from Mycobacterium lepraemurium

The two phages obtained from mycobacterium lepraemurium strain "Douglas" by using M. segmatis ATCC 607 as a non-lysogenic indicator (kindly supplied by L. Sula and named as AL1 and 1/1) were adsorbed on M. Smegmatis ATCC 607 with a P 45'/P0 of 0.046 and 0.01, respectively. Ultrastructural studies showed that these phages could be classified as Bradley type B1.

Presence of lipids in mycobacteriophage i3

The presence of lipids has been demonstrated in mycobacteriophage I3. The total lipid was composed of 69% phospholipids and 31% neutral lipids. More than two-thirds of phospholipids present in the phage were synthesized in the host prior to infection. The fatty acid composition of the phage differed markedly from that of its host, both in chain length and the degree of saturation. The phage lipid was mostly composed of saturated fatty acids of which more than 50% were short chain fatty acids. Changes in growth temperatures reflected variations in fatty acid composition, characteristic of the phage, and which were distinctly different from those of the host. Electron microscopic observations revealed that the phage has a membranous bilayer structure. The presence of lipids may facilitate the phage-host interaction especially in lipid-rich organisms like mycobacteria.

The tadpole-shaped structures in human non-necrotizing granulomas

We scrutinized the secondary lysosomal vesicle of the epitheloid cell from 9 patients whose biopsy specimens show multiple non-necrotizing granulomas by light microscopy (LM). In 4 of the 9 patients, we found tadpole-shaped structures (TSS) approximately tenfold larger than the size of the mycobacteriophage by transmission electron microscopy (TEM). In addition, we used a plasma etching method on epon-embedded tissue and successfully demonstrated the stereoscopic appearance of the TSS by scanning electron microscopy (SEM). The identified TSS were further analyzed with an X-ray energy dispersive spectrometer for their microchemistry. The TSS appeared to be integral structures by TEM and SEM and did not contain any nonbiologic elements when analyzed with the X-ray energy dispersive spectrometer. Their location as well as their morphologic features and microchemistry suggested that the TSS are a microorganism and related to the formation of the granulomas in our 4 patients.

Characterisation of mycobacteriophage ATCC 11759. Unusual physiocochemical properties of its DNA

Growth conditions and a purification procedure for mycobacteriophage ATCC 11759, a lytic phage for Mycobacterium smegmatis, are described. The phage is a large DNA phage with a very long tail (240 nm). A study of its DNA revealed three interesting features. 1. After denaturation the DNA molecule yields two strands of different buoyant densities. 2. The native DNA has unusual physical properties: its buoyant density in CsC1 is very low (1.654 g/cm3), its sedimentation rate is lower than expected for the molecular weight, its thermal stability at low ionic strength is high. 3. The DNA (in its native form or after reannealing) is resistant to various restriction endonucleases.

Interaction of Mycobacterium leprae and mycobacteriophage D29

This study of the interaction between Mycobacterium leprae and the mycobacteriophage D29 showed that the viruses caused a patchy damage of cell wall structure and the accumulation in the host of internal crystalline structures. Whether the observed ultrastructural alterations were caused by the replication of D29 was not clear. Mitomycin C also caused the accumulation of crystalline structures in M. leprae.

Structure of native and chloroform-methanol-treated mycobacteriophage R1

The morphologies of native and chloroform-methanol-treated mycobacteriophage R1 were compared by electron microscopy, utilizing three negative stains. R1 was determined to be a complex phage. The head appears as an elongated cylinder with a pointed end (93 +/- 3 by 42 +/- 3 nm) constructed from an orderly arrangement of capsomeres. The phage tail measures 209 +/- 11 by 11 +/- 1 nm and possesses a striated surface with two base plates at its distal end. Treatment of R1 with chloroform-methanol resulted in disruption of both the head and tail structures and was accompanied by loss of infectivity. However, because no likely lipid-containing structure was observed in native phages, there is the possibility that the mechanism of chloroform-methanol inactivation is something other than lipid extraction.

Lysogeny associated with mucoid variation in Mycobacterium kansasii

Ten of 200 strains of Mycobacterium kansasii were found to produce very mucoid growth on Löwenstein-Jensen medium. By electronmicroscopy these 10 strains were found to be lysogenic, whereas no phage was observed in cultures of 30 non-mucoid strains. The cultural and biochemical properties of the lysogenic strains are compared with those of non-lysogenic strains, and the morphology of the phages is described.

Biochemical and morphological characterization of mycobacteriophage R1

Large-scale propagation of mycobacteriophage R1 in broth culture has allowed the isolation of quantities of virus sufficient for characterization of its nucleic acid and lipid components as well as investigation of its ultrastructural attributes. Analysis of R1 DNA indicates that it is double stranded and possesses a molecular weight of 2.5 X 10(7) and a guanine-plus-cytosine content of 65.7 +/- 0.5%. The lipid fraction of R1 accounts for 14% of the total dry weight of the virus, 20% of which was identified as free or esterified sterols. A rapid loss of viral titer occurred after seconds of exposure to organic solvents. This result suggests that the lipid fractions of R1 is essential for its infectivity. Electron microscopic investigation of solvent-extracted R1 showed extensive deterioration of its normal morphology, including nucleocapsid disintegration and base plate separation. Routine phosphotungstate preparations demonstrated a particle with an oval head and a noncontractile tail. Altering the pH of the phosphotungstate negative stain from neutrality damage the viral particles. Uranyl formate-contrasted specimens displayed an elongated hexagonal nucleocapsid with a neck region; the cross-striated tail possessed a starlike base plate.

Chemical and physical properties of mycobacteriophage D29

Mycobacteriophage D29 has a head of uniform size (average diameter 65 nm) and regular shape and a tail of variable length. The stability of the bacteriophage is optimal between pH 9 and 10. The virus contain double-stranded DNA and six structural polypeptides, three major and three minor. The molecular weights of these six polypeptides, as determined by polyacrylamide gel electrophoresis in the presence of dodecylsulfate, are 150 000, 138 000, 13 000, 66 000 and 24 000. The virus contains no lipids as shown by (a) the lack of structural changes after inactivation of the bacteriophage with chloroform, (b) the absence of lipids containing [32P]phosphate or [35S]sulfate in labeled virus, and (c) the absence of an electron paramagnetic resonance spectrum in bacteriophage which had been incubated with a nitroxide-containing fatty acid.

A study on the receptor for a mycobacteriophage : phage phlei

From Mycobacterium phlei, glycolipid fractions have been isolated which inactivate phage Phlei. On the basis of the characteristics of the inactivation (specificity, kinetics, requirement for Ca++) typical of the phage-host cell system, it was concluded that these fractions contain the receptor sites for phage Phlei ; this conclusion was supported by electron microscopic studies. All the active fractions contain four kinds of components : fatty acids, glycerol, sugars (D-lyxose, 6-0-methyl-D-glucose, and low amounts of glucose and mannose), and water-soluble acids. These acids are isolated by degradation of the receptor fractions as oxalic and pyruvic acids. Variations of the ratio oxalic acid/pyruvic acid according to the mode of degradation and the absence of the peak characteristic of the protons of a pyruvic acid residue in the NMR spectrum, suggest that these acids might arise from the splitting of oxaloacetic acid. A tentative structure of the receptor is proposed, in many monoglycerides are linked through keto-acid to a polysaccharide core.

Biophysical properties of mycobacteriophages

Biophysical characterization of two mycobacteriophages (Phlei phage and Butyricum phage) was carried out. Biophysical parameters obtained were: (i) buoyant densities in CsCl of I . 51 g/ml for both phages; (ii) sedimentation coefficient of 490 S and 410 S; (iii) DNA content of 42 and 34% and (iv) mol. wt. calculated by electron microscopic dimensions to be 123 x 10(6) and 116 x 10(6) for Butyricum and Phlei phage, respectively.

The nature and incidence of lysogeny in Mycobacterium fortuitum

Ten of 28 strain of Mycobacterium fortuitum (ranae) were found to be associated with bacteriophage; three were pseudolysogenic, one liberated a phage that lysed a sensitive indicator strain, two liberated morphologically complete phages that did not lyse any of the strains used in this study and four liberated morphologically defective phages. The lysogenic and defectively lysogenic strains showed anomalies in cultural, biochemical and antigenic properties and in susceptibility to superinfecting phages. In view of the high frequency of lysogeny found in M. fortuitum, the role of bacteriophage in the variation of properties, including pathogenicity, of mycobacteria of greater clinical importance merits further consideration.

Growth inhibitory activity of deoxyribonucleic acid-containing factor(s) isolated from lepromatous lesions

Deoxyribonucleic acid-containing factor(s) isolated from Mycobacterium leprae suspensions obtained from lepromas of nine patients showed growth inhibitory activity against Micrococcus and both orange-red-pigmented and coccoid mutants of mycobacteria. No growth inhibition was observed for parent mycobacterial species, Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus epidermidis.