An Unusual Phage Repressor Encoded by Mycobacteriophage BPs

Temperate bacteriophages express transcription repressors that maintain lysogeny by down-regulating lytic promoters and confer superinfection immunity. Repressor regulation is critical to the outcome of infection—lysogenic or lytic growth—as well as prophage induction into lytic replication. Mycobacteriophage BPs and its relatives use an unusual integration-dependent immunity system in which the phage attachment site (attP) is located within the repressor gene (33) such that site-specific integration leads to synthesis of a prophage-encoded product (gp33¹⁰³) that is 33 residues shorter at its C-terminus than the virally-encoded protein (gp33¹³⁶). However, the shorter form of the repressor (gp33¹⁰³) is stable and active in repression of the early lytic promoter P_R, whereas the longer virally-encoded form (gp33¹³⁶) is inactive due to targeted degradation via a C-terminal ssrA-like tag. We show here that both forms of the repressor bind similarly to the 33–34 intergenic regulatory region, and that BPs gp33¹⁰³ is a tetramer in solution. The BPs gp33¹⁰³ repressor binds to five regulatory regions spanning the BPs genome, and regulates four promoters including the early lytic promoter, P_R. BPs gp33¹⁰³ has a complex pattern of DNA recognition in which a full operator binding site contains two half sites separated by a variable spacer, and BPs gp33¹⁰³ induces a DNA bend at the full operator site but not a half site. The operator site structure is unusual in that one half site corresponds to a 12 bp palindrome identified previously, but the other half site is a highly variable variant of the palindrome.

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

Selective identification of new therapeutic targets of Mycobacterium tuberculosis by IVIAT approach

The in vivo induced antigen technology (IVIAT)(1) has been used for the identification of open reading frames (ORFs) which could be possible therapeutic targets. A recombinant lambdagt11:: Mycobacterium tuberculosis H37Rv expression library was screened with pooled TB patient sera preabsorbed with in vitro grown M. tuberculosis H37Rv. Preabsorption of pooled TB patient sera allowed identification of antigens specifically expressed or upregulated during infection and growth in vivo. Six ORFs were identified, of which four (rv0287, rv2402, rv3878 and rv1045) were of hypothetical functions. Rv0287 is a probable regulatory protein. Rv3878 is present uniquely in M. tuberculosis H37Rv and is a part of RDI deletion region of M. bovis BCG, which includes esat 6 region. This could be exploited as a tool for diagnosis. Two ORFs were assigned function solely on the basis of homology, dnaQ (rv3711c) and lpdA (rv3303c). dnaQ codes for the epsilon subunit of DNA polymerase III, which is responsible for the proofreading activity of the complex. lpdA codes for dihydrolipoamide dehydrogenase, which is a part of many multienzyme complexes such as pyruvate dehydrogenase, keto-acid dehydrogenase and alpha-ketoglutarate dehydrogenase. These two enzymes appear to be potential targets for drug development.

Transcriptional regulation and immunity in mycobacteriophage Bxb1

Mycobacteriophage Bxb1 is a temperate phage of Mycobacterium smegmatis that shares a similar genome organization to mycobacteriophage L5, although the two phages are heteroimmune. We have investigated the regulatory circuitry of Bxb1 and found that it encodes a repressor, gp69, which regulates at least two promoters, an early lytic promoter, Pleft, and the divergent promoter, Pright. Bxb1 gp69 is 41% identical to the L5 repressor (gp71) and binds to repressor binding sites that conform to a similar, but distinct, 13 bp asymmetric consensus sequence to that for the L5 gp71 binding sites. The two phage repressors have a strong preference for their cognate binding sites, thus accounting for their immunity phenotypes. The Bxb1 genome contains 34 putative repressor binding sites located throughout the genome, but situated within short intergenic spaces and orientated in only one direction relative to the direction of transcription. Comparison with the locations of repressor binding sites within the L5 genome provides insights into how these unusual regulatory systems evolve.

The effect of mycobacteriophage particles on cell-mediated immune reactions

Suspensions of mycobacteriophages added to cultures of white blood cells (WBC's) reduce the phytohaemagglutinin (PHA) stimulated blast responses. Ultraviolet (UV) inactivation of the phages abolishes the inhibitory effect. Buffy coat cells from guinea pigs inoculated with mycobacteriophages and mice inoculated with these phages or with lysogenic mycobacteria show, without prior in vitro exposure to the antigen, significant reductions in the rate of their migration. This "spontaneous" migration inhibition is removed by prior treatment of the cells with trypsin or puromycin.

Lysogeny in the mycobacteria. II. Alterations of bacterial antigens mediated by mycobacteriophage

Using the agglutination test and the indirect fluorescent antibody test it was demonstrated that lysogenization of the rough variant of Mycobacterium smegmatis ATCC 607 by mycobacteriophages D29 and B4 was accompanied by the appearance of new bacterial antigens. Each phage mediated a different bacterial antigen. That the new bacterial antigens were phage mediated was demonstrated by the loss of the new antigens when the bacterial culture was "cured" of the prophage.