Effect of a cohesive end mismatch on viable phages production.

<p>Effect of a cohesive end mismatch on viable phages production.</p

Bacteria and Phages.

<p>Bacteria and Phages.</p

Annealed cohesive ends of phage chromosomes with cohesive end mismatches.

<p>A. The mismatch of a phage DNA with a ceL^N15/ceR^λ mismatch. B. The mismatch of a phage DNA with a ceL^λ/ceR^N15 mismatch. Mismatched bp are underlined and in bold. Highly conserved bp flanking the nick sites are highlighted in grey.</p

Packaging termination does not depend on <i>cosB</i> specificity^a.

<p>Packaging termination does not depend on <i>cosB</i> specificity<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#t005fn001" target="_blank">^a</a>.</p

Comparison of the <i>cos</i>es and terminase small subunit genes of λ, 21 and N15.

<p>A. Complex <i>cos</i> structure of phages λ, 21, Monarch. R3, R2 and R1 sequences are TerS binding sites, and I1 is an IHF binding site. B. Simple <i>cos</i> of N15 and relatives [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#pone.0141934.ref058" target="_blank">58</a>]. rR2 is a proposed accessory TerS binding site in the <i>cos</i> of N15 and relatives.</p

The terminases of λ and λ N15^hy4 do not show <i>cosN</i> specificity.

<p>The terminases of λ and λ N15^hy4 do not show <i>cosN</i> specificity.</p

Both cohesive end alleles are found in the progeny of phages with mismatched cohesive ends.

<p>Both cohesive end alleles are found in the progeny of phages with mismatched cohesive ends.</p

Helper packaging strategy.

<p>The large and small rectangles represent the envelope and chromosome of an <i>E</i>. <i>coli</i> cell with three prophages. Prophages1 and 2 are inserted in tandem in the bacterial chromosome, and the circle represents a third, heat-inducible plasmid prophage, the helper prophage. Induction of the helper prophage to lytic growth provides packaging components for both helper DNA and prophage DNA, provided the helper’s terminase can initiate packaging at the <i>cos</i> of upstream prophage 1 and terminate packaging at the <i>cos</i> of downstream prophage 2. The DNA packaged from the tandem prophages is represented by the horizontal arrow. The tandem prophages are not heat-inducible and remain repressed during the experiment.</p

Packaging specificities of phages λ, 21 and N15^a.

<p>Packaging specificities of phages λ, 21 and N15<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#t006fn001" target="_blank">^a</a>.</p

Alignments of the <i>cosB</i> and TerS DNA packaging recognition elements of λ-like bacteriophages.

<p>A. Alignment of R3 sequences of 21, Monarch, N15, and λ. Numbering is rightwards from the first base of the left cohesive end of each phage. Putative R3 sequences are highlighted in grey. The boundaries and locations of the R3 elements are only approximate and are mostly based on sequence conservation among the R3, R2 and R1 elements. Residues 56 and 59 in R3^λ and R3²¹ are important for recognition by TerS and are highlighted in green [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#pone.0141934.ref056" target="_blank">56</a>]. The CG→TA change at R3^λ bp 58 (highlighted in green) renders λ IHF-dependent for plaque formation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#pone.0141934.ref049" target="_blank">49</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#pone.0141934.ref070" target="_blank">70</a>][<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141934#pone.0141934.ref062" target="_blank">62</a>]. B. Alignments of the left ends of TerS subunits. Proposed recognition helixes are highlighted in grey and residues 20 and 24 of TerS²¹ and TerS^λ, known to be involved in packaging recognition and discrimination, are highlighted in green.</p