Genetics of critical contacts and clashes in the DNA packaging specificities of bacteriophages λ and 21

Abstract

The cos sites in λ and 21 chromosomes contain binding sites that recruit terminase to initiate DNA packaging. The small subunits of terminase, gpNu1 (λ) and gp1 (21), have winged helix-turn-helix DNA binding domains, where the recognition helixes differ in four of nine residues. To initiate packaging, the small subunit binds three R sequences in the cosB subsite. λ and 21 cannot package each other's DNA, due to recognition helix and R sequence differences. In λ and 21 cosBs, two bp, tri1 and tri2, are conserved in the R sequences yet differ between the phages; they are proposed to play a role in phage-specific packaging by λ and 21. Genetic experiments done with mixed and matched terminase and cosB alleles show packaging specificity depends on favorable contacts and clashes. These interactions indicate that the recognition helixes orient with residues 20 and 24 proximal to tri2 and tri1, respectively.

Bacteriophage lambda: Early pioneer and still relevant

“…Neither of these proteins is present in the completed virion. Mike Feiss and coworkers performed extensive and informative genetic analyses of lambda DNA packaging (Sippy et al , 2014; Feiss and Rao, 2012 and references therein), and Carlos Catalano's laboratory has studied its biochemistry ( e.g. , Andrews and Catalano, 2013; Singh et al , 2013).…”

DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch

“…The strong identity of R3 N15 and R3 Monarch is apparent, as is the lack of similarity of R3 N15 and R3 Monarch to R3 λ and R3 21 . In R3 λ and R3 21 , bp 56 and bp 59 are critical for TerS recognition [ 56 ]. R3 λ bp 58 is also important for TerS λ recognition [ 55 ].…”

“…The R1 sequence of cosB λ plays such a role [ 55 ]. Examination of prophages in Genebank identified an additional five prophages that have the R3 and rR2 sequences found in N15’s cosB [ 56 ]. In sum, two strikingly different cosB structures, complex and simple, are found in the λ-like phages.…”

“…Examination of the recognition helix and cosB R site sequences shows significant differences that account for the specificity difference ( Fig 2 ) [ 20 , 57 ]. Genetic analysis identified recognition helix:R site contacts that differ between λ and 21, plus clashes involved in discrimination by TerS λ and TerS 21 against the heterologous DNA [ 56 ]. Looking at TerS N15 and R3 N15 suggests that N15, and its relatives with simple cosB s might have a novel packaging specificity distinct from the λ and 21 specificities ( Fig 2 )[ 58 ].…”

“…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 R3 21 are important for recognition by TerS and are highlighted in green [ 56 ]. The CG→TA change at R3 λ bp 58 (highlighted in green) renders λ IHF-dependent for plaque formation [ 49 , 70 ][ 62 ].…”