Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex

Abstract

The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein–DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.

Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa

“…Except for nine hypothetical proteins, the single-stranded DNAbinding protein (gp36), ATP-dependent helicase (gp55), primase (gp56), putative transcriptional regulators (gp28 and gp34), and putative transcription factor (gp48) are present only in phage YA3. The homology of the CI (gp50) and Cro (gp51) analogs of these two phages are also relatively low (identity 18.0%, similarity 31.5% and identity 34.3%, similarity 47.1%, respectively), which is consistent with their poor sequence conservation between different phages (Dubrava et al, 2010;Hall et al, 2019). As for the promoters, we found three positive promoters in front of orf19, orf51, and orf64 (named PP1 -PP3 ) and four reverse promoters upstream of orf18, orf45, orf49, and orf67 (named PR1 -PR4 ) in the Ab31 genome (Figure 5).…”