Abstract
Despite decades of intensive research on bacteriophage lambda, a relatively uncharacterized region remains between the exo and xis genes. Collectively, exo-xis region genes are expressed during the earliest stages of the lytic developmental cycle and are capable of affecting the molecular events associated with the lysogenic-lytic developmental decision. In Shiga toxin-producing E. coli (STEC) and enterohemorragic E. coli (EHEC) that are responsible for food- and water-borne outbreaks throughout the world, there are distinct differences of exo-xis region genes from their counterparts in lambda phage. Together, these differences may help EHEC-specific phage and their bacterial hosts adapt to the complex environment within the human intestine. Only one exo-xis region protein, Ea8.5, has been solved to date. Here, I have used the AlphaFold and RoseTTAFold machine learning algorithms to predict the structures of six exo-xis region proteins from lambda and STEC/EHEC phages. Together, the models suggest possible roles for exo-xis region proteins in transcription and the regulation of RNA polymerase.
Highlights
Over the past forty years, enterohemorrhagic E. coli (EHEC) O157:H7 [1] and newer serotypes such as O104:H4 [2] have been responsible for numerous outbreaks of food poisoning throughout the world [3]
When the predicted structure of Orf60a was compared to the protein structure database, it compared favorably to a family of small DNA binding domains (DBDs) that use a β-sheet to interact with the major groove [47,48,49,50]
The predicted structures by AlphaFold and RoseTTAFold both describe a protein that is composed of a winged helix-turn-helix DNA binding domain (DBD), followed by a PVQ-repeat leading into a carboxy-terminal coiled-coil domain (Figure 9a)
Summary
Over the past forty years, enterohemorrhagic E. coli (EHEC) O157:H7 [1] and newer serotypes such as O104:H4 [2] have been responsible for numerous outbreaks of food poisoning throughout the world [3]. Antibiotic treatment of EHEC infections, is counterproductive because drugs that produce a stress response may stimulate the lysogenic-lytic transition and the consequent production of Shiga toxin [7,8,9]. Comparative genomics studies have helped reveal the wide diversity that is possible among Shiga-toxin producing bacteriophages (Stx+ phages) This diversity is likely accompanied by a myriad of ways that Stx+ phages may affect the virulence of their bacterial host. A set of relatively uncharacterized open reading frames (ORFs) between the exonuclease gene (exo) and the excisionase gene (xis) in lambdoid bacteriophages has been shown to affect the lysogenic-lytic developmental decision These so-called exo-xis region genes tend to produce a greater effect in Stx+ phages than λ, the most studied archetype and logical reference for comparison. Further explorations of the exo-xis region have the potential to reveal new insights into the lysogenic-lytic developmental decision and new therapeutic routes to combat infection
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