Abstract
The bacteriophage T4 early gene product MotB binds tightly but nonspecifically to DNA, copurifies with the host Nucleoid Associated Protein (NAP) H-NS in the presence of DNA and improves T4 fitness. However, the T4 transcriptome is not significantly affected by a motB knockdown. Here we have investigated the phylogeny of MotB and its predicted domains, how MotB and H-NS together interact with DNA, and how heterologous overexpression of motB impacts host gene expression. We find that motB is highly conserved among Tevenvirinae. Although the MotB sequence has no homology to proteins of known function, predicted structure homology searches suggest that MotB is composed of an N-terminal Kyprides-Onzonis-Woese (KOW) motif and a C-terminal DNA-binding domain of oligonucleotide/oligosaccharide (OB)-fold; either of which could provide MotB’s ability to bind DNA. DNase I footprinting demonstrates that MotB dramatically alters the interaction of H-NS with DNA in vitro. RNA-seq analyses indicate that expression of plasmid-borne motB up-regulates 75 host genes; no host genes are down-regulated. Approximately 1/3 of the up-regulated genes have previously been shown to be part of the H-NS regulon. Our results indicate that MotB provides a conserved function for Tevenvirinae and suggest a model in which MotB functions to alter the host transcriptome, possibly by changing the association of H-NS with the host DNA, which then leads to conditions that are more favorable for infection.
Highlights
Bacteriophage genes of unknown function comprise an abundance of ”dark matter” in the biological universe [1]
These analyses predicted that MotB contains two domains (Figure 1), an N-terminal domain (NTD) related to the Kyprides-OnzonisWoese (KOW) motif [36] and a C-terminal domain (CTD) related to the DNA-binding domain of oligonucleotide/oligosaccharide (OB)-fold [37]
The ongoing arms race between bacteria and lytic phages involves early phage genes that are needed to take over the host and host genes that can respond to this challenge
Summary
Bacteriophage genes of unknown function comprise an abundance of ”dark matter” in the biological universe [1]. One such gene is the phage T4 motB, which encodes an early gene product. Nonessential under normal laboratory conditions, our previous work has demonstrated that a motB knockdown yields a 2-fold lower burst than wild type (WT) T4, indicating that it contributes to phage fitness and that purified MotB binds tightly to both unmodified and T4 modified (5-glucosylated, hydroxymethylated cytosine) DNA [2]. MotB was named as a modifier of transcription, from very early work suggesting that a large T4 genomic deletion that removed motB affects some T4 middle gene expression [4]. Our global transcriptomic analyses have demonstrated that a T4 motB knockdown does not significantly affect T4 RNA levels [2]
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