Abstract
Virus production in the deep-sea environment has been found to be high, and viruses have been suggested to play significant roles in the overall functioning of this ecosystem. Nevertheless, little is known about these viruses, including the mechanisms that control their production, which makes them one of the least understood biological entities on Earth. Previously, we isolated the filamentous phage SW1, whose virus production and gene transcription were found to be active at low temperatures, from a deep-sea bacterium, Shewanella piezotolerans WP3. In this study, the operon structure of phage SW1 is presented, which shows two operons with exceptionally long 5′ and 3′ untranslated regions (UTRs). In addition, the 5′UTR was confirmed to significantly influence the RNA stability of the SW1 transcripts. Our study revealed novel regulation of the operon and led us to propose a unique regulatory mechanism for Inoviruses. This type of RNA-based regulation may represent a mechanism for significant viral production in the cold deep biosphere.
Highlights
Our data showed that SW1 possesses a novel regulatory system, which is significantly different from the Vibrio phage CTXΦ, and may provide a mechanism for significant viral production in the deep-sea environment
SW1 contains 9 ORFs, 8 of which are oriented in one direction, and the last ORF, fpsR, encodes a putative repressor in the reverse direction[17,18]
To elucidate its regulatory function, the fpsR gene was cloned into the expression vector pET-24b, and the binding of FpsR to the fpsA promoter (PfpsA) and fpsR promoter (PfpsR) was assessed using an electrophoretic mobility shift assay (EMSA) (Fig. 3)
Summary
The phage-borne regulator was shown to be able to bind to the promoter region of fpsA which encoded a replication protein of SW1. The RNA decay assay indicated that the two long 5′ UTRs regulated the RNA stability of phage SW1.
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