Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in <em>Chromobacterium violaceum</em>

Abstract

CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus <em>Chromobacterium violaceum</em>. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e⁻⁰⁷) corresponding to a hypothetical protein OR16_04617 from <em>Cupriavidus basilensis</em> OR16, which failed to provide insight into the function of CV_2116. The <em>CV_2116</em> gene was cloned into the p15TvLic expression plasmid, transformed into <em>E. coli</em>, and ¹³C- and ¹⁵N-labeled NMR samples of CV_2116 were overexpressed in <em>E. coli</em> and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β -sheets in the <em>N</em>-terminal two-thirds of the protein and one α-helix in the <em>C</em>-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of <em>CV_2116</em> encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, <em>C. violaceum</em> exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, <em>C. violaceum</em> has been shown to contain four prophage elements and <em>CV_2116</em> resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in <em>C. violaceum</em>.

Keywords

• CV_2116
• &lt;em&gt;Chromobacterium violaceum&lt;/em&gt;
• NMR
• solution structure
• structural genomics
• bacteriophage tail assembly
• prophage
• lateral gene transfer