Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus

• Published in: Journal of molecular biology 2020-06, Vol.432 (14), p.4139-4153
• Main Authors: González, Brenda, Monroe, Lyman, Li, Kunpeng, Yan, Rui, Wright, Elena, Walter, Thomas, Kihara, Daisuke, Weintraub, Susan T., Thomas, Julie A., Serwer, Philip, Jiang, Wen
• Format: Article
• Language: English
• Subjects: Bacteriophages - genetics; Bacteriophages - ultrastructure; Capsid Proteins - genetics; Cryoelectron Microscopy; decoration proteins; DNA condensates; DNA packaging; DNA Packaging - genetics; DNA, Viral - genetics; DNA, Viral - ultrastructure; Humans; Lysinibacillus; Nucleic Acid Conformation; phage G; Virus Assembly - genetics
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2020.05.016

Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Å resolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G. [Display omitted] •Cryo-EM reveals structure of phage G capsid at 6.1 Å resolution.•Interactions of the phage G decoration protein trimer with the major capsid protein shell resemble those of Lambda and TW1 phages.•Cryo-EM micrographs of phage G reveal condensed, smaller-than-capsid DNA densities.•Mass spectrometry analysis of phage G identifies (1) all major capsid components and (2) the prohead protease responsible for the processing of the major capsid protein, gp27.•Phage G structural studies led to proteomic and genomic analyses that revised the identity of the phage G host from Bacillus megaterium to a Lysinibacillus species.