Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages - PubMed (original) (raw)

Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages

Jing Liu et al. J Bacteriol. 2004 Jul.

Abstract

Most of the known prohead maturation proteases in double-stranded-DNA bacteriophages are shown, by computational methods, to fall into two evolutionarily independent clans of serine proteases, herpesvirus assemblin-like and ClpP-like. Phylogenetic analysis suggests that these two types of phage prohead protease genes displaced each other multiple times while preserving their exact location within the late operons of the phage genomes.

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Figures

FIG. 1.

FIG. 1.

Structures of HCMV protease (PDB code 1CMV) and ClpP protease from E. coli (PDB code 1TYF). The α-helices are blue, and the β-strands are orange. The residues in the catalytic triad are shown with balls and sticks. They are His63-Ser132-His157 in HCMV protease and Ser97-His122-Asp171 in E. coli ClpP protease. The structures were drawn by using the program MOLSCRIPT (19).

FIG. 2.

FIG. 2.

Multiple-sequence alignment of protease clan SH members. The left column is the gi number for each sequence followed by the name of the virus or phage. The identifiers of herpesvirus proteases with known three-dimensional structures are shown in bold blue font. Distances, in amino acid residues, from the ends of each sequence and between the blocks with highest sequence similarities are shown in parentheses. Consensus positions of the structural elements are shown above the alignment. Yellow shading indicates the conservation of hydrophobic residues, gray shading indicates the conservation of residues with small side chains (A, G, and S), and a white font on a black background indicates the conservation of negatively charged residues (D and E). The catalytic Ser, His, and Asp/Glu residues in the catalytic triad are in white font on a red background, except that the His in the third position of the triad in all herpesvirus proteases is on a blue background. (A) Representatives from family S21 with known three-dimensional structures. HSV-2, herpes simplex virus 2; VZV, varicella-zoster virus; EBV, Epstein-Barr virus; KSHV, Kaposi's sarcoma-associated herpesvirus. (B) Representatives from family U35. (C) Representatives from family U9.

FIG. 3.

FIG. 3.

Multiple-sequence alignment of protease clan SK members. Designations are as described in the legend to Fig. 2. Species abbreviations: Ec, E. coli; Bs, Bacillus subtilis; Lp, Lactobacillus plantarum; At, Arabidopsis thaliana; Sco, Streptomyces coelicolor A3(2); Sy, Synechocystis sp. strain PCC 6803; Bh, Bacillus halodurans; Pf, Pyrococcus furiosus DSM 3638; Mj, Methanococcus jannaschii; Rc, Rickettsia conorii.

FIG. 4.

FIG. 4.

Phylogenetic tree constructed by using the sequence alignment of phage portal proteins. Sequences of the portal proteins from phages and prophages were aligned by using the T-Coffee (23) and CLUSTAL_X (34) programs, followed by manual validation and the removal of poorly aligned regions. The phylogenetic tree was constructed by using the neighbor-joining method as implemented in the NEIGHBOR program, and subsets of the data were used to rebuild the tree multiple times. The root was set to midpoint by the RETREE program of the PHYLIP package (10), and the consensus tree was subsequently reviewed by TreeView (24). Bootstrap values were estimated by resampling the set of the alignment 100 times (see the supplemental material). The level of bootstrap support is marked by small circles in the following colors: red (90 to 100%), yellow (80 to 90%), green (70 to 80%), and blue (50 to 70%). The nodes with <40% support are unlabeled. Phages that encode prohead protease belonging to clan SH are shaded in pink, and those that encode prohead protease belonging to clan SK are shaded in gray.

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