Defense islands in bacterial and archaeal genomes and prediction of novel defense systems

Abstract

The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic "sinks" that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.

Fig. 1.

Identification of genomic islands.

Fig. 2.

Analysis of proximity between sets of genes in prokaryotic genomes.

Fig. 3.

Genomes in which the distribution of distances between defense genes significantly deviates from the random expectation.

Fig. 4.

Distribution of island lengths. Defense, DIs; Mobilome, mobilome islands; All, all islands of nonnegative genes.

Fig. 5.

Scaling of the defense and mobilome genes with the genome size (total number of genes). (A) Defense and mobilome genes. (B) Scaling of different defense systems.

Fig. 6.

Core elements and diversity of the Pgl defense system. The genes in predicted operons containing the three core genes and additional components of the Pgl system are shown by arrows, with the size roughly proportional to the size of the corresponding gene. Arrows for the three core genes are outlined in red; homologous genes are represented by arrows of the same color. Variable components are represented by gray arrows. The domains identified in the Pgl system proteins are shown above the respective arrows; COG or Pfam families are indicated in parentheses. Abbreviations: Pgl, phage growth limitation; MIT, microtubule interacting and trafficking (domain); GIY-YIG, conserved motif in a nuclease family (pfam01541).

Fig. 7.

Operons and domain organization of COG1479 genes, predicted new defense system components. (A) Operons containing COG1479 genes. The designations are as in Fig. 6. The arrows corresponding to genes encoding RM system subunits are red; the arrows that denote the core genes of Pgl systems are colored as in Fig. 6. (B) Domain organization of several proteins containing the core COG1479 domain. The lengths of the proteins and domains are shown roughly to scale. The core COG1479 domain is shown by a thick red outline. HNH is a motif conserved in the corresponding family of nucleases.

Fig. 8.

A predicted novel TA system. (A) Two distinct operons containing genes coding for members of the protein family with an HxH motif. The structures of representatives of the DUF3532 and DUF2442 families are shown. The PDB codes are indicated. The ribbon diagrams were generated using the Jmol server (http://www.jmol.org/). For the DUF2424 structure, two folds of the two domains are denoted according to the fold assignment in the SCOP database (3, 64). (B) Multiple-sequence alignment of the HxH motif-containing family. Secondary structure prediction is shown beneath the alignment as follows: H, α-helix; E, extended conformation (β-strand). The sequences are denoted by their GI numbers and species names. The conserved amino acids are in bold. The coloring is based on the consensus shown at the bottom of the alignment; h, hydrophobic residues (WFYMLIVACTH); p, polar residues (EDKRNQHTS); s, small residues (ACDGNPSTV); a, aromatic residues (YWF).

Fig. 9.

Two examples of putative novel defense system components identified in high-density DIs. Designations are as in Fig. 6. The arrows corresponding to genes encoding subunits of RM systems are yellow; TA components are magenta. Arrows for genes encoding putative novel components of defense systems described in this work are outlined in red. Abbreviations: RM, restriction modification; HNH, a motif conserved in the corresponding family of nucleases; Fic, toxin of the corresponding family; PHD, antitoxin of the corresponding family; TOPRIM, conserved catalytic domain of topoisomerases, primases, and OLD family nucleases (4).

Fig. 10.

The extreme abundance of defense systems in the M. aeruginosa genome. (A) Distribution of defense genes in the M. aeruginosa NIES 843 and Paenibacillus sp. strain JDR-2 genomes. (B) Examples of DIs containing putative novel defense system components. Designations are as in Fig. 6. The arrows denoting cas genes are blue, TA system components are magenta, and transposable elements are black. PIN, RHH, PHD, HTH, RelE, HicA, HicB, MNT, HEPN, and COG4636 are predicted TA system components described in detail previously (55). FS, frameshift; VPEP, family of proteins containing a VPEP motif (28). The cas gene nomenclature is given in accordance with the recently proposed classification (54). Proteins annotated as hypothetical are indicated by asterisks.