Trends in Microbiology
The PIN-domain toxin–antitoxin array in mycobacteria
Introduction
Proteins containing PIN-domains (homologues of the pilT N-terminal domain) are found in the genomes of a wide range of prokaryotes and eukaryotes. The biochemical and biological functions of these proteins is uncertain, however, recent work has resulted in a convergence of opinion. In eukaryotes PIN-domain proteins function as ribonucleases 1, 2 with activity linked to RNAi and nonsense-mediated RNA degradation 1, 3. In prokaryotes, the majority of PIN-domain proteins are the toxic components (by virtue of their ribonuclease activity) of chromosomally encoded toxin-antitoxin (TA) operons 4, 5, 6. A striking feature of the PIN-domain TA operons is their abundance in the genomes of several unrelated prokaryotes. For example, the genome of Mycobacterium tuberculosis harbours 38 PIN-domain TA operons 3, 7 (Arcus, V.L., unpublished results) and the hypertheromophilic chrenarchaeote, Sulfolobus tokodaii, has 25 PIN-domain TAs [6]. These arrays of PIN-domain TA operons in various unrelated prokaryotic genomes pose questions as to their evolutionary origins and contemporary functional significance. Recent results, which suggest that TA operons confer advantages on competing mobile genetic elements 8, 9, combined with the association of PIN-domain TA operons with potential mobile elements in M. tuberculosis, point to the horizontal gene pool as the primary source of TA operons. Indeed, their abundance within the genomes of bacteria such as M. tuberculosis could reflect recent and rapid evolution fuelled by the acquisition of new DNA. Contemporary functions for TA operons are various but point collectively toward a general role in the facilitation of persistence in organisms that inhabit variable and frequently stressful environments [6].
Section snippets
Toxin–antitoxin protein pairs
Toxin–antitoxin (TA) protein pairs were discovered more than 20 years ago as factors that protect low copy number plasmids in bacteria from segregational loss 10, 11. One protein of the pair is toxic to the cell and stable, whereas its cognate antitoxin is unstable and requires continuous transcription to inhibit the toxin. Thus, if the plasmid is not correctly segregated during cell division, one daughter cell lacks the plasmid and is left with just the TA proteins – one stable and toxic, the
PIN-domain proteins
PIN-domain-containing proteins are encoded within the genomes of organisms that span the three domains of life. The PIN-domain was first annotated on the basis of sequence similarity to the N-terminal domain of the type IV pili protein, pilT, from Myxococcus xanthus (PIN, PilT N-terminus) [20], and is represented in the Pfam database (http://www.sanger.ac.uk/Software/Pfam) as PF01850, currently with 468 members. This number is likely to be an underestimate because the Superfamily database,
The biochemical function of PIN-domain proteins
Recent work on the structure and function of PIN-domain-containing proteins in the hyperthermophilic crenarchaeote Pyrobaculum aerophilum and the human pathogen Mycobacterium tuberculosis 22, 23 has focused on a small, well-conserved family of PIN-domains with four homologues in each organism (these eight proteins belong to a ‘Cluster of Orthologous’ proteins, COG4113, NCBI). By solving the 3D structure of one member of the family, a structural and functional relationship was shown between the
Several microorganisms have expanded cohorts of PIN-domain proteins
Bioinformatic surveys of PIN-domain proteins across many fully sequenced organisms showed that several organisms (notably Mycobacterium tuberculosis and Archeoglobus fulgidus) have a dramatically expanded cohort of PIN-domain proteins in their genomes 3, 4. Several other prokaryotic genomes, whose cohort of PIN domains exceeds ten, include Gloeobacter violaceus (a Cyanobacterium and obligate photoautotroph), Nitrosomonas europaea (a Gram-negative obligate chemolithoautotroph) and several
PIN-domain proteins in mycobacteria
M. tuberculosis has 48 PIN-domain-containing proteins [3], which are highly diverse at the DNA sequence level. These PIN-domains can be discovered by protein sequence-based Hidden Markov Model (HMM) methods, such as those used by the TIGRFAM database (47 PIN domains in M. tuberculosis) [7], or structure-based HMM methods such as those used by the Superfamily database [21] (46 PIN-domain sequences in M. tuberculosis, E-values <0.01). Alternatively, using an approach similar to that used by
Possible biological roles for PIN-domain toxin-antitoxin proteins
In assessing the possible reasons for the expanded repertoires of PIN-domain TAs in the mycobacteria and several other evolutionarily distant organisms, it is important to differentiate between the factors leading to their incorporation and/or expansion in the genome, and the consequences of their incorporation (i.e. their present biological functions), which might be only distantly related to their function at the time of incorporation.
The evolutionary origins of TA elements are unclear;
Conclusions
Bioinformaticians were the first to hypothesize a biochemical role for PIN-domain proteins as ribonucleases [1] and suggested that they represented the toxic components of prokaryotic TA operons [3]. Subsequent structural [23], biochemical and microbiological experiments [5] have confirmed these hypotheses. However, there is much yet to learn about these TA systems. For example, are the PIN-domains sequence specific ribonucleases similar to the toxin MazF? What are the targets for the toxic
References (30)
- et al.
PIN domains in nonsense-mediated mRNA decay and RNAi
Curr. Biol.
(2000) Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA
J. Mol. Biol.
(2003)Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
J. Mol. Biol.
(2001)The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology
Tuberculosis (Edinb.)
(2003)Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease
J. Biol. Chem.
(2004)Disruption of the mycobacterial cell entry gene of Mycobacterium bovis BCG results in a mutant that exhibits a reduced invasiveness for epithelial cells
FEMS Microbiol. Lett.
(1999)Characterization of the Mycobacterium tuberculosis region containing the mpt83 and mpt70 genes
FEMS Microbiol. Lett.
(2001)PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA
RNA
(2004)- et al.
New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system
Genome Biol.
(2003) - et al.
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
Nucleic Acids Res.
(2005)
Characterization of a novel toxin-antitoxin module, VapBC, encoded by Leptospira interrogans chromosome
Cell Res.
Prokaryotic toxin-antitoxin stress response loci
Nat. Rev. Microbiol.
The TIGRFAMs database of protein families
Nucleic Acids Res.
Selection for plasmid post-segregational killing depends on multiple infection: evidence for the selection of more virulent parasites through parasite-level competition
Proc. R. Soc. Lond. B. Biol. Sci.
Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids
Proc. Natl. Acad. Sci. U. S. A.
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