Inteins are selfish genetic elements that disrupt the sequence of protein-coding genes and are excised post-translationally. Most inteins also contain a HEN (homing endonuclease) domain, which is important for their horizontal transmission. The present review focuses on the evolution of inteins and their nested HENs, and highlights several unsolved questions that could benefit from molecular genetic approaches. Such approaches can be well carried out in halophilic archaea, which are naturally intein-rich and have highly developed genetic tools for their study. In particular, the fitness effects of habouring an intein/HEN can be tested in direct competition assays, providing additional insights that will improve current evolutionary models.

HENs (homing endonucleases)

HENs are a large and diverse class of selfish elements found in archaea, bacteria and lower eukaryotes, and their respective viruses. HENs recognize and cleave specifically long target sequences (12–40 bp) that typically occur only once in a given genome [1,2]. Remarkably, HENs are found almost exclusively within self-splicing selfish elements, namely introns, which excise themselves at the mRNA level, and inteins, which splice out of the protein product [3] (Figure 1a). HENs contribute to the horizontal propagation of these selfish elements into intron-less or intein-less alleles, by cleaving the vacant allele to induce homologous recombination or reverse transcription (Figure 1b). Since HENs within group I introns were reviewed recently [4], we focus on HENs occupying inteins, examine the interesting evolutionary questions they bring up, and propose ways in which molecular biology experiments can help resolve undecided evolutionary conundrums.

Protein splicing and homing

Figure 1
Protein splicing and homing

(a) Inteins and protein splicing. (b) Target invasion by HENs.

Figure 1
Protein splicing and homing

(a) Inteins and protein splicing. (b) Target invasion by HENs.

Mutualism between selfish elements

Although it is obvious that inteins can profit from horizontal invasion, how and why the HEN benefits from its association with the intein is less obvious. Since HENs typically confer no selective advantage upon their host organism, they can only persist as long as the rate of their dissemination surpasses the rate of their degeneration via genetic drift or counterselection. The rate of dissemination is in turn dependent on the availability of homing targets, which are also subjects of mutation and selection. If cleavage by the HEN is by any degree toxic to the host, mutations in the target site may be selected that prevent it from being recognized or cleaved. Even if the HEN is neutral with respect to the survival of the host, the sequence of the target site may drift faster than can be accommodated by the evolution of the HEN. The long-term survival of a HEN is therefore dependent on the conservation of its target site. This target site is also the eventual insertion site of the HEN, and an insertion in a conserved locus will often dramatically reduce host fitness. Conversely, a HEN will cause no harm in terms of target disruption if it inhabits an intein, since it will be spliced out, preserving the function of their hosting gene. Moreover, inteins, whether with or without a HEN, tend to occupy conserved regions of essential genes [5,6]. This is the intein's intrinsic way of avoiding degeneration, since any disabling mutation in its splicing domain will create a permanent insertion in the essential gene and will therefore be eradicated. Thus, in this association, we observe mutualism between selfish elements: the HEN benefits from being nested within a spliceable ORF (open reading frame) integrated within a conserved site (the intein), while at the same time providing that ORF with transmissibility.

How did the mutualism between selfish elements evolve?

Free-standing HENs are known to exist in bacteriophages, where they can cleave the DNA of a competing bacteriophage, but not the one carrying them, thus providing a fitness advantage when two or more phages infect a host cell [7]. How HENs became associated with inteins remains unclear. However, two recent studies in bacteriophages may have revealed the process underlying the mutualistic association of introns and HENs, which is highly likely to be relevant also to inteins. In the cyanophage S-PM2, a free-standing HEN, similar in sequence to DNA resolvases, was observed close to the psbA gene, which contains a group I intron lacking a nested HEN [8]. This HEN, F-CphI, was shown to be unable to cleave the intron-containing psbA gene, but does cleave efficiently empty (intron-free) psbA alleles just a few nucleotides from the intron insertion site [9]. Furthermore, Bonocora and Shub [10] showed that, in a gene encoding DNA polymerase in T3 and T7 bacteriophages, there exists a site adjacent to an intron insertion point, which can be targeted by either an intron-nested HEN (T7) or a free-standing HEN (T3), again implying that HENs that target intron insertion sites can gradually become associated with introns. It is expected that the mutualistic relationship between the two elements was stabilized once they became physically associated.

How do HENs avoid degeneration?

The potential mutational drift of the target site mentioned above is not the only threat for the survival of HENs. Somewhat paradoxically, the very proliferation of a HEN may sow the seeds of its own destruction: in order to prevail on an evolutionary timescale, a HEN must also overcome the danger of target site depletion as a result of its own fixation in the population. Extensive horizontal propagation of the HEN could lead to fixation, with the HEN occupying every allele of the hosting gene in the population. Once fixation is achieved, no vacancy is left for further homing. Subsequently, there will be no selective pressure favouring the conservation of the HEN, making degeneration via accumulation of mutations inevitable (Figure 2). Indeed, inteins in various species were found to encode degenerated HENs, characterized by an accumulation of asynonymous mutations [11,12] and a lack of activity in in vitro cleavage assays [13,14]. Intriguingly, functionally degenerate HENs within inteins, unlike those that reside in introns, still show signs of purifying selection and maintain several highly conserved positions, perhaps suggesting that some positions within the HEN domain are also important for the protein-splicing reaction of the intein or for its overall structure [12].

The homing cycle

One possible getaway from the fixation-degeneration deadlock is to invade new niches, in other species, via horizontal transfer (Figure 2). However, quite often, HEN phylogenies agree with those of the host organism, implying that many HENs do nevertheless persist in a specific locus through evolutionary timescales. How then do they escape the fixation-degeneration catch? The canonical model of HEN evolution proposed by Burt and Koufopanou [1], called ‘the HEN cycle’ or the ‘homing cycle’ [2], addresses this enigma by invoking the recycling of homing targets. It proclaims that, while HEN propagation acts to exhaust all available targets, there is also an opposing process, namely precise intron/intein loss, which provides the supply of fresh targets (Figure 2). Indeed, phylogenetic analyses support the idea of frequent intron/intein loss, as very often several species in a genus harbour an intron that is not found in other species of that genus. Analogously, at the subspecies level, the HEN may persist while avoiding fixation if sporadic populations exist with and without the intron, and these populations exhibit low gene flow among them.

Although one can imagine a precise deletion of an intron by homologous recombination with its own cDNA, explaining how an intein will be precisely deleted is not easy. Homologous recombination between an intein-containing and a vacant allele will tend to result in gene conversion events in which the former is duplicated, rather than the latter. This is due to the fact that HEN activity (the creation of a double-strand break at the vacant allele) promotes gene conversion. Thus one has to posit that HEN degeneration or inactivation is a necessary step that always precedes intein deletion. However, even if such degeneration has already taken place, coming into contact with such a vacant allele should be a relatively rare event, requiring horizontal gene transfer from another population or species, and, as long as some parts of the population still have an active HEN, these events are unlikely to efficiently compete with homing. Moreover, recombination that is not triggered by HEN cleavage has a similar propensity to result in intein gain as it does to result in intein loss. Recently, both experimental data from euascomycetes species [15] and mathematical modelling [16] have shown that HENs can be maintained for very long evolutionary periods even in the absence of horizontal gene transfer. In fact, all three types of homing site can coexist in a well-mixed population assuming that the reduction in fitness resulting from carrying a dysfunctional HEN is higher than the reduction in fitness due to its functional counterpart [16].

However, currently, there is no specific evidence in support of that assumption. When the cost to host fitness of the functional HEN was actually higher than the cost of its dysfunctional counterpart, only periodic solutions were obtained [16], with typical allele frequencies that are lower than commonly observed in the natural populations surveyed to date [15]. Several alternative routes for HEN persistence have been suggested [2]. One such scenario that is in agreement with selfish element mutualism, states that inteins may be lost along with their resident HENs if they (and not the HENs as above) are detrimental to the fitness of their hosts [15]. This toxicity cannot be remedied by mutations that interfere with efficient splicing, because the intein is usually inserted in a conserved site of a vital protein. However, if individuals that possess the vacant allele are still present in the population, the fitness cost of the intein is likely to drive the vacant allele to fixation, resulting in eventual intein loss. Nonetheless, the intein can be actively propagated by its nesting HEN, and if the adverse effect is relatively minor, a dynamic equilibrium can result, since, on one hand, intein-less hosts are more fit, but, on the other, homing allows the invasion of the intein into vacant alleles. This balance will ensure a constant supply of vacant targets, and therefore a continuous selective pressure acting to conserve the homing ability of the HEN. Thus, paradoxically, by residing within inteins that cause a slight reduction in fitness, HENs can be protected from the fixation-degeneration mechanism. Gogarten and Hilario [2] pointed out that, although this dynamic equilibrium may be too precise and fragile to be maintained within a population, a balance between decreased host fitness and increased spreading of the intein, combined with a complex population structure (i.e. several subpopulations in which the fitness disadvantage and the homing efficiency could vary) can generate long persistence without requiring a homing cycle. Furthermore, even if the homing cycle does exist, it could be operating only within specific subpopulations, whereas in the meta-population, the HEN-mobilized intein never reaches fixation [2].

Another intriguing alternative to the homing cycle is that the HEN itself may confer some selective advantage on its host. Although the ability to cut the DNA of competing viruses can surely be an asset to HEN-containing bacteriophages [17], other benefits, such as a beneficial role in chromosomal DNA rearrangement, as described in the thermophilic archaeon Pyrococcus kodakaraensis [18], may be less obvious and more difficult to demonstrate. Another case that illustrates such possible mechanisms is that of the ‘HO’ HEN of Saccharomyces cerevisiae, derived from the intein VDE [VMA1 (vacuolar membrane ATPase 1)-derived endonuclease], which no longer propagates an intein but has been ‘domesticated’ and now mediates a new role, that of a mating-type switch, in that yeast [12].

Halophilic archaea as a model genetic system to study inteins and their HENs

Clearly, it is often difficult to decide between the different evolutionary scenarios presented above on the basis of mathematical modelling and phylogenetic reconstruction alone, no matter how well executed. Furthermore, incorporating experimental observations can help to define better the assumptions and parameters of the models. Ideally, studies of HEN evolution should incorporate population genetics studies, involving the comparison of inteins from same-species isolates [19,20] and molecular genetics studies, measuring the influence on fitness of HEN and/or intein presence in vivo and quantifying homing efficiency in a natural-like laboratory experiment that could involve both intra- and inter-species homing. Currently, the best example of such a genetic approach is the landmark intron study by Aagaard et al. [21], which showed that when the 23S rRNA HEN-containing intron of the archaeal hyperthermophile Desulfurococcus mobilis was artificially introduced into another hyperthermophilic archaeon, Sulfolobus acidocaldarius, it quickly spread through the S. acidocaldarius population, presumably by archaeal mating [2224] or conjugation [25] and intron-containing cells obtained a fitness advantage over their intron-free counterparts. Such an approach could easily be extended in intein research into a more natural-like experimental setting, where HEN genes are studied in their organisms of origin.

We propose that halophilic archaea (haloarchaea), which are easier to grow and manipulate than thermophiles, represent an ideal prokaryotic model system for the study of inteins/HENs due to several unique properties as follows.

(i) They harbour a multitude of inteins. Archaea in general and haloarchaea in particular tend to contain many inteins. For example, the square archaeon Haloquadratum walsbyi contains 14 putative inteins according to the intein database InBase [26]. Haloarchaea often harbour different inteins in the same gene. The gene encoding DNA polymerase B in haloarchaea (polB), for example, can contain at least four different inteins, and at least one species (H. walsbyi) has inteins occupying three possible locations [27]. An intein is occasionally conserved both in terms of the position of insertion and in terms of sequence similarity, across relatively remote haloarchaeal species. For example, the polB intein of Haloferax volcanii is homologous with one of the polB inteins in H. walsbyi.

(ii) Haloarchaea undergo horizontal gene transfer by the well-documented and highly efficient cell mating process [2224], which can allow DNA exchange within and even between species and therefore can facilitate the spread of a HEN to empty alleles within a population. Thus one can potentially monitor the dynamic of homing in real time.

(iii) Haloarchaea, in particular H. volcanii and Halobacterium salinarum, have become the most extensively used model organisms for molecular genetic studies of archaea because of the wide range of available genetic tools [28], such as shuttle vectors [29,30], the ability to manipulate their DNA by transformation [31,32], the existence of a strongly inducible promoter [33], as well as a targeted allele-exchange and gene-knockout system [34]. Finally, haloarchaea can also be harnessed to identify additional functions of HENs, which can be studied relatively simply, because host proteins can be engineered to be affinity-tagged, facilitating co-immunopurification experiments.

One can envisage several ways to use molecular genetics for the study of the evolutionary questions outlined above, by performing fairly straightforward experiments. (i) An intein-containing gene can be cured of its intein (or just the HEN domain) and compared with its wild-type counterpart, both in terms of individual growth/fitness and in direct competition experiments. (ii) A new intein can be introduced into a currently vacant site and the effects similarly examined. (iii) The invasion of a HEN-containing intein in a formerly intein-less population, can be monitored, by introducing a small number of intein/HEN-positive cells into a large intein-free population, then taking samples periodically and quantifying the fraction of intein-containing cells in the population (e.g. by quantitative real-time PCR). We have recently performed the first experiment (i), and showed that, under laboratory conditions, curing of an intein/HEN did not result in any change in fitness [35]

To date, intein/HEN research has already supplied many surprises, some of which have found industrial applications such as split inteins [36] or engineered HENs for gene therapy [37]. The future of intein/HEN research lies in combining multiple approaches including mathematical modelling, genomics, population genetics and molecular genetics. One can easily envision quantitative parameters derived from large population genetics surveys as well as molecular experiments being fed back into the existing mathematical models, increasing their predictive power. Conversely, new models and genomic observations will yield new hypotheses that need to be tested. Only by integrating multiple disciplines in the study of inteins/HENs could we hope to unravel the complex evolutionary puzzles that they are.

Molecular Biology of Archaea II: A Biochemical Society Focused Meeting held at Robinson College, Cambridge, U.K., 16–18 August 2010. Organized and Edited by Stephen Bell (Oxford, U.K.) and Finn Werner (University College London, U.K.).

Abbreviations

     
  • HEN

    homing endonuclease

  •  
  • ORF

    open reading frame

Funding

Work in the Gophna laboratory is supported by the James S. McDonnell Foundation and the Israeli Ministry of Health. Work in the Kupiec laboratory is supported by the James S. McDonnell Foundation, the Israeli Science Foundation and the Israel Cancer Research Fund.

References

References
1
Burt
A.
Koufopanou
V.
Homing endonuclease genes: the rise and fall and rise again of a selfish element
Curr. Opin. Genet. Dev.
2004
, vol. 
14
 (pg. 
609
-
615
)
2
Gogarten
J.P.
Hilario
E.
Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements
BMC Evol. Biol.
2006
, vol. 
6
 pg. 
94
 
3
Pietrokovski
S.
Intein spread and extinction in evolution
Trends Genet.
2001
, vol. 
17
 (pg. 
465
-
472
)
4
Nielsen
H.
Johansen
S.D.
Group I introns: moving in new directions
RNA Biol.
2009
, vol. 
6
 (pg. 
375
-
383
)
5
Edgell
D.R.
Stanger
M.J.
Belfort
M.
Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene
J. Mol. Biol.
2004
, vol. 
343
 (pg. 
1231
-
1241
)
6
Swithers
K.S.
Senejani
A.G.
Fournier
G.P.
Gogarten
J.P.
Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements
BMC Evol. Biol.
2009
, vol. 
9
 pg. 
303
 
7
Edgell
D.R.
Fast
N.M.
Doolittle
W.F.
Selfish DNA: the best defense is a good offense
Curr. Biol.
1996
, vol. 
6
 (pg. 
385
-
388
)
8
Mann
N.H.
Clokie
M.R.
Millard
A.
Cook
A.
Wilson
W.H.
Wheatley
P.J.
Letarov
A.
Krisch
H.M.
The genome of S-PM2, a “photosynthetic” T4-type bacteriophage that infects marine Synechococcus strains
J. Bacteriol.
2005
, vol. 
187
 (pg. 
3188
-
3200
)
9
Zeng
Q.
Bonocora
R.P.
Shub
D.A.
A free-standing homing endonuclease targets an intron insertion site in the psbA gene of cyanophages
Curr. Biol.
2009
, vol. 
19
 (pg. 
218
-
222
)
10
Bonocora
R.P.
Shub
D.A.
A likely pathway for formation of mobile group I introns
Curr. Biol.
2009
, vol. 
19
 (pg. 
223
-
228
)
11
Okuda
Y.
Sasaki
D.
Nogami
S.
Kaneko
Y.
Ohya
Y.
Anraku
Y.
Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts
Yeast
2003
, vol. 
20
 (pg. 
563
-
573
)
12
Koufopanou
V.
Burt
A.
Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis
Mol. Biol. Evol.
2005
, vol. 
22
 (pg. 
1535
-
1538
)
13
Saves
I.
Morlot
C.
Thion
L.
Rolland
J.L.
Dietrich
J.
Masson
J.M.
Investigating the endonuclease activity of four Pyrococcus abyssi inteins
Nucleic Acids Res.
2002
, vol. 
30
 (pg. 
4158
-
4165
)
14
Posey
K.L.
Koufopanou
V.
Burt
A.
Gimble
F.S.
Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species
Nucleic Acids Res.
2004
, vol. 
32
 (pg. 
3947
-
3956
)
15
Butler
M.I.
Gray
J.
Goodwin
T.J.
Poulter
R.T.
The distribution and evolutionary history of the PRP8 intein
BMC Evol. Biol.
2006
, vol. 
6
 pg. 
42
 
16
Yahara
K.
Fukuyo
M.
Sasaki
A.
Kobayashi
I.
Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer
Proc. Natl. Acad. Sci. U.S.A.
2009
, vol. 
106
 (pg. 
18861
-
18866
)
17
Goodrich-Blair
H.
Shub
D.A.
Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers
Cell
1996
, vol. 
84
 (pg. 
211
-
221
)
18
Nishioka
M.
Fujiwara
S.
Takagi
M.
Imanaka
T.
Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1
Nucleic Acids Res.
1998
, vol. 
26
 (pg. 
4409
-
4412
)
19
Wikmark
O.G.
Einvik
C.
De Jonckheere
J.F.
Johansen
S.D.
Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron
BMC Evol. Biol.
2006
, vol. 
6
 pg. 
39
 
20
Nomura
N.
Morinaga
Y.
Kogishi
T.
Kim
E.J.
Sako
Y.
Uchida
A.
Heterogeneous yet similar introns reside in identical positions of the rRNA genes in natural isolates of the archaeon Aeropyrum pernix
Gene
2002
, vol. 
295
 (pg. 
43
-
50
)
21
Aagaard
C.
Dalgaard
J.Z.
Garrett
R.A.
Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron− cells of Sulfolobus acidocaldarius
Proc. Natl. Acad. Sci. U.S.A.
1995
, vol. 
92
 (pg. 
12285
-
12289
)
22
Mevarech
M.
Werczberger
R.
Genetic transfer in Halobacterium volcanii
J. Bacteriol.
1985
, vol. 
162
 (pg. 
461
-
462
)
23
Rosenshine
I.
Mevarech
M.
Rodriguez-Valera
F.
The kinetic of the genetic exchange process in Halobacterium volcanii mating
General and Applied Aspects of Halophilic Microorganisms
1991
New York
Plenum Press
(pg. 
265
-
270
)
24
Ortenberg
R.
Tchelet
R.
Mevarech
M.
Oren
A.
A model for the genetic exchange system of the extremely halophilic archaeon Haloferax volcanii
Microbiology and Biogeochemistry of Hypersaline Environments
1999
Boca Raton
CRC Press
(pg. 
331
-
338
)
25
Stedman
K.M.
She
Q.
Phan
H.
Holz
I.
Singh
H.
Prangishvili
D.
Garrett
R.
Zillig
W.
pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: insights into recombination and conjugation in Crenarchaeota
J. Bacteriol.
2000
, vol. 
182
 (pg. 
7014
-
7020
)
26
Perler
F.B.
InBase: the Intein Database
Nucleic Acids Res.
2002
, vol. 
30
 (pg. 
383
-
384
)
27
MacNeill
S.A.
The haloarchaeal chromosome replication machinery
Biochem. Soc. Trans.
2009
, vol. 
37
 (pg. 
108
-
113
)
28
Allers
T.
Mevarech
M.
Archaeal genetics: the third way
Nat. Rev. Genet.
2005
, vol. 
6
 (pg. 
58
-
73
)
29
Holmes
M.
Pfeifer
F.
Dyall-Smith
M.
Improved shuttle vectors for Haloferax volcanii including a dual-resistance plasmid
Gene
1994
, vol. 
146
 (pg. 
117
-
121
)
30
Holmes
M.L.
Nuttall
S.D.
Dyall-Smith
M.L.
Construction and use of halobacterial shuttle vectors and further studies on Haloferax DNA gyrase
J. Bacteriol.
1991
, vol. 
173
 (pg. 
3807
-
3813
)
31
Cline
S.W.
Lam
W.L.
Charlebois
R.L.
Schalkwyk
L.C.
Doolittle
W.F.
Transformation methods for halophilic archaebacteria
Can. J. Microbiol.
1989
, vol. 
35
 (pg. 
148
-
152
)
32
Cohen
A.
Lam
W.L.
Charlebois
R.L.
Doolittle
W.F.
Schalkwyk
L.C.
Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea
Proc. Natl. Acad. Sci. U.S.A.
1992
, vol. 
89
 (pg. 
1602
-
1606
)
33
Large
A.
Stamme
C.
Lange
C.
Duan
Z.
Allers
T.
Soppa
J.
Lund
P.A.
Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene
Mol. Microbiol.
2007
, vol. 
66
 (pg. 
1092
-
1106
)
34
Bitan-Banin
G.
Ortenberg
R.
Mevarech
M.
Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene
J. Bacteriol.
2003
, vol. 
185
 (pg. 
772
-
778
)
35
Naor
A.
Lazary
R.
Barzel
A.
Papke
R.T.
Gophna
U.
In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii
PLoS ONE
2011
 
in the press
36
Sun
W.
Yang
J.
Liu
X.Q.
Synthetic two-piece and three-piece split inteins for protein trans-splicing
J. Biol. Chem.
2004
, vol. 
279
 (pg. 
35281
-
35286
)
37
Paques
F.
Duchateau
P.
Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy
Curr. Gene Ther.
2007
, vol. 
7
 (pg. 
49
-
66
)