Mobility and Consecutive Exonic Sequence Variations

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nadl-i4-orfl and coxl-i7~$. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nadl-iCorfl and coxl-i7-orf2appeared highly invasive. Sequence comparisons in the nadli4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. G ROUP I introns are nonessential genetic elements. Most confer no apparent selective advantage at the individual level (SERAPHIN et al. 198'7) but have spread in the course of evolution because endowed with invasive properties imparted by the product of the open reading frames (ORFs) they contain (LAMBOWITZ and BELFORT 1993). Their homing from intron-containing gene to cognate intronless allele is dependent upon this product, a site-specific endonuclease that creates a double-strand break at the exon-exon junction of the intronless allele ( JACQUIER and DUJON 1985; MACREADIE et al. 1985; COLLEAUX et al. 1986). The two distinct domains of mobile group I introns (catalytic core and endonuclease-encoding ORF) are supposed to have evolved independently ( LAMBOWITZ and BELFORT 1993). The presence of related intronic ORFs in divergent organisms was already proposed to be the result of genetic exchanges involving the ORF sequence independently of the intron (MICHEL and DU.JON 1986). Likewise, the presence in highly conserved introns of ORFs potentially encoding endonucleases that vary in both sequence and position (i .e, , CUMMINGS and DOMENICO 1988; MOTA and COLLINS 1988; SHUB et al. 1988) also strongly suggests that the ORFs rather than the introns were the original mobile elements ( BELL-PEDERSEN et al. 1990). Moreover, OW-encoding, or potentially encoding, endonucleases similar to those found in group I introns have been identified in various Corresponding author: C. H. Sellem, Centre de GCnCtique MolCculaire, C.N.R.S., 1, avenue de la Terrasse, 91198 Gifsur-Yvette, France. E-mail: [email protected] Genetics 143 777-788 (June, 1996) other contexts such as in an archeal intron (DALGAARD et al. 1993) and as free standing sequences, inside (i.e., the inteins; COOPER and STEVENS 1995) or outside (SHARMA et al. 1992; PEL and GRIVEL 1993; PAQUIN et al. 1994) gene context. In some of these cases, the ORFs were described as optional and proposed to be recent acquisitions, but their mobility as independent genetic entities has only been demonstrated in the case of inteins ( GIMBLE and THORNER 1992). Colonization of preexisting group I introns by independent mobile ORFs is supported by a few examples of optional ORFs (MOTA and COLLINS 1988; BECHHOFER et al. 1994; BINISZKIEWICZ et al. 1994; DE JONCKHEERE and BROWN 1994). Different mechanisms of acquisition have been proposed (LOIZOS et al. 1994; VADER et al. 1994), but no experimental evidence of mobility of such ORFs, from OW-containing intron to cognate OW-less allele, has