The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

“The rRNA sequences were aligned initially using ClustalX ( Thompson et al. 1997 ).”

“Dictyostelium discoideum and Acanthamoeba castellanii are thought to be more distant relatives of this group that diverge before the split of fungi and metazoa ( Baldauf et al. 2000; Van der Peer et al. 2000; Lang et al. 2002).”

“The identity elements and antideterminants of tRNAs are key aspects of the molecules that play a crucial role in the proper aminoacylation and prevention of misacylation of a tRNA (Giegé et al. 1998).”

“The branching order of the species within Ascomycota agrees with Bullerwell et al. (2003a) and Kurtzman and Robnett (2003), and that within Chytridiomycota agrees with Bullerwell et al. (2003b).”

“The grouping of fungi and metazoa, proposed by Baldauf & Palmer (1993), is supported by all the studies cited in the previous paragraph.”

“Winchell (2002) and Halanych (2004) for the relationship between the animal phyla.”

“(v) Ascomycota (group containing Yarrowia and relatives) Knight et al. (2001a) list a single change in the ancestor of Metazoa, Acanthamoeba and Fungi.”

“The three theories explaining codon reassignment are not exclusive considering that the ‘‘ambiguous intermediate’’ stage can be preceded by a significant decrease in the content of GCrich codons, so that codon reassignment might be driven by a combination of evolutionary mechanisms (56), often under the pressure for g…”

“changes, for reviews see [24–26]).”

“This tRNA-Trp mutation has also been observed in mitochondrial genomes that have the UGA StopRTrp recoding [24].”

“Splitting a two-codon family into separate single codons is possible in the case of Met and Trp codons, but this does not increase the number of amino acids encoded in either case; and, in many mitochondrial codes, Met and Trp both have two codons (Sengupta et al., 2007).”

“, 2009), as well as in mitochondria (Sengupta et al., 2007).”

“Remarkably, these mitochondrial protein-coding genes are translated using genetic codes different from the standard (nuclear) genetic code in many living eukaryotes 10 .”

“We have shown that the codon disappearance mechanism is a good explanation of some (but by no means all) the codon reassignments that occur in mitochondrial genomes [11].”

“This lack of phylogenetic signal may be caused by the strong A þ T bias of mitochondrial genomes or by multiple independent changes in the mitochondrial genetic code along the evolution of eukaryotes (such process is known to occur at a higher rate in the mitochondrial genome than in the nuclear genome; e.g., Knight e…”

“Still, any adaptive nature of the later changes in the genetic code has continued to be doubted, because there was apparently little to be gained from code alterations in modern organisms (9).”

“The changes corresponding to the gain and loss events are known in a large number of other cases too (Sengupta et al. 2007); thus, the biochemical details responsible for codon reassignments in the modern phase are fairly well understood.”

“These mechanisms fit the general ‘gain and loss’ framework, where ‘gain’ refers to acquisition of a new tRNA specificity, typically resulting from duplication of a tRNA gene, whereas ‘loss’ is elimination of a tRNA specificity, typically via deletion [11,23,24].”

“However, deviations in sense and nonsense codon use are found in bacteria, archaea, and both nuclear and organellar eukaryotic genomes (2, 3).”

“Loss of the Q modification and subsequent GA pairing is relevant with respect to the origin of several variant genetic codes in mitochondrial genomes (Yokobori et al. 2001; Sengupta et al. 2007).”

“While codon disappearance seems likely for the stop-to-sense codon changes of mitochondria, it is unlikely that the original codon would disappear entirely in sense-to-sense changes (Sengupta et al., 2007).”

“Simulation study on codon reassignment [54]suggested that the pathway of codon reassignment in favor of either “codon capture” or “ambiguous codon” depends on the initial conditions such as genome size and number of codons in interest.”

“This is why it is easier to detect codon reassignments that include stop codons, and might be the reason why most detected variations in genetic codes involve stop codons (Massey and Garey, 2007; Sengupta et al., 2007; McCutcheon et al., 2009; McCutcheon, 2010; Turmel et al., 2010).”

“All mitochondrial protein-coding genes commence with a classical methionine codon (ATG) and terminate with TAA, the preferred fungal mitochondrial termination codon [31].”

“…that the H. sapiens mitochondria with 22 tRNA species must gain some flexibility (each tRNA decodes two or four codons) in the decoding process (20–22) without loosing fidelity in contrast to E. coli with 45 tRNA species (or 41 anticodons) and H. sapiens cyto-plasms with 46 tRNA species (28,29).”

“These results offer empirical substantiation of previous models on stop codon reassignment (Osawa and Jukes 1989, 1995; Andersson and Kurland 1991; Sengupta and Higgs 2005; Sengupta et al. 2007).”

“Release factors 7,25 and tRNAs 26,27 with altered specificities suggest it is feasible to engineer attenuated UGA recognition, mitigating translation factor competition to free TGA alongside TAG for reassignment.”

“In Kluvyeromyces lactis, the mitochondrial genome lacks both CUN codons and any tRNA reading such codons (7).”

“Such avoidance of certain codon families would facilitate the evolutionary loss of the associated tRNA [33-35], although it is not always clear whether the avoidance is the cause or the consequence of the loss of the associated tRNA.”

“Unique features include RNA-poor mitoribosomes [25], partial stop codons in some transcripts that are completed by polyadenylation [21, 26], bicistronic transcripts [27], and unique genetic code [28].”

“Such avoidance of certain codon families would facilitate the evolutionary loss of the associated tRNA (Higgs et al. 2003; Sengupta and Higgs 2005; Sengupta et al. 2007), although it is not always clear whether the avoidance is the cause or the consequence of the loss of the associated tRNA.”

“Authors' response: There are a number of alternative genetic codes, for example in Candida albicans [38] and the ciliates Tetrahymena thermophila and Paramecium tetraurelia [39], not to mention in mitochondrial genomes [37].”

“Arg-tRNAUCU gene, which has been proposed as the initial step for these reassignments [68].”

“Full list o f a u th o r inform ation is available a t th e e n d o f th e article Two main models have been proposed to explain the evo­ lutionary changes in the genetic code [reviewed in [4-7]].”

“lactis; (Sengupta et al. 2007)].”

“According to previous studies that tried to explain the codon reassignments in mt genetic codes of eukaryotes, several mechanisms have been suggested to explain these alterations (Sengupta et al., 2005; Sengupta et al., 2007; Sengupta and Higgs, 2015).”

“Interestingly, codon reassignments are particularly frequent in metazoan mitochondria (Figure 1), where more than 10 variants have been described (Knight et al. 2001; Abascal et al. 2006a; Sengupta et al. 2007).”

“tionary scenario, which was based mainly on theoretical considerations and included a temporary ambiguous decoding system, was initially proposed by Schultz and Yarus (the ‘ambiguous intermediate’ theory; Schultz and Yarus, 1994; 1996) and further developed by others to explain the emergence of TilS in bacteria (Silva…”

“Stramenopiles universally lack mitochondrial-encoded threonine tRNA [41], contain a fused version of the glycolysis enzymes glyceraldehyde-3-phosphate dehydrogenase and triosephosphate isomerase [42, 43], and have relocalized the ATP-yielding part of glycolysis from the cytosol to the mitochondria…”

“For example, the UGA codon in mitochondria of many eukaryotes (other than land plants) codes for tryptophan rather than a stop (7); AGR codons (R=A or G) in inchordata mitochondria code for glycine rather than arginine (8); and CUN codons (N=A, U, G or C) in yeast mitochondria code for threonine instead of leucine (9).”

“AUA(Ile ! Met) has been described in the mitochondrial genome of yeast, metazoa, and Xanthophyceae (Ehara et al. 1997; Yokobori et al. 2001; Sengupta et al. 2007).”

“A connection between alterations of tRNA identity by RNA editing and variation of the genetic code was discussed in (12,22).”

“More recently, reassignment scenarios have been discussed within an extended gain– loss framework of codons and tRNAs, pointing out that it is necessary to consider the details of each case carefully (11).”

“This enrichment is effectuated by alterations in the mitochondrial genetic code that have occurred several times independently during the Cambrian radiation [26,27].”

“In addition, the structure of the genetic code implies a further mechanism against frameshifted translation.”

“For mitochondrial code variants this is recently described in [8].”

“Evolutionary emergence of these alterations is driven by genome reduction and mutational bias toward A?T residues, which are involved in the replacement of UAG(stop) by UAA and the emergence of UGA(Trp) from UGG(Trp) (Osawa and Jukes 1989; Sengupta et al. 2007).”

“…of how such codes could evolve, and the basic conclusion is that random events, like the disappearance of a codon, loss of a tRNA gene, or mutations in a tRNA gene that allow it to recognize other codons, drive this comparably modern evolution (Sengupta and Higgs 2005, Sengupta et al. 2007).”

“…fungi (3 times independently), chlorophytes, rhodophytes, stramenopiles (twice independently), kinetoplastids, diatoms, prymnesiophytes (surveyed in Sengupta et al. 2007), chlorarachniophytes (Inagaki et al. 1998) and prasinophytes (Turmel et al. 1999, 2010) Glutamine UAA and UAG Tetrahymena…”

“It should be noted that we do not attempt to explain the original emergence of the Standard Code itself or the codon reassignments during emergence of alternate codes (extensive studies can be found in Crick 1968; Ardell 1998; Freeland et al. 2000; Silva et al. 2004; Sengupta and Higgs 2005; Sengupta et al. 2007), or…”

“…lead to a reversion to the standard genetic code, as seems to be the case of AUA decoded normally as isoleucine in mitochondria of certain bilaterian invertebrates despite the fact that AUA encodes methionine in most bilaterians and is likely the ancestral state for the whole group 23,128 .”

“Almost all eukaryotes in which UGA is decoded by tRNA have the UCA anticodon [13].”

“Two main mechanisms have been proposed to explain how they may have evolved despite the large fitness cost that is expected to be associated with the modification of a codon [9,23,24]: through an ambiguous intermediate state and through the reassignment of a temporarily unused codon.”

“Further, several methanogenic archaea rewire the amber stop codon into a signal for incorporation of the 22nd amino acid, pyrrolysine (Pyl) (13,14), whereas the anomalous recognition of the AUA codon by tRNAMet alters the meaning of this particular triplet from isoleucine (Ile) to methionine (Met) in the mitochondria…”

“Simulation studies on codon reassignment (Sengupta et al. 2007) suggest that the pathway of codon reassignment in favour of either “codon capture” or “ambiguous codon” depends on initial conditions such as genome size and number of codons involved.”

“After a long debate on the origin of the modern genetic code variants [50,51], there is compelling evidence now to indicate that deviant genetic codes like those in animal mitochondria primarily evolve to match the amino acid requirements of the encoded proteins [18,51,52] rather than having their…”

“For instance, the mitochondrial code differs from the conventional code, shedding light on the coevolutionary dynamics between mitochondria and host cells [37].”

“Sengupta et al. (2007), for example, assume that sense-to-sense codon reassignment is deleterious in its initial stages and is followed by a lengthy period of adjustment in which an initially maladapted genome adapts to the new code.”

“The reappearance of UGA with the new meaning as a tryptophan codon in distantly related chlorophytes is then an exemplar manifestation of the codon disappearance model of codon reassignment [54].”

“The Codon Capture, also termed the Codon Disappearance theory, proposed by Osawa and Jukes in 1989, postulates that genetic code alterations are the result of neutral changes associated with the GC/AT content balance [35–38].”

“8, Moreover, during translation, mRNA triplets may, in some cases, have an additional meaning than they have according to the genetic code.”