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.”

“xa, the relationships between groups in the very earliest parts of the eukaryotic tree have proved difficult to resolve (Lang et al. 1999; Baldauf et al. 2000; Van der Peer et al. 2000; Baldauf 2003; Philippe et al. 2004). Our aim here was not to resolve these early branches, but to obtain trees that would allow for a…”

“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).”

“A reviewer of this paper pointed out that Osawa and Jukes (1989) , the original proponents of the CD model, insisted that, according to their theory, every single occurrence of the codon must disappear from the genome before the reassignment occurred.”

“This mechanism is expected in the theory due to the analogy of the problem with compensatory mutation theory (Kimura, 1985; Higgs, 1998, 2000).”

“This mechanism is expected in the theory due to the analogy of the problem with compensatory mutation theory (Kimura 1985; Higgs 1998 2000).”

“We have followed Mallatt & Winchell (2002) and Halanych (2004) for the relationship between the animal phyla.”

“Telford et al. (2000) have also discussed these two alternative scenarios in a parsimony treatment, however they did not consider the position of the tRNA-Ile(CAU) gene loss, or the fact that there are several independent modifications to the tRNA-Met, both of which are essential points in our…”

“Amoebidium parasiticum and Monosiga brevicollis are thought to be the closest unicellular relatives of the metazoa, and are therefore also included in this group.”

“(vi). Rhodophyta (Chondrus, Porphyra): Fig. 2 and Burger et al. (1999) .”

“It is known that many protein genes formerly present on the mitochondrial genome have been transferred to the nuclear genome (Blanchard and Lynch, 2000).”

“We attempted to answer this question with the kinetoplastids, Trypanosoma brucei and Leishmania tarentolae, which possess no mitochondrial tRNAs and where import is known to occur (Simpson et al. 1989; Hancock and Hajduk 1990; Schneider andMarechal-Drouard 2000).”

“4), which suggests that it was lost after the divergence of the phylum Porifera from other metazoan phyla.”

“We believe that there is a good case that positive selection was important in the establishment of the canonical code (Freeland et al. 2003; Ardell & Sella, 2002) and that this accounts for the non-randomness and apparent optimization of the code.”

“This was proposed by Schultz and Yarus (1994, 1996).”

“2 and Turmel et al. (1999).”

“and Burger et al. (1995). (iii).”

“We attempted to answer this question with the kinetoplastids, Trypanosoma brucei and Leishmania tarentolae, which possess no mitochondrial tRNAs and where import is known to occur (Simpson et al. 1989; Hancock and Hajduk 1990; Schneider and Marechal-Drouard 2000 ).”

“For the arrangement of the species within the Stramenopiles, we used the results of a much larger scale study with the nuclear small subunit rRNA gene ( Van der Peer et al. 1996 ).”

“tRNA is imported to the mitochondrion and then undergoes a base modification so that it can translate both UGA and UGG (Alfonzo et al. 1999).”

“Now that many complete genomes of organisms and organelles are available, there is ample evidence that the genetic code is not as universal (Knight et al. 2001a; Yokobori et al. 2001; Santos et al. 2004) as previously believed (Crick 1968).”

“Kurzman & Robnett (2003) and Diezmann et al. (2004) have considered the phylogeny of these groups using nuclear genes, and find that Candida, Kluyveromyces, Saccharomyces and Pichia are all paraphyletic.”

“It has previously been shown that codon usage patterns differ between the intronic ORFs and the other genes (Bullerwell et al. 2003; Talla et al. 2005).”

“However, Massey et al. (2006) have now shown that there is selection against the ambiguous CUG codons that causes them to become very rare in their original Leu positions.”

“Nedelcu et al. (2000) identified a tRNA-Arg(UCU) that should interact with AGA, and a tRNA-Ile(UAU) that should interact with AUA.”

“However, it has been suggested that ambiguous translation may be favorable (Santos et al. 1999).”

“This was proposed by Schultz and Yarus (1994, 1996).”

“Reassignments of UAG stop codons Two cases of reassignment of UAG from Stop to Leu are known: one in the two chytrids, Rhyzophidium and Spizellomyces (Fig.”

“Seif et al. (2005) argue that this has occurred in Mortierella and Schizosaccharomyces, where there is evidence of a small number of UGA acting as Trp codons that are translated very inefficiently by the standard Trp tRNA with CCA anticodon.”

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

“This point has been suggested previously (Saks et al. 1998), but as far as we are aware, there is no direct evidence that this occurs.”

“Multiple sequence alignments were carried out using T-COFFEE ( Notredame et al. 2000 ) and the alignment was edited to remove columns having more than 20% gaps.”

“It has been suggested that deletion of a tRNA gene might be favored since it reduces the total length of the genome and hence allows more rapid replication ( Andersson and Kurland 1991, 1995 ).”

“Stramenopiles and alveolates are two groups that are thought to be monophyletic according to Wolters (1991) and Saunders et al . (1995) .”

“Although there is general agreement on the definitions of the major eukaryotic taxa, the relationships between groups in the very earliest parts of the eukaryotic tree have proved difficult to resolve (Lang et al. 1999; Baldauf et al. 2000; Van der Peer et al. 2000; Baldauf 2003; Philippe et al. 2004).”

“It has previously been shown that codon usage patterns differ between the intronic ORFs and the other genes (Bullerwell et al. 2003; Talla et al. 2005).”

“These authors also show that the unmodified CAU anticodon can translate both codons if the base in the 37th position of the tRNA is t 6 A (N 6 - threonylcarbamoyladenosine) instead of A (see also Kuchino et al. 1987).”

“The codon usage of Chlamydomonas reinhardtii is markedly different from C. eugametos (Table 5 and Denovan-Wright et al. 1998).”

“Also in some echinoderms, the mutation of the base immediately adjacent to the 5’ end of the anticodon from a U to a C seems to help the GUU anticodon to recognize AAA (Castrasena et al. 1998).”

“floridae (Boore et al. 1999) and Epigonichthys maldivensis (Nohara et al.”

“In C. glabrata, Koszul et al. (2003) conclude that AUA is associated with Met based on comparison of C. glabrata sequences with S. cerevisiae sequences from which they find that 8 out of 16 AUA codons in C.glabrata appear at conserved Met sites encoded by AUA in S. cerevisiae.”

“The corresponding tRNA-Arg is also deleted in this species (Kerscher et al. 2001).”

“For this reason, wobble position U’s are often modified when they occur in tRNAs for two-codon families only (Yokobori et al. 2001).”

“In the case of the tRNA-Asn(GUU), mispairing with AAA is prevented by post-transcriptional modification of the wobble position G to Queuosine (Q), which allows pairing with U and C but inhibits pairing with A (Morris et al. 1999).”

“) Another study suggesting that ambiguous translation is deleterious is that by Kim et al. (2000), who studied many examples of anticodon mutations in tRNA-Phe from E.”

“(xi) Bacillariophyta (Skeletonema, Thalassiosira) - Fig 3 and Ehara et al. (2000) (xii) Kinetoplastida (Trypanosoma, Leishmania) - Inagaki et al. (1998).”

“There is evidence for this in Bacillus subtilis (Lovett et al. 1991, Matsugi et al. 1998), where UGA is ambiguous.”

“coli (Muramatsu et al. 1988) that the C at the wobble position undergoes a posttranscriptional base modification to K(2)C (lysidine), which allows this tRNA-Ile to pair with the AUA codon.”

“We interpret the decoding of AUA as Ile in Platyhelminths and Echinoderms/Hemichordates as indicating that an appropriate change in the tRNA-Met did not occur, and that AUA has always been Ile in these lineages.”

“In the remaining Metazoa (i.e. Bilateria) the loss of the tRNA-Arg(UCU) gives rise to subsequent changes in the genetic code.”

“We believe that there is a good case that positive selection was important in the establishment of the canonical code (Freeland et al. 2003; Ardell & Sella, 2002) and that this accounts for the non-randomness and apparent optimization of the code.”

“1999) and Epigonichthys maldivensis (Nohara et al. 2005), which also show no evidence of reassignment of AGA to Gly.”

“This mechanism is expected in the theory due to the analogy of the problem with compensatory mutation theory (Kimura, 1985; Higgs, 1998, 2000).”

“Since AGA was a moderately frequent codon for Ser prior to the reassignment, and since %A is high, we cannot argue that mutation pressure caused the disappearance of AGA and replacement by AGR prior to the change.”

“Many of the closest relatives to the species where UGA is reassigned have particularly low usage of UGA, e.g. Allomyces and Rhizopus, close relatives of the Basidiomycota, have 0; Cyanidioschyzon, close relative of Chondrus and Porphyra, has only 2; Scenedesmus and Chlamydomonas, close relatives of Pedinomonas, have 1…”

“Talla et al. (2005) argue that AUA is assigned toMet inK.”

“Before codon reassignment, tRNA-Met also has a CAU anticodon, which pairs with AUG only, but modification of the wobble-position C allows it to pair with both AUA and AUG ( Tomita et al. 1999b ).”

“A second similar case is the reassignment of UCA from Ser to Stop in Scenedesmus obliquus (Kück et al. 2000).”

“In the simulations of codon reassignment (Sengupta and Higgs 2005) it was possible to distinguish a few cases where this occurred.”

“The complete genome of Emiliana (Sanchez-Puerta et al. 2004) shows that it also possesses the reassignment.”

“Swire et al. (2005) did not distinguish between AI and UC.”

“Alternatively, in some Echinoderms (Matsuyama et al. 1998) and Molluscs (Tomita et al. 1998) a base modification from G to m 7 G also permits it to decode the entire AGN block as Ser.”

“(xi) Bacillariophyta (Skeletonema, Thalassiosira) - Fig 3 and Ehara et al. (2000) (xii) Kinetoplastida (Trypanosoma, Leishmania) - Inagaki et al. (1998).”

“It has previously been shown that codon usage patterns differ between the intronic ORFs and the other genes (Bullerwell et al. 2003; Talla et al. 2005).”

“This was originally proposed by Osawa and Jukes (1989, 1995) .”

“The fact that the tRNA-Thr(UAG) appears only in species where the tRNA-Leu(UAG) is absent suggests that the new gene evolved directly from the old tRNA-Leu(UAG) gene.”

“In mitochondrial genomes, the two strands of the genome are not equivalent, the four base frequencies are all different, and it is not true that πC = πG and πA = πU (see Urbina et al. 2006).”

“These species possess an unusual tRNA-Thr with anticodon UAG (Sibler et al. 1981; Osawa et al. 1990) and the usual tRNA-Leu(UAG) is not found in the genome.”

“There is evidence for this in Bacillus subtilis (Lovett et al. 1991, Matsugi et al. 1998), where UGA is ambiguous.”

“Another study suggesting ambiguous translation is deleterious is that of Kim et al. (2000), who studied many examples of anticodon mutations in tRNA-Phe from E. coli.”

“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).”