Hybridization between mitochondrial heavy strand tDNA and expressed light strand tRNA modulates the function of heavy strand tDNA as light strand replication origin

Seligmann, Hervé

doi:10.1016/j.jmb.2008.03.066

Cited by 53 publications

(26 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(A) Inversidens japanensis, (B) Quadrula quadrula and Venustaconcha ellipsiformis, and (C) Pyganodon grandis. Seligmann 2008). It is of interest to note that the prominent difference in AT-skew value for the cytb gene has not been observed in the M genomes of Q. quadrula and V. ellipsiformis, in the F genome of C. plicata (data not shown), or in the F or the M genome of P. grandis (Figure 4).…”

Section: Regions B C and A)mentioning

confidence: 88%

“…It should be noted that a similar pattern is observed for the F genome of H. cumingii (data not shown). Interestingly, this region (i.e., between trnH and trnS2) contains a noncoding region on the heavy strand capable of forming a stem-loop structure similar to that of other metazoan O L 's (e.g., Rodakis et al 2007;Seligmann 2008) (Figure S2,A and B). No clear skew pattern is observed for the M genome of I. japanensis; therefore, the location of its O L remains unclear.…”

Section: Regions B C and A)mentioning

confidence: 97%

See 1 more Smart Citation

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

et al. 2009

View full text Add to dashboard Cite

Doubly uniparental inheritance (DUI) of mitochondrial DNA in marine mussels (Mytiloida), freshwater mussels (Unionoida), and marine clams (Veneroida) is the only known exception to the general rule of strict maternal transmission of mtDNA in animals. DUI is characterized by the presence of genderassociated mitochondrial DNA lineages that are inherited through males (male-transmitted or M types) or females (female-transmitted or F types), respectively. This unusual system constitutes an excellent model for studying basic aspects of mitochondrial DNA inheritance and the evolution of mtDNA genomes in general.Here we compare published mitochondrial genomes of unionoid bivalve species with DUI, with an emphasis on characterizing unassigned regions, to identify regions of the F and M mtDNA genomes that could (i) play a role in replication or transcription of the mtDNA molecule and/or (ii) determine whether a genome will be transmitted via the female or the male gamete. Our results reveal the presence of one Fspecific and one M-specific open reading frames (ORFs), and we hypothesize that they play a role in the transmission and/or gender-specific adaptive functions of the M and F mtDNA genomes in unionoid bivalves. Three major unassigned regions shared among all F and M unionoid genomes have also been identified, and our results indicate that (i) two of them are potential heavy-strand control regions (O H ) for regulating replication and/or transcription and that (ii) multiple and potentially bidirectional light-strand origins of replication (O L ) are present in unionoid F and M mitochondrial genomes. We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or genderspecific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted.

show abstract

Section: Regions B C and A)mentioning

confidence: 88%

Section: Regions B C and A)mentioning

confidence: 97%

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

et al. 2009

View full text Add to dashboard Cite

show abstract

“…In human mitochondria, stem-loop DNA structures define replication origins (Hixson et al, 1986; Clayton, 1992, 2000; Seligmann and Krishnan, 2006; Seligmann et al, 2006a,b; Seligmann, 2008, 2010a, 2011; Seligmann and Labra, 2014). They guide RNA processing in mitochondria (Ojala et al, 1981), and in giant viruses and their virophages (Byrne et al, 2009; Claverie and Abergel, 2009).…”

Section: Introductionmentioning

confidence: 99%

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

Houmami

Seligmann

2017

Front. Genet.

Self Cite

View full text Add to dashboard Cite

We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa. (a) Polymerase-induced frameshift mutations occur preferentially at translational termination signals (nucleotide deletion is interpreted as termination of nucleotide polymerization, paralleling the role of stop codons in translation). (b) Stem-loop hairpin presence/absence modulates codon-amino acid assignments, showing that translational signals sometimes combine primary and secondary nucleotide structures (here codon and stem-loop). (c) Homopolymer nucleotide triplets (AAA, CCC, GGG, TTT) cause transcriptional and ribosomal frameshifts. Here we find in recently described human mitochondrial RNAs that systematically lack mono-, dinucleotides after each trinucleotide (delRNAs) that delRNA triplets include 2x more homopolymers than mitogenome regions not covered by delRNA. Further analyses of delRNAs show that the natural circular code X (a little-known group of 20 translational signals enabling ribosomal frame retrieval consisting of 20 codons {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} universally overrepresented in coding versus other frames of gene sequences), regulates frameshift in transcription and translation. This dual transcription and translation role confirms for X the hypothesis that translational signals were carried over from transcriptional signals.

show abstract

“…The second point relates to the fact that mitochondrial genomes, but not chloroplast nor nuclear genomes, break Chargaff's second parity rule that complementary nucleotides have almost equal frequencies in single stranded DNA (Nikolaou and Almirantis, 2006). This is presumably because of the usually unidirectional replication mode of mitochondria (Krishnan et al, 2004;Seligmann et al, 2006a,b;Seligmann, 2008Seligmann, , 2010bHolt and Reyes, 2012), but also because of the almost Ahyong et al, 2007. A genus name not within a rounded rectangular frame has a regular (not a swinger) 18S rDNA sequence, the right-pointing arrow originating at the genus name refers to the genus with the most similar A o -4T þ Co -4 G swinger 18S rDNA.…”

Section: Inverted Repeats and Ao-4 Tþc O -4 G Swinger Dnamentioning

confidence: 99%