Putative mitochondrial polypeptides coded by expanded quadruplet codons, decoded by antisense tRNAs with unusual anticodons

Ahmed, 2007, Frameshift signals in genes associated with the circular code, In Silico Biol., 7, 155

Ahmed, 2010, Essential molecular functions associated with circular code evolution, J. Theor. Biol., 264, 613, 10.1016/j.jtbi.2010.02.006

Ahmed, 2011, Circular code signal in frameshift genes, J. Comp. Sci. Syst. Biol., 4, 7

Akashi, 2002, Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis, Proc. Natl. Acad. Sci. U. S. A., 99, 3695, 10.1073/pnas.062526999

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucl. Acids Res., 25, 3389, 10.1093/nar/25.17.3389

Altschul, 2005, Protein database searches using compositionally adjusted substitution matrices, FEBS J., 272, 5101, 10.1111/j.1742-4658.2005.04945.x

Anderson, 2002, Exploring the limits of codon and anticodon size, Chem. Biol., 9, 237, 10.1016/S1074-5521(02)00094-7

Annex, 1990, Mitochondrial DNA structure and expression in specialized subtypes of mammalian triated muscle, Mol. Cell Biol., 10, 56171, 10.1128/MCB.10.11.5671

Ardell, 2001, On the evolution of redundancy in genetic codes, J. Mol. Evol., 53, 269, 10.1007/s002390010217

Arqués, 1996, A complementary circular code in the protein coding genes, J. Theor. Biol., 182, 45, 10.1006/jtbi.1996.0142

Arqués, 1997, A circular code in the protein coding genes of mitochondria, J. Theor. Biol., 189, 273, 10.1006/jtbi.1997.0513

Atkins, 2009, A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment, Microbiol. Mol. Biol. Rev., 73, 178, 10.1128/MMBR.00010-08

Barak, 1996, On the mechanism of leftward frameshifting at severeal hungry codons, J. Mol. Biol., 256, 676, 10.1006/jmbi.1996.0117

Baranov, 2009, Codon size reduction as the origin of the triplet genetic code, PloS One, 4, e5708, 10.1371/journal.pone.0005708

Basak, 2005, On the origin of genomic adaptation at high temperature for prokaryotic organisms, Biochem. Biophys. Res. Commun., 330, 629, 10.1016/j.bbrc.2005.02.134

Basak, 2005, Correlations between genomic GC levels and optimal growth temperatures: some comments, Biochem. Biophys. Res. Commun., 327, 969, 10.1016/j.bbrc.2004.12.100

Benjamini, 1995, Controlling for the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. B, 57, 289, 10.1111/j.2517-6161.1995.tb02031.x

Brzezniak, 2011, Human ELAC2 gene encodes the tRNAseZ responsible for mitochondrial tRNA 3′ processing which acts on precursors already cleaved by RNAseP, RNA Biol., 8, 1

Chen, 2010, Quadruplet codons: one small step for a ribosome, one giant leap for proteins: an expanded genetic code could address fundamental questions about algorithmic information, biological function, and the origins of life, Bioessays, 32, 650, 10.1002/bies.201000051

Chou, 1978, Prediction of the secondary structure of proteins from their amino acid sequence, Adv. Enzym. Rel. Areas Mol. Biol., 47, 45

Chrzanowska-Lightowlers, 2011, Termination or protein synthesis in mammal mitochondria, J. Biol. Chem., 286, 34479, 10.1074/jbc.R111.290585

Clayton, 2000, Transcription and replication of mitochondrial DNA, Human Reprod., 15, 11, 10.1093/humrep/15.suppl_2.11

De Magalhaes, 2009, A database of vertebrate longevity records and their relation to other life history traits, J. Evol. Biol., 22, 1770, 10.1111/j.1420-9101.2009.01783.x

De Magalhaes, 2009, Meta-analysis of age-related gene expression profiles identifies common signatures of aging, Bioinformatics, 25, 875, 10.1093/bioinformatics/btp073

Di Giulio, 2001, The late stage of the genetic code structuring took place at a high temperature, Gene, 261, 189, 10.1016/S0378-1119(00)00522-9

Dunham, 2007, Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit, RNA, 13, 817, 10.1261/rna.367307

Farabaugh, 1996, Programmed translational frameshifting, Microbiol. Rev., 60, 103, 10.1128/MMBR.60.1.103-134.1996

Faure, 2011, Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene, Biol. Direct., 6, 56, 10.1186/1745-6150-6-56

Florentz, 2003, Human mitochondrial tRNAs in health and disease, Cell. Mol. Life Sci., 60, 1356, 10.1007/s00018-003-2343-1

Freeland, 1998, The genetic code is one in a million, J. Mol. Evol., 47, 238, 10.1007/PL00006381

Glusman, G., 2009. Mining junk DNA to find hidden transcriptional gems. Genomic Signal Processing and Statistics. GENSIPS; IEEE International workshop, Minneapolis, MN.

Glusman, 2006, A third approach to gene prediction suggests thousands of additional human transcribed regions, PLOS Comp. Biol., 2, 160, 10.1371/journal.pcbi.0020018

Gonzalez, 2011, Circular codes revisited: A statistical approach, J. Theor. Biol., 275, 21, 10.1016/j.jtbi.2011.01.028

Gonzalez, 2012, On the origin of the mitochondrial genetic code: towards a unified mathematical framework for the management of genetic information, Nat. Prec., 10.1038/npre.2012.7136.1

Grantham, 1974, Amino acid difference formula to help explain protein evolution, Science, 185, 862, 10.1126/science.185.4154.862

Guilloux, 2012, The genetic code and its optimization for kinetic energy conservation in polypeptide chains, BioSystems, 109, 141, 10.1016/j.biosystems.2012.03.001

Hohsaka, 1999, Incorporation of two nonnatural amino acids into proteins through extension of the genetic code, Nucl. Acids Symp. Ser., 1999, 79, 10.1093/nass/42.1.79

Hoogsteen, 1963, The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine, Acta Crystallographica., 16, 907, 10.1107/S0365110X63002437

Hurst, 2001, High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes, Proc. Biol. Sci., 268, 493, 10.1098/rspb.2000.1397

Itzkovitz, 2007, The genetic code is nearly optimal for allowing additional information within protein-coding sequences, Genome Res., 17, 405, 10.1101/gr.5987307

Juehling, 2011, Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements, Nucl. Acids Res., 40, 2833, 10.1093/nar/gkr1131

Klobutcher, 2005, Sequencing of random Euplotes crassus macronuclear genes supports a high frequency of +1 translational frameshifting, Eukaryot. Cell, 4, 2098, 10.1128/EC.4.12.2098-2105.2005

Klobutcher, 2002, Shifty ciliates: frequent programmed translational frameshifting in euplotids, Cell, 111, 763, 10.1016/S0092-8674(02)01138-8

Korostelev, 2011, Structural aspects of translation termination on the ribosome, RNA, 17, 1409, 10.1261/rna.2733411

Krishnan, 2004, Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes, DNA Cell Biol., 23, 707, 10.1089/dna.2004.23.707

Lee, 2003, A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity, Nat. Genet., 33, 40, 10.1038/ng1056

Lehmann, 2006, Mitochondrial genome anatomy and species-specific lifespan, Rejuven. Res., 9, 223, 10.1089/rej.2006.9.223

Lindahl, 1993, Instability and decay of the primary structure of DNA, Nature, 362, 709, 10.1038/362709a0

Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucl. Acids Res., 25, 955, 10.1093/nar/25.5.0955

Macey, 1999, Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families, Mol. Phylogenet. Evol., 12, 250, 10.1006/mpev.1999.0615

Magliery, 2001, Expanding the genetic code: selection of efficient suppressors of four-base codons and identification of shifty four-base codons with a library approach in Escherichia coli, J. Mol. Biol., 307, 755, 10.1006/jmbi.2001.4518

Marashi, 2004, Correlations between genomic GC levels and optimal growth temperatures are not ‘robust’, Biochem. Biophys. Res. Commun., 325, 381, 10.1016/j.bbrc.2004.10.051

Mathews, 1999, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, J. Mol. Biol., 288, 911, 10.1006/jmbi.1999.2700

McCaldon, 1988, Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences, Proteins Struct. Funct. Bioinform., 4, 99, 10.1002/prot.340040204

Mercer, 2011, The human mitochondrial transcriptome, Cell, 146, 645, 10.1016/j.cell.2011.06.051

Michel, 2008, A 2006 review of circular codes in genes, Comput. Math. Appl., 55, 984, 10.1016/j.camwa.2006.12.090

Michel, 2012, Circular code motifs in transfer and 16S ribosomal RNAs: A possible translation code in genes, Comp. Biol. Chem., 37, 24, 10.1016/j.compbiolchem.2011.10.002

Mindell, 1998, An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles, Mol. Biol. Evol., 15, 1568, 10.1093/oxfordjournals.molbev.a025884

Moore, 2000, Quadruplet codons: implications for code expansion and the specification of translation step size, J. Mol. Biol., 298, 195, 10.1006/jmbi.2000.3658

Musto, 2004, Correlations between genomic GC levels and optimal growth temperatures in prokaryotes, FEBS Lett., 573, 73, 10.1016/j.febslet.2004.07.056

Musto, 2005, The correlation between genomic G+C and optimal growth temperature of prokaryotes is robust: A reply to Marashi and Ghalanbor, Biochem. Biophys. Res. Commun., 330, 357, 10.1016/j.bbrc.2005.02.133

Neumann, 2010, Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome, Nature, 464, 441, 10.1038/nature08817

Nikilova, 2011, Transient Hoogsteen base pairs in canonical duplex DNA, Nature, 470, 498, 10.1038/nature09775

Ninio, 1971, Codon-anticodon recognition: the missing triplet hypothesis, J. Mol. Biol., 56, 63, 10.1016/0022-2836(71)90084-2

O’Connor, 1989, tRNA hopping: enhancement by and expanded anticodon, EMBO J., 8, 4315, 10.1002/j.1460-2075.1989.tb08618.x

Pacheu-Grau, 2012, Read-through therapy for mitochondrial DNA nonsense mutations, Drug Discov. Today, 4, 1063, 10.1016/j.drudis.2012.04.012

Perneger, 1998, What is wrong with Bonferroni adjustments, Brit. Med. J., 136, 1236, 10.1136/bmj.316.7139.1236

Popadin, K., Bazykin, G., 2008. Nucleotide repeats in mitochondrial genome determine human lifespan. Nature Prec. hdl:10101/npre.2008.2399.1.

Rancurel, 2009, Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation, J. Virol., 83, 10719, 10.1128/JVI.00595-09

Ream, 2003, Base compositions of genes encoding α-Actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G+C content, Mol. Biol. Evol., 20, 105, 10.1093/molbev/msg008

Ren, 2012, Alternative reading frame selection mediated by tRNA-like domain of an internal ribosome entry site, Proc. Natl. Acad. Sci. U.S.A., 109, e630, 10.1073/pnas.1111303109

Richter, 2011, Translation termination in human mitochondrial ribosomes, Biochem. Soc. Trans., 38, 1523, 10.1042/BST0381523

Riddle, 1973, Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA, Nat. New Biol., 242, 230, 10.1038/newbio242230a0

Rocher, 2002, Base composition at mtDNA boundaries suggests a DNA triple helix model for human mitochondrial DNA large-scale rearrangements, Mol. Genetics Metab., 76, 123, 10.1016/S1096-7192(02)00024-0

Rodriguez, 2007, In vivo incorporation of multiple amino acids through nonsense and frameshift suppression, Proc. Natl. Acad. Sci. U. S. A., 103, 8650, 10.1073/pnas.0510817103

Schattner, 2005, The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs, Nucl. Acids Res., 33, W686, 10.1093/nar/gki366

Seligmann, H., Pollock, D.D., 2003. The ambush hypothesis: hidden stop codons prevent off-frame gene reading. Midsouth Computational Biology and Bioinformatics Society, Abstract 36.

Seligmann, 2004, The ambush hypothesis: off frame stop codons arrest early accidental frameshifted transcription, DNA Cell Biol., 23, 701, 10.1089/dna.2004.23.701

Seligmann, 2006, Possible multiple origins of replication in primate mitochondria: alternative role of tRNA sequences, J. Theor. Biol., 241, 321, 10.1016/j.jtbi.2005.11.035

Seligmann, 2006, Mitochondrial tRNA sequences as unusual replication origins: pathogenic implications for Homo sapiens, J. Theor. Biol., 243, 375, 10.1016/j.jtbi.2006.06.028

Seligmann, 2000, Evolution and ecology of developmental processes and of the resulting morphology: directional asymmetry in hindlimbs of Agamidae and Laceertidae (Reptilia: Lacertilia), Biol. J. Linn. Soc. (Lond.), 69, 461, 10.1111/j.1095-8312.2000.tb01219.x

Seligmann, 2003, Cost minimization of amino acid usages, J. Mol. Evol., 56, 151, 10.1007/s00239-002-2388-z

Seligmann, 2007, Cost minimization of ribosomal frameshifts, J. Theor. Biol., 249, 162, 10.1016/j.jtbi.2007.07.007

Seligmann, 2008, Hybridization between mitochondrial heavy strand tDNA and expressed light strand tRNA modulates the function of heavy strand tDNA as light strand replication origin, J. Mol. Biol., 379, 188, 10.1016/j.jmb.2008.03.066

Seligmann, 2010, The ambush hypothesis at the whole organism level: Off frame, ‘hidden’ stops in vertebrate mitochondrial genes increase developmental stability, Comput. Biol. Chem., 34, 80, 10.1016/j.compbiolchem.2010.03.001

Seligmann, 2010, Do anticodons of mysacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid?, BMC Mol. Biol., 11, 41, 10.1186/1471-2199-11-41

Seligmann, 2010, Avoidance of antisense antiterminator tRNA anticodons in vertebrate mitochondria, Biosystems, 101, 42, 10.1016/j.biosystems.2010.04.004

Seligmann, 2010, Undetected antisense tRNAs in mitochondria?, Biol. Direct., 5, 39, 10.1186/1745-6150-5-39

Seligmann, 2010, Mitochondrial tRNAs as light strand replication origins: similarity between anticodon loops and the loop of the light strand replication origin predicts initiation of DNA replication, Biosystems, 99, 85, 10.1016/j.biosystems.2009.09.003

Seligmann, 2011, Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion, Comput. Biol. Chem., 35, 81, 10.1016/j.compbiolchem.2011.03.001

Seligmann, 2011, Two genetic codes, one genome: Frameshifted primate mitochondrial genes code for additional proteins in presence of antisense antitermination tRNAs, Biosystems, 105, 271, 10.1016/j.biosystems.2011.05.010

Seligmann, 2011, Pathogenic mutations in antisense mitochondrial tRNAs, J. Theor. Biol., 269, 287, 10.1016/j.jtbi.2010.11.007

Seligmann, 2011, Mutation patterns due to converging mitochondrial replication and transcription increase lifespan, and cause growth rate-longevity tradeoffs

Seligmann, 2012, An overlapping genetic code for frameshifted overlapping genes in Drosophila mitochondria: Antisense antitermination tRNAs UAR insert serine, J. Theor. Biol., 298, 51, 10.1016/j.jtbi.2011.12.026

Seligmann, 2012, Overlapping genes coded in the 3′-to-5′-direction in mitochondrial genes and 3′-to-5′ polymerization of non-complementary RNA by an ‘invertase’, J. Theor. Biol., 215, 38, 10.1016/j.jtbi.2012.08.044

Seligmann, 2012, Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes, Curr. Genom., 13, 37, 10.2174/138920212799034802

Seligmann, 2012, Positive and negative cognate amino acid bias affects compositions of aminoacyl-tRNA synthetases and reflects functional constraints on protein structure, BIO, 2, 11, 10.5618/bio.2012.v2.n1.2

Seligmann, H. Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as a special case. Comp. Biol. Chem., in press-a.

Seligmann, H. Replicational mutation gradients, dipole moments, nearest neighbour effects and DNA polymerase gamma fidelity in human mitochondrial genomes. In: Stuart, D., (Ed.) The Mechanisms of DNA Replication. InTech Publisher. ISBN 980-953-307-590-2, in press-b.

Shah, 2010, Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias, PLoS Genet., 6, e1001128, 10.1371/journal.pgen.1001128

Sroga, 1992, Insertion (sufB) in the anticodon loop or base substitution (sufC) in the anticodon stem of tRNA(Pro)2 from Salmonella typhimurium induces suppression of frameshift mutations, Nucl. Acids Res., 20, 3463, 10.1093/nar/20.13.3463

Takamatsu, 2002, Regulation of mitochondrial D-loops by transcription factor A and single-stranded DNA-binding protein, EMBO Rep., 3, 451, 10.1093/embo-reports/kvf099

Temperley, 2010, Hungry codons promote frameshifting in human mitochondrial ribosomes, Science, 327, 301, 10.1126/science.1180674

Tse, 2010, Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes, BMC Genomics, 11, 491, 10.1186/1471-2164-11-491

Tuohy, 1992, Seven, eight and nine-membered anticodon loop mutants of tRNA(2Arg) which cause +1 frameshifting. Tolerance of DHU arm and other secondary mutations, J. Mol. Biol., 228, 1042, 10.1016/0022-2836(92)90313-9

Walker, 2008, Recognition and positioning of mRNA in the ribosome by tRNAs with expanded anticodons, J. Mol. Biol., 360, 599, 10.1016/j.jmb.2006.05.006

Walter, 1994, Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding, Proc. Natl. Acad. Sci. U. S. A., 91, 9218, 10.1261/rna.1970310

Wang, 2010, Reprogramming the genetic code: from triplet to quadruplet codes, Angew. Chem. Int. Ed., 51, 2288, 10.1073/pnas.91.20.9218

Wang, 2006, On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: Data quality and confounding factors, Biochem. Biophys. Res. Commun., 342, 681, 10.1002/anie.201105016

Wei, 2012, CONCORD: a consensus method for protein secondary structure prediction via Mixed Integer Linear Optimization, Proc. R. Soc. A, 468, 831, 10.1016/j.bbrc.2006.02.037

Young, 2010, Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandnard stop codons beginning with adenine in vertebrate mitochondria, RNA, 16, 1146, 10.1098/rspa.2011.0514

Zheng, 2010, Gene-centric association analysis for the correlation between guanin-cytosine content levels and temperature range conditions of prokaryotic species, BMC Bioinformatics, 11, S7, 10.1186/1471-2105-11-S11-S7