-
1
-
-
0032508543
-
Energetics of amino acid synthesis in hydrothermal ecosystems
-
COI: 1:CAS:528:DyaK1cXmtVWiurc%3D, PID: 9733509
-
Amend JP, Shock EL (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. Science 281:1659–1662
-
(1998)
Science
, vol.281
, pp. 1659-1662
-
-
Amend, J.P.1
Shock, E.L.2
-
2
-
-
0034837877
-
On the evolution of redundancy in genetic codes
-
COI: 1:CAS:528:DC%2BD3MXotVaiurg%3D, PID: 11675587
-
Ardell DH, Sella G (2001) On the evolution of redundancy in genetic codes. J Mol Evol 53:269–281
-
(2001)
J Mol Evol
, vol.53
, pp. 269-281
-
-
Ardell, D.H.1
Sella, G.2
-
3
-
-
84896733379
-
Revisiting the physico-chemical hypothesis of code origin: an analysis based on code-sequence coevolution in a finite population
-
COI: 1:CAS:528:DC%2BC2cXjs1Clu78%3D, PID: 24500541
-
Bandhu AV, Aggarwal N, Sengupta S (2013) Revisiting the physico-chemical hypothesis of code origin: an analysis based on code-sequence coevolution in a finite population. Orig Life Evol Biosph 43:465–489
-
(2013)
Orig Life Evol Biosph
, vol.43
, pp. 465-489
-
-
Bandhu, A.V.1
Aggarwal, N.2
Sengupta, S.3
-
4
-
-
55949132715
-
Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria
-
COI: 1:CAS:528:DC%2BD1cXhtleksrrO, PID: 18946048
-
Bender A, Hajieva P, Moosmann B (2008) Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. Proc Natl Acad Sci USA 105:16496–16501
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 16496-16501
-
-
Bender, A.1
Hajieva, P.2
Moosmann, B.3
-
5
-
-
84868685850
-
The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)
-
COI: 1:CAS:528:DC%2BC3sXitFKhs7c%3D, PID: 22793875
-
Bernhardt HS (2012) The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol Direct 7:23
-
(2012)
Biol Direct
, vol.7
, pp. 23
-
-
Bernhardt, H.S.1
-
6
-
-
63049130753
-
DNA before proteins? Recent discoveries in nucleic acid catalysis strengthen the case
-
COI: 1:CAS:528:DC%2BD1MXjs1ymt7k%3D, PID: 19215202
-
Burton AS, Lehman N (2009) DNA before proteins? Recent discoveries in nucleic acid catalysis strengthen the case. Astrobiology 9:125–130
-
(2009)
Astrobiology
, vol.9
, pp. 125-130
-
-
Burton, A.S.1
Lehman, N.2
-
7
-
-
84876783818
-
The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm
-
PID: 23615203
-
Caetano-Anollés G, Seufferheld MJ (2013) The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm. J Mol Microbiol Biotechnol 23:152–177
-
(2013)
J Mol Microbiol Biotechnol
, vol.23
, pp. 152-177
-
-
Caetano-Anollés, G.1
Seufferheld, M.J.2
-
8
-
-
84879702721
-
Expanded use of sense codons is regulated by modified cytidines in tRNA
-
COI: 1:CAS:528:DC%2BC3sXhtFejsLzM, PID: 23781103
-
Cantara WA, Murphy FV, Demirci H, Agris PF (2013) Expanded use of sense codons is regulated by modified cytidines in tRNA. Proc Natl Acad Sci USA 110:10964–10969
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 10964-10969
-
-
Cantara, W.A.1
Murphy, F.V.2
Demirci, H.3
Agris, P.F.4
-
9
-
-
84922022547
-
What RNA world? Why a peptide/RNA partnership merits renewed experimental attention
-
PID: 25625599
-
Carter CW (2015) What RNA world? Why a peptide/RNA partnership merits renewed experimental attention. Life 5:294–320
-
(2015)
Life
, vol.5
, pp. 294-320
-
-
Carter, C.W.1
-
10
-
-
0032584155
-
Codon reassignment and amino acid composition in hemichordate mitochondria
-
COI: 1:CAS:528:DyaK1cXitlKjtrY%3D, PID: 9520430
-
Castresana J, Feldmaier-Fuchs G, Pääbo S (1998) Codon reassignment and amino acid composition in hemichordate mitochondria. Proc Natl Acad Sci USA 95:3703–3707
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 3703-3707
-
-
Castresana, J.1
Feldmaier-Fuchs, G.2
Pääbo, S.3
-
11
-
-
77649336503
-
The origin of the biologically coded amino acids
-
COI: 1:CAS:528:DC%2BC3cXjtFynsLc%3D, PID: 20034500
-
Cleaves HJ (2010) The origin of the biologically coded amino acids. J Theor Biol 263:490–498
-
(2010)
J Theor Biol
, vol.263
, pp. 490-498
-
-
Cleaves, H.J.1
-
12
-
-
84896787870
-
Nature’s starships. I. Observed abundances and relative frequencies of amino acids in meteorites
-
Cobb AK, Pudritz RE (2014) Nature’s starships. I. Observed abundances and relative frequencies of amino acids in meteorites. Astrophys J 783:140
-
(2014)
Astrophys J
, vol.783
, pp. 140
-
-
Cobb, A.K.1
Pudritz, R.E.2
-
13
-
-
33846038387
-
Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome
-
COI: 1:CAS:528:DC%2BD2sXhsFygtw%3D%3D, PID: 17159993
-
Cochella L, Brunelle JL, Green R (2007) Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome. Nat Struct Mol Biol 14:30–36
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 30-36
-
-
Cochella, L.1
Brunelle, J.L.2
Green, R.3
-
14
-
-
84859593945
-
A new understanding of the decoding principle on the ribosome
-
COI: 1:CAS:528:DC%2BC38XksVehtL0%3D, PID: 22437501
-
Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G (2012) A new understanding of the decoding principle on the ribosome. Nature 484:256–259
-
(2012)
Nature
, vol.484
, pp. 256-259
-
-
Demeshkina, N.1
Jenner, L.2
Westhof, E.3
Yusupov, M.4
Yusupova, G.5
-
15
-
-
0036841366
-
Genetic code origin: are the pathways of type Glu-tRNA(Gln) –> Gln-tRNA(Gln) molecular fossils or not?
-
PID: 12399935
-
Di Giulio M (2002) Genetic code origin: are the pathways of type Glu-tRNA(Gln) –> Gln-tRNA(Gln) molecular fossils or not? J Mol Evol 55:616–622
-
(2002)
J Mol Evol
, vol.55
, pp. 616-622
-
-
Di Giulio, M.1
-
16
-
-
52449089127
-
An extension of the coevolution theory of the origin of the genetic code
-
PID: 18775066
-
Di Giulio M (2008) An extension of the coevolution theory of the origin of the genetic code. Biol Direct 3:37
-
(2008)
Biol Direct
, vol.3
, pp. 37
-
-
Di Giulio, M.1
-
17
-
-
0032976509
-
Physicochemical optimization in the genetic code origin as the number of codified amino acids increases
-
PID: 10368428
-
Di Giulio M, Medugno M (1999) Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 49:1–10
-
(1999)
J Mol Evol
, vol.49
-
-
Di Giulio, M.1
Medugno, M.2
-
18
-
-
0034781941
-
A blind empiricism against the coevolution theory of the origin of the genetic code
-
Di Gulio M (2001) A blind empiricism against the coevolution theory of the origin of the genetic code. J Mol Evol 53:724–732
-
(2001)
J Mol Evol
, vol.53
, pp. 724-732
-
-
Di Gulio, M.1
-
19
-
-
80054746223
-
An alternative to the RNA world hypothesis
-
Francis BR (2011) An alternative to the RNA world hypothesis. Trends Evol Biol 3:e2
-
(2011)
Trends Evol Biol
, vol.3
, pp. 2
-
-
Francis, B.R.1
-
20
-
-
84888646161
-
Evolution of the genetic code by incorporation of amino acids that improved or changed protein function
-
COI: 1:CAS:528:DC%2BC3sXhslWhsLbP, PID: 23743924
-
Francis BR (2013) Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 77:134–158
-
(2013)
J Mol Evol
, vol.77
, pp. 134-158
-
-
Francis, B.R.1
-
21
-
-
84922785133
-
The hypothesis that the genetic code originated in coupled synthesis of proteins and the evolutionary predecessors of nucleic acids in primitive cells
-
PID: 25679748
-
Francis BR (2015) The hypothesis that the genetic code originated in coupled synthesis of proteins and the evolutionary predecessors of nucleic acids in primitive cells. Life 5:467–505
-
(2015)
Life
, vol.5
, pp. 467-505
-
-
Francis, B.R.1
-
22
-
-
0031662136
-
The genetic code is one in a million
-
COI: 1:CAS:528:DyaK1cXmt1ansrs%3D, PID: 9732450
-
Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47:238–248
-
(1998)
J Mol Evol
, vol.47
, pp. 238-248
-
-
Freeland, S.J.1
Hurst, L.D.2
-
23
-
-
0142135398
-
The case for an error minimizing standard genetic code
-
COI: 1:CAS:528:DC%2BD3sXnt1KhtL0%3D, PID: 14604186
-
Freeland SJ, Wu T, Keulmann N (2003) The case for an error minimizing standard genetic code. Orig Life Evol Biosph 33:457–477
-
(2003)
Orig Life Evol Biosph
, vol.33
, pp. 457-477
-
-
Freeland, S.J.1
Wu, T.2
Keulmann, N.3
-
24
-
-
0035233646
-
Optimality of the genetic code with respect to protein stability and amino acid frequencies
-
Gilis D, Massar S, Cerf NJ, Rooman M (2001) Optimality of the genetic code with respect to protein stability and amino acid frequencies. Genome Biol 2:11
-
(2001)
Genome Biol
, vol.2
, pp. 11
-
-
Gilis, D.1
Massar, S.2
Cerf, N.J.3
Rooman, M.4
-
25
-
-
7544235210
-
On the optimality of the genetic code, with the consideration of termination codons
-
COI: 1:CAS:528:DC%2BD2cXpsVKnurc%3D, PID: 15527955
-
Goodarzi H, Nejad HA, Torabi N (2004) On the optimality of the genetic code, with the consideration of termination codons. Biosystems 77:163–173
-
(2004)
Biosystems
, vol.77
, pp. 163-173
-
-
Goodarzi, H.1
Nejad, H.A.2
Torabi, N.3
-
26
-
-
18844462433
-
On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices
-
COI: 1:CAS:528:DC%2BD2MXktVKnsLw%3D, PID: 15882694
-
Goodarzi H, Najafabadi HS, Hassani K, Nejad HA, Torabi N (2005) On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J Theor Biol 235:318–325
-
(2005)
J Theor Biol
, vol.235
, pp. 318-325
-
-
Goodarzi, H.1
Najafabadi, H.S.2
Hassani, K.3
Nejad, H.A.4
Torabi, N.5
-
27
-
-
0842267211
-
Kinetic determinants of high-fidelity tRNA discrimination on the ribosome
-
COI: 1:CAS:528:DC%2BD2cXhsFOiu7Y%3D, PID: 14759365
-
Gromadski KB, Rodnina MV (2004) Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell 13:191–200
-
(2004)
Mol Cell
, vol.13
, pp. 191-200
-
-
Gromadski, K.B.1
Rodnina, M.V.2
-
28
-
-
31544454704
-
A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity
-
COI: 1:CAS:528:DC%2BD28Xhslehu7o%3D, PID: 16455492
-
Gromadski KB, Daviter T, Rodnina MV (2006) A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol Cell 21:369–377
-
(2006)
Mol Cell
, vol.21
, pp. 369-377
-
-
Gromadski, K.B.1
Daviter, T.2
Rodnina, M.V.3
-
29
-
-
71849108697
-
Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes
-
COI: 1:CAS:528:DC%2BD1MXhsFGgtrjE, PID: 19931533
-
Grosjean H, de Crécy-Lagard V, Marck C (2010) Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett 584:252–264
-
(2010)
FEBS Lett
, vol.584
, pp. 252-264
-
-
Grosjean, H.1
de Crécy-Lagard, V.2
Marck, C.3
-
30
-
-
4243559860
-
Compensatory neutral mutations and the evolution of RNA
-
PID: 9720274
-
Higgs PG (1998) Compensatory neutral mutations and the evolution of RNA. Genetica 102–103:91–101
-
(1998)
Genetica
, vol.102-103
, pp. 91-101
-
-
Higgs, P.G.1
-
31
-
-
67449137928
-
A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code
-
PID: 19393096
-
Higgs PG (2009) A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biol Direct 4:16
-
(2009)
Biol Direct
, vol.4
, pp. 16
-
-
Higgs, P.G.1
-
32
-
-
84926186318
-
The RNA world: molecular co-operation at the origin of life
-
COI: 1:CAS:528:DC%2BC2cXhvF2js73M, PID: 25385129
-
Higgs PG, Lehman N (2015) The RNA world: molecular co-operation at the origin of life. Nat Rev Genet 16:7–17
-
(2015)
Nat Rev Genet
, vol.16
, pp. 7-17
-
-
Higgs, P.G.1
Lehman, N.2
-
33
-
-
35748957867
-
From protoplanetary disks to prebiotic amino acids and the origin of the genetic code
-
Pudritz RE, Higgs PG, Stone J, (eds), 3, Cambridge University Press, Cambridge
-
Higgs PG, Pudritz RE (2007) From protoplanetary disks to prebiotic amino acids and the origin of the genetic code. In: Pudritz RE, Higgs PG, Stone J (eds) Planetary systems and the origins of life. Cambridge Series in Astrobiology, vol 3. Cambridge University Press, Cambridge
-
(2007)
Planetary systems and the origins of life. Cambridge Series in Astrobiology
-
-
Higgs, P.G.1
Pudritz, R.E.2
-
34
-
-
67449120846
-
A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code
-
COI: 1:CAS:528:DC%2BD1MXotFWisrw%3D, PID: 19566427
-
Higgs PG, Pudritz RE (2009) A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9:483–490
-
(2009)
Astrobiology
, vol.9
, pp. 483-490
-
-
Higgs, P.G.1
Pudritz, R.E.2
-
35
-
-
0031081750
-
Aminoacyl-tRNA synthesis: divergent routes to a common goal
-
COI: 1:CAS:528:DyaK2sXht1Gnsr8%3D, PID: 9048478
-
Ibba M, Curnow AW, Söll D (1997) Aminoacyl-tRNA synthesis: divergent routes to a common goal. Trends Biochem Sci 22:39–42
-
(1997)
Trends Biochem Sci
, vol.22
, pp. 39-42
-
-
Ibba, M.1
Curnow, A.W.2
Söll, D.3
-
36
-
-
0034234758
-
The adaptor hypothesis revisited
-
COI: 1:CAS:528:DC%2BD3cXks12nur0%3D, PID: 10871880
-
Ibba M, Becker HD, Stathopoulos C, Tumbula DL, Söll D (2000) The adaptor hypothesis revisited. Trends Biochem Sci 25:311–316
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 311-316
-
-
Ibba, M.1
Becker, H.D.2
Stathopoulos, C.3
Tumbula, D.L.4
Söll, D.5
-
37
-
-
38949118287
-
Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection
-
COI: 1:CAS:528:DC%2BD1cXjtFCht7Y%3D, PID: 18048402
-
Jia W, Higgs PG (2008) Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol Biol Evol 25:339–351
-
(2008)
Mol Biol Evol
, vol.25
, pp. 339-351
-
-
Jia, W.1
Higgs, P.G.2
-
38
-
-
0037062978
-
The antiquity of RNA-based evolution
-
Joyce GF (2000) The antiquity of RNA-based evolution. Nature 418:214–221
-
(2000)
Nature
, vol.418
, pp. 214-221
-
-
Joyce, G.F.1
-
39
-
-
0015881599
-
Arginine as an evolutionary intruder into protein synthesis
-
COI: 1:CAS:528:DyaE3sXkvVymtbs%3D, PID: 4731949
-
Jukes TH (1973) Arginine as an evolutionary intruder into protein synthesis. Biochem Biophys Res Commun 53:709–714
-
(1973)
Biochem Biophys Res Commun
, vol.53
, pp. 709-714
-
-
Jukes, T.H.1
-
40
-
-
34547470915
-
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation
-
COI: 1:CAS:528:DC%2BD2sXnvFOnu78%3D, PID: 17592110
-
Kavran JM, Gundllapalli S, O’Donoghue P, Englert M, Söll D, Steitz TA (2007) Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc Natl Acad Sci USA 104:11268–11273
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 11268-11273
-
-
Kavran, J.M.1
Gundllapalli, S.2
O’Donoghue, P.3
Englert, M.4
Söll, D.5
Steitz, T.A.6
-
41
-
-
0033993457
-
Guilt by association: the arginine case revisited
-
COI: 1:CAS:528:DC%2BD3cXivFyjs7s%3D, PID: 10786841
-
Knight RD, Landweber LF (2000) Guilt by association: the arginine case revisited. RNA 6:499–510
-
(2000)
RNA
, vol.6
, pp. 499-510
-
-
Knight, R.D.1
Landweber, L.F.2
-
42
-
-
0035234558
-
Rewiring the keyboard: evolvability of the genetic code
-
COI: 1:CAS:528:DC%2BD3MXisVGjs7g%3D, PID: 11253070
-
Knight RD, Freeland SJ, Landweber LF (2001) Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2:49–58
-
(2001)
Nat Rev Genet
, vol.2
, pp. 49-58
-
-
Knight, R.D.1
Freeland, S.J.2
Landweber, L.F.3
-
43
-
-
84885791219
-
Genomically recoded organisms expand biological functions
-
COI: 1:CAS:528:DC%2BC3sXhs1WltrvI, PID: 24136966
-
Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ (2013) Genomically recoded organisms expand biological functions. Science 342:357–360
-
(2013)
Science
, vol.342
, pp. 357-360
-
-
Lajoie, M.J.1
Rovner, A.J.2
Goodman, D.B.3
Aerni, H.R.4
Haimovich, A.D.5
Kuznetsov, G.6
Mercer, J.A.7
Wang, H.H.8
Carr, P.A.9
Mosberg, J.A.10
Rohland, N.11
Schultz, P.G.12
Jacobson, J.M.13
Rinehart, J.14
Church, G.M.15
Isaacs, F.J.16
-
44
-
-
0023785307
-
The evolutionary transition from RNA to DNA in early cells
-
COI: 1:CAS:528:DyaL1cXls1Gku7g%3D, PID: 2464698
-
Lazcano A, Guerrero R, Margulis L, Oró J (1988) The evolutionary transition from RNA to DNA in early cells. J Mol Evol 27:283–290
-
(1988)
J Mol Evol
, vol.27
, pp. 283-290
-
-
Lazcano, A.1
Guerrero, R.2
Margulis, L.3
Oró, J.4
-
45
-
-
0023804470
-
Genetic code development by stop codon takeover
-
COI: 1:CAS:528:DyaL1MXjsVyjsQ%3D%3D, PID: 2477643
-
Lehman N, Jukes TH (1988) Genetic code development by stop codon takeover. J Theor Biol 135:203–214
-
(1988)
J Theor Biol
, vol.135
, pp. 203-214
-
-
Lehman, N.1
Jukes, T.H.2
-
46
-
-
84891815610
-
Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria
-
COI: 1:CAS:528:DC%2BC2cXkvFCl, PID: 24049072
-
Ling J, Daoud R, Lajoie MJ, Church GM, Söll D, Lang BF (2014) Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Res 42:499–508
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 499-508
-
-
Ling, J.1
Daoud, R.2
Lajoie, M.J.3
Church, G.M.4
Söll, D.5
Lang, B.F.6
-
47
-
-
0035936577
-
The molecular basis of nuclear genetic code change in ciliates
-
COI: 1:CAS:528:DC%2BD3MXhtVSgtbo%3D, PID: 11231122
-
Lozupone CA, Knight RD, Landweber LF (2001) The molecular basis of nuclear genetic code change in ciliates. Curr Biol 11:65–74
-
(2001)
Curr Biol
, vol.11
, pp. 65-74
-
-
Lozupone, C.A.1
Knight, R.D.2
Landweber, L.F.3
-
48
-
-
33745888090
-
On the evolution of the standard amino-acid alphabet
-
PID: 16515719
-
Lu Y, Freeland S (2006) On the evolution of the standard amino-acid alphabet. Genome Biol 7:102
-
(2006)
Genome Biol
, vol.7
, pp. 102
-
-
Lu, Y.1
Freeland, S.2
-
49
-
-
33645214213
-
Mutation pressure and the evolution of organelle genomic architecture
-
COI: 1:CAS:528:DC%2BD28Xis1equr0%3D, PID: 16556832
-
Lynch M, Koskella B, Schaack S (2006) Mutation pressure and the evolution of organelle genomic architecture. Science 311:1727–1730
-
(2006)
Science
, vol.311
, pp. 1727-1730
-
-
Lynch, M.1
Koskella, B.2
Schaack, S.3
-
50
-
-
0242417617
-
Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp
-
COI: 1:CAS:528:DC%2BD3sXjt1Sqtrk%3D, PID: 12670996
-
Massey SE, Moura G, Beltrão P, Almeida R, Garey JR, Tuite MF, Santos MA (2003) Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp. Genome Res 13:544–557
-
(2003)
Genome Res
, vol.13
, pp. 544-557
-
-
Massey, S.E.1
Moura, G.2
Beltrão, P.3
Almeida, R.4
Garey, J.R.5
Tuite, M.F.6
Santos, M.A.7
-
51
-
-
68249126127
-
Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont
-
PID: 19609354
-
McCutcheon JP, McDonald BR, Moran NA (2009) Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet 5:e1000565
-
(2009)
PLoS Genet
, vol.5
, pp. 1000565
-
-
McCutcheon, J.P.1
McDonald, B.R.2
Moran, N.A.3
-
52
-
-
71049150612
-
Prebiotic chemistry on the primitive earth
-
Miller SL, Cleaves HJ (2007) Prebiotic chemistry on the primitive earth. Orig Life 1:3–56
-
(2007)
Orig Life
, vol.1
, pp. 3-56
-
-
Miller, S.L.1
Cleaves, H.J.2
-
53
-
-
0017617331
-
Origin of organic compounds on the primitive earth and in meteorites
-
COI: 1:CAS:528:DyaE2sXosVyhtw%3D%3D, PID: 1018332
-
Miller SL, Urey HC, Oró J (1976) Origin of organic compounds on the primitive earth and in meteorites. J Mol Evol 9:59–72
-
(1976)
J Mol Evol
, vol.9
, pp. 59-72
-
-
Miller, S.L.1
Urey, H.C.2
Oró, J.3
-
54
-
-
0023942379
-
A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli
-
COI: 1:CAS:528:DyaL1cXltVKltb4%3D, PID: 3132458
-
Muramatsu T, Yokoyama S, Horie N, Matsuda A, Yamaizumi Z, Kuchino Y, Nishimura S, Miyazawa T (1988) A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J Biol Chem 263:9261–9267
-
(1988)
J Biol Chem
, vol.263
, pp. 9261-9267
-
-
Muramatsu, T.1
Yokoyama, S.2
Horie, N.3
Matsuda, A.4
Yamaizumi, Z.5
Kuchino, Y.6
Nishimura, S.7
Miyazawa, T.8
-
55
-
-
71549166642
-
Exceptional error minimization in putative primordial genetic codes
-
PID: 19925661
-
Novozhilov AS, Koonin EV (2009) Exceptional error minimization in putative primordial genetic codes. Biol Direct 4:44
-
(2009)
Biol Direct
, vol.4
, pp. 44
-
-
Novozhilov, A.S.1
Koonin, E.V.2
-
56
-
-
0024583607
-
Codon reassignment (codon capture) in evolution
-
COI: 1:CAS:528:DyaL1MXhs1yhsrs%3D, PID: 2499683
-
Osawa S, Jukes TH (1989) Codon reassignment (codon capture) in evolution. J Mol Evol 28:271–278
-
(1989)
J Mol Evol
, vol.28
, pp. 271-278
-
-
Osawa, S.1
Jukes, T.H.2
-
57
-
-
0025371613
-
Evolution of the mitochondrial genetic code III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria
-
COI: 1:CAS:528:DyaK3cXitFWrt7Y%3D, PID: 2111846
-
Osawa S, Collins D, Ohama T, Jukes TH, Watanabe K (1990) Evolution of the mitochondrial genetic code III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria. J Mol Evol 30:322–328
-
(1990)
J Mol Evol
, vol.30
, pp. 322-328
-
-
Osawa, S.1
Collins, D.2
Ohama, T.3
Jukes, T.H.4
Watanabe, K.5
-
58
-
-
0033168212
-
Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome
-
COI: 1:CAS:528:DyaK1MXksFKlt7c%3D, PID: 10393195
-
Pape T, Wintermeyer W, Rodnina M (1999) Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J 18:3800–3807
-
(1999)
EMBO J
, vol.18
, pp. 3800-3807
-
-
Pape, T.1
Wintermeyer, W.2
Rodnina, M.3
-
59
-
-
79955109293
-
Did evolution select a nonrandom “alphabet” of amino acids?
-
COI: 1:CAS:528:DC%2BC3MXkvFaltr0%3D, PID: 21434765
-
Philip GK, Freeland SJ (2011) Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology 11:235–240
-
(2011)
Astrobiology
, vol.11
, pp. 235-240
-
-
Philip, G.K.1
Freeland, S.J.2
-
60
-
-
77955955750
-
The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria
-
COI: 1:CAS:528:DC%2BC3cXhtVGrt7bM, PID: 20403966
-
Ran W, Higgs PG (2010) The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria. Mol Biol Evol 27:2129–2140
-
(2010)
Mol Biol Evol
, vol.27
, pp. 2129-2140
-
-
Ran, W.1
Higgs, P.G.2
-
61
-
-
0034610369
-
Testing a biosynthetic theory of the genetic code: fact or artifact?
-
COI: 1:CAS:528:DC%2BD3cXoslygu7c%3D, PID: 11087835
-
Ronneberg TA, Landweber LF, Freeland SJ (2000) Testing a biosynthetic theory of the genetic code: fact or artifact? Proc Natl Acad Sci USA 97:13690–13695
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 13690-13695
-
-
Ronneberg, T.A.1
Landweber, L.F.2
Freeland, S.J.3
-
62
-
-
84922595374
-
Recoded organisms engineered to depend on synthetic amino acids
-
COI: 1:CAS:528:DC%2BC2MXht1Omtr0%3D, PID: 25607356
-
Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ (2015) Recoded organisms engineered to depend on synthetic amino acids. Nature 518:89–93
-
(2015)
Nature
, vol.518
, pp. 89-93
-
-
Rovner, A.J.1
Haimovich, A.D.2
Katz, S.R.3
Li, Z.4
Grome, M.W.5
Gassaway, B.M.6
Amiram, M.7
Patel, J.R.8
Gallagher, R.R.9
Rinehart, J.10
Isaacs, F.J.11
-
63
-
-
1642513699
-
Driving change: the evolution of alternative genetic codes
-
COI: 1:CAS:528:DC%2BD2cXmvFyhug%3D%3D, PID: 14746991
-
Santos MA, Moura G, Massey SE, Tuite MF (2004) Driving change: the evolution of alternative genetic codes. Trends Genet 20:95–102
-
(2004)
Trends Genet
, vol.20
, pp. 95-102
-
-
Santos, M.A.1
Moura, G.2
Massey, S.E.3
Tuite, M.F.4
-
64
-
-
0028332057
-
Transfer RNA mutation and the malleability of the genetic code
-
COI: 1:CAS:528:DyaK2cXitFSjs7s%3D, PID: 8107079
-
Schultz DW, Yarus M (1994) Transfer RNA mutation and the malleability of the genetic code. J Mol Biol 235:1377–1380
-
(1994)
J Mol Biol
, vol.235
, pp. 1377-1380
-
-
Schultz, D.W.1
Yarus, M.2
-
65
-
-
0030138792
-
On malleability in the genetic code
-
COI: 1:CAS:528:DyaK28XjvVajsLo%3D, PID: 8662012
-
Schultz DW, Yarus M (1996) On malleability in the genetic code. J Mol Evol 42:597–601
-
(1996)
J Mol Evol
, vol.42
, pp. 597-601
-
-
Schultz, D.W.1
Yarus, M.2
-
66
-
-
0036214921
-
The impact of message mutation on the fitness of a genetic code
-
COI: 1:CAS:528:DC%2BD38XjtFymtLk%3D, PID: 11965436
-
Sella G, Ardell DH (2002) The impact of message mutation on the fitness of a genetic code. J Mol Evol 54:638–651
-
(2002)
J Mol Evol
, vol.54
, pp. 638-651
-
-
Sella, G.1
Ardell, D.H.2
-
67
-
-
22144437754
-
A unified model of codon reassignment in alternative genetic codes
-
COI: 1:CAS:528:DC%2BD2MXntVGksbY%3D, PID: 15781705
-
Sengupta S, Higgs PG (2005) A unified model of codon reassignment in alternative genetic codes. Genetics 170:831–840
-
(2005)
Genetics
, vol.170
, pp. 831-840
-
-
Sengupta, S.1
Higgs, P.G.2
-
68
-
-
34250704167
-
The mechanisms of codon reassignments in mitochondrial genetic codes
-
COI: 1:CAS:528:DC%2BD2sXms12jsLg%3D, PID: 17541678
-
Sengupta S, Yang X, Higgs PG (2007) The mechanisms of codon reassignments in mitochondrial genetic codes. J Mol Evol 64:662–688
-
(2007)
J Mol Evol
, vol.64
, pp. 662-688
-
-
Sengupta, S.1
Yang, X.2
Higgs, P.G.3
-
69
-
-
84931567021
-
Two perspectives on the origin of the standard genetic code
-
COI: 1:CAS:528:DC%2BC2MXhtVCqurY%3D, PID: 25585805
-
Sengupta S, Aggarwal N, Bandhu AV (2014) Two perspectives on the origin of the standard genetic code. Orig Life Evol Biosph 44:287–291
-
(2014)
Orig Life Evol Biosph
, vol.44
, pp. 287-291
-
-
Sengupta, S.1
Aggarwal, N.2
Bandhu, A.V.3
-
70
-
-
41849117355
-
From one amino acid to another: tRNA-dependent amino acid biosynthesis
-
COI: 1:CAS:528:DC%2BD1cXktl2ksrY%3D, PID: 18252769
-
Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Söll D (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res 36:1813–1825
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 1813-1825
-
-
Sheppard, K.1
Yuan, J.2
Hohn, M.J.3
Jester, B.4
Devine, K.M.5
Söll, D.6
-
71
-
-
79959458664
-
An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine
-
COI: 1:CAS:528:DC%2BC3MXnvVKnsbs%3D, PID: 21321019
-
Su D, Lieberman A, Lang BF, Simonovic M, Söll D, Ling J (2011) An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res 39:4866–4874
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 4866-4874
-
-
Su, D.1
Lieberman, A.2
Lang, B.F.3
Simonovic, M.4
Söll, D.5
Ling, J.6
-
72
-
-
0031051572
-
The “polysemous” codon—a codon with multiple amino acid assignment caused by dual specificity of tRNA identity
-
COI: 1:CAS:528:DyaK2sXitF2ltrY%3D, PID: 9118950
-
Suzuki T, Ueda T, Watanabe K (1997) The “polysemous” codon—a codon with multiple amino acid assignment caused by dual specificity of tRNA identity. EMBO J 16:1122–1134
-
(1997)
EMBO J
, vol.16
, pp. 1122-1134
-
-
Suzuki, T.1
Ueda, T.2
Watanabe, K.3
-
73
-
-
14644437032
-
Mitochondrial genetic codes evolve to match amino acid requirements of proteins
-
COI: 1:CAS:528:DC%2BD2MXhtVShtr0%3D, PID: 15696375
-
Swire J, Judson OP, Burt A (2005) Mitochondrial genetic codes evolve to match amino acid requirements of proteins. J Mol Evol 60:128–139
-
(2005)
J Mol Evol
, vol.60
, pp. 128-139
-
-
Swire, J.1
Judson, O.P.2
Burt, A.3
-
74
-
-
0033230183
-
Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria
-
COI: 1:CAS:528:DyaK1MXnt1Gku78%3D, PID: 10518623
-
Tomita K, Ueda T, Ishiwa S, Crain PF, McCloskey JA, Watanabe K (1999a) Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria. Nucleic Acids Res 27:4291–4297
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4291-4297
-
-
Tomita, K.1
Ueda, T.2
Ishiwa, S.3
Crain, P.F.4
McCloskey, J.A.5
Watanabe, K.6
-
75
-
-
0033118871
-
The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria
-
COI: 1:CAS:528:DyaK1MXisVCjt78%3D, PID: 10076000
-
Tomita K, Ueda T, Watanabe K (1999b) The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res 27:1683–1689
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1683-1689
-
-
Tomita, K.1
Ueda, T.2
Watanabe, K.3
-
76
-
-
4143139971
-
The triplet code from first principles
-
COI: 1:CAS:528:DC%2BD2cXmtlKnsLo%3D, PID: 15214800
-
Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dyn 22:1–11
-
(2004)
J Biomol Struct Dyn
, vol.22
-
-
Trifonov, E.N.1
-
77
-
-
0034618571
-
Domain-specific recruitment of amide amino acids for protein synthesis
-
COI: 1:CAS:528:DC%2BD3cXmsleksbc%3D, PID: 10993083
-
Tumbula DL, Becker HD, Chang WZ, Söll D (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature 407:106–110
-
(2000)
Nature
, vol.407
, pp. 106-110
-
-
Tumbula, D.L.1
Becker, H.D.2
Chang, W.Z.3
Söll, D.4
-
78
-
-
58149389394
-
Genetic code supports targeted insertion of two amino acids by one codon
-
COI: 1:CAS:528:DC%2BD1MXhvFeltw%3D%3D, PID: 19131629
-
Turanov AA, Lobanov AV, Fomenko DE, Morrison HG, Sogin ML, Klobutcher LA, Hatfield DL, Gladyshev VN (2009) Genetic code supports targeted insertion of two amino acids by one codon. Science 323:259–261
-
(2009)
Science
, vol.323
, pp. 259-261
-
-
Turanov, A.A.1
Lobanov, A.V.2
Fomenko, D.E.3
Morrison, H.G.4
Sogin, M.L.5
Klobutcher, L.A.6
Hatfield, D.L.7
Gladyshev, V.N.8
-
79
-
-
84856363808
-
Unassigned codons, nonsense suppression, and anticodon modifications in the evolution of the genetic code
-
COI: 1:CAS:528:DC%2BC3MXhs1Wks7%2FO, PID: 22076654
-
van der Gulik PT, Hoff WD (2011) Unassigned codons, nonsense suppression, and anticodon modifications in the evolution of the genetic code. J Mol Evol 73:59–69
-
(2011)
J Mol Evol
, vol.73
, pp. 59-69
-
-
van der Gulik, P.T.1
Hoff, W.D.2
-
80
-
-
33746092088
-
Collective evolution and the genetic code
-
COI: 1:CAS:528:DC%2BD28XntFWmsLg%3D, PID: 16818880
-
Vetsigian K, Woese C, Goldenfeld N (2006) Collective evolution and the genetic code. Proc Natl Acad Sci USA 103:10696–10701
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 10696-10701
-
-
Vetsigian, K.1
Woese, C.2
Goldenfeld, N.3
-
81
-
-
84877250387
-
The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome
-
COI: 1:CAS:528:DC%2BC3sXkvFyjs7g%3D, PID: 23542153
-
Voorhees RM, Mandal D, Neubauer C, Köhrer C, RajBhandary UL, Ramakrishnan V (2013) The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Nat Struct Mol Biol 20:641–643
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 641-643
-
-
Voorhees, R.M.1
Mandal, D.2
Neubauer, C.3
Köhrer, C.4
RajBhandary, U.L.5
Ramakrishnan, V.6
-
82
-
-
0019792825
-
Reasons for the occurrence of the twenty coded protein amino acids
-
COI: 1:CAS:528:DyaL3MXltFSls7g%3D, PID: 7277510
-
Weber AL, Miller SL (1981) Reasons for the occurrence of the twenty coded protein amino acids. J Mol Evol 17:273–284
-
(1981)
J Mol Evol
, vol.17
, pp. 273-284
-
-
Weber, A.L.1
Miller, S.L.2
-
83
-
-
0001155613
-
A co-evolution theory of the genetic code
-
COI: 1:CAS:528:DyaE2MXkt1ertbg%3D, PID: 1057181
-
Wong JT (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 72:1909–1912
-
(1975)
Proc Natl Acad Sci USA
, vol.72
, pp. 1909-1912
-
-
Wong, J.T.1
-
84
-
-
17844405021
-
Coevolution theory of the genetic code at age thirty
-
COI: 1:CAS:528:DC%2BD2MXjtlOjtr8%3D, PID: 15770677
-
Wong JT (2005) Coevolution theory of the genetic code at age thirty. BioEssays 27:416–425
-
(2005)
BioEssays
, vol.27
, pp. 416-425
-
-
Wong, J.T.1
-
85
-
-
84904582489
-
Emergence of life: from functional RNA selection to natural selection and beyond
-
COI: 1:CAS:528:DC%2BC2cXhs1Smsr3L
-
Wong JT (2014) Emergence of life: from functional RNA selection to natural selection and beyond. Front Biosci 19:1117–1150
-
(2014)
Front Biosci
, vol.19
, pp. 1117-1150
-
-
Wong, J.T.1
-
86
-
-
0034002683
-
RNA-ligand chemistry: a testable source for the genetic code
-
COI: 1:CAS:528:DC%2BD3cXivFyjs70%3D, PID: 10786839
-
Yarus M (2000) RNA-ligand chemistry: a testable source for the genetic code. RNA 6:475–484
-
(2000)
RNA
, vol.6
, pp. 475-484
-
-
Yarus, M.1
-
87
-
-
0034822301
-
Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity
-
COI: 1:CAS:528:DC%2BD3MXotVaiu74%3D, PID: 11675591
-
Yokobori S, Suzuki T, Watanabe K (2001) Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J Mol Evol 53:314–326
-
(2001)
J Mol Evol
, vol.53
, pp. 314-326
-
-
Yokobori, S.1
Suzuki, T.2
Watanabe, K.3
-
88
-
-
58149354143
-
Quality control by the ribosome following peptide bond formation
-
COI: 1:CAS:528:DC%2BD1MXitlShsw%3D%3D, PID: 19092806
-
Zaher HS, Green R (2009a) Quality control by the ribosome following peptide bond formation. Nature 457:161–166
-
(2009)
Nature
, vol.457
, pp. 161-166
-
-
Zaher, H.S.1
Green, R.2
-
89
-
-
60149099539
-
Fidelity at the molecular level: lessons from protein synthesis
-
COI: 1:CAS:528:DC%2BD1MXkvFGktr4%3D, PID: 19239893
-
Zaher HS, Green R (2009b) Fidelity at the molecular level: lessons from protein synthesis. Cell 136:746–762
-
(2009)
Cell
, vol.136
, pp. 746-762
-
-
Zaher, H.S.1
Green, R.2
|