Codon catalog usage is a genome strategy modulated for gene expressivity

Grantham, R.; Gautier, Christian; Gouy, Manolo; Jacobzone, M.; Mercier, Raphaël

doi:10.1093/nar/9.1.213-b

Cited by 924 publications

(483 citation statements)

References 41 publications

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“…To isolate full-length Spin cDNA from gibel carp, we designed four degenerate primers: skr1, skr2, skf1 and skf2 (Table 1) based on the conserved motif sequences of Spin/Ssty protein family and also the amino acid usage rates in fish proteins (Grantham et al, 1980(Grantham et al, , 1981. An about 250 bp fragment was amplified by Nested PCR from SMART cDNA library of gibel carp mature eggs, and was shown to have high similarity to human and mouse Spin gene.…”

Section: Cdna Cloning and Sequence Characterization Of Gibel Carp Spimentioning

confidence: 99%

Identification of a Spindlin homolog in gibel carp (Carassius auratus gibelio)

Wang

Sun

Mei

et al. 2005

Comparative Biochemistry and Physiology Part B: Biochemistry an

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Section: Cdna Cloning and Sequence Characterization Of Gibel Carp Spimentioning

confidence: 99%

Identification of a Spindlin homolog in gibel carp (Carassius auratus gibelio)

Wang

Sun

Mei

et al. 2005

Comparative Biochemistry and Physiology Part B: Biochemistry an

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“…CAC CAG CAT CAG GTA GTG GAT GGG GTT CAG CAT CTC CAG CAC-3 '; 35mer, 5 '-TT CTG GAT GCT CTC CAC ACA CTG GCC CTG CAG GGT-3') were synthesized by the modified triester method [16]. The base sequences of both probes were designed on the basis of partial amino acid sequences of human placental P'45OAaoM [17], using published data for codon usage frequencies [18]. All other materials including restriction endonucleases, [c+32P]dCTP and [y-'*P]ATP were obtained from commercial sources.…”

Section: Cdna Clonesmentioning

confidence: 99%

Alternative usage of different poly(A) addition signals for two major species of mRNA encoding human aromatase P‐450

Toda¹,

M²,

Mitsuuchi³

et al. 1989

FEBS Letters

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Two cDNA clones for human placental aromatase P-450 (P-450 AROM) have been isolated and sequenced. The insert of one clone (2894 bp) contains an open reading frame encoding a protein consisting of 503 amino acid residues together with a 49 bp S-untranslated stretch and a 1336 bp 3'-noncoding region to which a poly(A) tract is attached. Three potential poly(A) addition signals are detected in this 3'noncoding region. The other clone contains a shorter cDNA insert, the nucleotide sequence of which overlaps with most of the sequence of the longer cDNA insert (nucleotides 36-2355) except for one nucleotide substitution. The 3'noncoding region of this shorter cDNA is only 846 bp in length, but a poly(A) tract is also attached to its 3'-terminus. Northern blot analysis of human placental RNA reveals the presence of two major mRNA species of 3.4 and 2.9 kb when probes excised from the overlapping region of these two cDNAs are employed. The 2.9 kb mRNA is not detected, however, when a fragment of the non-overlapping region of the longer cDNA is used as a probe. It is therefore concluded that the two major species of P-4SOAROM mRNA are formed as a consequence of alternative processing of precursor mRNA(s).

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“…Grantham's genome hypothesis proposes that each species systematically uses certain synonymous codons (codons that code for the same amino acid) in coding sequences (2)(3)(4), in other words, that each species has a distinct codon bias. Many studies have since confirmed that, at least in prokaryotes, selective forces acting at the level of translation maintain biased codon usage (5)(6)(7).…”

mentioning

confidence: 99%

“…In contrast, explanation ii is referred to as a neutral or mutational explanation. Variation in codon bias among genes from the same organism has been shown to depend on many parameters, including expression level (4,5,11), amino acid composition (12)(13)(14)(15), gene length (16,17), mRNA structure (18)(19)(20), and protein level noise considerations (21). In most of these cases, evidence exists that selection at different steps during protein expression shapes codon bias.…”

mentioning

confidence: 99%

Codon usage between genomes is constrained by genome-wide mutational processes

Chen

Lee

Hottes

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

316

251

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Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genomewide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.

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Codon catalog usage is a genome strategy modulated for gene expressivity

Abstract: The nucleic acid sequence bank now contains 161

Cited by 924 publications

References 41 publications

Identification of a Spindlin homolog in gibel carp (Carassius auratus gibelio)

Identification of a Spindlin homolog in gibel carp (Carassius auratus gibelio)

Alternative usage of different poly(A) addition signals for two major species of mRNA encoding human aromatase P‐450

Codon usage between genomes is constrained by genome-wide mutational processes

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