DSP techniques for protein coding region identification based on background noise and nonlinear phase delay reduction from period-3 spectrum using zero phased anti-notch filter and Savitzky-Golay (S-G) filter

Abstract Genes that have undergone positive or diversifying selection are likely to be associated with adaptive divergence between species. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of synonymous fixed differences per synonymous site (ω = Ka/Ks). We used an evolutionary expressed sequence tag (EST) approach to estimate the distribution of ω among 304 orthologous loci between Arabidopsis thaliana and A. lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. We find that 14 of 304 genes (∼5%) have an estimated ω > 1 and are candidates for genes with increased selection intensities. Molecular population genetic analyses of 6 of these rapidly evolving protein loci indicate that, despite their high levels of between-species nonsynonymous divergence, these genes do not have elevated levels of intraspecific replacement polymorphisms compared to previously studied genes. A hierarchical Bayesian analysis of protein-coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to previously studied A. thaliana nuclear loci.

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Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication

Journal of General Virology ◽

10.1099/vir.0.052126-0 ◽

2013 ◽

Vol 94 (7) ◽

pp. 1486-1495 ◽

Cited By ~ 17

Author(s):

Graham J. Belsham

Keyword(s):

Disease Virus ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

Initiation Codon ◽

Coding Region ◽

Protein Coding ◽

Coding Sequence ◽

Bhk Cells ◽

Leader Protein ◽

Mouth Disease Virus

The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding sequence is lethal for the virus, whereas loss of the Lb coding sequence results in a virus that is viable in BHK cells. In addition, it is now shown that deletion of the ‘spacer’ region between these two initiation codons can be tolerated. Growth of the virus precisely lacking just the Lb coding sequence resulted in a previously undetected accumulation of frameshift mutations within the ‘spacer’ region. These mutations block the inappropriate fusion of amino acid sequences to the amino-terminus of the capsid protein precursor. Modification, by site-directed mutagenesis, of the Lab initiation codon, in the context of the virus lacking the Lb coding region, was also tolerated by the virus within BHK cells. However, precise loss of the Lb coding sequence alone blocked FMDV replication in primary bovine thyroid cells. Thus, the requirement for the Leader protein coding sequences is highly dependent on the nature and extent of the residual Leader protein sequences and on the host cell system used. FMDVs precisely lacking Lb and with the Lab initiation codon modified may represent safer seed viruses for vaccine production.

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Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila

Cell ◽

10.1016/0092-8674(84)90261-7 ◽

1984 ◽

Vol 38 (3) ◽

pp. 667-673 ◽

Cited By ~ 121

Author(s):

Michael Levine ◽

Gerald M. Rubin ◽

Robert Tjian

Keyword(s):

Dna Sequences ◽

Homeotic Genes ◽

Coding Region ◽

Protein Coding ◽

Human Dna

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An additional promoter within the protein-coding region of thepsbD-psbC gene cluster in tobacco chloroplast DNA

Nucleic Acids Research ◽

10.1093/nar/17.23.9583 ◽

1989 ◽

Vol 17 (23) ◽

pp. 9583-9591 ◽

Cited By ~ 59

Author(s):

Wen Biao Yao ◽

Bing Yuan Meng ◽

Minoru Tanaka ◽

Masahiro Sugiura

Keyword(s):

Chloroplast Dna ◽

Gene Cluster ◽

Coding Region ◽

Protein Coding ◽

Tobacco Chloroplast

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Structure and expression of canary myc family genes

Molecular and Cellular Biology ◽

10.1128/mcb.11.3.1770-1776.1991 ◽

1991 ◽

Vol 11 (3) ◽

pp. 1770-1776

Author(s):

R G Collum ◽

D F Clayton ◽

F W Alt

Keyword(s):

Untranslated Region ◽

Untranslated Regions ◽

Coding Region ◽

Protein Coding ◽

Coding Regions ◽

Neuronal Precursors ◽

Myc Gene ◽

Mature Neurons

We found that the canary N-myc gene is highly related to mammalian N-myc genes in both the protein-coding region and the long 3' untranslated region. Examined coding regions of the canary c-myc gene were also highly related to their mammalian counterparts, but in contrast to N-myc, the canary and mammalian c-myc genes were quite divergent in their 3' untranslated regions. We readily detected N-myc and c-myc expression in the adult canary brain and found N-myc expression both at sites of proliferating neuronal precursors and in mature neurons.

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The destabilizing elements in the coding region of c-fos mRNA are recognized as RNA

Molecular and Cellular Biology ◽

10.1128/mcb.13.8.5034-5042.1993 ◽

1993 ◽

Vol 13 (8) ◽

pp. 5034-5042

Author(s):

C L Wellington ◽

M E Greenberg ◽

J G Belasco

Keyword(s):

Codon Usage ◽

Mammalian Cells ◽

Mrna Decay ◽

Polypeptide Chain ◽

Coding Region ◽

Protein Coding ◽

Present Evidence ◽

Reading Frame ◽

Nascent Polypeptide

The protein-coding region of the c-fos proto-oncogene transcript contains elements that direct the rapid deadenylation and decay of this mRNA in mammalian cells. The function of these coding region instability determinants requires movement of ribosomes across mRNAs containing them. Three types of mechanisms could account for this translational requirement. Two of these possibilities, (i) that rapid mRNA decay might be mediated by the nascent polypeptide chain and (ii) that it might result from an unusual codon usage, have experimental precedent. Here, we present evidence that the destabilizing elements in the c-fos coding region are not recognized in either of these two ways. Instead, the ability of the c-fos coding region to function as a potent mRNA destabilizer when translated in the +1 reading frame indicates that the signals for rapid deadenylation and decay reside in the sequence or structure of the RNA comprising this c-fos domain.

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Identification of the principal promoter sequence of the c-H-ras transforming oncogene: deletion analysis of the 5'-flanking region by focus formation assay

Molecular and Cellular Biology ◽

10.1128/mcb.7.8.2933-2940.1987 ◽

1987 ◽

Vol 7 (8) ◽

pp. 2933-2940

Author(s):

H Honkawa ◽

W Masahashi ◽

S Hashimoto ◽

T Hashimoto-Gotoh

Keyword(s):

Dna Sequences ◽

Promoter Sequence ◽

Ras Oncogene ◽

Coding Region ◽

Focus Formation ◽

S1 Nuclease ◽

Protein Coding ◽

Consensus Sequences ◽

Flanking Region ◽

Virus C

A number of deletion mutants were isolated, including 5', 3', and internal deletions in the 5'-flanking region of the human cellular oncogene related to the Harvey sarcoma virus (c-H-ras), and their transforming activities were examined in NIH 3T3 cells. DNA sequences which could not be detected without losing transforming activity were localized to a relatively short stretch upstream of the region which showed homology to the 5'-flanking region of v-H-ras oncogene. S1 nuclease analysis indicated that there were two clusters of mRNA start sites at positions that were about 1,371 and 1,298 base pairs upstream of the first coding ATG. The minimum region required for promoter function was estimated to be a 51-base-pair-long (or less) DNA segment. The promoter was GC rich (78%) and did not contain the consensus sequences that are usually observed in PolII-directed promoters but contained a GC box within which one of the mRNA start sites was included. In addition, two sets of positive and negative elements seemed to be located between the promoter and the protein-coding region, which appeared to influence positively and negatively, respectively, the efficiency of transformation with the c-H-ras oncogene.

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Mammalian nonsense codons can be cis effectors of nuclear mRNA half-life

Molecular and Cellular Biology ◽

10.1128/mcb.14.12.8219-8228.1994 ◽

1994 ◽

Vol 14 (12) ◽

pp. 8219-8228

Author(s):

P Belgrader ◽

J Cheng ◽

X Zhou ◽

L S Stephenson ◽

L E Maquat

Keyword(s):

Triosephosphate Isomerase ◽

Blot Hybridization ◽

Mrna Level ◽

Coding Region ◽

Protein Coding ◽

Codon Recognition ◽

Reverse Transcription Pcr ◽

Nonsense Codon ◽

Bona Fide ◽

Nonsense Codons

Frameshift and nonsense mutations within the gene for human triosephosphate isomerase (TPI) that generate a nonsense codon within the first three-fourths of the protein coding region have been found to reduce the abundance of the product mRNA that copurifies with nuclei. The cellular process and location of the nonsense codon-mediated reduction have proven difficult to elucidate for technical reasons. We show here, using electron microscopy to judge the purity of isolated nuclei, that the previously established reduction to 25% of the normal mRNA level is evident for nuclei that are free of detectable cytoplasmic contamination. Therefore, the reduction is likely to be characteristic of bona fide nuclear RNA. Fully spliced nuclear mRNA is identified by Northern (RNA) blot hybridization and a reverse transcription-PCR assay as the species that undergoes decay in experiments that used the human c-fos promoter to elicit a burst and subsequent shutoff of TPI gene transcription upon the addition of serum to serum-deprived cells. Finally, the finding that deletion of a 5' splice site of the TPI gene results predominantly but not exclusively in the removal by splicing (i.e., skipping) of the upstream exon as a part of the flanking introns has been used to demonstrate that decay is specific to those mRNA products that maintain the nonsense codon. This result, together with our previous results that implicate translation by ribosomes and charged tRNAs in the decay mechanism, indicate that nonsense codon recognition takes place after splicing and triggers decay solely in cis. The possibility that decay takes place during the process of mRNA export from the nucleus to the cytoplasm is discussed.

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