Calculating Orthologous Protein-Coding Sequence Set Probability Using the Poisson Process

2021 ◽  
Author(s):  
Junfeng Liu ◽  
Yi Wang ◽  
Hongyu Zhao
Keyword(s):  
Poisson Process ◽  
Protein Coding ◽  
Orthologous Protein ◽  
Coding Sequence

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

2013 ◽  
Vol 94 (7) ◽  
pp. 1486-1495 ◽  
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.

Polyamine-mediated regulation of mouse ornithine decarboxylase is posttranslational

1989 ◽  
Vol 9 (12) ◽  
pp. 5484-5490
Author(s):  
T van Daalen Wetters ◽  
M Macrae ◽  
M Brabant ◽  
A Sittler ◽  
P Coffino
Keyword(s):  
Ornithine Decarboxylase ◽  
Translational Regulation ◽  
Feedback Inhibition ◽  
Chimeric Protein ◽  
Sequence Information ◽  
Pulse Label ◽  
Protein Coding ◽  
Coding Sequence ◽  
Series Of Experiments ◽  
The Difference

The activity of ornithine decarboxylase (ODC) is negatively regulated by intracellular polyamines, which thereby mediate a form of feedback inhibition of the initial enzyme in the pathway of their synthesis. This phenomenon has been believed to result, at least in part, from translational regulation. To investigate this further, we performed four series of experiments. First, we found that a chimeric protein encoded by an mRNA containing the ODC 5' leader sequence did not exhibit polyamine-dependent regulation. Second, we showed that transcripts containing the protein-coding sequence of ODC, but no other ODC-derived sequence information, exhibited regulation. Third, we found that the association of ODC mRNA with ribosomes was not altered when intracellular polyamine levels were modulated under conditions previously deemed to cause translational regulation. Last, we carried out experiments to measure the incorporation of [35S]methionine into ODC in polyamine-starved and polyamine-replete cells. Differential incorporation diminished progressively as pulse-label times were shortened; at the shortest labeling time used (4 min), the difference in favor of ODC in polyamine-starved cells was less than twofold. These findings suggest that it is necessary to reevaluate the question of whether polyamines cause alterations of translation of ODC mRNA.

scholarly journals Polyamine-mediated regulation of mouse ornithine decarboxylase is posttranslational.

1989 ◽  
Vol 9 (12) ◽  
pp. 5484-5490 ◽  
Author(s):  
T van Daalen Wetters ◽  
M Macrae ◽  
M Brabant ◽  
A Sittler ◽  
P Coffino
Keyword(s):  
Ornithine Decarboxylase ◽  
Translational Regulation ◽  
Feedback Inhibition ◽  
Chimeric Protein ◽  
Sequence Information ◽  
Pulse Label ◽  
Protein Coding ◽  
Coding Sequence ◽  
Series Of Experiments ◽  
The Difference

The activity of ornithine decarboxylase (ODC) is negatively regulated by intracellular polyamines, which thereby mediate a form of feedback inhibition of the initial enzyme in the pathway of their synthesis. This phenomenon has been believed to result, at least in part, from translational regulation. To investigate this further, we performed four series of experiments. First, we found that a chimeric protein encoded by an mRNA containing the ODC 5' leader sequence did not exhibit polyamine-dependent regulation. Second, we showed that transcripts containing the protein-coding sequence of ODC, but no other ODC-derived sequence information, exhibited regulation. Third, we found that the association of ODC mRNA with ribosomes was not altered when intracellular polyamine levels were modulated under conditions previously deemed to cause translational regulation. Last, we carried out experiments to measure the incorporation of [35S]methionine into ODC in polyamine-starved and polyamine-replete cells. Differential incorporation diminished progressively as pulse-label times were shortened; at the shortest labeling time used (4 min), the difference in favor of ODC in polyamine-starved cells was less than twofold. These findings suggest that it is necessary to reevaluate the question of whether polyamines cause alterations of translation of ODC mRNA.

Variation in protein-coding sequence and the genetic basis of cisplatin-induced toxicities among testicular cancer survivors (TCS) in the Platinum Study.

2016 ◽  
Vol 34 (15_suppl) ◽  
pp. 1537-1537 ◽  
Author(s):  
Eric R Gamazon ◽  
Heather E. Wheeler ◽  
Robert D. Frisina ◽  
Omar El Charif ◽  
Taisei Mushiroda ◽  
...  
Keyword(s):  
Testicular Cancer ◽  
Cancer Survivors ◽  
Genetic Basis ◽  
Protein Coding ◽  
Coding Sequence ◽  
Testicular Cancer Survivors

scholarly journals Structure of the human lactate dehydrogenase B gene

1989 ◽  
Vol 257 (3) ◽  
pp. 921-924 ◽  
Author(s):  
T Takeno ◽  
S S L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Translation Initiation ◽  
Initiation Site ◽  
Initiation Codon ◽  
Translation Initiation Site ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Sequence ◽  
Human Genomic ◽  
Human And Mouse

Human genomic clones containing parts of the lactate dehydrogenase B (LDH-B) gene (approx. 25 kb in length) were isolated and characterized. The protein-coding sequence of human LDH-B gene is interrupted by six introns at codons nos. 42-43, 82, 140, 198, 237 and 278-279, and the positions of these introns are homologous to those of LDH-A genes from man and mouse. The 5' non-coding region of human LDH-B gene is interrupted by an intron six nucleotide residues upstream of the ATG translation-initiation site, whereas those of human and mouse LDH-A genes are interrupted at 24 nucleotide residues 5' to the ATG initiation codon. As is the case of LDH-A genes from man and mouse, there is no intron in the 3' non-coding region of human LDH-B gene.

Cloning of a Complete Protein-Coding Sequence of Human Platelet-Type Phosphofructokinase Isozyme from Pancreatic Islet

1994 ◽  
Vol 198 (3) ◽  
pp. 990-998 ◽  
Author(s):  
K. Eto ◽  
H. Sakura ◽  
K. Yasuda ◽  
T. Hayakawa ◽  
E. Kawasaki ◽  
...  
Keyword(s):  
Pancreatic Islet ◽  
Human Platelet ◽  
Protein Coding ◽  
Coding Sequence ◽  
Complete Protein

The protein-coding sequence of the bovine ACTH-β-LPH precursor gene is split near the signal peptide region

Nature ◽  
1980 ◽  
Vol 287 (5784) ◽  
pp. 752-755 ◽  
Author(s):  
Shigetada Nakanishi ◽  
Yutaka Teranishi ◽  
Masaharu Noda ◽  
Mitsue Notake ◽  
Yumiko Watanabe ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Protein Coding ◽  
Coding Sequence ◽  
Signal Peptide Region ◽  
Peptide Region
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