scholarly journals Single-base deletion in GmCHR5 increases the genistein-to-daidzein ratio in soybean seed

2020 ◽  
Vol 70 (3) ◽  
pp. 265-276
Author(s):  
Md. Abdur Rauf Sarkar ◽  
Wakana Otsu ◽  
Akihiro Suzuki ◽  
Fumio Hashimoto ◽  
Toyoaki Anai ◽  
...  
Keyword(s):  
Soybean Seed ◽  
Single Base ◽  
Single Base Deletion

scholarly journals Heterotrimeric PCNA Increases the Activity and Fidelity of Dbh, a Y-family Translesion DNA Polymerase Prone to Creating Single-Base Deletion Mutations

2020 ◽  
Author(s):  
Yifeng Wu ◽  
William Jaremko ◽  
Ryan C. Wilson ◽  
Janice D. Pata
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Polymerase Activity ◽  
List Type ◽  
Single Base ◽  
Deletion Mutations ◽  
Single Base Deletion ◽  
Translesion Dna ◽  
Y Family

AbstractDbh is a Y-family translesion DNA polymerase from Sulfolobus acidocaldarius, an archaeal species that grows in harsh environmental conditions. Biochemically, Dbh displays a distinctive mutational profile, creating single-base deletion mutations at extraordinarily high frequencies (up to 50%) in specific repeat sequences. In cells, however, Dbh does not appear to contribute significantly to spontaneous frameshifts in these same sequence contexts. This suggests that either the error-prone DNA synthesis activity of Dbh is reduced in vivo and/or Dbh is restricted from replicating these sequences. Here, we test the hypothesis that the propensity for Dbh to make single base deletion mutations is reduced through interaction with the S. acidocaldarius heterotrimeric sliding clamp processivity factor, PCNA-123. We first confirm that Dbh physically interacts with PCNA-123, with the interaction requiring both the PCNA-1 subunit and the C-terminal 10 amino acids of Dbh, which contain a predicted PCNA-interaction peptide (PIP) motif. This interaction stimulates the polymerase activity of Dbh, even on short, linear primer-template DNA by increasing the rate of nucleotide incorporation. This stimulation requires an intact PCNA-123 heterotrimer and a DNA duplex length of at least 18 basepairs, the minimal length predicted from structural data to bind to both the polymerase and the clamp. Finally, we find that PCNA-123 increases the fidelity of Dbh on a single-base deletion hotspot sequence 3-fold by promoting an increase in the rate of correct, but not incorrect, nucleotide addition and propose that PCNA-123 induces Dbh to adopt a more active conformation that is less prone to creating deletions during DNA synthesis.HighlightsPCNA increases the fidelity of Dbh polymerase on a deletion-hotspot sequence.The interaction stimulates incorporation of the correct, but not incorrect, nucleotide.A minimal duplex length of 18 bp is required for PCNA to stimulate polymerase activity.Structural modeling suggests that PCNA induces a conformational change in Dbh.

A single-base deletion in soybean flavonol synthase gene is associated with magenta flower color

2006 ◽  
Vol 63 (1) ◽  
pp. 125-135 ◽  
Author(s):  
Ryoji Takahashi ◽  
Stephen M. Githiri ◽  
Kouta Hatayama ◽  
Emilyn G. Dubouzet ◽  
Norimoto Shimada ◽  
...  
Keyword(s):  
Flower Color ◽  
Flavonol Synthase ◽  
Single Base ◽  
Single Base Deletion

scholarly journals A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat

Genomics ◽  
2006 ◽  
Vol 88 (6) ◽  
pp. 698-705 ◽  
Author(s):  
Yasuko Ishida ◽  
Victor A. David ◽  
Eduardo Eizirik ◽  
Alejandro A. Schäffer ◽  
Beena A. Neelam ◽  
...  
Keyword(s):  
Coat Color ◽  
Domestic Cat ◽  
Single Base ◽  
Single Base Deletion ◽  
Color Phenotype ◽  
Coat Color Phenotype

A novel single-base deletion mutation of the RUNX2 gene in a Chinese family with cleidocranial dysplasia

2011 ◽  
Vol 10 (4) ◽  
pp. 3539-3544 ◽  
Author(s):  
C.Y. Fang ◽  
J.J Xue ◽  
L. Tan ◽  
C.H. Jiang ◽  
Q.P. Gao ◽  
...  
Keyword(s):  
Deletion Mutation ◽  
Chinese Family ◽  
Cleidocranial Dysplasia ◽  
Single Base ◽  
Single Base Deletion

scholarly journals Minor Groove Interactions at the DNA Polymerase β Active Site Modulate Single-base Deletion Error Rates

2000 ◽  
Vol 275 (36) ◽  
pp. 28033-28038 ◽  
Author(s):  
Wendy P. Osheroff ◽  
William A. Beard ◽  
Shang Yin ◽  
Samuel H. Wilson ◽  
Thomas A. Kunkel
Keyword(s):  
Dna Polymerase ◽  
Active Site ◽  
Minor Groove ◽  
Error Rates ◽  
Dna Polymerase Β ◽  
Single Base ◽  
Single Base Deletion
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