scholarly journals Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil

2020 ◽  
Vol 14 (4) ◽  
pp. 436-443 ◽  
Author(s):  
Mina Nakauchi ◽  
Emi Takashita ◽  
Seiichiro Fujisaki ◽  
Masayuki Shirakura ◽  
Rie Ogawa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Rapid Detection ◽  
Acidic Subunit ◽  
Influenza Polymerase

Proline-106 EPSPS Mutation Imparting Glyphosate Resistance in Goosegrass (Eleusine indica) Emerges in South America

Weed Science ◽  
2018 ◽  
Vol 67 (1) ◽  
pp. 48-56 ◽  
Author(s):  
Hudson K. Takano ◽  
Rafael R. Mendes ◽  
Leonardo B. Scoz ◽  
Ramiro F. Lopez Ovejero ◽  
Jamil Constantin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Rapid Detection ◽  
Resistance Mechanism ◽  
Fold Increase ◽  
In Planta ◽  
Eleusine Indica ◽  
Target Site Resistance ◽  
Resistance Trait

AbstractGlyphosate-resistant (GR) goosegrass [Eleusine indica(L.) Gaertn.] was recently identified in Brazil, but its resistance mechanism was unknown. This study elucidated the resistance mechanism in this species and developed a molecular marker for rapid detection of this target-site resistance trait. The resistance factor for the resistant biotype was 4.4-fold compared with the glyphosate-susceptible (GS) in greenhouse dose–response experiments. This was accompanied by a similar (4-fold) difference in the levels of in vitro andin plantashikimate accumulation in these biotypes. However, there was no difference in uptake, translocation, or metabolism of glyphosate between the GS and GR biotypes. Moreover, both biotypes showed similar values for 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number and transcription. Sequencing of a 330-bp fragment of theEPSPSgene identified a single-nucleotide polymorphism that led to a Pro-106-Ser amino acid substitution in the enzyme from the GR biotype. This mutation imparted a 3.8-fold increase in the amount of glyphosate required to inhibit 50% of EPSPS activity, confirming the role of this amino acid substitution in resistance to glyphosate. A quantitative PCR–based genotyping assay was developed for the rapid detection of resistant plants containing this Pro-106-Ser mutation.

Hubsm: A Novel Amino Acid Substitution Matrix for Comparing Hub Proteins

2017 ◽  
Vol 7 (8) ◽  
pp. 212
Author(s):  
Renganayaki G. ◽  
Achuthsankar S. Nair
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Low Complexity ◽  
Database Search ◽  
Substitution Matrix ◽  
Compositional Bias ◽  
Sequence Alignments ◽  
Amino Acid Substitution Matrix ◽  
Alignment Algorithms ◽  
Hub Proteins

Sequence alignment algorithms and  database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid.   In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the  residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs,  the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.

scholarly journals A large compressibility change of protein induced by a single amino acid substitution

1996 ◽  
Vol 5 (3) ◽  
pp. 542-545 ◽  
Author(s):  
Kunihiko Gekko ◽  
Youjiro Tamura ◽  
Eiji Ohmae ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Single Amino Acid Substitution ◽  
Single Amino Acid

Identification of a Functional Domain Within the Essential Core of Histone H3 That Is Required for Telomeric and HM Silencing in Saccharomyces cerevisiae

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 447-452 ◽  
Author(s):  
Jeffrey S Thompson ◽  
Marilyn L Snow ◽  
Summer Giles ◽  
Leslie E McPherson ◽  
Michael Grunstein
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Amino Acid Substitution ◽  
Histone H3 ◽  
Single Amino Acid ◽  
Functional Domain ◽  
Partial Loss ◽  
Histone Fold ◽  
Gal1 Promoter ◽  
Substitution Mutations

Abstract Fourteen novel single-amino-acid substitution mutations in histone H3 that disrupt telomeric silencing in Saccharomyces cerevisiae were identified, 10 of which are clustered within the α1 helix and L1 loop of the essential histone fold. Several of these mutations cause derepression of silent mating locus HML, and an additional subset cause partial loss of basal repression at the GAL1 promoter. Our results identify a new domain within the essential core of histone H3 that is required for heterochromatin-mediated silencing.

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