Analysis of the molecular evolution of histone variant H2A.Z using a linker-mediated complex strategy and yeast genetic complementation

2021 ◽  
Author(s):  
Saho Kitagawa ◽  
Masayuki Kusakabe ◽  
Daisuke Takahashi ◽  
Takumi Narimiya ◽  
Yu Nakabayashi ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Evolutionary Conservation ◽  
Histone Variant ◽  
Genetic Complementation ◽  
Yeast Genetic

Abstract The histone variant H2A.Z is deposited into chromatin by specific machinery and is required for genome functions. Using a linker-mediated complex strategy combined with yeast genetic complementation, we demonstrate evolutionary conservation of H2A.Z together with its chromatin incorporation and functions. This approach is applicable to the evolutionary analyses of proteins that form complexes with interactors.

scholarly journals Molecular evolution of the histone variant H2A.Z

2019 ◽  
Vol 35 (3) ◽  
pp. 217-218
Author(s):  
S. Kitagawa ◽  
M. Kusakabe ◽  
H. Oku ◽  
D. Takahashi ◽  
T. Narimiya ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Histone Variant

scholarly journals Molecular Evolution of Lysine Biosynthesis in Agaricomycetes

2021 ◽  
Vol 8 (1) ◽  
pp. 37
Author(s):  
Zili Song ◽  
Maoqiang He ◽  
Ruilin Zhao ◽  
Landa Qi ◽  
Guocan Chen ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Evolutionary Relationship ◽  
Deep Understanding ◽  
Evolutionary Conservation ◽  
Fungal Species ◽  
Lysine Biosynthesis ◽  
Tertiary Structures ◽  
Saccharopine Dehydrogenase ◽  
Homocitrate Synthase ◽  
Substrate Binding Sites

As an indispensable essential amino acid in the human body, lysine is extremely rich in edible mushrooms. The α-aminoadipic acid (AAA) pathway is regarded as the biosynthetic pathway of lysine in higher fungal species in Agaricomycetes. However, there is no deep understanding about the molecular evolutionary relationship between lysine biosynthesis and species in Agaricomycetes. Herein, we analyzed the molecular evolution of lysine biosynthesis in Agaricomycetes. The phylogenetic relationships of 93 species in 34 families and nine orders in Agaricomycetes were constructed with six sequences of LSU, SSU, ITS (5.8 S), RPB1, RPB2, and EF1-α datasets, and then the phylogeny of enzymes involved in the AAA pathway were analyzed, especially homocitrate synthase (HCS), α-aminoadipate reductase (AAR), and saccharopine dehydrogenase (SDH). We found that the evolution of the AAA pathway of lysine biosynthesis is consistent with the evolution of species at the order level in Agaricomycetes. The conservation of primary, secondary, predicted tertiary structures, and substrate-binding sites of the enzymes of HCS, AAR, and SDH further exhibited the evolutionary conservation of lysine biosynthesis in Agaricomycetes. Our results provide a better understanding of the evolutionary conservation of the AAA pathway of lysine biosynthesis in Agaricomycetes.

scholarly journals A benchmark of gene expression tissue-specificity metrics

2015 ◽  
Author(s):  
Nadezda Kryuchkova ◽  
Marc Robinson-Rechavi
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Expression Pattern ◽  
Tissue Specificity ◽  
Evolutionary Rate ◽  
Evolutionary Conservation ◽  
Rna Seq ◽  
Functional Feature ◽  
Tissue Specific

One of the major properties of genes is their expression pattern. Notably, genes are often classified as tissue-specific or housekeeping. This property is of interest to molecular evolution as an explanatory factor of, e.g., evolutionary rate, as well as a functional feature which may in itself evolve. While many different methods of measuring tissue specificity have been proposed and used for such studies, there has been no comparison or benchmarking of these methods to our knowledge, and little justification of their use. In this study we compare nine measures of tissue-specificity. Most methods were established for ESTs and microarrays, and several were later adapted to RNA-seq. We analyze their capacity to distinguish gene categories, their robustness to the choice and number of tissues used, and their capture of evolutionary conservation signal.

Molecular evolution of a cytochrome P450 for the synthesis of potential antidepressant (2R,6R)-hydroxynorketamine

2021 ◽  
Author(s):  
Ansgar Bokel ◽  
Michael C. Hutter ◽  
Vlada B. Urlacher
Keyword(s):  
Cytochrome P450 ◽  
Molecular Evolution ◽  
Cytochrome P450 Monooxygenase ◽  
P450 Monooxygenase ◽  
Effective Synthesis

Engineered cytochrome P450 monooxygenase CYP154E1 enables the effective synthesis of the potential antidepressant (2R,6R)-hydroxynorketamine via N-demethylation and regio- and stereoselective hydroxylation of (R)-ketamine.

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