scholarly journals Structure and function of the chromatin remodeler SMARCAD1 with its nucleosome substrate

2021 ◽  
Author(s):  
Jonathan Markert ◽  
Keda Zhou ◽  
Karolin Luger
Keyword(s):  
De Novo ◽  
Structure And Function ◽  
Dependent Manner ◽  
Nucleosome Assembly ◽  
Chromatin Remodeler ◽  
Chromatin Remodelers ◽  
Histone Octamer ◽  
Disease Information ◽  
Unique Manner ◽  
And Function

AbstractThe ATP-dependent chromatin remodeler SMARCAD1 acts on nucleosomes during DNA repair and transcription, but despite its implication in disease, information on its structure and function is scarce. Chromatin remodelers use a variety of ways to engage nucleosomes, and outcomes of the ATP-dependent reactions vary widely. Here we show that SMARCAD1 transfers the entire histone octamer from one DNA segment to another in an ATP-dependent manner but is also capable of de novo nucleosome assembly from histone octamer, due to its ability to bind all histones simultaneously. We describe the cryoEM structure of SMARCAD1 in complex with a nucleosome and show that it engages its substrate unlike any other chromatin remodeler. Our combined data allow us to put forward a testable model for SMARCAD1 mechanism.One-Sentence SummaryThe single subunit chromatin remodeler SMARCAD1 engages nucleosomes in a unique manner and transfers the entire histone octamer.

scholarly journals riboCIRC: a comprehensive database of translatable circRNAs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huihui Li ◽  
Mingzhe Xie ◽  
Yan Wang ◽  
Ludong Yang ◽  
Zhi Xie ◽  
...  
Keyword(s):  
De Novo ◽  
Species Conservation ◽  
Structure And Function ◽  
Research Community ◽  
Genome Browser ◽  
Valuable Resource ◽  
Sequence Structure ◽  
A Genome ◽  
Context Specific ◽  
And Function

AbstractriboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com.

Response to: De Novo Kidney Transplantation Without Use of Calcineurin Inhibitors Preserves Renal Structure and Function at 2 Years

2005 ◽  
Vol 5 (5) ◽  
pp. 1169-1169
Author(s):  
Stuart M. Flechner ◽  
Caroline M. Lanigan ◽  
Daniel R. Salomon ◽  
James T. Burke ◽  
Kim Solez
Keyword(s):  
Kidney Transplantation ◽  
De Novo ◽  
Calcineurin Inhibitors ◽  
Structure And Function ◽  
Renal Structure ◽  
And Function

Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin

2018 ◽  
Vol 54 (34) ◽  
pp. 4356-4359 ◽  
Author(s):  
Lu-Lu Yin ◽  
Hong Yuan ◽  
Ke-Jie Du ◽  
Bo He ◽  
Shu-Qin Gao ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Heme Proteins ◽  
De Novo ◽  
Structure And Function ◽  
Intramolecular Disulfide Bond ◽  
And Function

The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.

scholarly journals Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits

2016 ◽  
Vol 113 (29) ◽  
pp. E4151-E4160 ◽  
Author(s):  
Selom K. Doamekpor ◽  
Joong-Won Lee ◽  
Nathaniel L. Hepowit ◽  
Cheng Wu ◽  
Clement Charenton ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Quality ◽  
E3 Ligase ◽  
Structure And Function ◽  
Dependent Manner ◽  
Ribosomal Subunits ◽  
Terminal Domain ◽  
Cell Extracts ◽  
And Function

The Ltn1 E3 ligase (listerin in mammals) has emerged as a paradigm for understanding ribosome-associated ubiquitylation. Ltn1 binds to 60S ribosomal subunits to ubiquitylate nascent polypeptides that become stalled during synthesis; among Ltn1’s substrates are aberrant products of mRNA lacking stop codons [nonstop translation products (NSPs)]. Here, we report the reconstitution of NSP ubiquitylation in Neurospora crassa cell extracts. Upon translation in vitro, ribosome-stalled NSPs were ubiquitylated in an Ltn1-dependent manner, while still ribosome-associated. Furthermore, we provide biochemical evidence that the conserved N-terminal domain (NTD) plays a significant role in the binding of Ltn1 to 60S ribosomal subunits and that NTD mutations causing defective 60S binding also lead to defective NSP ubiquitylation, without affecting Ltn1’s intrinsic E3 ligase activity. Finally, we report the crystal structure of the Ltn1 NTD at 2.4-Å resolution. The structure, combined with additional mutational studies, provides insight to NTD’s role in binding stalled 60S subunits. Our findings show that Neurospora extracts can be used as a tool to dissect mechanisms underlying ribosome-associated protein quality control and are consistent with a model in which Ltn1 uses 60S subunits as adapters, at least in part via its NTD, to target stalled NSPs for ubiquitylation.

scholarly journals Two Distantly Homologous DnaG Primases from Thermoanaerobacter tengcongensis Exhibit Distinct Initiation Specificities and Priming Activities

2010 ◽  
Vol 192 (11) ◽  
pp. 2670-2681 ◽  
Author(s):  
Jie Li ◽  
Jingfang Liu ◽  
Ligang Zhou ◽  
Huadong Pei ◽  
Jian Zhou ◽  
...  
Keyword(s):  
Amino Acids ◽  
De Novo ◽  
Thermophilic Bacterium ◽  
Structure And Function ◽  
Thermoanaerobacter Tengcongensis ◽  
Wide Range ◽  
Dna Binding Affinity ◽  
Template Specificity ◽  
And Function

ABSTRACT Primase, encoded by dnaG in bacteria, is a specialized DNA-dependent RNA polymerase that synthesizes RNA primers de novo for elongation by DNA polymerase. Genome sequence analysis has revealed two distantly related dnaG genes, TtdnaG and TtdnaG 2, in the thermophilic bacterium Thermoanaerobacter tengcongensis. Both TtDnaG (600 amino acids) and TtDnaG2 (358 amino acids) exhibit primase activities in vitro at a wide range of temperatures. Interestingly, the template recognition specificities of these two primases are quite distinctive. When trinucleotide-specific templates were tested, TtDnaG initiated RNA primer synthesis efficiently only on templates containing the trinucleotide 5′-CCC-3′, not on the other 63 possible trinucleotides. When the 5′-CCC-3′ sequence was flanked by additional cytosines or guanines, the initiation efficiency of TtDnaG increased remarkably. Significantly, TtDnaG could specifically and efficiently initiate RNA primer synthesis on a limited set of tetranucleotides composed entirely of cytosines and guanines, indicating that TtDnaG initiated RNA primer synthesis more preferably on GC-containing tetranucleotides. In contrast, it seemed that TtDnaG2 had no specific initiation nucleotides, as it could efficiently initiate RNA primer synthesis on all templates tested. The DNA binding affinity of TtDnaG2 was usually 10-fold higher than that of TtDnaG, which might correlate with its high activity but low template specificity. These distinct priming activities and specificities of TtDnaG and TtDnaG2 might shed new light on the diversity in the structure and function of the primases.

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