journal
https://read.qxmd.com/read/38499483/despite-the-odds-formation-of-the-sars-cov-2-methylation-complex
#21
JOURNAL ARTICLE
Alex Matsuda, Jacek Plewka, Michał Rawski, André Mourão, Weronika Zajko, Till Siebenmorgen, Leanid Kresik, Kinga Lis, Alisha N Jones, Magdalena Pachota, Abdulkarim Karim, Kinga Hartman, Shivlee Nirwal, Ravi Sonani, Yuliya Chykunova, Igor Minia, Paweł Mak, Markus Landthaler, Marcin Nowotny, Grzegorz Dubin, Michael Sattler, Piotr Suder, Grzegorz M Popowicz, Krzysztof Pyrć, Anna Czarna
Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes...
March 18, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38499482/exhaustive-identification-of-genome-wide-binding-events-of-transcriptional-regulators
#22
JOURNAL ARTICLE
Anna Nordin, Pierfrancesco Pagella, Gianluca Zambanini, Claudio Cantù
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives...
March 18, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38499480/engineering-an-escherichia-coli-strain-for-production-of-long-single-stranded-dna
#23
JOURNAL ARTICLE
Konlin Shen, Jake J Flood, Zhihuizi Zhang, Alvin Ha, Brian R Shy, John E Dueber, Shawn M Douglas
Long single-stranded DNA (ssDNA) is a versatile molecular reagent with applications including RNA-guided genome engineering and DNA nanotechnology, yet its production is typically resource-intensive. We introduce a novel method utilizing an engineered Escherichia coli 'helper' strain and phagemid system that simplifies long ssDNA generation to a straightforward transformation and purification procedure. Our method obviates the need for helper plasmids and their associated contamination by integrating M13mp18 genes directly into the E...
March 18, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38485701/substrate-specificity-of-mycobacterium-tuberculosis-trna-terminal-nucleotidyltransferase-toxin-ment3
#24
JOURNAL ARTICLE
Jun Liu, Yuka Yashiro, Yuriko Sakaguchi, Tsutomu Suzuki, Kozo Tomita
Mycobacterium tuberculosis transfer RNA (tRNA) terminal nucleotidyltransferase toxin, MenT3, incorporates nucleotides at the 3'-CCA end of tRNAs, blocking their aminoacylation and inhibiting protein synthesis. Here, we show that MenT3 most effectively adds CMPs to the 3'-CCA end of tRNA. The crystal structure of MenT3 in complex with CTP reveals a CTP-specific nucleotide-binding pocket. The 4-NH2 and the N3 and O2 atoms of cytosine in CTP form hydrogen bonds with the main-chain carbonyl oxygen of P120 and the side chain of R238, respectively...
March 15, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477398/molecular-basis-of-a-thaliana-keops-complex-in-biosynthesizing-trna-t6a
#25
JOURNAL ARTICLE
Xinxing Zheng, Chenchen Su, Lei Duan, Mengqi Jin, Yongtao Sun, Li Zhu, Wenhua Zhang
In archaea and eukaryotes, the evolutionarily conserved KEOPS is composed of four core subunits-Kae1, Bud32, Cgi121 and Pcc1, and a fifth Gon7/Pcc2 that is found in fungi and metazoa. KEOPS cooperates with Sua5/YRDC to catalyze the biosynthesis of tRNA N6-threonylcarbamoyladenosine (t6A), an essential modification needed for fitness of cellular organisms. Biochemical and structural characterizations of KEOPSs from archaea, yeast and humans have determined a t6A-catalytic role for Kae1 and auxiliary roles for other subunits...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477394/molecular-mechanism-of-the-one-component-regulator-rccr-on-bacterial-metabolism-and-virulence
#26
JOURNAL ARTICLE
Yibo Zhu, Xingyu Mou, Yingjie Song, Qianqian Zhang, Bo Sun, Huanxiang Liu, Hong Tang, Rui Bao
The regulation of carbon metabolism and virulence is critical for the rapid adaptation of pathogenic bacteria to host conditions. In Pseudomonas aeruginosa, RccR is a transcriptional regulator of genes involved in primary carbon metabolism and is associated with bacterial resistance and virulence, although the exact mechanism is unclear. Our study demonstrates that PaRccR is a direct repressor of the transcriptional regulator genes mvaU and algU. Biochemical and structural analyses reveal that PaRccR can switch its DNA recognition mode through conformational changes triggered by KDPG binding or release...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477377/determinants-of-crispr-cas12a-nuclease-activation-by-dna-and-rna-targets
#27
JOURNAL ARTICLE
Eric A Nalefski, Remy M Kooistra, Ishira Parikh, Samantha Hedley, Karunya Rajaraman, Damian Madan
The RNA-guided CRISPR-associated (Cas) enzyme Cas12a cleaves specific double-stranded (ds-) or single-stranded (ss-) DNA targets (in cis), unleashing non-specific ssDNA cleavage (in trans). Though this trans-activity is widely coopted for diagnostics, little is known about target determinants promoting optimal enzyme performance. Using quantitative kinetics, we show formation of activated nuclease proceeds via two steps whereby rapid binding of Cas12a ribonucleoprotein to target is followed by a slower allosteric transition...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477356/defining-the-contribution-of-microrna-specific-argonautes-with-slicer-capability-in-animals
#28
JOURNAL ARTICLE
Anisha Pal, Vaishnav Vasudevan, François Houle, Michael Lantin, Katherine A Maniates, Miguel Quévillon Huberdeau, Allison L Abbott, Martin J Simard
microRNAs regulate gene expression through interaction with an Argonaute protein. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicer residues in the canonical microRNA pathway is still unclear in animals. To address this, we created Caenorhabditis elegans strains with mutated slicer residues in the endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477352/atrx-guards-against-aberrant-differentiation-in-mesenchymal-progenitor-cells
#29
JOURNAL ARTICLE
Yan Fang, Douglas Barrows, Yakshi Dabas, Thomas S Carroll, Sam Singer, William D Tap, Benjamin A Nacev
Alterations in the tumor suppressor ATRX are recurrently observed in mesenchymal neoplasms. ATRX has multiple epigenetic functions including heterochromatin formation and maintenance and regulation of transcription through modulation of chromatin accessibility. Here, we show in murine mesenchymal progenitor cells (MPCs) that Atrx deficiency aberrantly activated mesenchymal differentiation programs. This includes adipogenic pathways where ATRX loss induced expression of adipogenic transcription factors and enhanced adipogenic differentiation in response to differentiation stimuli...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477346/uncovering-the-gacs-mediated-role-in-evolutionary-progression-through-trajectory-reconstruction-in-pseudomonas-aeruginosa
#30
JOURNAL ARTICLE
Bo Jiang, Huifang Qiu, Chenghui Lu, Mingqi Lu, Yuanhao Li, Weijun Dai
The genetic diversities of subpopulations drive the evolution of pathogens and affect their ability to infect hosts and cause diseases. However, most studies to date have focused on the identification and characterization of adaptive mutations in single colonies, which do not accurately reflect the phenotypes of an entire population. Here, to identify the composition of variant subpopulations within a pathogen population, we developed a streamlined approach that combines high-throughput sequencing of the entire population cells with genotyping of single colonies...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477342/an-autocatalytic-crispr-cas-amplification-effect-propelled-by-the-lna-modified-split-activators-for-dna-sensing
#31
JOURNAL ARTICLE
Ke Sun, Lei Pu, Chuan Chen, Mutian Chen, Kaiju Li, Xinqiong Li, Huanqing Li, Jia Geng
CRISPR-Cas systems with dual functions offer precise sequence-based recognition and efficient catalytic cleavage of nucleic acids, making them highly promising in biosensing and diagnostic technologies. However, current methods encounter challenges of complexity, low turnover efficiency, and the necessity for sophisticated probe design. To better integrate the dual functions of Cas proteins, we proposed a novel approach called CRISPR-Cas Autocatalysis Amplification driven by LNA-modified Split Activators (CALSA) for the highly efficient detection of single-stranded DNA (ssDNA) and genomic DNA...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38477328/an-anticodon-sensing-t-boxzyme-generates-the-elongator-nonproteinogenic-aminoacyl-trna-in-situ-of-a-custom-made-translation-system-for-incorporation
#32
JOURNAL ARTICLE
Wei Lu, Naohiro Terasaka, Yuriko Sakaguchi, Takeo Suzuki, Tsutomu Suzuki, Hiroaki Suga
In the hypothetical RNA world, ribozymes could have acted as modern aminoacyl-tRNA synthetases (ARSs) to charge tRNAs, thus giving rise to the peptide synthesis along with the evolution of a primitive translation apparatus. We previously reported a T-boxzyme, Tx2.1, which selectively charges initiator tRNA with N-biotinyl-phenylalanine (BioPhe) in situ in a Flexible In-vitro Translation (FIT) system to produce BioPhe-initiating peptides. Here, we performed in vitro selection of elongation-capable T-boxzymes (elT-boxzymes), using para-azido-l-phenylalanine (PheAZ) as an acyl-donor...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471818/crispr-antiphage-defence-mediated-by-the-cyclic-nucleotide-binding-membrane-protein-csx23
#33
JOURNAL ARTICLE
Sabine Grüschow, Stuart McQuarrie, Katrin Ackermann, Stephen McMahon, Bela E Bode, Tracey M Gloster, Malcolm F White
CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae...
March 13, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471819/viral-reprogramming-of-host-transcription-initiation
#34
JOURNAL ARTICLE
Nathan A Ungerleider, Claire Roberts, Tina M O'Grady, Trang T Nguyen, Melody Baddoo, Jia Wang, Eman Ishaq, Monica Concha, Meggie Lam, Jordan Bass, Truong D Nguyen, Nick Van Otterloo, Nadeeshika Wickramarachchige-Dona, Dorota Wyczechowska, Maria Morales, Tianfang Ma, Yan Dong, Erik K Flemington
Viruses are master remodelers of the host cell environment in support of infection and virus production. For example, viruses typically regulate cell gene expression through modulating canonical cell promoter activity. Here, we show that Epstein Barr virus (EBV) replication causes 'de novo' transcription initiation at 29674 new transcription start sites throughout the cell genome. De novo transcription initiation is facilitated in part by the unique properties of the viral pre-initiation complex (vPIC) that binds a TATT[T/A]AA, TATA box-like sequence and activates transcription with minimal support by additional transcription factors...
March 12, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471816/catalytic-residues-of-microrna-argonautes-play-a-modest-role-in-microrna-star-strand-destabilization-in-c-elegans
#35
JOURNAL ARTICLE
Kasuen Kotagama, Acadia L Grimme, Leah Braviner, Bing Yang, Rima M Sakhawala, Guoyun Yu, Lars Kristian Benner, Leemor Joshua-Tor, Katherine McJunkin
Many microRNA (miRNA)-guided Argonaute proteins can cleave RNA ('slicing'), even though miRNA-mediated target repression is generally cleavage-independent. Here we use Caenorhabditis elegans to examine the role of catalytic residues of miRNA Argonautes in organismal development. In contrast to previous work, mutations in presumed catalytic residues did not interfere with development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the catalytic residue mutants, with the largest effect observed in embryos...
March 12, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471814/correction-to-a-dual-activity-topoisomerase-complex-promotes-both-transcriptional-activation-and-repression-in-response-to-starvation
#36
(no author information available yet)
No abstract text is available yet for this article.
March 12, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471813/correction-to%C3%A2-pathbank-2-0-the-pathway-database-for-model-organism-metabolomics
#37
(no author information available yet)
No abstract text is available yet for this article.
March 12, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471810/structural-basis-of-how-mgme1-processes-dna-5-ends-to-maintain-mitochondrial-genome-integrity
#38
JOURNAL ARTICLE
Eric Y C Mao, Han-Yi Yen, Chyuan-Chuan Wu
Mitochondrial genome maintenance exonuclease 1 (MGME1) helps to ensure mitochondrial DNA (mtDNA) integrity by serving as an ancillary 5'-exonuclease for DNA polymerase γ. Curiously, MGME1 exhibits unique bidirectionality in vitro, being capable of degrading DNA from either the 5' or 3' end. The structural basis of this bidirectionally and, particularly, how it processes DNA from the 5' end to assist in mtDNA maintenance remain unclear. Here, we present a crystal structure of human MGME1 in complex with a 5'-overhang DNA, revealing that MGME1 functions as a rigid DNA clamp equipped with a single-strand (ss)-selective arch, allowing it to slide on single-stranded DNA in either the 5'-to-3' or 3'-to-5' direction...
March 12, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471808/correction-to-cell-cycle-regulated-dna-methyltransferase-fluorescent-tracking-of-a-dna-strand-separation-mechanism-and-identification-of-the-responsible-protein-motif
#39
(no author information available yet)
No abstract text is available yet for this article.
March 12, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38471806/comprehensive-transcriptome-analysis-reveals-altered-mrna-splicing-and-post-transcriptional-changes-in-the-aged-mouse-brain
#40
JOURNAL ARTICLE
Nisha Hemandhar Kumar, Verena Kluever, Emanuel Barth, Sebastian Krautwurst, Mattia Furlan, Mattia Pelizzola, Manja Marz, Eugenio F Fornasiero
A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse brain, combining short- and long-read sequencing technologies with extensive bioinformatic analyses. Our findings encompass a spectrum of age-related changes, including differences in isoform usage, decreased mRNA dynamics and a module showing increased expression of neuronal genes...
March 12, 2024: Nucleic Acids Research
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