Article
Biochemistry & Molecular Biology
Zhiling Kuang, Jiyuan Ke, Jiong Hong, Zhongliang Zhu, Liwen Niu
Summary: PCI domain proteins play important roles in post-transcriptional gene regulation. In this study, the structure of yeast Thp3-Csn12-Sem1 ternary complex was determined, revealing significant structural differences compared to the Sac3-Thp1-Sem1 complex. This structure provides a foundation for further exploring its specific recruitment to the spliceosome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Congyao Xu, Xiaofeng Fang, Tiancong Lu, Caroline Dean
Summary: The study reveals that the Arabidopsis floral repressor gene FLC is co-transcriptionally repressed by COOLAIR, with the involvement of AGO1 in promoting COOLAIR splicing dynamics and chromatin silencing. AGO1 is shown to associate with COOLAIR and influence its processing, leading to the resolution of R-loops and local chromatin environment conducive to low transcription initiation. These findings suggest a conserved cotranscriptional regulation mechanism involving AGO1 that influences transcriptional output.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Sam Balzarini, Roosje Van Ende, Arnout Voet, Koen Geuten
Summary: Despite progress in methodology, a widely applicable, easily scalable, and cost-effective procedure for isolating specific RNPs is still lacking. We present the Silica-based Acidic Phase Separation (SAPS)-capture workflow, which combines previously described techniques in a versatile, optimal, and cost-effective protocol. This method isolates specific RNPs from pre-purified samples, resulting in an increased RNP/bead ratio and reduced experimental cost. Validation experiments were conducted using yeast and Arabidopsis, demonstrating the applicability of this procedure to study the ribonome of any RNA molecule in any organism or tissue type.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Alejandro Collin, Araceli Gonzalez-Jimenez, Maria del Carmen Gonzalez-Jimenez, Manuel J. Alfonso, Olga Calvo
Summary: Saccharomyces cerevisiae Sub1 is a transcriptional stimulatory protein that shares homology with the ssDNA binding domain (ssDBD) of human PC4. This study reveals the key residues responsible for DNA-ScSub1 interaction in vivo, localized in the ssDBD, and demonstrates that the carboxyl-terminal (CT) region is required for transcription elongation. These findings indicate that Sub1 plays a dual role in transcription, participating in initiation through the ssDBD and in elongation through the CT region.
Article
Biochemistry & Molecular Biology
Ophelie Lautier, Arianna Penzo, Jerome O. Rouviere, Guillaume Chevreux, Louis Collet, Isabelle Loiodice, Angela Taddei, Frederic Devaux, Martine A. Collart, Benoit Palancade
Summary: The research reveals that the formation of the nuclear pore complex involves co-translational events in the cytoplasm and nucleus. Different NPC subunits establish binary interactions during translation. Localized translation ensures the proper delivery of proteins to the pore and the nucleus.
Article
Genetics & Heredity
Magdalena Boguta
Summary: The control of assembly of yeast RNA polymerases (RNAPs) is not well understood. A recent study suggests that the early-stage assembly of RNAP III complex may occur through a co-translational mechanism, with the involvement of the Rbs1 protein.
Article
Multidisciplinary Sciences
Mustafa Malik Ghulam, Mathieu Catala, Gaspard Reulet, Michelle S. Scott, Sherif Abou Elela
Summary: We demonstrate that gene duplication in yeast serves as a stress-adaptation mechanism by modulating the global proteome through differential expression of ribosomal protein paralogs. This mechanism controls translation through differential acetylation of ribosomal proteins, favoring the translation of genes with short open reading frames under normal conditions and increasing translation of genes with long open reading frames after exposure to drugs. This study identifies a natural program where changing the ratio of proteins produced from duplicated genes modifies translation in response to drugs, regardless of ribosome number.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jinfan Wang, Byung-Sik Shin, Carlos Alvarado, Joo-Ran Kim, Jonathan Bohlen, Thomas E. Dever, Joseph D. Puglisi
Summary: Through real-time single-molecule fluorescence spectroscopy, it has been found that the eukaryotic 43S preinitiation complex engages with mRNA through a slow, ATP-dependent process and proceeds to scan rapidly and directionally along the 5' untranslated region (5' UTR). Scanning ribosomes can traverse RNA secondary structures, but hairpin structures near the start codons drive them backward in the 5' direction, requiring rescanning.
Article
Biochemistry & Molecular Biology
Celia Jeronimo, Andrew Angel, Vu Q. Nguyen, Jee Min Kim, Christian Poitras, Elie Lambert, Pierre Collin, Jane Mellor, Carl Wu, Francois Robert
Summary: Research has shown that the histone chaperone FACT binds to transcribed chromatin, predominantly recognizing the +1 nucleosome, as it is partially unwrapped by RNAPII, and spreads to downstream nucleosomes with the assistance of the chromatin remodeler Chd1.
Article
Biochemistry & Molecular Biology
Sebastien Alphonse, Ankan Banerjee, Swathi Dantuluri, Stewart Shuman, Ranajeet Ghose
Summary: Tpt1, an essential component of the fungal and plant tRNA splicing machinery, catalyzes transfer of an internal RNA 2'-PO4 to NAD(+) yielding RNA 2'-OH and ADP-ribose-1',2'-cyclic phosphate products. NMR structures of the Tpt1 ortholog from the bacterium Runella slithyformis (RslTpt1) were reported, showing significant inter-lobe dynamics in the free and NAD(+)-bound states. Functional analysis indicated that substrate affinity is primarily determined by the ADP moiety and NAD(+) interacts with specific residues essential for Tpt1 activity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sebastien Alphonse, Ankan Banerjee, Swathi Dantuluri, Stewart Shuman, Ranajeet Ghose
Summary: The NMR structures of RsITpt1 in free and NAD(+) bound states reveal substantial inter-lobe dynamics. ITC measurements show that substrate affinity is primarily determined by the ADP moiety. NAD(+)-induced chemical shift perturbations are localized to the C-lobe of RsITpt1.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosomal RNA is a crucial component of ribosomes, playing a key role in peptide bond formation and accurate genetic code decoding. Recent research suggests that ribosomal RNA modifications are not 100% complete, leading to heterogeneous populations of ribosomes. Accumulated knowledge from yeast is valuable in understanding the role of ribosomal RNA modifications in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Lina Liu, Jiaju Xu, Ruiying Na, Renpeng Du, Wenxiang Ping, Jingping Ge, Dan Zhao
Summary: In this study, the extraction, purification, and characterization of an exopolysaccharide (EPS) from Saccharomyces cerevisiae Y3 were investigated. The EPS was found to be a hetero-polysaccharide composed of various sugars and exhibited good hydrophilicity, thermal stability, and antioxidation ability.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Zhanna Hakhverdyan, Kelly R. Molloy, Sarah Keegan, Thurston Herricks, Dante M. Lepore, Mary Munson, Roman Subbotin, David Fenyo, John D. Aitchison, Javier Fernandez-Martinez, Brian T. Chait, Michael P. Rout
Summary: Cellular processes are largely carried out by dynamic macromolecular assemblies, such as the nuclear pore complex (NPC), which mediates selective macromolecular transport between the nucleus and cytoplasm. While all NPC components turnover slowly, their exchange rates vary significantly, with scaffold-forming Nups exchanging slowly and connector Nups exchanging more rapidly. Targeted perturbations in NPC structure revealed a dynamic resilience to damage, opening a new understanding of macromolecular assembly dynamics.
Article
Multidisciplinary Sciences
Gerald Ryan R. Aquino, Philipp Hackert, Nicolai Krogh, Kuan-Ting Pan, Mariam Jaafar, Anthony K. Henras, Henrik Nielsen, Henning Urlaub, Katherine E. Bohnsack, Markus T. Bohnsack
Summary: Early pre-60S ribosomal particles are complex structures undergoing dynamic changes, with RNA helicase Dbp7 playing a key role in regulating the assembly process. Dbp7 influences compaction of domain V/VI and impacts binding and activity of factors like ribosomal protein uL3 in early ribosomal assembly.
NATURE COMMUNICATIONS
(2021)