Decapping NAD-RNAs: TIR domain-containing proteins stand out for specificity
Trends Biochem Sci. 2024 Apr 26:S0968-0004(24)00101-4. doi: 10.1016/j.tibs.2024.04.004. Online ahead of print.ABSTRACTA recently characterized RNA modification is NAD+-modified RNAs (NAD-RNAs). Various enzymes decap NAD-RNAs, and Wang and Yu et al. now describe another, namely Toll/interleukin-1 receptor (TIR) domain-containing proteins of bacteria and Archaea. TIR decapping products are a specific variant of cyclic ADP ribose (ADPR)-RNAs (v-cADPR-RNAs), opening a new window to the NAD-RNA world.PMID:38677919 | DOI:10.1016/j.tibs.2024.04.004 (Source: Trends in Biochemical Sciences)
Source: Trends in Biochemical Sciences - April 27, 2024 Category: Biochemistry Authors: Dechang Cao Source Type: research
The YTHDF proteins display distinct cellular functions on m < sup > 6 < /sup > A-modified RNA
Trends Biochem Sci. 2024 Apr 26:S0968-0004(24)00086-0. doi: 10.1016/j.tibs.2024.04.001. Online ahead of print.ABSTRACTYTHDF proteins are main cytoplasmic 'reader' proteins of RNA N6-methyladenosine (m6A) methylation in mammals. They are largely responsible for m6A-mediated regulation in the cell cytosol by controlling both mRNA translation and degradation. Recent functional and mechanistic investigations of the YTHDF proteins revealed that these proteins have different functions to enable versatile regulation of the epitranscriptome. Their divergent functions largely originate from their different amino acid sequences in t...
Source: Trends in Biochemical Sciences - April 27, 2024 Category: Biochemistry Authors: Zhongyu Zou Chuan He Source Type: research
A team of chaperones play to win in the bacterial periplasm
Trends Biochem Sci. 2024 Apr 26:S0968-0004(24)00081-1. doi: 10.1016/j.tibs.2024.03.015. Online ahead of print.ABSTRACTThe survival and virulence of Gram-negative bacteria require proper biogenesis and maintenance of the outer membrane (OM), which is densely packed with β-barrel OM proteins (OMPs). Before reaching the OM, precursor unfolded OMPs (uOMPs) must cross the whole cell envelope. A network of periplasmic chaperones and proteases maintains unfolded but folding-competent conformations of these membrane proteins in the aqueous periplasm while simultaneously preventing off-pathway aggregation. These periplasmic protei...
Source: Trends in Biochemical Sciences - April 27, 2024 Category: Biochemistry Authors: Taylor Devlin Karen G Fleming Source Type: research
Decapping NAD-RNAs: TIR domain-containing proteins stand out for specificity
Trends Biochem Sci. 2024 Apr 26:S0968-0004(24)00101-4. doi: 10.1016/j.tibs.2024.04.004. Online ahead of print.ABSTRACTA recently characterized RNA modification is NAD+-modified RNAs (NAD-RNAs). Various enzymes decap NAD-RNAs, and Wang and Yu et al. now describe another, namely Toll/interleukin-1 receptor (TIR) domain-containing proteins of bacteria and Archaea. TIR decapping products are a specific variant of cyclic ADP ribose (ADPR)-RNAs (v-cADPR-RNAs), opening a new window to the NAD-RNA world.PMID:38677919 | DOI:10.1016/j.tibs.2024.04.004 (Source: Trends in Biochemical Sciences)
Source: Trends in Biochemical Sciences - April 27, 2024 Category: Biochemistry Authors: Dechang Cao Source Type: research
The YTHDF proteins display distinct cellular functions on m < sup > 6 < /sup > A-modified RNA
Trends Biochem Sci. 2024 Apr 26:S0968-0004(24)00086-0. doi: 10.1016/j.tibs.2024.04.001. Online ahead of print.ABSTRACTYTHDF proteins are main cytoplasmic 'reader' proteins of RNA N6-methyladenosine (m6A) methylation in mammals. They are largely responsible for m6A-mediated regulation in the cell cytosol by controlling both mRNA translation and degradation. Recent functional and mechanistic investigations of the YTHDF proteins revealed that these proteins have different functions to enable versatile regulation of the epitranscriptome. Their divergent functions largely originate from their different amino acid sequences in t...
Source: Trends in Biochemical Sciences - April 27, 2024 Category: Biochemistry Authors: Zhongyu Zou Chuan He Source Type: research
A team of chaperones play to win in the bacterial periplasm
Trends Biochem Sci. 2024 Apr 26:S0968-0004(24)00081-1. doi: 10.1016/j.tibs.2024.03.015. Online ahead of print.ABSTRACTThe survival and virulence of Gram-negative bacteria require proper biogenesis and maintenance of the outer membrane (OM), which is densely packed with β-barrel OM proteins (OMPs). Before reaching the OM, precursor unfolded OMPs (uOMPs) must cross the whole cell envelope. A network of periplasmic chaperones and proteases maintains unfolded but folding-competent conformations of these membrane proteins in the aqueous periplasm while simultaneously preventing off-pathway aggregation. These periplasmic protei...
Source: Trends in Biochemical Sciences - April 27, 2024 Category: Biochemistry Authors: Taylor Devlin Karen G Fleming Source Type: research
CellVis2: a conference on visualizing the molecular cell
Trends Biochem Sci. 2024 Apr 25:S0968-0004(24)00079-3. doi: 10.1016/j.tibs.2024.03.013. Online ahead of print.ABSTRACTIn January 2024, a targeted conference, 'CellVis2', was held at Scripps Research in La Jolla, USA, the second in a series designed to explore the promise, practices, roadblocks, and prospects of creating, visualizing, sharing, and communicating physical representations of entire biological cells at scales down to the atom.PMID:38670884 | DOI:10.1016/j.tibs.2024.03.013 (Source: Trends in Biochemical Sciences)
Source: Trends in Biochemical Sciences - April 26, 2024 Category: Biochemistry Authors: Ludovic Autin David S Goodsell Ivan Viola Arthur Olson Source Type: research
CellVis2: a conference on visualizing the molecular cell
Trends Biochem Sci. 2024 Apr 25:S0968-0004(24)00079-3. doi: 10.1016/j.tibs.2024.03.013. Online ahead of print.ABSTRACTIn January 2024, a targeted conference, 'CellVis2', was held at Scripps Research in La Jolla, USA, the second in a series designed to explore the promise, practices, roadblocks, and prospects of creating, visualizing, sharing, and communicating physical representations of entire biological cells at scales down to the atom.PMID:38670884 | DOI:10.1016/j.tibs.2024.03.013 (Source: Trends in Biochemical Sciences)
Source: Trends in Biochemical Sciences - April 26, 2024 Category: Biochemistry Authors: Ludovic Autin David S Goodsell Ivan Viola Arthur Olson Source Type: research
Tyrosine - a structural glue for hierarchical protein assembly
Trends Biochem Sci. 2024 Apr 22:S0968-0004(24)00080-X. doi: 10.1016/j.tibs.2024.03.014. Online ahead of print.ABSTRACTProtein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their na...
Source: Trends in Biochemical Sciences - April 23, 2024 Category: Biochemistry Authors: Anton Maraldo Jelena Rnjak-Kovacina Christopher Marquis Source Type: research
Tyrosine - a structural glue for hierarchical protein assembly
Trends Biochem Sci. 2024 Apr 22:S0968-0004(24)00080-X. doi: 10.1016/j.tibs.2024.03.014. Online ahead of print.ABSTRACTProtein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their na...
Source: Trends in Biochemical Sciences - April 23, 2024 Category: Biochemistry Authors: Anton Maraldo Jelena Rnjak-Kovacina Christopher Marquis Source Type: research
Tyrosine - a structural glue for hierarchical protein assembly
Trends Biochem Sci. 2024 Apr 22:S0968-0004(24)00080-X. doi: 10.1016/j.tibs.2024.03.014. Online ahead of print.ABSTRACTProtein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their na...
Source: Trends in Biochemical Sciences - April 23, 2024 Category: Biochemistry Authors: Anton Maraldo Jelena Rnjak-Kovacina Christopher Marquis Source Type: research
Beneath the surface: endosomal GPCR signaling
Trends Biochem Sci. 2024 Apr 19:S0968-0004(24)00072-0. doi: 10.1016/j.tibs.2024.03.006. Online ahead of print.ABSTRACTG protein-coupled receptors (GPCRs) located at the cell surface bind extracellular ligands and convey intracellular signals via activation of heterotrimeric G proteins. Traditionally, G protein signaling was viewed to occur exclusively at this subcellular region followed by rapid desensitization facilitated by β-arrestin (βarr)-mediated G protein uncoupling and receptor internalization. However, emerging evidence over the past 15 years suggests that these βarr-mediated events do not necessarily terminate...
Source: Trends in Biochemical Sciences - April 20, 2024 Category: Biochemistry Authors: Emmanuel Flores-Espinoza Alex R B Thomsen Source Type: research
Understanding the dynamic design of the spliceosome
Trends Biochem Sci. 2024 Apr 18:S0968-0004(24)00078-1. doi: 10.1016/j.tibs.2024.03.012. Online ahead of print.ABSTRACTThe spliceosome catalyzes the splicing of pre-mRNAs. Although the spliceosome evolved from a prokaryotic self-splicing intron and an associated protein, it is a vastly more complex and dynamic ribonucleoprotein (RNP) whose function requires at least eight ATPases and multiple RNA rearrangements. These features afford stepwise opportunities for multiple inspections of the intron substrate, coupled with spliceosome disassembly for substrates that fail inspection. Early work using splicing-defective pre-mRNAs ...
Source: Trends in Biochemical Sciences - April 19, 2024 Category: Biochemistry Authors: Irene Beusch Hiten D Madhani Source Type: research
Thiol dioxygenases: from structures to functions
Trends Biochem Sci. 2024 Apr 15:S0968-0004(24)00073-2. doi: 10.1016/j.tibs.2024.03.007. Online ahead of print.ABSTRACTThiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of...
Source: Trends in Biochemical Sciences - April 15, 2024 Category: Biochemistry Authors: Monica Perri Francesco Licausi Source Type: research
Thiol dioxygenases: from structures to functions
Trends Biochem Sci. 2024 Apr 15:S0968-0004(24)00073-2. doi: 10.1016/j.tibs.2024.03.007. Online ahead of print.ABSTRACTThiol oxidation to dioxygenated sulfinic acid is catalyzed by an enzyme family characterized by a cupin fold. These proteins act on free thiol-containing molecules to generate central metabolism precursors and signaling compounds in bacteria, fungi, and animal cells. In plants and animals, they also oxidize exposed N-cysteinyl residues, directing proteins to proteolysis. Enzyme kinetics, X-ray crystallography, and spectroscopy studies prompted the formulation and testing of hypotheses about the mechanism of...
Source: Trends in Biochemical Sciences - April 15, 2024 Category: Biochemistry Authors: Monica Perri Francesco Licausi Source Type: research
