Publications

tRNA Val allows four-way decoding with unmodified uridine at the wobble position in Lactobacillus casei

developer — Tue, 26 Nov 2024 13:51:44 +0000

tRNA Val allows four-way decoding with unmodified uridine at the wobble position in Lactobacillus casei developer mar 26/11/2024 - 14:51

Modifications at the wobble position (position 34) of tRNA facilitate interactions that enable or stabilize non-Watson–Crick base pairs. In bacterial tRNA, 5-hydroxyuridine (ho 5 U) derivatives xo 5 U present at the wobble positions of tRNAs are responsible for the recognition of NYN codon families. These modifications of U34 allow base-pairing not only with A and G but also with U, and in some cases, C. mo 5 U was originally found in Gram-positive bacteria, and cmo 5 U and mcmo 5 U were found in Gram-negative bacteria. tRNAs of Mycoplasma species, mitochondria, and chloroplasts adopt four-way decoding in which unmodified U34 recognizes codons ending in A, G, C, and U. Lactobacillus casei , Gram-positive bacteria, and lactic acid bacteria lack the modification enzyme genes for xo 5 U biosynthesis. Nevertheless, L. casei has only one type of tRNA Val with the anticodon UAC [tRNA Val (UAC)]. However, the genome of L. casei encodes an undetermined tRNA (tRNA Und ) gene, and the sequence corresponding to the anticodon region is GAC. Here, we confirm that U34 in L. casei tRNA Val is unmodified and that there is no tRNA Und expression in the cells. In addition, in vitro transcribed tRNA Und was not aminoacylated by L. casei valyl-tRNA synthetase, suggesting that tRNA Und is not able to accept valine, even if expressed in cells. Correspondingly, native tRNA Val (UAC) with unmodified U34 bound to all four valine codons in the ribosome A site. This suggests that L. casei tRNA Val decodes all valine codons by four-way decoding, similarly to tRNAs from Mycoplasma species, mitochondria, and chloroplasts.

Bactériologie

Off RNA 2024 Riko Sugita, Vincent Guerineau, David Touboul, Satoko Yoshizawa, Kazuyuki Takai, Chie Tomikawa false 10.1261/rna.080155.124 lun 18/11/2024 - 16:23

Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome.

developer — Wed, 13 Nov 2024 13:08:32 +0000

Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome. developer mer 13/11/2024 - 14:08

Gene expression in bacterial cells is dependent on a gene&prime s position along the genome, mainly because of the effects of neighbouring genes&prime expression, but also because of the local activity of nucleoid proteins, differing levels of DNA supercoiling and changes in gene copy number with growth rate and growth phase. This genome position dependence can be a source of specific regulation, however, in some cases it is necessary to have gene expression insulated from these local effects. Escherichia coli cells express ribosomal RNA from multiple operons found at different sites along the genome. The number of ribosomal operons varies in different strains and correlates with the maximal growth rate. rRNA promoters are under the regulation of Fis, H-NS, DNA supercoiling and ppGpp. These factors are known to result in growth phase and growth rate dependent regulation of gene expression. Here we show that the combined action of Fis and H-NS also provides insulation from the activity of both local and global regulatory factors. Furthermore, our results indicate that the presence of a divergently expressed gene can also act as an insulator revealing a DNA supercoiling gradient from the origin to the terminus. The organisation of ribosomal promoters therefore has been selected to allow for gene duplication independently of the influence of local genome organisation and neighbouring genes&prime activity.

Sciences du Vivant

Off 2024 Elisa Brambilla, Malikmohamed Yousuf, Qing Zhang, Gladys Mbemba, Cyriane Oeuvray, Damel Mektepbayeva, Anne Olliver, Marco Cosentino Lagomarsino, Bianca Sclavi false 10.1101/2024.03.27.586983 jeu 28/03/2024 - 16:24

Ca 2+ regulation of Myosin II and Myosin VI during rupture of the Shigella -containing vacuole

developer — Tue, 12 Nov 2024 13:08:13 +0000

Ca 2+ regulation of Myosin II and Myosin VI during rupture of the Shigella -containing vacuole developer mar 12/11/2024 - 14:08

Shigella , the causative agent of bacillary dysentery, invades epithelial cells to colonize the intestinal mucosa. Following invasion, Shigella is enclosed in a vacuole that needs to rupture for bacterial intra-cytosolic replication. We show here that rupture of the Shigella vacuole requires Ca 2+ influx leading to long lasting local Ca 2+ increases that regulate actin dynamics affecting the Shigella vacuole integrity. These Ca 2+ increases promote vacuolar rupture by activating myosin II associated with actin filaments in membrane ruffles distant from the vacuole, while tethering myosin VI at the actin coat-surrounded vacuole. Ca 2+ depletion and myosin II inhibition impair formation of the actin coat and vacuole rupture. Inhibition of myosin VI also delays rupture of vacuoles but lead to their tumbling. These findings highlight a role for Ca 2+ in coordinating actin–based forces and constraints during early rupture steps of bacterial vacuole, that pull on vacuolar membranes and tether them to the actin cortex via myosin II and VI, respectively, a process relevant to intracellular pathogen and endomembrane trafficking.

Sciences du Vivant

Off 2024 Mariette Bonnet, Chun Hui Sun, Jost Enninga, Anne Houdusse, Guy Tran van Nhieu false 10.1101/2024.05.22.595272 dim 10/11/2024 - 14:08

Triphenylamine Sensitized 8‐Dimethylaminoquinoline: An Efficient Two‐Photon Caging Group for Intracellular Delivery

developer — Sat, 12 Oct 2024 10:03:25 +0000

Triphenylamine Sensitized 8‐Dimethylaminoquinoline: An Efficient Two‐Photon Caging Group for Intracellular Delivery developer sam 12/10/2024 - 12:03

Abstract Triphenylamine‐sensitized 8‐dimethylaminoquinoline (TAQ) probes showed fair two‐photon absorption and fragmentation cross sections in releasing kainate and GABA ligands. The water‐soluble PEG and TEG‐analogs allowed cell internalization and efficient light‐gated liberation of the rhodamine reporter under UV and two‐photon (NIR) irradiation conditions.

Chimie

Off Chemistry - A European Journal 2024 Delphine Rigault, Philippe Nizard, Jonathan Daniel, Mireille Blanćhard-Desce, Patrick Tauc, Hamid Dhimane, Peter Dalko false 10.1002/chem.202401289 jeu 22/08/2024 - 16:24

Stimulation of ATP Hydrolysis by ssDNA Provides the Necessary Mechanochemical Energy for G4 Unfolding

developer — Sat, 12 Oct 2024 10:03:25 +0000

Stimulation of ATP Hydrolysis by ssDNA Provides the Necessary Mechanochemical Energy for G4 Unfolding developer sam 12/10/2024 - 12:03

The G-quadruplex (G4) is a distinct geometric and electrophysical structure compared to classical doublestranded DNA, and its stability can impede essential cellular processes such as replication, transcription, and translation. This study focuses on the BsPif1 helicase, revealing its ability to bind independently to both single-stranded DNA (ssDNA) and G4 structures. The unfolding activity of BsPif1 on G4 relies on the presence of a single tail chain, and the covalent continuity between the single tail chain and the G4 0 s main chain is necessary for efficient G4 unwinding. This suggests that ATP hydrolysis-driven ssDNA translocation exerts a pull force on G4 unwinding. Molecular dynamics simulations identified a specific region within BsPif1 that contains five crucial amino acid sites responsible for G4 binding and unwinding. A "molecular wire stripper" model is proposed to explain BsPif1 0 s mechanism of G4 unwinding. These findings provide a new theoretical foundation for further exploration of the G4 development mechanism in Pif1 family helicases.

Biologie structurale

Off Journal of Molecular Biology 2024 Yang-Xue Dai, Xiao-Lei Duan, Wen-Tong Fu, Shan Wang, Na-Nv Liu, Hai-Hong Li, Xia Ai, Hai-Lei Guo, Cel Areny Navés, Elisabeth Bugnard, Daniel Auguin, Xi-Miao Hou, Stephane Rety, Xu-Guang Xi false 10.1016/j.jmb.2023.168373 lun 01/01/2024 - 00:00

The catalytic triad of rice NARROW LEAF1 involves H234

developer — Fri, 11 Oct 2024 10:02:38 +0000

The catalytic triad of rice NARROW LEAF1 involves H234 developer ven 11/10/2024 - 12:02

NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.

Amélioration des plantes

Off Nature Plants 2024 Ling-Yun Huang, Na-Nv Liu, Wei-Fei Chen, Xia Ai, Hai-Hong Li, Ze-Lin Zhang, Xi-Miao Hou, Philippe Fossé, Olivier Mauffret, Dong-Sheng Lei, Stephane Rety, Xu-Guang Xi false 10.1038/s41477-024-01668-1 mer 10/04/2024 - 16:24

Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition

developer — Thu, 10 Oct 2024 10:00:48 +0000

Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition developer jeu 10/10/2024 - 12:00

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.

Biologie structurale

Off Nucleic Acids Research 2024 Ben-Ge Xin, Ling-Yun Huang, Ling-Gang Yuan, Na-Nv Liu, Hai-Hong Li, Xia Ai, Dong-Sheng Lei, Xi-Miao Hou, Stephane Rety, Xu-Guang Xi false 10.1093/nar/gkae138 lun 01/01/2024 - 00:00

Direct single-cell observation of a key Escherichia coli cell-cycle oscillator

developer — Thu, 05 Sep 2024 06:14:21 +0000

Direct single-cell observation of a key Escherichia coli cell-cycle oscillator developer jeu 05/09/2024 - 08:14

Initiation of DNA replication in Escherichia coli is coupled to cell size via the DnaA protein, whose activity is dependent on its nucleotide-bound state. However, the oscillations in DnaA activity have never been observed at the single-cell level. By measuring the volume-specific production rate of a reporter protein under control of a DnaA-regulated promoter, we could distinguish two distinct cell-cycle oscillators. The first, driven by both DnaA activity and SeqA repression, shows a causal relationship with cell size and divisions, similarly to initiation events. The second one, a reporter of DnaA activity alone, loses the synchrony and causality properties. Our results show that transient inhibition of gene expression by SeqA keeps the oscillation of volume-sensing DnaA activity in phase with the subsequent division event and suggest that DnaA activity peaks do not correspond directly to initiation events.

Sciences du Vivant

Off Science Advances 2024 Ilaria Iuliani, Gladys Mbemba, Marco Cosentino Lagomarsino, Bianca Sclavi false 10.1126/sciadv.ado5398 ven 19/07/2024 - 16:24

Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition

developer — Fri, 23 Feb 2024 07:26:55 +0000

Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition developer ven 23/02/2024 - 08:26

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary str uct ures and organizing ribonucleoprotein comple x es. In our study, w e conducted a systematic analysis of the helicase-related activities of Esc heric hia coli HrpA and presented the str uct ures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP h y droly sis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core pla y s an essential role in unwinding RNA / RNA and RNA / DNA duple x es, the N-terminal e xtension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA / DNA duple x un winding. Import antly, the APHB domain is implicated in binding to non-canonical DNA str uct ures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase comple x. T his research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a f oundation f or further in v estigations into the recognition and functional implications of i-motif DNA str uct ures in various biological processes. Gr aphical abstr act

Biologie structurale

Off Nucleic Acids Research 2024 Ben-Ge Xin, Ling-Yun Huang, Ling-Gang Yuan, Na-Nv Liu, Hai-Hong Li, Xia Ai, Dong-Sheng Lei, Xi-Miao Hou, Stephane Rety, Xu-Guang Xi 1 10.1093/nar/gkae138 lun 01/01/2024 - 00:00

Stimulation of ATP Hydrolysis by ssDNA Provides the Necessary Mechanochemical Energy for G4 Unfolding

developer — Wed, 31 Jan 2024 01:44:10 +0000

Stimulation of ATP Hydrolysis by ssDNA Provides the Necessary Mechanochemical Energy for G4 Unfolding developer mer 31/01/2024 - 02:44

Biochimie, Biologie Moléculaire