MST kinases in innate immune signaling

The mammalian STE20-like (MST) protein kinases are composed of MST1, MST2, MST3, MST4 and YSK1. They play crucial roles in cell growth, migration, polarity and apoptosis. Dysfunction of these kinases often leads to diseases. MST kinases are extensively involved in development and function of immune system. Here, we review recent progresses on the regulatory function of MST kinases in innate immune signaling

Fine-Tuning Stomatal Movement Through Small Signaling Peptides

As sessile organisms, plants are continuously exposed to a wide range of environmental stress. In addition to their crucial roles in plant growth and development, small signaling peptides are also implicated in sensing environmental stimuli. Notably, recent studies in plants have revealed that small signaling peptides are actively involved in controlling stomatal aperture to defend against biotic and abiotic stress. This review illustrates our growing knowledge of small signaling peptides in the modulation of stomatal aperture and highlights future challenges to decipher peptide signaling pathways in guard cells

How does cohesin organize the 3D genome?

Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. I will present direct evidence that cohesin extrudes DNA loops that are anchored by CTCF proteins in specific orientations. CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging of CTCF-cohesin collisions, we demonstrate that the N-terminus of CTCF must be oriented towards cohesin to block its ability to compact DNA. C-terminally oriented CTCF accelerates DNA compaction by cohesin. Oriented inactive Cas9 and Cas12a ribonucleoproteins exhibit similar polar effects on DNA compaction by cohesin. RNA-DNA hybrids (R-loops), such as those that occur at highly transcribed genes, efficiently block cohesin-mediated DNA compaction. Our results explain long-standing puzzles regarding how CTCF and transcription shape the 3D genome. © FASEB

Finite-Time Speed Control of Marine Diesel Engine Based on ADRC

In this paper, in order to handle the nonlinear system and the sophisticated disturbance in the marine engine, a finite-time convergence control method is proposed for the diesel engine rotating speed control. First, the mean value model is established for the diesel engine, which can represent response of engine fuel injection to engine speed. Then, in order to deal with parameter perturbation and load disturbance of the marine diesel engine, a finite-time convergence active disturbance rejection control (ADRC) is proposed. At the last, simulation experiments are conducted to verify the effectiveness of the proposed controller under the different load disturbances for the 7RT-Flex60C marine diesel engine. The simulation results demonstrate that the proposed control scheme has better control effect and stronger anti-interference ability than the linear ADRC

CTCF and R-loops are boundaries of cohesin-mediated DNA looping

Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries. © 2023 Elsevier Inc.FALS

The structural basis of the activation and inhibition of DSR2 NADase by phage proteins

Abstract DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD+. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while suppressed by the SPbeta phage-encoded DSAD1 protein, enabling phages to evade the host defense. However, the molecular mechanisms of activation and inhibition of DSR2 remain elusive. Here, we report the cryo-EM structures of apo DSR2, DSR2-TTP-NAD+ and DSR2-DSAD1 complexes. DSR2 assembles into a head-to-head tetramer mediated by its Sir2 domain. The C-terminal helical regions of DSR2 constitute four partner-binding cavities with opened and closed conformation. Two TTP molecules bind to two of the four C-terminal cavities, inducing conformational change of Sir2 domain to activate DSR2. Furthermore, DSAD1 competes with the activator for binding to the C-terminal cavity of DSR2, effectively suppressing its enzymatic activity. Our results provide the mechanistic insights into the DSR2-mediated anti-phage defense system and DSAD1-dependent phage immune evasion

Statistics of Data Reduction and Structure Refinement.

a<p>Data for the highest resolution bin is in parentheses.</p>b<p><i>R</i>_merge = Σ|Ii−Im|/ΣIi, where Ii is the intensity of the measured reflection and Im is the mean intensity of all symmetry-related reflections.</p>c<p><i>R</i>_work = Σ| |Fobs|−|Fcalc| |/Σ|Fobs|, where Fobs and Fcalc are observed and calculated structure factors, respectively. <i>R</i>_free = Σ_T| |Fobs|−|Fcalc| |/Σ_T|Fobs|, where T denotes a test data set of about 5% of the total reflections randomly chosen and set aside prior to refinement.</p>d<p>RMSD = root-mean-square deviation.</p

The Crystal Structure of <em>Arabidopsis</em> VSP1 Reveals the Plant Class C-Like Phosphatase Structure of the DDDD Superfamily of Phosphohydrolases

<div><p><em>Arabidopsis thaliana</em> vegetative storage proteins, VSP1 and VSP2, are acid phosphatases and belong to the haloacid dehalogenase (HAD) superfamily. In addition to their potential nutrient storage function, they were thought to be involved in plant defense and flower development. To gain insights into the architecture of the protein and obtain clues about its function, we have tested their substrate specificity and solved the structure of VSP1. The acid phosphatase activities of these two enzymes require divalent metal such as magnesium ion. Conversely, the activity of these two enzymes is inhibited by vanadate and molybdate, but is resistant to inorganic phosphate. Both VSP1 and VSP2 did not exhibit remarkable activities to any physiological substrates tested. In the current study, we presented the crystal structure of recombinant VSP1 at 1.8 Å resolution via the selenomethionine single-wavelength anomalous diffraction (SAD). Specifically, an α-helical cap domain on the top of the α/β core domain is found to be involved in dimerization. In addition, despite of the low sequence similarity between VSP1 and other HAD enzymes, the core domain of VSP1 containing conserved active site and catalytic machinery displays a classic haloacid dehalogenase fold. Furthermore, we found that VSP1 is distinguished from bacterial class C acid phosphatase P4 by several structural features. To our knowledge, this is the first study to reveal the crystal structure of plant vegetative storage proteins.</p> </div

Relative activities of VSP1 and VSP2 toward different substrates.

<p>ND, not detectable.</p><p>Relative activities are expressed as the percentage of the activity with <i>p</i>NPP. The results are the average of the values determined in triplicates and the respective standard error is constantly lower than 10%.</p

Comparison between VSP1 and P4 in active sites and dimer patterns.

<p>(A) Residues in the catalytic site of VSP1. Magnesium ions and water molecules are colored by green and red, respectively. (B) Residues in the catalytic site of P4. Magnesium ion and water molecules are colored by green and red, respectively. (C) Hydrophobic core between two VSP1 monomers. Two VSP1 monomers are colored magenta and cyan, respectively. (D) Hydrogen bonds between two VSP1 monomers. Two VSP1 monomers are colored magenta and cyan, respectively. (E) Interaction pattern of VSP1 dimer. One monomer is coloured magenta, while the N-terminal helices of the other monomer are coloured cyan. (F) Interaction pattern of P4 dimer. One monomer is colored yellow, while the N-terminal helices of the other monomer are colored green. The magenta VSP1 monomer in (E) and the yellow P4 monomer in (F) are aligned.</p