cell biology

Intrinsically disordered regions in TRPV2 mediate protein-protein interactions

Transient receptor potential (TRP) ion channels are gated by diverse intra- and extracellular stimuli leading to cation inflow (Na+, Ca2+) regulating many cellular processes and initiating organismic somatosensation. *

Structures of most TRP channels have been solved. However, structural and sequence analysis showed that ~30% of the TRP channel sequences, mainly the N- and C-termini, are intrinsically disordered regions (IDRs). Unfortunately, very little is known about IDR ‘structure’, dynamics and function, though it has been shown that they are essential for native channel function. *

In the article “Intrinsically disordered regions in TRPV2 mediate protein-protein interactions”, Raghavendar R. Sanganna Gari, Grigory Tagiltsev, Ruth A. Pumroy, Yining Jiang, Martin Blackledge, Vera Y. Moiseenkova-Bell and Simon Scheuring imaged TRPV2 channels in membranes using high-speed atomic force microscopy (HS-AFM). *

The dynamic single molecule imaging capability of HS-AFM allowed the authors to visualize IDRs and revealed that N-terminal IDRs were involved in intermolecular interactions. Their work provides evidence about the ‘structure’ of the TRPV2 IDRs, and that the IDRs may mediate protein-protein interactions. *

In total, 1.5 µl of the TRPV2 reconstituted vesicles were deposited on a 1.5-mm2 freshly cleaved mica surface, which was glued with epoxy to the quartz sample stage. After 20–30 min incubation, the sample was gently rinsed with imaging buffer (20 mM Hepes, pH 8.0, 150 mM NaCl) and mounted in the HS-AFM fluid cell. All images in this study were taken using a HS-AFM operated in amplitude modulation mode using optimized scan and feedback parameters and lab-built amplitude detectors and free amplitude stabilizers. *

Short (8 µm) cantilevers (NanoWorld Ultra-Short Cantilevers for High-Speed AFM USC-F1.2-k0.15) with nominal spring constant of 0.15 N/m, resonance frequency of 0.6 MHz, and a quality factor of ∼1.5 in liquid were used. AFM probes were sharpened using oxygen plasma etching to obtain better resolution. *

Fig. 1 from “Intrinsically disordered regions in TRPV2 mediate protein-protein interactions” by Raghavendar R. Sanganna Gari et al. :TRPV2 reconstitution for HS-AFM analysis. b Overview HS-AFM images (Supplementary Movie 1) of TRPV2 (windmill-shaped molecules) in soy polar lipid membranes on mica (dark background areas). False color scale: 0–9 nm. The white oversaturated areas have a height of ~26 nm and represent likely non-ruptured small vesicles. NanoWorld-USC-F1.2-k0.15 AFM probes were used for the HS-AFM — Fig. 1 from “Intrinsically disordered regions in TRPV2 mediate protein-protein interactions” by Raghavendar R. Sanganna Gari et al. :
TRPV2 reconstitution for HS-AFM analysis.
b Overview HS-AFM images (Supplementary Movie 1) of TRPV2 (windmill-shaped molecules) in soy polar lipid membranes on mica (dark background areas). False color scale: 0–9 nm. The white oversaturated areas have a height of ~26 nm and represent likely non-ruptured small vesicles.

*Raghavendar R. Sanganna Gari, Grigory Tagiltsev, Ruth A. Pumroy, Yining Jiang, Martin Blackledge, Vera Y. Moiseenkova-Bell and Simon Scheuring
Intrinsically disordered regions in TRPV2 mediate protein-protein interactions
Communications Biology volume 6, Article number: 966 (2023)
DOI: https://doi.org/10.1038/s42003-023-05343-7

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The article “Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response” by Raghavendar R. Sanganna Gari, Grigory Tagiltsev, Ruth A. Pumroy, Yining Jiang, Martin Blackledge, Vera Y. Moiseenkova-Bell and Simon Scheuring is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third-party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.

Cell surface fluctuations regulate early embryonic lineage sorting

In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive.*

In the article “Cell surface fluctuations regulate early embryonic lineage sorting” Ayaka Yanagida, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, Ruby Peters, Henry De Belly, Davide A.D. Cassani, Sarra Achouri Raphael Blumenfeld, Kristian Franze, Edouard Hannezo, Ewa K. Paluch, Jennifer Nichols and Kevin J. Chalut investigate the mechanical basis of EPI and PrE sorting. *

The authors find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting.*

These differential surface fluctuations systematically correlate with differential cellular fluidity, which Ayaka Yanagida et al. propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, A. Yanagida et al. identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.*

The surface tension of cells was measured using an Atomic Force Microscopy (AFM) based technique with a commercially available stand-alone platform for cell adhesion and cytomechanics studies mounted on an inverted confocal microscope.*

pEPI (epiblast , EPI, founder of the fetus) and pPrE (primitive endoderm, founder of the yolk sac ) tension measurements were performed using NanoWorld ARROW-TL1Au tipless silicon AFM cantilevers (nominal spring constant of 0.03 N/m).*
Sensitivity was calibrated by acquiring a force curve on a glass coverslip. Spring constant was calibrated by the thermal noise fluctuation method. Z-length parameter and setpoint force were set at 30 μm and 10 nN, respectively. Constant height mode was selected. The measurement was carried on by lowering the tipless AFM cantilever onto an empty area next to a target cell. Once the cantilever retracted (by roughly 30 μm), it was positioned above the target cell and run a compression for 200 seconds. During the constant height compression, the force acting on the AFM cantilever was recorded. After initial force relaxation, the resulting force value was used to extract surface tension.*

ES cells tension measurements were performed using the same commercial platform for cell adhesion and cytomechanics studies and a DSD2 Differential Spinning Disk both mounted on an inverted microscope.*

NanoWorld tipless silicon AFM cantilevers of the ARROW-TL1 type were chosen (nominal spring constant of 0.03 N/m). Sensitivity was calibrated by acquiring a force curve on glass. Spring constant was calibrated by the thermal noise fluctuation method. Z-length parameter and setpoint force were set at 80 μm and 4 nN, respectively. Constant height mode was selected. The measurement was carried on by lowering the tipless AFM cantilever onto an empty area next to a target cell. Once the AFM cantilever retracted (by roughly 80 μm), it was positioned above the target cell and a compression was run for 50 seconds. During the constant height compression, the force acting on the AFM cantilever was recorded. After initial force relaxation, the resulting force value was used to extract surface tension. A confocal stack was acquired using a ×40/1.1 NA water immersion objective.*

Figure 4 from Ayaka Yanagida et al. “Cell surface fluctuations regulate early embryonic lineage sorting”:
Differences in ezrin-mediated surface fluctuations regulate cell sorting
(A) Representative images of constitutively active Ezrin-IRES-mCherry (CA-EZR) ES cells, showing a high degree of pERM variability in the low mCherry-expressing ES cells. Surface fluctuations of single CA-EZR cells without Dox and WT H2B-BFP, and CA-EZR ES cells with or without Dox in 2i+LIF. L, M, and H indicate low, medium, and high expression of mCherry as assessed by the 3-quantiles of expression in the mCherry-expressing cells. Surface fluctuations were normalized by the mean of the Dox− surface fluctuations in each of the experiments or the mean of the WT H2B-BFP surface fluctuations. p values were calculated using one-way ANOVA, with the p values above each group representing the outcome of pairwise comparison with Dox−, and the p value above all values in CA-EZR Dox+ condition representing the comparison of all groups.
(B) The surface tension of dissociated Dox-treated CA-EZR ES cells measured using the AFM technique presented in Chugh et al., 2017
is plotted against the intensity of mCherry to show that there is no correlation between CA-EZR expression and surface tension. On the right is the surface tension of dissociated WT H2B-BFP ES cells and Dox-treated CA-EZR ES cells. p value was calculated by two-way ANOVA using cell type and experimental replicate as variables.
(C) θ of the homotypic doublets that can be formed from CA-EZR ES cells with or without Dox.
(D) Representative images of CA-EZR ES cells and WT H2B-BFP ES cells aggregated with or without Dox. The line drawn through the center of the aggregates represents the line over which we found an intensity profile in (E).
(E) Representative comparison of BFP and mCherry line scan signals in the CA-EZR and H2B-BFP ES cells aggregates with or without Dox, using the line across the images in (D).
(F) Schematic showing how the radial average (dipole moment) R is calculated, along with model examples of R for distributions shown.
(G) R of aggregates of CA-EZR and H2B-BFP ES cells.

*Ayaka Yanagida, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, Ruby Peters, Henry De Belly, Davide A.D. Cassani, Sarra Achouri Raphael Blumenfeld, Kristian Franze, Edouard Hannezo, Ewa K. Paluch, Jennifer Nichols and Kevin J. Chalut
Cell surface fluctuations regulate early embryonic lineage sorting
Cell, Volume 185, Issue 5, 3 March 2022, Pages 777-793.e20
DOI: https://doi.org/10.1016/j.cell.2022.01.022

The article “Cell surface fluctuations regulate early embryonic lineage sorting” by Ayaka Yanagida, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, Ruby Peters, Henry De Belly, Davide A.D. Cassani, Sarra Achouri Raphael Blumenfeld, Kristian Franze, Edouard Hannezo, Ewa K. Paluch, Jennifer Nichols and Kevin J. Chalut is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third-party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.

Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division

Bacterial cell division is a complex process requiring the coordination of multiple components to allow the appropriate spatial and temporal control of septum formation and cell scission. *

Peptidoglycan (PG) is the major structural component of the septum, and recent studies by Katarzyna Wacnik et al., in the human pathogen Staphylococcus aureus have revealed a complex, multistage PG architecture that develops during septation. *

Penicillin-binding proteins (PBPs) are essential for the final steps of PG biosynthesis; their transpeptidase activity links the peptide side chains of nascent glycan strands. PBP1 is required for cell division in S. aureus. *

In the article “Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division” Katarzyna Wacnik, Vincenzo A. Rao, Xinyue Chen, Lucia Lafage, Manuel Pazos, Simon Booth, Waldemar Vollmer, Jamie K. Hobbs, Richard J. Lewis and Simon J. Foster demonstrate that it has multiple essential functions associated with its enzymatic activity and as a regulator of division. *

Loss of PBP1, or just its C-terminal PASTA domains, results in cessation of division at the point of septal plate formation. The PASTA domains can bind PG and thereby potentially coordinate the cell division process. The transpeptidase activity of PBP1 is also essential, but its loss leads to a strikingly different phenotype of thickened and aberrant septa, which is phenocopied by the morphological effects of adding the PBP1-specific β-lactam, meropenem. Together, these results lead to a model for septal PG synthesis where PBP1 enzyme activity is required for the characteristic architecture of the septum and PBP1 protein molecules enable the formation of the septal plate. *

Bacterial cell wall peptidoglycan is essential, and its synthesis is the target of clinically important antibiotics such as β-lactams. β-lactams target penicillin-binding proteins (PBPs) that assemble new peptidoglycan from its building blocks. *

The human pathogen Staphylococcus aureus only has two essential PBPs that can carry out all the functions necessary for growth and division. *

In the absence of the confounding antibiotic resistance-associated PBP PBP2A, the PBP1 transpeptidase activity is required for cell division, and in the article “Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division”, Katarzyna Wacnik et al. state that they have found that it has several essential functions, both as an enzyme and as a coordinator by binding to cell division proteins and to its peptidoglycan product, via its PASTA domains. *

This has led to a new model for cell division with PBP1 responsible for the synthesis of the characteristic architectural features of the septum. *

NanoWorld Ultra-Short Cantilevers for High-Speed AFM of the USC-F0.3-k0.3 AFM probe type (nominal spring constant of 0.3 N/m and resonant frequency (in liquid) of ~150 kHz (300 kHz in air) were used for the Atomic Force Microscopy imaging.

Supplemental Material from Katarzyna Wacnik et al 2022 “Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division” FIG S5: Gallery of AFM images of S. aureus Δpbp1, pbp1ΔPASTA, and pbp1*. (A) Diagram of the section through of the cell with progressing septum (top) and AFM topographic images (bottom) of unfinished (i) and closed (ii) septa, parallel to the plane of the image, in SH1000 WT. Sacculi (images to the left, scale bars = 500 nm, data scales [z]: 200 [top] and 250 nm [bottom]) and higher-magnification scans (images to the right, scale bars = 50 nm, data scales [z]: 80 [top] and 40 nm [bottom]) of the boxed areas from the images to the left. (B) AFM topographic images of unfinished septa, parallel to the plane of the image, in Δpbp1 (from left to right, scale bars = 500, 50, and 50 nm; data scales [z] 500, 120, and 150 nm), pbp1ΔPASTA (from left to right, scale bars = 500, 50, and 50 nm; data scales [z] 693, 80, and 100 nm), and pbp1* (from left to right, scale bars = 500, 50, and 50 nm; data scales [z] 500, 80, and 25 nm) grown in the absence of inducer for 2 h. Images to the left are sacculi, while images in the center (1) and to the right (2) are higher-magnification scans of the boxed areas of the images on the left. (C) AFM topographic images (right) of the external nascent ring architecture in SH1000 WT (wt; from top to bottom, scale bars = 500 and 50 nm; data scales [z], 100 and 20 nm) and mutants Δpbp1 (top to bottom, scale bars = 500 and 50 nm; data scales [z], 400 and 60 nm) and pbp1ΔPASTA (from top to bottom, scale bars = 500 and 50 nm; data scales [z], 350 and 100 nm) grown in the absence of inducer for 2 h. The top images are the external surface of sacculi, while the bottom images are higher-magnification scans of the boxed areas of the top images. The arrows indicate piecrusts of the next division plane, which dissects the previous division septum. Arrowheads indicate abnormal features, holes, in the PG ring architecture. On the left is an interpretive diagram of a section through the cell wall (i) and the corresponding external surface (ii) as viewed by AFM. The mature cell wall of a newly separated daughter cell is shown in blue, which has both internally and externally mesh-structured PG. The newly exposed septum has an external ring-structured PG (green) and a mesh-like cytoplasmic facing PG (yellow). Data are representative of two independent experiments. NanoWorld Ultra-Short Cantilevers for High-Speed Atomic Force Microscopy of the USC-F0.3-k0.3 AFM probe type were used. — Supplemental Material from Katarzyna Wacnik et al 2022 “Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division” FIG S5: Gallery of AFM images of S. aureus Δpbp1, pbp1ΔPASTA, and pbp1*. (A) Diagram of the section through of the cell with progressing septum (top) and AFM topographic images (bottom) of unfinished (i) and closed (ii) septa, parallel to the plane of the image, in SH1000 WT. Sacculi (images to the left, scale bars = 500 nm, data scales [z]: 200 [top] and 250 nm [bottom]) and higher-magnification scans (images to the right, scale bars = 50 nm, data scales [z]: 80 [top] and 40 nm [bottom]) of the boxed areas from the images to the left. (B) AFM topographic images of unfinished septa, parallel to the plane of the image, in Δpbp1 (from left to right, scale bars = 500, 50, and 50 nm; data scales [z] 500, 120, and 150 nm), pbp1ΔPASTA (from left to right, scale bars = 500, 50, and 50 nm; data scales [z] 693, 80, and 100 nm), and pbp1* (from left to right, scale bars = 500, 50, and 50 nm; data scales [z] 500, 80, and 25 nm) grown in the absence of inducer for 2 h. Images to the left are sacculi, while images in the center (1) and to the right (2) are higher-magnification scans of the boxed areas of the images on the left. (C) AFM topographic images (right) of the external nascent ring architecture in SH1000 WT (wt; from top to bottom, scale bars = 500 and 50 nm; data scales [z], 100 and 20 nm) and mutants Δpbp1 (top to bottom, scale bars = 500 and 50 nm; data scales [z], 400 and 60 nm) and pbp1ΔPASTA (from top to bottom, scale bars = 500 and 50 nm; data scales [z], 350 and 100 nm) grown in the absence of inducer for 2 h. The top images are the external surface of sacculi, while the bottom images are higher-magnification scans of the boxed areas of the top images. The arrows indicate piecrusts of the next division plane, which dissects the previous division septum. Arrowheads indicate abnormal features, holes, in the PG ring architecture. On the left is an interpretive diagram of a section through the cell wall (i) and the corresponding external surface (ii) as viewed by AFM. The mature cell wall of a newly separated daughter cell is shown in blue, which has both internally and externally mesh-structured PG. The newly exposed septum has an external ring-structured PG (green) and a mesh-like cytoplasmic facing PG (yellow). Data are representative of two independent experiments.

*Katarzyna Wacnik, Vincenzo A. Rao, Xinyue Chen, Lucia Lafage, Manuel Pazos, Simon Booth, Waldemar Vollmer, Jamie K. Hobbs, Richard J. Lewis and Simon J. Foster
Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division
American Society for Microbiology Journals, (2022) mBio, Vol. 13, No. 4
DOI: https://doi.org/10.1128/mbio.00669-22

The article “Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division” by Katarzyna Wacnik, Vincenzo A. Rao, Xinyue Chen, Lucia Lafage, Manuel Pazos, Simon Booth, Waldemar Vollmer, Jamie K. Hobbs, Richard J. Lewis and Simon J. Foster is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third-party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.