scholarly journals A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly

2019 ◽  
Vol 117 (1) ◽  
pp. 388-394 ◽  
Author(s):  
Jonathan Herrmann ◽  
Po-Nan Li ◽  
Fatemeh Jabbarpour ◽  
Anson C. K. Chan ◽  
Ivan Rajkovic ◽  
...  

Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that theCaulobacter crescentusSLP readily crystallizes into sheets in vitro via a calcium-triggered multistep assembly pathway. This pathway involves 2 domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2-dimensional (2D) crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using a time course of electron cryo-microscopy (Cryo-EM) imaging reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the 2 domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.

2019 ◽  
Author(s):  
Jonathan Herrmann ◽  
Po-Nan Li ◽  
Fatemeh Jabbarpour ◽  
Anson C. K. Chan ◽  
Ivan Rajkovic ◽  
...  

AbstractSurface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the C. crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multi-step assembly pathway. This pathway involves two domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2D crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using time-resolved electron cryo-microscopy (Cryo-EM) reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the two domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.Significance StatementMany microbes assemble a crystalline protein layer on their outer surface as an additional barrier and communication platform between the cell and its environment. Surface layer proteins efficiently crystallize to continuously coat the cell and this trait has been utilized to design functional macromolecular nanomaterials. Here, we report that rapid crystallization of a bacterial surface layer protein occurs through a multi-step pathway involving a crystalline intermediate. Upon calcium-binding, sequential changes occur in the structure and arrangement of the protein, which are captured by time-resolved small angle x-ray scattering and transmission electron cryo-microscopy. We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization in vivo.


2020 ◽  
Vol 117 (3) ◽  
pp. 1485-1495 ◽  
Author(s):  
Amir Bitran ◽  
William M. Jacobs ◽  
Xiadi Zhai ◽  
Eugene Shakhnovich

Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins’ sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins’ sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.


2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Fatima Saleh ◽  
Alice Carstairs ◽  
S. Leah Etheridge ◽  
Paul Genever

Wnt signalling has been implicated in the regulation of stem cell self-renewal and differentiation; however, the majority of in vitro studies are carried out using monolayer 2D culture techniques. Here, we used mesenchymal stromal cell (MSC) EGFP reporter lines responsive to Wnt pathway activation in a 3D spheroid culture system to mimic better the in vivo environment. Endogenous Wnt signalling was then investigated under basal conditions and when MSCs were induced to undergo osteogenic and adipogenic differentiation. Interestingly, endogenous Wnt signalling was only active during 3D differentiation whereas 2D cultures showed no EGFP expression throughout an extended differentiation time-course. Furthermore, exogenous Wnt signalling in 3D adipogenic conditions inhibited differentiation compared to unstimulated controls. In addition, suppressing Wnt signalling by Dkk-1 restored and facilitated adipogenic differentiation in MSC spheroids. Our findings indicate that endogenous Wnt signalling is active and can be tracked in 3D MSC cultures where it may act as a molecular switch in adipogenesis. The identification of the signalling pathways that regulate MSCs in a 3D in vivo-like environment will advance our understanding of the molecular mechanisms that control MSC fate.


2014 ◽  
Vol 56 ◽  
pp. 167-180 ◽  
Author(s):  
Philipp Trepte ◽  
Nadine Strempel ◽  
Erich E. Wanker

PolyQ (polyglutamine) diseases such as HD (Huntington's disease) or SCA1 (spinocerebellar ataxia type 1) are neurodegenerative disorders caused by abnormally elongated polyQ tracts in human proteins. PolyQ expansions promote misfolding and aggregation of disease-causing proteins, leading to the appearance of nuclear and cytoplasmic inclusion bodies in patient neurons. Several lines of experimental evidence indicate that this process is critical for disease pathogenesis. However, the molecular mechanisms underlying spontaneous polyQ-containing aggregate formation and the perturbation of neuronal processes are still largely unclear. The present chapter reviews the current literature regarding misfolding and aggregation of polyQ-containing disease proteins. We specifically focus on studies that have investigated the amyloidogenesis of polyQ-containing HTTex1 (huntingtin exon 1) fragments. These protein fragments are disease-relevant and play a critical role in HD pathogenesis. We outline potential mechanisms behind mutant HTTex1 aggregation and toxicity, as well as proteins and small molecules that can modify HTTex1 amyloidogenesis in vitro and in vivo. The potential implications of such studies for the development of novel therapeutic strategies are discussed.


2015 ◽  
Vol 197 (19) ◽  
pp. 3216-3227 ◽  
Author(s):  
Sao-Mai Nguyen-Mau ◽  
So-Young Oh ◽  
Daphne I. Schneewind ◽  
Dominique Missiakas ◽  
Olaf Schneewind

ABSTRACTBacillus anthracisvegetative forms assemble an S-layer comprised of two S-layer proteins, Sap and EA1. A hallmark of S-layer proteins are their C-terminal crystallization domains, which assemble into a crystalline lattice once these polypeptides are deposited on the bacterial surface via association between their N-terminal S-layer homology domains and the secondary cell wall polysaccharide. Here we show thatslaQ, encoding a small cytoplasmic protein conserved among pathogenic bacilli elaborating S-layers, is required for the efficient secretion and assembly of Sap and EA1. S-layer protein precursors cosediment with SlaQ, and SlaQ appears to facilitate Sap assembly. Purified SlaQ polymerizes and when mixed with purified Sap promotes thein vitroformation of tubular S-layer structures. A model is discussed whereby SlaQ, in conjunction with S-layer secretion factors SecA2 and SlaP, promotes localized secretion and S-layer assembly inB. anthracis.IMPORTANCES-layer proteins are endowed with the propensity for self-assembly into crystalline arrays. Factors promoting S-layer protein assembly have heretofore not been reported. We identifiedBacillus anthracisSlaQ, a small cytoplasmic protein that facilitates S-layer protein assemblyin vivoandin vitro.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1158-1158
Author(s):  
Ermelinda Porpiglia ◽  
Ying Liu ◽  
Ramona Pop ◽  
Merav Socolovsky

Abstract Tissue hypoxia triggers the erythropoietic stress response, where high blood erythropoietin (Epo) stimulates increased red blood cell production rate. Stat5 is rapidly phosphorylated following ligation of the Epo receptor (EpoR) in erythroid cells in vitro and is required for normal erythropoiesis [Socolovsky et al. Blood, 2001; Cui et al., Mol Cel Biol, 2004]. Stat5-deficient mice, and mice expressing a truncated EpoR lacking Stat5 docking sites, are impaired in their response to erythropoietic stress, suggesting thatStat5 mediates EpoR signaling during stress [Socolovsky et al., 2001; Menon et al., J Clin Invest, 2006]. The identity of the erythroid progenitors in which Stat5 becomes active during stress, and the time-course of its activation, are not known. Recently, we developed flow-cytometric techniques that identify stress-responsive erythroblast subsets directly in freshly-explanted mouse hematopoietic tissue [Liu et al., Blood 2006]. Here we combined these techniques with intracellular flow-cytometry [Krutzik et al, J Immunol., 2005], to measure Stat5 activation within early erythroblasts in vivo. We mimicked the effects of acute erythropoietic stress by injecting adult Balb/C mice with a single dose of Epo (10 IU/gram sub-cutaneously), and harvested spleen and bone marrow at different time points following Epo injection. These cells were labeled for the cell-surface markers Ter119 and CD71, and intracellularly with a specfic antibody against phospho-Stat5. Serum Epo was measured by ELISA. Baseline Epo (10 to 50 mU/ml) increased to 600 mU/ml by 10 minutes post injection, peaked by 6 hours and remained high (over 5000 mU/ml) for 24 hours. Stat5 phosphorylation (=phospho-Stat5) was apparent by 15 minutes in both bone-marrow and spleen. In both tissues, it was highest in the least differentiated, ProE and Ery.A erythroblasts (Ter119-med CD71-high, and Ter119-high CD71-high FSC-high, respectively, Liu et al. 2006). In bone-marrow, the percentage of ProE that were positive for phospho-Stat5 (phospho-Stat5+) increased from a baseline of less than 1% to 65% by 30 minutes, but declined to 10% of ProE by 6 hours. This low-level of phospho-Stat5+ cells was maintained for the ensuing 10 hours. Of interest, in spite of the large variations in the percent of phospho-Stat5+ cells, the median phospho-Stat5 signal remained constant within the phospho-Stat5+ erythroblasts. This suggests that erythroblasts are either ‘on’ or ‘off’ with respect to Stat5 activation, and that the principal variant is the fraction of cells that are ‘on’ in the tissue. The decline in phospho-Stat5+ cells by 6 hours occurred in spite of persisting, high serum Epo, suggesting the activation of negative feedback mechanisms that limit EpoR signaling. We also noted a clear difference in the sensitivity of otherwise similar erythroblast subsets between spleen and bone-marrow: in spleen, a smaller percentage of erythroblasts became phospho-Stat5+, the signal was slower to develop and diminished sooner than in bone-marrow. We conclude that Stat5 phosphorylation occurs rapidly upon an increase in serum Epo, but is likely to be damped from its peak by negative feedback meachanisms. Spleen erythroblasts are less sensitive than bone-marrow erythroblasts to Epo activation. Further, the principal regulation of the phospho-Stat5 signal appears to be at the level of the tissue, where the main variable is the fraction of cells expressing phospho-Stat5, rather than the level of phospho-Stat5 per cell. The molecular mechanisms responsible for this type of regulation remain to be elucidated.


F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 43 ◽  
Author(s):  
Ho Man Tang ◽  
C. Conover Talbot Jr ◽  
Ming Chiu Fung ◽  
Ho Lam Tang

Anastasis (Greek for "rising to life") is a cell recovery phenomenon that rescues dying cells from the brink of cell death. We recently discovered anastasis to occur after the execution-stage of apoptosis in vitro and in vivo. Promoting anastasis could in principle preserve injured cells that are difficult to replace, such as cardiomyocytes and neurons. Conversely, arresting anastasis in dying cancer cells after cancer therapies could improve treatment efficacy. To develop new therapies that promote or inhibit anastasis, it is essential to identify the key regulators and mediators of anastasis – the therapeutic targets. Therefore, we performed time-course microarray analysis to explore the molecular mechanisms of anastasis during reversal of ethanol-induced apoptosis in mouse primary liver cells. We found striking changes in transcription of genes involved in multiple pathways, including early activation of pro-cell survival, anti-oxidation, cell cycle arrest, histone modification, DNA-damage and stress-inducible responses, and at delayed times, angiogenesis and cell migration. Validation with RT-PCR confirmed similar changes in the human liver cancer cell line, HepG2, during anastasis. Here, we present the time-course whole-genome gene expression dataset revealing gene expression profiles during the reversal of apoptosis. This dataset provides important insights into the physiological, pathological, and therapeutic implications of anastasis.


2019 ◽  
Author(s):  
Colin J. Comerci ◽  
Jonathan Herrmann ◽  
Joshua Yoon ◽  
Fatemeh Jabbarpour ◽  
Xiaofeng Zhou ◽  
...  

AbstractBacteria assemble the cell envelope using localized enzymes to account for growth and division of a topologically complicated surface1–3. However, a regulatory pathway has not been identified for assembly and maintenance of the surface layer (S-layer), a 2D crystalline protein coat surrounding the curved 3D surface of a variety of bacteria4,5. By specifically labeling, imaging, and tracking native and purified RsaA, the S-layer protein (SLP) fromC. crescentus, we show that protein self-assembly alone is sufficient to assemble and maintain the S-layerin vivo. By monitoring the location of newly produced S-layer on the surface of living bacteria, we find that S-layer assembly occurs independently of the site of RsaA secretion and that localized production of new cell wall surface area alone is insufficient to explain S-layer assembly patterns. When the cell surface is devoid of a pre-existing S-layer, the location of S-layer assembly depends on the nucleation characteristics of SLP crystals, which grow by capturing RsaA molecules freely diffusing on the outer bacterial surface. Based on these observations, we propose a model of S-layer assembly whereby RsaA monomers are secreted randomly and diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated into growing 2D S-layer crystals. The complicated topology of the cell surface enables formation of defects, gaps, and grain boundaries within the S-layer lattice, thereby guiding the location of S-layer assembly without enzymatic assistance. This unsupervised mechanism poses unique challenges and advantages for designing treatments targeting cell surface structures or utilizing S-layers as self-assembling macromolecular nanomaterials. As an evolutionary driver, 2D protein self-assembly rationalizes the exceptional S-layer subunit sequence and species diversity6.


2016 ◽  
Vol 36 (suppl_1) ◽  
Author(s):  
Allison Ostriker ◽  
Kristen Leslie ◽  
Kathleen Martin

Coronary allograft vasculopathy (CAV) occurs in 50% of heart transplant recipients at 10 years after surgery. Allograft failure secondary to CAV accounts for 30% of deaths in transplant recipients. CAV is characterized by concentric neointimal hyperplasia (NIH) in the graft vasculature results in ischemic injury. T cell-derived INF-γ is a well-established driver of NIH in CAV. The molecular mechanisms engaged by IFN-γ in vascular smooth muscle cells (VSMCs) in CAV are not fully elucidated. Our group recently showed that TET methylcytosine dioxygenase 2 is a regulator of VSMC phenotype. We hypothesized, therefore, that IFN-γ modulates TET2 expression and/or function in VSMCs. We found, using a single minor histocompatibility mismatch aorta interposition graft model of CAV, that TET2 expression was decreased in vivo in the graft neointima as compared to in control tissue. Further, we found that IFN-y was sufficient to repress TET2 gene transcription in human VSMC in vitro, and this repression was not reversed by mTOR inhibition. We then sought to determine if repression of TET2 is sufficient to exacerbate neointimal hyperplasia in the aorta graft model. We found that NIH was exacerbated in aorta grafts from VSMC-specific, inducible, TET2 knockout (iKO) donors versus controls. Neither T cell recruitment, nor STAT1 activation, was increased in the iKO grafts versus controls; while time course analysis showed that neointimal cells were primarily recipient-derived, suggesting a non-cell autonomous mechanism. Western blot analysis of VSMCs stimulated with IFN-γ for 0-120 minutes suggested that, in addition to STAT1 activation, IFN-γ decreases β-catenin signaling. ChIP-PCR studies showed that STAT1, but not LEF1 (a β-catenin coactivator), occupancy increased at the TET2 promotor following INF-γ stimulation. Studies are ongoing to further elucidate the requirement for STAT1 and/or β-catenin in IFN-γ-dependent repression of TET2 in VSMCs and the non-autonomous role of TET2 on mediating NIH progression in CAV. Since IFN-y-dependent repression of TET2 is not reversed by rapamycin, elucidating this pathway represents an opportunity for developing complementary therapies to mTOR inhibition that may result in improved outcomes and fewer side effects.


F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 43 ◽  
Author(s):  
Ho Man Tang ◽  
C. Conover Talbot Jr ◽  
Ming Chiu Fung ◽  
Ho Lam Tang

Apoptosis is a type of programmed cell death that is essential for normal organismal development and homeostasis of multicellular organisms by eliminating unwanted, injured, or dangerous cells. This cell suicide process is generally assumed to be irreversible. However, accumulating studies suggest that dying cells can recover from the brink of cell death. We recently discovered an unexpected reversibility of the execution-stage of apoptosis in vitro and in vivo, and proposed the term anastasis (Greek for “rising to life”) to describe this cell recovery phenomenon. Promoting anastasis could in principle preserve injured cells that are difficult to replace, such as cardiomyocytes and neurons. Conversely, arresting anastasis in dying cancer cells after cancer therapies could improve treatment efficacy. To develop new therapies that promote or inhibit anastasis, it is essential to identify the key regulators and mediators of anastasis – the therapeutic targets. Therefore, we performed time-course microarray analysis to explore the molecular mechanisms of anastasis during reversal of ethanol-induced apoptosis in mouse primary liver cells. We found striking changes in transcription of genes involved in multiple pathways, including early activation of pro-survival genes, cell cycle arrest, stress-inducible responses, and at delayed times, cell migration and angiogenesis. Here, we present the time-course whole-genome gene expression dataset revealing gene expression profiles during the reversal of apoptosis. This dataset provides important insights into the physiological, pathological, and therapeutic implications of anastasis.


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