scholarly journals Computational Modeling of C-Terminal Tails to Predict the Calcium-Dependent Secretion of Endoplasmic Reticulum Resident Proteins

2021 ◽  
Vol 9 ◽  
Author(s):  
Kathleen A. Trychta ◽  
Bing Xie ◽  
Ravi Kumar Verma ◽  
Min Xu ◽  
Lei Shi ◽  
...  

The lumen of the endoplasmic reticulum (ER) has resident proteins that are critical to perform the various tasks of the ER such as protein maturation and lipid metabolism. These ER resident proteins typically have a carboxy-terminal ER retention/retrieval sequence (ERS). The canonical ERS that promotes ER retrieval is Lys-Asp-Glu-Leu (KDEL) and when an ER resident protein moves from the ER to the Golgi, KDEL receptors (KDELRs) in the Golgi recognize the ERS and return the protein to the ER lumen. Depletion of ER calcium leads to the mass departure of ER resident proteins in a process termed exodosis, which is regulated by KDELRs. Here, by combining computational prediction with machine learning-based models and experimental validation, we identify carboxy tail sequences of ER resident proteins divergent from the canonical “KDEL” ERS. Using molecular modeling and simulations, we demonstrated that two representative non-canonical ERS can stably bind to the KDELR. Collectively, we developed a method to predict whether a carboxy-terminal sequence acts as a putative ERS that would undergo secretion in response to ER calcium depletion and interacts with the KDELRs. The interaction between the ERS and the KDELR extends beyond the final four carboxy terminal residues of the ERS. Identification of proteins that undergo exodosis will further our understanding of changes in ER proteostasis under physiological and pathological conditions where ER calcium is depleted.

2021 ◽  
Author(s):  
Kathleen A Trychta ◽  
Bing Xie ◽  
Ravi Verma ◽  
Min Xu ◽  
Lei Shi ◽  
...  

The lumen of the endoplasmic reticulum (ER) has resident proteins that are critical to perform the various tasks of the ER such as protein maturation and lipid metabolism. These ER resident proteins typically have a carboxy-terminal ER retention sequence (ERS). The canonical ERS is Lys-Asp-Glu-Leu (KDEL) and when an ER resident protein moves from the ER to the Golgi, KDEL receptors (KDELRs) in the Golgi recognize the ERS and return the protein to the ER lumen. Depletion of ER calcium leads to the mass departure of ER resident proteins in a process termed exodosis, which is also regulated by KDELRs. Here, by combining computational prediction with machine learning-based models and experimental validation, we identify carboxy tail sequences of ER resident proteins divergent from the canonical KDEL ERS. Using molecular modeling and simulations, we demonstrated that two representative non-canonical ERS can stably bind to the KDELR. Collectively, we developed a method to predict whether a carboxy-terminal sequence acts as a putative ERS that would undergo secretion in response to ER calcium depletion and interact with the KDELRs. Identification of proteins that undergo exodosis will further our understanding of changes in ER proteostasis under physiological and pathological conditions where ER calcium is depleted.


2014 ◽  
Vol 25 (18) ◽  
pp. 2828-2839 ◽  
Author(s):  
Mark J. Henderson ◽  
Emily S. Wires ◽  
Kathleen A. Trychta ◽  
Christopher T. Richie ◽  
Brandon K. Harvey

Endoplasmic reticulum (ER) calcium homeostasis is disrupted in diverse pathologies, including neurodegeneration, cardiovascular diseases, and diabetes. Temporally defining calcium dysregulation during disease progression, however, has been challenging. Here we describe secreted ER calcium-monitoring proteins (SERCaMPs), which allow for longitudinal monitoring of ER calcium homeostasis. We identified a carboxy-terminal modification that is sufficient to confer release of a protein specifically in response to ER calcium depletion. A Gaussia luciferase (GLuc)–based SERCaMP provides a simple and sensitive method to monitor ER calcium homeostasis in vitro or in vivo by analyzing culture medium or blood. GLuc-SERCaMPs revealed ER calcium depletion in rat primary neurons exposed to various ER stressors. In vivo, ER calcium disruption in rat liver was monitored over several days by repeated sampling of blood. Our results suggest that SERCaMPs will have broad applications for the long-term monitoring of ER calcium homeostasis and the development of therapeutic approaches to counteract ER calcium dysregulation.


2020 ◽  
Author(s):  
Steffen Preissler ◽  
Claudia Rato ◽  
Yahui Yan ◽  
Luke A. Perera ◽  
Aron Czako ◽  
...  

AbstractThe metazoan endoplasmic reticulum (ER) serves both as a hub for maturation of secreted proteins and as an intracellular calcium storage compartment, facilitating calcium release-dependent cellular processes. ER calcium depletion robustly activates the unfolded protein response (UPR). However, it is unclear how fluctuations in ER calcium impact organellar proteostasis. Here we report that calcium selectively affects the dynamics of the abundant metazoan ER Hsp70 chaperone BiP, by enhancing its affinity for ADP. In the calcium replete ER, ADP rebinding to post-ATP hydrolysis BiP-substrate complexes competes with ATP binding during both spontaneous and co-chaperone-assisted nucleotide exchange, favouring substrate retention. Conversely, in the calcium depleted ER, relative acceleration of ADP-to-ATP exchange favours substrate release. These findings explain the rapid dissociation of certain substrates from BiP observed in the calcium-depleted ER and suggest a mechanism for tuning ER quality control and coupling UPR activity to signals that mobilise ER calcium in secretory cells.


eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Steffen Preissler ◽  
Claudia Rato ◽  
Yahui Yan ◽  
Luke A Perera ◽  
Aron Czako ◽  
...  

The metazoan endoplasmic reticulum (ER) serves both as a hub for maturation of secreted proteins and as an intracellular calcium storage compartment, facilitating calcium-release-dependent cellular processes. ER calcium depletion robustly activates the unfolded protein response (UPR). However, it is unclear how fluctuations in ER calcium impact organellar proteostasis. Here, we report that calcium selectively affects the dynamics of the abundant metazoan ER Hsp70 chaperone BiP, by enhancing its affinity for ADP. In the calcium-replete ER, ADP rebinding to post-ATP hydrolysis BiP-substrate complexes competes with ATP binding during both spontaneous and co-chaperone-assisted nucleotide exchange, favouring substrate retention. Conversely, in the calcium-depleted ER, relative acceleration of ADP-to-ATP exchange favours substrate release. These findings explain the rapid dissociation of certain substrates from BiP observed in the calcium-depleted ER and suggest a mechanism for tuning ER quality control and coupling UPR activity to signals that mobilise ER calcium in secretory cells.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2621-2621
Author(s):  
Susanne Vejda ◽  
Katarzyna Piwocka ◽  
Thomas G. Cotter ◽  
Gerald C. O’Sullivan ◽  
Sharon L. McKenna

Abstract The Bcr-Abl oncoprotein plays a major role in the development and progression of chronic myeloid leukemia (CML). Several studies have suggested that the expression levels of Bcr-Abl are elevated at disease progression to blast crisis (BC) and that this plays significant role in the achievement of drug resistance. We have established cell lines expressing low (C2 cells) and high levels (C4 cells) of Bcr-Abl to study the molecular mechanisms involved in disease progression especially with regard to drug resistance. Microarray analysis revealed that Bcr-Abl expressing cells exhibit increased expression of various endoplasmic reticulum (ER) resident proteins indicating that the ER is a novel target of Bcr-Abl. Recently, this organelle has been described as an important apoptotic gateway. Indeed, by measuring calcium levels (steady state and following drug treatment) in the ER and cytoplasm we could elucidate that the calcium dependent apoptotic signaling is disturbed in Bcr-Abl transformed cells. Moreover, inhibition of Bcr-Abl activity by Imatinib reversed this phenotype indicating that Bcr-Abl is directly modulating calcium homeostasis by yet unknown mechanisms. Two Bcr-Abl expressing human cell lines, K562 and BV173, also showed reduced amounts of calcium in the ER compared to the Bcr-Abl negative cell lines HL60 and Jurkat. Etoposide was chosen for apoptosis induction as this drug was classified to target not only the mitochondria (classical mitochondrial pathway) but also the ER (calcium dependent apoptotic pathway). Cell death was induced in the parental and Bcr-Abl transformed cell lines and calcium changes in the cytosol and the mitochondria were measured using organelle specific calcium probes. In C2 and C4 cells an early mitochondrial calcium overload was absent possibly due to the decreased amount of free releasable calcium in the ER. Moreover, other ER/calcium activated pathways were greatly diminished, such as cytosolic calcium elevation and calpain activation during apoptosis. It has been shown that decreased levels of releasable calcium in the ER is associated with cell survival. It is possible therefore that Bcr-Abl may exert some of its pro-survival or anti-apoptotic effects at the ER, by directly influencing the levels of releasable calcium. This study demonstrates a novel downstream consequence of Bcr-Abl signaling. The ability to negate calcium dependent apoptotic signaling is likely to be a major pro-survival mechanism in Bcr-Abl transformed cells.


2020 ◽  
Vol 11 (10) ◽  
Author(s):  
Ilaria Genovese ◽  
Flavia Giamogante ◽  
Lucia Barazzuol ◽  
Theo Battista ◽  
Annarita Fiorillo ◽  
...  

Abstract Dysregulation of calcium signaling is emerging as a key feature in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD), and targeting this process may be therapeutically beneficial. Under this perspective, it is important to study proteins that regulate calcium homeostasis in the cell. Sorcin is one of the most expressed calcium-binding proteins in the human brain; its overexpression increases endoplasmic reticulum (ER) calcium concentration and decreases ER stress in the heart and in other cellular types. Sorcin has been hypothesized to be involved in neurodegenerative diseases, since it may counteract the increased cytosolic calcium levels associated with neurodegeneration. In the present work, we show that Sorcin expression levels are strongly increased in cellular, animal, and human models of AD, PD, and HD, vs. normal cells. Sorcin partially colocalizes with RyRs in neurons and microglia cells; functional experiments with microsomes containing high amounts of RyR2 and RyR3, respectively, show that Sorcin is able to regulate these ER calcium channels. The molecular basis of the interaction of Sorcin with RyR2 and RyR3 is demonstrated by SPR. Sorcin also interacts with other ER proteins as SERCA2 and Sigma-1 receptor in a calcium-dependent fashion. We also show that Sorcin regulates ER calcium transients: Sorcin increases the velocity of ER calcium uptake (increasing SERCA activity). The data presented here demonstrate that Sorcin may represent both a novel early marker of neurodegenerative diseases and a response to cellular stress dependent on neurodegeneration.


2014 ◽  
Vol 26 (1) ◽  
pp. 497-515 ◽  
Author(s):  
Dongsheng Tian ◽  
Junxia Wang ◽  
Xuan Zeng ◽  
Keyu Gu ◽  
Chengxiang Qiu ◽  
...  

1978 ◽  
Vol 56 (9) ◽  
pp. 920-925 ◽  
Author(s):  
N. G. Seidah ◽  
R. Routhier ◽  
M. Caron ◽  
M. Chrétien ◽  
S. Demassieux ◽  
...  

In this paper, we present the amino-terminal sequence of rat tonin, an endopeptidase responsible for the conversion of angiotensinogen, the tetradecapeptide renin substrate, or angiotensin I to angiotensin II. It is shown that isoleucine and proline occupy the amino- and carboxy-terminal residues respectively. The N-terminal sequence analysis permitted the identification of 34 out of the first 40 residue s of the single polypeptide chain composed of 272 amino acids. The se results showed an extensive homology with the sequence of many serine proteases of the trypsin–chymotrypsin family. This information, coupled with the slow inhibition of tonin by diisopropylfluorophosphate, classified this enzyme as a selective endopeptidase of the active serine protease family.


1995 ◽  
Vol 224 (2) ◽  
pp. 588-596 ◽  
Author(s):  
J.M. Bailey ◽  
O. Tu ◽  
G. Issai ◽  
A. Ha ◽  
J.E. Shively

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