Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling
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PROVIDER: PRJNA897861 | ENA |
REPOSITORIES: ENA
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Project description:Increasing evidence suggests that ribosome composition and modifications contribute to translation control. Much less is known about the regulatory roles of mRNA binding by ribosomal proteins to specific mRNA translation and ribosome specialization. Here we used CRISPR-Cas9, to mutate the RPS26 C-terminal tail (RPS26dC) predicted to bind AUG upstream nucleotides at the exit channel. RPS26 binding to positions -10 to -16 of short 5’UTR mRNAs exerts positive and negative effects on translation directed by Kozak and TISU, respectively. Consistent with that, shortening the 5′UTR from 16 to 10 nt diminished Kozak and enhanced TISU-driven translation. As TISU is resistant and Kozak is sensitive to energy stress, we examined stress responses and found that the RPS26dC mutation confers resistance to glucose starvation and mTOR inhibition. Furthermore, the basal mTOR activity is reduced while AMPK is activated in RPS26dC cells, mirroring energy-deprived WT cells. Likewise, the translatome of RPS26dC cells is correlated to glucose-starved WT cells. Our findings uncover the central roles of RPS26 C-terminal RNA binding in energy metabolism, in the translation of mRNAs bearing specific features and in the translation tolerance of TISU genes to energy stress.
2023-04-12 | GSE217180 | GEO
Project description:Increasing evidence suggests that ribosome composition and modifications contribute to translation control. Whether direct mRNA binding by ribosomal proteins regulates the translation of specific mRNA and contributes to ribosome specialization has been poorly investigated. Here, we used CRISPR-Cas9 to mutate the RPS26 C-terminus (RPS26dC) predicted to bind AUG upstream nucleotides at the exit channel. RPS26 binding to positions -10 to -16 of short 5' untranslated region (5'UTR) mRNAs exerts positive and negative effects on translation directed by Kozak and Translation Initiator of Short 5'UTR (TISU), respectively. Consistent with that, shortening the 5'UTR from 16 to 10 nt diminished Kozak and enhanced TISU-driven translation. As TISU is resistant and Kozak is sensitive to energy stress, we examined stress responses and found that the RPS26dC mutation confers resistance to glucose starvation and mTOR inhibition. Furthermore, the basal mTOR activity is reduced while AMP-activated protein kinase is activated in RPS26dC cells, mirroring energy-deprived wild-type (WT) cells. Likewise, the translatome of RPS26dC cells is correlated to glucose-starved WT cells. Our findings uncover the central roles of RPS26 C-terminal RNA binding in energy metabolism, in the translation of mRNAs bearing specific features and in the translation tolerance of TISU genes to energy stress.
| S-EPMC10201367 | biostudies-literature
Project description:Amino acids (aa) are not only building blocks for proteins, but also signalling molecules, with the mammalian target of rapamycin complex 1 (mTORC1) acting as a key mediator. However, little is known about whether aa, independently of mTORC1, activate other kinases of the mTOR signalling network. To delineate aa-stimulated mTOR network dynamics, we here combine a computational–experimental approach with text mining-enhanced quantitative proteomics. We report that AMP-activated protein kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR complex 2 (mTORC2) are acutely activated by aa-readdition in an mTORC1-independent manner. AMPK activation by aa is mediated by Ca2+/calmodulin-dependent protein kinase kinase β (CaMKKβ). In response, AMPK impinges on the autophagy regulators Unc-51-like kinase-1 (ULK1) and c-Jun. AMPK is widely recognized as an mTORC1 antagonist that is activated by starvation. We find that aa acutely activate AMPK concurrently with mTOR. We show that AMPK under aa sufficiency acts to sustain autophagy. This may be required to maintain protein homoeostasis and deliver metabolite intermediates for biosynthetic processes.
2016-12-12 | PXD003073 | Pride
Project description:Translation of TOP mRNAs encoding protein synthesis machinery is strictly regulated by an amino acid sensing mTOR pathway. However, its regulatory mechanism remains elusive. Here, we demonstrate that TOP mRNA translation positively correlates with its poly(A) tail length under mTOR active/amino acid-rich condition, suggesting that TOP mRNAs are post-transcriptionally controlled by poly(A) tail length regulation. Consistent with this, tail length of TOP mRNAs dynamically fluctuates in response to amino acid availability. Poly(A) tail shortens under mTOR active/ amino acid-rich condition, whereas the long-tailed TOP mRNAs accumulate under mTOR inactive/amino acid-starved (AAS) condition. An RNA-binding protein LARP1 that specifically binds to TOP mRNAs is indispensable for the process. We also show that LARP1 interacts with non-canonical poly(A) polymerases, PAPD4, PAPD5 and PAPD7 and induces post-transcriptional polyadenylation of the target when tethered to the mRNA. Our findings illustrate that LARP1 contributes to the selective accumulation of TOP mRNAs with long poly(A) tail under AAS, resulting in accelerated ribosomal loading onto TOP mRNAs for the resumption of translation after AAS.
2022-09-22 | GSE145744 | GEO
Project description:DallePezze2016 - Activation of AMPK and mTOR
by amino acids (Model 3)
This model is as described in
the Supplementary Software 3 of the reference publication: SBML
model similar to Model S2, but including a more complex p70-S6K
module.
This model is described in the article:
A systems study reveals
concurrent activation of AMPK and mTOR by amino acids.
Dalle Pezze P, Ruf S, Sonntag AG,
Langelaar-Makkinje M, Hall P, Heberle AM, Razquin Navas P, van
Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B,
Deitersen J, Stork B, Fäßler E, Schäuble S, Hahn
U, Horvatovich P, Shanley DP, Thedieck K.
Nat Commun 2016 Nov; 7: 13254
Abstract:
Amino acids (aa) are not only building blocks for proteins,
but also signalling molecules, with the mammalian target of
rapamycin complex 1 (mTORC1) acting as a key mediator. However,
little is known about whether aa, independently of mTORC1,
activate other kinases of the mTOR signalling network. To
delineate aa-stimulated mTOR network dynamics, we here combine
a computational-experimental approach with text mining-enhanced
quantitative proteomics. We report that AMP-activated protein
kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR
complex 2 (mTORC2) are acutely activated by aa-readdition in an
mTORC1-independent manner. AMPK activation by aa is mediated by
Ca2+/calmodulin-dependent protein kinase kinase ? (CaMKK?). In
response, AMPK impinges on the autophagy regulators Unc-51-like
kinase-1 (ULK1) and c-Jun. AMPK is widely recognized as an
mTORC1 antagonist that is activated by starvation. We find that
aa acutely activate AMPK concurrently with mTOR. We show that
AMPK under aa sufficiency acts to sustain autophagy. This may
be required to maintain protein homoeostasis and deliver
metabolite intermediates for biosynthetic processes.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000640.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000640 | BioModels
Project description:Sonntag2012 - mTOR model - IRS dependent regulation of AMPK by insulin
TSC1-TSC2 complex has two states: 1)
active (TSC1_TSC2_pS1387), regulated by AMPK_pT172; 2) inactive
(TSC1_TSC2_pT1462) regulated by Akt_pT308. Particularly, mTORC1 is
inhibited by TSC1_TSC2 in active state. AMPK is activated at T172
by the species IRS1_p activated by the insulin receptor upon
insulin stimulation. Consequently, AMPK_pT172 is inhibited by
mTORC1_pS2448 indirectly by the p70-S6K-negative feedback loop.
This model is described in the article:
A modelling-experimental
approach reveals insulin receptor substrate (IRS)-dependent
regulation of adenosine monosphosphate-dependent kinase (AMPK)
by insulin.
Sonntag AG, Dalle Pezze P, Shanley
DP, Thedieck K.
FEBS J. 2012 Sep; 279(18):
3314-3328
Abstract:
Mammalian target of rapamycin (mTOR) kinase responds to
growth factors, nutrients and cellular energy status and is a
central controller of cellular growth. mTOR exists in two
multiprotein complexes that are embedded into a complex
signalling network. Adenosine monophosphate-dependent kinase
(AMPK) is activated by energy deprivation and shuts off
adenosine 5'-triphosphate (ATP)-consuming anabolic processes,
in part via the inactivation of mTORC1. Surprisingly, we
observed that AMPK not only responds to energy deprivation but
can also be activated by insulin, and is further induced in
mTORC1-deficient cells. We have recently modelled the mTOR
network, covering both mTOR complexes and their insulin and
nutrient inputs. In the present study we extended the network
by an AMPK module to generate the to date most comprehensive
data-driven dynamic AMPK-mTOR network model. In order to define
the intersection via which AMPK is activated by the insulin
network, we compared simulations for six different hypothetical
model structures to our observed AMPK dynamics. Hypotheses
ranking suggested that the most probable intersection between
insulin and AMPK was the insulin receptor substrate (IRS) and
that the effects of canonical IRS downstream cues on AMPK would
be mediated via an mTORC1-driven negative-feedback loop. We
tested these predictions experimentally in multiple set-ups,
where we inhibited or induced players along the insulin-mTORC1
signalling axis and observed AMPK induction or inhibition. We
confirmed the identified model and therefore report a novel
connection within the insulin-mTOR-AMPK network: we conclude
that AMPK is positively regulated by IRS and can be inhibited
via the negative-feedback loop.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000580.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000580 | BioModels
Project description:Translation of TOP mRNAs encoding protein synthesis machinery is strictly regulated by an amino acid sensing mTOR pathway. However, its regulatory mechanism remains elusive. Here, we demonstrate that TOP mRNA translation positively correlates with its poly(A) tail length under mTOR active/amino acid-rich condition, suggesting that TOP mRNAs are post-transcriptionally controlled by poly(A) tail length regulation. Consistent with this, tail length of TOP mRNAs dynamically fluctuates in response to amino acid availability. Poly(A) tail shortens under mTOR active/ amino acid-rich condition, whereas the long-tailed TOP mRNAs accumulate under mTOR inactive/amino acid-starved (AAS) condition. An RNA-binding protein LARP1 that specifically binds to TOP mRNAs is indispensable for the process. We also show that LARP1 interacts with non-canonical poly(A) polymerases, PAPD4, PAPD5 and PAPD7 and induces post-transcriptional polyadenylation of the target when tethered to the mRNA. Our findings illustrate that LARP1 contributes to the selective accumulation of TOP mRNAs with long poly(A) tail under AAS, resulting in accelerated ribosomal loading onto TOP mRNAs for the resumption of translation after AAS.
2022-09-19 | GSE137807 | GEO
Project description:DallePezze2016 - Activation of AMPK and mTOR
by amino acids (Model 1)
This model is as described in
Supplementary Software 2 of the reference publication:
SBML
model including only the canonical amino acid input on
mTORC1.
This model is described in the article:
A systems study reveals
concurrent activation of AMPK and mTOR by amino acids.
Dalle Pezze P, Ruf S, Sonntag AG,
Langelaar-Makkinje M, Hall P, Heberle AM, Razquin Navas P, van
Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B,
Deitersen J, Stork B, Fäßler E, Schäuble S, Hahn
U, Horvatovich P, Shanley DP, Thedieck K.
Nat Commun 2016 Nov; 7: 13254
Abstract:
Amino acids (aa) are not only building blocks for proteins,
but also signalling molecules, with the mammalian target of
rapamycin complex 1 (mTORC1) acting as a key mediator. However,
little is known about whether aa, independently of mTORC1,
activate other kinases of the mTOR signalling network. To
delineate aa-stimulated mTOR network dynamics, we here combine
a computational-experimental approach with text mining-enhanced
quantitative proteomics. We report that AMP-activated protein
kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR
complex 2 (mTORC2) are acutely activated by aa-readdition in an
mTORC1-independent manner. AMPK activation by aa is mediated by
Ca2+/calmodulin-dependent protein kinase kinase ? (CaMKK?). In
response, AMPK impinges on the autophagy regulators Unc-51-like
kinase-1 (ULK1) and c-Jun. AMPK is widely recognized as an
mTORC1 antagonist that is activated by starvation. We find that
aa acutely activate AMPK concurrently with mTOR. We show that
AMPK under aa sufficiency acts to sustain autophagy. This may
be required to maintain protein homoeostasis and deliver
metabolite intermediates for biosynthetic processes.
This model is hosted on
BioModels Database
and identified by:
MODEL1705030000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1705030000 | BioModels
Project description:DallePezze2016 - Activation of AMPK and mTOR
by amino acids (Model 2)
This
model is as described in the Supplementary Software 2 of the
reference publication:
SBML
model including four amino acids input in the network (simple
p70-S6K module).
This model is described in the article:
A systems study reveals
concurrent activation of AMPK and mTOR by amino acids.
Dalle Pezze P, Ruf S, Sonntag AG,
Langelaar-Makkinje M, Hall P, Heberle AM, Razquin Navas P, van
Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B,
Deitersen J, Stork B, Fäßler E, Schäuble S, Hahn
U, Horvatovich P, Shanley DP, Thedieck K.
Nat Commun 2016 Nov; 7: 13254
Abstract:
Amino acids (aa) are not only building blocks for proteins,
but also signalling molecules, with the mammalian target of
rapamycin complex 1 (mTORC1) acting as a key mediator. However,
little is known about whether aa, independently of mTORC1,
activate other kinases of the mTOR signalling network. To
delineate aa-stimulated mTOR network dynamics, we here combine
a computational-experimental approach with text mining-enhanced
quantitative proteomics. We report that AMP-activated protein
kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR
complex 2 (mTORC2) are acutely activated by aa-readdition in an
mTORC1-independent manner. AMPK activation by aa is mediated by
Ca2+/calmodulin-dependent protein kinase kinase ? (CaMKK?). In
response, AMPK impinges on the autophagy regulators Unc-51-like
kinase-1 (ULK1) and c-Jun. AMPK is widely recognized as an
mTORC1 antagonist that is activated by starvation. We find that
aa acutely activate AMPK concurrently with mTOR. We show that
AMPK under aa sufficiency acts to sustain autophagy. This may
be required to maintain protein homoeostasis and deliver
metabolite intermediates for biosynthetic processes.
This model is hosted on
BioModels Database
and identified by:
MODEL1705030001.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1705030001 | BioModels
Project description:5’-AMP-Activated Protein Kinase (Ampk) is an energy gatekeeper that responds to decreases in available ATP by inhibiting energy-consuming processes like protein synthesis and promoting energy-generating processes like glucose uptake. Recently, our lab showed that Lkb1, a previously unstudied kinase in B cell immunology and the main upstream kinase of Ampk, had a critical and unexpected role in B cell activation and germinal center formation. In T cells knockout of the downstream target Ampk, only partially phenocopies Lkb1 deletion, so we sought to determine whether the role of Lkb1 in B cells depends on Ampk. We find Ampk is activated upon B cell stimulation in vitro. Surprisingly, however, Ampk activation occurs in the absence of energetic stress, and B cells continue to grow and divide despite Ampk activity. We performed an IP-MS substrate screen to identify Ampk targets and only identified a limited repertoire of canonical targets, and many non-canonical targets. Despite activation of Ampk and the major role of Lkb1 in B cell activation, B cell specific deletion of Ampk does not significantly affect B cell activation, differentiation, carbon handling, gene expression, or humoral immune responses. The only major effect of Ampk loss was accelerated downregulation of IgD during stimulation, which was preceded by downregulation of the IgD regulator Zfp318. Early activation of Ampk by pharmacological means also has little impact on B cell function, although treatment with the biguanide Phenformin critically impairs germinal center formation and class switch recombination in vivo, but does not significantly impair antigen-specific antibody responses. Combined, our results suggest an unexpected and unexplained activation of Ampk in B cells.
2019-06-16 | GSE121025 | GEO