Cargando…

Modelling phagosomal lipid networks that regulate actin assembly

BACKGROUND: When purified phagosomes are incubated in the presence of actin under appropriate conditions, microfilaments start growing from the membrane in a process that is affected by ATP and the lipid composition of the membrane. Isolated phagosomes are metabolically active organelles that contai...

Descripción completa

Detalles Bibliográficos
Autores principales: Kühnel, Mark, Mayorga, Luis S, Dandekar, Thomas, Thakar, Juilee, Schwarz, Roland, Anes, Elsa, Griffiths, Gareth, Reich, Jens
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628873/
https://www.ncbi.nlm.nih.gov/pubmed/19061496
http://dx.doi.org/10.1186/1752-0509-2-107
_version_ 1782163740853010432
author Kühnel, Mark
Mayorga, Luis S
Dandekar, Thomas
Thakar, Juilee
Schwarz, Roland
Anes, Elsa
Griffiths, Gareth
Reich, Jens
author_facet Kühnel, Mark
Mayorga, Luis S
Dandekar, Thomas
Thakar, Juilee
Schwarz, Roland
Anes, Elsa
Griffiths, Gareth
Reich, Jens
author_sort Kühnel, Mark
collection PubMed
description BACKGROUND: When purified phagosomes are incubated in the presence of actin under appropriate conditions, microfilaments start growing from the membrane in a process that is affected by ATP and the lipid composition of the membrane. Isolated phagosomes are metabolically active organelles that contain enzymes and metabolites necessary for lipid interconversion. Hence, addition of ATP, lipids, and actin to the system alter the steady-state composition of the phagosomal membrane at the same time that the actin nucleation is initiated. Our aim was to model all these processes in parallel. RESULTS: We compiled detailed experimental data on the effects of different lipids and ATP on actin nucleation and we investigated experimentally lipid interconversion and ATP metabolism in phagosomes by using suitable radioactive compounds. In a first step, a complex lipid network interconnected by chemical reactions catalyzed by known enzymes was modelled in COPASI (Complex Pathway Simulator). However, several lines of experimental evidence indicated that only the phosphatidylinositol branch of the network was active, an observation that dramatically reduced the number of parameters in the model. The results also indicated that a lipid network-independent ATP-consuming activity should be included in the model. When this activity was introduced, the set of differential equations satisfactorily reproduced the experimental data. On the other hand, a molecular mechanism connecting membrane lipids, ATP, and the actin nucleation process is still missing. We therefore adopted a phenomenological (black-box) approach to represent the empirical observations. We proposed that lipids and ATP influence the dynamic interconversion between active and inactive actin nucleation sites. With this simple model, all the experimental data were satisfactorily fitted with a single positive parameter per lipid and ATP. CONCLUSION: By establishing an active 'dialogue' between an initial complex model and experimental observations, we could narrow the set of differential equations and parameters required to characterize the time-dependent changes of metabolites influencing actin nucleation on phagosomes. For this, the global model was dissected into three sub-models: ATP consumption, lipid interconversion, and nucleation of actin on phagosomal membranes. This scheme allowed us to describe this complex system with a relatively small set of differential equations and kinetic parameters that satisfactorily reproduced the experimental data.
format Text
id pubmed-2628873
institution National Center for Biotechnology Information
language English
publishDate 2008
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-26288732009-01-21 Modelling phagosomal lipid networks that regulate actin assembly Kühnel, Mark Mayorga, Luis S Dandekar, Thomas Thakar, Juilee Schwarz, Roland Anes, Elsa Griffiths, Gareth Reich, Jens BMC Syst Biol Research Article BACKGROUND: When purified phagosomes are incubated in the presence of actin under appropriate conditions, microfilaments start growing from the membrane in a process that is affected by ATP and the lipid composition of the membrane. Isolated phagosomes are metabolically active organelles that contain enzymes and metabolites necessary for lipid interconversion. Hence, addition of ATP, lipids, and actin to the system alter the steady-state composition of the phagosomal membrane at the same time that the actin nucleation is initiated. Our aim was to model all these processes in parallel. RESULTS: We compiled detailed experimental data on the effects of different lipids and ATP on actin nucleation and we investigated experimentally lipid interconversion and ATP metabolism in phagosomes by using suitable radioactive compounds. In a first step, a complex lipid network interconnected by chemical reactions catalyzed by known enzymes was modelled in COPASI (Complex Pathway Simulator). However, several lines of experimental evidence indicated that only the phosphatidylinositol branch of the network was active, an observation that dramatically reduced the number of parameters in the model. The results also indicated that a lipid network-independent ATP-consuming activity should be included in the model. When this activity was introduced, the set of differential equations satisfactorily reproduced the experimental data. On the other hand, a molecular mechanism connecting membrane lipids, ATP, and the actin nucleation process is still missing. We therefore adopted a phenomenological (black-box) approach to represent the empirical observations. We proposed that lipids and ATP influence the dynamic interconversion between active and inactive actin nucleation sites. With this simple model, all the experimental data were satisfactorily fitted with a single positive parameter per lipid and ATP. CONCLUSION: By establishing an active 'dialogue' between an initial complex model and experimental observations, we could narrow the set of differential equations and parameters required to characterize the time-dependent changes of metabolites influencing actin nucleation on phagosomes. For this, the global model was dissected into three sub-models: ATP consumption, lipid interconversion, and nucleation of actin on phagosomal membranes. This scheme allowed us to describe this complex system with a relatively small set of differential equations and kinetic parameters that satisfactorily reproduced the experimental data. BioMed Central 2008-12-05 /pmc/articles/PMC2628873/ /pubmed/19061496 http://dx.doi.org/10.1186/1752-0509-2-107 Text en Copyright © 2008 Kühnel et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Kühnel, Mark
Mayorga, Luis S
Dandekar, Thomas
Thakar, Juilee
Schwarz, Roland
Anes, Elsa
Griffiths, Gareth
Reich, Jens
Modelling phagosomal lipid networks that regulate actin assembly
title Modelling phagosomal lipid networks that regulate actin assembly
title_full Modelling phagosomal lipid networks that regulate actin assembly
title_fullStr Modelling phagosomal lipid networks that regulate actin assembly
title_full_unstemmed Modelling phagosomal lipid networks that regulate actin assembly
title_short Modelling phagosomal lipid networks that regulate actin assembly
title_sort modelling phagosomal lipid networks that regulate actin assembly
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628873/
https://www.ncbi.nlm.nih.gov/pubmed/19061496
http://dx.doi.org/10.1186/1752-0509-2-107
work_keys_str_mv AT kuhnelmark modellingphagosomallipidnetworksthatregulateactinassembly
AT mayorgaluiss modellingphagosomallipidnetworksthatregulateactinassembly
AT dandekarthomas modellingphagosomallipidnetworksthatregulateactinassembly
AT thakarjuilee modellingphagosomallipidnetworksthatregulateactinassembly
AT schwarzroland modellingphagosomallipidnetworksthatregulateactinassembly
AT aneselsa modellingphagosomallipidnetworksthatregulateactinassembly
AT griffithsgareth modellingphagosomallipidnetworksthatregulateactinassembly
AT reichjens modellingphagosomallipidnetworksthatregulateactinassembly