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An integrative approach for modeling and simulation of heterocyst pattern formation in cyanobacteria filaments.

Torres-Sánchez A, Gómez-Gardeñes J, Falo F - PLoS Comput. Biol. (2015)

Bottom Line: As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion.In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally.Finally, we discuss the validity and possible improvements of the model.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza, Spain; Laboratori de Càlcul Numèric, Universitat de Politècnica de Catalunya, Barcelona, Spain.

ABSTRACT
Heterocyst differentiation in cyanobacteria filaments is one of the simplest examples of cellular differentiation and pattern formation in multicellular organisms. Despite of the many experimental studies addressing the evolution and sustainment of heterocyst patterns and the knowledge of the genetic circuit underlying the behavior of single cyanobacterium under nitrogen deprivation, there is still a theoretical gap connecting these two macroscopic and microscopic processes. As an attempt to shed light on this issue, here we explore heterocyst differentiation under the paradigm of systems biology. This framework allows us to formulate the essential dynamical ingredients of the genetic circuit of a single cyanobacterium into a set of differential equations describing the time evolution of the concentrations of the relevant molecular products. As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion. These two ingredients allow us to understand the principles by which heterocyst patterns can be generated and sustained. In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally. Finally, we discuss the validity and possible improvements of the model.

No MeSH data available.


Related in: MedlinePlus

Main components and interactions involved in the reaction to combined nitrogen deprivation in cyanobacteria.Rectangular boxes represent genes (ntcA, hetR and patS) while rounded boxes and circles represent transcription factors (NtcA, HetR and PatS) and smaller molecules (2-OG and cN) respectively. Normal-tipped and flat-tipped arrows stand for up-regulating and down-regulating processes respectively. Dashed lines stand for indirect or imperfectly understood interactions. The accumulation of 2-OG enhances the DNA-binding activity of NtcA, which in turn up-regulates the transcription of ntcA and hetR. HetR activates ntcA and hetR (composing the central NtcA-HetR autoregulatory loop), the inhibitor patS and other genes that lead to nitrogen fixation and the morphological changes involved in heterocyst differentiation. 2-OG and cN levels are linked through the GS/GOGAT cycle (see Fig. 2).
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pcbi.1004129.g001: Main components and interactions involved in the reaction to combined nitrogen deprivation in cyanobacteria.Rectangular boxes represent genes (ntcA, hetR and patS) while rounded boxes and circles represent transcription factors (NtcA, HetR and PatS) and smaller molecules (2-OG and cN) respectively. Normal-tipped and flat-tipped arrows stand for up-regulating and down-regulating processes respectively. Dashed lines stand for indirect or imperfectly understood interactions. The accumulation of 2-OG enhances the DNA-binding activity of NtcA, which in turn up-regulates the transcription of ntcA and hetR. HetR activates ntcA and hetR (composing the central NtcA-HetR autoregulatory loop), the inhibitor patS and other genes that lead to nitrogen fixation and the morphological changes involved in heterocyst differentiation. 2-OG and cN levels are linked through the GS/GOGAT cycle (see Fig. 2).

Mentions: Heterocyst development begins with sensing combined-nitrogen (cN) limitation and ends with nitrogen fixation in mature heterocysts. This process is usually completed after 20 hours at 30∘C [9]. In Fig. 1 we show a basic scheme of the genetic circuit including the most relevant elements and their respective interactions. Here we explain the main features of this genetic circuit.


An integrative approach for modeling and simulation of heterocyst pattern formation in cyanobacteria filaments.

Torres-Sánchez A, Gómez-Gardeñes J, Falo F - PLoS Comput. Biol. (2015)

Main components and interactions involved in the reaction to combined nitrogen deprivation in cyanobacteria.Rectangular boxes represent genes (ntcA, hetR and patS) while rounded boxes and circles represent transcription factors (NtcA, HetR and PatS) and smaller molecules (2-OG and cN) respectively. Normal-tipped and flat-tipped arrows stand for up-regulating and down-regulating processes respectively. Dashed lines stand for indirect or imperfectly understood interactions. The accumulation of 2-OG enhances the DNA-binding activity of NtcA, which in turn up-regulates the transcription of ntcA and hetR. HetR activates ntcA and hetR (composing the central NtcA-HetR autoregulatory loop), the inhibitor patS and other genes that lead to nitrogen fixation and the morphological changes involved in heterocyst differentiation. 2-OG and cN levels are linked through the GS/GOGAT cycle (see Fig. 2).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4376521&req=5

pcbi.1004129.g001: Main components and interactions involved in the reaction to combined nitrogen deprivation in cyanobacteria.Rectangular boxes represent genes (ntcA, hetR and patS) while rounded boxes and circles represent transcription factors (NtcA, HetR and PatS) and smaller molecules (2-OG and cN) respectively. Normal-tipped and flat-tipped arrows stand for up-regulating and down-regulating processes respectively. Dashed lines stand for indirect or imperfectly understood interactions. The accumulation of 2-OG enhances the DNA-binding activity of NtcA, which in turn up-regulates the transcription of ntcA and hetR. HetR activates ntcA and hetR (composing the central NtcA-HetR autoregulatory loop), the inhibitor patS and other genes that lead to nitrogen fixation and the morphological changes involved in heterocyst differentiation. 2-OG and cN levels are linked through the GS/GOGAT cycle (see Fig. 2).
Mentions: Heterocyst development begins with sensing combined-nitrogen (cN) limitation and ends with nitrogen fixation in mature heterocysts. This process is usually completed after 20 hours at 30∘C [9]. In Fig. 1 we show a basic scheme of the genetic circuit including the most relevant elements and their respective interactions. Here we explain the main features of this genetic circuit.

Bottom Line: As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion.In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally.Finally, we discuss the validity and possible improvements of the model.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza, Spain; Laboratori de Càlcul Numèric, Universitat de Politècnica de Catalunya, Barcelona, Spain.

ABSTRACT
Heterocyst differentiation in cyanobacteria filaments is one of the simplest examples of cellular differentiation and pattern formation in multicellular organisms. Despite of the many experimental studies addressing the evolution and sustainment of heterocyst patterns and the knowledge of the genetic circuit underlying the behavior of single cyanobacterium under nitrogen deprivation, there is still a theoretical gap connecting these two macroscopic and microscopic processes. As an attempt to shed light on this issue, here we explore heterocyst differentiation under the paradigm of systems biology. This framework allows us to formulate the essential dynamical ingredients of the genetic circuit of a single cyanobacterium into a set of differential equations describing the time evolution of the concentrations of the relevant molecular products. As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion. These two ingredients allow us to understand the principles by which heterocyst patterns can be generated and sustained. In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally. Finally, we discuss the validity and possible improvements of the model.

No MeSH data available.


Related in: MedlinePlus