BioModels Database logo

BioModels Database

spacer

BIOMD0000000437 - Tseng2012 - Circadian clock of N.crassa

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 22496627
Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM.
Comprehensive modelling of the Neurospora circadian clock and its temperature compensation.
PLoS Comput. Biol. 2012; 8(3): e1002437
University of Manchester, Manchester, United Kingdom.  [more]
Model
Original Model: BIOMD0000000437.origin
Submitter: Yu-yao Tseng
Submission ID: MODEL1212150000
Submission Date: 15 Dec 2012 17:15:20 UTC
Last Modification Date: 25 Feb 2015 12:54:12 UTC
Creation Date: 26 Feb 2013 14:39:12 UTC
Encoders:  Vijayalakshmi Chelliah
   Yu-yao Tseng
set #1
bqmodel:isDerivedFrom BioModels Database Leloup1999_CircadianRhythms_Neurospora
PubMed 17965132
PubMed 15653726
set #2
bqbiol:hasTaxon Taxonomy Neurospora crassa
set #3
bqbiol:isVersionOf Gene Ontology temperature compensation of the circadian clock
Notes
Tseng2012 - Circadian clock of N.crassa

A comprehensive model of the circardian clock of fungal Neurospora crassa , which encompasses existing knowledge of the biochemistry of Neurospora clock, is described by Tseng et al. (2012). The model is validated against a wide range of experimental phenotypes and has been used to investigate possible molecular explanations of temperature compensation.

This model is described in the article:

Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM
PLoS Comput. Biol. [2012 ; Volume: 8 (Issue: 3 )] Page info: e1002437

Abstract:

Circadian clocks provide an internal measure of external time allowing organisms to anticipate and exploit predictable daily changes in the environment. Rhythms driven by circadian clocks have a temperature compensated periodicity of approximately 24 hours that persists in constant conditions and can be reset by environmental time cues. Computational modelling has aided our understanding of the molecular mechanisms of circadian clocks, nevertheless it remains a major challenge to integrate the large number of clock components and their interactions into a single, comprehensive model that is able to account for the full breadth of clock phenotypes. Here we present a comprehensive dynamic model of the Neurospora crassa circadian clock that incorporates its key components and their transcriptional and post-transcriptional regulation. The model accounts for a wide range of clock characteristics including: a periodicity of 21.6 hours, persistent oscillation in constant conditions, arrhythmicity in constant light, resetting by brief light pulses, and entrainment to full photoperiods. Crucial components influencing the period and amplitude of oscillations were identified by control analysis. Furthermore, simulations enabled us to propose a mechanism for temperature compensation, which is achieved by simultaneously increasing the translation of frq RNA and decreasing the nuclear import of FRQ protein.

Figure 3 of the reference publication has been reproduced using Copasi 4.8 (Build 35).

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.

Model
Publication ID: 22496627 Submission Date: 15 Dec 2012 17:15:20 UTC Last Modification Date: 25 Feb 2015 12:54:12 UTC Creation Date: 26 Feb 2013 14:39:12 UTC
Mathematical expressions
Reactions
Time re01 re02 re03
re04 re05 re06 re07
re08 re09 re10 re11
re12 re13 re14 re15
re16 re17 re18 re19
re20 re21 re22 re23
re24 re25 re26 re27
re28 re29 re30 re31
re32 re33 re34 re35
re36 re37 re38 re39
Rules
Assignment Rule (variable: total_FRQ) Assignment Rule (variable: total_WC1) Assignment Rule (variable: total_FRQc) Assignment Rule (variable: total_FRQn)
Assignment Rule (variable: total_hypo_FRQ) Assignment Rule (variable: total_hyper_FRQ) Assignment Rule (variable: c_hypoFRQ_to_hyperFRQ) Assignment Rule (variable: n_hypoFRQ_to_hyperFRQ)
Assignment Rule (variable: total_VVD) Assignment Rule (variable: Period) Assignment Rule (variable: total_WC2) Assignment Rule (variable: total_hypoWCC)
Assignment Rule (variable: total_WCCn) Assignment Rule (variable: total_hyperWCC) Assignment Rule (variable: hyper_hypo_WCC)  
Events
n_CYCLE light_on light_off calculate_period_find_frq_level_A
calculate_period_find_Y calculate_period_find_X    
Physical entities
Compartments Species
default Period T X
Y c_hypoFRQ_to_hyperFRQ cycle
frq_level_A n_hypoFRQ_to_hyperFRQ time
total_FRQ total_FRQc total_FRQn
total_VVD total_WC1 total_WC2
total_WCCn total_hyper_FRQ total_hypoWCC
total_hypo_FRQ line line2
line3 total_hyperWCC hyper_hypo_WCC
Cytoplasm VVDc WC1c WC2c
degraded_VVDc degraded_WC1c degraded_WC2c
degraded_frq_mRNA degraded_hyperFRQc degraded_hyperWCCc
degraded_vvd_mRNA degraded_wc1_mRNA degraded_wc2_mRNA
frq_mRNA hyperFRQc hyperWCCc
hypoFRQc hypoWCCc vvd_mRNA
wc1_mRNA wc2_mRNA  
Nucleus L_WCC L_WCCVVDn VVDn
active_hypoWCCn degraded_L_WCCCVVDn degraded_VVDn
degraded_active_hypoWCCn degraded_hyperFFCn degraded_hyperWCCn
frq_gene hyperFRQn hyperWCCn
hypoFRQn hypoWCCn vvd_gene
wc1_gene wc2_gene  
Global parameters
k_01 K_01 H_01 k_05
k_14 k_06 k_07 k_13
k_23 K_02 H_02 k_35
k_30 k_31 k_32 k_02a01
k_03 k_09 k_10 k_11
k_21 k_18 k_29 k_19
k_24 k_15 k_20 k_17
k_34 k_33 k_25 k_22
on off k_08 k_12
k_37 k_16 k_38 T_light_on
k_26 k_01a k_02a02 kact_L_WCC_light
k_36 k_04 k_09a k_03i
k_03a k_02 k_27 k_28
k_39 LP LP2 LP3
Reactions (40)
 
 Time [time] → [T];  
 
 re01 [frq_gene] → [frq_mRNA];   {active_hypoWCCn} , {L_WCC} , {active_hypoWCCn} , {L_WCC}
 
 re02 [wc1_gene] → [wc1_mRNA];   {active_hypoWCCn} , {L_WCC} , {active_hypoWCCn} , {L_WCC}
 
 re03 [wc2_gene] → [wc2_mRNA];   {hypoFRQn} , {hypoWCCn} , {hypoWCCn} , {hypoFRQn}
 
 re04 [vvd_gene] → [vvd_mRNA];   {L_WCC} , {L_WCC}
 
 re05 [frq_mRNA] → [hypoFRQc];   {frq_mRNA}
 
 re06 [wc1_mRNA] → [WC1c];   {wc1_mRNA}
 
 re07 [wc2_mRNA] → [WC2c];   {wc2_mRNA}
 
 re08 [vvd_mRNA] → [VVDc];   {vvd_mRNA}
 
 re09 [frq_mRNA] → [degraded_frq_mRNA];   {hypoFRQc} , {frq_mRNA} , {hypoFRQc}
 
 re10 [wc1_mRNA] → [degraded_wc1_mRNA];   {wc1_mRNA}
 
 re11 [wc2_mRNA] → [degraded_wc2_mRNA];   {wc2_mRNA}
 
 re12 [vvd_mRNA] → [degraded_vvd_mRNA];   {vvd_mRNA}
 
 re13 [WC1c] + [WC2c] → [hypoWCCc];   {WC1c} , {WC2c}
 
 re14 [hypoFRQc] → [hypoFRQn];   {hypoFRQc}
 
 re15 [hypoWCCc] → [hypoWCCn];   {hypoWCCc}
 
 re16 [VVDc] → [VVDn];   {VVDc}
 
 re17 [hypoFRQn] → [hypoFRQc];   {hypoFRQn}
 
 re18 [hyperFRQn] → [hyperFRQc];   {hyperFRQn}
 
 re19 [hyperWCCn] → [hyperWCCc];   {hyperWCCn}
 
 re20 [hypoFRQc] → [hyperFRQc];   {hypoFRQc}
 
 re21 [hypoFRQn] → [hyperFRQn];   {hypoFRQn}
 
 re22 [hypoWCCc] → [hyperWCCc];   {hypoWCCc}
 
 re23 [hypoWCCn] → [hyperWCCn];   {hypoFRQn} , {hypoWCCn} , {hypoFRQn}
 
 re24 [hyperWCCc] → [hypoWCCc];   {hyperWCCc}
 
 re25 [hypoWCCn] → [active_hypoWCCn];   {hypoWCCn}
 
 re26 [hypoWCCn] → [L_WCC];   {hypoWCCn}
 
 re27 [VVDn] + [L_WCC] → [L_WCCVVDn];   {VVDn} , {L_WCC}
 
 re28 [L_WCCVVDn] → [hypoWCCn] + [VVDn];   {L_WCCVVDn}
 
 re29 [hyperFRQc] → [degraded_hyperFRQc];   {hyperFRQc}
 
 re30 [hyperFRQn] → [degraded_hyperFFCn];   {hyperFRQn}
 
 re31 [WC1c] → [degraded_WC1c];   {WC1c}
 
 re32 [WC2c] → [degraded_WC2c];   {WC2c}
 
 re33 [hyperWCCc] → [degraded_hyperWCCc];   {hyperWCCc}
 
 re34 [hyperWCCn] → [degraded_hyperWCCn];   {hyperWCCn}
 
 re35 [active_hypoWCCn] → [degraded_active_hypoWCCn];   {active_hypoWCCn}
 
 re36 [L_WCC] → [degraded_L_WCCCVVDn];   {L_WCC}
 
 re37 [VVDc] → [degraded_VVDc];   {VVDc}
 
 re38 [VVDn] → [degraded_VVDn];   {VVDn}
 
 re39 [L_WCCVVDn] → [degraded_L_WCCCVVDn];   {L_WCCVVDn}
 
Rules (15)
 
 Assignment Rule (name: total_FRQ) total_FRQ = hypoFRQc+hyperFRQc+hypoFRQn+hyperFRQn
 
 Assignment Rule (name: total_WC1) total_WC1 = WC1c+hypoWCCc+hyperWCCc+hypoWCCn+hyperWCCn+active_hypoWCCn+L_WCC+L_WCCVVDn
 
 Assignment Rule (name: total_FRQc) total_FRQc = hypoFRQc+hyperFRQc
 
 Assignment Rule (name: total_FRQn) total_FRQn = hypoFRQn+hyperFRQn
 
 Assignment Rule (name: total_hypo_FRQ) total_hypo_FRQ = hypoFRQn+hypoFRQc
 
 Assignment Rule (name: total_hyper_FRQ) total_hyper_FRQ = hyperFRQn+hyperFRQc
 
 Assignment Rule (name: c_hypoFRQ_to_hyperFRQ) c_hypoFRQ_to_hyperFRQ = hypoFRQc/hyperFRQc
 
 Assignment Rule (name: n_hypoFRQ_to_hyperFRQ) n_hypoFRQ_to_hyperFRQ = hypoFRQn/hyperFRQn
 
 Assignment Rule (name: total_VVD) total_VVD = VVDn+VVDc+L_WCCVVDn
 
 Assignment Rule (name: Period) Period = Y-X
 
 Assignment Rule (name: total_WC2) total_WC2 = WC2c+hypoWCCc+hypoWCCn+hyperWCCn+hyperWCCc+active_hypoWCCn+L_WCC
 
 Assignment Rule (name: total_hypoWCC) total_hypoWCC = hypoWCCc+hypoWCCn
 
 Assignment Rule (name: total_WCCn) total_WCCn = hypoWCCn+hyperWCCn+active_hypoWCCn+L_WCC
 
 Assignment Rule (name: total_hyperWCC) total_hyperWCC = hyperWCCn+hyperWCCc
 
 Assignment Rule (name: s61) hyper_hypo_WCC = total_hyperWCC/total_hypoWCC
 
Events (6)
 
 n_CYCLE
cycle = cycle+1
 
 light_on
k_26 = kact_L_WCC_light
 
 light_off
k_26 = 0
 
 calculate_period_find_frq_level_A
frq_level_A = frq_mRNA
 
 calculate_period_find_Y
Y = T
 
 calculate_period_find_X
X = T
 
   Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
  Period
Compartment: default
Initial amount: 0.0
 
 T
Compartment: default
Initial amount: 0.0
 
 X
Compartment: default
Initial amount: 0.0
 
 Y
Compartment: default
Initial amount: 0.0
 
  c_hypoFRQ_to_hyperFRQ
Compartment: default
Initial amount: 0.0
 
 cycle
Compartment: default
Initial amount: 0.0
 
 frq_level_A
Compartment: default
Initial amount: 0.0
 
  n_hypoFRQ_to_hyperFRQ
Compartment: default
Initial amount: 0.0
 
 time
Compartment: default
Initial amount: 0.0
 
  total_FRQ
Compartment: default
Initial amount: 0.0
 
  total_FRQc
Compartment: default
Initial amount: 0.0
 
  total_FRQn
Compartment: default
Initial amount: 0.0
 
  total_VVD
Compartment: default
Initial amount: 0.0
 
  total_WC1
Compartment: default
Initial amount: 0.0
 
  total_WC2
Compartment: default
Initial amount: 0.0
 
  total_WCCn
Compartment: default
Initial amount: 0.0
 
  total_hyper_FRQ
Compartment: default
Initial amount: 0.0
 
  total_hypoWCC
Compartment: default
Initial amount: 0.0
 
  total_hypo_FRQ
Compartment: default
Initial amount: 0.0
 
 line
Compartment: default
Initial amount: 1.8728
 
 line2
Compartment: default
Initial amount: 0.985
 
 line3
Compartment: default
Initial amount: 1.67
 
  total_hyperWCC
Compartment: default
Initial amount: 0.0
 
  hyper_hypo_WCC
Compartment: default
Initial amount: 0.0
 
 Cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 VVDc
Compartment: Cytoplasm
Initial amount: 0.0
 
 WC1c
Compartment: Cytoplasm
Initial concentration: 0.039
 
 WC2c
Compartment: Cytoplasm
Initial concentration: 6.11815
 
 degraded_VVDc
Compartment: Cytoplasm
Initial amount: 0.0
 
 degraded_WC1c
Compartment: Cytoplasm
Initial concentration: 0.0
 
 degraded_WC2c
Compartment: Cytoplasm
Initial concentration: 0.0
 
 degraded_frq_mRNA
Compartment: Cytoplasm
Initial concentration: 0.0
 
 degraded_hyperFRQc
Compartment: Cytoplasm
Initial amount: 0.0
 
 degraded_hyperWCCc
Compartment: Cytoplasm
Initial amount: 0.0
 
 degraded_vvd_mRNA
Compartment: Cytoplasm
Initial amount: 0.0
 
 degraded_wc1_mRNA
Compartment: Cytoplasm
Initial concentration: 0.0
 
 degraded_wc2_mRNA
Compartment: Cytoplasm
Initial concentration: 0.0
 
 frq_mRNA
Compartment: Cytoplasm
Initial concentration: 0.22321
 
 hyperFRQc
Compartment: Cytoplasm
Initial amount: 0.368117
 
 hyperWCCc
Compartment: Cytoplasm
Initial amount: 0.496374
 
 hypoFRQc
Compartment: Cytoplasm
Initial amount: 0.619449
 
 hypoWCCc
Compartment: Cytoplasm
Initial amount: 0.4285
 
 vvd_mRNA
Compartment: Cytoplasm
Initial amount: 0.0
 
 wc1_mRNA
Compartment: Cytoplasm
Initial concentration: 0.5218
 
 wc2_mRNA
Compartment: Cytoplasm
Initial concentration: 0.636098
 
 Nucleus Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 L_WCC
Compartment: Nucleus
Initial amount: 0.0
 
 L_WCCVVDn
Compartment: Nucleus
Initial amount: 0.0
 
 VVDn
Compartment: Nucleus
Initial amount: 0.0
 
 active_hypoWCCn
Compartment: Nucleus
Initial amount: 0.05281
 
 degraded_L_WCCCVVDn
Compartment: Nucleus
Initial concentration: 0.0
 
 degraded_VVDn
Compartment: Nucleus
Initial amount: 0.0
 
 degraded_active_hypoWCCn
Compartment: Nucleus
Initial amount: 0.0
 
 degraded_hyperFFCn
Compartment: Nucleus
Initial concentration: 0.0
 
 degraded_hyperWCCn
Compartment: Nucleus
Initial amount: 0.0
 
 frq_gene
Compartment: Nucleus
Initial concentration: 1.0
Constant
 
 hyperFRQn
Compartment: Nucleus
Initial amount: 0.07298
 
 hyperWCCn
Compartment: Nucleus
Initial amount: 0.1573204
 
 hypoFRQn
Compartment: Nucleus
Initial amount: 0.394774
 
 hypoWCCn
Compartment: Nucleus
Initial amount: 0.47086
 
 vvd_gene
Compartment: Nucleus
Initial amount: 1.0
 
 wc1_gene
Compartment: Nucleus
Initial concentration: 1.0
Constant
 
 wc2_gene
Compartment: Nucleus
Initial concentration: 1.0
Constant
 
Global Parameters (56)
 
   k_01
Value: 7.3   (Units: substance)
Constant
 
   K_01
Value: 0.1   (Units: substance)
Constant
 
   H_01
Value: 4.0   (Units: substance)
Constant
 
   k_05
Value: 0.19   (Units: substance)
 
   k_14
Value: 0.1   (Units: substance)
Constant
 
   k_06
Value: 0.226   (Units: substance)
Constant
 
   k_07
Value: 1.0   (Units: substance)
Constant
 
   k_13
Value: 0.472   (Units: substance)
Constant
 
   k_23
Value: 0.6   (Units: substance)
Constant
 
   K_02
Value: 0.475   (Units: substance)
Constant
 
   H_02
Value: 12.0   (Units: substance)
Constant
 
   k_35
Value: 1.29   (Units: substance)
Constant
 
   k_30
Value: 0.27   (Units: substance)
Constant
 
   k_31
Value: 0.135   (Units: substance)
Constant
 
   k_32
Value: 0.085   (Units: substance)
Constant
 
   k_02a01
Value: 1.2   (Units: substance)
Constant
 
   k_03
Value: 1.6   (Units: substance)
Constant
 
   k_09
Value: 2.0   (Units: substance)
Constant
 
   k_10
Value: 2.4   (Units: substance)
Constant
 
   k_11
Value: 2.5   (Units: substance)
Constant
 
   k_21
Value: 0.1   (Units: substance)
Constant
 
   k_18
Value: 0.3   (Units: substance)
Constant
 
   k_29
Value: 0.27   (Units: substance)
Constant
 
   k_19
Value: 0.29   (Units: substance)
Constant
 
   k_24
Value: 0.3   (Units: substance)
Constant
 
   k_15
Value: 0.3   (Units: substance)
Constant
 
   k_20
Value: 0.1   (Units: substance)
Constant
 
   k_17
Value: 0.1   (Units: substance)
Constant
 
   k_34
Value: 0.05   (Units: substance)
Constant
 
   k_33
Value: 0.05   (Units: substance)
Constant
 
   k_25
Value: 0.15   (Units: substance)
Constant
 
   k_22
Value: 0.3   (Units: substance)
Constant
 
   on
Value: 96.0
Constant
 
   off
Value: 120.0
Constant
 
   k_08
Value: 0.68   (Units: substance)
Constant
 
   k_12
Value: 6.2   (Units: substance)
Constant
 
   k_37
Value: 0.24   (Units: substance)
Constant
 
   k_16
Value: 0.3   (Units: substance)
Constant
 
   k_38
Value: 0.24   (Units: substance)
Constant
 
   T_light_on
Value: 1.0E7   (Units: substance)
Constant
 
   k_26  
 
   k_01a
Value: 320.0   (Units: substance)
Constant
 
   k_02a02
Value: 90.0   (Units: substance)
Constant
 
   kact_L_WCC_light
Value: 5.0   (Units: substance)
Constant
 
   k_36
Value: 6.0   (Units: substance)
Constant
 
   k_04
Value: 800.0   (Units: substance)
Constant
 
   k_09a
Value: 0.356   (Units: substance)
Constant
 
   k_03i
Value: 0.03   (Units: substance)
Constant
 
   k_03a
Value: 0.03   (Units: substance)
Constant
 
   k_02
Value: 1.19   (Units: substance)
Constant
 
   k_27
Value: 20.0   (Units: substance)
Constant
 
   k_28
Value: 1.8   (Units: substance)
Constant
 
   k_39
Value: 0.75   (Units: substance)
Constant
 
   LP
Value: 60.0   (Units: substance)
Constant
 
   LP2
Constant
 
   LP3
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000437

Curator's comment: (updated: 26 Feb 2013 14:38:54 GMT)

Figure 3 of the reference publication has been reproduced. The data were obtained by simulating the model using Copasi v4.8 (Build 35) and plots were made using Gnuplot.

spacer
spacer