title: Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA in Saccharomyces cerevisiae: experimental and computational evidences.
abstract: BACKGROUND
  The cAMP-dependent protein kinase regulatory network (PKA-RN) regulates metabolism, memory, learning, development, and response to stress. Previous models of this network considered the catalytic subunits (CS) as a single entity, overlooking their functional individualities. Furthermore, PKA-RN dynamics are often measured through cAMP levels in nutrient-depleted cells shortly after being fed with glucose, dismissing downstream physiological processes.
  
  
  RESULTS
  Here we show that temperature stress, along with deletion of PKA-RN genes, significantly affected HSE-dependent gene expression and the dynamics of the PKA-RN in cells growing in exponential phase. Our genetic analysis revealed complex regulatory interactions between the CS that influenced the inhibition of Hsf1/Skn7 transcription factors. Accordingly, we found new roles in growth control and stress response for Hsf1/Skn7 when PKA activity was low (cdc25Δ cells). Experimental results were used to propose an interaction scheme for the PKA-RN and to build an extension of a classic synchronous discrete modeling framework. Our computational model reproduced the experimental data and predicted complex interactions between the CS and the existence of a repressor of Hsf1/Skn7 that is activated by the CS. Additional genetic analysis identified Ssa1 and Ssa2 chaperones as such repressors. Further modeling of the new data foresaw a third repressor of Hsf1/Skn7, active only in the absence of Tpk2. By averaging the network state over all its attractors, a good quantitative agreement between computational and experimental results was obtained, as the averages reflected more accurately the population measurements.
  
  
  CONCLUSIONS
  The assumption of PKA being one molecular entity has hindered the study of a wide range of behaviors. Additionally, the dynamics of HSE-dependent gene expression cannot be simulated accurately by considering the activity of single PKA-RN components (i.e., cAMP, individual CS, Bcy1, etc.). We show that the differential roles of the CS are essential to understand the dynamics of the PKA-RN and its targets. Our systems level approach, which combined experimental results with theoretical modeling, unveils the relevance of the interaction scheme for the CS and offers quantitative predictions for several scenarios (WT vs. mutants in PKA-RN genes and growth at optimal temperature vs. heat shock).
authors.affiliation: Instituto de Biología, Universidad Nacional Autónoma de México, 04510, México, D.F., Mexico. slandero@gmail.com.
authors.forename: Sergio
authors.initials: S
authors.lastname: Pérez-Landero
authors.affiliation: Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico. motta@icf.unam.mx.
authors.forename: Santiago
authors.initials: S
authors.lastname: Sandoval-Motta
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico. cma@ibt.unam.mx.
authors.forename: Claudia
authors.initials: C
authors.lastname: Martínez-Anaya
authors.affiliation: Present Address: Department of Anesthesiology, Pharmacology & Therapeutics, The University of British Columbia, Vancouver, V6T 1Z4, BC, Canada. yrying@mail.ubc.ca.
authors.forename: Runying
authors.initials: R
authors.lastname: Yang
authors.affiliation: Present Address: Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, 62209, Cuernavaca, Mor., Mexico. jordi@uaem.mx.
authors.forename: Jorge Luis
authors.initials: JL
authors.lastname: Folch-Mallol
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico. luzma@ibt.unam.mx.
authors.forename: Luz María
authors.initials: LM
authors.lastname: Martínez
authors.affiliation: Present Address: Grupo La Florida México, Tlalnepantla, 54170, Edo. de Méx., Mexico. lventura@grupolaflorida.com.
authors.forename: Larissa
authors.initials: L
authors.lastname: Ventura
authors.affiliation: Present Address: El Colegio de la Frontera Sur, 30700, Tapachula, Chis., Mexico. kguillen@ecosur.mx.
authors.forename: Karina
authors.initials: K
authors.lastname: Guillén-Navarro
authors.affiliation: Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico. max@icf.unam.mx.
authors.forename: Maximino
authors.initials: M
authors.lastname: Aldana-González
authors.affiliation: Instituto de Biología, Universidad Nacional Autónoma de México, 04510, México, D.F., Mexico. jorge.nieto@ib.unam.mx.
authors.forename: Jorge
authors.initials: J
authors.lastname: Nieto-Sotelo
mesh_terms: D055162:Biocatalysis; D054751:Cyclic AMP-Dependent Protein Kinase Catalytic Subunits / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D017353:Gene Deletion; D015966:Gene Expression Regulation, Fungal; D006360:Heat-Shock Proteins / Q000378:metabolism*; D018869:Heat-Shock Response; D008954:Models, Biological; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism* / Q000502:physiology; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; C067168:HSF1 protein, S cerevisiae; D006360:Heat-Shock Proteins; D012333:RNA, Messenger; C083962:SKN7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D054751:Cyclic AMP-Dependent Protein Kinase Catalytic Subunits