Yeast Cell Cycle Logic Model

This is a multi-value logic model of the yeast cell cycle network. The model is built using the GINsim software, to open this file, simply open GINsim and load the file. Black circles are phenomenological nodes, white circles are genomic regulatory elements, green circles are checkpoint nodes, red circles are lncRNA nodes, white rectangles are protein or protein complex nodes, and blue rectangles are the S_proteins and G2_proteins nodes responsible for activating nodes from S and G2 phases, respectively. The lncRNA-protein interactions were predicted independently for the SEY6210 and BY4742 strains.   </p

Network of coevolutions in the Sox9 proteins.

(A) The coevolutions are shown using D. rerio Sox9a, M. albus Sox9b and H. sapiens Sox9 as the reference sequences. The graph nodes indicate the amino acid with its corresponding position number in the reference sequence. The edges (lines) connect the pair of coevolving amino acids inferred from the CAPS program. Each amino acid is colored based on its localization in the corresponding Sox9 domain: DIM (purple), HMG box (light blue), K2 (orange), PQA (dark cyan) and PQS (red). The range (begin-end) of each domain is also depicted in the scheme. The sign for truncated regions (//) is used for fitting the figure dimensions. (B) The Sox9 multiple protein sequence alignment is indicated. The color of each domain follows the description aforementioned. Upper green bars evidence high conserved sites.</p

Network model.

Black circles are phenomenological nodes, white circles are genomic regulatory elements, green circles are checkpoint nodes, red circles are lncRNA nodes, white rectangles are protein or protein complex nodes, and blue rectangles are the S_proteins and G2_proteins nodes responsible for activating nodes from S and G2 phases, respectively. The lncRNA-protein interactions were predicted independently for the SEY6210 and BY4742 strains. The computational GINsim model is available at https://figshare.com/articles/software/Yeast_Cell_Cycle_Logic_Model/14503035.</p

Oligonucleotides used in this study.

Bold nucleotides indicate the genomic target sequence. “Δ1”: oligonucleotides used to obtain the SEY6210 lnc9136Δ1 mutant; “Δ2”: oligonucleotides used to obtain the SEY6210 lnc9136Δ2; *: phosphorylated primer end. Details of target-homology repairs and Cas9 cleavage loci are shown in S4 Fig.</p

Node types, range of values, and their biological meaning.

’a’ indicates that this node type also has some nodes that reach only three values. Thus, ’1’ and ’2’ indicate normal and high levels (or activity), respectively. ’b’, the checkpoint node Mating is a Boolean node. Then, ’0’ or ’1’ indicate inactivation or activation of the Mating node, respectively. ’c’ refers to the lncRNAs or selected genes for the experimental model simulations (details provided in the ‘Simulating the effects of ethanol stress-responsive lncRNAs and ethanol on the cell cycle’ in the Materials and Methods section).</p

Sequences of lncRNAs studied here in FASTA format.

Name; strain: genomic coordinates start-end; orientation. (PDF)</p

Simulating the SEY6210 cell cycle under ethanol stress with <i>in silico</i> overexpression of lnc9136 (the third experimental model simulation in Fig 1).

The box color indicates the node levels in each simulation state. The simulation presented a cyclic attractor related to a functional cell cycle, which includes all states depicted on the X-axis. Thus, the functional cell cycle is evidenced when the simulation outcomes cyclic attractors presenting the activation of all phenomenological nodes, further inhibited when the MITOSIS_EXIT node reaches ’2’, and restarting the cell cycle (MASS returning to ’0’), as observed here (see details in the ’Model cycling rationale’ in the Materials and Methods). The upper picture in the box on the left is the LT cell cycle arrest mechanism reported in Fig 4, while the bottom picture reports our suggested M arrest skip mechanism that may occur in cells under ethanol stress. The red ’X’ depicts suppression of a given regulation. The red ’X’ on the edge head ended at the Swe1 node, indicates that this node was blocked neither by Gin4 nor Hsl1 when lnc9136 was overexpressed under ethanol (EtOH) stress.</p

Fig 4 -

Cell cycle predictions of the LT (A) and HT (B) phenotypes under ethanol stress (the first experimental model simulation in Fig 1). The box color indicates the node values in each simulation state. Cell cycle arrest is defined when the simulation usually displays single-state attractors without the MASS node returning to ’0’, as observed here; otherwise, the simulation of the model returned a functional cell cycle. The M phase arrest in the LT (A) is evidenced here by MASS > ’0’ and MITOSIS_EXIT = ’1’. G1 arrest in the HT (B) is evidenced here by the MASS > ’0’, and DNA_Replication = ’0’. Details concerning arrests are reported in the ’Model cycling rationale’ and Eq 1 in the Materials and Methods section. Since the model simulations in A and B represented cell cycle arrests, the attractors are the last states depicted on the X-axis.</p

Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9

<div><p>Sox9 plays an important role in a large variety of developmental pathways in vertebrates. It is composed of three domains: high-mobility group box (HMG box), dimerization (DIM) and transactivation (TAD). One of the main processes for regulation and variability of the pathways involving Sox9 is the self-gene expression regulation of Sox9. However, the subsequent roles of the Sox9 domains can also generate regulatory modulations. Studies have shown that TADs can bind to different types of proteins and its function seems to be influenced by DIM. Therefore, we hypothesized that both domains are directly associated and can be responsible for the functional variability of Sox9. We applied a method based on a broad phylogenetic context, using sequences of the HMG box domain, to ensure the homology of all the Sox9 copies used herein. The data obtained included 4,921 sequences relative to 657 metazoan species. Based on coevolutionary and selective pressure analyses of the Sox9 sequences, we observed coevolutions involving DIM and TADs. These data, along with the experimental data from literature, indicate a functional relationship between these domains. Moreover, DIM and TADs may be responsible for the functional plasticity of Sox9 because they are more tolerant for molecular changes (higher Ka/Ks ratio than the HMG box domain). This tolerance could allow a differential regulation of target genes or promote novel targets during transcriptional activation. In conclusion, we suggest that DIM and TADs functional association may regulate differentially the target genes or even promote novel targets during transcription activation mediated by Sox9 paralogs, contributing to the subfunctionalization of Sox9a and Sox9b in teleosts.</p></div

State transition graph of the yeast cell cycle without perturbation.

The box color indicates the node values in each state. The ’X’ axis contains all the states of the attractor. The functional cell cycle is observed when the simulation results in cyclic attractors presenting the activation of all phenomenological nodes, further inhibited when the MITOSIS_EXIT node reaches ’2’ and restarting the cell cycle (MASS returning to ’0’), as observed here. The boxes on the left side show the key events along the systems evolution. The numbers on the left side of phenomenological nodes represent the order of node activation to emulate a functional cell cycle. (PDF)</p