Data on dynamic study of cytoophidia in Saccharomyces cerevisiae

The data in this paper are related to the research article entitled “Filamentation of metabolic enzymes in Saccharomyces cerevisiae” Q.J. Shen et al. (2016) [1]. Cytoophidia are filamentous structures discovered in fruit flies (doi:10.1016/S1673-8527(09)60046-1) J.L. Liu (2010) [2], bacteria (doi:10.1038/ncb2087) M. Ingerson-Mahar et al. (2010) [3], yeast (doi:10.1083/jcb.201003001; doi:10.1242/bio.20149613) C. Noree et al. (2010) and J. Zhang, L. Hulme, J.L. Liu (2014) [4], [5] and human cells (doi:10.1371/journal.pone.0029690; doi:10.1016/j.jgg.2011.08.004) K. Chen et al. (2011) and W.C. Carcamo et al. (2011) ( [6], [7]. However, there is little research on the motility of the cytoophidia. Here we selected cytoophidia formed by 6 filament-forming proteins in the budding yeast S. cerevisiae, and performed living-cell imaging of cells expressing the proteins fused with GFP. The dynamic features of the six types of cytoophidia were analyzed. In the data, both raw movies and analysed results of the dynamics of cytoophidia are presented.

Dynamic feature of the above 6 kinds of cytoophidia are shown separately, which can be useful to be compared with other results.
We provide an effective method for tracking and analyzing the cytoophidia in budding yeast.

Data
In the data, Fig. 1 shows the location accuracy for the cytoophidia in fixed budding yeast, demonstrating that our tracking method is suitable for the foci and filament of cytoophidia. Fig. 2 is the summary of the dynamic analysis for 5 kinds of cytoophidia: Acc1p, Asn1p, Gcd2p, Gdb1p, and Pfk2p. Movie 1-6 are the raw videos of budding yeast expressing 6 kinds of GFP-fused proteins respectively. Movie 7-8 show the typically movements of the fast and slow Glt1p cytoophidia respectively.

Live cell imaging
S. cerevisiae strains used here were derived from the yeast GFP clone collection comprising of 4159 GFP tagged open reading frames (ORF) [8]. All strains were shaken at 32°C for 24 h before the live cell imaging. Cells at stationary stage were pipetted onto Glass Bottom Dishes (MatTek Corporation, Ashland, MA) with appropriate dilution in PBS. The cells dispersed in a single layer on the bottom. After 30 min incubating at room temperature, the cells were imaged using the 63X objective on a laser-scanning confocal microscope (Leica TCS SP5 II confocal microscope). Time-lapse videos were taken at 1.29 s intervals between each frame over 10 min of real time. All the videos were captured at room temperature. At least 3 videos for each sample were taken with random fields containing filaments.
For the immobilized cytoophidia, cells were fixed in 4% paraformaldehyde (PFA) for 10 min, and then washed by PBS.

Tracking
Tracking of the cytoophidia was performed by using the ImageJ plugin Particle Tracker [9]. The effectiveness of the software for tracking the filament-formed cytoophidia was proved. In each frame, the cytoophidia were localized first. The greatest number of clearly visible cytoophidia were need to be captured. Generally, the parameter radius was set to 5-7 pixels and the percentile was set to 0.3-0.5% in Particle Tracker software. In the linking step, the parameters of linking range and displacement were set to 2 frames and 5 pixels respectively. All the linking parameters for each kind of cytoophidia were optically checked. The trajectories were saved in txt format for further analysis.

Dynamic analysis
Only the trajectories longer than 15 frames (approximately 20 s) were selected. The MSD of each trajectory was calculated by the equation where τ is the time lag. Then the first 15 points of MSD were fitted by the power law equation The exponent α indicates the non-linear relationship of MSD with time, carrying information about the motion type of the diffusion [10]: ɑ $1 corresponds to free Brownian motion (i.e. free diffusion), αo1 sub-diffusion (i.e. diffusion within a crowded medium), α41 super-diffusion (i.e. diffusion overlaid with directed motion). Similarly, the diffusion coefficient D is determined by fitting the 3 initial points of the MSD curves with All the analyses were performed using a user-defined program in Matlab.