Models and experiments to understand cell size control

MODELS AND EXPERIMENTS TO

UNDERSTAND CELL SIZE CONTROL

Attila Csikász-Nagy

Randall Division of Cell and Molecular Biophysics

Institute for Mathematical and Molecular Biomedicine

Marti Aldea

Cell size in eukaryotes

Salamander larvae

Size control in budding yeast

V_B V_S

T₁ α

Critical size depends on growth rate 10 20 30 40 50 60 0.00 0.05 0.10 0.15 0.20 0.25 0.30 V o lu m e a t S ta rt (V s, µ m 3 )

Growth rate in G1 (α, µm3_/min) Glu Gal Raf• Eth

• • •

V_B V_S

T₁ α

Computational model matches experimental results T im e (a rb it ra ry sc a le ) ─ Pre-Start ─Post-Start 0 20 40 60 80 100 120 140 160 0 10 20 30 40 50 60 70 V o lu m e (µ m 3) Vi Vs Vb Vd’ Experimental Model 0 20 40 60 80 0 500 1000 1500 2000 2500 3000 V o lu m e (µ m 3) Time (min) ─ Pre-Start ─Post-Start Time (min) T1 10 20 30 40 50 60 70 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 V o lu m e a t S ta rt (V s, µ m 3 )

Growth rate in G1 (α, µm3/min Glu Gal Raf• Eth

Computational model explains growth rate dependent size

Growth rate in G1 (α, µm3_/min)

10 20 30 40 50 60 0 0.1 0.2 0.3 V o lu m e a t S ta rt (V s, µ m 3) Vs=f(αααα) 10 20 30 40 50 60 0 0.1 0.2 0.3

Growth rate in G1 (α, µm3_/min)

V o lu m e a t S ta rt (V s, µ m 3) Vs=k Generation # 1 1000 0 60 20 40 V s (µ m 3) T 1 ( m in ) 0 300 100 200 Vs=36.9 µm3_{(CV 17.3%)} T1=62.5 min (CV 57.6%) Vs=f(α) T1 T1’ Vs’=f(α’) Slow (α’) Fast (α) Vs=37.2 µm3_{(CV 17.1%)} Generation # 1 1000 0 60 20 40 V s (µ m 3) T 1 ( m in ) 0 300 100 200 T1=72.8 min (CV 70.4%) Slow (α’) Fast (α) T1 T1’ Vs=k Growth rate dependent critical size Fixed critical size

Size control perturbation in mutants 10 20 30 40 50 60 70 80 90 100 0.0 0.1 0.2 0.3 0.4 0.5 0.6 10 20 30 40 50 60 70 80 90 100 0.0 0.1 0.2 0.3 0.4 0.5 10 20 30 40 50 60 70 80 90 100 0.0 0.1 0.2 0.3 0.4 10 20 30 40 50 60 0.0 0.1 0.2 0.3 10 20 30 40 50 60 0.0 0.1 0.2 0.3 10 20 30 40 50 60 0.0 0.1 0.2 0.3 10 20 30 40 0.0 0.1 0.2 V s ( µ m 3) V s ( µ m 3) whi3 whi5N cln3 ydj1 cln1,2 sfp1 oCLN3 α(µm3_/min) α(µm3_/min) α(µm3_/min) α(µm3_{/min) α(µm}3_/min) V s ( µ m 3) V s ( µ m 3) V s ( µ m 3) V s ( µ m 3) V s ( µ m 3) α(µm3_{/min) α(µm}3_/min)

wild-type wild-type wild-type

wild-type

wild-type

wild-type wild-type

Hsp40, DnaJ

chaperon

Chaperons connects growth to cell size? Swi6 Swi4, Mbp1

ER

nucleus

0.4 0.6 0.8 1 1.2 1.4 1.6 0 100 200 300 400 0 0.1 0.2 0.3 0 100 200 300 400 0.4 0.6 0.8 1 1.2 1.4 1.6 0 100 200 300 400 0 0.1 0.2 0.3 0 100 200 300 400

Mass doubling time: 140 min α = 0.004

Mass doubling time: 350 min α = 0.0027 cell mass cell volume Ydj1_free Cln3_folded cell mass cell volume Ydj1_free Cln3_folded

The ‘speedometer’ model

Time (min) Time (min)

y = 128.42x + 0.6609 R² = 0.9946 0.4 0.8 1.2 1.6 0 0.002 0.004 0.006 Vs α 10 20 30 40 50 60 0.00 0.05 0.10 0.15 0.20 0.25 0.30 V o lu m e a t S ta rt (V s, µ m 3 )

Growth rate in G1 (α, µm3_/min) Glu Gal Raf• Eth

• • •

Building and analyzing a network of size regulators

S. pombe size mutants S. pombe size mutants + first neighbours

Centrality rank Merged 1 lsk6 2 ter1 3 bdf2 4 hln4 5 tea1 6 hkv3 7 erm0 8 paa1 9 cbi11 10 cid14 11 ssr3 12 skv3 13 lcf2 14 prp17 15 cdc22 16 act1 17 hsq13 18 rpb5 19 cmh6 20 rpt5 Centrality rank Size mutants 1 prp17 2 scd1 3 cbp1 4 slx8 5 spi1 6 wee1 7 bdf2 8 tea1 9 paa1 10 cid14 11 act1 12 rpb7 13 ssr3 14 cdc22 15 fib1 16 mto1 17 rpt5 18 adh1 19 cpc2 20 rpn11

ORF IDs Protein Names Attribute Systematic IDs Protein Names Attribute Protein Names TAIR iD

S. cerevisiae S. cerevisiae S. cerevisiae S. pombe S. pombe S. pombe H. sapiens A. thaliana

YCR009C RVS161 larger:

Actin cytoskeleton SPBC725.09c hob3 long BIN3 At4g27270

YDL082W RPL13A smaller:

Ribosomal subunits SPAC664.05 rpl13 germination RPL13 At2g44950

YDL136W RPL35B smaller:

Ribosomal subunits SPCC613.05c rpl35 spores RPL35 At2g09990

YHR001W QCR10 smaller:

Mitochondrial function SPBC1271.12 kes1 misshapen OSBPL10 At5g57240

YHR158C KEL1 smaller:

Morphology function SPCC1223.06 tea1 curved RABEPK At3g05420

YJL187C SWE1 smaller:

Cell cycle regulator SPCC18B5.03 wee1 small WEE2 At1g51850

YNL148C ALF1 larger:

Cell cycle regulator SPAC13D6.05 alp11 curved TBCB At3g10220

YOL004W SIN3 larger:

RNA Pol II complex SPBC12C2.10c pst1 lon SIN3A At5g10960

YPL031C PHO85 smaller:

DNG Glicerol SPCC16C4.11 pef1 misshapen CDK5 At5g39840

YPR135W POB1 larger:

Cell cycle regulator SPAPB1E7.02c mcl1 long WDHD1 At3g42660

… … … …

Translating yeast data to other organisms

Marti Aldea _{Rafael Carazo-Salas} Shaun N. Thomas

Size control in Arabidopsis

Measuring at various time points:

- Size of leaves

- Size of floral ramp

- Root length

- Root diameter

- Size of silique

- Number of seeds

- Size of seeds

Checking the expression of candidate genes in different size apple varieties to identify control on fruit size.

Acknowledgements

Thank you!

Thank you!

Thank you!

Thank you!

Aldea group

Rafael Carazo-Salas Zoltán Dúl

Shaun B. Thomas