The microtubule skeleton and the evolution of neuronal complexity in vertebrates

Nataliya Trushina, Armen Mulkidjanian and and Roland Brandt

Supplementary material

Table S1: Tubulin genes of well-annotated organisms including pseudogenes and tubulin-like genes.

Rattus Rattus Mus musculus Homo sapiens Mus musculus Homo sapiens norvegicus norvegicus alpha-tubulins beta-tubulins TUBA1A TUBA1A TUBA1A TUBB1 TUBB1 TUBB TUBA1B TUBA1B TUBA1B TUBB2A TUBB2A TUBB1 TUBA1C TUBA1C TUBA1C TUBB2A-PS1 TUBB2B TUBB1P1 TUBA3A TUBA3A TUBA3C TUBB2A-PS2 TUBB3 TUBB1P2 TUBA3B TUBA3B TUBA3D TUBB2B TUBB4A TUBB2A TUBA4A TUBA4A TUBA3E TUBB3 TUBB4B TUBB2B TUBA8 TUBA8 TUBA3FP TUBB3-PS1 TUBB5 TUBB2BP1 TUBAL3 TUBAL3 TUBA3GP TUBB4A TUBB6 TUBB3 TUBA4A TUBB4B TUBB3P1 TUBA4B TUBB4B-PS1 TUBB3P2 TUBA8 TUBB4B-PS2 TUBB4A TUBAL3 TUBB5 TUBB4AP1 TUBAP TUBB6 TUBB4B TUBAP2 TUBB4BP1 TUBAP3 TUBB4BP2 TUBAP4 TUBB4BP3 TUBB4BP4 TUBB4BP5 TUBB4BP6 TUBB4BP7 TUBB6 TUBB6P1 TUBB7P TUBB8 TUBB8P1 TUBB8P10 TUBB8P11 TUBB8P12 TUBB8P2 TUBB8P3 TUBB8P4 TUBB8P5 TUBB8P6 TUBB8P7

Table S2: IDs of protein sequences used for multiple alignments. Organism MAPT MAP2 MAP6 STMN1 SNCA

Homo sapiens A0A024RA17 P11137 Q96JE9 P16949 P37840

Macaca mulatta P57786 XP_014966342 XP_014970708 A0A1D5RIA2 P61143

Rattus P19332 XP_008765428 Q63560 P13668 P37377 norvegicus

Mus musculus P10637 P20357 Q7TSJ2 P54227 O55042

Gallus gallus A0A1D6UPR2 XP_015144832 O73737 P31395 Q9I9H1

Taeniopygia H0YUJ8 ACH45686 Q4JHT6 guttata

Pelodiscus K7FNJ0 XP_006127432 K7FTW8 K7FQZ9 K7FW98 sinensis

Anolis G1KTS4 G1KKT3 H9GIU4 H9GPR1 R4GAF5 carolinensis

Xenopus Q0P4W8 XP_012826494 B0S4Q5 NP_001007972 A4IH15 tropicalis

Latimeria H3B3D6 XP_014349527 H3BB05 XP_006001589 chalumnae

Oryzias latipes H2MMP5 H2MB24 - ENSORLP00020013247 A0A090D865 map6a

H2LLC9 - map6b

Danio rerio E7FH04 - E7F624 - map6a Q1RLQ1 - stmn1b mapta

X1WE77 - E7FFM0 - Q568Q7 - stmn1b maptb map6b

Petromyzon S4RCW8 marinus

Eptatretus ENSEBUP00000021068 burgeri

Figure S1: Mean numbers of orthologs for each group of selected human microtubule skeleton components with divergence times between Mammals and other groups of vertebrates shown in Figure 2. A. The mean numbers of orthologs of genes for groups predicted with high confidence for vertebrate organisms from Ensembl genome browser are presented. Divergence times between Mammals and other groups of vertebrates are the same as presented in Figure 2C. Lines represent a linear fit to the data. The respective R2 values are shown in the graphs. Note that the mean numbers of orthologs tend to increase from lower to higher vertebrates for tubulin-sequestering proteins, MT-binding proteins and structure proteins.

Figure S2: Predicted disorder of MAP2 throughout evolution of vertebrates. A. Disorder prediction plot of human MAP2 (1827 aa) is shown on the left. For the prediction, the program IUPred2A with prediction type “long disorder” was used. A disorder prediction map of MAP2 for selected organisms is shown on the right. The different regions of MAP2 are indicated below. B. Quantitative evaluation of disorder of different regions of MAP2 (as indicated in A) for selected organisms is shown. The respective R2 values are shown in the graphs. The species are color coded from yellow to orange as shown in Figure 2. Note that none of the regions exhibits a clear trend of disorder change throughout evolution.

Figure S3: Predicted disorder of -synuclein throughout evolution of vertebrates. A. Disorder prediction plot of human -synuclein (140 aa) (coded by the SNCA gene) is shown on the left. For the prediction, the program IUPred2A with prediction type “long disorder” was used. A disorder prediction map of -synuclein for selected organisms is shown on the right. B. Quantitative evaluation of disorder of -synuclein for selected organisms is shown. The respective R2 value is shown in the graph. The species are color coded from yellow to orange as shown in Figure 2. Note that the sequence does not exhibit a trend for disorder increase throughout evolution but rather indicates a decrease in disorder.

Figure S4: Predicted disorder of tau, MAP6, stathmin 1, MAP2, and -synuclein with divergence times between Mammals and other groups of vertebrates shown in Figure 2. Quantitative evaluation of disorder of regions of tau and MAP6 (as indicated in Figure 4), stathmin 1 (as indicated in Figure 5), MAP2 (as indicated in Figure S2) and -synuclein (as indicated in Figure S3). Lines represent a linear fit to the data. The respective R2 values are shown in the graphs. Note that the predicted disorder in tau’s N-terminal part and in MAP6 still tends to increase after organism grouping by higher taxons.