Ureaplasma diversum protein interaction networks: evidence of horizontal gene
transfer and evolution of reduced genomes among the Mollicutes
Joana Kästle Silva1, Lucas Miranda Marques2,3, Jorge Timenetsky3, Sávio Torres de
Farias1
1 Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Brazil 2 Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da
Conquista, Brazil3 Department of Microbiology, Institute of Biomedical Science, University of São Paulo,
São Paulo, Brazil
Correspondence and reprints: Savio Torres de Farias – [email protected]
Authors correspondence
Joana Kastle – [email protected]
Lucas Miranda Marques – [email protected]
Jorge Timenetsky – [email protected]
Supplementary information
Table 1. U. diversum PPI network parameters and the centralty measures of the 10 random networks used for validation.
Clust. Coef. Centrality
U. diversum 0.613 0.359
Random_1 0.230 0.073
Random_2 0.229 0.077
Random_3 0.230 0.087
Random_4 0.231 0.087
Random_5 0.231 0.057
Random_6 0.229 0.060
Random_7 0.230 0.067
Random_8 0.232 0.080
Random_9 0.232 0.083
Random_10 0.230 0.073
Table 2. Urease PPI network parameters in the analysed species.
Clust.
coefficient
Network
centrality
Charact. Path
length
U. diversum 0.934 0.222 1.182
U. urealyticum 0.858 0.467 1.382
U. parvum 0.899 0.444 1.364
C. urealyticum 0.877 0.444 1.356
C. glurucolyticum 0.783 0.489 1.40
S. aureus 0.888 0.378 1.309
Table 3. Topological parameters of the PPI networks involved in purine metabolism.
Clust. Coefficient Network centrality Characteristic path
length
U. diversum 0.934 0.182 1.154
U. urealyticum 0.938 0.154 1.132
U. parvum 0.928 0.179 1.154
M. hominis 0.954 0.061 1.051
M. pneumoniae 0.921 0.242 1.205
M. genitalium 0.945 0.167 1.141
Table 4. Network parameters of the pyrimidine metabolism subnetworks in the investigated
groups.
Clust. coefficient Network
centralization
Charact. Path length
U. diversum 0.841 0.167 1.220
U. urealyticum 0.834 0.163 1.206
U. parvum 0.872 0.210 1.183
M. hominis 0.679 0.218 1.341
M. pneumoniae 0.818 0.275 1.238
M.genitalium 0.863 0.176 1.152
C. urealyticum 0.811 0.289 1.236
Figure 1 Intersection of the urease PPI network in the species evaluated for horizontal transfer
events.
Figure 4. Pyrimidine metabolism PPI networks in a) U. diversum, b) U. urealyticum and c) U. parvum.
Figure 5. 16s trees for species when were identified lateral gene transfer. (A) Urease lateral gene transfer and (B) purine and pyrimidine lateral gene transfer.