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 – stfarias@yahoo.com.br

Authors correspondence

Joana Kastle – joana_kaestle@hotmail.com

Lucas Miranda Marques – lmirandamarques@gmail.com

Jorge Timenetsky – joti@usp.br

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 2. Urease subnetworks in (A) U. diversum, (B) U. urealyticum and U. parvum

Figure 3. Purine metabolism PPI networks in a) U. diversum, b) U. urealyticum and c) U. parvum.

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.