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What are the Evolutionary Origins of Mitochondria? A Complex Network Approach.

Carvalho DS, Andrade RF, Pinho ST, Góes-Neto A, Lobão TC, Bomfim GC, El-Hani CN - PLoS ONE (2015)

Bottom Line: The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c).In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor.Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.

View Article: PubMed Central - PubMed

Affiliation: General Biology Department, Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil.

ABSTRACT
Mitochondria originated endosymbiotically from an Alphaproteobacteria-like ancestor. However, it is still uncertain which extant group of Alphaproteobacteria is phylogenetically closer to the mitochondrial ancestor. The proposed groups comprise the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. In this study, we apply a new complex network approach to investigate the evolutionary origins of mitochondria, analyzing protein sequences modules in a critical network obtained through a critical similarity threshold between the studied sequences. The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c). In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor. Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.

No MeSH data available.


Dendrogram produced by the successive elimination of links with largest value of betweenness for ATP synthase subunits 4 and b at σ = 35%.The branching event separating the two groups occurs after the elimination of the two links that can be identified in Fig 10. The dynamical process of connection elimination clearly indicates three further important branching events: the first separates C3 from the group C1+C2, the second separates C1 from C2, and the third separates C4 from C5.
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pone.0134988.g011: Dendrogram produced by the successive elimination of links with largest value of betweenness for ATP synthase subunits 4 and b at σ = 35%.The branching event separating the two groups occurs after the elimination of the two links that can be identified in Fig 10. The dynamical process of connection elimination clearly indicates three further important branching events: the first separates C3 from the group C1+C2, the second separates C1 from C2, and the third separates C4 from C5.

Mentions: In a similar way to the discussion of the results for ATP synthase subunits 9 and c, this discussion is supported by a sequence of graphs in Figs 7–11. The dataset for the subunits 4 and b includes 122 protein sequences: 27% (n = 33) mitochondrial, 73% (n = 89) alphaproteobacterial. The critical network occurs at σ = σmax = 36% (Fig 7). The network at this value displays six communities, which are divided into two larger clusters and one additional disconnected community (Fig 8a). In the first cluster there is one community containing mitochondrial sequences, while the remaining mitochondrial sequences are found in the second cluster. In the first cluster, we find the following communities: C1—Rhodobacterales, Rhizobiales and clusters SAR11 and SAR116; C2 –mitochondrial sequences from plants; and C3—Rhodobacterales, Rhodospirillales, Sphingomonadales, and Caulobacterales. In the second cluster, we find two further communities: C4—mitochondrial sequences from fungi; C5—mitochondrial sequences from metazoans. Finally, C6 is an isolated community containing sequences from Rickettsia.


What are the Evolutionary Origins of Mitochondria? A Complex Network Approach.

Carvalho DS, Andrade RF, Pinho ST, Góes-Neto A, Lobão TC, Bomfim GC, El-Hani CN - PLoS ONE (2015)

Dendrogram produced by the successive elimination of links with largest value of betweenness for ATP synthase subunits 4 and b at σ = 35%.The branching event separating the two groups occurs after the elimination of the two links that can be identified in Fig 10. The dynamical process of connection elimination clearly indicates three further important branching events: the first separates C3 from the group C1+C2, the second separates C1 from C2, and the third separates C4 from C5.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4557972&req=5

pone.0134988.g011: Dendrogram produced by the successive elimination of links with largest value of betweenness for ATP synthase subunits 4 and b at σ = 35%.The branching event separating the two groups occurs after the elimination of the two links that can be identified in Fig 10. The dynamical process of connection elimination clearly indicates three further important branching events: the first separates C3 from the group C1+C2, the second separates C1 from C2, and the third separates C4 from C5.
Mentions: In a similar way to the discussion of the results for ATP synthase subunits 9 and c, this discussion is supported by a sequence of graphs in Figs 7–11. The dataset for the subunits 4 and b includes 122 protein sequences: 27% (n = 33) mitochondrial, 73% (n = 89) alphaproteobacterial. The critical network occurs at σ = σmax = 36% (Fig 7). The network at this value displays six communities, which are divided into two larger clusters and one additional disconnected community (Fig 8a). In the first cluster there is one community containing mitochondrial sequences, while the remaining mitochondrial sequences are found in the second cluster. In the first cluster, we find the following communities: C1—Rhodobacterales, Rhizobiales and clusters SAR11 and SAR116; C2 –mitochondrial sequences from plants; and C3—Rhodobacterales, Rhodospirillales, Sphingomonadales, and Caulobacterales. In the second cluster, we find two further communities: C4—mitochondrial sequences from fungi; C5—mitochondrial sequences from metazoans. Finally, C6 is an isolated community containing sequences from Rickettsia.

Bottom Line: The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c).In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor.Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.

View Article: PubMed Central - PubMed

Affiliation: General Biology Department, Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil.

ABSTRACT
Mitochondria originated endosymbiotically from an Alphaproteobacteria-like ancestor. However, it is still uncertain which extant group of Alphaproteobacteria is phylogenetically closer to the mitochondrial ancestor. The proposed groups comprise the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. In this study, we apply a new complex network approach to investigate the evolutionary origins of mitochondria, analyzing protein sequences modules in a critical network obtained through a critical similarity threshold between the studied sequences. The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c). In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor. Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.

No MeSH data available.