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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.


Community structure revealed by the color representation of the neighborhood matrices (NM) of two networks based on the dataset for ATP synthase subunits 4 and b at values σ = 36%—top panel—and σ = 35%—bottom panel.The discussion in the caption of Fig 2 on color codes and other features of the graphs also applies. At σ = 35%, six relevant communities are identified as Ci, i = 1–6, Only C6 is separated from all the other five communities. At σ = 36%, the large group splits into two subgroups, respectively formed by C1, C2, C3, and C4, C5. Different color codes indicate larger paths, linking nodes from C3 and C5 when σ = 35%, but which are no longer present at σ = 36%.
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pone.0134988.g008: Community structure revealed by the color representation of the neighborhood matrices (NM) of two networks based on the dataset for ATP synthase subunits 4 and b at values σ = 36%—top panel—and σ = 35%—bottom panel.The discussion in the caption of Fig 2 on color codes and other features of the graphs also applies. At σ = 35%, six relevant communities are identified as Ci, i = 1–6, Only C6 is separated from all the other five communities. At σ = 36%, the large group splits into two subgroups, respectively formed by C1, C2, C3, and C4, C5. Different color codes indicate larger paths, linking nodes from C3 and C5 when σ = 35%, but which are no longer present at σ = 36%.

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)

Community structure revealed by the color representation of the neighborhood matrices (NM) of two networks based on the dataset for ATP synthase subunits 4 and b at values σ = 36%—top panel—and σ = 35%—bottom panel.The discussion in the caption of Fig 2 on color codes and other features of the graphs also applies. At σ = 35%, six relevant communities are identified as Ci, i = 1–6, Only C6 is separated from all the other five communities. At σ = 36%, the large group splits into two subgroups, respectively formed by C1, C2, C3, and C4, C5. Different color codes indicate larger paths, linking nodes from C3 and C5 when σ = 35%, but which are no longer present at σ = 36%.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134988.g008: Community structure revealed by the color representation of the neighborhood matrices (NM) of two networks based on the dataset for ATP synthase subunits 4 and b at values σ = 36%—top panel—and σ = 35%—bottom panel.The discussion in the caption of Fig 2 on color codes and other features of the graphs also applies. At σ = 35%, six relevant communities are identified as Ci, i = 1–6, Only C6 is separated from all the other five communities. At σ = 36%, the large group splits into two subgroups, respectively formed by C1, C2, C3, and C4, C5. Different color codes indicate larger paths, linking nodes from C3 and C5 when σ = 35%, but which are no longer present at σ = 36%.
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.