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

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.

Evidence that a respiratory shield in Escherichia coli protects a low-molecular-mass FeII pool from O2-dependent oxidation

“…At a later stage in evolution, an ancestor of ␣-proteobacteria was engulfed by a proto-eukaryotic host, culminating in a symbiotic relationship in which mitochondria provided chemical energy to the host via OXPHOS (49). Mitochondria and their bacterial ancestors share similar iron-rich respiration-related proteins as well as a suite of proteins involved in ISC biosynthesis (50,51).…”

Peptidoglycan in obligate intracellular bacteria

“…These intracellular bacteria typically replicate either free in the eukaryotic cytoplasm, or within specialised vacuoles. It is hypothesised that an early mutualistic adaptation between bacteria and archaea led to the emergence of modern mitochondria and chloroplasts (Bonen et al, 1977;Kuntzel et al, 1981;Carvalho et al, 2015). The major groups of obligate intracellular bacteria are the phylogenetically distinct Chlamydiales and Rickettsiales orders, as well as Coxiella, Buchnera and Mycobacterium leprae ( Fig.…”

Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes

“…Despite the fact that the network with the biggest distance was obtained at 75% identity, the community structure was already too fragmented to answer questions about the evolution of the gene families analyzed in the phylogeny ( Figure S1A). A similar situation occurred in [18], and the problem was solved by analyzing other networks in different peaks. Here we attempted to solve this problem by analyzing the network at 51% in order to find the last network where all sequences were connected.…”

“…Network approaches have also been successfully applied to study fungi evolution based on enzymes related to the chitin synthase pathway [17]. Recently, Carvalho et al [18] have used a network-based approach to address the origin of the mitochondria, providing a new perspective on the study mitochondrial evolution.…”