What do metabolism and mitochondria have in common

So, comparative genomic analysis has allowed a reconstruction of two possible reductive pathways in the bioenergetic capacity of bacteria evolving into mitochondria Fig. How can we establish which of these pathways is most likely, and thus identify extant models for proto-mitochondria? Probabilistic approaches based upon the frequency of gene loss from each subset would not produce conclusive evidence, because of the biased phylogenetic distribution of available bacterial genomes.

We have then carried out the classical phylogenomic approach of computing the overall relationships of the organisms in the model of Fig.

Although the obtained trees could be globally consistent with the sequence of either pathway A or B, they did not offer discriminatory evidence in favour of one or the other, while consistently placing Midichloria and other Rickettsiales close to the mitochondrial clade. This tree topology has been reported before [1] , [4] , [5] , [21] but is inconsistent with our new model of Fig.

We next followed the alternative approach of exploiting the molecular diversity of key bioenergetic proteins, including their multiple duplication [34].

To enhance the discriminatory power of this approach, we have chosen proteins of energy metabolism that have a clear bacterial origin, but are encoded or located in different compartments of eukaryotic cells cf. The hypothesis underlying our approach is that such diverse proteins, as well as their genetic clusters, would present transition forms between bacteria and mitochondria predominantly in those organisms that are close to the proto-mitochondrial lineage.

The first bioenergetic system we considered is N metabolism, the presence or absence of which sharply determines the pathways leading to the mitochondria of fungi and metazoans Fig. Structurally, NirBD is characterised by the fusion of the small protein NirD - belonging to the Rieske superfamily of Fe-S proteins coordinated by histidines and cysteines [37] - at the C-terminus of the NirB protein, which catalyses the reduction of nitrite and is structurally related to sulfite reductase SiR [38].

Interstingly, the distribution of NirB is restricted to a relatively narrow group of facultatively anaerobic bacteria [38] , [39] , but that of NirBD is much narrower Table 1. The gene clusters are related to the Nas operon of Klebsiella Fig. A — The diagram shows the gene clusters of assimilatory, NAD P H-dependent nitrate reduction in bacteria and eukaryotes.

The various elements of Nas operon of Klebsiella [36] and the NiiA-NiaD operon in fungi [35] are colour coded as indicated in the quandrant on the top right. B — Possible molecular evolution of fungal NiaD nitrate reductase. Each domain is identified by a specific symbol - see the text for details. C — Representative distance tree of various proteins containing the bacterial FNR-like conserved domain. The tree was obtained with Neighbour Joining maximal distance 0.

This reductase subunit of methane monooxygenase contains a FNR-like domain similar to that of assimilatory nitrate reductases [43] lying in a sister group as indicated. Among the bacteria associated with pathway A and B in Fig. Roseobacter litoralis and Magnetospirillum have NirB w ithin an operon similar to that of Klebsiella Fig.

This situation may well arise from secondary loss of metabolic traits in ecologically specialised organisms such as dimorphic Maricaulis and predatory Micavibrio. A typical Molybdenum cofactor-binding domain Moco occupies the N-terminus and includes a terminal part binding another molibdopterin cofactor as in NapA periplasmic and NasA cytoplasmic reductases [36] — [40].

This is followed by an intermediate domain homologous to the small redox protein flavodoxin Fig. The C-terminus then contains a flavoprotein reacting with the electron donor NAD P H which, in combination with flavodoxin, forms a domain closely related to sulfite reductase CysJ of E. The CysJ- related domain belongs to the superfamily of Ferredoxin Reductase-like domains, cd FNR-like [41] , which includes also the C-terminal domain of fungal nitrate reductase, NiaD [35] , [40].

In particular, flavodoxin reductases of the genus Methylobacterium and the reductase subunits of soluble methane monoxygenase [42] , [43] MMO, present also in close relatives of Beijerinckia such as Methylocella were consistently found in sister clades to NiaD and related proteins of fungi, heterokonts and Acanthamoeba Fig.

Notably, the gene of this protein is located at the beginning of Beijerinckia nitrate assimilation operon Fig. Its Nitric Oxide dioxygenase activity is also similar to that of the hybrid nitrate reductase of microalgae from the heterokont group, e. Asaia , represent the likely precursors of eukaryotic, NiaD -related nitrate reductase Table 1 and Fig.

The parallel evolution of mitochondrial sulfite oxidase, which shares the same cytochrome b 5 and Moco domains with eukaryotic assimilatory nitrate reductases Fig. To test alternative evolutionary pathways for mitochondria Fig. In eukaryotes, this enzyme complex is embedded in the inner mitochondrial membrane, combining catalytic subunits of bacterial origin with various nuclear-encoded subunits of unknown function.

Although all aa 3 -type oxidases are of type A according to the classification of heme-copper oxygen reductases [26] , the complexity of their gene clusters has not been considered before. Here, we have analysed in depth this complexity for it provides valuable phylogenetic information.

Various aspects of our analysis are presented below in the following order: 1, diversity of COX operons; 2, evolution of COX operons; 3, possible COX operons of proto-mitochondria; 4, evolution of the molecular architecture of COX 3; 5, phylogenetic distribution of COX operons. We have initially undertaken a systematic analysis of the genomic diversity of aa 3 -type oxidases. The scrutiny of all the gene clusters containing proteobacterial COX subunits [46] — [51] suggests that they fall into three distinctive types of COX operons, which we called type a, b and a—b transition Fig.

These subtypes form coherent clades in the phylogenetic trees of their COX 1 subunit Fig. Despite the variation in gene sequence, all COX operons appear to derive from the core structure of the ctaA-G operon of Bacillus subtilis [46] — [51] Fig.

A — Graphical representation of aa 3 oxidase gene clusters. DUF; question mark within hexagon, completely unknown protein. Distance between genes is arbitrary. The synthenic diads of protist mitochondria [48] are shown below the blue line. Each of the recognised subfamilies of COX 3 [41] is represented by a different colour, as indicated in the middle of the illustration. B - Representative distance tree of COX 1 proteins.

The group containing bacterial and mitochondrial proteins mito. Protein length and type of COX operon are annotated on the right of the tree. C — Simplified pattern of typical phylogenetic trees of COX 1 proteins. The tree is modelled to match distance trees of nitrate reductase Fig. Branch length is arbitrary. S2 in File S1. However, the diverse forms of short hypothetical proteins that intermix with COX subunits Fig.

Therefore, we have developed a method that quantifies the sequence similarity with the COX IV proteins from Rhodobacter [53] and Thermus [47] , [54] , for which the 3D structure is available see Fig. S2 in File S1 and its legend for details. Strong sequence similarity with these COX 4 proteins was found in the C-terminal extension of bacterial COX 1 proteins that are to aa long, as well as in mitochondrial COX 1 of the pathogenic fungus, Zymoseptoria tritici [55] Fig. S2A in File S1.

Morever, the C-terminal part of the mtDNA-encoded COX 1 of ciliates, an ancient and diverse phylum of unicellular eukaryotes [56] , shows some sequence similarity encompassing both transmembrane helices of COX 4 proteins Fig. S2A and B in File S1.

Although this similarity is clearly weaker than that observed with bacterial COX 1 proteins, it lies in a conserved region among ciliates Fig. The identification of COX 4-like proteins has been combined with phylogenetic analysis to deduce the possible evolution of COX operons. These proteins are characteristic of caa 3 oxidases [46] , [47] , as well as of COX operon type a, which can therefore be considered the ancestral form of proteobacterial gene clusters for aa 3 -type oxidases Fig.

The differentiation into other types of COX operons can be evaluated also from the phylogenetic trees of the catalytic subunit COX 1, the analysis of which has offered new evidence for discriminating the evolutionary pathways in Fig. Mitochondrial COX 1 proteins cluster in a monophyletic clade that lies in sister position of closely packed bacterial sub-branches, especially that containing Rhodospirillales Fig. This overall tree topology is consistently found with all methods, whereas the branching order within the group containing the mitochondrial clade may vary, depending upon the method and taxa used to construct the phylogenetic trees Fig.

Nevertheless, it is noteworthy that all the proteins belonging to COX operon type b lie in the same group containing the mitochondrial clade, as exemplified in Fig. Hence, bacteria having only COX operon type b cannot be the ancestors of mitochondria. We then needed additional information to identify which of the organisms containing multiple COX operons may be close to proto-mitochondria.

To this end, we next moved to the analysis of COX proteins of unicellular eukaryotes. Are these cues pointing to the original COX operon s of proto-mitochondria? To answer this question, we searched the available mtDNA genomes of unicellular eukaryotes. The COX 1 protein of another hyphotrich, Monoeuplotes minuta [58] , appears to contain a split version of COX 3 having its initial two transmembrane helices separated from the subsequent 5-transmembrane helices domain by the major part of COX 1 Fig.

The mtDNA of ciliates often contains split genes [56] , [58] , but in this case an ancestral splitting of COX 3 must have been subsequently intermixed with the COX 1 gene. The alternative possibility would be that COX 3 splitting may reflect a fusion between precursors of mitochondrial COX 3, since in Monoeuplotes it occurs within the region joining the two transmembrane domains which form the V-shaped structure of the protein [53] , [59] - [61].

Light grey areas indicate transmembrane helices TM. B — Graphical representation of COX fused proteins. The hydrophobic peaks in the hydropathy profile of the proteins, which was obtained using the program WHAT [81] with a fixed scanning window of 19 residues, is represented by the sharp triangles, that are commensurated to the peak height maximum in the hydrophobicity profile and width of the predicted TM [81] , which closely correspond to those observed in 3D-structures [47] , [54] , [61].

The gene sequence closely resembles the core structure of a COX operon of type a - in the opposite order of transcription cf. In view of the consensus that a single event of symbiosis originated all mitochondria [1] — [10] and considering the presence of COX 11 COX 3 syntheny in Jakobide mitochondria [48] , a feature characteristic of COX operon type b Figs. Differential loss of either operon might further explain some differences in the mtDNA-coded proteins of ciliates and other unicellular eukaryotes, as well as the different types of accessory subunits of their bioenergetic complexes [1].

In the 3D structures available for cytochrome c oxidases, the initial two transmembrane helices of the 7- helices COX 3 protein that is present in mitochondria and bacterial COX operon type b Fig.

The tight binding of two specific forms of these PL to mitochondrial COX 3 appears to modulate the entry of oxygen into the binuclear catalytic centre of the enzyme [60]. PL-binding residues are present also in other parts of the COX 3 protein that are common to all its forms and tend to be conserved [59] — [62]. A — Heatmap for the strength of phospholipid binding by COX 3 proteins. The table summarises the molecular features of PL-binding sites residues in aligned COX 3 proteins Table S4 in File S1 ; it is colour mapped according to the number of conserved sites to represent the increasing PL-binding strength along bacterial and mitochondrial protein sequences, as indicated by the legend on the right of the table.

PL-binding is considered weak when less than 3 sites are conserved for each PL, the nomenclature of which is taken from Ref. PE, phosphatidyl-ethanolamine; PG, phosphatidyl-glycerol. The list includes conserved amino acids corresponding to E90 in beef COX 3, which lies near bound PL modulating oxygen entry into the catalytic site of the oxidase [60]. B - Representative distance tree of COX 3 proteins. The tree was obtained as described in the legend of Fig.

The group containing bacterial proteins from COX operon type b and their mitochondrial homologues is enclosed in a blue square as in Fig. Quantitative evaluation of the PL-binding strength further refines the evolutionary relationship among COX 3 proteins. To acquire further information for differentiating the pathways of mitochondrial evolution in Fig. This implies that Roseobacter and Micavibrio cannot be related to the ancestors of mitochondria, as for Pelagibacter and similar marine organisms.

Conversely, COX operon type a-I has the broadest phylogenetic distribution among all types of COX operon, encompassing taxonomic groups beyond the phylum of proteobacteria such as Planctomycetes [50]. Indeed, the Nrf -like gene cluster that is associated with this COX operon was originally discovered in ancient eubacteria including Planctomycetes [63]. In cells, mitochondria create an interconnected reticulum. Disturbances in mitochondrial metabolism are known to play a role not only in rare genetics disorders, but have also been implicated in many common diseases of aging.

Conventional studies of mitochondrial metabolism are based on the isolation of intact organelles. Today, we classify prokaryotes and eukaryotes based on differences in their cellular contents Figure 5. Figure 5: Typical prokaryotic left and eukaryotic right cells In prokaryotes, the DNA chromosome is in contact with the cellular cytoplasm and is not in a housed membrane-bound nucleus.

In eukaryotes, however, the DNA takes the form of compact chromosomes separated from the rest of the cell by a nuclear membrane also called a nuclear envelope. Eukaryotic cells also contain a variety of structures and organelles not present in prokaryotic cells.

Throughout the course of evolution, organelles such as mitochondria and chloroplasts a form of plastid may have arisen from engulfed prokaryotes. A paradigm gets shifty. Nature , All rights reserved. Mitochondria — often called the powerhouses of the cell — enable eukaryotes to make more efficient use of food sources than their prokaryotic counterparts. That's because these organelles greatly expand the amount of membrane used for energy-generating electron transport chains.

In addition, mitochondria use a process called oxidative metabolism to convert food into energy, and oxidative metabolism yields more energy per food molecule than non-oxygen-using, or anaerobic , methods. Energywise, cells with mitochondria can therefore afford to be bigger than cells without mitochondria.

Within eukaryotic cells, mitochondria function somewhat like batteries, because they convert energy from one form to another: food nutrients to ATP. Accordingly, cells with high metabolic needs can meet their higher energy demands by increasing the number of mitochondria they contain. For example, muscle cells in people who exercise regularly possess more mitochondria than muscle cells in sedentary people. Prokaryotes, on the other hand, don't have mitochondria for energy production, so they must rely on their immediate environment to obtain usable energy.

Prokaryotes generally use electron transport chains in their plasma membranes to provide much of their energy. The actual energy donors and acceptors for these electron transport chains are quite variable, reflecting the diverse range of habitats where prokaryotes live.

In aerobic prokaryotes, electrons are transferred to oxygen, much as in the mitochondria. The challenges associated with energy generation limit the size of prokaryotes. As these cells grow larger in volume, their energy needs increase proportionally. However, as they increase in size, their surface area — and thus their ability to both take in nutrients and transport electrons — does not increase to the same degree as their volume.

As a result, prokaryotic cells tend to be small so that they can effectively manage the balancing act between energy supply and demand Figure 6. Figure 6: The relationship between the radius, surface area, and volume of a cell Note that as the radius of a cell increases from 1x to 3x left , the surface area increases from 1x to 9x, and the volume increases from 1x to 27x. This page appears in the following eBook.

Aa Aa Aa. Eukaryotic Cells. Figure 1: A mitochondrion. Figure 2: A chloroplast. What Defines an Organelle? Why Is the Nucleus So Important? Why Are Mitochondria and Chloroplasts Special? In her lab at Baylor College of Medicine, Dr. Wang works with C. In this study, Wang and Lin compared two groups of worms. One group received bacteria that had been grown in a nutritionally rich environment. The other group of worms received the same type of bacteria, but it had grown in nutritionally poor conditions.

Both groups of worms received the same amount and type of nutrients, the only difference was the type of environment in which the bacteria had grown before they were administered to the worms.

Interestingly, the worms carrying bacteria that came from a nutritionally poor environment had in their bodies twice the amount of fat present in the worms living with the bacteria coming from the nutritionally rich environment.