Origins and Evolution of Pathways of Anaerobic Metabolism in the Animal Kingdom

Energetic characteristics and functional roles define two maintypes of anaerobicpathways in the animal kingdom: high efficiency/lowrates of energy production pathways geared to anoxia survival(aspartate-succinate and glucose-succinate pathways), and lowefficiency?/high rates of energy production pathways gearedto maintaining or increasing metabolic activity (multiple opinepathways and lactate pathway). The aspartate-succinate and opinepathways require both amino acids and carbohydrate as substrates,whereas the glucose-succinate and lactate pathways are dependenton carbohydrate only. Phylogenetic, functional and chemicalconsiderations indicate an evolutionary progression from aminoacid-linked to carbohydrate-based anaerobic pathways. The tauropineand strombine pathwaysare possibly the most ancient opine pathwaysso far discovered, and the octopine pathway the most advanced.The roles of the aspartate-succinate and opine pathways mayoriginally have been not too dissimilar. A hierarchy of "ratesof energy production pathways" of phosphagen > lactate >octopine > other opine pathways is proposed, which definesmuch of their phylogenetic selection and how they are used.The different properties of phosphocreatine compared to otherphosphagens is indicated to have been a key factor in the emergenceof vertebrates     

Origin and Evolution of Plastids and Photosynthesis in Eukaryotes

Recent progress in understanding the origins of plastids from endosymbiotic cyanobacteria is reviewed. Establishing when during geological time the endosymbiosis occurred remains elusive, but progress has been made in defining the cyanobacterial lineage most closely related to plastids, and some mechanistic insight into the possible existence of cryptic endosymbioses perhaps involving Chlamydia-like infections of the host have also been presented. The phylogenetic affinities of the host remain obscure. The existence of a second lineage of primary plastids in euglyphid amoebae has now been confirmed, but the quasipermanent acquisition of plastids by animals has been shown to be more ephemeral than initially suspected. A new understanding of how plastids have been integrated into their hosts by transfer of photosynthate, by endosymbiotic gene transfer and repatriation of gene products back to the endosymbiont, and by regulation of endosymbiont division is presented in context.Photosynthesis is biology’s equivalent of alchemy converting a common substance (CO₂) into a precious one (reduced carbon compounds rich in chemical energy). Freely available light energy is initially converted to precious chemical energy in the form of ATP. This energy, and the reducing power generated by splitting water molecules to release electrons, is used to fix carbon from atmospheric CO₂ and generate reduced carbon compounds that underpin the biosphere. It is estimated that plants and algae convert 258 billion tons of carbon dioxide into biomass by photosynthesis annually (Geider et al. 2001). Microfossils in ancient stromatolites indicate that cyanobacterium-like organisms had invented this process—or an early, perhaps nonoxygenic, version of it—at least 3.5 byo (billions of years old) (Lowe 1980; Walter et al. 1980; Schopf 1993). These photosynthetic prokaryotes substantially predate eukaryotes, which emerged much later (Rasmussen et al. 2008; Koonin 2010). The common ancestor of all eukaryotes entered into an endosymbiotic partnership with an α-proteobacterium that evolved into the mitochondrion, now the site of aerobic respiration in most eukaryotes (Gray 2012); animals and fungi are heterotrophic descendants of this partnership. Another lineage, which eventually produced the plants, entered into a second endosymbiotic partnership, this time with a cyanobacterium, which transplanted photosynthetic alchemy into eukaryotes to create plastids (Gray and Archibald 2012). This review will highlight recent progress in our understanding of the origin and evolution of plastids.     

New Developments in Selenium Biochemistry: Selenocysteine Biosynthesis in Eukaryotes and Archaea

We used comparative genomics and experimental analyses to show that (1) eukaryotes and archaea, which possess the selenocysteine (Sec) protein insertion machinery contain an enzyme, O-phosphoseryl-transfer RNA (tRNA)^[Ser]Sec kinase (designated PSTK), which phosphorylates seryl-tRNA^[Ser]Sec to form O-phosphoseryl-tRNA^[Ser]Sec and (2) the Sec synthase (SecS) in mammals is a pyridoxal phosphate-containing protein previously described as the soluble liver antigen (SLA). SecS uses the product of PSTK, O-phosphoseryl-tRNA^[Ser]Sec, and selenophosphate as substrates to generate selenocysteyl-tRNA^[Ser]Sec. Sec could be synthesized on tRNA^[Ser]Sec from selenide, adenosine triphosphate (ATP), and serine using tRNA^[Ser]Sec, seryl-tRNA synthetase, PSTK, selenophosphate synthetase, and SecS. The enzyme that synthesizes monoselenophosphate is a previously identified selenoprotein, selenophosphate synthetase 2 (SPS2), whereas the previously identified mammalian selenophosphate synthetase 1 did not serve this function. Monoselenophosphate also served directly in the reaction replacing ATP, selenide, and SPS2, demonstrating that this compound was the active selenium donor. Conservation of the overall pathway of Sec biosynthesis suggests that this pathway is also active in other eukaryotes and archaea that contain selenoproteins. X.-M. Xu and B. A. Carlson contributed equally to the studies described herein.     

Biochemistry and Metabolism of Giardia

Giardia lamblia, an aerotolerant anaerobe, respires in the presence of oxygen by a flavin, iron-sulfur protein-mediated electron transport system. Glucose appears to be the only sugar catabolized by the Embden-Meyerhof-Pamas and hexose monophosphate pathways, and energy is produced by substrate level phosphorylation. Substrates are incompletely oxidized to CO₂, ethanol and acetate by nonsedimentable enzymes. The lack of incorporation of inosine, hypoxanthine, xanthine, formate or glycine into nucleotides indicates an absence of de novo purine synthesis. Only adenine, adenosine, guanine and guanosine are salvaged, and no interconversion of these purines was detected. Salvage of these purines and their nucleosides is accomplished by adenine phosphoribosyltransferase, adenosine hydrolase, guanosine phosphonbosyltransferase and guanine hydrolase. The absence of de novo pyrimidine synthesis was confirmed by the lack of incorporation of bicarbonate, orotate and aspartate into nucleotides, and by the lack of detectable levels of the enzymes of de novo pyrimidine synthesis. Salvage appears to be accomplished by the action of uracil phosphoribosyltransferase, uridine hydrolase, uridine phosphotransferase, cytidine deaminase, cytidine hydrolase, cytosine phosphoribosyltransferase and thymidine phosphotransferase. Nucleotides of uracil may be converted to nucleotides of cytosine by cytidine triphosphate synthetase, but thymidylate synthetase and dihydrofolate reductase activities were not detected. Uptake of pyrmidine nucleosides, and perhaps pyrimidines, appears to be accomplished by carrier-mediated transport, and the common site for uptake of uridine and cytidine is distinct from the site for thymidine. Thymine does not appear to be incorporated into nucleotide pools. Giardia trophozoites appear to rely on preformed lipids rather than synthesizing them de novo. Major lipids include phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingomyelin, sterol (probably cholesterol) and mono-, di- and triacylglycer-ides. The lipid composition of the cysts of G. lamblia isolated from gerbils and G. muris isolated from mice are similar to those obtained from the trophozoites of G. lamblia grown in vitro. The activities of several hydrolases of G. lamblia have been shown to be confined to a single lysosome-like particle population with an equilibrium density of approximately 1.15 in sucrose. Contrary to the trophozoites of Entamoeba and the trichomonads, Giardia trophozoites appear to lack most carbohydrate splitting hydrolases. Calmodulin has been reported in G. lamblia trophozoites, and it appears to have properties similar to the calmodulin isolated from other eucaryotic cells.     

Comparative Study of the Energy Metabolism of Anaerobic Alkaliphiles from Soda Lakes

We investigated the influence of inhibitors of energy metabolism and ionophores on the growth and formation of metabolic products in alkaliphilic anaerobes characterized by various catabolism types. It was shown that blockage of oxidative phosphorylation by the addition of N,N-dicyclohexylcarbodiimide (DCCD), an inhibitor of F₁F₀ ATP synthase, resulted in a complete arrest of the growth of the acetogenic bacterium Tindallia magadiensis with arginine as an electron acceptor. In the presence of pyruvate, substrate-level phosphorylation occurred. The methylotrophic methanogenic archaebacterium Methanosalsus zhilinae did not grow with DCCD and vanadate, an inhibitor of ₁₂ ATPase, suggesting the presence of two ATPase types in this species. In the saccharolytic alkaliphiles Halonatronum saccharophilum, Amphibacillus tropicus, and Spirochaeta alkalica (which are characterized by different pH optima), the contribution of the H⁺ gradient to the energy metabolism and, presumably, to the maintenance of the intracellular pH level decreased with an increase in the degree of alkaliphily. Based on the data of an inhibitor assay using protonophores, monensin, and amiloride, we suggest that all of the bacteria tested depend on H⁺and Na⁺ gradients. The Na⁺/H⁺ antiport appears to be a universal mechanism of regulating the intracellular pH level and the interaction between the Na⁺ and H⁺ cycles in bacterial cells cultivated under alkaline conditions.     

Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea

Background

The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best.

Methodology/Principal Findings

While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex—all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea.

Conclusion/Significance

This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.     

Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes

Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness of functional modules in eukaryotes and probe the biological and methodological factors influencing our estimates. We have collected various datasets of protein complexes and pathways in Saccheromyces cerevisiae. We define orthologous groups on 34 eukaryotic genomes and measure the extent of cohesive evolution of sets of orthologous groups of which members constitute a known complex or pathway. Within this framework it appears that most functional modules evolve flexibly rather than cohesively. Even after correcting for uncertain module definitions and potentially problematic orthologous groups, only 46% of pathways and complexes evolve more cohesively than random modules. This flexibility seems partly coupled to the nature of the functional module because biochemical pathways are generally more cohesively evolving than complexes.     

Biochemistry and Physiology of Alligator Metabolism in vivo

The metabolic rate of the alligator is a direct function ofthe volume of blood flowing through the capillaries/unit time/unitweight, which in turn, is determined by the heart rate and thestroke volume. For an animal with such a low metabolic rate,the heart rate is relatively rapid, in part because the heartis relatively small. Metabolic rate of the smallest alligatorexceeds that of the largest by about 25 to 1. Lowering the temperaturedecreases blood flow without decreasing the oxygen and substrateextracted from each liter. Metabolic rate (oxygen consumption)is expressed by the equation M.R. = F(A – V), where Fis the blood flow and A – V is the oxygen A – Vdifference. For the catabolism of compounds in which oxygenis not directly involved, the expression is V = KF[S], whereV is the velocity of the reaction, F is the blood flow, and[S] is the concentration of the substrate. K is a constant,differing for each catabolite, but having about the same valuefor any one catabolite in vertebrates, cold- or warm-blooded.Enzyme kinetics in a live vertebrate has little in common withthat determined in the usual experiments in vitro. A 70 kg alligatorat 28°C has a blood flow of 0.2 liters/min, a stroke volumeof 6.3 ml, a circulation time of 27 min, and it produces about72 kcal/day, or about 4% of that of a man of equal size.     

Anaerobic Amino Acid Metabolism

Anoxic stress induces a strong change in sugar, protein, and amino acid metabolism in higher plants. Sugars are rapidly consumed through the anaerobic glycolysis to sustain energy production. Protein degradation under anoxia is a mechanism to release free amino acids contributing in this way to maintaining the osmotic potential of the tissue under stress. Among free amino acids, a particular role is played by glutamic acid, being a precursor of some characteristic compounds of the anaerobic metabolism (alanine, -aminobutyric acid, and putrescine). The glutamine synthetase/glutamate synthase cycle contributes to ammonia reassimilation and primary assimilation of nitrate, and resynthesizes constantly glutamate for the synthesis of other compounds. Some polypeptides involved in these pathways are expressed under anoxia. The importance of amino acid metabolism for the response to anaerobic stress is discussed.     

A New Aspect to the Origin and Evolution of Eukaryotes

One of the most important omissions in recent evolutionary theory concerns how eukaryotes could emerge and evolve. According to the currently accepted views, the first eukaryotic cell possessed a nucleus, an endomembrane system, and a cytoskeleton but had an inefficient prokaryotic-like metabolism. In contrast, one of the most ancient eukaryotes, the metamonada Giardia lamblia, was found to have formerly possessed mitochondria. In sharp contrast with the traditional views, this paper suggests, based on the energetic aspect of genome organization, that the emergence of eukaryotes was promoted by the establishment of an efficient energy-converting organelle, such as the mitochondrion. Mitochondria were acquired by the endosymbiosis of ancient α-purple photosynthetic Gram-negative eubacteria that reorganized the prokaryotic metabolism of the archaebacterial-like ancestral host cells. The presence of an ATP pool in the cytoplasm provided by this cell organelle allowed a major increase in genome size. This evolutionary change, the remarkable increase both in genome size and complexity, explains the origin of the eukaryotic cell itself. The loss of cell wall and the appearance of multicellularity can also be explained by the acquisition of mitochondria. All bacteria use chemiosmotic mechanisms to harness energy; therefore the periplasm bounded by the cell wall is an essential part of prokaryotic cells. Following the establishment of mitochondria, the original plasma membrane-bound metabolism of prokaryotes, as well as the funcion of the periplasm providing a compartment for the formation of different ion gradients, has been transferred into the inner mitochondrial membrane and intermembrane space. After the loss of the essential function of periplasm, the bacterial cell wall could also be lost, which enabled the naked cells to establish direct connections among themselves. The relatively late emergence of mitochondria may be the reason why multicellularity evolved so slowly. Received: 29 May 1997 / Accepted: 9 October 1997     

Evolution of Mitochondria Reconstructed from the Energy Metabolism of Living Bacteria

The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.     

The Evolution of Fatty Acid Desaturases and Cytochrome b5 in Eukaryotes

Desaturases that introduce double bonds into the fatty acids are involved in the adaptation of membrane fluidity to changes in the environment. Besides, polyunsaturated fatty acids (PUFAs) are increasingly recognized as important pharmaceutical and nutraceutical compounds. To successfully engineer organisms with increased stress tolerance or the ability to synthesize valuable PUFAs, detailed knowledge about the complexity of the desaturase family as well as understanding of the coevolution of desaturases and their cytochrome b5 electron donors is needed. We have constructed phylogenies of several hundred desaturase sequences from animals, plants, fungi and bacteria and of the cytochrome b5 domains that are fused to some of these enzymes. The analysis demonstrates the existence of three major desaturase acyl-CoA groups that share few similarities. Our results indicate that the fusion of Δ⁶-desaturase-like enzymes with their cytochrome b5 electron donor was a single event that took place in the common ancestor of all eukaryotes. We also propose the Δ⁶-desaturase-like enzymes as the most probable donor of the cytochrome b5 domain found in fungal Δ⁹-desaturases and argue that the recombination most likely happened soon after the separation of the animal and fungal ancestors. These findings answer some of the previously unresolved questions and contribute to the quickly expanding field of research on desaturases.     

Aerobic and Anaerobic Starvation Metabolism in Methanotrophic Bacteria

The capacity for anaerobic metabolism of endogenous and selected exogenous substrates in carbon- and energy-starved methanotrophic bacteria was examined. The methanotrophic isolate strain WP 12 survived extended starvation under anoxic conditions while metabolizing 10-fold less endogenous substrate than did parallel cultures starved under oxic conditions. During aerobic starvation, the cell biomass decreased by 25% and protein and lipids were the preferred endogenous substrates. Aerobic protein degradation (24% of total protein) took place almost exclusively during the initial 24 h of starvation. Metabolized carbon was recovered mainly as CO(inf2) during aerobic starvation. In contrast, cell biomass decreased by only 2.4% during anaerobic starvation, and metabolized carbon was recovered mainly as organic solutes in the starvation medium. During anaerobic starvation, only the concentration of intracellular low-molecular-weight compounds decreased, whereas no significant changes were measured for cellular protein, lipids, polysaccharides, and nucleic acids. Strain WP 12 was also capable of a limited anaerobic glucose metabolism in the absence of added electron acceptors. Small amounts of CO(inf2) and organic acids, including acetate, were produced from exogenous glucose under anoxic conditions. Addition of potential anaerobic electron acceptors (fumarate, nitrate, nitrite, or sulfate) to starved cultures of the methanotrophs Methylobacter albus BG8, Methylosinus trichosporium OB3b, and strain WP 12 did not stimulate anaerobic survival. However, anaerobic starvation of these bacteria generally resulted in better survival than did aerobic starvation. The results suggest that methanotrophic bacteria can enter a state of anaerobic dormancy accompanied by a severe attenuation of endogenous metabolism. In this state, maintenance requirements are presumably provided for by fermentation of certain endogenous substrates. In addition, low-level catabolism of exogenous substrates may support long-term anaerobic survival of some methanotrophic bacteria.     

Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes

LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.