Breath-giving cooperation: critical review of origin of mitochondria hypotheses Major unanswered questions point to the importance of early ecology

The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria

TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels

TransportDB () is a comprehensive database resource of information on cytoplasmic membrane transporters and outer membrane channels in organisms whose complete genome sequences are available. The complete set of membrane transport systems and outer membrane channels of each organism are annotated based on a series of experimental and bioinformatic evidence and classified into different types and families according to their mode of transport, bioenergetics, molecular phylogeny and substrate specificities. User-friendly web interfaces are designed for easy access, query and download of the data. Features of the TransportDB website include text-based and BLAST search tools against known transporter and outer membrane channel proteins; comparison of transporter and outer membrane channel contents from different organisms; known 3D structures of transporters, and phylogenetic trees of transporter families. On individual protein pages, users can find detailed functional annotation, supporting bioinformatic evidence, protein/DNA sequences, publications and cross-referenced external online resource links. TransportDB has now been in existence for over 10 years and continues to be regularly updated with new evidence and data from newly sequenced genomes, as well as having new features added periodically

Comparative molecular biological analysis of membrane transport genes in organisms

Comparative analyses of membrane transport genes revealed many differences in the features of transport homeostasis in eight diverse organisms, ranging from bacteria to animals and plants. In bacteria, membrane-transport systems depend mainly on single genes encoding proteins involved in an ATP-dependent pump and secondary transport proteins that use H+ as a co-transport molecule. Animals are especially divergent in their channel genes, and plants have larger numbers of P-type ATPase and secondary active transporters than do other organisms. The secondary transporter genes have diverged evolutionarily in both animals and plants for different co-transporter molecules. Animals use Na+ ions for the formation of concentration gradients across plasma membranes, dependent on secondary active transporters and on membrane voltages that in turn are dependent on ion transport regulation systems. Plants use H+ ions pooled in vacuoles and the apoplast to transport various substances; these proton gradients are also dependent on secondary active transporters. We also compared the numbers of membrane transporter genes in Arabidopsis and rice. Although many transporter genes are similar in these plants, Arabidopsis has a more diverse array of genes for multi-efflux transport and for response to stress signals, and rice has more secondary transporter genes for carbohydrate and nutrient transport

Metatranscriptomic analysis of community structure and metabolism of the rhizosphere microbiome.

Plant-microbe interactions in the rhizosphere, the region of soil influenced by plant roots, are integral to biogeochemical cycling, and maintenance of plant health and productivity. Interactions between model plants and microbes are well understood, but relatively little is about the plant microbiome. Here, comparative metatranscriptomics was used to determine taxonomic compositions and metabolic responses of microbes in soil and the rhizospheres of wheat, oat and pea. Additionally a wild-type oat was compared to a mutant (sad1) deficient in production of antifungal avenacins. Analyses of taxonomic compositions and functions based on rRNA and protein coding genes agreed that rhizosphere microbiomes differed from soil and between plant species. Pea had a stronger effect than wheat and oat, suggesting distinct cereal and legume microbiomes. Proportions of eukaryotic rRNA in the oat and pea rhizospheres were more than fivefold higher than in the wheat rhizosphere or soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, while the pea rhizosphere was highly enriched for fungi. Only the eukaryotic community was distinct from wild-type oat in the sad1 mutant, suggesting avenacins have a broader role than protecting from fungal pathogens. The addition of an internal RNA standard allowed quantitative determination of global transcriptional activity in each environment. This was generally higher in the rhizospheres, particularly pea, than in soil. Taxa known to possess metabolic traits potentially important for rhizosphere colonisation, plant growth promotion and pathogenesis were selected by plants. Such traits included cellulose and other plant polymer degradation, nitrogen fixation, hydrogen oxidation, methylotrophy and antibiotic production. These functions were also more highly expressed in rhizospheres than soil. Microbes also induced functions involved in chemotaxis, motility, attachment, pathogenesis, responses to oxidative stress, cycling of nitrogen and sulphur, acquisition of phosphorous, iron and other metals, as well as metabolism of a variety of sugars, aromatics, organic and amino acids, many plant species specific. Profiling microbial communities with metatranscriptomics allowed comparison of relative and quantitative abundance of microbes and their metabolism, from multiple samples, across all domains of life, without PCR bias. This revealed profound differences in the taxonomic composition and metabolic functions of rhizosphere microbiomes between crop plants and soil

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

<p>Abstract</p> <p>Background</p> <p>A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution.</p> <p>Results</p> <p>Our experimentation with <it>E. coli </it>and yeast proteins with 16 different carefully composed reference sets of genomes revealed that the phyletic patterns of proteins in prokaryotes alone could be adequate enough to make reasonably accurate functional linkage predictions. A slight improvement in performance is observed on adding few eukaryotes into the reference set, but a noticeable drop-off in performance is observed with increased number of eukaryotes. Inclusion of most parasitic, pathogenic or vertebrate genomes and multiple strains of the same species into the reference set do not necessarily contribute to an improved sensitivity or accuracy. Interestingly, we also found that evolutionary histories of individual pathways have a significant affect on the performance of the PPC approach with respect to a particular reference set. For example, to accurately predict functional links in carbohydrate or lipid metabolism, a reference set solely composed of prokaryotic (or bacterial) genomes performed among the best compared to one composed of genomes from all three super-kingdoms; this is in contrast to predicting functional links in translation for which a reference set composed of prokaryotic (or bacterial) genomes performed the worst. We also demonstrate that the widely used random null model to quantify the statistical significance of profile similarity is incomplete, which could result in an increased number of false-positives.</p> <p>Conclusion</p> <p>Contrary to previous proposals, it is not merely the number of genomes but a careful selection of informative genomes in the reference set that influences the prediction accuracy of the PPC approach. We note that the predictive power of the PPC approach, especially in eukaryotes, is heavily influenced by the primary endosymbiosis and subsequent bacterial contributions. The over-representation of parasitic unicellular eukaryotes and vertebrates additionally make eukaryotes less useful in the reference sets. Reference sets composed of highly non-redundant set of genomes from all three super-kingdoms fare better with pathways showing considerable vertical inheritance and strong conservation (e.g. translation apparatus), while reference sets solely composed of prokaryotic genomes fare better for more variable pathways like carbohydrate metabolism. Differential performance of the PPC approach on various pathways, and a weak positive correlation between functional and profile similarities suggest that caution should be exercised while interpreting functional linkages inferred from genome-wide large-scale profile comparisons using a single reference set.</p

Domain-based approaches to understanding phylogeny and orthology

Domain-based approaches are used in phylogenetic reconstruction and functional identification. Two groups of ionotropic glutamate receptors (iGluR???s) were identified with the topology of the binding core and pore-loop of the eukaryotic iGluR???s. Group 1 has a potassium-like selectivity filter and Group 2 is most closely related to eukaryotic iGluR???s. The relationship among them was investigated in this research. Then, the domain complexity of proteins was analysed on a comprehensive basis. Our results showed that bacterial and archaeal proteins are as complex as eukaryotic proteins in domain abundance, but more promiscuous. Proteins emerged in early stage are also more promiscuous, but with low domain abundance. The possible application of protein comparison based on domain content was also suggested in this research and could be used to help the identification of function and orthology. Therefore, domain-based approaches are proved to be useful in many areas of proteome research, including functional annotation, evolutionary illustration, and protein-protein network construction

Structural and organisational conditions for the appearance of a functionally integrated organisation in the transition from prokaryotic to eukaryotic cell

211 p.The concept of functional (or physiological) integration is explanatorily relevant to both biology andphilosophy of biology, but it suffers from two main related problems: first, it is an umbrella termencompassing any causal interdependence of functions, thus being unsuitable for characterisingbiological organisations as physiologic units; secondly, it lacks a unified theoretical framework tounderstand this concept. This PhD thesis aims to investigate the relationship between functionalintegration and biological individuality by studying the nature and the role of physiological integration inone of the major evolutionary transitions: the origin of the eukaryotic cell from the prokaryotic one. Themethodology employed is the so-called ¿organizational approach¿ that combines the descriptive approachof the methodological naturalism with the normative evaluation of the epistemic and practicalconsequences of the theoretical frameworks of life sciences. At the core of this work is the examinationof the physic-chemical and structural-functional conditions that allowed the transformation of aprokaryote into a eukaryotic cell and that determined a very specific kind of functionally integratedorganisation in eukaryotes. The thesis puts forward a theoretical proposal for functional integrationconsisting in the global capacity, enabled by specific spatial constraints, of a biological organisation toperform system-level regulation, spatio-temporal coordination of the parts, and system-levelreproduction. This proposal for functional integration has important consequences for understandingimportant issues of theoretical biology and philosophy of biology, such as biological individuality,biological autonomy, and major transitions in evolution

Structural and organisational conditions for the appearance of a functionally integrated organisation in the transition from prokaryotic to eukaryotic cell

211 p.The concept of functional (or physiological) integration is explanatorily relevant to both biology andphilosophy of biology, but it suffers from two main related problems: first, it is an umbrella termencompassing any causal interdependence of functions, thus being unsuitable for characterisingbiological organisations as physiologic units; secondly, it lacks a unified theoretical framework tounderstand this concept. This PhD thesis aims to investigate the relationship between functionalintegration and biological individuality by studying the nature and the role of physiological integration inone of the major evolutionary transitions: the origin of the eukaryotic cell from the prokaryotic one. Themethodology employed is the so-called ¿organizational approach¿ that combines the descriptive approachof the methodological naturalism with the normative evaluation of the epistemic and practicalconsequences of the theoretical frameworks of life sciences. At the core of this work is the examinationof the physic-chemical and structural-functional conditions that allowed the transformation of aprokaryote into a eukaryotic cell and that determined a very specific kind of functionally integratedorganisation in eukaryotes. The thesis puts forward a theoretical proposal for functional integrationconsisting in the global capacity, enabled by specific spatial constraints, of a biological organisation toperform system-level regulation, spatio-temporal coordination of the parts, and system-levelreproduction. This proposal for functional integration has important consequences for understandingimportant issues of theoretical biology and philosophy of biology, such as biological individuality,biological autonomy, and major transitions in evolution