Biomedical subjects
D Moreira
Publications and source records attributed to D Moreira.
Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton.
Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2-5 microm from the aphotic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.
Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front.
To contribute to the understanding of deep-sea planktonic communities, we explored the prokaryotic diversity of a 3000 m deep site at the Antarctic Polar Front using molecular methods. Bacterial 16S rDNA-amplified sequences corresponded to the as yet uncultivated groups SAR11, within the alpha-Proteobacteria, and SAR324, within the delta-Proteobacteria, as well as to the gamma-Proteobacteria, Cytophagales, Planctomyces, Gram-positives, and the group of environmental sequences SAR406. Among them, gamma-proteobacterial sequences were the most abundant and diverse. Within Archaea, and using six different primer sets for 16S rDNA amplification, only euryarchaeotal sequences were retrieved. Most of them clustered with the Thermoplasma-related marine groups II and III, but some corresponded to a recently described group of marine sequences emerging at the base of haloarchaea. Our data suggest that gamma-Proteobacteria and Euryarchaeota may be dominant elements in terms of genetic diversity of the two prokaryotic domains in this deep-sea pelagic area.
Sure facts and open questions about the origin and evolution of photosynthetic plastids.
Some eukaryotic groups carry out photosynthesis thanks to plastids, which are endosymbiotic organelles derived from cyanobacteria. Increasing evidence suggests that the plastids from green plants, red algae, and glaucophytes arose directly from a single common primary symbiotic event between a cyanobacterium and a phagotrophic eukaryotic host. They are therefore known as primary plastids. All other lineages of photosynthetic eukaryotes seem to have acquired their plastids by secondary or tertiary endosymbioses, which are established between eukaryotic algae, already containing plastids, and other eukaryotic hosts. Both primary and secondary symbioses have been followed by extensive plastid genome reduction through gene loss and gene transfer to the host nucleus. All this makes the reconstruction of the evolutionary history of plastids a very complex task, indissoluble from the resolution of the general phylogeny of eukaryotes.
A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions.
During our study of the 16S rRNA gene sequence-based archaeal diversity of a deep-sea site located at a 3,000 m depth at the Antarctic Polar Front, we detected several phylotypes ascribed to already known Group II and III Euryarchaeota, and a cluster of distinct sequences that branched off at the base of haloarchaea. The position of this lineage (marine Group IV) was very robust using distance (neighbour-joining) and maximum-likelihood methods. Subsequently, we designed specific primers for the detection of this archaeal group in other marine environments using polymerase chain reaction amplification and sequence comparison. Group IV archaea were found in the Antarctic area (across a gradient from the Southern ocean to the South Atlantic), and also in North Atlantic and Mediterranean waters. In all oceanic locations, Group IV archaea were never detected in surface waters, but were vertically distributed in the deepest part of the water column.
New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence.
The phylum Euglenozoa consists of three distinct groups: the euglenoids, diplonemids and kinetoplastids. The phylogenetic position of the diplonemids within this phylum remains unsettled, since both morphological and molecular data produce weak and contradictory results. It is shown here that taxonomic sampling, G+C content bias, mutational saturation and differences of evolutionary rate among lineages are major factors affecting the topology of the small-subunit rRNA euglenozoan tree. When these problems are minimized by using a larger diplonemid sampling (including a sequence of environmental origin) and correcting for G+C bias (by using both paralinear distances or an unbiased dataset), a diplonemids+euglenoids sisterhood is retrieved. Bootstrap support for this relationship is still moderate, but it is retrieved by all analysis methods, overcoming previously reported disagreements. In addition, the inclusion of a large number of euglenoid sequences in the analysis improves some phylogenetic relationships within this group. Some problematic taxa, such as the species Khawkinea quartana, are now placed with high bootstrap support and monophyly is found for two interesting groups (the photosynthetic genera Eutreptia+Eutreptiella and the loricate genera Strombomonas+Trachelomonas), although with weak statistical support.
Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions.
The current paradigm of eukaryotic evolution is based primarily on comparative analysis of ribosomal RNA sequences. It shows several early-emerging lineages, mostly amitochondriate, which might be living relics of a progressive assembly of the eukaryotic cell. However, the analysis of slow-evolving positions, carried out with the newly developed slow-fast method, reveals that these lineages are, in terms of nucleotide substitution, fast-evolving ones, misplaced at the base of the tree by a long branch attraction artefact. Since the fast-evolving groups are not always the same, depending on which macromolecule is used as a marker, this explains most of the observed incongruent phylogenies. The current paradigm of eukaryotic evolution thus has to be seriously re-examined as the eukaryotic phylogeny is presently best summarized by a multifurcation. This is consistent with the Big Bang hypothesis that all extant eukaryotic lineages are the result of multiple cladogeneses within a relatively brief period, although insufficiency of data is also a possible explanation for the lack of resolution. For further resolution, rare evolutionary events such as shared insertions and/or deletions or gene fusions might be helpful.
The origin of red algae and the evolution of chloroplasts.
Chloroplast structure and genome analyses support the hypothesis that three groups of organisms originated from the primary photosynthetic endosymbiosis between a cyanobacterium and a eukaryotic host: green plants (green algae + land plants), red algae and glaucophytes (for example, Cyanophora). Although phylogenies based on several mitochondrial genes support a specific green plants/red algae relationship, the phylogenetic analysis of nucleus-encoded genes yields inconclusive, sometimes contradictory results. To address this problem, we have analysed an alternative nuclear marker, elongation factor 2, and included new red algae and protist sequences. Here we provide significant support for a sisterhood of green plants and red algae. This sisterhood is also significantly supported by a multi-gene analysis of a fusion of 13 nuclear markers (5,171 amino acids). In addition, the analysis of an alternative fusion of 6 nuclear markers (1,938 amino acids) indicates that glaucophytes may be the closest relatives to the green plants/red algae group. Thus, our study provides evidence from nuclear markers for a single primary endosymbiosis at the origin of these groups, and supports a kingdom Plantae comprising green plants, red algae and glaucophytes.
The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome.
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The new phylogeny of eukaryotes.
Molecular phylogeny has been regarded as the ultimate tool for the reconstruction of relationships among eukaryotes-especially the different protist groups-given the difficulty in interpreting morphological data from an evolutionary point of view. In fact, the use of ribosomal RNA as a marker has provided the first well resolved eukaryotic phylogenies, leading to several important evolutionary hypotheses. The most significant is that several early-emerging, amitochondriate lineages, are living relics from the early times of eukaryotic evolution. The use of alternative protein markers and the recognition of several molecular phylogeny reconstruction artefacts, however, have strongly challenged these ideas. The putative early emerging lineages have been demonstrated as late-emerging ones, artefactually misplaced to the base of the tree. The present state of eukaryotic evolution is best described by a multifurcation, in agreement with the 'big bang' hypothesis that assumes a rapid diversification of the major eukaryotic phyla. For further resolution, the analysis of genomic data through improved phylogenetic methods will be required.
A mitochondrial origin for eukaryotic C2H2 zinc finger regulators?
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Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacterial replication machinery.
In contrast to the universality of other central genetic mechanisms, the replication machinery of Bacteria is clearly different from those of Archaea and Eukaryotes. A large number of bacterial genes involved in DNA replication can also be found in plasmids and phages. Based on this, it has been recently proposed that the ancestral bacterial genes were displaced by non-orthologous replication genes from plasmids and phages, which would explain the profound difference between Bacteria and the other domains of life. The alternative hypothesis is that these DNA replication genes have been frequently transferred from bacterial hosts to the genomes of their plasmids and phages. The phylogenetic analysis of the bacterial DNA replication proteins most abundant in databases (replicative helicase DnaB, single-strand binding protein Ssb and topoisomerase TopB) presented here supports the latter hypothesis. Each protein tree shows that sequences from plasmids and phages branch close to their bacterial-specific hosts, suggesting multiple independent horizontal transfers. Therefore, there is no evidence so far for non-orthologous gene displacement of these genes.
Molecular phylogeny: pitfalls and progress.
Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects.
Biochemical analysis of the interaction between elongation factor 1alpha and alpha/beta-tubulins from a ciliate, Tetrahymena pyriformis.
The interaction between elongation factor 1alpha (EF-1alpha) and alpha/beta-tubulins has been analyzed in vivo and in vitro. An association of both alpha- and beta-tubulins with EF-1alpha in the lysate of Tetrahymena pyriformis was detected by co-immunoprecipitation analysis. In contrast, in vitro biomolecular interaction analysis with glutathione S-transferase (GST) fusion proteins revealed that GST-beta-tubulin, but not GST-alpha-tubulin, can bind to GST-EF-1alpha. Two beta-tubulin binding sites have been identified to reside in the domains I and III of EF-1alpha. In addition, beta-tubulin itself seems to have two distinct interaction sites for each of the domains. Since domain II of EF-1alpha did not interact with beta-tubulin, we have re-evaluated the phylogenetic status of ciliates using EF-1alpha sequences devoid of domain II. The phylogenetic tree thus obtained was significantly different from that inferred from the whole sequence of EF-1alpha, suggesting the presence of functional constraints on the molecular evolution of EF-1alpha.
Respiratory chains in the last common ancestor of living organisms.
Sequences in current databases show that a number of proteins involved in respiratory processes are homologous in archaeal and bacterial species. In particular, terminal oxidases belonging to oxygen, nitrate, sulfate, and sulfur respiratory pathways have been sequenced in members of both domains. They include cytochrome oxidase, nitrate reductase, adenylylsulfate reductase, sulfite reductase, and polysulfide reductase. These proteins can be assigned to the last common ancestor of living organisms assuming that the deepest split of the three domains of life occurred between Archaea and Bacteria and that they were not acquired through lateral gene transfer by one of these domains. These molecular data indicate that several of the most important respiratory pathways arose early in evolution and that the last common ancestor of living organisms was not a simple organism in its energetic metabolism. Rather, it may have been able to gain energy by means of at least four electron transport chains, and therefore it may have been prepared to face a wide range of environmental conditions.
Metabolic symbiosis at the origin of eukaryotes.
Thirty years after Margulis revived the endosymbiosis theory for the origin of mitochondria and chloroplasts, two novel symbiosis hypotheses for the origin of eukaryotes have been put forward. Both propose that eukaryotes arose through metabolic symbiosis (syntrophy) between eubacteria and methanogenic Archaea. They also propose that this was mediated by interspecies hydrogen transfer and that, initially, mitochondria were anaerobic. These hypotheses explain the mosaic character of eukaryotes (i.e. an archaeal-like genetic machinery and a eubacterial-like metabolism), as well as distinct eukaryotic characteristics (which are proposed to be products of symbiosis). Combined data from comparative genomics, microbial ecology and the fossil record should help to test their validity.
Smr: a bacterial and eukaryotic homologue of the C-terminal region of the MutS2 family.
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Horizontal transfers confuse the prokaryotic phylogeny based on the HSP70 protein family.
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