Microbial genescapes: a prokaryotic view of the yeast genome

We examine the translated open reading frames (ORFs) of the yeast Saccharomyces cerevisiae, focusing on those that have FASTA matches in phyletically defined sets of completely sequenced genomes. On this basis, we identify archaeal yeast, bacterial yeast, universal yeast, and yeast ORFs that do not have a match in any of nine prokaryote genomes. Similarly, we examine the yeast mitochondrial genome and the subset of the yeast nuclear ORFs identified as being involved in mitochondrial biogenesis. For the yeast ORFs that match one or more ORFs in these prokaryote genomes, we examine the phyletic and functional distributions of these matches as a function of match strength. These results provide genome level insights into the origin of the eukaryotic cell and the origin of mitochondria. More generally, they exemplify how the growing database of prokaryote genome sequences can help us understand eukaryote genomes.     

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary

Applied Microbiology and Biotechnology - There are close exchanges between sediment and water in estuaries; however, the patterns of prokaryotic community assembly in these two habitat types are...     

Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes

Here, we present a comprehensive analysis of solute transport systems encoded within the completely sequenced genomes of 18 prokaryotic organisms. These organisms include four Gram-positive bacteria, seven Gram-negative bacteria, two spirochetes, one cyanobacterium and four archaea. Membrane proteins are analyzed in terms of putative membrane topology, and the recognized transport systems are classified into 76 families, including four families of channel proteins, four families of primary carriers, 54 families of secondary carriers, six families of group translocators, and eight unclassified families. These families are analyzed in terms of the paralogous and orthologous relationships of their protein members, the substrate specificities of their constituent transporters and their distributions in each of the 18 organisms studied. The families vary from large superfamilies with hundreds of represented members, to small families with only one or a few members. The mode of transport generally correlates with the primary mechanism of energy generation, and the numbers of secondary transporters relative to primary transporters are roughly proportional to the total numbers of primary H(+) and Na(+) pumps in the cell. The phosphotransferase system is less prevalent in the analyzed bacteria than previously thought (only six of 14 bacteria transport sugars via this system) and is completely lacking in archaea and eukaryotes. Escherichia coli is shown to be exceptionally broad in its transport capabilities and therefore, at a membrane transport level, does not appear representative of the bacteria thus far sequenced. Archaea and spirochetes exhibit fewer proteins with multiple transmembrane segments and fewer net transporters than most bacteria. These results provide insight into the relevance of transport to the overall physiology of prokaryotes.     

Identification and phyletic distribution of the plasma esterases of some anthropoid primates

Using electrophoresis, specific staining, and selective inhibition, we examined and identified esterase components in the plasma of 13 anthropoid species: 5 hominoids, 7 cercopithecoids, and 1 platyrrhine. Most species, unlike humans, exhibited one or more arylesterase and/or carboxylesterase components as well as cholinesterase and albumin-associated arylesterase. A distinctive arylesterase probably indicates pregnancy in cercopithecoids. While some characters (such as the net charge of the cholinesterase molecule) were extremely uniform across all taxa examined, other quantitative and qualitative traits showed intra- and interspecific variation. Comparison of a cladogram with the distribution of traits shows that the least phyletically stable traits are, in general, those that also exhibit intraspecific polymorphism. One genus-specific, and therefore relatively conservative, trait (weak dimer-dimer bonding in the cholinesterase molecule) evidently appeared independently among papionin cercopithecoids and hominoids. The most parsimonious interpretation of this distribution reinforces the notion of a Pan-Gorilla-Homoclade sororally related to Pongo.In general, plasma esterases are an underexploited source of genetic markers in primates.     

Osmoadaptation mechanisms in prokaryotes: distribution of compatible solutes

Microorganisms respond to osmotic stress mostly by accumulating compatible solutes, either by uptake from the medium or by de novo synthesis. These osmotically active molecules preserve the positive turgor pressure required for cell division. The diversity of compatible solutes is large but falls into a few major chemical categories; they are usually small organic molecules such as amino acids or their derivatives, and carbohydrates or their derivatives. Some are widely distributed in nature while others seem to be exclusively present in specific groups of organisms. This review discusses the diversity and distribution of known classes of compatible solutes found in prokaryotes as well as the increasing knowledge of the genes and pathways involved in their synthesis. The alternative roles of some archetypal compatible solutes not subject to osmoregulatory constraints are also discussed.     

Predicted structure and phyletic distribution of the RNA-binding protein Hfq

Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The predicted structure aligns with most major features of the Methanobacterium thermoautotrophicum LSm protein structure. Conserved residues in Hfq are positioned at the same structural locations responsible for subunit assembly and RNA interaction in Sm proteins. A highly conserved portion of Hfq assumes a structural fold similar to the Sm2 motif of Sm proteins. The evolution of the Hfq protein was explored by conducting a BLAST search of microbial genomes followed by phylogenetic analysis. Approximately half of the 140 complete or nearly complete genomes examined contain at least one gene coding for Hfq. The presence or absence of Hfq closely followed major bacterial clades. It is absent from high-level clades and present in the ancient Thermotogales-Aquificales clade and all proteobacteria except for those that have undergone major reduction in genome size. Residues at three positions in Hfq form signatures for the beta/gamma proteobacteria, alpha proteobacteria and low GC Gram-positive bacteria groups.     

Diversity and distribution of hemerythrin-like proteins in prokaryotes

Hemerythrins are oxygen-binding proteins found in the body fluids and tissues of certain invertebrates. Oxygen is bound at a nonheme iron centre consisting of two oxo-bridged iron atoms bound to a characteristic set of conserved histidine: aspartate and glutamate residues with the motifs H-HxxxE-HxxxH-HxxxxD. It has recently been demonstrated biochemically that two bacterial proteins bearing the same motifs do in fact possess similar iron centres and bind oxygen in the same way. The recent profusion of prokaryotic genomic sequence data has shown that proteins bearing hemerythrin motifs are present in a wide variety of bacteria, and a few archaea. Some of these are short proteins as in eukaryotes; others appear to consist of a hemerythrin domain fused to another domain, generally a putative signal transduction domain such as a methyl-accepting chemotaxis protein, a histidine kinase, or a GGDEF protein (cyclic di-GMP synthase). If, as initial evidence suggests, these are in fact hemerythrin-like oxygen-binding proteins, then their diversity in prokaryotes far exceeds that seen in eukaryotes. Here, a survey is presented of prokaryotic protein sequences bearing hemerythrin-like motifs, for which the designation 'bacteriohemerythrins' is proposed, and their functions are speculated.     

A phyletic perspective on the allometry of plant biomass-partitioning patterns and functionally equivalent organ-categories

Biomass-partitioning patterns influence the functioning of aquatic and terrestrial vegetation at all levels, ranging from individual growth and reproduction to the flow of mass and energy through entire communities. For this reason, leaf, stem and root dry biomass-partitioning patterns across taxonomically and ecologically diverse seed plants (spermatophytes) have been intensively investigated, both empirically and theoretically. By contrast, phyletically disparate plants (e.g. green and brown algal macrophytes, mosses and pteridophytes) have not been examined to determine whether the partitioning of their body parts into 'leaf', 'stem' and 'root' analogs accords with that of spermatophytes. In this review, the biomass-partitioning patterns of siphonous and brown algal macrophytes, mosses and pteridophytes were compared allometrically with those of spermatophytes and were shown to be largely in statistical accordance (thus lending support to the hypothesis that a single scaling relationship exists across eukaryotic photoautotrophs). This concordance is argued to support the hypothesis of functional equivalence across analogous, but developmentally different, body parts, a feature that permits the use of simpler biological model systems with which to derive analytical explanations for the biomass-partitioning patterns reported for more complex seed plants.     

Taxonomic patterns in the nitrogen assimilation of soil prokaryotes

Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with ¹⁵N. Following incubation with ¹⁵ , distinct patterns of ¹⁵N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated ¹⁵N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased ¹⁵N use by Firmicutes and Bacteriodetes. While is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with ¹⁵N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment.     

Occurrence of lignin degradation genotypes and phenotypes among prokaryotes

A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.     

Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms

Microbial biogeography studies expend much effort in determining whether environmental selection or stochastic processes related to dispersal are more important in shaping community composition. While both types of factors are possibly influential, it is tacitly assumed that protists, or microbial eukaryotes in general, behave biogeographically as prokaryotes because of their small physical size. However, direct evidence for this in exactly the same environment and at the same phylogenetic depth is lacking. In this study, we compared the structure of both prokaryotic and eukaryotic components of microbial communities forming biofilms on mineral substrates in different geographic locations at the level of small-subunit (SSU) rRNA-based operational taxonomic units (OTUs). These microbial communities are subjected to strong environmental selection and contain significant proportions of extremophilic microorganisms adapted to desiccation and UV radiation. We find that the nature of the substrate as well as climatic variables and geography influences microbial community structure. However, constrained correspondence analyses and distance-decay curves showed that, whereas the substrate type was the most significant factor structuring bacterial communities, geographic location was the most influential factor for microbial eukaryote communities. Biological explanations implying a higher dispersal success for bacteria combined with more mobile lifestyles for predatory protists may underlie these different prokaryote versus microbial eukaryote biogeographic patterns.     

Avoid your neighbours: size-determined spatial distribution patterns among northern pike individuals

The spatial distribution of individual animals may both cause and be caused by intra- and/or interspecific interactions. This work aims primarily on effects of intraspecific interactions. Agonistic and unequally strong interactions among conspecifics should make the within-population distribution of individuals to be characterised by spatial avoidance of potentially risky conspecifics, according to the individual risks perceived. This process should affect individual performance and involve individual tradeoffs, as failing to adequately avoid risky conspecifics could incur unnecessary costs, while, at the same time, successful conspecific avoidance may reduce access to patches favourable for e.g. foraging or sheltering. Intraspecific agonistic behaviours, such as cannibalism and competition, are likely to have prominent effects in size-structured populations. It is therefore reasonable to assume spatial avoidance of intraspecific risks according to individuals' size relationships in such populations. With this field investigation I show that individuals of northern pike spatially avoid larger conspecifics. This avoidance creates a size-influenced and spatially clumped distribution pattern among pike individuals. At low pike densities, however, distances between individuals increase, allowing for an even distribution pattern to appear. The spatial distribution patterns among piscivore individuals should affect both the individual performance of predators and the potential for spatial anti-predatory responses of their prey, and hence be a factor in consumer–resource interactions.     

Shared strategies in gene organization among prokaryotes and eukaryotes

Although genes in prokaryotes and eukaryotes are transcribed and translated by very different mechanisms, they may be organized in their respective chromosomes in surprisingly similar ways. Here, I examine common modes of maintaining nonrandom gene organization in both prokaryotes and eukaryotes, the different ways these organizations have likely arisen, and classes of organization that may be unique to one group or the other.     

Cleavage patterns, cell-lineages and cell specification are clues to phyletic lineages in Spiralia

Embryos of molluscs, annelids, nemerteans and platyhelminthes show remarkable intra- and interphyletic resemblances and differences in mesentoblast, dorso-ventral axis and trochoblast specification. These variations have been used to investigate their evolutionary relationship. In molluscs and annelids a heterochronic shift parallels evolutionary relations based on adult characters. Nemerteans and platyhelminthes lack trochal cells and differ in the specification of the mesodermal precursor cell. Nemerteans also differ fundamentally with respect to axis specification related to the first cleavage. Therefore, close phylogenetic relations exist between molluscs and annelids, whereas nemerteans and platyhelminthes are only remotely related with each other and with molluscs and annelids.     

Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns

Background

Phyletic patterns denote the presence and absence of orthologous genes in completely sequenced genomes and are used to infer functional links between genes, on the assumption that genes involved in the same pathway or functional system are co-inherited by the same set of genomes. However, this basic premise has not been quantitatively tested, and the limits of applicability of the phyletic-pattern method remain unknown.

Results

We characterized a hierarchy of 3,688 phyletic patterns encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes, using different distances, clustering algorithms, and measures of cluster quality. The most sensitive set of parameters recovered 223 clusters, each consisting of genes that belong to the same metabolic pathway or functional system. Fifty-six clusters included unexpected genes with plausible functional links to the rest of the cluster. Only a small percentage of known pathways and multiprotein complexes are co-inherited as one cluster; most are split into many clusters, indicating that gene loss and displacement has occurred in the evolution of most pathways.

Conclusions

Phyletic patterns of functionally linked genes are perturbed by differential gains, losses and displacements of orthologous genes in different species, reflecting the high plasticity of microbial genomes. Groups of genes that are co-inherited can, however, be recovered by hierarchical clustering, and may represent elementary functional modules of cellular metabolism. The phyletic patterns approach alone can confidently predict the functional linkages for about 24% of the entire data set.     

Karyomorphological parameters and C-band distribution suggest phyletic relationships within the subtribeLimodorinae (Orchidaceae)

Karyotype attributes and heterochromatin distribution were used to characterize fourteen taxa of the subtribeLimodorinae (Orchidaceae). The karyotypes were established using morphometrical parameters following Feulgen staining and C-banding. No significant differences in heterochromatin content were found between specimens collected from various sites. Four species of theEpipactis helleborine group possess some chromosome pairs with quite similar heterochromatin patterns; some differences were found inE. distans with respect to other species of this group.Epipactis palustris differed significantly from otherEpipactis species in its different karyotype and its numerous terminal C-bands. The largest differences from the other genera were shown inLimodorum as far as karyomorphology and heterochromatin patterns were concerned. C-band distribution indicated similarity among non-homologous chromosomes, supporting a possible palaeo-polyploid origin for theCephalanthera andEpipactis karyotypes.     

WD-repeat protein encoding genes among prokaryotes of theStreptomyces genus

Southern hybridization with probes designed for detection of WD-repeats coding sequences gave positive results in 21 streptomycete strains indicating that WD-repeats encoding genes are massively spread among streptomycetes. One of them, thewdlA gene ofStreptomyces lincolnensis, codes for a 971 amino acid protein with seven WD-repeats in its C-terminus, two transmembrane domains and an ATP/GTP binding site upstream of the WD-repeat region.