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PubMed1996

Ancestral relationships of the major eukaryotic lineages.

Molecular systematics has revolutionized our understanding of microbial evolution. Phylogenetic frameworks relating all organisms in this biosphere can be inferred from comparisons of slowly evolving molecules such as the small and large subunit ribosomal RNAs. Unlike today's text book standard, the "Five Kingdoms" (plants, animals, fungi, protists and bacteria), molecular studies define three primary lines of descent (Eukaryotes, Eubacteria, and Archaebacteria). Within the Eukaryotes, the "higher" kingdoms (Fungi, Plantae, and Animalia) are joined by at least two novel complex evolutionary assemblages, the "Alveolates" (ciliates, dinoflagellates and apicomplexans) and the "Stramenopiles" (diatoms, oomycetes, labyrinthulids, brown algae and chrysophytes). The separation of these eukaryotic groups (described as the eukaryotic "crown") occurred approximately 10(9) years ago and was preceded by a succession of earlier diverging protist lineages, some as ancient as the separation of the prokaryotic domains. The molecular phylogenies suggest that multiple endosymbiotic events introduced plastids into discrete eukaryotic lineages.

Animal Population Groups↗
PubMed1994

Trachoma and LGV biovars of Chlamydia trachomatis share the same glycosaminoglycan-dependent mechanism for infection of eukaryotic cells.

A sulphated glycosaminoglycan-dependent mechanism of microbial infection for mammalian cells was characterized for the Chlamydia trachomatis trachoma and lymphogranuloma venereum (LGV) biovars. We demonstrated that the trachoma and LGV biovars compete for the same receptor(s) on host cells and that their infectivity was inhibited by heparin or heparan sulphate. Using a specific heparan sulphate lyase (heparitinase) to treat organisms, the infectivity of both biovars was abolished. Furthermore, exogenous heparan sulphate rescued chlamydial infectivity following treatment with heparitinase and the restored infectivity was neutralized by an anti-heparan sulphate monoclonal antibody. These data suggest that heparan sulphate-like-mediated interactions between C. trachomatis and eukaryotic cells are essential for infectivity.

Animals↗
PubMed2004

Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains.

Originally identified from eukaryotes, the Mg2+- or Mn2+-dependent protein phosphatases (PPMs) are a diverse group of enzymes whose members include eukaryotic PP2C and some prokaryotic serine/threonine phosphatases. In a previous study, unexpectedly large numbers of PPMs were identified in two Streptomyces genomes. In this work, a phylogenetic analysis was performed with all the PPMs available from a wide variety of microbial sources to determine the evolutionary origin of the Streptomyces PPM proteins. Consistent with earlier hypotheses, the results suggested that the microbial PPMs were relatively recent additions from eukaryotic sources. Results also indicated that the Streptomyces PPMs were divided into two major subfamilies at an early stage of their emergence in Streptomyces genomes. The first subfamily, which contains only six Streptomyces PPMs, possesses a catalytic domain whose sequence and architecture are similar to that of eukaryotic PPMs; the second subfamily contains 89 Streptomyces PPMs that lack the 5a and 5b catalytic domain motifs, similar to the PPMs SpoIIE and RsbU of Bacillus subtilis. Significant gene duplication was observed for the PPMs in the second subfamily. In addition, more than half (54 %) of the Streptomyces PPMs from the second subfamily were found to have at least one additional sensory domain, most commonly the PAS or the GAF domain. Phylogenetic analysis showed that these domains tended to be clustered according to the putative physiological functions rather than taxonomic relationship, implying that they might have arisen as a result of domain recruitment in a late evolutionary stage. This study provides an insight into how Streptomyces spp. may have expanded their PPM-based signal transduction networks to enable them to respond to a greater range of environmental changes.

Catalytic Domain↗
PubMed2006

New opportunities revealed by biotechnological explorations of extremophiles.

Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of potential applications for biotechnology. More recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles.

Archaea↗
PubMed2000

The Santa Barbara Basin is a symbiosis oasis.

It is generally agreed that the origin and initial diversification of Eucarya occurred in the late Archaean or Proterozoic Eons when atmospheric oxygen levels were low and the risk of DNA damage due to ultraviolet radiation was high. Because deep water provides refuge against ultraviolet radiation and early eukaryotes may have been aerotolerant anaerobes, deep-water dysoxic environments are likely settings for primeval eukaryotic diversification. Fossil evidence shows that deep-sea microbial mats, possibly of sulphur bacteria similar to Beggiatoa, existed during that time. Here we report on the eukaryotic community of a modern analogue, the Santa Barbara Basin (California, USA). The Beggiatoa mats of these severely dysoxic and sulphidic sediments support a surprisingly abundant protistan and metazoan meiofaunal community, most members of which harbour prokaryotic symbionts. Many of these taxa are new to science, and both microaerophilic and anaerobic taxa appear to be represented. Compared with nearby aerated sites, the Santa Barbara Basin is a 'symbiosis oasis' offering a new source of organisms for testing symbiosis hypotheses of eukaryogenesis.

Animals↗
PubMed1992

On the nature of global classification.

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

Biological Evolution↗
PubMed2000

MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region.

Our challenge in annotating the 2.91-Mb Adh region of the Drosophila melanogaster genome was to identify genetic and genomic features automatically, completely, and precisely within a 6-week period. To do so, we augmented the MAGPIE microbial genome annotation system to handle eukaryotic genomic sequence data. The new configuration required the integration of eukaryotic gene-finding tools and DNA repeat tools into the automatic data collection module. It also required us to define in MAGPIE new strategies to combine data about eukaryotic exon predictions with functional data to refine the exon predictions. At the heart of the resulting new eukaryotic genome annotation system is a reverse comparison of public protein and complementary DNA sequences against the input genome to identify missing exons and to refine exon boundaries. The software modules that add eukaryotic genome annotation capability to MAGPIE are available as EGRET (Eukaryotic Genome Rapid Evaluation Tool).

Alcohol Dehydrogenase↗
PubMed1998

Hemoglobin biosynthesis in Vitreoscilla stercoraria DW: cloning, expression, and characterization of a new homolog of a bacterial globin gene.

In the strictly aerobic, gram-negative bacterium Vitreoscilla strain C1, oxygen-limited growth conditions create a more than 50-fold increase in the expression of a homodimeric heme protein which was recognized as the first bacterial hemoglobin (Hb). The recently determined crystal structure of Vitreoscilla Hb has indicated that the heme pocket of microbial globins differs from that of eukaryotic Hbs. In an attempt to understand the diverse functions of Hb-like proteins in prokaryotes, we have cloned and characterized the gene (vgb) encoding an Hb-like protein from another strain of Vitreoscilla, V. stercoraria DW. Several silent changes were observed within the coding region of the V. stercoraria vgb gene. Apart from that, V. stercoraria Hb exhibited interesting differences between the A and E helices. Compared to its Hb counterpart from Vitreoscilla strain C1, the purified preparation of V. stercoraria Hb displays a slower autooxidation rate. The differences between Vitreoscilla Hb and V. stercoraria Hb were mapped onto the three-dimensional structure of Vitreoscilla Hb, which indicated that the four changes, namely, Ile7Val, Ile9Thr, Ile10Ser, and Leu62Val, present within the V. stercoraria Hb fall in the region where the A and E helices contact each other. Therefore, alteration in the relative orientation of the A and E helices and the corresponding conformational change in the heme binding pocket of V. stercoraria Hb can be correlated to its slower autooxidation rate. In sharp contrast to the oxygen-regulated biosynthesis of Hb in Vitreoscilla strain C1, production of Hb in V. stercoraria has been found to be low and independent of oxygen control, which is supported by the absence of a fumarate and nitrate reductase regulator box within the V. stercoraria vgb promoter region. Thus, the regulation mechanisms of the Hb-encoding gene appear to be quite different in the two closely related species of Vitreoscilla. The relatively slower autooxidation rate of V. stercoraria Hb, lack of oxygen sensitivity, and constitutive production of Hb suggest that it may have some other function(s) in the cellular physiology of V. stercoraria DW, together with facilitated oxygen transport, predicted for earlier reported Vitreoscilla Hb.

Amino Acid Sequence↗
PubMed1994

Partial purification and characterization of DNA topoisomerase II from Plasmodium falciparum.

DNA topoisomerase II from Plasmodium falciparum was partially purified by FPLC using three columns: Econo-Pac Q, heparin-agarose and Mono Q. The enzyme showed ATP- and Mg2 +/- dependent activities in a decatenation assay, with optimum concentrations of 0.5 and 10 mM, respectively. Furthermore, highest activity was detected in the presence of 100 mM KCI. Enzyme decatenation activity was not inhibited by the DNA topoisomerase I inhibitor, camptothecin, but was sensitive to both prokaryotic and eukaryotic DNA topoisomerase II inhibitors.

Animals↗
PubMed1999

Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment.

Microbial populations, their distributions, and their aquatic environments were studied over a year (1997) at an acid mine drainage (AMD) site at Iron Mountain, Calif. Populations were quantified by fluorescence in situ hybridizations with group-specific probes. Probes were used for the domains Eucarya, Bacteria, and Archaea and the two species most widely studied and implicated for their role in AMD production, Thiobacillus ferrooxidans and Leptospirillum ferrooxidans. Results show that microbial populations, in relative proportions and absolute numbers, vary spatially and seasonally and correlate with geochemical and physical conditions (pH, temperature, conductivity, and rainfall). Bacterial populations were in the highest proportion (>95%) in January. Conversely, archaeal populations were in the highest proportion in July and September ( approximately 50%) and were virtually absent in the winter. Bacterial and archaeal populations correlated with conductivity and rainfall. High concentrations of dissolved solids, as reflected by high conductivity values (up to 125 mS/cm), occurred in the summer and correlated with high archaeal populations and proportionally lower bacterial populations. Eukaryotes were not detected in January, when total microbial cell numbers were lowest (<10(5) cells/ml), but eukaryotes increased at low-pH sites ( approximately 0.5) during the remainder of the year. This correlated with decreasing water temperatures (50 to 30 degrees C; January to November) and increasing numbers of prokaryotes (10(8) to 10(9) cells/ml). T. ferrooxidans was in highest abundance (>30%) at moderate pHs and temperatures ( approximately 2.5 and 20 degrees C) in sites that were peripheral to primary acid-generating sites and lowest (0 to 5%) at low-pH sites (pH approximately 0.5) that were in contact with the ore body. L. ferrooxidans was more widely distributed with respect to geochemical conditions (pH = 0 to 3; 20 to 50 degrees C) but was more abundant at higher temperatures and lower pHs ( approximately 40 degrees C; pH approximately 0.5) than T. ferrooxidans.

Archaea↗
PubMedDate not supplied

[Homologous protein domains in superkingdoms Archaea, Bacteria, and Eukaryota and the problem of the origin of eukaryotes].

The distribution of protein domains was analyzed in superkingdoms Archaea, Bacteria, and Eukaryota. About a half of eukaryotic domains have prokaryotic origin. Many domains related to information processing in the nucleocytoplasm were inherited from archaea. Sets of domains associated with metabolism and regulatory and signaling systems were inherited from bacteria. Many signaling and regulatory domains common for bacteria and eukaryotes were responsible for the cellular interaction of bacteria with other components of the microbial community but were involved in coordination of the activity of eukaryotic organelles and cells in multicellular organisms. Many eukaryotic domains of bacterial origin could not originate from ancestral mitochondria and plastids but rather were adopted from other bacteria. An archaeon with the induced incorporation of alien genetic material could be the ancestor of the eukaryotic nucleocytoplasm.

Animals↗
PubMed1994

A simple method to eliminate mycoplasma from cell cultures.

The efficacy of several antibiotic treatments to eliminate mycoplasma from Vero cells contaminated chronically with Mycoplasma orale II were tested. Minocyclin, Kanamycin, Tylosine and Roxitromycin, at non cytotoxic concentrations, were assayed alone or in different combinations. Mycoplasma contamination was effectively eradicated without recurrence once the following regimen was applied: Incubation of contaminated cells with Tylosine (250 micrograms/ml) for 12 days followed by incubation with Minocycline (5 micrograms/ml) for 10 days. This treatment was not deleterious for cell growth, it was effective after only one application and it was successful to eradicate mycoplasma from other contaminated eukaryotic continuous cell lines.

Animals↗
PubMed2003

Sedimentary microbial community dynamics in a regulated stream: East Fork of the Little Miami River, Ohio.

A field study was conducted in the Lower East Fork of the Little Miami River, a regulated stream in Clermont county, Ohio, to determine how changes in streamflow, water temperature and photo-period affect sediment microbial community structure. Surface sediment cores were collected from sampling stations spanning 60 river kilometers three to four times per year between October 1996 and October 1999. During the final year of the field study, water temperature, water depth, conductivity, total suspended solids, dissolved organic carbon, instantaneous streamflow velocity, sediment grain size and sediment organic matter were determined. Total microbial biomass was measured using the phospholipid phosphate technique (PLP) and ranged between 2 and 134 nmol PLP * g(-1) dry weight sediment with a mean of 25 nmol PLP * g(-1). Microbial community structure was determined using the phospholipid fatty acid analysis and indicated seasonal shifts in sedimentary microbial community composition. January to June sedimentary microbial biomass was predominately prokaryotic (60% +/- 2), whereas microeukaryotes dominated samples collected during the late summer (55% +/- 2.4) and fall (60% +/- 2). These changes were correlated with stream discharge and water temperature. Microbial community structure varied spatially about a reservoir with prokaryotic biomass dominant at upstream stations and eukaryotic biomass dominant at downstream stations. These findings reveal that sedimentary microbial communities in streams are dynamic responding to the seasonal variation of environmental factors.

Ecosystem↗
PubMed2005

DING proteins are from Pseudomonas.

DING proteins have been described as animal and plant proteins with potential biomineralisation, receptor or signalling roles that have been characterised by an N-terminal DINGGG-sequence. However, these sequences have only ever been identified as either N-terminal peptides or partial cDNA sequences, and have yet to be detected in any of the many genomic animal and plant genomes now available. Microbial relatives of the DING proteins have been described, which appear to be periplasmic phosphate-binding proteins. Recently, full-length Pseudomonas aeruginosa UCBPP-PA14 and Hypericum perforatum genes have been sequenced that show high homology to the published DING protein N-terminal sequences, and small peptides previously identified in conjunction with the peptide sequencing of DING proteins can also be mapped to regions across these full-length sequences. Searching with these sequences identifies other plant and animal cDNA fragments in the public nucleotide databases, and, additionally, an unordered rat genomic contig that contains a DING-like sequence on a small fragment. Analysing the codon usage of these DNA sequences identifies all of these sequences as of Pseudomonas origin, suggesting that DING proteins do not exist in eukaryotes, but instead are potentially due to microbial contamination or infection.

Amino Acid Sequence↗
PubMed2006

Sphingolipids as targets for microbial infections.

Sphingolipids had long been regarded as merely structural components of eukaryotic cellular membranes. Research has discovered sphingolipids to have crucial roles in cellular processes as bioactive molecules. Lately, there has also been an increased interest in sphingolipids and sphingolipid-metabolizing enzymes as mediators of microbial pathogenicity and as potential targets for the development of new therapeutics. This minireview will provide a comprehensive analysis of sphingolipid pathways in mammalian and microbial cells, highlighting their uniqueness and discussing their potential as therapeutic targets for microbial infections.

Animals↗
PubMed1999

Unexpected population distribution in a microbial mat community: sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia.

The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with group-specific hybridization probes to quantify 16S rRNA extracted from 100-microm depth intervals. This revealed a preferential localization of SRB within the region defined by the oxygen chemocline. Among the different groups of SRB quantified, including members of the provisional families "Desulfovibrionaceae" and "Desulfobacteriaceae," Desulfonema-like populations dominated and accounted for up to 30% of total rRNA extracted from certain depth intervals of the chemocline. These data suggest that recognized genera of SRB are not necessarily restricted by high levels of oxygen in this mat community and the possibility of significant sulfur cycling within the chemocline. In marked contrast, eukaryotic populations in this community demonstrated a preference for regions of anoxia.

Anaerobiosis↗