| 1. |
- Andersson, Jan O, et al.
(author)
-
A century of typhus, lice and Rickettsia
- 2000
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In: Research in Microbiology. - : EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER. - 0923-2508 .- 1769-7123. ; 151:2, s. 143-150
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Journal article (peer-reviewed)abstract
- At the beginning of the 20th century, it was discovered at the Pasteur Institute in Tunis that epidemic typhus is transmitted by the human body louse. The complete genome sequence of its causative agent, Rickettsia prowazekii, was determined at Uppsala University in Sweden at the end of the century. In this mini-review, we discuss insights gained from the genome sequence of this fascinating and deadly organism.
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| 2. |
- Naumov, Gennadi I., et al.
(author)
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Genetic characterization of the nonconventional yeast Hansenula anomala
- 2001
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In: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 152:6, s. 551-562
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Journal article (peer-reviewed)abstract
- We describe genetic, molecular and taxonomic characteristics of the yeast Hansenula anomala. Pulsed-field gel electrophoresis of chromosomal DNAs from 19 H. anomala strains and related species indicated that H. anomala had a clearly different karyotype. Chromosome length polymorphism of the H. anomala strains was independent of their geographic origin and source of isolation. The strains were classified into four groups of similar karyotypes and one strain showed a unique profile. The sizes of chromosomes ranged from 850 to 3500 kb in different strains. The haploid chromosome number of H. anomala is at least nine. We have found RAPD primers discriminating at both the species and strain levels. All the primers tested except the M13 core sequence generated unique patterns with most strains. The results indicate the usefulness of PCR analysis with primer M13 for identification of the H. anomala species. Screening of the CBS (Utrecht) collection strains of H. anomala showed that they are rather difficult objects for genetic hybridization analysis. The strains have low fertility, viz. very poor sporulation, low mating type activities and, as a rule, nonviable ascospores. The majority of the hybrids obtained are polyploid, probably tetraploid, as judged by the segregation of control auxotrophic markers. Nevertheless, some monosporic cultures of the strains studied, including the biocontrol yeast J121, formed diploid hybrids with regular meiotic segregation of control auxotrophic markers. As a rule, H. anomala isolates are homothallic, showing delayed self-diploidization. Rare stable heterothallic strains of H. anomala also occur.
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| 3. |
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| 4. |
- Campos, Manuel, et al.
(author)
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The type II secretion system : a dynamic fiber assembly nanomachine
- 2013
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 164:6, s. 545-555
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Journal article (peer-reviewed)abstract
- Type II secretion systems (T2SSs) share common origins and structure with archaeal flagella (archaella) and pili, bacterial competence systems and type IV pili. All of these systems use a conserved ATP-powered machinery to assemble helical fibers that are anchored in the plasma membrane. The T2SSs assemble pseudopili, periplasmic filaments that promote extracellular secretion of folded periplasmic proteins. Comparative analysis of T2SSs and related fiber assembly nanomachines might provide important clues on their functional specificities and dynamics. This review focuses on recent developments in the study of pseudopilus structure and biogenesis, and discusses mechanistic models of pseudopilus function in protein secretion.
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| 5. |
- Christel, Stephan, et al.
(author)
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Comparison of Boreal Acid Sulfate Soil Microbial Communities in Oxidative and Reductive Environments
- 2019
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In: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 170:6-7, s. 288-295
-
Journal article (peer-reviewed)abstract
- Due to land uplift after the last ice age, previously stable Baltic Sea sulfidic sediments are becoming dry land. When these sediments are drained, the sulfide minerals are exposed to air and can release large amounts of metals and acid into the environment. This can cause severe ecological damage such as fish kills in rivers feeding the northern Baltic Sea. In this study, five sites were investigated for the occurrence of acid sulfate soils and their geochemistry and microbiology was identified. The pH and soil chemistry identified three of the areas as having classical acid sulfate soil characteristics and culture independent identification of 16S rRNA genes identified populations related to acidophilic bacteria capable of catalyzing sulfidic mineral dissolution, including species likely adapted to low temperature. These results were compared to an acid sulfate soil area that had been flooded for ten years and showed that the previously oxidized sulfidic materials had an increased pH compared to the unremediated oxidizied layers. In addition, the microbiology of the flooded soil had changed such that alkalinity producing ferric and sulfate reducing reactions had likely occurred. This suggested that flooding of acid sulfate soils mitigates their environmental impact.
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| 6. |
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| 7. |
- Fuxelius, Hans-Henrik, et al.
(author)
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The genomic and metabolic diversity of Rickettsia
- 2007
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 158:10, s. 745-753
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Journal article (peer-reviewed)abstract
- Comparative genomics of Rickettsia and Orientia has revealed an exciting interplay between reductive evolutionary forces acting on metabolic genes in all species and proliferation of mobile genetic elements in some species. These contradictory evolutionary forces highlight the influence of chance, adaptation and host-cell exploitation during the evolution of intracellular bacteria.
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| 8. |
- Goncalves, Odete Sofia Lopes, et al.
(author)
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The repeated 36 amino acid motif of Chlamydia trachomatis Hc2 protein binds to the major groove of DNA
- 2019
-
In: Research in Microbiology. - : ELSEVIER. - 0923-2508 .- 1769-7123. ; 170:6-7, s. 256-262
-
Journal article (peer-reviewed)abstract
- The gram-negative, obligate intracellular human pathogen, Chlamydia trachomatis has a bi-phasic developmental cycle. The histone H1-like C. trachomatis DNA binding protein, Hc2, is produced late during the developmental cycle when the dividing reticulate body transforms into the smaller, metabolically inactive elementary body. Together with Hc1, the two proteins compact the chlamydial chromosome and arrest replication and transcription. Hc2 is heterogeneous in length due to variation in the number of lysine rich pentamers. Six pentamers and one hexamer constitute a 36 amino acid long repetitive unit that, in spite of variations, is unique for Chlamydiaceae. Using synthetic peptides, the DNA-binding capacity of the 36 amino acid peptide and that of a randomized peptide was analyzed. Both peptides bound and compacted plasmid DNA, however, electron microscopy of peptide/DNA complexes showed major differences in the resulting aggregated structures. Fluorescence spectroscopy was used to analyze the binding. After complexing plasmid DNA with each of three different intercalating dyes, increasing amounts of peptides were added and fluorescence spectroscopy performed. The major groove binder, methyl green, was displaced by both peptides at low concentrations, while the minor groove binder, Hoechts, and the intercalating dye, Ethidium Bromide, were displaced only at high concentrations of peptides. (C) 2019 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
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| 9. |
- González, Carolina, et al.
(author)
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Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis.
- 2014
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 165:9, s. 726-734
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Journal article (peer-reviewed)abstract
- Acidophilic microorganisms inhabit low pH environments such as acid mine drainage that is generated when sulfide minerals are exposed to air. The genome sequence of the psychrotolerant Acidithiobacillus ferrivorans SS3 was compared to a metagenome from a low temperature acidic stream dominated by an A. ferrivorans-like strain. Stretches of genomic DNA characterized by few matches to the metagenome, termed 'metagenomic islands', encoded genes associated with metal efflux and pH homeostasis. The metagenomic islands were enriched in mobile elements such as phage proteins, transposases, integrases and in one case, predicted to be flanked by truncated tRNAs. Cus gene clusters predicted to be involved in copper efflux and further Cus-like RND systems were predicted to be located in metagenomic islands and therefore, constitute part of the flexible gene complement of the species. Phylogenetic analysis of Cus clusters showed both lineage specificity within the Acidithiobacillus genus as well as niche specificity associated with an acidic environment. The metagenomic islands also contained a predicted copper efflux P-type ATPase system and a polyphosphate kinase potentially involved in polyphosphate mediated copper resistance. This study identifies genetic variability of low temperature acidophiles that likely reflects metal resistance selective pressures in the copper rich environment.
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| 10. |
- Grones, Peter
(author)
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Characterization of newly identified DnaA and DnaB proteins from Acetobacter
- 2016
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 167, s. 655-668
-
Journal article (peer-reviewed)abstract
- Although chromosomal replication is an essential feature of the bacterial life cycle, the replication mechanism and involved molecular players have never been properly characterized in the Acetobacter genera. Thanks to whole-genome sequencing, the unknown replication proteins from Acetobacter pasteurianus and Acetobacter orleanensis, DnaA-like and DnaB-like, could be identified. Despite the low nucleotide or amino acid similarity to the respective orthologs from Escherichia coli, their involvement during replication regulation was corroborated by artificial microRNA. In the Acetobacter genome, a novel replication origin, oriAo, was detected with three 9-nucleotide-long DnaA boxes to which DnaA-like proteins bind actively. Bacterial two-hybrid systems and co-immunoprecipitation confirmed the homologous and heterologous interactions between DnaA-like and DnaB-like proteins with their E. coli orthologs. This communication is due to the conserved tryptophan at position 6 for E. coli or 25 for Acetobacter that unables DnaA-like proteins to form oligomeric protein structures after its substitution. Altogether, these results provide novel insights into the genome replication mechanism in Acetobacter. (C) 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
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| 11. |
- Jonsson, Anders, et al.
(author)
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Reduced activity of glutamine synthetase in Rhodospirillum rubrum mutants lacking the adenylyltransferase GlnE
- 2009
-
In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 160:8, s. 581-4
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Journal article (peer-reviewed)abstract
- In the nitrogen-fixing bacterium Rhodospirillum rubrum, the GlnE adenylyltransferase (encoded by glnE) catalyzes reversible adenylylation of glutamine synthetase, thereby regulating nitrogen assimilation. We have generated glnE mutant strains that are unable to adenylylate glutamine synthetase (GS). Surprisingly, the activity of GS was lower in the mutants than in the wild type, even when grown in nitrogen-fixing conditions. Our results support the proposal that R. rubrum can only cope with the absence of an adenylylation system in the presence of lowered GS expression or activity. In general terms, this report also provides further support for the central role of GS in bacterial metabolism.
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| 12. |
- Kupka, Daniel, et al.
(author)
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Oxidation of elemental sulfur, tetrathionate and ferrous iron by the psychrotolerant Acidithiobacillus strain SS3.
- 2009
-
In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 160:10, s. 767-774
-
Journal article (peer-reviewed)abstract
- Mesophilic iron and sulfur-oxidizing acidophiles are readily found in acid mine drainage sites and bioleaching operations, but relatively little is known about their activities at suboptimal temperatures and in cold environments. The purpose of this work was to characterize the oxidation of elemental sulfur (S(0)), tetrathionate (S4O6(2-)) and ferrous iron (Fe2+) by the psychrotolerant Acidithiobacillus strain SS3. The rates of elemental sulfur and tetrathionate oxidation had temperature optima of 20 degrees and 25 degrees C, respectively, determined using a temperature gradient incubator that involved narrow (1.1 degrees C) incremental increases from 5 degrees to 30 degrees C. Activation energies calculated from the Arrhenius plots were 61 and 89 kJ mol(-1) for tetrathionate and 110 kJ mol(-1) for S(0) oxidation. The oxidation of elemental sulfur produced sulfuric acid at 5 degrees C and decreased the pH to approximately 1. The low pH inhibited further oxidation of the substrate. In media with both S(0) and Fe2+, oxidation of elemental sulfur did not commence until all available ferrous iron was oxidized. These data on sequential oxidation of the two substrates are in keeping with upregulation and downregulation of several proteins previously noted in the literature. Ferric iron was reduced to Fe2+ in parallel with elemental sulfur oxidation, indicating the presence of a sulfur:ferric iron reductase system in this bacterium.
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| 13. |
- Liu, Junfa, et al.
(author)
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Elevated CpxR~P levels repress the Ysc-Yop type III secretion system of Yersinia pseudotuberculosis
- 2012
-
In: Research in Microbiology. - Elsevier : Elsevier BV. - 0923-2508 .- 1769-7123. ; 163:8, s. 518-530
-
Journal article (peer-reviewed)abstract
- One way that Gram-negative bacteria respond to extracytoplasmic stress is through the CpxA-CpxR system. An activated CpxA sensor kinase phosphorylates the CpxR response regulator to instigate positive auto-amplification of Cpx pathway activation, as well as synthesis of various bacterial survival factors. In the absence of CpxA, human enteropathogenic Yersinia pseudotuberculosis accumulates high CpxR~P levels aided by the action of low molecular weight phosphodonors such as acetyl~P. Critically, these bacteria are also defective for plasmid encoded Ysc-Yop-dependent type III synthesis and secretion, an essential determinant of virulence. Herein, we investigated whether elevated CpxR~P levels account for lost Ysc-Yop function. Decisively, reducing CpxR~P in Yersinia defective for CpxA phosphatase activity - through incorporating second-site suppressor mutations in ackA-pta or cpxR - dramatically restored Ysc-Yop T3S function. Moreover, the repressive effect of accumulated CpxR~P is a direct consequence of binding to the promoter regions of the T3S genes. Thus, Cpx pathway activation has two consequences in Yersinia; one, to maintain quality control in the bacterial envelope, and the second, to restrict ysc-yop gene expression to those occasions where it will have maximal effect.
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| 14. |
- Maisnier-Patin, Sophie, et al.
(author)
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Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution
- 2004
-
In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 155:5, s. 360-369
-
Journal article (peer-reviewed)abstract
- Compensatory mutations, due to their ability to mask the deleterious effects of another mutation, are important for the adaptation and evolution of most organisms. Resistance to antibiotics, antivirals, antifungals, herbicides and insecticides is usually associated with a fitness cost. As a result of compensatory evolution, the initial fitness costs conferred by resistance mutations (or other deleterious mutations) can often be rapidly and efficiently reduced. Such compensatory evolution is potentially of importance for (i) the long-term persistence of drug resistance, (ii) reducing the rate of fitness loss associated with the accumulation of deleterious mutations in small asexual populations, and (iii) the evolution of complexity of cellular processes.
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| 15. |
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| 16. |
- Moore, Edward R.B. 1954, et al.
(author)
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Microbial systematics and taxonomy: relevance for a microbial commons.
- 2010
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In: Research in microbiology. - : Elsevier BV. - 1769-7123 .- 0923-2508. ; 161:6, s. 430-8
-
Research review (peer-reviewed)abstract
- The issues of microbial taxonomy and potential interactions with a microbial commons are discussed, with emphasis on three components: characterization; classification; and nomenclature. The current state of technology and the spectrum of methods that are used for phenotypic and genotypic characterization of prokaryotes, classification at different taxonomic levels and points of prokaryote nomenclature are reviewed. While all taxonomic ranks comprise a cohesive systematic framework for microorganisms, the prokaryotic genus and species provide the "working unit" of taxonomy. Since 2004, the number of validly published genera and species has increased by approximately 50%. Extensive development of technology will continue to enable ever higher resolution characterization and more refined classification of microorganisms. Characterization and classification at the species level may be most relevant for bacterial taxonomy, although reproducible differentiation at the strain level will probably prove to be more relevant for a microbial commons. A dynamic microbial taxonomy, albeit with well-founded and stable guidelines for defining microorganisms, provides an efficient organizational system for dealing with the enormous spectrum of microbial diversity.
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| 17. |
- Ni, Gaofeng, et al.
(author)
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Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms
- 2016
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 167:7, s. 568-575
-
Journal article (peer-reviewed)abstract
- Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72 +/- 9 mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105 +/- 42 mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology. (C) 2016 The Authors. Published by Elsevier Masson SAS on behalf of Institut Pasteur.
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| 18. |
- Nilsson, Daniel P.G., et al.
(author)
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Physico-chemical characterization of single bacteria and spores using optical tweezers
- 2023
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In: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 174:6
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Journal article (peer-reviewed)abstract
- Spore-forming pathogenic bacteria are adapted for adhering to surfaces, and their endospores can tolerate strong chemicals making decontamination difficult. Understanding the physico-chemical properties of bacteria and spores is therefore essential in developing antiadhesive surfaces and disinfection techniques. However, measuring physico-chemical properties in bulk does not show the heterogeneity between cells. Characterizing bacteria on a single-cell level can thereby provide mechanistic clues usually hidden in bulk measurements. This paper shows how optical tweezers can be applied to characterize single bacteria and spores, and how physico-chemical properties related to adhesion, fluid dynamics, biochemistry, and metabolic activity can be assessed.
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| 19. |
- Otto, Karen
(author)
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Biophysical approaches to study the dynamic process of bacterial adhesion.
- 2008
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 159:6, s. 415-22
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Journal article (peer-reviewed)abstract
- Recent applications of biophysical techniques to the study of adhesion and biofilm formation are playing an important role in broadening our understanding of bacterial interactions. While non-invasive methods enable measurement of adhesion kinetics in real time, single-cell approaches provide information about adhesion forces mediated by specific cell surface structures. Promising approaches are presented in this review.
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| 20. |
- Poole, Anthony M
(author)
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Horizontal gene transfer and the earliest stages of the evolution of life
- 2009
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In: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 160:7, s. 473-480
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Journal article (peer-reviewed)abstract
- Horizontal gene transfer (HGT) has been suggested to be the dominant hereditary process at the earliest stages of evolution. I examine this suggestion within the context of the problem of genetic parasites and suggest that extreme rates of transfer may in fact negatively impact evolutionary transitions. In regard to the proposal that HGT is Lamarckian, the apparent conflict between HGT and Darwinian evolution is easily avoided by considering HGT at the appropriate level of selection.
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| 21. |
- Poole, Anthony M., et al.
(author)
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Reconciling an archaeal origin of eukaryotes with engulfment : a biologically plausible update of the Eocyte hypothesis
- 2011
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 162:1, s. 71-76
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Journal article (peer-reviewed)abstract
- An archaeal origin of eukaryotes is often equated with the engulfment of the bacterial ancestor of mitochondria by an archaeon. Such an event is problematic in that it is not supported by archaeal cell biology. We show that placing phylogenetic results within a stem-and-crown framework eliminates such incompatibilities, and that an archaeal origin for eukaryotes (as suggested from recent phylogenies) can be uncontroversially reconciled with phagocytosis as the mechanism for engulfment of the mitochondrial ancestor. This is significant because it eliminates a perceived problem with eukaryote origins: that an archaeal origin of eukaryotes (as under the Eocyte hypothesis) cannot be reconciled with existing cell biological mechanisms through which bacteria may take up residence inside eukaryote cells.
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| 22. |
- Roth, John R, et al.
(author)
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Amplification-mutagenesis : how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation
- 2004
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 155:5, s. 342-351
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Journal article (peer-reviewed)abstract
- The behavior of a particular bacterial genetic system has been interpreted as evidence that selective stress induces general mutagenesis or even preferentially directs mutations to sites that improve growth (adaptive mutation). It has been proposed that changes in mutability are a programmed response to stress in non-growing cells. In contrast, the amplification-mutagenesis model suggests that stress has no direct effect on the mutation rate and that mutations arise in cells growing under strong selection. In this model, stress serves only as a selective pressure that favors cells with multiple copies of a growth-limiting gene. Mutations are made more probable because more target copies are added to the selection plate-more cells with more mutational targets per cell. The amplification-mutagenesis process involves standard genetic events and therefore should apply to all biological systems. Idiosyncrasies of the particular system described here accelerate this process, allowing an evolutionary series of events to be completed in only a few days.
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| 23. |
- Sepúlveda-Rebolledo, Pedro, et al.
(author)
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Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives
- 2024
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In: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 175:1-2
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Journal article (peer-reviewed)abstract
- Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.
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| 24. |
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| 25. |
- Steger, Kristin, et al.
(author)
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Effects of differing temperature management on development of Actinobacteria populations during composting
- 2007
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 158:7, s. 617-624
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Journal article (peer-reviewed)abstract
- Actinobacteria are believed to play a major role in organic matter degradation and humification processes in composts. In this study, the effects of different temperature regimes on the succession of Actinobacteria populations during composting were investigated in a laboratory reactor. Phospholipid fatty acid (PLFA) was used to investigate quantitative changes in the overall microbial biomass and community structure, and in the size of Actinobacteria populations. Qualitative changes were determined using PCR-DGGE (denaturing gradient gel electrophoresis) and sequencing of 16S rRNA genes with Actinobacteria-specific primers. The peak in total microbial biomass was roughly twice as high and delayed in trials where the maximum temperature was 40 °C, compared to those where it was 55 or 67 °C. There was a shift from members of Corynebacterium, Rhodococcus and Streptomyces at the onset to species of thermotolerant Actinobacteria in the cooling phase, e.g. Saccharomonospora viridis, Thermobifida fusca and Thermobispora bispora. In conclusion, temperature was an important selective factor for the development of Actinobacteria populations in composts, and they constituted a substantial part of the community in the later compost stages.
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| 26. |
- Svanström, Åsa, et al.
(author)
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Intracellular trehalase activity is required for development, germination and heat-stress resistance of Aspergillus niger conidia
- 2013
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 164, s. 91-99
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Journal article (peer-reviewed)abstract
- The disaccharide trehalose is known as a stress protectant in several kinds of organisms, including fungi, where it is a major carbohydrate in resting structures, e.g. asexual conidia. The gene encoding the enzyme responsible for degradation of intracellular trehalose, treB, was deleted and the phenotype was analyzed in terms of morphology, trehalose content during conidial outgrowth and stress tolerance. The mutant conidiophores produced fewer and less viable spores, and during early stages of germination the internal levels of trehalose were higher compared to the wild type. When subjecting the mutant to various stresses (weak acid and salt), no increased sensitivity could be observed, but in line with previous observations, e.g. in Aspergillus nidulans, Aspergillus niger Delta treB spores in a very early stage of germination were less sensitive to heat stress. In contrast, when subjecting resting spores to 55 degrees C, an intact treB gene was essential for survival. This finding suggests that trehalose mobilization is required to facilitate cell recovery after heat-induced damage. (C) 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
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| 27. |
- Teixeira, Pedro Filipe, et al.
(author)
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Diazotrophic growth of Rhodospirillum rubrum with 2-oxoglutarate as sole carbon source affects the regulation of nitrogen metabolism as well as the soluble proteome
- 2010
-
In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 161:8, s. 651-659
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Journal article (peer-reviewed)abstract
- 2-Oxoglutarate plays a central role as a signal in the regulation of nitrogen metabolism in the phototrophic diazotroph Rhodospirillum rubrum. In order to further study the role of this metabolite, we have constructed an R. rubrum strain that has the capacity to grow on 2-oxoglutarate as sole carbon source, in contrast to wild-type R. rubrum. This strain has the same growth characteristics as wild-type with malate as carbon source, but showed clear metabolic differences when 2-oxoglutarate was used. Among other things, the regulation of nitrogen metabolism is altered, which can be related to different modification profiles of the regulatory PII proteins.
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| 28. |
- Wittorf, Lea, et al.
(author)
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Expression of nirK and nirS genes in two strains of Pseudomonas stutzeri harbouring both types of NO-forming nitrite reductases
- 2018
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 169, s. 343-347
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Journal article (peer-reviewed)abstract
- Reduction of nitrite to nitric oxide in denitrification is catalysed by two different nitrite reductases, encoded by nirS or nirK. Long considered mutually exclusive and functionally redundant in denitrifying bacteria, we show expression of both genes co-occurring in Pseudomonas stutzeri. The differential expression patterns between strain AN10 and JM300 in relation to oxygen and nitrate and their different denitrification phenotypes, with AN10 reducing nitrate more rapidly and accumulating nitrite, suggest that nirS and nirK can have different roles. Dissimilar gene arrangements and transcription factors in the nir gene neighbourhoods could explain the observed differences in gene expression and denitrification activity. (C) 2018 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
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| 29. |
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| 30. |
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| 31. |
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| 32. |
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| 33. |
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| 34. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes
- 2012
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508. ; 163:6-7, s. 407-412
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Journal article (peer-reviewed)abstract
- Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package – Megraft – that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.
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| 35. |
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| 36. |
- Jaen-Luchoro, Daniel, et al.
(author)
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Corynebacterium genitalium sp. nov., nom. rev. and Corynebacterium pseudogenitalium sp. nov., nom. rev., two old species of the genus Corynebacterium described from clinical and environmental samples
- 2023
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508. ; 174:1-2
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Journal article (peer-reviewed)abstract
- Two Corynebacterium species were proposed decades ago, isolated from clinical samples and divided into biovars: "Corynebacterium genitalium" biovars I-V and "Corynebacterium pseudogenitalium" biovars C1 -C6. Several biovars have been re-classified as new species. Nevertheless, biovar I and C5, together with their respective specific epithets "Corynebacterium genitalium" and "Corynebacterium pseudogenitalium", remained not validly published after more than 40 years. Several more strains, temptatively classified as "C. genitalium" biovar I and "Corynebacterium pseudogenitalium" C5, have been isolated from clinical and environmental samples. Both species presented Gram-positive, non-spore forming rod-shaped cells, able to grow aerobically with CO2. Core-genome analysis identified "C. genitalium" to be most closely related to Corynebacterium tuscaniense, Corynebacterium urinipleomorphum, Corynebacterium aquatimens and C appendicis, and Corynebacterium gottingense as the most closely related species to "C. pseudogenitalium". Comprehensive genomic, genotypic, phenotypic analyses, as well as chemotaxonomic, support the proposal for "C. genitalium" and "C. pseudogenitalium" as distinct species within the genus Corynebacterium. The designated type strains of the two species are Furness 392-1T = ATCC 33030T = CCUG 38989T = CCM 9178T = DSM 113155T for C. genitalium sp. nov., nom. rev., and Furness 162-C2T = ATCC 33039T = CCUG 27540T = CCM 9177T = DSM 113154T for C. pseudogenitalium sp. nov., nom. rev. (c) 2022 The Author(s). Published by Elsevier Masson SAS on behalf of Institut Pasteur. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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- Talla, E., et al.
(author)
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Insights into the pathways of iron- and sulfur-oxidation, and biofilm formation from the chemolithotrophic acidophile Acidithiobacillus ferrivorans CF27
- 2014
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508. ; 165:9, s. 753-760
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Journal article (peer-reviewed)abstract
- The iron-oxidizing acidithiobacilli cluster into at least four groups, three of which (Acidithiobacillus ferrooxidans, Acidithiobacillus ferridurans and Acidithiobacillus ferrivorans) have been designated as separate species. While these have many physiological traits in common, they differ in some phenotypic characteristics including motility, and pH and temperature minima. In contrast to At. ferrooxidans and At. ferridurans, all At. ferrivorans strains analysed to date possess the iro gene (encoding an iron oxidase) and, with the exception of strain CF27, the rusB gene encoding an iso-rusticyanin whose exact function is uncertain. Strain CF27 differs from other acidithiobacilli by its marked propensity to form macroscopic biofilms in liquid media. To identify the genetic determinants responsible for the oxidation of ferrous iron and sulfur and for the formation of extracellular polymeric substances, the genome of At. ferrivorans CF27 strain was sequenced and comparative genomic studies carried out with other Acidithiobacillus spp.. Genetic disparities were detected that indicate possible differences in ferrous iron and reduced inorganic sulfur compounds oxidation pathways among iron-oxidizing acidithiobacilli. In addition, strain CF27 is the only sequenced Acidithiobacillus spp. to possess genes involved in the biosynthesis of fucose, a sugar known to confer high thickening and flocculating properties to extracellular polymeric substances.
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