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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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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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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 163:6-7, s. 407-412
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Campos, Manuel, et al.
(författare)
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The type II secretion system : a dynamic fiber assembly nanomachine
- 2013
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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 164:6, s. 545-555
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Tidskriftsartikel (refereegranskat)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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| 4. |
- González, Carolina, et al.
(författare)
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Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis.
- 2014
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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 165:9, s. 726-734
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Liu, Junfa, et al.
(författare)
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Elevated CpxR~P levels repress the Ysc-Yop type III secretion system of Yersinia pseudotuberculosis
- 2012
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Ingår i: Research in Microbiology. - Elsevier : Elsevier BV. - 0923-2508 .- 1769-7123. ; 163:8, s. 518-530
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Moore, Edward R.B. 1954, et al.
(författare)
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Microbial systematics and taxonomy: relevance for a microbial commons.
- 2010
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Ingår i: Research in microbiology. - : Elsevier BV. - 1769-7123 .- 0923-2508. ; 161:6, s. 430-8
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Forskningsöversikt (refereegranskat)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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| 7. |
- Poole, Anthony M., et al.
(författare)
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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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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 162:1, s. 71-76
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Tidskriftsartikel (refereegranskat)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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| 8. |
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| 9. |
- Svanström, Åsa, et al.
(författare)
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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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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 164, s. 91-99
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Tidskriftsartikel (refereegranskat)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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| 10. |
- Talla, E., et al.
(författare)
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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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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 165:9, s. 753-760
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Tidskriftsartikel (refereegranskat)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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| 11. |
- Teixeira, Pedro Filipe, et al.
(författare)
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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
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Ingår i: Research in Microbiology. - : Elsevier BV. - 0923-2508 .- 1769-7123. ; 161:8, s. 651-659
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Tidskriftsartikel (refereegranskat)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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