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  • 1.
    Andersson, Siv G. E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Goodman, A. L.
    Bacterial genomes: Next generation sequencing technologies for studies of bacterial ecosystems2012In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 15, no 5, p. 603-604Article in journal (Other academic)
  • 2.
    Bernander, Rolf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    Ettema, Thijs J.G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Molecular Evolution.
    FtsZ-less cell division in archaea and bacteria2010In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 13, no 6, p. 747-752Article in journal (Refereed)
    Abstract [en]

    A dedicated cell division machinery is needed for efficient proliferation of an organism. The eukaryotic actin-myosin based mechanism and the bacterial FtsZ-dependent machinery have both been characterized in detail, and a third division mechanism, the Cdv system, was recently discovered in archaea from the Crenarchaeota phylum. Despite these findings, division mechanisms remain to be identified in, for example, organisms belonging to the bacterial PVC superphylum, bacteria with extremely reduced genomes, wall-less archaea and bacteria, and in archaea that carry out the division process without cell constriction. Cytokinesis mechanisms in these clades and individual taxa are likely to include adaptation of host functions to division of bacterial symbionts, transfer of bacterial division genes into the host genome, vesicle formation without a dedicated constriction machinery, cross-wall formation without invagination, as well as entirely novel division mechanisms.

  • 3.
    Einarsson, Elin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Ma'ayeh, Showgy Y.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Svärd, Staffan G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    An up-date on Giardia and giardiasis2016In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 34, p. 47-52Article, review/survey (Refereed)
    Abstract [en]

    Giardia intestinalis is a non-invasive protozoan parasite infecting the upper small intestine causing acute, watery diarrhea or giardiasis in 280 million people annually. Asymptomatic infections are equally common and recent data have suggested that infections even can be protective against other diarrhea! diseases. Most symptomatic infections resolve spontaneously but infections can lead to chronic disease and treatment failures are becoming more common world-wide. Giardia infections can also result in irritable bowel syndrome (IBS) and food allergies after resolution. Until recently not much was known about the mechanism of giardiasis or the cause of post-giardiasis syndromes and treatment failures, but here we will describe the recent progress in these areas.

  • 4. Gerdes, Kenn
    et al.
    Wagner, Gerhart H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    RNA antitoxins2007In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 10, no 2, p. 117-124Article, review/survey (Refereed)
    Abstract [en]

    Recent genomic analyses revealed a surprisingly large number of toxin–antitoxin loci in free-living prokaryotes. The antitoxins are proteins or antisense RNAs that counteract the toxins. Two antisense RNA-regulated toxin–antitoxin gene families, hok/sok and ldr, are unrelated sequence-wise but have strikingly similar properties at the level of gene and RNA organization. Recently, two SOS-induced toxins were found to be regulated by RNA antitoxins. One such toxin, SymE, exhibits similarity with MazE antitoxin and, surprisingly, inhibits translation. Thus, it is possible that an ancestral antitoxin gene evolved into the present toxin gene (symE) whose translation is repressed by an RNA antitoxin (SymR).

  • 5. Giraud, A
    et al.
    Radman, M
    Matic, I
    Taddei, F
    The rise and fall of mutator bacteria.2001In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 4, no 5, p. 582-5Article in journal (Refereed)
    Abstract [en]

    Bacteria with elevated mutation rates are frequently found among natural isolates. This is probably because of their ability to generate genetic variability, the substrate for natural selection. However, such high mutation rates can lead to the loss of vital functions. The evolution of bacterial populations may happen through alternating periods of high and low mutation rates. The cost and benefits of high mutation rates in the course of bacterial adaptive evolution are reviewed.

  • 6.
    Hagström, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    The challenges of integrating two genomes in one cell2018In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 41, p. 89-94Article, review/survey (Refereed)
    Abstract [en]

    Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria. Recent findings suggest that the mitochondria! genome is retained to avoid conflicting signals between protein targeting pathways in the cell. However, if the selective pressure for oxygenic respiration is lost, the mitochondrial genome will start to deteriorate and soon be lost.

  • 7. Hirt, Robert P.
    et al.
    Alsmark, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Embley, T. Martin
    Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites2015In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 23, p. 155-162Article, review/survey (Refereed)
    Abstract [en]

    Our knowledge of the extent and functional impact of lateral gene transfer (LGT) from prokaryotes to eukaryotes, outside of endosymbiosis, is still rather limited. Here we review the recent literature, focusing mainly on microbial parasites, indicating that LGT from diverse prokaryotes has played a significant role in the evolution of a number of lineages, and by extension throughout eukaryotic evolution. As might be expected, taxonomic biases for donor prokaryotes indicate that shared habitat is a major factor driving transfers. The LGTs identified predominantly affect enzymes from metabolic pathways, but over a third of LGT are genes for putative proteins of unknown function. Finally, we discuss the difficulties in analysing LOT among eukaryotes and suggest that high-throughput methodologies integrating different approaches are needed to achieve a more global understanding of the importance of LGT in eukaryotic evolution.

  • 8.
    Hughes, Diarmaid
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Dan I
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Selection of resistance at lethal and non-lethal antibiotic concentrations2012In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 15, no 5, p. 555-560Article in journal (Refereed)
    Abstract [en]

    Much of what we currently know about the genetics and evolution of antibiotic-resistance is based on selections with lethal drug concentrations that allow the detection of rare mutants with strong phenotypes. These data may be misleading with regard to the evolution of antibiotic resistance in natural environments, because bacteria are frequently exposed to concentration gradients of antibiotics. A significant part of antibiotic-resistance evolution may occur when bacteria are exposed to non-lethal concentrations of drug. High-resolution competition assays show that resistance mutations are rapidly enriched, and selected de novo, at very low antibiotic concentrations. Genomic analysis is providing a better understanding of how frequent and small-effect mutations selected at very low antibiotic concentrations contribute to the step-wise development of antibiotic resistance.

  • 9.
    Johansson, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Lovmar, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Rate and accuracy of bacterial protein synthesis revisited2008In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 11, no 2, p. 141-147Article, review/survey (Refereed)
    Abstract [en]

    Our understanding of the accuracy of tRNA selection on the messenger RNA programmed ribosome has recently increased dramatically because of high-resolution crystal structures of the ribosome, cryo-electron microscopy reconstructions of its functional complexes, and fast kinetics experiments. Application of single-molecule spectroscopy with fluorescence resonance energy transfer to studies of tRNA selection by the ribosome has also provided new, albeit controversial, insights. Interestingly, when the fundamental trade-off between rate and accuracy in substrate-selective biosynthetic reactions is taken into account, some aspects of the current models of ribosome function appear strikingly suboptimal in the context of growing bacterial cells.

  • 10.
    Jones, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Elf, Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Bursting onto the scene?: Exploring stochastic mRNA production in bacteria2018In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 45, p. 124-130Article, review/survey (Refereed)
    Abstract [en]

    Recent large-scale measurements of gene expression variability (or noise) in E. coli have led to the unexpected conclusion that the variability is in large part dictated by and increasing with the mean level of expression. Here we review the evidence for this apparent universal trend in variability, as well as for the related idea that transcription is fundamentally bursty. We examine recently proposed mechanisms for burstiness and universality and argue that they do not explain important features of observed data. Finally, we discuss potential limitations and pitfalls in the interpretation of experimental measurements of cell-to-cell variability.

  • 11.
    Lundgren, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Archaeal cell cycle progress2005In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 8, no 6, p. 662-668Article in journal (Refereed)
    Abstract [en]

    The discovery of multiple chromosome replication origins in Sulfolobus species has added yet another eukaryotic trait to the archaea, and brought new levels of complexity to the cell cycle in terms of initiation of chromosome replication, replication termination and chromosome decatenation. Conserved repeated DNA elements — origin recognition boxes — have been identified in the origins of replication, and shown to bind the Orc1/Cdc6 proteins involved in cell cycle control. The origin recognition boxes aid in the identification and characterization of new origins, and their conservation suggests that most archaea have a similar replication initiation mechanism. Cell-cycle-dependent variation in Orc1/Cdc6 levels has been demonstrated, reminiscent of variations in cyclin levels during the eukaryotic cell cycle. Information about archaeal chromosome segregation is also accumulating, including the identification of a protein that binds to short regularly spaced repeats that might constitute centromer-like elements. In addition, studies of cell-cycle-specific gene expression have potential to reveal, in the near future, missing components in crenarchaeal chromosome replication, genome segregation and cell division. Together with an increased number of physiological and cytological investigations of the overall organization of the cell cycle, rapid progress of the archaeal cell cycle field is evident, and archaea, in particular Sulfolobus species, are emerging as simple and powerful models for the eukaryotic cell cycle.

  • 12. Mira, Alex
    et al.
    Klasson, Lisa
    Andersson, Siv G E
    Microbial genome evolution: sources of variability.2002In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 5, no 5, p. 506-12Article in journal (Refereed)
    Abstract [en]

    Comparative genome analyses of close relatives have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. The genomes of free-living bacteria often carry phages and repetitive sequences that mediate genomic rearrangements in contrast to the small genomes of obligate host-associated bacteria. This suggests that genomic stability correlates with the genomic content of repeated sequences and movable genetic elements, and thereby with bacterial lifestyle. Genes with unknown functions present in a single species tend to be shorter than conserved, functional genes, indicating that the fraction of unique genes in microbial genomes has been overestimated.

  • 13.
    Sällström, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Genome reduction in the alpha-Proteobacteria2005In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 8, no 5, p. 579-585Article in journal (Refereed)
    Abstract [en]

    More than 20 α-proteobacterial genomes are currently available. These range in size from 1–9 Mb and represent excellent model systems for evolutionary studies of the organizational features of bacterial genomes. Computational inferences have shown that genome reductions have occurred independently in lineages such as Rickettsia and Bartonella that are associated with intracellular lifestyles. Analyses of these reduced genomes have provided insights into the evolution of vector-borne transmission pathways. Further research into the population biology of bacteria, arthropods and vertebrate hosts will help to refine the biology of host–pathogen interactions and will facilitate the design of vaccines and vector-control programs.

  • 14.
    Sällström, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Genome reduction in the alpha-Proteobacteria2005In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 8, no 5, p. 579-585Article in journal (Refereed)
    Abstract [en]

    More than 20 alpha-proteobacterial genomes are currently available. These range in size from 1–9 Mb and represent excellent model systems for evolutionary studies of the organizational features of bacterial genomes. Computational inferences have shown that genome reductions have occurred independently in lineages such as Rickettsia and Bartonella that are associated with intracellular lifestyles. Analyses of these reduced genomes have provided insights into the evolution of vector-borne transmission pathways. Further research into the population biology of bacteria, arthropods and vertebrate hosts will help to refine the biology of host–pathogen interactions and will facilitate the design of vaccines and vector-control programs.

  • 15. Vogel, Jörg
    et al.
    Wagner, Gerhart E. H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Target identification of small noncoding RNAs in bacteria2007In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 10, no 3, p. 262-270Article, review/survey (Refereed)
    Abstract [en]

    Small noncoding RNAs have been discovered at a staggering rate in Escherichia coli and many other bacteria. Most of the sRNAs of known function regulate gene expression by binding to specific mRNAs or proteins. Given the scores of sRNAs of unknown function, the identification of their cellular targets has become urgent. Here, we review the diverse strategies that have been used to identify and validate bacterial sRNA targets. These include the pulse-expression of sRNAs followed by global transcriptome analysis (microarrays), new biocomputational prediction algorithms, and novel gfp reporter gene fusions to validate candidate target gene regulation.

1 - 15 of 15
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