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  • 1. Asiegbu, F O
    et al.
    Choi, W B
    Li, G S
    Nahalkova, Jarmila
    Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden.
    Dean, R A
    Isolation of a novel antimicrobial peptide gene (Sp-AMP) homologue from Pinus sylvestris (Scots pine) following infection with the root root fungus Heterobasidion annosum2003Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 228, nr 1, s. 27-31Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new family of antimicrobial peptide homologues termed Sp-Amp has been discovered in Pinus sylvestris (Scots pine). This is the first report of such proteins to be characterized in a conifer species. Sp-AMP1 was identified in a substructured cDNA library of root tissue infected with the root rot fungus Heterobasidion annosum and encodes a mature peptide of 79 amino acid residues. Three additional members of the Sp-AMP family (Sp-AMPs 2-4) encode cysteine-rich proteins of 105 amino acids, each containing an N-terminal region with a probable cleavage signal sequence. Northern analysis confirmed that Sp-AMP expression is elevated in Scots pine roots upon infection with H. annosum. These peptides share 64% amino acid identity with a mature protein from Macadamia integrifolia (MiAMP1), which allowed us to build a homology model for preliminary analysis. Southern analyses further confirmed that several copies of the gene are present in the Scots pine genome. The potential significance of Sp-AMP in the H. annosum-conifer pathosystem is discussed.

  • 2. Asiegbu, F.O.
    et al.
    Choi, W.
    Li, G.
    Nahalkova, Jarmila
    Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden.
    Dean, R.A.
    Isolation of a novel antimicrobal peptide gene (Sp-AMP) homologue from Pinus sylvestris (Scots pine) following infection with the root rot fungus Heterobasidion annosum2003Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 228, nr 1, s. 27-31Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new family of antimicrobial peptide homologues termed Sp-Amp has been discovered in Pinus sylvestris (Scots pine). This is the first report of such proteins to be characterized in a conifer species. Sp-AMP1 was identified in a substructured cDNA library of root tissue infected with the root rot fungus Heterobasidion annosum and encodes a mature peptide of 79 amino acid residues. Three additional members of the Sp-AMP family (Sp-AMPs 2–4) encode cysteine-rich proteins of 105 amino acids, each containing an N-terminal region with a probable cleavage signal sequence. Northern analysis confirmed that Sp-AMP expression is elevated in Scots pine roots upon infection with H. annosum. These peptides share 64% amino acid identity with a mature protein from Macadamia integrifolia (MiAMP1), which allowed us to build a homology model for preliminary analysis. Southern analyses further confirmed that several copies of the gene are present in the Scots pine genome. The potential significance of Sp-AMP in the H. annosum–conifer pathosystem is discussed.

  • 3. Bontempi, EJ
    et al.
    Garcia, GA
    Buschiazzo, A
    Henriksson, Jan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi, Medicinsk genetik.
    Pravia, CA
    Ruiz, AM
    Pettersson, Ulf
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi, Medicinsk genetik.
    Pszenny, V
    The tyrosine aminotransferase from Trypanosoma rangeli: sequence andgenomic characterization2000Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 189, nr 2, s. 253-257Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The complete sequence and genomic characterization of the tyrosine aminotransferase (TAT) gene from Trypanosoma rangeli is reported. The gene was found to be organized in a tandem multicopy gene array. A homologous mRNA species (2.5 kb) was identified in the epimastigote form of the parasite. From the deduced amino acid sequence, the gene encodes a protein of 420 amino acids with a predicted molecular mass of 46.4 kDa and a theoretical pI of 6.23. A high sequence identity was found with the Trypanosoma cruzi, human and rat enzymes. All the essential residues for TAT enzymatic activity are conserved, as well as a pyridoxal-phosphate attachment site typical of class-I aminotransferases. The recombinant enzyme was recognized by a monoclonal antibody against the T. cruzi enzyme. Additionally, the recombinant protein showed enzymatic activity when incubated with L-tyrosine and 2-oxoglutaric acid as substrates.

  • 4.
    Camsund, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Devine, Ellenor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Holmqvist, Marie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Peter, Yohanoun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Lindblad, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Stensjö, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    A HupS-GFP fusion protein demonstrates a heterocyst specific localisation of the uptake hydrogenase in the cyanobacterium Nostoc punctiformeIngår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968Artikel i tidskrift (Refereegranskat)
  • 5.
    Camsund, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Molekylär biomimetik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Devine, Ellenor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Holmqvist, Marie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Yohanoun, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Lindblad, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Stensjö, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    A HupS-GFP fusion protein demonstrates a heterocyst-specific localization of the uptake hydrogenase in Nostoc punctiforme2011Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 316, nr 2, s. 152-159Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    All diazotrophic filamentous cyanobacteria contain an uptake hydrogenase that is involved in the reoxidation of H-2 produced during N-2-fixation. In Nostoc punctiforme ATCC 29133, N-2-fixation takes place in the microaerobic heterocysts, catalysed by a nitrogenase. Although the function of the uptake hydrogenase may be closely connected to that of nitrogenase, the localization in cyanobacteria has been under debate. Moreover, the subcellular localization is not understood. To investigate the cellular and subcellular localization of the uptake hydrogenase in N. punctiforme, a reporter construct consisting of the green fluorescent protein (GFP) translationally fused to HupS, within the complete hupSL operon, was constructed and transferred into N. punctiforme on a self-replicative vector by electroporation. Expression of the complete HupS-GFP fusion protein was confirmed by Western blotting using GFP antibodies. The N. punctiforme culture expressing HupS-GFP was examined using laser scanning confocal microscopy, and fluorescence was exclusively detected in the heterocysts. Furthermore, the fluorescence in mature heterocysts was localized to several small or fewer large clusters, which indicates a specificity of the subcellular localization of the uptake hydrogenase.

  • 6.
    Christel, Stephan
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden..
    Fridlund, Jimmy
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden..
    Buetti-Dinh, Antoine
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden..
    Buck, Moritz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Watkin, Elizabeth L.
    Curtin Univ, Sch Biomed Sci, CHIRI Biosci, Perth, WA 6845, Australia..
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, S-39182 Kalmar, Sweden..
    RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans2016Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 363, nr 7, artikel-id fnw057Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDA genes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdr genes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.

  • 7.
    Corcoll, Natalia
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, SE-40530 Gothenburg, Sweden..
    Osterlund, Tobias
    Chalmers, Dept Math Sci, SE-41296 Gothenburg, Sweden..
    Sinclair, Lucas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Eiler, Alexander
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Kristiansson, Erik
    Chalmers, Dept Math Sci, SE-41296 Gothenburg, Sweden..
    Backhaus, Thomas
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, SE-40530 Gothenburg, Sweden..
    Eriksson, K. Martin
    Chalmers, Dept Mech & Maritime Sci, SE-41296 Gothenburg, Sweden..
    Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing2017Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 364, nr 14, artikel-id fnx139Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol (R) Reagent (PlantDNAzol) and the FastDNA (R) SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 mu g g wet wt(-1)). Lower amounts of DNA were obtained (<37 mu g g wet wt(-1)) with the Power Plant (R) Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm (R) DNA Isolation Kit (PowerBiofilm) methods, but integrity and purity of the extracted DNA were higher. Results from 16S rRNA amplicon sequencing demonstrate that the choice of a DNA extraction method significantly influences the bacterial community profiles generated. A higher number of bacterial OTUs were detected when DNA was extracted with the PowerBiofilm and the PlantDNAzol methods. Overall, this study demonstrates the potential bias in metagenomic diversity estimates associated with different DNA extraction methods.

  • 8.
    Dombrowski, Nina
    et al.
    Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Texas Austin, Marine Sci Inst, Dept Marine Sci, 750 Channel View Dr, Port Aransas, TX 78373 USA.
    Lee, Jun-Hoe
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Williams, Tom A.
    Univ Bristol, Sch Biol Sci, Life Sci Bldg,24 Tyndall Ave, Bristol BS8 1TQ, Avon, England.
    Offre, Pierre
    Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands.
    Spang, Anja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands.
    Genomic diversity, lifestyles and evolutionary origins of DPANN archaea2019Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 366, nr 2, artikel-id fnz008Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Archaea-a primary domain of life besides Bacteriahave for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.

  • 9.
    Li, Xin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Mustila, Henna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Magnuson, Ann
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Stensjö, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Homologous overexpression of NpDps2 and NpDps5 increases the tolerance for oxidative stress in the multicellular cyanobacterium Nostoc punctiforme2018Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 365, nr 18, artikel-id fny198Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The filamentous cyanobacterium Nostoc punctiforme has several oxidative stress-managing systems, including Dps proteins. Dps proteins belong to the ferritin superfamily and are involved in abiotic stress management in prokaryotes. Previously, we found that one of the five Dps proteins in N. punctiforme, NpDps2, was critical for H2O2 tolerance. Stress induced by high light intensities is aggravated in N. punctiforme strains deficient of either NpDps2, or the bacterioferritin-like NpDps5. Here, we have investigated the capacity of NpDps2 and NpDps5 to enhance stress tolerance by homologous overexpression of these two proteins in N. punctiforme. Both overexpression strains were found to tolerate twice as high concentrations of added H2O2 as the control strain, indicating that overexpression of either NpDps2 or NpDps5 will enhance the capacity for H2O2 tolerance. Under high light intensities, the overexpression of the two NpDps did not enhance the tolerance against general light-induced stress. However, overexpression of the heterocyst-specific NpDps5 in all cells of the filament led to a higher amount of chlorophyll-binding proteins per cell during diazotrophic growth. The OENpDps5 strain also showed an increased tolerance to ammonium-induced oxidative stress. Our results provide information of how Dps proteins may be utilised for engineering of cyanobacteria with enhanced stress tolerance.

  • 10.
    Li, Xin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Sandh, Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap, Mikrobiell kemi.
    Nenninger, Anja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Muro-Pastor, Alicia M.
    Stensjo, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Differential transcriptional regulation of orthologous dps genes from two closely related heterocyst-forming cyanobacteria2015Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 362, nr 6, artikel-id fnv017Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In cyanobacteria, DNA-binding proteins from starved cells (Dps) play an important role in the cellular response to oxidative and nutritional stresses. In this study, we have characterized the cell-type specificity and the promoter regions of two orthologous dps genes, Npun_R5799 in Nostoc punctiforme and alr3808 in Anabaena sp. PCC 7120. A transcriptional start site (TSS), identical in location to the previously identified proximal TSS of alr3808, was identified for Npun_R5799 under both combined nitrogen supplemented and N-2-fixing growth conditions. However, only alr3808 was also transcribed from a second distal TSS. Sequence homologies suggest that the promoter region containing the distal TSS is not conserved upstream of orthologous genes among heterocyst-forming cyanobacteria. The analysis of promoter GFP-reporter strains showed a different role in governing cell-type specificity between the proximal and distal promoter of alr3808. We here confirmed the heterocyst specificity of the distal promoter of alr3808 and described a very early induction of its expression during proheterocyst differentiation. In contrast, the complete promoters of both genes were active in all cells. Even though Npun_R5799 and alr3808 are orthologs, the regulation of their respective expression differs, indicating distinctions in the function of these cyanobacterial Dps proteins depending on the strain and cell type.

  • 11.
    Loftsdottir, Heidur
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper. SVA, Dept Microbiol, Natl Vet Inst, S-75189 Uppsala, Sweden..
    Söderlund, Robert
    SVA, Dept Microbiol, Natl Vet Inst, S-75189 Uppsala, Sweden.;Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, S-75007 Uppsala, Sweden..
    Jinnerot, Tomas
    SVA, Dept Microbiol, Natl Vet Inst, S-75189 Uppsala, Sweden..
    Eriksson, Erik
    SVA, Dept Microbiol, Natl Vet Inst, S-75189 Uppsala, Sweden..
    Bongcam-Rudloff, Erik
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, S-75007 Uppsala, Sweden..
    Aspan, Anna
    SVA, Dept Microbiol, Natl Vet Inst, S-75189 Uppsala, Sweden..
    Dynamics of insertion sequence element IS629 inactivation of verotoxin 2 genes in Escherichia coli O157:H72017Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 364, nr 8, artikel-id fnx074Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There are several anecdotal reports of insertion sequence (IS) element inactivation of verotoxin genes among enterohaemorrhagic Escherichia coli of the serotype O157:H7, a pathogen causing severe gastrointestinal disease in infected humans. These insertions can be expected to drastically reduce the virulence of the bacteria. IS element inactivation has been shown to be reversible in model systems, suggesting the possibility of spontaneous restoration of virulence. In this study, traditional and high-throughput sequencing was used to characterise three patterns of IS629 inactivation of verotoxin 2 genes in EHEC O157:H7, caused by insertion or insertion followed by partial deletion. At least one of the patterns of inactivation appears to have persisted several years among cattle O157:H7, indicating it has no major effect on fitness in the animal reservoir. Digital PCR was used to directly quantify the reversal rates of the insertional inactivation of a selected isolate under laboratory conditions. Inserts were found to be absent from in the order of 1/10(5) of individual genomes, with significantly higher loss frequencies observed in cultures under nutrient-poor conditions. We conclude that strains with this type of inactivation found in food or animal samples should be considered a threat to human health, and may pose a challenge for PCR-based detection methods.

  • 12.
    Macvanin, Mirjana
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Hughes, Diarmaid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Hyper-susceptibility of a fusidic acid-resistant mutant of Salmonella to different classes of antibiotics2005Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 247, nr 2, s. 215-220Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Fusidic acid resistance (FusR) in Salmonella enterica serovar Typhimurium is caused by mutations in fusA, encoding elongation factor G (EF-G). Pleiotropic phenotypes are observed in FusR mutants. Thus, the fusA1 allele (EF-G P413L) is associated with slow growth rate, reduced ppGpp and RpoS levels, reduced heme levels, and increased sensitivity to oxidative stress. The fusA1–15 allele, (EF-G P413L and T423I) derived from fusA1 in a selection for growth rate compensation, is partially compensated in each of these phenotypic defects but maintains its resistance to fusidic acid. We show here that the fusA1 allele is associated with sensitivity to ultraviolet light and increased susceptibility to the inhibitory action of several unrelated antibiotic classes (β-lactam, fluoroquinolone, aminoglycoside, rifampicin, and chloramphenicol). The fusA1–15 allele, in contrast, is less susceptible to UV and to other antibiotics than fusA1. The hyper-susceptibility to multiple antibiotics associated with fusA1 and fusA1–15 is revealed in a novel growth competition assay at sub-MIC concentrations, but not in a standard MIC assay.

  • 13.
    Martinez, Javier
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Henrikson, Jan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Rydåker, Maria
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Cazzulo, J J
    Pettersson, Ulf
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Genes for cysteine proteinases from Trypanosoma rangeli1995Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 129, nr 2-3, s. 135-141Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    PCR amplification of genomic DNA from the American trypanosome, Trypanosoma rangeli, using as primers oligonucleotides derived from the gene of cruzipain, the major cysteine proteinase (CP) from Trypanosoma cruzi, allowed the production of a probe which was used to obtain three clones encoding a CP with 70% overall identity with cruzipain. The genes are organized in tandem, with a monomere size of approximately 2 kbp, located on two chromosomes which, in some parasite isolates, have a high molecular mass (higher than 5.7 Mbp), and in others are much smaller (about 500 kbp). The low expression of this CP at the protein level correlates well with the low level of specific mRNA found in Northern blots.

  • 14.
    Nahalkova, Jarmila
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolutionsbiologi, Molekylär evolution.
    Fatehi, Jamshid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolutionsbiologi, Molekylär evolution.
    Red fluorescent protein (DsRed2) as a novel reporter in Fusarium oxysporum f. sp. Lycopersici2003Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 225, nr 2, s. 305-309Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    pAn-DsRed2 vector was constructed for constitutive cytoplasmic expression of the red fluorescent protein (DsRed2) under control of the glyceraldehyde-3-phosphate dehydrogenase gene promoter from Aspergillus nidulans. DsRed2-transformation of two Fusarium oxysporum f. sp. lycopersici strains pathogenic against tomato host resulted in bright red cytoplamic fluorescence of the fungus. The transformants were screened based on the hygromycin B resistance, brightness, stability and rate of appearance of the DsRed2 fluorescence. The transormed fungi were growing normally and their pathogenicity did not change after transformation procedure. The function of novel DsRed2 marker was verified by fluorescence microscopy of the infected tomato seedlings. The results indicate that DsRed2 can be used as a efficient novel reporter gene for monitoring of the F. oxysporum within the host tissues.

  • 15.
    Nahalkova, Jarmila
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolutionsbiologi, Molekylär evolution.
    Fatehi, Jamshid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolutionsbiologi, Molekylär evolution.
    Red fluorescent protein (DsRed2) as a novel reporter in Fusarium oxysporum f. sp lycopersiei2003Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 225, nr 2, s. 305-309Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    pAn-DsRed2 vector was constructed for constitutive cytoplasmic expression of the red fluorescent protein (DsRed2) under control of the glyceraldehyde-3-phosphate dehydrogenase gene promoter from Aspergillus nidulans. DsRed2-transformation of two Fusarium oxysporum f. sp. lycopersici strains pathogenic against tomato host resulted in bright red cytoplamic fluorescence of the fungus. The transformants were screened based on the hygromycin B resistance, brightness, stability and rate of appearance of the DsRed2 fluorescence. The transormed fungi were growing normally and their pathogenicity did not change after transformation procedure. The function of novel DsRed2 marker was verified by fluorescence microscopy of the infected tomato seedlings. The results indicate that DsRed2 can be used as a efficient novel reporter gene for monitoring of the F oxysporum within the host tissues.

  • 16.
    Nahalkova, Jarmila
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Molekylär evolution.
    Fatehi, Jamshid
    Olivain, Chantal
    Alabouvette, Claude
    Tomato root colonization by fluorescent-tagged pathogenic and protective strains of Fusarium oxysporum in hydroponic culture differs from root colonization in soil2008Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 286, nr 2, s. 152-157Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The colonization process of tomato roots inoculated separately or/and simultaneously by a pathogenic Fusarium oxysporum f. sp. lycopersici strain Fol8 and the protective F. oxysporum strain Fo47, genetically tagged with the red and green fluorescent protein genes, respectively, was studied in a hydroponic culture. Plants were coinoculated with Fol8 and Fo47 at two conidial concentration ratios of 1/1 and 1/100, in which biological control was not effective or effective, respectively. First observation of fungi on root was possible 48 h after inoculation at a high inoculum level and 5 days post inoculation at the lower concentration of inoculum. The pattern of root colonization was similar for both strains with the initial development of hyphal network on the upper part of taproot, followed by the growth of hyphae towards the elongation zone, lateral roots and root apices. Finally, the whole elongation zone and root apex were invaded by both strains but no specific infection sites were observed. When coinoculated, both strains could grow very closely or even at the same spot on the root surface. At the nonprotective ratio, Fol8 was the successful colonizer, but application of Fo47 at a concentration 100 times > , Fol8 delayed vessel colonization by the pathogen.

  • 17. Nikolausz, Marcell
    et al.
    Sipos, Rita
    Révész, Sára
    Szekely, Anna
    Department of Microbiology, Eötvös Loránd University of Science, Budapest, Hungary.
    Márialigeti, Károly
    Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels2005Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 244, s. 385-390Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) was isolated from the background smear rather than from discrete bands of the DGGE gel. The ‘‘interband’’ region was considered as a potential source of less dominant members of natural microbial communities. Surprisingly, instead of detecting new bands from the re-amplified PCR products, patterns very similar to the original ones were obtained regardless of the position of the ‘‘interband’’ region. The results suggest that the separation of amplicons by DGGE may not be perfect and band re-amplification based sequence analyses need careful interpretation.

  • 18.
    Pettersson, B. M. Fredrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Kemisk biologi.
    Nitharwal, Ram Gopal
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Kemisk biologi.
    Das, Sarbashis
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
    Behra, Krishna P. R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Benedik, Evgen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Arasu, Uma T.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Islam, Nurul M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Dasgupta, Santanu
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Bhattacharya, Alok
    Kirsebom, Leif A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Kemisk biologi.
    Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions2013Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 342, nr 2, s. 98-105Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Like other bacteria, Mycobacterium spp. have developed different strategies in response to environmental changes such as nutrient limitations and other different stress situations. We have identified candidate genes (rsb genes) from Mycobacterium marinum involved in the regulation of the activity of the alternative sigma factor, sigma F. This is a homolog of the master regulator of general stress response, sigma B, and the sporulation-specific sigma factor, sigma F, in Bacillus subtilis. The organization of these genes in M.marinum and B.subtilis is similar. Transcriptome and qRT-PCR data show that these genes are indeed expressed in M.marinum and that the levels of expression vary with growth phase and exposure to stress. In particular, cold stress caused a significant rise in the expression of all identified rsb and sigF genes. We discuss these data in relation to what is currently known for other Mycobacterium spp.

  • 19.
    Sandh, Gustaf
    et al.
    Botaniska Institutionen Stockholms Universitet.
    El-Shehawy, Rehab
    Botaniska Institutionen Stockholms Universitet.
    Díez, Beatriz
    Botaniska Institutionen Stockholms Universitet.
    Bergman, Birgitta
    Botaniska Institutionen Stockholms Universitet.
    Temporal separation of cell division and diazotrophy in the marine diazotrophic cyanobacterium Trichodesmium erythraeum IMS101.2009Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 295, nr 2, s. 281-8Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Examination of the diurnal patterns of basic cellular processes in the marine nonheterocystous diazotrophic cyanobacterium Trichodesmium revealed that the division of cells occurred throughout the diurnal cycle, but that it oscillated and peaked at an early stage in the dark period. Transcription of the early cell division gene ftsZ and the occurrence of the FtsZ protein showed a similar diurnal rhythmicity that preceded the division of cells. DNA replication (dnaA gene transcription) occurred before the transcription of ftsZ and hetR, the latter encoding the key heterocyst differentiation protein. Transcription of ftsZ and hetR in turn preceded the development of the nitrogen-fixing diazocytes and nifH transcription, and were at the minimum when diazotrophy was at the maximum. The nifH gene transcription showed a negative correlation to the circadian clock gene kaiC. Together, the data show a temporal separation between cell division and diazotrophy on a diurnal basis.

  • 20.
    Székely, Anna J.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Univ S Florida, Coll Marine Sci, St Petersburg, FL 33701 USA..
    Breitbart, Mya
    Univ S Florida, Coll Marine Sci, St Petersburg, FL 33701 USA..
    Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology2016Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 363, nr 6, artikel-id fnw027Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics.

  • 21.
    Wang, Helen
    et al.
    Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.
    Franke, CC
    Nordlund, Stefan
    Noren, Agneta
    Reversible membrane association of dinitrogenase reductase activating glycohydrolase in the regulation of nitrogenase activity in Rhodospirillum rubrum; dependence on GlnJ and AmtB12005Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 253, nr 2, s. 273-279Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the photosynthetic bacterium Rhodospirillum rubrum nitrogenase activity is regulated by reversible ADP-ribosylation of dinitrogenase reductase in response to external so called "switch-off" effectors. Activation of the modified, inactive form is catalyzed by dinitrogenase reductase activating glycohydrolase (DRAG) which removes the ADP-ribose moiety. This study addresses the signal transduction between external effectors and DRAG. R. rubrum, wild-type and P(II) mutant strains, were studied with respect to DRAG localization. We conclude that GlnJ clearly has an effect on the association of DRAG to the membrane in agreement with the effect on regulation of nitrogenase activity. Furthermore, we have generated a R. rubrum mutant lacking the putative ammonium transporter AmtB1 which was shown not to respond to "switch-off" effectors; no loss of nitrogenase activity and no ADP-ribosylation. Interestingly, DRAG was mainly localized to the cytosol in this mutant. Overall the results support our model in which association to the membrane is part of the mechanism regulating DRAG activity.

  • 22.
    Wang, Helen
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Waluk, Dominik
    Dixon, Ray
    Nordlund, Stefan
    Norén, Agneta
    Energy shifts induce membrane sequestration of DraG in Rhodospirillum rubrum independent of the ammonium transporters and diazotrophic conditions.2018Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 365, nr 16, artikel-id fny176Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Metabolic regulation of Rhodospirillum rubrum nitrogenase is mediated at the post-translational level by the enzymes DraT and DraG when subjected to changes in nitrogen or energy status. DraT is activated during switch-off, while DraG is inactivated by reversible membrane association. We confirm here that the ammonium transporter, AmtB1, rather than its paralog AmtB2, is required for ammonium induced switch-off. Amongst several substitutions at the N100 position in DraG, only N100K failed to locate to the membrane following ammonium shock, suggesting loss of interaction through charge repulsion. When switch-off was induced by lowering energy levels, either by darkness during photosynthetic growth or oxygen depletion under respiratory conditions, reversible membrane sequestration of DraG was independent of AmtB proteins and occurred even under non-diazotrophic conditions. We propose that under these conditions, changes in redox status or possibly membrane potential induce interactions between DraG and another membrane protein in response to the energy status.

  • 23.
    Wang, Sheng-Bing
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Cantlay, Stuart
    Nordberg, Niklas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Letek, Michal
    Gil, A
    Flärdh, Klas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Domains involved in the in vivo function and oligomerization of apical growth determinant DivIVA in Streptomyces coelicolor2009Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 297, nr 1, s. 101-109Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The coiled-coil protein DivIVA is a determinant of apical growth and hyphal branching in Streptomyces coelicolor. We have investigated the properties of this protein and the involvement of different domains in its essential function and subcellular targeting. In S. coelicolor cell extracts, DivIVA was present as large oligomeric complexes that were not strongly membrane associated. The purified protein could self-assemble into extensive protein filaments in vitro. Two large and conspicuous segments in the amino acid sequence of streptomycete DivIVAs not present in other homologs, an internal PQG-rich segment and a carboxy-terminal extension, are shown to be dispensable for the essential function in S. coelicolor. Instead, the highly conserved amino-terminal of 22 amino acids was required and affected establishment of new DivIVA foci and hyphal branches, and an essential coiled-coil domain affected oligomerization of the protein.

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