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Javadi, A., Söderholm, N., Olofsson, A., Flärdh, K. & Sandblad, L. (2019). Assembly mechanisms of the bacterial cytoskeletal protein FilP. Life Science Alliance, 2(3), Article ID e201800290.
Open this publication in new window or tab >>Assembly mechanisms of the bacterial cytoskeletal protein FilP
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2019 (English)In: Life Science Alliance, ISSN 2575-1077, Vol. 2, no 3, article id e201800290Article in journal (Refereed) Published
Abstract [en]

Despite low-sequence homology, the intermediate filament (IF)–like protein FilP from Streptomyces coelicolor displays structural and biochemical similarities to the metazoan nuclear IF lamin. FilP, like IF proteins, is composed of central coiled-coil domains interrupted by short linkers and flanked by head and tail domains. FilP polymerizes into repetitive filament bundles with paracrystalline properties. However, the cations Na+ and K+ are found to induce the formation of a FilP hexagonal meshwork with the same 60-nm repetitive unit as the filaments. Studies of polymerization kinetics, in combination with EM techniques, enabled visualization of the basic building block — a transiently soluble rod-shaped FilP molecule—and its assembly into protofilaments and filament bundles. Cryoelectron tomography provided a 3D view of the FilP bundle structure and an original assembly model of an IF-like protein of prokaryotic origin, thereby enabling a comparison with the assembly of metazoan IF.

Place, publisher, year, edition, pages
Life Science Alliance, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-161722 (URN)10.26508/lsa.201800290 (DOI)000473222200011 ()31243049 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationThe Kempe FoundationsSwedish Research Council, 2011-05198
Available from: 2019-07-26 Created: 2019-07-26 Last updated: 2019-10-14Bibliographically approved
Zhang, H., Söderholm, N., Sandblad, L., Wiklund, K. & Andersson, M. (2019). DSeg: a dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures. Microscopy and Microanalysis, 25(3), 711-719
Open this publication in new window or tab >>DSeg: a dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures
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2019 (English)In: Microscopy and Microanalysis, ISSN 1431-9276, E-ISSN 1435-8115, Vol. 25, no 3, p. 711-719Article in journal (Refereed) Published
Abstract [en]

Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.

Place, publisher, year, edition, pages
Cambridge University Press, 2019
Keywords
filamentous, hyphae, image segmentation, MATLAB, software, quantitative measurement
National Category
Biophysics
Research subject
Computerized Image Analysis; cell research
Identifiers
urn:nbn:se:umu:diva-150686 (URN)10.1017/S1431927619000308 (DOI)000474798800016 ()30894244 (PubMedID)
Note

Originally included in thesis in manuscript form.

The program is available at https://sourceforge.net/projects/dseg-software

Available from: 2018-08-15 Created: 2018-08-15 Last updated: 2019-08-07Bibliographically approved
Sen, B. C., Wasserstrom, S., Findlay, K., Söderholm, N., Sandblad, L., von Wachenfeldt, C. & Flardh, K. (2019). Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.. Molecular Microbiology, 112(1), 184-198
Open this publication in new window or tab >>Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.
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2019 (English)In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 112, no 1, p. 184-198Article in journal (Refereed) Published
Abstract [en]

Bacterial cell division is orchestrated by the Z ring, which is formed by single-stranded treadmilling protofilaments of FtsZ. In Streptomyces, during sporulation, multiple Z rings are assembled and lead to formation of septa that divide a filamentous hyphal cell into tens of prespore compartments. We describe here mutant alleles of ftsZ in Streptomyces coelicolor and Streptomyces venezuelae that perturb cell division in such a way that constriction is initiated along irregular spiral-shaped paths rather than as regular septa perpendicular to the cell length axis. This conspicuous phenotype is caused by amino acid substitutions F37I and F37R in beta strand S2 of FtsZ. The F37I mutation leads, instead of regular Z rings, to formation of relatively stable spiral-shaped FtsZ structures that are capable of initiating cell constriction. Further, we show that the F37 mutations affect the polymerization properties and impair the cooperativity of FtsZ assembly in vitro. The results suggest that specific residues in beta strand S2 of FtsZ affect the conformational switch in FtsZ that underlies assembly cooperativity and enable treadmilling of protofilaments, and that these features are required for formation of regular Z rings. However, the data also indicate FtsZ-directed cell constriction is not dependent on assembly cooperativity.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-161837 (URN)10.1111/mmi.14262 (DOI)000474705900012 ()31002418 (PubMedID)
Available from: 2019-08-08 Created: 2019-08-08 Last updated: 2019-08-08Bibliographically approved
Söderholm, N., Javadi, A., Sierra Flores, I., Flärdh, K. & Sandblad, L. (2018). Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins. Scientific Reports, 8, Article ID 16524.
Open this publication in new window or tab >>Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 16524Article in journal (Refereed) Published
Abstract [en]

Coiled-coil domains of intermediate filaments (IF) and prokaryotic IF-like proteins enable oligomerisation and filamentation, and no additional function is ascribed to these coiled-coil domains. However, an IF-like protein from Streptomyces reticuli was reported to display cellulose affinity. We demonstrate that cellulose affinity is an intrinsic property of the IF-like proteins FilP and Scy and the coiled-coil protein DivIVA from the genus Streptomyces. Furthermore, IF-like proteins and DivIVA from other prokaryotic species and metazoan IF display cellulose affinity despite having little sequence homology. Cellulose affinity-based purification is utilised to isolate native FilP protein from the whole cell lysate of Scoelicolor. Moreover, cellulose affinity allowed for the isolation of IF and IF-like protein from the whole cell lysate of Ccrescentus and a mouse macrophage cell line. The binding to cellulose is mediated by certain combinations of coiled-coil domains, as demornstrated for FilP and lamin. Fusions of target proteins to cellulose-binding coiled-coil domains allowed for cellulose-based protein purification. The data presented show that cellulose affinity is a novel function of certain coiled-coil domains of IF and IF-like proteins from evolutionary diverse species.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-154062 (URN)10.1038/s41598-018-34886-7 (DOI)000449499500013 ()30410115 (PubMedID)
Funder
The Kempe FoundationsSwedish Research Council, 349-2007-8673Swedish Research Council, 2016-06598
Available from: 2018-12-19 Created: 2018-12-19 Last updated: 2019-10-14Bibliographically approved
Paulsson, M., Che, K. F., Ahl, J., Tham, J., Sandblad, L., Smith, M. E., . . . Riesbeck, K. (2018). Bacterial Outer Membrane Vesicles Induce Vitronectin Release Into the Bronchoalveolar Space Conferring Protection From Complement-Mediated Killing. Frontiers in Microbiology, 9, Article ID 1559.
Open this publication in new window or tab >>Bacterial Outer Membrane Vesicles Induce Vitronectin Release Into the Bronchoalveolar Space Conferring Protection From Complement-Mediated Killing
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2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 1559Article in journal (Refereed) Published
Abstract [en]

Pathogens causing pneumonia utilize the complement regulator vitronectin to evade complement-mediated killing. Although vitronectin is associated with several chronic lung diseases, the role of bronchoalveolar vitronectin in pneumonia has not been studied. This study sought to reveal the involvement of vitronectin in the bronchoalveolar space during pneumonia, to assess the effect of outer membrane vesicles and endotoxin on vitronectin release, and to determine whether bacterial pathogens utilize pulmonary vitronectin for evasion. Vitronectin was analyzed in cell-free bronchoalveolar lavage fluid harvested from patients with pneumonia (n = 8) and from healthy volunteers after subsegmental endotoxin instillation (n = 13). Vitronectin binding by Pseudomonas aeruginosa and Haemophilus influenzae was analyzed, and subsequent complement evasion was assessed by serum challenge. The effects of outer membrane vesicles on vitronectin production in mouse lungs and human type II alveolar epithelial cells (A549) were determined. We detected increased vitronectin concentrations in lavage fluid during pneumonia (p = 0.0063) and after bronchial endotoxin challenge (p = 0.016). The capture of vitronectin by bacteria significantly reduced complement-mediated lysis. Following challenge with vesicles, vitronectin was detected in mouse bronchoalveolar space, and mouse alveolar epithelial cells in vivo as well as A549 cells in vitro contained increased levels of vitronectin. Taken together, outer membrane vesicles and endotoxin from Gram-negative bacteria induce vitronectin, which is released into the bronchoalveolar space, and used for evasion of complement-mediated clearance.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
alveolar epithelial cells, complement regulators, endotoxin, outer membrane vesicles, Haemophilus influenzae, immune evasion, pneumonia, Pseudomonas aeruginosa
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-150722 (URN)10.3389/fmicb.2018.01559 (DOI)000438515800001 ()30061873 (PubMedID)2-s2.0-85049840858 (Scopus ID)
Available from: 2018-08-29 Created: 2018-08-29 Last updated: 2018-08-29Bibliographically approved
Taheri, N., Mahmud, A. K., Sandblad, L., Fällman, M., Wai, S. N. & Fahlgren, A. (2018). Campylobacter jejuni bile exposure influences outer membrane vesicles protein content and bacterial interaction with epithelial cells. Scientific Reports, 8, Article ID 16996.
Open this publication in new window or tab >>Campylobacter jejuni bile exposure influences outer membrane vesicles protein content and bacterial interaction with epithelial cells
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 16996Article in journal (Refereed) Published
Abstract [en]

Campylobacter jejuni is a prevalent human pathogen and a major cause of bacterial gastroenteritis in the world. In humans, C. jejuni colonizes the intestinal tract and its tolerance to bile is crucial for bacteria to survive and establish infection. C. jejuni produces outer membrane vesicles (OMVs) which have been suggested to be involved in virulence. In this study, the proteome composition of C. jejuni OMVs in response to low concentration of bile was investigated. We showed that exposure of C. jejuni to low concentrations of bile, similar to the concentration in cecum, induced significant changes in the protein profile of OMVs released during growth without affecting the protein profile of the bacteria. This suggests that bile influences a selective packing of the OMVs after bacterial exposure to low bile. A low concentration of bile was found to increase bacterial adhesion to intestinal epithelial cells, likely by an enhanced hydrophobicity of the cell membrane following exposure to bile. The increased bacterial adhesiveness was not associated with increased invasion, instead bile exposure decreased C. jejuni invasion. OMVs released from bacteria upon exposure to low bile showed to increase both adhesion and invasion of non-bile-exposed bacteria into intestinal epithelial cells. These findings suggest that C. jejuni in environments with low concentrations of bile produce OMVs that facilitates colonization of the bacteria, and this could potentially contribute to virulence of C. jejuni in the gut.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018
National Category
Microbiology Cell Biology
Identifiers
urn:nbn:se:umu:diva-153787 (URN)10.1038/s41598-018-35409-0 (DOI)000450411700027 ()
Funder
Carl Tryggers foundation
Available from: 2018-12-03 Created: 2018-12-03 Last updated: 2019-01-18Bibliographically approved
Rajan, A., Persson, B. D., Frängsmyr, L., Olofsson, A., Sandblad, L., Heino, J., . . . Arnberg, N. (2018). Enteric species F human adenoviruses use laminin-binding integrins as co-receptors for infection of Ht-29 cells. Scientific Reports, 8(1), Article ID 10019.
Open this publication in new window or tab >>Enteric species F human adenoviruses use laminin-binding integrins as co-receptors for infection of Ht-29 cells
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, no 1, article id 10019Article in journal (Refereed) Published
Abstract [en]

The enteric species F human adenovirus types 40 and 41 (HAdV-40 and -41) are the third most common cause of infantile gastroenteritis in the world. Knowledge about HAdV-40 and -41 cellular infection is assumed to be fundamentally different from that of other HAdVs since HAdV-40 and -41 penton bases lack the αV-integrin-interacting RGD motif. This motif is used by other HAdVs mainly for internalization and endosomal escape. We hypothesised that the penton bases of HAdV-40 and -41 interact with integrins independently of the RGD motif. HAdV-41 transduction of a library of rodent cells expressing specific human integrin subunits pointed to the use of laminin-binding α2-, α3- and α6-containing integrins as well as other integrins as candidate co-receptors. Specific laminins prevented internalisation and infection, and recombinant, soluble HAdV-41 penton base proteins prevented infection of human intestinal HT-29 cells. Surface plasmon resonance analysis demonstrated that HAdV-40 and -41 penton base proteins bind to α6-containing integrins with an affinity similar to that of previously characterised penton base:integrin interactions. With these results, we propose that laminin-binding integrins are co-receptors for HAdV-40 and -41.

Place, publisher, year, edition, pages
Springer Nature, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-146978 (URN)10.1038/s41598-018-28255-7 (DOI)000437097000036 ()29968781 (PubMedID)2-s2.0-85049507353 (Scopus ID)
Note

Originally included in thesis in manuscript form.

Available from: 2018-04-24 Created: 2018-04-24 Last updated: 2018-08-29Bibliographically approved
Brännström, K., Gharibyan, A. L., Islam, T., Iakovleva, I., Nilsson, L., Lee, C. C., . . . Olofsson, A. (2018). Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips. Data in Brief, 19, 1166-1170
Open this publication in new window or tab >>Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips
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2018 (English)In: Data in Brief, E-ISSN 2352-3409, Vol. 19, p. 1166-1170Article in journal (Refereed) Published
Abstract [en]

We demonstrate the use of Scanning Electron microscopy (SEM) in combination with Surface Plasmon Resonance (SPR) to probe and verify the formation of amyloid and its morphology on an SPR chip. SPR is a technique that measures changes in the immobilized weight on the chip surface and is frequently used to probe the formation and biophysical properties of amyloid structures. In this context it is of interest to also monitor the morphology of the formed structures. The SPR chip surface is made of a layer of gold, which represent a suitable material for direct analysis of the surface using SEM. The standard SPR chip used here (CM5-chip, GE Healthcare, Uppsala, Sweden) can easily be disassembled and directly analyzed by SEM. In order to verify the formation of amyloid fibrils in our experimental conditions we analyzed also in-solution produced structures by using Transmission Electron Microscopy (TEM). For further details and experimental findings, please refer to the article published in Journal of Molecular Biology, (Brännström K. et al., 2018) [1].

Place, publisher, year, edition, pages
Elsevier, 2018
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-149049 (URN)10.1016/j.dib.2018.05.129 (DOI)000449869100149 ()30228999 (PubMedID)2-s2.0-85047834173 (Scopus ID)
Note

Refers to: Kristoffer Brännström, Tohidul Islam, Anna L. Gharibyan, Irina Iakovleva, Lina Nilsson, Cheng Choo Lee, Linda Sandblad, Annelie Pamrén, Anders Olofsson. The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation. Journal of Molecular Biology, Volume 430, Issue 13, 22 June 2018, Pages 1940-1949

Available from: 2018-06-14 Created: 2018-06-14 Last updated: 2019-02-04Bibliographically approved
Brännström, K., Islam, T., Gharibyan, A. L., Iakovleva, I., Nilsson, L., Lee, C. C., . . . Olofsson, A. (2018). The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation. Journal of Molecular Biology, 430(13), 1940-1949
Open this publication in new window or tab >>The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation
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2018 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 430, no 13, p. 1940-1949Article in journal (Refereed) Published
Abstract [en]

Fibril formation of the amyloid-β peptide (Aβ) follows a nucleation-dependent polymerization process and is associated with Alzheimer's disease. Several different lengths of Aβ are observed in vivo, but Aβ1-40 and Aβ1-42 are the dominant forms. The fibril architectures of Aβ1-40 and Aβ1-42 differ and Aβ1-42 assemblies are generally considered more pathogenic. We show here that monomeric Aβ1-42 can be cross-templated and incorporated into the ends of Aβ1-40 fibrils, while incorporation of Aβ1-40 monomers into Aβ1-42 fibrils is very poor. We also show that via cross-templating incorporated Aβ monomers acquire the properties of the parental fibrils. The suppressed ability of Aβ1-40 to incorporate into the ends of Aβ1-42 fibrils and the capacity of Aβ1-42 monomers to adopt the properties of Aβ1-40 fibrils may thus represent two mechanisms reducing the total load of fibrils having the intrinsic, and possibly pathogenic, features of Aβ1-42 fibrils in vivo. We also show that the transfer of fibrillar properties is restricted to fibril-end templating and does not apply to cross-nucleation via the recently described path of surface-catalyzed secondary nucleation, which instead generates similar structures to those acquired via de novo primary nucleation in the absence of catalyzing seeds. Taken together these results uncover an intrinsic barrier that prevents Aβ1-40 from adopting the fibrillar properties of Aβ1-42 and exposes that the transfer of properties between amyloid-β fibrils are determined by their path of formation.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Aβ, Cross-templating, Fibril, Surface Plasmon resonance, Thioflavin-T
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-148050 (URN)10.1016/j.jmb.2018.05.001 (DOI)29751013 (PubMedID)2-s2.0-85047103029 (Scopus ID)
Available from: 2018-06-14 Created: 2018-06-14 Last updated: 2018-06-14Bibliographically approved
Nilsson, L., Pamrén, A., Islam, T., Brännström, K., Golchin, S. A., Pettersson, N., . . . Olofsson, A. (2018). Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates. Journal of Molecular Biology, 430(17), 2722-2733
Open this publication in new window or tab >>Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates
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2018 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 430, no 17, p. 2722-2733Article in journal (Refereed) Published
Abstract [en]

The pathological Aβ aggregates associated with Alzheimer's disease follow a nucleation-dependent path of formation. A nucleus represents an oligomeric assembly of Aβ peptides that acts as a template for subsequent incorporation of monomers to form a fibrillar structure. Nuclei can form de novo or via surface-catalyzed secondary nucleation, and the combined rates of elongation and nucleation control the overall rate of fibril formation. Transthyretin (TTR) obstructs Aβ fibril formation in favor of alternative non-fibrillar assemblies, but the mechanism behind this activity is not fully understood. This study shows that TTR does not significantly disturb fibril elongation; rather, it effectively interferes with the formation of oligomeric nuclei. We demonstrate that this interference can be modulated by altering the relative contribution of elongation and nucleation, and we show how TTR's effects can range from being essentially ineffective to almost complete inhibition of fibril formation without changing the concentration of TTR or monomeric Aβ.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Aβ, Surface Plasmon Resonance, Thioflavin-T, amyloid, transthyretin
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-148930 (URN)10.1016/j.jmb.2018.06.005 (DOI)000441645300013 ()29890120 (PubMedID)
Funder
The Dementia Association - The National Association for the Rights of the DementedThe Kempe FoundationsSwedish Research CouncilMagnus Bergvall FoundationTorsten Söderbergs stiftelse
Available from: 2018-06-14 Created: 2018-06-14 Last updated: 2018-09-05Bibliographically approved
Projects
3D electron microscopy visualization of the bacterial cytoskeleton [2011-05198_VR]; Umeå UniversityNanoSPAM: National Nodes for Sample Preparation And Microscopy [2018-06478_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3492-3287

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