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Jaiman, D., Nagampalli, R. & Persson, K. (2023). A comparative analysis of lipoprotein transport proteins: LolA and LolB from Vibrio cholerae and LolA from Porphyromonas gingivalis. Scientific Reports, 13(1), Article ID 6605.
Open this publication in new window or tab >>A comparative analysis of lipoprotein transport proteins: LolA and LolB from Vibrio cholerae and LolA from Porphyromonas gingivalis
2023 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1, article id 6605Article in journal (Refereed) Published
Abstract [en]

In Gram-negative bacteria, N-terminal lipidation is a signal for protein trafficking from the inner membrane (IM) to the outer membrane (OM). The IM complex LolCDE extracts lipoproteins from the membrane and moves them to the chaperone LolA. The LolA-lipoprotein complex crosses the periplasm after which the lipoprotein is anchored to the OM. In γ-proteobacteria anchoring is assisted by the receptor LolB, while a corresponding protein has not been identified in other phyla. In light of the low sequence similarity between Lol-systems from different phyla and that they may use different Lol components, it is crucial to compare representative proteins from several species. Here we present a structure-function study of LolA and LolB from two phyla: LolA from Porphyromonas gingivalis (phylum bacteroidota), and LolA and LolB from Vibrio cholerae (phylum proteobacteria). Despite large sequence differences, the LolA structures are very similar, hence structure and function have been conserved throughout evolution. However, an Arg-Pro motif crucial for function in γ-proteobacteria has no counterpart in bacteroidota. We also show that LolA from both phyla bind the antibiotic polymyxin B whereas LolB does not. Collectively, these studies will facilitate the development of antibiotics as they provide awareness of both differences and similarities across phyla.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Biochemistry and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-207883 (URN)10.1038/s41598-023-33705-y (DOI)000997547300091 ()37095149 (PubMedID)2-s2.0-85153687027 (Scopus ID)
Funder
Swedish Research Council, 2007-08673Swedish Research Council, 2016-05009Lars Hierta Memorial Foundation
Available from: 2023-05-08 Created: 2023-05-08 Last updated: 2023-09-05Bibliographically approved
Kurata, T., Saha, C. K., Buttress, J. A., Mets, T., Brodiazhenko, T., Turnbull, K. J., . . . Atkinson, G. C. (2022). A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains. Proceedings of the National Academy of Sciences of the United States of America, 119(6), Article ID e2102212119.
Open this publication in new window or tab >>A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains
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2022 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 6, article id e2102212119Article in journal (Refereed) Published
Abstract [en]

Toxin–antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids as well as temperate bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analyzed the conservation of genomic neighborhoods using our computational tool FlaGs (for flanking genes), which allows high-throughput detection of TA-like operons. Focusing on the widespread but poorly experimentally characterized antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have named the domain Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralized TA pairs. While the majority of validated PanA-neutralized toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises transcription and translation as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralization mechanisms employed by Type II TA systems. Finally, through directed evolution, we have selected PanA variants that can neutralize noncognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain.

Place, publisher, year, edition, pages
National Academy of Sciences, 2022
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-192632 (URN)10.1073/pnas.2102212119 (DOI)000758481100014 ()35121656 (PubMedID)2-s2.0-85124146792 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW 2020.0037Swedish Research Council, 2017-03783Swedish Research Council, 2019-01085Ragnar Söderbergs stiftelse, Fellowship grantThe Kempe Foundations, SMK-1858.3Carl Tryggers foundation , CTS19:24The Kempe Foundations, ScholarshipThe Kempe Foundations, Fall 2020Swedish Research Council, 2018-00956
Available from: 2022-02-21 Created: 2022-02-21 Last updated: 2023-09-05Bibliographically approved
Toh, E., Baryalai, P., Nadeem, A., Aung, K. M., Chen, S., Persson, K., . . . Wai, S. N. (2022). Bacterial protein MakA causes suppression of tumour cell proliferation via inhibition of PIP5K1α/Akt signalling. Cell Death and Disease, 13(12), Article ID 1024.
Open this publication in new window or tab >>Bacterial protein MakA causes suppression of tumour cell proliferation via inhibition of PIP5K1α/Akt signalling
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2022 (English)In: Cell Death and Disease, ISSN 2041-4889, E-ISSN 2041-4889, Vol. 13, no 12, article id 1024Article in journal (Refereed) Published
Abstract [en]

Recently, we demonstrated that a novel bacterial cytotoxin, the protein MakA which is released by Vibrio cholerae, is a virulence factor, causing killing of Caenorhabditis elegans when the worms are grazing on the bacteria. Studies with mammalian cell cultures in vitro indicated that MakA could affect eukaryotic cell signalling pathways involved in lipid biosynthesis. MakA treatment of colon cancer cells in vitro caused inhibition of growth and loss of cell viability. These findings prompted us to investigate possible signalling pathways that could be targets of the MakA-mediated inhibition of tumour cell proliferation. Initial in vivo studies with MakA producing V. cholerae and C. elegans suggested that the MakA protein might target the PIP5K1α phospholipid-signalling pathway in the worms. Intriguingly, MakA was then found to inhibit the PIP5K1α lipid-signalling pathway in cancer cells, resulting in a decrease in PIP5K1α and pAkt expression. Further analyses revealed that MakA inhibited cyclin-dependent kinase 1 (CDK1) and induced p27 expression, resulting in G2/M cell cycle arrest. Moreover, MakA induced downregulation of Ki67 and cyclin D1, which led to inhibition of cell proliferation. This is the first report about a bacterial protein that may target signalling involving the cancer cell lipid modulator PIP5K1α in colon cancer cells, implying an anti-cancer effect.

Place, publisher, year, edition, pages
Springer Nature, 2022
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-201753 (URN)10.1038/s41419-022-05480-7 (DOI)000895373300001 ()36473840 (PubMedID)2-s2.0-85143300255 (Scopus ID)
Funder
Swedish Research Council, 2018-02914Swedish Research Council, 2019-01720Swedish Research Council, 2019-01318Swedish Research Council, 2016-05009Swedish Cancer Society, CAN-2017-419Swedish Cancer Society, 2020-711Swedish Cancer Society, CAN-2017-381The Kempe Foundations, JCK-1728The Kempe Foundations, SMK-1553The Kempe Foundations, JCK2931.1U9Malmö University
Available from: 2022-12-21 Created: 2022-12-21 Last updated: 2023-09-05Bibliographically approved
Nadeem, A., Berg, A., Pace, H., Alam, A., Toh, E., Ådén, J., . . . Wai, S. N. (2022). Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae. eLIFE, 11, Article ID e73439.
Open this publication in new window or tab >>Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae
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2022 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 11, article id e73439Article in journal (Refereed) Published
Abstract [en]

The α-pore-forming toxins (α-PFTs) from pathogenic bacteria damage host cell membranes by pore formation. We demonstrate a remarkable, hitherto unknown mechanism by an α-PFT protein from Vibrio cholerae. As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other α-PFTs. In contrast, MakA in isolation induces tube-like structures in acidic endosomal compartments of epithelial cells in vitro. The present study unravels the dynamics of tubular growth, which occurs in a pH-, lipid-, and concentration-dependent manner. Within acidified organelle lumens or when incubated with cells in acidic media, MakA forms oligomers and remodels membranes into high-curvature tubes leading to loss of membrane integrity. A 3.7 Å cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. MakA forms a pinecone-like spiral with a central cavity and a thin annular lipid bilayer embedded between the MakA transmembrane helices in its active α-PFT conformation. Our study provides insights into a novel tubulation mechanism of an α-PFT protein and a new mode of action by a secreted bacterial toxin.

Place, publisher, year, edition, pages
eLife Sciences Publications, Ltd, 2022
Keywords
Vibrio cholerae, MakA, lipid
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-192300 (URN)10.7554/eLife.73439 (DOI)2-s2.0-85124321786 (Scopus ID)
Funder
Swedish Research Council, 2018–02914Swedish Research Council, 2016–05009Swedish Research Council, 2019–01720Swedish Research Council, 2016–06963Swedish Research Council, 2019–02011Swedish Cancer Society, 2017–419Swedish Cancer Society, 2020–711The Kempe Foundations, JCK-1728The Kempe Foundations, SMK-1756.2The Kempe Foundations, SMK-1553The Kempe Foundations, JCK-1724The Kempe Foundations, SMK-1961Knut and Alice Wallenberg FoundationFamiljen Erling-Perssons Stiftelse
Available from: 2022-02-08 Created: 2022-02-08 Last updated: 2024-01-12Bibliographically approved
Nadeem, A., Nagampalli, R., Toh, E., Alam, A., Myint, S. L., Heidler, T., . . . Persson, K. (2021). A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion. Proceedings of the National Academy of Sciences of the United States of America, 118(47), Article ID e2111418118.
Open this publication in new window or tab >>A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion
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2021 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 47, article id e2111418118Article in journal (Refereed) Published
Abstract [en]

Vibrio cholerae, responsible for outbreaks of cholera disease, is a highly motile organism by virtue of a single flagellum. We describe how the flagellum facilitates the secretion of three V. cholerae proteins encoded by a hitherto-unrecognized genomic island. The proteins MakA/B/E can form a tripartite toxin that lyses erythrocytes and is cytotoxic to cultured human cells. A structural basis for the cytolytic activity of the Mak proteins was obtained by X-ray crystallography. Flagellum-facilitated secretion ensuring spatially coordinated delivery of Mak proteins revealed a role for the V. cholerae flagellum considered of particular significance for the bacterial environmental persistence. Our findings will pave the way for the development of diagnostics and therapeutic strategies against pathogenic Vibrionaceae.

National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-191257 (URN)10.1073/pnas.2111418118 (DOI)000727697700014 ()34799450 (PubMedID)2-s2.0-85121209218 (Scopus ID)
Funder
Swedish Research Council, 2016-05009Swedish Research Council, 2018-02914Swedish Research Council, 2019-01720Swedish Research Council, 2007-08673The Kempe Foundations, SMK-1756.2The Kempe Foundations, SMK-1553The Kempe Foundations, JCK-1728Swedish Cancer Society, 2017-419The Kempe Foundations, SMK-1961Swedish Research Council
Available from: 2022-01-12 Created: 2022-01-12 Last updated: 2023-05-11Bibliographically approved
Heidler, T. & Persson, K. (2021). Crystallization of Recombinant Fimbrial Proteins of Porphyromonas gingivalis (1ed.). In: Keiji Nagano and Yoshiaki Hasegawa (Ed.), Periodontal Pathogens: Methods and Protocols (pp. 87-96). Humana Press
Open this publication in new window or tab >>Crystallization of Recombinant Fimbrial Proteins of Porphyromonas gingivalis
2021 (English)In: Periodontal Pathogens: Methods and Protocols / [ed] Keiji Nagano and Yoshiaki Hasegawa, Humana Press, 2021, 1, p. 87-96Chapter in book (Refereed)
Abstract [en]

Porphyromonas gingivalis fimbriae play a critical role in colonization. Elucidation of the fimbrial structure in atomic detail is important for understanding the colonization mechanism and to provide means to combat periodontitis. X-ray crystallography is a technique that is used to obtain detailed information of proteins along with bound ligands and ions. Crystallization of the protein of interest is the first step toward structure determination. Unfortunately it is not possible to predict the crystallization condition of a certain protein or even if the protein can be crystallized. Protein crystallization is, on the contrary, a matter of trial and error. However, the best strategy for success is to focus on the protein purification step to obtain a sample that is pure, stable, homogeneous and of high concentration. This chapter addresses general methods for crystallization of fimbrial proteins.

Place, publisher, year, edition, pages
Humana Press, 2021 Edition: 1
Series
Methods in Molecular Biology (MIMB), ISSN 1064-3745, E-ISSN 1940-6029 ; 2210
Keywords
Protein purification, Crystallization, Optimization, Fimbriae
National Category
Microbiology in the medical area Structural Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-184186 (URN)10.1007/978-1-0716-0939-2_9 (DOI)32815130 (PubMedID)2-s2.0-85090229731 (Scopus ID)978-1-0716-0938-5 (ISBN)978-1-0716-0941-5 (ISBN)978-1-0716-0939-2 (ISBN)
Available from: 2021-06-10 Created: 2021-06-10 Last updated: 2021-11-26Bibliographically approved
Graça, A. T., Hall, M., Persson, K. & Schröder, W. P. (2021). High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Scientific Reports, 11(1), Article ID 15534.
Open this publication in new window or tab >>High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction
2021 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 1, article id 15534Article in journal (Refereed) Published
Abstract [en]

In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.

Place, publisher, year, edition, pages
Nature Publishing Group, 2021
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-186557 (URN)10.1038/s41598-021-94914-x (DOI)000683319500011 ()2-s2.0-85111686355 (Scopus ID)
Available from: 2021-08-11 Created: 2021-08-11 Last updated: 2024-01-30Bibliographically approved
Nadeem, A., Alam, A., Toh, E., Myint, S. L., Ur Rehman, Z., Liu, T., . . . Wai, S. N. (2021). Phosphatidic acid-mediated binding and mammalian cell internalization of the Vibrio cholerae cytotoxin MakA. PLoS Pathogens, 17(3), Article ID 1009414.
Open this publication in new window or tab >>Phosphatidic acid-mediated binding and mammalian cell internalization of the Vibrio cholerae cytotoxin MakA
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2021 (English)In: PLoS Pathogens, ISSN 1553-7366, E-ISSN 1553-7374, Vol. 17, no 3, article id 1009414Article in journal (Refereed) Published
Abstract [en]

Vibrio cholerae is a noninvasive intestinal pathogen extensively studied as the causative agent of the human disease cholera. Our recent work identified MakA as a potent virulence factor of V. cholerae in both Caenorhabditis elegans and zebrafish, prompting us to investigate the potential contribution of MakA to pathogenesis also in mammalian hosts. In this study, we demonstrate that the MakA protein could induce autophagy and cytotoxicity of target cells. In addition, we observed that phosphatidic acid (PA)-mediated MakA-binding to the host cell plasma membranes promoted macropinocytosis resulting in the formation of an endomembrane-rich aggregate and vacuolation in intoxicated cells that lead to induction of autophagy and dysfunction of intracellular organelles. Moreover, we functionally characterized the molecular basis of the MakA interaction with PA and identified that the N-terminal domain of MakA is required for its binding to PA and thereby for cell toxicity. Furthermore, we observed that the ΔmakA mutant outcompeted the wild-type V. cholerae strain A1552 in the adult mouse infection model. Based on the findings revealing mechanistic insights into the dynamic process of MakA-induced autophagy and cytotoxicity we discuss the potential role played by the MakA protein during late stages of cholera infection as an anti-colonization factor.

Place, publisher, year, edition, pages
Public Library of Science, 2021
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-181991 (URN)10.1371/journal.ppat.1009414 (DOI)000631027700007 ()33735319 (PubMedID)2-s2.0-85103129339 (Scopus ID)
Available from: 2021-04-12 Created: 2021-04-12 Last updated: 2023-05-11Bibliographically approved
Heidler, T. ., Ernits, K., Ziolkowska, A., Claesson, R. & Persson, K. (2021). Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide. Communications Biology, 4(1), Article ID 106.
Open this publication in new window or tab >>Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide
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2021 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 4, no 1, article id 106Article in journal (Refereed) Published
Abstract [en]

The Gram-negative bacterium Porphyromonas gingivalis is a secondary colonizer of the oral biofilm and is involved in the onset and progression of periodontitis. Its fimbriae, of type-V, are important for attachment to other microorganisms in the biofilm and for adhesion to host cells. The fimbriae are assembled from five proteins encoded by the mfa1 operon, of which Mfa5 is one of the ancillary tip proteins. Here we report the X-ray structure of the N-terminal half of Mfa5, which reveals a von Willebrand factor domain and two IgG-like domains. One of the IgG-like domains is stabilized by an intramolecular isopeptide bond, which is the first such bond observed in a Gram-negative bacterium. These features make Mfa5 structurally more related to streptococcal adhesins than to the other P. gingivalis Mfa proteins. The structure reported here indicates that horizontal gene transfer has occurred among the bacteria within the oral biofilm.

Place, publisher, year, edition, pages
Springer Nature, 2021
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-180642 (URN)10.1038/s42003-020-01621-w (DOI)000613287300001 ()33495563 (PubMedID)2-s2.0-85099767147 (Scopus ID)
Available from: 2021-02-24 Created: 2021-02-24 Last updated: 2021-02-24Bibliographically approved
Persson, K. & Backman, L. (2021). Structural and functional characterization of a plant alpha-actinin. FEBS Open Bio, 11(8), 2198-2210
Open this publication in new window or tab >>Structural and functional characterization of a plant alpha-actinin
2021 (English)In: FEBS Open Bio, E-ISSN 2211-5463, Vol. 11, no 8, p. 2198-2210Article in journal (Refereed) Published
Abstract [en]

The Australian tree malletwood (Rhodamnia argentea) is unique. The genome of malletwood is the only known plant genome that contains a gene coding for an α-actinin-like protein. Several organisms predating the animal-plant bifurcation express an α-actinin or α-actinin-like protein. Therefore, it appears that plants in general, but not malletwood, have lost the α-actinin or α-actinin-like gene during evolution. In order to characterize its structure and function, we synthesized the gene and expressed the recombinant R. argentea protein. The results clearly show that this protein has all properties of genuine α-actinin. The N-terminal actin-binding domain (ABD), with two calponin homology motifs, is very similar to the ABD of any α-actinin. The C-terminal calmodulin-like domain, as well as the intervening rod domain, are also similar to the corresponding regions in other α-actinins. The R. argentea α-actinin-like protein dimerises in solution and thereby can cross-link actin filaments. Based on these results, we believe the R. argentea protein represents a genuine α-actinin, making R. argentea unique in the plant world.

Place, publisher, year, edition, pages
John Wiley & Sons, 2021
Keywords
alpha-actinin, actin-binding protein, protein structure, plant
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-185731 (URN)10.1002/2211-5463.13222 (DOI)000666949800001 ()34110107 (PubMedID)2-s2.0-85108808150 (Scopus ID)
Funder
Carl Tryggers foundation Swedish Research Council, Dnr 2016-05009
Available from: 2021-07-04 Created: 2021-07-04 Last updated: 2022-01-12Bibliographically approved
Projects
Structure and function of bacterial proteins involved in oral biofilm formation [2011-04186_VR]; Umeå UniversityDeciphering the assembly mechanisms of bacterial fimbriae-a novel donor-strand mechanism [2016-05009_VR]; Umeå University; Publications
Heidler, T. & Persson, K. (2021). Crystallization of Recombinant Fimbrial Proteins of Porphyromonas gingivalis (1ed.). In: Keiji Nagano and Yoshiaki Hasegawa (Ed.), Periodontal Pathogens: Methods and Protocols (pp. 87-96). Humana Press
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-0807-0348

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