umu.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Obi, Ikenna
Alternative names
Publications (10 of 11) Show all publications
Deiana, M., Chand, K., Jamroskovic, J., Obi, I., Chorell, E. & Sabouri, N. (2019). A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission. Angewandte Chemie International Edition
Open this publication in new window or tab >>A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission
Show others...
2019 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773Article in journal (Refereed) Epub ahead of print
Abstract [en]

The design of turn‐on dyes with optical signals sensitive to the formation of supramolecular structures provides fascinating and underexplored opportunities for G‐quadruplex (G4) DNA detection and characterization. Here, we show a new switching mechanism that relies on the recognition‐driven disaggregation (on‐signal) of an ultrabright coumarin‐quinazoline conjugate. The synthesized probe selectively lights‐up parallel G4 DNA structures via the disassembly of its supramolecular state, demonstrating outputs that are easily integrable into a label free molecular logic system. Finally, our molecule preferentially stains the G4‐rich nucleoli of cancer cells.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2019
National Category
Natural Sciences Medical and Health Sciences
Research subject
Medical Biochemistry
Identifiers
urn:nbn:se:umu:diva-164662 (URN)10.1002/anie.201912027 (DOI)000497789300001 ()31644837 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW2015-0189Swedish Research Council, VR-NT 2017-05235Swedish Research Council, VR-MH 2018-02651The Kempe Foundations, SMK-1632
Available from: 2019-10-25 Created: 2019-10-25 Last updated: 2019-12-16
Jamroskovic, J., Obi, I., Movahedi, A., Chand, K., Chorell, E. & Sabouri, N. (2019). Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay. DNA Repair, 82, Article ID 102678.
Open this publication in new window or tab >>Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay
Show others...
2019 (English)In: DNA Repair, ISSN 1568-7864, E-ISSN 1568-7856, Vol. 82, article id 102678Article in journal (Refereed) Published
Abstract [en]

In order to understand in which biological processes the four-stranded G-quadruplex (G4) DNA structures play a role, it is important to determine which predicted regions can actually adopt a G4 structure. Here, to identify DNA regions in Schizosaccharomyces pombe that fold into G4 structures, we first optimized a quantitative PCR (qPCR) assay using the G4 stabilizer, PhenDC3. We call this method the qPCR stop assay, and used it to screen for G4 structures in genomic DNA. The presence of G4 stabilizers inhibited DNA amplification in 14/15 unexplored genomic regions in S. pombe that encompassed predicted G4 structures, suggesting that at these sites the stabilized G4 structure formed an obstacle for the DNA polymerase. Furthermore, the formation of G4 structures was confirmed by complementary in vitro assays. In vivo, the S. pombe G4 unwinder Pif1 helicase, Pfh1, was associated with tested G4 sites, suggesting that the G4 structures also formed in vivo. Thus, we propose that the confirmed G4 structures in S. pombe form an obstacle for replication in vivo, and that the qPCR stop assay is a method that can be used to identify G4 structures. Finally, we suggest that the qPCR stop assay can also be used for identifying G4 structures in other organisms, as well as being adapted to screen for novel G4 stabilizers.

Keywords
G-quadruplex DNA, Schizosaccharomyces pombe, G4 stabilizer PhenDC3, Pif1 family helicase Pfh1, DNA replication, Quantitative PCR
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Biochemistry
Identifiers
urn:nbn:se:umu:diva-162927 (URN)10.1016/j.dnarep.2019.102678 (DOI)000491627000009 ()31473486 (PubMedID)2-s2.0-85071382717 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW2015-0189The Kempe Foundations, SMK1449 and SMK1632Swedish Society for Medical Research (SSMF)
Available from: 2019-09-02 Created: 2019-09-02 Last updated: 2019-11-20Bibliographically approved
Thanikkal, E. J., Kumar Gahlot, D., Liu, J., Fredriksson Sundbom, M., Gurung, J. M., Ruuth, K., . . . Francis, M. S. (2019). The Yersinia pseudotuberculosis Cpx envelope stress system contributes to transcriptional activation of rovM. Virulence, 10(1), 37-57
Open this publication in new window or tab >>The Yersinia pseudotuberculosis Cpx envelope stress system contributes to transcriptional activation of rovM
Show others...
2019 (English)In: Virulence, ISSN 2150-5594, E-ISSN 2150-5608, Vol. 10, no 1, p. 37-57Article in journal (Refereed) Published
Abstract [en]

The Gram-negative enteropathogen Yersinia pseudotuberculosis possesses a number of regulatory systems that detect cell envelope damage caused by noxious extracytoplasmic stresses. The CpxA sensor kinase and CpxR response regulator two-component regulatory system is one such pathway. Active Cpx signalling upregulates various factors designed to repair and restore cell envelope integrity. Concomitantly, this pathway also down-regulates key determinants of virulence. In Yersinia, cpxA deletion accumulates high levels of phosphorylated CpxR (CpxR~P). Accumulated CpxR~P directly repressed rovA expression and this limited expression of virulence-associated processes. A second transcriptional regulator, RovM, also negatively regulates rovA expression in response to nutrient stress. Hence, this study aimed to determine if CpxR~P can influence rovA expression through control of RovM levels. We determined that the active CpxR~P isoform bound to the promoter of rovM and directly induced its expression, which naturally associated with a concurrent reduction in rovA expression. Site-directed mutagenesis of the CpxR~P binding sequence in the rovM promoter region desensitised rovM expression to CpxR~P. These data suggest that accumulated CpxR~P inversely manipulates the levels of two global transcriptional regulators, RovA and RovM, and this would be expected to have considerable influence on Yersinia pathophysiology and metabolism.

Place, publisher, year, edition, pages
Taylor & Francis Group, 2019
Keywords
Environmental stress responsiveness, gene expression control, metabolic networks, microbial behaviour, growth and survival, fitness
National Category
Microbiology Microbiology in the medical area
Research subject
Microbiology; Molecular Biology; Infectious Diseases
Identifiers
urn:nbn:se:umu:diva-154425 (URN)10.1080/21505594.2018.1556151 (DOI)000453473300001 ()30518290 (PubMedID)
Funder
Swedish Research Council, 2009-3660Swedish Research Council, 2014-6652
Available from: 2018-12-17 Created: 2018-12-17 Last updated: 2019-03-05Bibliographically approved
Lekmeechai, S., Su, Y.-C., Brant, M., Alvarado-Kristensson, M., Vallström, A., Obi, I., . . . Riesbeck, K. (2018). Helicobacter pylori Outer Membrane Vesicles Protect the Pathogen From Reactive Oxygen Species of the Respiratory Burst. Frontiers in Microbiology, 9, Article ID 1837.
Open this publication in new window or tab >>Helicobacter pylori Outer Membrane Vesicles Protect the Pathogen From Reactive Oxygen Species of the Respiratory Burst
Show others...
2018 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 1837Article in journal (Refereed) Published
Abstract [en]

Outer membrane vesicles (OMVs) play an important role in the persistence of Helicobacter pylori infection. Helicobacter OMVs carry a plethora of virulence factors, including catalase (KatA), an antioxidant enzyme that counteracts the host respiratory burst. We found KatA to be enriched and surface-associated in OMVs compared to bacterial cells. This conferred OMV-dependent KatA activity resulting in neutralization of H2O2 and NaClO, and rescue of surrounding bacteria from oxidative damage. The antioxidant activity of OMVs was abolished by deletion of KatA. In conclusion, enrichment of antioxidative KatA in OMVs is highly important for efficient immune evasion.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
H. pylori, KatA, outer membrane vesicles, oxidative burst, reactive oxygen species
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-152205 (URN)10.3389/fmicb.2018.01837 (DOI)000443976200001 ()30245670 (PubMedID)
Available from: 2018-10-25 Created: 2018-10-25 Last updated: 2018-10-25Bibliographically approved
Skoog, E. C., Padra, M., Åberg, A., Gideonsson, P., Obi, I., Quintana-Hayashi, M. P., . . . Linden, S. K. (2017). BabA dependent binding of Helicobacter pylori to human gastric mucins cause aggregation that inhibits proliferation and is regulated via ArsS. Scientific Reports, 7, Article ID 40656.
Open this publication in new window or tab >>BabA dependent binding of Helicobacter pylori to human gastric mucins cause aggregation that inhibits proliferation and is regulated via ArsS
Show others...
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 40656Article in journal (Refereed) Published
Abstract [en]

Mucins in the gastric mucus layer carry a range of glycan structures, which vary between individuals, can have antimicrobial effect or act as ligands for Helicobacter pylori. Mucins from various individuals and disease states modulate H. pylori proliferation and adhesin gene expression differently. Here we investigate the relationship between adhesin mediated binding, aggregation, proliferation and adhesin gene expression using human gastric mucins and synthetic adhesin ligand conjugates. By combining measurements of optical density, bacterial metabolic activity and live/dead stains, we could distinguish bacterial aggregation from viability changes, enabling elucidation of mechanisms behind the anti-prolific effects that mucins can have. Binding of H. pylori to Leb-glycoconjugates inhibited the proliferation of the bacteria in a BabA dependent manner, similarly to the effect of mucins carrying Leb. Furthermore, deletion of arsS lead to a decrease in binding to Leb-glycoconjugates and Leb-decorated mucins, accompanied by decreased aggregation and absence of anti-prolific effect of mucins and Leb-glycoconjugates. Inhibition of proliferation caused by adhesin dependent binding to mucins, and the subsequent aggregation suggests a new role of mucins in the host defense against H. pylori. This aggregating trait of mucins may be useful to incorporate into the design of adhesin inhibitors and other disease intervention molecules.

National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-132309 (URN)10.1038/srep40656 (DOI)000392344400001 ()28106125 (PubMedID)
Available from: 2017-04-07 Created: 2017-04-07 Last updated: 2018-06-09Bibliographically approved
Olofsson, A., Nygård Skalman, L., Obi, I., Lundmark, R. & Arnqvist, A. (2014). Uptake of Helicobacter pylori vesicles is facilitated by clathrin-dependent and clathrin-independent endocytic pathways. mBio, 5(3), e00979-14
Open this publication in new window or tab >>Uptake of Helicobacter pylori vesicles is facilitated by clathrin-dependent and clathrin-independent endocytic pathways
Show others...
2014 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 5, no 3, p. e00979-14-Article in journal (Refereed) Published
Abstract [en]

UNLABELLED: Bacteria shed a diverse set of outer membrane vesicles that function as transport vehicles to deliver effector molecules and virulence factors to host cells. Helicobacter pylori is a gastric pathogen that infects half of the world's population, and in some individuals the infection progresses into peptic ulcer disease or gastric cancer. Here we report that intact vesicles from H. pylori are internalized by clathrin-dependent endocytosis and further dynamin-dependent processes, as well as in a cholesterol-sensitive manner. We analyzed the uptake of H. pylori vesicles by gastric epithelial cells using a method that we refer to as quantification of internalized substances (qIS). The qIS assay is based on a near-infrared dye with a cleavable linker that enables the specific quantification of internalized substances after exposure to reducing conditions. Both chemical inhibition and RNA interference in combination with the qIS assay showed that H. pylori vesicles enter gastric epithelial cells via both clathrin-mediated endocytosis and additional endocytic processes that are dependent on dynamin. Confocal microscopy revealed that H. pylori vesicles colocalized with clathrin and dynamin II and with markers of subsequent endosomal and lysosomal trafficking. Interestingly, however, knockdown of components required for caveolae had no significant effect on internalization and knockdown of components required for clathrin-independent carrier (CLIC) endocytosis increased internalization of H. pylori vesicles. Furthermore, uptake of vesicles by both clathrin-dependent and -independent pathways was sensitive to depletion, but not sequestering, of cholesterol in the host cell membrane suggesting that membrane fluidity influences the efficiency of H. pylori vesicle uptake.

IMPORTANCE: Bacterial vesicles act as long-distance tools to deliver toxins and effector molecules to host cells. Vesicles can cause a variety of host cell responses via cell surface-induced cell signaling or internalization. Vesicles of diverse bacterial species enter host cells via different endocytic pathways or via membrane fusion. With the combination of a fluorescence-based quantification assay that quantifies internalized vesicles in a large number of cells and either chemical inhibition or RNA interference, we show that clathrin-mediated endocytosis is the major pathway for uptake of Helicobacter pylori vesicles and that lipid microdomains of the host cell membrane affect uptake of vesicles via clathrin-independent pathways. Our results provide important insights about membrane fluidity and its important role in the complex process that directs the H. pylori vesicle to a specific endocytic pathway. Understanding the mechanisms that operate in vesicle-host interactions is important to fully recognize the impact of vesicles in pathogenesis.

National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-90953 (URN)10.1128/mBio.00979-14 (DOI)000338875900050 ()24846379 (PubMedID)
Available from: 2014-07-04 Created: 2014-07-04 Last updated: 2018-06-07Bibliographically approved
Obi, I. & Francis, M. (2013). Demarcating SurA activities required for outer membrane targeting of Yersinia pseudotuberculosis adhesins. Infection and Immunity, 81(7), 2296-2308
Open this publication in new window or tab >>Demarcating SurA activities required for outer membrane targeting of Yersinia pseudotuberculosis adhesins
2013 (English)In: Infection and Immunity, ISSN 0019-9567, E-ISSN 1098-5522, Vol. 81, no 7, p. 2296-2308Article in journal (Refereed) Published
Abstract [en]

SurA is a periplasmic protein folding factor involved in chaperoning and trafficking of outer membrane proteins across the Gram-negative bacterial periplasm. In addition, SurA also possesses peptidyl-prolyl cis/trans isomerase activity. In enteropathogenic Yersinia pseudotuberculosis, we have previously reported that SurA is needed for bacterial virulence and envelope integrity. In this study, we investigated the role of SurA in the assembly of important Yersinia adhesins. Using genetic mutation, biochemical characterization and an in vitro-based bacterial host cell association assay, we confirmed that surface localization of the invasin adhesin is dependent on SurA. As a surA deletion also has some impact on the levels of individual components of the BAM complex in the Yersinia outer membrane, abolished invasin surface assembly could reflect both a direct loss of SurA-dependent periplasmic targeting as well as a potentially compromised BAM complex assembly platform in the outer membrane. To varying degrees, the assembly of two other adhesins, Ail and the pH 6 antigen fibrillum PsaA also depend on SurA. Consequently, loss of SurA leads to a dramatic reduction in Yersinia attachment to eukaryotic host cells. Genetic complementation of surA deletion mutants indicated a prominent role for SurA chaperone function in outer membrane protein assembly. Significantly, the N-terminus of SurA contributed most of this SurA chaperone function. Despite a dominant chaperoning role, it was also evident that SurA isomerization activity did make a modest contribution to this assembly process.

Place, publisher, year, edition, pages
Washington: American Society for Microbiology, 2013
Keywords
outer membrane proteins, chaperone, peptidyl-prolyl cis/trans isomerase, OmpA, type three secretion
National Category
Microbiology Biochemistry and Molecular Biology
Research subject
Microbiology; Infectious Diseases; Molecular Biology; Biochemistry
Identifiers
urn:nbn:se:umu:diva-72864 (URN)10.1128/IAI.01208-12 (DOI)000320307300003 ()
Funder
Swedish Research Council, 2009-3660Swedish Research Council, 2006-3869
Available from: 2013-06-14 Created: 2013-06-14 Last updated: 2018-06-08Bibliographically approved
Liu, J., Thanikkal, E., Obi, I. & Francis, M. (2012). Elevated CpxR~P levels repress the Ysc-Yop type III secretion system of Yersinia pseudotuberculosis. Research in Microbiology, 163(8), 518-530
Open this publication in new window or tab >>Elevated CpxR~P levels repress the Ysc-Yop type III secretion system of Yersinia pseudotuberculosis
2012 (English)In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123, Vol. 163, no 8, p. 518-530Article in journal (Refereed) Published
Abstract [en]

One way that Gram-negative bacteria respond to extracytoplasmic stress is through the CpxA-CpxR system. An activated CpxA sensor kinase phosphorylates the CpxR response regulator to instigate positive auto-amplification of Cpx pathway activation, as well as synthesis of various bacterial survival factors. In the absence of CpxA, human enteropathogenic Yersinia pseudotuberculosis accumulates high CpxR~P levels aided by the action of low molecular weight phosphodonors such as acetyl~P. Critically, these bacteria are also defective for plasmid encoded Ysc-Yop-dependent type III synthesis and secretion, an essential determinant of virulence. Herein, we investigated whether elevated CpxR~P levels account for lost Ysc-Yop function. Decisively, reducing CpxR~P in Yersinia defective for CpxA phosphatase activity - through incorporating second-site suppressor mutations in ackA-pta or cpxR - dramatically restored Ysc-Yop T3S function. Moreover, the repressive effect of accumulated CpxR~P is a direct consequence of binding to the promoter regions of the T3S genes. Thus, Cpx pathway activation has two consequences in Yersinia; one, to maintain quality control in the bacterial envelope, and the second, to restrict ysc-yop gene expression to those occasions where it will have maximal effect.

Place, publisher, year, edition, pages
Elsevier: , 2012
Keywords
Extracytoplasmic stress, CpxA, AckA, Pta, virulence
National Category
Microbiology Microbiology in the medical area
Research subject
Microbiology; Molecular Biology
Identifiers
urn:nbn:se:umu:diva-60454 (URN)10.1016/j.resmic.2012.07.010 (DOI)
Funder
Swedish Research Council
Available from: 2012-10-19 Created: 2012-10-13 Last updated: 2018-06-08Bibliographically approved
Liu, J., Obi, I. R., Thanikkal, E. J., Kieselbach, T. & Francis, M. S. (2011). Phosphorylated CpxR Restricts Production of the RovA Global Regulator in Yersinia pseudotuberculosis. PLoS ONE, 6(8), e23314
Open this publication in new window or tab >>Phosphorylated CpxR Restricts Production of the RovA Global Regulator in Yersinia pseudotuberculosis
Show others...
2011 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 8, p. e23314-Article in journal (Refereed) Published
Abstract [en]

Background: RovA is a global transcriptional regulator of gene expression in pathogenic Yersinia. RovA levels are kept in check by a sophisticated layering of distinct transcriptional and post-transcriptional regulatory mechanisms. In the enteropathogen Y. pseudotuberculosis, we have previously reported that the extracytoplasmic stress sensing CpxA-CpxR two-component regulatory system modulates rovA expression.

Methodology/Principal Findings: In this study, we characterized CpxR phosphorylation (CpxR similar to P) in vitro, and determined that phosphorylation was necessary for CpxR to efficiently bind to the PCR-amplified upstream regulatory region of rovA. The precise CpxR similar to P binding site was mapped by a nuclease protection assay and directed mutagenesis confirmed that in vivo binding to the rovA promoter inhibits transcription. Reduced RovA production was most pronounced following CpxR, P accumulation in the Yersinia cytoplasm during chronic Cpx pathway activation and by the indiscriminate phosphodonor action of acetyl phosphate.

Conclusions/Significance: Cpx pathway activation restricts levels of the RovA global regulator. The regulatory influence of CpxR similar to P must therefore extend well beyond periplasmic quality control in the Yersinia envelope, to include genes involved in environmental survival and pathogenicity.

Place, publisher, year, edition, pages
Public Library of Science, 2011
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-46172 (URN)10.1371/journal.pone.0023314 (DOI)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2011-08-29 Created: 2011-08-29 Last updated: 2018-06-08Bibliographically approved
Obi, I., Nordfelth, R. & Francis, M. (2011). Varying dependency of periplasmic peptidylprolyl cis-trans isomerases in promoting Yersinia pseudotuberculosis stress tolerance and pathogenicity. Biochemical Journal, 439(2), 321-332
Open this publication in new window or tab >>Varying dependency of periplasmic peptidylprolyl cis-trans isomerases in promoting Yersinia pseudotuberculosis stress tolerance and pathogenicity
2011 (English)In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 439, no 2, p. 321-332Article in journal (Refereed) Published
Abstract [en]

Periplasmic PPIases (peptidylprolyl cis-trans isomerases) catalyse the cis-trans isomerization of peptidyl-prolyl bonds, which is a rate-limiting step during protein folding. We demonstrate that the surA, ppiA, ppiD, fkpA and fklB alleles each encode a periplasmic PPIase in the bacterial pathogen Yersinia pseudotuberculosis. Of these, four were purified to homogeneity. Purified SurA, FkpA and FklB, but not PpiD, displayed detectable PPIase activity in vitro. Significantly, only Y. pseudotuberculosis lacking surA caused drastic alterations to the outer membrane protein profile and FA (fatty acid) composition. They also exhibited aberrant cellular morphology, leaking LPS (lipopolysaccharide) into the extracellular environment. The SurA PPIase is therefore most critical for maintaining Y. pseudotuberculosis envelope integrity during routine culturing. On the other hand, bacteria lacking either surA or all of the genes ppiA, ppiD, fkpA and fklB were sensitive to hydrogen peroxide and were attenuated in mice infections. Thus Y. pseudotuberculosis exhibits both SurA-dependent and -independent requirements for periplasmic PPIase activity to ensure in vivo survival and a full virulence effect in a mammalian host.

Place, publisher, year, edition, pages
United Kingdom: Portland Press Limited, 2011
Keywords
chaperone, immunosuppressant, infection, membrane biogenesis, periplasmic peptidylprolyl cis–trans isomerase, protein folding, survival
National Category
Microbiology
Research subject
Microbiology; Molecular Biology; Biochemistry
Identifiers
urn:nbn:se:umu:diva-48067 (URN)10.1042/BJ20110767 (DOI)21726196 (PubMedID)
Funder
Swedish Research Council, 2006-3869Swedish Research Council, 2009-3660
Available from: 2011-10-10 Created: 2011-10-07 Last updated: 2018-06-08Bibliographically approved
Organisations

Search in DiVA

Show all publications