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Zlatkov, N. & Uhlin, B. E. (2020). Unconventional Cyclic di-GMP Signaling in Escherichia coli (1ed.). In: Chou, Shan-Ho; Guiliani, Nicolas; Lee, Vincent T.; Römling, Ute (Ed.), Microbial Cyclic Di-Nucleotide Signaling: (pp. 487-517). Cham: Springer International Publishing
Open this publication in new window or tab >>Unconventional Cyclic di-GMP Signaling in Escherichia coli
2020 (English)In: Microbial Cyclic Di-Nucleotide Signaling / [ed] Chou, Shan-Ho; Guiliani, Nicolas; Lee, Vincent T.; Römling, Ute, Cham: Springer International Publishing , 2020, 1, p. 487-517Chapter in book (Other academic)
Abstract [en]

The species Escherichia coli represents an unfathomable variety of commensal, pathogenic, and environmental strains. The conventional cyclic di-GMP signaling in E. coli controls sessility-motility changes linked to commensalism and/or pathogenicity. Extraintestinal Pathogenic E. coli (ExPEC) are “commensals” that can cause an array of infections outside the gastrointestinal tract. To accommodate their pathogenic lifestyle with the commensal one, ExPEC biology is shaped not only by the presence of specific virulence genes and pathoadaptive mutations but also by regulatory adaptations. Bioinformatic and genetic studies indicate that the cyclic di-GMP signaling network is included in the adaptation process. For example, some neuroinvasive ExPEC were found to maintain reduced cyclic di-GMP levels due to RpoS deactivation, resulting in loss of appearance of the rugose morphotype. Moreover, ExPEC has a diversified repertoire of cyclic di-GMP degrading enzymes obtained by acquisition of novel genes often associated with fimbrial biogenesis gene clusters (e.g., sfaY/papY/focY) and by modification or deletion of specific core genome genes. For example, the majority of ExPEC contains a shortened allelic variant of the ycgG gene and some ExPEC strains do not even carry the genetic locus. New combinations of regulators offer a new cyclic di-GMP platform for S-fimbrial biogenesis and for new metabolic capabilities leading to citrate utilization and ferric citrate uptake. In this review, we outline the prerequisites for the unconventional signaling network, the rationale behind its existence in ExPEC, and future perspectives in studies of ExPEC.

Place, publisher, year, edition, pages
Cham: Springer International Publishing, 2020 Edition: 1
Keywords
ExPEC, NMEC, Pathoadaptation, RpoS, Citrate, Ferric citrate, S-fimbriae
National Category
Natural Sciences Medical and Health Sciences
Research subject
Microbiology
Identifiers
urn:nbn:se:umu:diva-169131 (URN)10.1007/978-3-030-33308-9_29 (DOI)978-3-030-33307-2 (ISBN)978-3-030-33308-9 (ISBN)
Funder
Swedish Research Council, 2015-03007Swedish Research Council, 2015-06824Swedish Research Council, 2016-06598Swedish Research Council, 349-2007-8673Swedish Research Council, 829-2006-7431
Available from: 2020-03-21 Created: 2020-03-21 Last updated: 2020-03-23Bibliographically approved
Zlatkov, N. & Uhlin, B. E. (2019). Absence of Global Stress Regulation in Escherichia coli Promotes Pathoadaptation and Novel c-di-GMP-dependent Metabolic Capability. Scientific Reports, 9, Article ID 2600.
Open this publication in new window or tab >>Absence of Global Stress Regulation in Escherichia coli Promotes Pathoadaptation and Novel c-di-GMP-dependent Metabolic Capability
2019 (English)In: Scientific Reports, ISSN 2045-2322, Vol. 9, article id 2600Article in journal (Refereed) Published
Abstract [en]

athoadaptive mutations linked to c-di-GMP signalling were investigated in neonatal meningitis-causing Escherichia coli (NMEC). The results indicated that NMEC strains deficient in RpoS (the global stress regulator) maintained remarkably low levels of c-di-GMP, a major bacterial sessility-motility switch. Deletion of ycgG2, shown here to encode a YcgG allozyme with c-di-GMP phosphodiesterase activity, and the restoration of RpoS led to a decrease in S-fimbriae, robustly produced in artificial urine, hinting that the urinary tract could serve as a habitat for NMEC. We showed that NMEC were skilled in aerobic citrate utilization in the presence of glucose, a property that normally does not exist in E. coli. Our data suggest that this metabolic novelty is a property of extraintestinal pathogenic E. coli since we reconstituted this ability in E. coli UTI89 (a cystitis isolate) via deactivation rpoS; additionally, a set of pyelonephritis E. coli isolates were shown here to aerobically use citrate in the presence of glucose. We found that the main reason for this metabolic capability is RpoS inactivation leading to the production of the citrate transporter CitT, exploited by NMEC for ferric citrate uptake dependent on YcgG2 (an allozyme with c-di-GMP phosphodiesterase activity).

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
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-155827 (URN)10.1038/s41598-019-39580-w (DOI)000459399400069 ()30796316 (PubMedID)
Note

Originally included in thesis in manuscript form.

Available from: 2019-01-29 Created: 2019-01-29 Last updated: 2019-05-22Bibliographically approved
Zlatkov, N. (2019). Regulatory mechanisms involved in pathoadaptation of extraintestinal pathogenic Escherichia coli. (Doctoral dissertation). Umeå: Umeå Universitet
Open this publication in new window or tab >>Regulatory mechanisms involved in pathoadaptation of extraintestinal pathogenic Escherichia coli
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Establishment of commensal bacteria within a new niche of their host usually promotes the transition from commensalism to pathogenicity. Extraintestinal Pathogenic Escherichia coli (ExPEC) represent different pathovars with biphasic lifestyle – they can reside in the gut as commensals or they can escape and cause diseases elsewhere in the human body. Depending on the disease they are linked to, ExPEC can be divided into Uropathogenic E. coli (UPEC), Newborn Meningitis-causing E. coli (NMEC) and Sepsis-associated E. coli (SEPEC).

Pathoadaptive mutations linked to c-di-GMP signaling were investigated in the NMEC strain IHE3034 which lacks the main global stress regulator RpoS. We investigated the role of ycgG2 in the lifestyle of NMEC. Deletion of ycgG2, shown by us to encode an YcgG allozyme with c-di-GMP phosphodiesterase (PDE) activity, and the restored RpoS led to a decrease in the S-fimbriae, otherwise robustly produced in artificial urine, hinting that the urinary tract could serve as a habitat for NMEC. We showed that NMEC were capable of aerobic citrate utilization in the presence of a co-substrate - a property that normally does not exist in E. coli. Our data hint that this metabolic upgrade is enhanced by the lack, or reduced activity, of c-di-GMP PDEs. We also found that citrate utilization is a property of ExPEC, since we reconstituted it in E. coli UTI89 (a cystitis isolate) via inactivation of its RpoS, and since a set of pyelonephritis E. coli isolates use citrate aerobically in the presence of glucose. The main reason for this metabolic capability is the absence of RpoS which leads to the production of the citrate transporter CitT. Furthermore, we highlighted the deletion of the fec operon (required for the ferric citrate uptake) in a large group of different ExPEC strains and we showed that NMEC can use CitT for in vitro ferric citrate uptake dependent on YcgG2 as an alternative system.

Another pathoadaptive mutation which influences the fitness of ExPEC is the clyA (cytolysin A) gene inactivation, resulting from different deletions in different ExPEC genomes. When we restored the clyA+ locus, the UPEC strain 536 displayed increased susceptibility to antimicrobial peptides and urea. We also showed that the ClyA expression in 536 was increased by the presence of the DNA-binding regulator SfaX and another stand-alone PDE similar to YcgG2, called SfaY. The results were further confirmed by ClyA downregulation in NMEC deficient in SfaY and SfaX.

We also studied the role of sfaY - a gene coding for another stand-alone c-di-GMP PDE. The expression of sfaY is under the regulation of the main promoter of the horizontally acquired sfa gene cluster. The latter is responsible for the regulation and assembly of the virulence-associated S-fimbriae, via which ExPEC bacteria bind to sialylated receptors. We found that NMEC are competent for filamentation because of a c-di-GMP-dependent program under the control of a phase-variation event which selectively turns ‘ON’ the sfa promoter in a subpopulation of bacteria. When SfaY is present, c-di-GMP levels are reduced, thus inducing the SOS stress response via the canonical LexA-RecA pathway. The signaling resulted in an internal differentiation of the bacterial population into a subpopulation exhibiting a filamentous morphotype (bacteria with induced SOS stress response) and a subpopulation of small motile and non-motile bacteria. Hence, this molecular program could serve as a clue to explain the formation of the intracellular bacterial communities observed during urinary tract infection by UPEC.

Place, publisher, year, edition, pages
Umeå: Umeå Universitet, 2019. p. 74
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 2008
Keywords
ExPEC, PAIs, pathoadaptation, citrate, metabolism, filamentation, toxins
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Cell and Molecular Biology
Research subject
Molecular Biology; Microbiology
Identifiers
urn:nbn:se:umu:diva-155816 (URN)978-91-7855-002-9 (ISBN)
Public defence
2019-02-20, Major Groove, NUS byggnad 6L, Norrlands universitetssjukhus, Umeå, 09:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council, 2015-03007, 2015-06824, 2016-06598, 349-2007-8673, 829-2006-7431
Available from: 2019-01-30 Created: 2019-01-28 Last updated: 2019-01-29Bibliographically approved
Dimova, L. G., Zlatkov, N., Verkade, H. J., Uhlin, B. E. & Tietge, U. J. F. (2017). High- cholesterol diet does not alter gut microbiota composition in mice. Nutrition & Metabolism, 14, Article ID 15.
Open this publication in new window or tab >>High- cholesterol diet does not alter gut microbiota composition in mice
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2017 (English)In: Nutrition & Metabolism, ISSN 1743-7075, E-ISSN 1743-7075, Vol. 14, article id 15Article in journal (Refereed) Published
Abstract [en]

Introduction: Western diet containing both saturated fat and cholesterol impairs cardio- metabolic health partly by modulating diversity and function of the microbiota. While diet containing only high fat has comparable effects, it is unclear how diets only enriched in cholesterol impact the microbiota. Therefore, we aimed to characterize the response of host and microbiota to a high cholesterol ( HC) diet in mice susceptible to cardio- metabolic disease. Methods: LDLR knockout mice received either 1.25% HC or no cholesterol containing control diet ( NC) for 12 weeks before characterizing host cholesterol metabolism and intestinal microbiota composition ( next generation sequencing). Results: HC diet substantially increased plasma ( 1.6- fold) and liver cholesterol levels ( 21- fold), biliary cholesterol secretion ( 4.5- fold) and fecal neutral sterol excretion ( 68- fold, each p < 0.001) but not fecal bile acid excretion. Interestingly, despite the profound changes in intestinal cholesterol homeostasis no differences in microbial composition between control and HC- fed mice were detected. In both groups the main phyla were Bacteroidetes ( 55%), Firmicutes ( 27%) and Verrucomicrobia ( 14%). Conclusion: Our results demonstrate that in mice HC diet alone does not alter the microbiota composition despite inducing substantial adaptive changes in whole body cholesterol homeostasis. The impact of Western diet on intestinal microbiota thus appears to be mediated exclusively by its high fat content.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD, 2017
Keywords
Diet, Cholesterol, microbiota, Ldlr-knockout, Bile, Neutral sterols
National Category
Nutrition and Dietetics
Identifiers
urn:nbn:se:umu:diva-136088 (URN)10.1186/s12986-017-0170-x (DOI)000396910300001 ()28239402 (PubMedID)
Available from: 2017-06-14 Created: 2017-06-14 Last updated: 2019-01-29Bibliographically approved
Enow Oben Ayuk, C., Oscarsson, J., Zlatkov, N., Westermark, M., Duperthuy, M., Wai, S. N. & Uhlin, B. E. (2014). Elevated recombinant clyA gene expression in the uropathogenic Escherichia coli strain 536, a clue to explain pathoadaptive mutations in a subset of extraintestinal E. coli strains. BMC Microbiology, 14, 216
Open this publication in new window or tab >>Elevated recombinant clyA gene expression in the uropathogenic Escherichia coli strain 536, a clue to explain pathoadaptive mutations in a subset of extraintestinal E. coli strains
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2014 (English)In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 14, p. 216-Article in journal (Refereed) Published
Abstract [en]

There are at least four different variants of ΔclyA, suggesting that such deletions in clyA have arisen at more than one occasion. On the basis of this occurrence of the truncated clyA genes, we considered that there may be a patho-adaptive selection for deletions in clyA in extraintestinal pathogenic E. coli. In E. coli K-12 the clyA gene has been viewed as “cryptic” since it is tightly silenced by the nucleoid structuring protein H-NS. We constructed a restored clyA+ locus in derivatives of the UPEC strain 536 for further investigation of this hypothesis and, in particular, how the gene would be expressed. Our results show that the level of clyA+ expression is highly increased in the UPEC derivatives in comparison with the non-pathogenic E. coli K-12. Transcription of the clyA+ gene was induced to even higher levels when the SfaX regulatory protein was overproduced. The derivative with a restored clyA+ locus displayed a somewhat slower growth than the parental UPEC strain 536 when a sub-inhibitory concentration of the antimicrobial peptide Polymyxin B was added to the growth medium.

Place, publisher, year, edition, pages
BioMed Central, 2014
Keywords
ClyA cytolysin, Pathoadaptive mutations, clyA gene expression, Extraintestinal Escherichia coli, SfaX regulatory protein
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-93657 (URN)10.1186/s12866-014-0216-4 (DOI)000341665100001 ()
Available from: 2014-09-29 Created: 2014-09-29 Last updated: 2019-01-28Bibliographically approved
Zlatkov, N. & Uhlin, B. E.C-di-GMP-mediated Morphotypic Pathoadaptability of Neonatal Meningitis Escherichia coli.
Open this publication in new window or tab >>C-di-GMP-mediated Morphotypic Pathoadaptability of Neonatal Meningitis Escherichia coli
(English)Manuscript (preprint) (Other academic)
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-155828 (URN)
Available from: 2019-01-29 Created: 2019-01-29 Last updated: 2019-01-29
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3318-9084

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