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Article ; Online: Diverse functions for acyltransferase-3 proteins in the modification of bacterial cell surfaces.

Pearson, Caroline / Tindall, Sarah / Potts, Jennifer R / Thomas, Gavin H / van der Woude, Marjan W

2022 Volume 168, Issue 3

Abstract: The acylation of sugars, most commonly via acetylation, is a widely used mechanism in bacteria that uses a simple chemical modification to confer useful traits. For structures like lipopolysaccharide, capsule and peptidoglycan, that function outside of ... ...

Abstract	The acylation of sugars, most commonly via acetylation, is a widely used mechanism in bacteria that uses a simple chemical modification to confer useful traits. For structures like lipopolysaccharide, capsule and peptidoglycan, that function outside of the cytoplasm, their acylation during export or post-synthesis requires transport of an activated acyl group across the membrane. In bacteria this function is most commonly linked to a family of integral membrane proteins - acyltransferase-3 (AT3). Numerous studies examining production of diverse extracytoplasmic sugar-containing structures have identified roles for these proteins in
MeSH term(s)	Acetylation ; Acylation ; Acyltransferases/genetics ; Acyltransferases/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Bacterial Proteins/metabolism ; Peptidoglycan/metabolism
Chemical Substances	Bacterial Proteins ; Peptidoglycan ; Acyltransferases (EC 2.3.-)
Language	English
Publishing date	2022-03-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1180712-x
ISSN	1465-2080 ; 1350-0872
ISSN (online)	1465-2080
ISSN	1350-0872
DOI	10.1099/mic.0.001146
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Article ; Online: A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer.

Newman, Kahlan E / Tindall, Sarah N / Mader, Sophie L / Khalid, Syma / Thomas, Gavin H / Van Der Woude, Marjan W

eLife

2023 Volume 12

Abstract: Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance ... ...

Abstract	Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism are largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified, and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens.
MeSH term(s)	Acetyltransferases/genetics ; Acetyltransferases/metabolism ; Bacteria/metabolism ; Acylation ; Protein Structure, Secondary
Chemical Substances	Acetyltransferases (EC 2.3.1.-)
Language	English
Publishing date	2023-01-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.81547
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Article ; Online: Spatial Organization of Expanding Bacterial Colonies Is Affected by Contact-Dependent Growth Inhibition.

Bottery, Michael J / Passaris, Ioannis / Dytham, Calvin / Wood, A Jamie / van der Woude, Marjan W

Current biology : CB

2019 Volume 29, Issue 21, Page(s) 3622–3634.e5

Abstract: Identifying how microbes are able to manipulate, survive, and thrive in complex multispecies communities has expanded our understanding of how microbial ecosystems impact human health and the environment. The ability of bacteria to negatively affect ... ...

Abstract	Identifying how microbes are able to manipulate, survive, and thrive in complex multispecies communities has expanded our understanding of how microbial ecosystems impact human health and the environment. The ability of bacteria to negatively affect neighbors, through explicit toxin delivery systems, provides them with an opportunity to manipulate the composition of growing microbial communities. Contact-dependent inhibition (CDI) systems (a Type Vb secretion system) are a distinct subset of competition systems whose contribution to shaping the development of spatially structured bacterial communities are yet to be fully understood. Here, we compare the impact of different CDI systems, at both the single-cell and population level, to determine the key drivers of CDI-mediated competition within spatially structured bacterial populations. Through an iterative approach using both an Escherichia coli experimental system and computational modeling, we show that CDI systems have subtle and system-specific effects at the single-cell level, generating single-cell-wide boundaries between CDI-expressing inhibitor cells and their neighboring targets. Despite the subtle effects of CDI at a single-cell level, CDI systems greatly diminished the ability of susceptible targets to expand their range during colony growth. The inoculum density of the population, together with the CDI system-specific variables of the speed of inhibition after contact and biological cost of CDI, strongly affects CDI-mediated competition. In contrast, the magnitude of the toxin-induced growth retardation of target cells only weakly impacts the composition of the population. Our work reveals how distinct CDI systems can differentially affect the composition and spatial arrangement of bacterial populations.
MeSH term(s)	Computational Biology ; Contact Inhibition ; Escherichia coli/physiology ; Microbial Interactions ; Microorganisms, Genetically-Modified/physiology ; Models, Biological ; Population Dynamics ; Salmonella typhimurium/genetics ; Spatial Analysis
Language	English
Publishing date	2019-10-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2019.08.074
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Article ; Online: Phase variation: how to create and coordinate population diversity.

van der Woude, Marjan W

Current opinion in microbiology

2011 Volume 14, Issue 2, Page(s) 205–211

Abstract: Phase variation yields phenotypic heterogeneity in a clonal population as the result of one of a limited number of known molecular mechanisms. These include slipped strand mispairing, site-specific recombination and epigenetic regulation mediated by DNA ... ...

Abstract	Phase variation yields phenotypic heterogeneity in a clonal population as the result of one of a limited number of known molecular mechanisms. These include slipped strand mispairing, site-specific recombination and epigenetic regulation mediated by DNA methylation. Recently new regulatory variants utilizing these mechanisms have been identified, which is facilitating the identification of additional phase variation events solely from genome sequence analysis. Furthermore, it is becoming increasingly clear that in many cases phase variation control is integrated with regulatory networks and with cellular processes of a growing cell. This review focuses specifically on these recent advances in the understanding of the regulation of phase variation.
MeSH term(s)	Antigens, Bacterial/biosynthesis ; Bacteria/classification ; Bacteria/genetics ; Bacteria/growth & development ; Bacteria/immunology ; Bacterial Physiological Phenomena ; Bacterial Typing Techniques ; Gene Expression Regulation, Bacterial ; Phenotype ; Serotyping
Chemical Substances	Antigens, Bacterial
Language	English
Publishing date	2011-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2011.01.002
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Zs.A 5514: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase.

Pearson, Caroline R / Tindall, Sarah N / Herman, Reyme / Jenkins, Huw T / Bateman, Alex / Thomas, Gavin H / Potts, Jennifer R / Van der Woude, Marjan W

mBio

2020 Volume 11, Issue 4

Abstract: Membrane bound acyltransferase-3 (AT3) domain-containing proteins are implicated in a wide range of carbohydrate O-acyl modifications, but their mechanism of action is largely unknown. O-antigen acetylation by AT3 domain-containing acetyltransferases ... ...

Abstract	Membrane bound acyltransferase-3 (AT3) domain-containing proteins are implicated in a wide range of carbohydrate O-acyl modifications, but their mechanism of action is largely unknown. O-antigen acetylation by AT3 domain-containing acetyltransferases of
MeSH term(s)	Acetylation ; Acyltransferases/genetics ; Acyltransferases/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Carbohydrate Metabolism ; Computer Simulation ; Models, Molecular ; Salmonella enterica/enzymology ; Salmonella enterica/genetics ; Substrate Specificity ; Virulence
Chemical Substances	Bacterial Proteins ; Acyltransferases (EC 2.3.-)
Language	English
Publishing date	2020-08-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.01364-20
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Article: Re-examining the role and random nature of phase variation.

van der Woude, Marjan W

FEMS microbiology letters

2006 Volume 254, Issue 2, Page(s) 190–197

Abstract: Phase variation in bacteria is often considered a random process that has evolved to facilitate immune evasion in a host. Here, alternative biological roles for this process are presented and discussed, incorporating recent studies on nonpathogenic and ... ...

Abstract	Phase variation in bacteria is often considered a random process that has evolved to facilitate immune evasion in a host. Here, alternative biological roles for this process are presented and discussed, incorporating recent studies on nonpathogenic and commensal bacterial species. Furthermore, the integration of phase variation into bacterial regulatory networks and the relevance of this for considering phase variation as a random process are reviewed. Novel approaches are needed to study phase variation and its biological roles, but the insights obtained can contribute significantly to our understanding of the dynamic behaviour of bacterial populations and their interactions with the environment.
MeSH term(s)	Adaptation, Physiological ; Animals ; Bacteria/genetics ; Bacteria/growth & development ; Bacteria/metabolism ; Bacteria/pathogenicity ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biofilms/growth & development ; Gene Expression Regulation, Bacterial ; Humans ; Phenotype
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2006-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1111/j.1574-6968.2005.00038.x
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Article ; Online: Establishing and maintaining sequestration of Dam target sites for phase variation of agn43 in Escherichia coli.

Kaminska, Renata / van der Woude, Marjan W

Journal of bacteriology

2010 Volume 192, Issue 7, Page(s) 1937–1945

Abstract: Phase variation of the outer membrane protein Ag43 encoded by agn43 in Escherichia coli is controlled by an epigenetic mechanism. Sequestration of the regulatory region from Dam-dependent methylation has to be established and maintained throughout a ... ...

Abstract	Phase variation of the outer membrane protein Ag43 encoded by agn43 in Escherichia coli is controlled by an epigenetic mechanism. Sequestration of the regulatory region from Dam-dependent methylation has to be established and maintained throughout a generation to obtain and maintain the OFF phase. This work shows that hemimethylated DNA, which is formed by the passage of the DNA replication fork in an ON-phase cell, can be sequestered from methylation by OxyR binding, which is thus a key event for the switch from ON to OFF. No evidence was found that the protein SeqA, which also binds to the region, is involved in sequestration. To facilitate the dissection of this process further, a novel approach was introduced that does not alter the sequence of the regulatory region or the cellular concentration of Dam or OxyR, which consists of inserting auxiliary OxyR binding sites upstream of the regulatory region. Using this strategy, it was shown that the ON-to-OFF switch frequency can be modulated without changing the OFF-to-ON frequency. The data support a model in which in an ON-phase cell, the subcellular OxyR availability at the replication fork as it passes through the agn43 regulatory region is key for initiating an ON-to-OFF switch. In contrast, this availability is not a determining factor for the switch from OFF to ON. This finding shows that different variables affect these two stochastic events. This provides new insight into the events determining the stochastic nature of epigenetic phase variation.
MeSH term(s)	Adhesins, Bacterial/biosynthesis ; Adhesins, Escherichia coli ; DNA, Bacterial/metabolism ; Electrophoretic Mobility Shift Assay ; Epigenesis, Genetic ; Escherichia coli/genetics ; Escherichia coli/physiology ; Escherichia coli Proteins/biosynthesis ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Models, Biological ; Protein Binding ; Repressor Proteins/metabolism ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/metabolism
Chemical Substances	Adhesins, Bacterial ; Adhesins, Escherichia coli ; DNA, Bacterial ; Escherichia coli Proteins ; Repressor Proteins ; antigen 43, E coli ; oxyR protein, E coli ; Site-Specific DNA-Methyltransferase (Adenine-Specific) (EC 2.1.1.72) ; dam protein, E coli (EC 2.1.1.72)
Language	English
Publishing date	2010-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.01629-09
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Article ; Online: Control of gene expression at a bacterial leader RNA, the agn43 gene encoding outer membrane protein Ag43 of Escherichia coli.

Wallecha, Anu / Oreh, Heather / van der Woude, Marjan W / deHaseth, Pieter L

Journal of bacteriology

2014 Volume 196, Issue 15, Page(s) 2728–2735

Abstract: The family of agn alleles in Escherichia coli pathovars encodes autotransporters that have been implicated in biofilm formation, autoaggregation, and attachment to cells. The alleles all have long leader RNAs preceding the Ag43 translation initiation ... ...

Abstract	The family of agn alleles in Escherichia coli pathovars encodes autotransporters that have been implicated in biofilm formation, autoaggregation, and attachment to cells. The alleles all have long leader RNAs preceding the Ag43 translation initiation codon. Here we present an analysis of the agn43 leader RNA from E. coli K-12. We demonstrate the presence of a rho-independent transcription terminator just 28 bp upstream of the main translation start codon and show that it is functional in vitro. Our data indicate that an as-yet-unknown mechanism of antitermination of transcription must be operative in earlier phases of growth. However, as bacterial cell cultures mature, progressively fewer transcripts are able to bypass this terminator. In the K-12 leader sequence, two in-frame translation initiation codons have been identified, one upstream and the other downstream of the transcription terminator. For optimal agn43 expression, both codons need to be present. Translation from the upstream start codon leads to increased downstream agn43 expression. Our findings have revealed two novel modes of regulation of agn43 expression in the leader RNA in addition to the previously well-characterized regulation of phase variation at the agn43 promoter.
MeSH term(s)	5' Untranslated Regions/genetics ; Adhesins, Escherichia coli/genetics ; Bacterial Outer Membrane Proteins/genetics ; Escherichia coli K12/genetics ; Gene Expression Regulation, Bacterial/genetics ; Genes, Reporter ; Promoter Regions, Genetic/genetics ; RNA Stability ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; Terminator Regions, Genetic/genetics ; Transcription, Genetic
Chemical Substances	5' Untranslated Regions ; Adhesins, Escherichia coli ; Bacterial Outer Membrane Proteins ; RNA, Bacterial ; RNA, Messenger ; antigen 43, E coli
Language	English
Publishing date	2014-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.01680-14
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Article ; Online: Spatial Dependence of DNA Damage in Bacteria due to Low-Temperature Plasma Application as Assessed at the Single Cell Level.

Privat-Maldonado, Angela / O'Connell, Deborah / Welch, Emma / Vann, Roddy / van der Woude, Marjan W

Scientific reports

2016 Volume 6, Page(s) 35646

Abstract: Low temperature plasmas (LTPs) generate a cocktail of reactive nitrogen and oxygen species (RNOS) with bactericidal activity. The RNOS however are spatially unevenly distributed in the plasma. Here we test the hypothesis that this distribution will ... ...

Abstract	Low temperature plasmas (LTPs) generate a cocktail of reactive nitrogen and oxygen species (RNOS) with bactericidal activity. The RNOS however are spatially unevenly distributed in the plasma. Here we test the hypothesis that this distribution will affect the mechanisms underpinning plasma bactericidal activity focussing on the level of DNA damage in situ. For the first time, a quantitative, single cell approach was applied to assess the level of DNA damage in bacteria as a function of the radial distance from the centre of the plasma jet. Salmonella enterica on a solid, dry surface was treated with two types of LTP: an atmospheric-pressure dielectric barrier discharge plasma jet (charged and neutral species) and a radio-frequency atmospheric-pressure plasma jet (neutral species). In both cases, there was an inverse correlation between the degree of DNA damage and the radial distance from the centre of the plasma, with the highest DNA damage occurring directly under the plasma. This trend was also observed with Staphylococcus aureus. LTP-generated UV radiation was eliminated as a contributing factor. Thus valuable mechanistic information can be obtained from assays on biological material, which can inform the development of LTP as a complementary or alternative therapy for (topical) bacterial infections.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; DNA Damage ; Microbial Viability/drug effects ; Plasma Gases/pharmacology ; Salmonella enterica/drug effects ; Salmonella enterica/physiology ; Single-Cell Analysis ; Spatial Analysis ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/physiology
Chemical Substances	Anti-Bacterial Agents ; Plasma Gases
Language	English
Publishing date	2016-10-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep35646
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Article ; Online: A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants.

Diard, Médéric / Bakkeren, Erik / Lentsch, Verena / Rocker, Andrea / Bekele, Nahimi Amare / Hoces, Daniel / Aslani, Selma / Arnoldini, Markus / Böhi, Flurina / Schumann-Moor, Kathrin / Adamcik, Jozef / Piccoli, Luca / Lanzavecchia, Antonio / Stadtmueller, Beth M / Donohue, Nicholas / van der Woude, Marjan W / Hockenberry, Alyson / Viollier, Patrick H / Falquet, Laurent /

Wüthrich, Daniel / Bonfiglio, Ferdinando / Loverdo, Claude / Egli, Adrian / Zandomeneghi, Giorgia / Mezzenga, Raffaele / Holst, Otto / Meier, Beat H / Hardt, Wolf-Dietrich / Slack, Emma

Nature microbiology

2021 Volume 6, Issue 7, Page(s) 830–841

Abstract: The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune ... ...

Abstract	The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance
MeSH term(s)	Administration, Oral ; Animals ; Antibodies, Bacterial/immunology ; Antigenic Variation ; Bacterial Proteins/genetics ; Evolution, Molecular ; Genetic Fitness ; Hexosyltransferases/genetics ; Immune Evasion ; Immunity, Mucosal ; Immunoglobulin A/immunology ; Intestines/immunology ; Intestines/microbiology ; Mice ; Mutation ; O Antigens/genetics ; O Antigens/immunology ; Salmonella Infections/microbiology ; Salmonella Infections/prevention & control ; Salmonella Vaccines/administration & dosage ; Salmonella Vaccines/immunology ; Salmonella typhimurium/genetics ; Salmonella typhimurium/immunology ; Salmonella typhimurium/pathogenicity ; Vaccines, Attenuated/administration & dosage ; Vaccines, Attenuated/immunology ; Virulence
Chemical Substances	Antibodies, Bacterial ; Bacterial Proteins ; Immunoglobulin A ; O Antigens ; Salmonella Vaccines ; Vaccines, Attenuated ; Hexosyltransferases (EC 2.4.1.-) ; O-antigen polymerase (EC 2.4.1.-)
Language	English
Publishing date	2021-05-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-021-00911-1
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