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Article ; Online: Rok from B. subtilis: Bridging genome structure and transcription regulation.

Erkelens, Amanda M / van Erp, Bert / Meijer, Wilfried J J / Dame, Remus T

2024

Abstract: Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid-associated proteins and liquid-liquid phase separation, and has to ... ...

Abstract	Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid-associated proteins and liquid-liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram-positive bacterium Bacillus subtilis as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the B. subtilis chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA-DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok-mediated gene repression. Lastly, we investigate which features characterize H-NS-like proteins, a family that, at present, lacks a clear definition.
Language	English
Publishing date	2024-03-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.15250
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Article ; Online: Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity.

Forrest, David / Warman, Emily A / Erkelens, Amanda M / Dame, Remus T / Grainger, David C

Nature communications

2022 Volume 13, Issue 1, Page(s) 1149

Abstract: Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing ... ...

Abstract	Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli.
MeSH term(s)	Bacillus subtilis/genetics ; Bacillus subtilis/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; DNA ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Transcription, Genetic
Chemical Substances	Bacterial Proteins ; DNA (9007-49-2) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2022-03-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28747-1
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Article: Specific DNA binding of archaeal histones HMfA and HMfB.

Erkelens, Amanda M / Henneman, Bram / van der Valk, Ramon A / Kirolos, Nancy C S / Dame, Remus T

Frontiers in microbiology

2023 Volume 14, Page(s) 1166608

Abstract: In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. ... ...

Abstract	In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial sequence "Clone20," a high-affinity model sequence for binding of the histones from
Language	English
Publishing date	2023-04-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1166608
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Article: System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on

Du, Chao / Willemse, Joost / Erkelens, Amanda M / Carrion, Victor J / Dame, Remus T / van Wezel, Gilles P

mSystems

2022 Volume 7, Issue 3, Page(s) e0006122

Abstract: Bacterial chromosome structure is, to a great extent, organized by a diverse group of proteins collectively referred to as nucleoid-associated proteins (NAPs). Many NAPs have been well studied ... ...

Abstract	Bacterial chromosome structure is, to a great extent, organized by a diverse group of proteins collectively referred to as nucleoid-associated proteins (NAPs). Many NAPs have been well studied in
Language	English
Publishing date	2022-05-16
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/msystems.00061-22
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Article ; Online: DNA-bridging by an archaeal histone variant via a unique tetramerisation interface.

Ofer, Sapir / Blombach, Fabian / Erkelens, Amanda M / Barker, Declan / Soloviev, Zoja / Schwab, Samuel / Smollett, Katherine / Matelska, Dorota / Fouqueau, Thomas / van der Vis, Nico / Kent, Nicholas A / Thalassinos, Konstantinos / Dame, Remus T / Werner, Finn

Communications biology

2023 Volume 6, Issue 1, Page(s) 968

Abstract: In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into 'hypernucleosome' particles of varying sizes with each dimer ... ...

Abstract	In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into 'hypernucleosome' particles of varying sizes with each dimer wrapping 30 bp of DNA. These are composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension enabling homotetramerisation. The 1.9 Å X-ray structure of a dimeric MJ1647 species, structural modelling of the tetramer, and site-directed mutagenesis reveal that the C-terminal tetramerization module consists of two alpha helices in a handshake arrangement. Unlike canonical histones, MJ1647 tetramers can bridge two DNA molecules in vitro. Using single-molecule tethered particle motion and DNA binding assays, we show that MJ1647 tetramers bind ~60 bp DNA and compact DNA in a highly cooperative manner. We furthermore show that MJ1647 effectively competes with the transcription machinery to block access to the promoter in vitro. To the best of our knowledge, MJ1647 is the first histone shown to have DNA bridging properties, which has important implications for genome structure and gene expression in archaea.
MeSH term(s)	Histones/genetics ; DNA/genetics ; Archaea/genetics ; Biological Assay ; Eukaryota ; Polymers
Chemical Substances	Histones ; DNA (9007-49-2) ; Polymers
Language	English
Publishing date	2023-09-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05348-2
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Article ; Online: The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues.

Erkelens, Amanda M / Qin, Liang / van Erp, Bert / Miguel-Arribas, Andrés / Abia, David / Keek, Helena G J / Markus, Dorijn / Cajili, Marc K M / Schwab, Samuel / Meijer, Wilfried J J / Dame, Remus T

Nucleic acids research

2022

Abstract: Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of ...

Abstract	Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family.
Language	English
Publishing date	2022-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac1064
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Zs.A 1067: Show issues

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Article ; Online: Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.

Karlsson, Elin / Paissoni, Cristina / Erkelens, Amanda M / Tehranizadeh, Zeinab A / Sorgenfrei, Frieda A / Andersson, Eva / Ye, Weihua / Camilloni, Carlo / Jemth, Per

The Journal of biological chemistry

2020 Volume 295, Issue 51, Page(s) 17698–17712

Abstract: Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular ... ...

Abstract	Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway.
MeSH term(s)	Amino Acid Sequence ; Animals ; CREB-Binding Protein/chemistry ; CREB-Binding Protein/genetics ; CREB-Binding Protein/metabolism ; Evolution, Molecular ; Humans ; Hydrophobic and Hydrophilic Interactions ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/classification ; Intrinsically Disordered Proteins/genetics ; Intrinsically Disordered Proteins/metabolism ; Kinetics ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Nuclear Receptor Coactivator 3/chemistry ; Nuclear Receptor Coactivator 3/genetics ; Nuclear Receptor Coactivator 3/metabolism ; Phylogeny ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Domains ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; Sequence Alignment ; Static Electricity
Chemical Substances	Intrinsically Disordered Proteins ; Recombinant Proteins ; CREB-Binding Protein (EC 2.3.1.48) ; CREBBP protein, human (EC 2.3.1.48) ; NCOA3 protein, human (EC 2.3.1.48) ; Nuclear Receptor Coactivator 3 (EC 2.3.1.48)
Language	English
Publishing date	2020-12-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA120.015645
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Uc I Zs.108: Show issues

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Article ; Online: Novel anti-repression mechanism of H-NS proteins by a phage protein.

Bdira, Fredj Ben / Erkelens, Amanda M / Qin, Liang / Volkov, Alexander N / Lippa, Andrew M / Bowring, Nicholas / Boyle, Aimee L / Ubbink, Marcellus / Dove, Simon L / Dame, Remus T

Nucleic acids research

2021 Volume 49, Issue 18, Page(s) 10770–10784

Abstract: H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These ... ...

Abstract	H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; DNA/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Gene Silencing ; Models, Molecular ; Protein Binding ; Pseudomonas/genetics ; Pseudomonas/growth & development ; Pseudomonas/virology ; Pseudomonas Phages/physiology ; Trans-Activators/chemistry ; Trans-Activators/metabolism ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	Bacterial Proteins ; DNA-Binding Proteins ; H-NS protein, bacteria ; MvaT protein, Pseudomonas ; Trans-Activators ; Viral Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2021-09-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab793
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Article ; Online: Mechanical and structural properties of archaeal hypernucleosomes.

Henneman, Bram / Brouwer, Thomas B / Erkelens, Amanda M / Kuijntjes, Gert-Jan / van Emmerik, Clara / van der Valk, Ramon A / Timmer, Monika / Kirolos, Nancy C S / van Ingen, Hugo / van Noort, John / Dame, Remus T

Nucleic acids research

2020 Volume 49, Issue 8, Page(s) 4338–4349

Abstract: Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone-DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of ... ...

Abstract	Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone-DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of DNA wrapped around an 'endless' histone-protein core. However, if and how such a hypernucleosome structure assembles on a long DNA substrate and which interactions provide for its stability, remains unclear. Here, we describe micromanipulation studies of complexes of the histones HMfA and HMfB with DNA. Our experiments show hypernucleosome assembly which results from cooperative binding of histones to DNA, facilitated by weak stacking interactions between neighboring histone dimers. Furthermore, rotational force spectroscopy demonstrates that the HMfB-DNA complex has a left-handed chirality, but that torque can drive it in a right-handed conformation. The structure of the hypernucleosome thus depends on stacking interactions, torque, and force. In vivo, such modulation of the archaeal hypernucleosome structure may play an important role in transcription regulation in response to environmental changes.
MeSH term(s)	Archaeal Proteins/chemistry ; DNA, Archaeal/chemistry ; Histones/chemistry ; Mechanical Phenomena ; Methanobacteriales/chemistry ; Nucleosomes/chemistry ; Protein Multimerization
Chemical Substances	Archaeal Proteins ; DNA, Archaeal ; Histones ; Nucleosomes ; histone HMf
Language	English
Publishing date	2020-12-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa1196
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