1
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Islam F, Mishra PP. Molecular Insight into the Structural Dynamics of Holliday Junctions Modulated by Integration Host Factor. J Phys Chem B 2024; 128:5642-5657. [PMID: 38812070 DOI: 10.1021/acs.jpcb.4c02997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The integration host factor (IHF) in Escherichia coli is a nucleoid-associated protein with multifaceted roles that encompass DNA packaging, viral DNA integration, and recombination. IHF binds to double-stranded DNA featuring a 13-base pair (bp) consensus sequence with high affinity, causing a substantial bend of approximately 160° upon binding. Although wild-type IHF (WtIHF) is principally involved in DNA bending to facilitate foreign DNA integration into the host genome, its engineered counterpart, single-chain IHF (ScIHF), was specifically designed for genetic engineering and biotechnological applications. Our study delves into the interactions of both IHF variants with Holliday junctions (HJs), pivotal intermediates in DNA repair, and homologous recombination. HJs are dynamic structures capable of adopting open or stacked conformations, with the open conformation facilitating processes such as branch migration and strand exchange. Using microscale thermophoresis, we quantitatively assessed the binding of IHF to four-way DNA junctions that harbor specific binding sequences H' and H1. Our findings demonstrate that both IHF variants exhibit a strong affinity for HJs, signifying a structure-based recognition mechanism. Circular dichroism (CD) experiments unveiled the impact of the protein on the junction's conformation. Furthermore, single-molecule Förster resonance energy transfer (smFRET) confirmed the influence of IHF on the junction's dynamicity. Intriguingly, our results revealed that WtIHF and ScIHF binding shifts the population toward the open conformation of the junction and stabilizes it in that state. In summary, our findings underscore the robust affinity of the IHF for HJs and its capacity to stabilize the open conformation of these junctions.
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Affiliation(s)
- Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
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2
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Royzenblat SK, Freddolino L. Spatio-temporal organization of the E. coli chromosome from base to cellular length scales. EcoSal Plus 2024:eesp00012022. [PMID: 38864557 DOI: 10.1128/ecosalplus.esp-0001-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.
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Affiliation(s)
- Sonya K Royzenblat
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lydia Freddolino
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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3
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Battaglia C, Michieletto D. Loops are geometric catalysts for DNA integration. Nucleic Acids Res 2024:gkae484. [PMID: 38864388 DOI: 10.1093/nar/gkae484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024] Open
Abstract
The insertion of DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of DNA insertions are not random and the physical mechanisms underlying the integration site selection are poorly understood. Here, we perform Molecular Dynamics simulations to study the insertion of DNA elements, such as viral DNA or transposons, into naked DNA or chromatin substrates. More specifically, we explore the role of loops within the polymeric substrate and discover that they act as 'geometric catalysts' for DNA integration by reducing the energy barrier for substrate deformation. Additionally, we discover that the 1D pattern and 3D conformation of loops have a marked effect on the distribution of integration sites. Finally, we show that loops may compete with nucleosomes to attract DNA integrations. These results may be tested in vitro and they may help to understand patterns of DNA insertions with implications in genome evolution and engineering.
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Affiliation(s)
- Cleis Battaglia
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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4
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Hustmyer CM, Landick R. Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression. Mol Microbiol 2024. [PMID: 38847475 DOI: 10.1111/mmi.15283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
DNA in bacterial chromosomes is organized into higher-order structures by DNA-binding proteins called nucleoid-associated proteins (NAPs) or bacterial chromatin proteins (BCPs). BCPs often bind to or near DNA loci transcribed by RNA polymerase (RNAP) and can either increase or decrease gene expression. To understand the mechanisms by which BCPs alter transcription, one must consider both steric effects and the topological forces that arise when DNA deviates from its fully relaxed double-helical structure. Transcribing RNAP creates DNA negative (-) supercoils upstream and positive (+) supercoils downstream whenever RNAP and DNA are unable to rotate freely. This (-) and (+) supercoiling generates topological forces that resist forward translocation of DNA through RNAP unless the supercoiling is constrained by BCPs or relieved by topoisomerases. BCPs also may enhance topological stress and overall can either inhibit or aid transcription. Here, we review current understanding of how RNAP, BCPs, and DNA topology interplay to control gene expression.
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Affiliation(s)
- Christine M Hustmyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Lamoureux CR, Phaneuf PV, Palsson B, Zielinski D. Escherichia coli non-coding regulatory regions are highly conserved. NAR Genom Bioinform 2024; 6:lqae041. [PMID: 38774514 PMCID: PMC11106028 DOI: 10.1093/nargab/lqae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/05/2024] [Accepted: 05/15/2024] [Indexed: 05/24/2024] Open
Abstract
Microbial genome sequences are rapidly accumulating, enabling large-scale studies of sequence variation. Existing studies primarily focus on coding regions to study amino acid substitution patterns in proteins. However, non-coding regulatory regions also play a distinct role in determining physiologic responses. To investigate intergenic sequence variation on a large-scale, we identified non-coding regulatory region alleles across 2350 Escherichia coli strains. This 'alleleome' consists of 117 781 unique alleles for 1169 reference regulatory regions (transcribing 1975 genes) at single base-pair resolution. We find that 64% of nucleotide positions are invariant, and variant positions vary in a median of just 0.6% of strains. Additionally, non-coding alleles are sufficient to recover E. coli phylogroups. We find that core promoter elements and transcription factor binding sites are significantly conserved, especially those located upstream of essential or highly-expressed genes. However, variability in conservation of transcription factor binding sites is significant both within and across regulons. Finally, we contrast mutations acquired during adaptive laboratory evolution with wild-type variation, finding that the former preferentially alter positions that the latter conserves. Overall, this analysis elucidates the wealth of information found in E. coli non-coding sequence variation and expands pangenomic studies to non-coding regulatory regions at single-nucleotide resolution.
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Affiliation(s)
- Cameron R Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Patrick V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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6
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Shepherd JW, Guilbaud S, Zhou Z, Howard JAL, Burman M, Schaefer C, Kerrigan A, Steele-King C, Noy A, Leake MC. Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA. Nat Commun 2024; 15:2748. [PMID: 38553446 PMCID: PMC10980717 DOI: 10.1038/s41467-024-47126-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/21/2024] [Indexed: 04/02/2024] Open
Abstract
Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.
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Affiliation(s)
- Jack W Shepherd
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
- Department of Biology, University of York, York, YO10 5DD, England
| | - Sebastien Guilbaud
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Zhaokun Zhou
- Guangdong Provincial Key Lab of Robotics and Intelligent System, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jamieson A L Howard
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Matthew Burman
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Adam Kerrigan
- The York-JEOL Nanocentre, University of York, York, YO10 5BR, England
| | - Clare Steele-King
- Bioscience Technology Facility, University of York, York, YO10 5DD, England
| | - Agnes Noy
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England.
- Department of Biology, University of York, York, YO10 5DD, England.
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7
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Su X, Jin X, Wang Z, Duan S. Unraveling Exogenous DNA Processing in Cas4-Lacking Crispr Systems: A Novel Bypass Pathway Explored. Adv Biol (Weinh) 2024; 8:e2300454. [PMID: 38072634 DOI: 10.1002/adbi.202300454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/09/2023] [Indexed: 03/16/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are widely distributed adaptive immune systems found in prokaryotes. The process involves three main stages: adaptation, expression, and interference. While the adaptation stage has been extensively studied, there is still an incomplete understanding of the mechanisms underlying the capture, trimming, and integration of exogenous DNA. For instance, Cas4, a CRISPR-Cas protein with endonuclease activity, is responsible for selecting and processing protospacer adjacent motif (PAM) sequences. However, some CRISPR isoforms lack Cas4 activity, relying on other enzymes for adaptive immunity. Recently, Wang et al. presented a novel model of exogenous DNA processing in a type I-E CRISPR system lacking Cas4 in a Nature article. This model integrates protospacer processing into CRISPR arrays through fine-tuned synthases formed by DnaQ-like exonuclease (DEDDh) and Cas1-Cas2 complexes. Their study introduces a novel model, shedding new light on the evolution of CRISPR adaptive immunity. This perspective comprehensively examines the fundamental process of CRISPR adaptive immunity, detailing both the classical pathway mediated by Cas4 and the alternative pathway mediated by DEDDh. Furthermore, a thorough evaluation of Wang et al.'s work is conducted, highlighting its strengths, weaknesses, and existing research challenges.
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Affiliation(s)
- Xinming Su
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
| | - Xiaoyu Jin
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
| | - Zehua Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
- Department of Clinical Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310000, China
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8
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Rashid FZM, Crémazy FGE, Hofmann A, Forrest D, Grainger DC, Heermann DW, Dame RT. The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli. Nat Commun 2023; 14:7478. [PMID: 37978176 PMCID: PMC10656529 DOI: 10.1038/s41467-023-43322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay, Versailles, 78180, France
| | - Andreas Hofmann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Dieter W Heermann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - Remus T Dame
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands.
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9
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Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega M, Isupov M, Harmer N, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo M, Contestabile R, Vallone B, Tramonti A, Montemiglio L. Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR. Nucleic Acids Res 2023; 51:8237-8254. [PMID: 37378428 PMCID: PMC10450172 DOI: 10.1093/nar/gkad552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.
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Affiliation(s)
- Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Anna Barile
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy
| | - Mirella Vivoli Vega
- School of Biochemistry, University of Bristol, University Walk, BS8 1TD Bristol, UK
| | - Michail N Isupov
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Elena Gugole
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Paolo Swuec
- Cryo-Electron Microscopy Core Facility, Human Technopole, Milano 20157, Italy
| | - Martino Bolognesi
- Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy
| | - Anita Scipioni
- Department of Chemistry, Sapienza, University of Rome, Rome 00185, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Martino Luigi Di Salvo
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, Rome 00185, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
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10
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Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M. Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Res 2023; 51:5864-5882. [PMID: 37207342 PMCID: PMC10287934 DOI: 10.1093/nar/gkad397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.
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Affiliation(s)
- Aleix Tarrés-Solé
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Joachim M Gerhold
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Olivier Piétrement
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | | | - Elena Ruiz-López
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Inserm, CNRS and Université de Montpellier, France, Sébastien Lyonnais, UAR 3725 CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Joaquim Roca
- Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Maria Solà
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
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11
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Nambiar K, P SK, Devaraj D, Sevanan M. Development of biopolymers from microbes and their environmental applications. PHYSICAL SCIENCES REVIEWS 2023. [DOI: 10.1515/psr-2022-0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Abstract
Inventions begin with the invasion of humans and furnish a better livelihood. In some cases, it turns out to be imperative. The environmental issues of using synthetic polymers, including bio-incompatibility, toxicity, high cost, poor hydrophilicity, and pro-inflammatory degradation of byproducts, are increasing the need for and application of eco-friendly, alternative polymeric substances from medicine to biotechnology, which includes the industries of medicine, cosmetics, confectionery, wastewater treatment, etc., as tissue scaffolds, wound dressings, drug packaging material, dermal fillers, moisturising cream, carriers, sun protectants, antiperspirants, and deodorants; gelling agents; stabilisers, emulsifiers, photographic films, etc. Biopolymers are available in different compounds, produced by microbes, plants, and animals, where microbes, for example, Pseudomonas aeruginosa and Kamagataeibacter sucrofermetans, retain these compounds at an exorbitant level, helping them to sustain adverse conditions. Moreover, compared to plant and animal biopolymers, microbial biopolymers are preferred due to their ease of production, design, and processing at an industrial levels. In this regard, polyhydroxyalkanoates (PHA) and poly-3-hydroxybutyrate (PHB) have together attained assiduity for their biodegradable properties and possess similar features as petrochemical-based polymers, commonly synthetic polymers like polyethylene, polypropylene, etc. This attributes to its non-toxic nature, i.e., it behaves eco-friendly by degrading the components through a carbon-neutral energy cycle to carbon dioxide and water, which lessens the dependence on petroleum-based polymers. This chapter contemplates the methods to develop biopolymers from microbes and their environmental applications, focusing on the confiscation of heavy metals, organic dyes or oils, etc.
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Affiliation(s)
- Krishnanjana Nambiar
- Department of Biotechnology , Karunya Institute of Technology and Sciences, Deemed to be University , Coimbatore , India
| | - Saravana Kumari P
- Department of Microbiology , Rathnavel Subramaniam College of Arts and Science , Coimbatore , India
| | - Dheeksha Devaraj
- Department of Biotechnology , Karunya Institute of Technology and Sciences, Deemed to be University , Coimbatore , India
| | - Murugan Sevanan
- Department of Biotechnology , Karunya Institute of Technology and Sciences, Deemed to be University , Coimbatore , India
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12
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Fosado YAG, Howard J, Weir S, Noy A, Leake MC, Michieletto D. Fluidification of Entanglements by a DNA Bending Protein. PHYSICAL REVIEW LETTERS 2023; 130:058203. [PMID: 36800460 DOI: 10.1103/physrevlett.130.058203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
In spite of the nanoscale and single-molecule insights into nucleoid associated proteins (NAPs), their role in modulating the mesoscale viscoelasticity of entangled DNA has been overlooked so far. By combining microrheology and molecular dynamics simulation, we find that the abundant NAP "integration host factor" (IHF) lowers the viscosity of entangled λDNA 20-fold at physiological concentrations and stoichiometries. Our results suggest that IHF may play a previously unappreciated role in resolving DNA entanglements and in turn may be acting as a "genomic fluidizer" for bacterial genomes.
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Affiliation(s)
- Yair A G Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jamieson Howard
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - Simon Weir
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Agnes Noy
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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13
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Hołówka J, Łebkowski T, Feddersen H, Giacomelli G, Drużka K, Makowski Ł, Trojanowski D, Broda N, Bramkamp M, Zakrzewska-Czerwińska J. Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin. Front Microbiol 2023; 14:1146406. [PMID: 36960278 PMCID: PMC10028186 DOI: 10.3389/fmicb.2023.1146406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) crucially contribute to organizing bacterial chromatin and regulating gene expression. Among the most highly expressed NAPs are the HU and integration host factor (IHF) proteins, whose functional homologues, HupB and mycobacterial integration host factor (mIHF), are found in mycobacteria. Despite their importance for the pathogenicity and/or survival of tubercle bacilli, the role of these proteins in mycobacterial chromosome organization remains unknown. Here, we used various approaches, including super-resolution microscopy, to perform a comprehensive analysis of the roles of HupB and mIHF in chromosome organization. We report that HupB is a structural agent that maintains chromosome integrity on a local scale, and that the lack of this protein alters chromosome morphology. In contrast, mIHF is a highly dynamic protein that binds DNA only transiently, exhibits susceptibility to the chromosomal DNA topology changes and whose depletion leads to the growth arrest of tubercle bacilli. Additionally, we have shown that depletion of Mycobacterium smegmatis integration host factor (msIHF) leads to chromosome shrinkage and replication inhibition.
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Affiliation(s)
- Joanna Hołówka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- *Correspondence: Joanna Hołówka,
| | - Tomasz Łebkowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Helge Feddersen
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Karolina Drużka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Łukasz Makowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Damian Trojanowski
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Natalia Broda
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
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14
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Chen S, Hu M, Hu A, Xue Y, Wang S, Liu F, Li C, Zhou X, Zhou J. The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2. MOLECULAR PLANT PATHOLOGY 2022; 23:1487-1507. [PMID: 35819797 PMCID: PMC9452768 DOI: 10.1111/mpp.13244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Dickeya zeae is an aggressive bacterial phytopathogen that infects a wide range of host plants. It has been reported that integration host factor (IHF), a nucleoid-associated protein consisting of IHFα and IHFβ subunits, regulates gene expression by influencing nucleoid structure and DNA bending. To define the role of IHF in the pathogenesis of D. zeae MS2, we deleted either and both of the IHF subunit encoding genes ihfA and ihfB, which significantly reduced the production of cell wall-degrading enzymes (CWDEs), an unknown novel phytotoxin and the virulence factor-modulating (VFM) quorum-sensing (QS) signal, cell motility, biofilm formation, and thereafter the infection ability towards both potato slices and banana seedlings. To characterize the regulatory pathways of IHF protein associated with virulence, IHF binding sites (consensus sequence 5'-WATCAANNNNTTR-3') were predicted and 272 binding sites were found throughout the genome. The expression of 110 tested genes was affected by IHF. Electrophoretic mobility shift assay (EMSA) showed direct interaction of IhfA protein with the promoters of vfmE, speA, pipR, fis, slyA, prtD, hrpL, hecB, hcp, indA, hdaA, flhD, pilT, gcpJ, arcA, arcB, and lysR. This study clarified the contribution of IHF in the pathogenic process of D. zeae by controlling the production of VFM and putrescine QS signals, phytotoxin, and indigoidine, the luxR-solo system, Fis, SlyA, and FlhD transcriptional regulators, and secretion systems from type I to type VI. Characterization of the regulatory networks of IHF in D. zeae provides a target for prevention and control of plant soft rot disease.
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Affiliation(s)
- Shanshan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Anqun Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Si Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Fan Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Chuhao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
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15
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Chen J, Gissendanner CR, Tikhe CV, Li HF, Sun Q, Husseneder C. Genomics and Geographic Diversity of Bacteriophages Associated With Endosymbionts in the Guts of Workers and Alates of Coptotermes Species (Blattodea: Rhinotermitidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.881538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Subterranean termites depend nutritionally on their gut microbiota, which includes protozoa as well as taxonomically and functionally diverse bacteria. Our previous metavirome study revealed a high diversity and novel families of bacteriophages in the guts of Coptotermes formosanus workers from New Orleans, Louisiana, United States. Two assembled bacteriophage genomes (Phages TG-crAlp-04 and 06, family Podoviridae) existed in all colonies and showed similarity to a prophage (ProJPt-Bp1) previously sequenced from a bacterial endosymbiont (Candidatus Azobacteroides pseudotrichonymphae, CAP) of protozoa in the gut of a termite species of the genus Prorhinotermes from Taiwan. In this study the genomes of Phage TG-crAlp-04 and 06 were subjected to detailed functional annotation. Both phage genomes contained conserved genes for DNA packaging, head and tail morphogenesis, and phage replication. Approximately 30% of the amino acid sequences derived from genes in both genomes matched to those of ProJPt-Bp1 phage or other phages from the crAss-like phage group. No integrase was identified; the lack of a lysogeny module is a characteristic of crAss-like phages. Primers were designed to sequence conserved genes of the two phages and their putative host bacterium (CAP) to detect their presence in different termite species from native and introduced distribution ranges. Related strains of the host bacterium were found across different termite genera and geographic regions. Different termite species had separate CAP strains, but intraspecific geographical variation was low. These results together with the fact that CAP is an important intracellular symbiont of obligate cellulose-digesting protozoa, suggest that CAP is a core gut bacterium and co-evolved across several subterranean termite species. Variants of both crAss-like phages were detected in different Coptotermes species from the native and introduced range, but they did not differentiate by species or geographic region. Since similar phages were detected in different termite species, we propose the existence of a core virome associated with core bacterial endosymbionts of protozoa in the guts of subterranean termites. This work provides a strong basis for further study of the quadripartite relationship of termites, protozoa, bacteria, and bacteriophages.
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16
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Watson GD, Chan EW, Leake MC, Noy A. Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF. Comput Struct Biotechnol J 2022; 20:5264-5274. [PMID: 36212531 PMCID: PMC9519438 DOI: 10.1016/j.csbj.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022] Open
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17
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Shepherd JW, Leake MC. The End Restraint Method for Mechanically Perturbing Nucleic Acids In Silico. Methods Mol Biol 2022; 2476:249-262. [PMID: 35635708 DOI: 10.1007/978-1-0716-2221-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical perturbation is due to molecular machines such as topoisomerases which must stretch and twist DNA as part of various functions including DNA repair and replication. While the broad-scale mechanical response of nucleic acids to tension and torsion is well characterized, detail at the single base pair level is beyond the limits of even super-resolution imaging. Here, we present a straightforward, flexible, and extensible umbrella-sampling protocol to twist and stretch nucleic acids in silico using the popular biomolecular simulation package Amber-though the principles we describe are applicable also to other packages such as GROMACS. We discuss how to set up the simulation system, decide force fields and solvation models, and equilibrate. We then introduce the torsionally constrained stretching protocol, and finally we present some analysis techniques we have used to characterize structural motif formation. Rather than defining forces or fictional pseudoatoms, we instead define a fixed translation of specified atoms between each umbrella-sampling step, which allows comparison with experiment without needing to estimate applied forces by simply using the fractional end-to-end displacement as a comparison metric. We hope that this easy-to-implement solution will be valuable for interrogating optical and magnetic tweezers data on nucleic acids at base pair resolution.
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Affiliation(s)
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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18
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Ma X, Ma L, Huo YX. Reconstructing the transcription regulatory network to optimize resource allocation for robust biosynthesis. Trends Biotechnol 2021; 40:735-751. [PMID: 34895933 DOI: 10.1016/j.tibtech.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An ideal microbial cell factory (MCF) should deliver maximal resources to production, which conflicts with the microbe's native growth-oriented resource allocation strategy and can therefore lead to early termination of the high-yield period. Reallocating resources from growth to production has become a critical factor in constructing robust MCFs. Instead of strengthening specific biosynthetic pathways, emerging endeavors are focused on rearranging the gene regulatory network to fundamentally reprogram the resource allocation pattern. Combining this idea with transcriptional regulation within the hierarchical regulatory network, this review discusses recent engineering strategies targeting the transcription machinery, module networks, regulatory edges, and bottom network layer. This global view will help to construct a production-oriented phenotype that fully harnesses the potential of MCFs.
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Affiliation(s)
- Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China; Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, People's Republic of China.
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