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Book: SMC complexes

Badrinarayanan, Anjana

methods and protocols

(Methods in molecular biology ; 2004 ; Springer protocols)

2019

Author's details	edited by Anjana Badrinarayanan
Series title	Methods in molecular biology ; 2004 Springer protocols
Collection
Language	English
Size	xiii, 336 Seiten, Illustrationen
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book
HBZ-ID	HT020082247
ISBN	978-1-4939-9519-6 ; 9781493995202 ; 1-4939-9519-7 ; 1493995200
Database	Catalogue ZB MED Medicine, Health

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Shelf mark	Loan status	Location
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Article ; Online: SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function.

Kamat, Aditya / Badrinarayanan, Anjana

Current opinion in microbiology

2023 Volume 73, Page(s) 102323

Abstract: Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS- ... ...

Abstract	Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS-independent DDRs have also been discovered. Studies further report diversity in the types of repair proteins present across bacterial species as well as differences in their mechanisms of action. Although the primary function of DDRs is preservation of genome integrity, the diverse organization, conservation, and function of bacterial DDRs raises important questions about how genome error correction mechanisms could influence or be influenced by the genomes that encode them. In this review, we discuss recent insights on three SOS-independent bacterial DDRs. We consider open questions in our understanding of how diversity in response and repair mechanisms is generated, and how action of these pathways is regulated in cells to ensure maintenance of genome integrity.
MeSH term(s)	DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; SOS Response, Genetics ; Bacteria/genetics ; Bacteria/metabolism ; DNA Damage ; DNA Repair ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism
Chemical Substances	DNA, Bacterial ; Bacterial Proteins
Language	English
Publishing date	2023-05-04
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2023.102323
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Article ; Online: Fluorescence Recovery After Photobleaching (FRAP) to Study Dynamics of the Structural Maintenance of Chromosome (SMC) Complex in Live Escherichia coli Bacteria.

Badrinarayanan, Anjana / Leake, Mark C

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2476, Page(s) 31–41

Abstract: MukBEF, a structural maintenance of chromosome (SMC) complex, is an important molecular machine for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or "foci") composed of molecular assemblies ...

Abstract	MukBEF, a structural maintenance of chromosome (SMC) complex, is an important molecular machine for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or "foci") composed of molecular assemblies in the cell, where it is thought to carry out most of its chromosome-associated activities. Here, we outline the technique of fluorescence recovery after photobleaching (FRAP) as a method to study the properties of YFP-tagged MukB in fluorescent foci. This method can provide important insight into the dynamics of MukB on DNA and be used to study its biochemical properties in vivo.
MeSH term(s)	Chromosomal Proteins, Non-Histone/genetics ; Chromosomes ; Escherichia coli/chemistry ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Fluorescence Recovery After Photobleaching ; Repressor Proteins/genetics
Chemical Substances	Chromosomal Proteins, Non-Histone ; Escherichia coli Proteins ; MukB protein, E coli ; Repressor Proteins
Language	English
Publishing date	2022-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2221-6_4
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Article ; Online: SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function

Kamat, Aditya / Badrinarayanan, Anjana

Current Opinion in Microbiology. 2023 June, v. 73 p.102323-

2023

Abstract	Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS-independent DDRs have also been discovered. Studies further report diversity in the types of repair proteins present across bacterial species as well as differences in their mechanisms of action. Although the primary function of DDRs is preservation of genome integrity, the diverse organization, conservation, and function of bacterial DDRs raises important questions about how genome error correction mechanisms could influence or be influenced by the genomes that encode them. In this review, we discuss recent insights on three SOS-independent bacterial DDRs. We consider open questions in our understanding of how diversity in response and repair mechanisms is generated, and how action of these pathways is regulated in cells to ensure maintenance of genome integrity.
Keywords	DNA damage ; genome ; microbiology
Language	English
Dates of publication	2023-06
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2023.102323
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria.

Kamat, Aditya / Tran, Ngat T / Sharda, Mohak / Sontakke, Neha / Le, Tung B K / Badrinarayanan, Anjana

PLoS biology

2024 Volume 22, Issue 3, Page(s) e3002540

Abstract: DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The ... ...

Abstract	DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.
MeSH term(s)	Prevalence ; Bacteria/genetics ; DNA Methylation/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; DNA Repair ; Protein Processing, Post-Translational ; DNA Damage/genetics ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; DNA, Bacterial/metabolism
Chemical Substances	Transcription Factors ; Bacterial Proteins ; DNA, Bacterial
Language	English
Publishing date	2024-03-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3002540
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Article ; Online: Chromosome organization shapes replisome dynamics in Caulobacter crescentus.

Zhang, Chen / Joseph, Asha Mary / Casini, Laurent / Collier, Justine / Badrinarayanan, Anjana / Manley, Suliana

Nature communications

2024 Volume 15, Issue 1, Page(s) 3460

Abstract: DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial ... ...

Abstract	DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial species, driving the hypothesis that a physical linker may tether them together. However, replisome splitting has also been reported in many of the same species, leaving the principles behind replisome organization a long-standing puzzle. Here, by tracking the replisome β-clamp subunit in live Caulobacter crescentus, we find that rapid DNA segregation can give rise to a second focus which resembles a replisome, but does not replicate DNA. Sister replisomes can remain colocalized, or split apart to travel along DNA separately upon disruption of chromosome inter-arm alignment. Furthermore, chromosome arm-specific replication-transcription conflicts differentially modify replication speed on the two arms, facilitate the decoupling of the two replisomes. With these observations, we conclude that the dynamic chromosome organization flexibly shapes the organization of sister replisomes, and we outline principles which can help to reconcile previously conflicting models of replisome architecture.
MeSH term(s)	Caulobacter crescentus/metabolism ; Caulobacter crescentus/genetics ; DNA Replication ; Chromosomes, Bacterial/metabolism ; Chromosomes, Bacterial/genetics ; Bacterial Proteins/metabolism ; Bacterial Proteins/genetics ; DNA, Bacterial/metabolism ; DNA, Bacterial/genetics ; Chromosome Segregation
Chemical Substances	Bacterial Proteins ; DNA, Bacterial
Language	English
Publishing date	2024-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47849-6
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Article ; Online: DarT-mediated mtDNA damage induces dynamic reorganization and selective segregation of mitochondria.

Dua, Nitish / Seshadri, Akshaya / Badrinarayanan, Anjana

The Journal of cell biology

2022 Volume 221, Issue 10

Abstract: Mitochondria are dynamic organelles that play essential roles in cell growth and survival. Processes of fission and fusion are critical for the distribution, segregation, and maintenance of mitochondria and their genomes (mtDNA). While recent work has ... ...

Abstract	Mitochondria are dynamic organelles that play essential roles in cell growth and survival. Processes of fission and fusion are critical for the distribution, segregation, and maintenance of mitochondria and their genomes (mtDNA). While recent work has revealed the significance of mitochondrial organization for mtDNA maintenance, the impact of mtDNA perturbations on mitochondrial dynamics remains less understood. Here, we develop a tool to induce mitochondria-specific DNA damage using a mitochondrial-targeted base modifying bacterial toxin, DarT. Following damage, we observe dynamic reorganization of mitochondrial networks, likely driven by mitochondrial dysfunction. Changes in the organization are associated with the loss of mtDNA, independent of mitophagy. Unexpectedly, perturbation to exonuclease function of mtDNA replicative polymerase, Mip1, results in rapid loss of mtDNA. Our data suggest that, under damage, partitioning of defective mtDNA and organelle are de-coupled, with emphasis on mitochondrial segregation independent of its DNA. Together, our work underscores the importance of genome maintenance on mitochondrial function, which can act as a modulator of organelle organization and segregation.
MeSH term(s)	Bacterial Toxins ; DNA Damage ; DNA Polymerase I ; DNA, Mitochondrial/genetics ; Exonucleases ; Mitochondria/genetics ; Mitochondrial Dynamics/genetics ; Mitophagy/genetics
Chemical Substances	Bacterial Toxins ; DNA, Mitochondrial ; DNA Polymerase I (EC 2.7.7.7) ; Exonucleases (EC 3.1.-)
Language	English
Publishing date	2022-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.202205104
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Article ; Online: Visualizing mutagenic repair: novel insights into bacterial translesion synthesis.

Joseph, Asha Mary / Badrinarayanan, Anjana

FEMS microbiology reviews

2020 Volume 44, Issue 5, Page(s) 572–582

Abstract: DNA repair is essential for cell survival. In all domains of life, error-prone and error-free repair pathways ensure maintenance of genome integrity under stress. Mutagenic, low-fidelity repair mechanisms help avoid potential lethality associated with ... ...

Abstract	DNA repair is essential for cell survival. In all domains of life, error-prone and error-free repair pathways ensure maintenance of genome integrity under stress. Mutagenic, low-fidelity repair mechanisms help avoid potential lethality associated with unrepaired damage, thus making them important for genome maintenance and, in some cases, the preferred mode of repair. However, cells carefully regulate pathway choice to restrict activity of these pathways to only certain conditions. One such repair mechanism is translesion synthesis (TLS), where a low-fidelity DNA polymerase is employed to synthesize across a lesion. In bacteria, TLS is a potent source of stress-induced mutagenesis, with potential implications in cellular adaptation as well as antibiotic resistance. Extensive genetic and biochemical studies, predominantly in Escherichia coli, have established a central role for TLS in bypassing bulky DNA lesions associated with ongoing replication, either at or behind the replication fork. More recently, imaging-based approaches have been applied to understand the molecular mechanisms of TLS and how its function is regulated. Together, these studies have highlighted replication-independent roles for TLS as well. In this review, we discuss the current status of research on bacterial TLS, with emphasis on recent insights gained mostly through microscopy at the single-cell and single-molecule level.
MeSH term(s)	Bacteria/genetics ; DNA Repair ; DNA, Bacterial/genetics ; DNA-Directed DNA Polymerase/metabolism ; Microscopy ; Mutagenesis ; Optical Imaging ; Single-Cell Analysis
Chemical Substances	DNA, Bacterial ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2020-06-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	283740-7
ISSN	1574-6976 ; 0168-6445
ISSN (online)	1574-6976
ISSN	0168-6445
DOI	10.1093/femsre/fuaa023
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Article ; Online: Tracking Bacterial Chromosome Dynamics with Microfluidics-Based Live Cell Imaging.

Raghunathan, Suchitha / Badrinarayanan, Anjana

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2004, Page(s) 223–238

Abstract: In bacteria, chromosomes are highly organized within the limited volume of the cell to form a nucleoid. Recent application of microscopy and chromosome conformation capture techniques have together provided a comprehensive understanding of the nature of ... ...

Abstract	In bacteria, chromosomes are highly organized within the limited volume of the cell to form a nucleoid. Recent application of microscopy and chromosome conformation capture techniques have together provided a comprehensive understanding of the nature of this organization and the role of factors such as the structural maintenance of chromosomes (SMC) proteins in the establishment and maintenance of the same. In this chapter, we outline a microfluidics-based approach for live cell imaging of Escherichia coli chromosome dynamics in wild-type cells. This assay can be used to track the activity of the SMC complex, MukBEF, on DNA and assess the impact of perturbations such as DNA damage on chromosome organization and segregation.
MeSH term(s)	Chromosomes, Bacterial/metabolism ; DNA, Bacterial/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Microfluidics/methods
Chemical Substances	DNA, Bacterial ; Escherichia coli Proteins
Language	English
Publishing date	2019-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9520-2_17
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Article ; Online: Live-Cell Fluorescence Imaging of RecN in Caulobacter crescentus Under DNA Damage.

Chimthanawala, Afroze / Badrinarayanan, Anjana

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2004, Page(s) 239–250

Abstract: Structural maintenance of chromosomes (SMC) proteins play a central role in the organization, segregation and maintenance of chromosomes across domains of life. In bacteria, an SMC-family protein, RecN, has been implicated to have important functions in ... ...

Abstract	Structural maintenance of chromosomes (SMC) proteins play a central role in the organization, segregation and maintenance of chromosomes across domains of life. In bacteria, an SMC-family protein, RecN, has been implicated to have important functions in DNA damage repair. Recent studies have suggested that RecN is required to increase chromosome cohesion in response to DNA damage and may also stimulate specific events during recombination-based repair. While biochemical and genetic assays provide insights into mechanism of action of RecN and other repair factors, in vivo understanding of activity and regulation of proteins can be predominantly gained via microscopy-based approaches. Here, we describe a protocol to study the localization of fluorescently tagged RecN to a site-specific double-strand break (DSB) in Caulobacter crescentus. We further outline a method to probe RecN dynamics in cells with a single, nonreplicating chromosome. This technique can be used to study the early steps of recombination-based repair and understand the regulation of protein recruitment to and further association with sites of damage.
MeSH term(s)	Bacterial Proteins/genetics ; Caulobacter crescentus/genetics ; Chromosome Segregation/genetics ; Chromosomes, Bacterial/genetics ; DNA Breaks, Double-Stranded ; DNA Damage/genetics ; DNA Restriction Enzymes/genetics ; DNA, Bacterial/genetics ; Fluorescence ; Recombinational DNA Repair/genetics
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; DNA Restriction Enzymes (EC 3.1.21.-)
Language	English
Publishing date	2019-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9520-2_18
Database	MEDical Literature Analysis and Retrieval System OnLINE

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