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Article ; Online: Swarming Motility Assays in Salmonella.

Partridge, Jonathan D / Harshey, Rasika M

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

2023 Volume 2646, Page(s) 147–158

Abstract: Salmonella enterica has six subspecies, of which the subspecies enterica is the most important for human health. The dispersal and infectivity of this species are dependent upon flagella-driven motility. Two kinds of flagella-mediated movements have been ...

Abstract	Salmonella enterica has six subspecies, of which the subspecies enterica is the most important for human health. The dispersal and infectivity of this species are dependent upon flagella-driven motility. Two kinds of flagella-mediated movements have been described-swimming individually in bulk liquid and swarming collectively over a surface substrate. During swarming, the bacteria acquire a distinct physiology, the most significant consequence of which is acquisition of adaptive resistance to antibiotics. Described here are protocols to cultivate, verify, and study swimming and swarming motility in S. enterica, and an additional "border-crossing" assay, where cells "primed" to swarm are presented with an environmental challenge such as antibiotics to assess their propensity to handle the challenge.
MeSH term(s)	Humans ; Salmonella enterica ; Cell Movement ; Flagella/physiology ; Bacterial Proteins ; Movement
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2023-02-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3060-0_13
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Second Role for the Second Messenger Cyclic-di-GMP in E. coli: Arresting Cell Growth by Altering Metabolic Flow.

Hwang, YuneSahng / Harshey, Rasika M

mBio

2023 Volume 14, Issue 2, Page(s) e0061923

Abstract: c-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. ... ...

Abstract	c-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. Their catalytic activity is modulated by c-di-GMP binding to autoinhibitory sites (I-sites). YfiN is a conserved inner membrane DGC that lacks these sites. Instead, YfiN activity is directly repressed by periplasmic YfiR, which is inactivated by redox stress. In Escherichia coli, an additional envelope stress causes YfiN to relocate to the mid-cell to inhibit cell division by interacting with the division machinery. Here, we report a third activity for YfiN in E. coli, where cell growth is inhibited without YfiN relocating to the division site. This action of YfiN is only observed when the bacteria are cultured on gluconeogenic carbon sources, and is dependent on absence of the autoinhibitory sites. Restoration of I-site function relieves the growth-arrest phenotype, and disabling this function in a heterologous DGC causes acquisition of this phenotype. Arrested cells are tolerant to a wide range of antibiotics. We show that the likely cause of growth arrest is depletion of cellular GTP from run-away synthesis of c-di-GMP, explaining the dependence of growth arrest on gluconeogenic carbon sources that exhaust more GTP during production of glucose. This is the first report of c-di-GMP-mediated growth arrest by altering metabolic flow.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Second Messenger Systems ; Cyclic GMP/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Biofilms ; Phosphorus-Oxygen Lyases/genetics ; Phosphorus-Oxygen Lyases/metabolism ; Guanosine Triphosphate/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial
Chemical Substances	bis(3',5')-cyclic diguanylic acid (61093-23-0) ; Cyclic GMP (H2D2X058MU) ; Escherichia coli Proteins ; Phosphorus-Oxygen Lyases (EC 4.6.-) ; Guanosine Triphosphate (86-01-1) ; Bacterial Proteins
Language	English
Publishing date	2023-04-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00619-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Goodbye PAM: Phage λ's Red recombination system cripples PAMs and helps dodge CRISPR attacks.

Ho, Khang / Harshey, Rasika M

Cell host & microbe

2021 Volume 29, Issue 10, Page(s) 1469–1471

Abstract: Ever wondered how the phage λ Red recombination system resembles the Red Queen? Hossain et al. (2021) provide an answer in this issue of Cell Host & Microbe. They show that Red debilitates PAM sequences by mutagenic repair of CRISPR-targeted DNA breaks ... ...

Abstract	Ever wondered how the phage λ Red recombination system resembles the Red Queen? Hossain et al. (2021) provide an answer in this issue of Cell Host & Microbe. They show that Red debilitates PAM sequences by mutagenic repair of CRISPR-targeted DNA breaks in infecting λ, thus shaping the phage-CRISPR arms race.
MeSH term(s)	Bacteriophage lambda/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Recombination, Genetic
Language	English
Publishing date	2021-10-15
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2021.09.011
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Article: Flagellar motor remodeling during swarming requires FliL.

Partridge, Jonathan D / Dufour, Yann / Hwang, YuneSahng / Harshey, Rasika M

bioRxiv : the preprint server for biology

2023

Abstract: FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are ... ...

Abstract	FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. Bacterial physiology and morphology are also altered during swarming to cope with the challenges of surface navigation. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria -
Language	English
Publishing date	2023-07-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.14.549092
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Article: Iron Memory in

Bhattacharyya, Souvik / Bhattarai, Nabin / Pfannenstiel, Dylan M / Wilkins, Brady / Singh, Abhyudai / Harshey, Rasika M

bioRxiv : the preprint server for biology

2023

Abstract: The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered ... ...

Abstract	The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when
Language	English
Publishing date	2023-05-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.19.541523
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Article ; Online: Flagellar motor remodeling during swarming requires FliL.

Partridge, Jonathan D / Dufour, Yann / Hwang, YuneSahng / Harshey, Rasika M

Molecular microbiology

2023 Volume 120, Issue 5, Page(s) 670–683

Abstract	FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria-Escherichia coli, Bacillus subtilis, and Proteus mirabilis. During swarming, all these bacteria show increased cell speed and a skewed motor bias that suppresses cell tumbling. We demonstrate that these altered motor parameters, or "motor remodeling," require FliL. Both swarming and motor remodeling can be restored in an E. coli fliL mutant by complementation with fliL genes from P. mirabilis and B. subtilis, showing conservation of a swarming-associated FliL function across phyla. In addition, we demonstrate that the strong interaction we reported earlier between FliL and the flagellar MS-ring protein FliF is confined to the RBM-3 domain of FliF that links the periplasmic rod to the cytoplasmic C-ring. This interaction may explain several phenotypes associated with the absence of FliL.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Membrane Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Movement ; Flagella/metabolism
Chemical Substances	Bacterial Proteins ; Membrane Proteins
Language	English
Publishing date	2023-09-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.15148
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Article ; Online: A heritable iron memory enables decision-making in

Bhattacharyya, Souvik / Bhattarai, Nabin / Pfannenstiel, Dylan M / Wilkins, Brady / Singh, Abhyudai / Harshey, Rasika M

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 48, Page(s) e2309082120

Abstract: The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered ... ...

Abstract	The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when
MeSH term(s)	Escherichia coli/genetics ; Iron ; Anti-Bacterial Agents
Chemical Substances	Iron (E1UOL152H7) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2309082120
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Article: Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of

Walker, David M / Harshey, Rasika M

Mobile DNA

2020 Volume 11, Page(s) 26

Abstract: Background: The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the : Results: We tracked Mu transposition from six different starting locations on the : Conclusions: The results in this study ... ...

Abstract	Background: The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the Results: We tracked Mu transposition from six different starting locations on the Conclusions: The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.
Language	English
Publishing date	2020-07-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2536054-1
ISSN	1759-8753
ISSN	1759-8753
DOI	10.1186/s13100-020-00217-9
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Article ; Online: Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series.

Partridge, Jonathan D / Harshey, Rasika M

Journal of visualized experiments : JoVE

2020 , Issue 159

Abstract: Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of ...

Abstract	Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of movement. Here we demonstrate a combination of three of these methodologies. Motility in soft agar is the oldest, offering a strong selection for isolating gain-of-function suppressor mutations in motility-impaired strains, where motility is restored through a second mutation. The cell-tethering technique, first employed to demonstrate the rotary nature of the flagellar motor, can be used to assess the impact of signaling effectors on the motor speed and its ability to switch rotational direction. The "border-crossing" assay is more recent, where swimming bacteria can be primed to transition into moving collectively as a swarm. In combination, these protocols represent a systematic and powerful approach to identifying components of the motility machinery, and to characterizing their role in different facets of swimming and swarming. They can be easily adapted to study motility in other bacterial species.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/physiology ; Escherichia coli Proteins/genetics ; Flagella/metabolism ; Genes, Suppressor ; Microbiological Techniques/methods ; Movement ; Mutation/genetics
Chemical Substances	Escherichia coli Proteins
Language	English
Publishing date	2020-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/61364
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Article ; Online: Dead cells release a ‘necrosignal’ that activates antibiotic survival pathways in bacterial swarms

Souvik Bhattacharyya / David M. Walker / Rasika M. Harshey

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 12

Abstract: Swarming bacterial populations can exhibit antibiotic resistance, despite sustaining considerable cell death. Here, Bhattacharyya et al. show that killed cells release periplasmic protein AcrA, which activates efflux pumps on the surface of live cells, ... ...

Abstract	Swarming bacterial populations can exhibit antibiotic resistance, despite sustaining considerable cell death. Here, Bhattacharyya et al. show that killed cells release periplasmic protein AcrA, which activates efflux pumps on the surface of live cells, thus enhancing antibiotic resistance in the surviving cells.
Keywords	Science ; Q
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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