Phenotypic memory in quorum sensing DOI Creative Commons

Ghazaleh Ostovar,

James Q. Boedicker

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 20, 2023

Abstract Quorum sensing (QS) is a regulatory mechanism used by bacteria to coordinate group behavior in response high cell densities. During QS, cells monitor the concentration of external signals, known as autoinducers, proxy for density. QS often involves positive feedback loops, leading upregulation genes associated with signal production and detection. This results distinct steady-state concentrations QS-related molecules QS-ON QS-OFF states. Due slow decay rates biomolecules such proteins, even after removal initial stimuli, can retain elevated levels QS-associated extended periods time. persistence stimuli has potential impact future denoting memory past exposure. phenomenon, which consequence carry-over rather than genetic inheritance, “phenotypic” memory. theoretical study aims investigate presence phenotypic conditions that influence this Numerical simulations based on ordinary differential equations analytical modeling were gene expression sudden changes density extracellular concentrations. The model examined effect various cellular parameters strength dynamics. findings revealed transient QS-responsive genes. These consequences depend strongly how was perturbed, well parameters, including Fold Change QS-regulated genes, autoinducer synthesis rate, threshold required activation, growth rate. Author summary Bacteria use quorum collaborate when their numbers are high. Cells produce detect signals trigger certain proteins behavior. Interestingly, produced during process linger gone. these form “memory”, temporarily changed events recent past. Our focuses exploring factors it. To do this, we models examine history exposure affect cells. We found prior respond future, but only under specific conditions. research contributes our understanding adapt environmental changes.

Language: Английский

The molecular architecture of the nuclear basket DOI Creative Commons
Digvijay Singh, Neelesh Soni, Joshua Hutchings

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(19), P. 5267 - 5281.e13

Published: Aug. 9, 2024

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), protozoa (T. gondii). integrative modeling, computed a model yeast that revealed how hub nucleoporins (Nups) ring binds to basket-forming Mlp/Tpr proteins: coiled-coil domains form struts basket, while their unstructured termini constitute distal densities, which potentially serve as docking site for preprocessing before

Language: Английский

Citations

27
Legacy effects of rhizodeposits on soil microbiomes: A perspective DOI Creative Commons
P. Nannipieri, S. Emilia Hannula, Giacomo Pietramellara

et al.

Soil Biology and Biochemistry, Journal Year: 2023, Volume and Issue: 184, P. 109107 - 109107

Published: June 25, 2023

Plant legacy effects observed in plant-soil feedback experiments have largely been attributed to the root or litter material of previous plant. The rhizodeposits are defined as changes soil microbiome that remain after a plant has died removed from and caused by release substances various compositions living plants (rhizodeposits). Rhizodeposit-mediated ignored mainly due high spatial temporal variability difficulties quantifying tracking them rhizosphere. In this perspective article, we discuss what is known about provide ideas for future improve understanding phenomenon. Only few studies separate rhizodeposit-mediated decomposition. Results these indicate on microbial communities may persist several months years, especially if same crop cultivated persistently years 'conditioning' phase. fungal usually last longer than those bacterial life-cycle strategies (spore formation) slower reproduction rates, compared communities. We highlight need further experimentation investigate influence length conditioning phase persistence effect, differentiate effect exudates sloughed cells, simple sugars molecular-weight derived compounds with antimicrobial properties, explore whether species diversity influences nature legacy. To address questions, propose use contemporary tools such stable isotope probing, genetics, reverse microdialysis. think harnessing could be promising approach sustainable production creating disease-suppressive soils simulating growth-promoting micro-organisms within systems.

Language: Английский

Citations

29
Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops DOI Creative Commons
Mohamed R. Abdelfadil, Sascha Patz, Steffen Kolb

et al.

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: July 18, 2024

Abstract Background Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets untangle rhizosphere structure of two groups non-halophytes. aimed for identification marker being adapted high three independent approaches. Results Fifteen studies met selection criteria downstream analysis, consisting 40 representing diverse non-halophyte species. Microbiome structural analysis revealed distinct compositions halophytes face salt concentrations compared grown at low or from For concentrations, we discovered genera were independently detected through core microbiome, key hub by network random forest analysis. These Thalassospira , Erythrobacter Marinobacter . Conclusions Our level is critical factor affecting microbiome assembly plants. Detecting across high-halophytes may help select Bacteria might improve tolerance non-halophytic

Language: Английский

Citations

4
The Molecular Architecture of the Nuclear Basket DOI Creative Commons
Digvijay Singh, Neelesh Soni, Joshua Hutchings

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 28, 2024

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi (yeast;

Language: Английский

Citations

3
Phenotypic memory in quorum sensing DOI Creative Commons

Ghazaleh Ostovar,

James Q. Boedicker

PLoS Computational Biology, Journal Year: 2024, Volume and Issue: 20(7), P. e1011696 - e1011696

Published: July 8, 2024

Quorum sensing (QS) is a regulatory mechanism used by bacteria to coordinate group behavior in response high cell densities. During QS, cells monitor the concentration of external signals, known as autoinducers, proxy for density. QS often involves positive feedback loops, leading upregulation genes associated with signal production and detection. This results distinct steady-state concentrations QS-related molecules QS-ON QS-OFF states. Due slow decay rates biomolecules such proteins, even after removal initial stimuli, can retain elevated levels QS-associated extended periods time. persistence stimuli has potential impact future indicating memory past exposure. phenomenon, which consequence carry-over rather than genetic inheritance, "phenotypic" memory. theoretical study aims investigate presence phenotypic conditions that influence this Numerical simulations based on ordinary differential equations analytical modeling were gene expression sudden changes density extracellular concentrations. The model examined effect various cellular parameters strength dynamics. findings revealed transient QS-responsive genes. These consequences depend strongly how was perturbed, well parameters, including Fold Change QS-regulated genes, autoinducer synthesis rate, threshold required activation, growth rate.

Language: Английский

Citations

3
Phenotypic heterogeneity follows a growth-viability tradeoff in response to amino acid identity DOI Creative Commons
Kiyan Shabestary, Cinzia Klemm, Benedict Carling

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 2, 2024

Abstract In their natural environments, microorganisms mainly operate at suboptimal growth conditions with fluctuations in nutrient abundance. The resulting cellular adaptation is subject to conflicting tasks: or survival maximisation. Here, we study this by systematically measuring the impact of a nitrogen downshift 24 sources on metabolism single-cell level. Saccharomyces lineages grown rich media and exposed gradually differentiate form two subpopulations different cell sizes where one favours while other viability an extended chronological lifespan. This differentiation asymmetrical daughter cells representing new differentiated state increased viability. We characterise metabolic response using RNA sequencing, biosensors transcription factor-tagged GFP library coupled high-throughput microscopy, imaging more than 800,000 cells. find that subpopulation associated dormant quiescent displaying differences MAPK signalling. Depending identity source present, into can be actively maintained, attenuated, aborted. These results establish amino acids as important signalling molecules for formation genetically identical subpopulations, involved lifespan rate determination.

Language: Английский

Citations

3
Self-Organization and Memory in a Disordered Solid Subject to Random Driving DOI
Muhittin Mungan, Dheeraj Kumar, Sylvain Patinet

et al.

Physical Review Letters, Journal Year: 2025, Volume and Issue: 134(17)

Published: April 30, 2025

We consider self-organization and memory formation in a mesoscopic model of an amorphous solid subject to protocol random shear confined strain range ±ϵ_{max}. develop proper readout protocols show that the response driven system self-organizes retain range, which can be subsequently retrieved. Our findings generalize previous results obtained upon oscillatory driving suggest disordered materials emerge under more general conditions, such as interacting with its fluctuating environment. Self-organization correlation between dynamics environment, providing thereby elementary mechanism for sensing. conclude by discussing our their potential relevance adaptation simple organisms lacking brain changing environments.

Language: Английский

Citations

0
Engineering plasmid copy number heterogeneity for dynamic microbial adaptation DOI
Shalni Kumar, Andrew Lezia,

Jeff Hasty

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(8), P. 2173 - 2184

Published: June 18, 2024

Language: Английский

Citations

2
Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing DOI

Alex W. Walls,

Adam Rosenthal

Transcription, Journal Year: 2024, Volume and Issue: 15(1-2), P. 48 - 62

Published: March 14, 2024

Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, engage both competition cooperation with neighbors. While we typically think bacterial adaptation as group behavior, where all cells respond unison, there often mixture phenotypic responses within population, distinct types arise. A primary phenomenon driving these transcriptional heterogeneity. Given mRNA transcripts are extremely short-lived compared eukaryotes, state closely associated physiology, thus the transcriptome acts snapshot behavior bacterium. Therefore, application single-cell transcriptomics microbial populations will provide novel insight into cellular differentiation ecology. In this review, an overview heterogeneity systems, discuss findings already provided by approaches, plot new avenues inquiry regulation, biology, mechanisms made possible when communities analyzed at resolution.

Language: Английский

Citations

1
A protein condensation network contextualises cell fate decisions DOI Creative Commons
Thomas R. Peskett, Sung Sik Lee, Yves Barral

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 18, 2024

Summary For cells to thrive, they must make appropriate fate decisions based on a myriad of internal and external stimuli. But how do integrate these different forms information contextualise their decisions? Old yeast showed an ability dampen proliferation as entered senescence. Conversely, had enhanced promote during escape from pheromone stimulation. A network nucleoprotein condensation states involving processing bodies (P-bodies) the prion-like RNA-binding protein, Whi3, controlled opposing decisions. In old but not in young cells, Whi3 was both necessary sufficient for senescence entry. localised age-dependent P-bodies. Preventing formation stopped driving Challenging with stimulus, pheromone, revealed that condensates second function: potentiating cell’s trigger mating response. These findings identify biomolecular integrator contextual decisions, enabling them navigate overlapping life events.

Language: Английский

Citations

1