Bacillus subtilis utilizes the DNA damage response to manage multicellular development

Gozzi, Kevin; Ching, Carly; Paruthiyil, Srinand; Zhao, Yongmei; Godoy-Carter, Veronica; Chai, Yunrong

doi:10.1038/s41522-017-0016-3

Cited by 31 publications

(44 citation statements)

References 43 publications

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“…The existence of a front suggests that colony expansion rate is nutrient-limited [43], and that the ∼ 1 mm width of the matrix-producing region may be set by a nutrient penetration depth, D/q, where D is the nutrient diffusivity and q is the nutrient uptake rate [44]. The accumulation of metabolic by-products, such as reactive oxygen species [45], has been recently shown to lead to decreased matrix gene expression in developing biofilms. Thus, metabolic gradients and nutrient-depletion dynamics likely drive the transition from matrix production to sporulation during front propagation.…”

Section: Discussionmentioning

confidence: 99%

Matrix production inBacillus subtilisbiofilms is localized to a propagating front

Srinivasan

Vladescu

Koehler

et al. 2017

Preprint

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Bacterial biofilms are surface attached microbial communities encased in self-produced extracellular polymeric substances (EPS). Development of a mature biofilm must require coordinating cell differentiation and multicellular activity at scales much larger than the single microbial unit. Here we demonstrate that during development of Bacillus subtilis biofilms, EPS matrix production is localized to a front propagating at the periphery. We show that within the front, cells switch off matrix production and transition to sporulation after a set time delay of ∼ 100 min. Correlation analyses of fluctuations in fluorescence reporter activity reveals that the front emerges from a pair of gene expression waves of matrix production and sporulation. The expression waves travel across cells that are immobilized in the biofilm matrix, in contrast to active cell migration or horizontal colony spreading. A single length scale and time scale couples the spatiotemporal propagation of both fronts throughout development, with the front displacement obeying a t 1/2 scaling law. As a result, gene expression patterns within the advancing fronts collapse to self-similar expression profiles. Our results indicate that development of bacterial biofilms may be governed by universal wave-like dynamics localized to a self-similar front.The vast majority of bacteria do not exist as solitary cells but within structurally complex communities known as bacterial biofilms [1]. From dental plaques to the alkaline hot springs of Yellowstone, bacteria in natural aquatic and terrestrial ecosystems [2][3][4][5] exist in these surface-associated aggregates encased in a self-produced matrix, known as the extracellular polymeric substance (EPS) [6][7][8]. The EPS matrix is primarily composed of exopolysachharides and proteins [9]. The production of EPS facilitates the construction of sophisticated threedimensional structures [10]. Additionally, the rigid scaffold supports the immobilization of individual microorganisms, allowing for cellular signaling and the creation of localized homeostatic zones [11]. Thus, the EPS matrix supports the biofilm's robust physiology by facilitating reproducible spatial patterns of gene expression, cellular differentiation, and morphology in a manner analogous to multicellular organisms [12][13][14][15]. As a result, biofilms are capable of performing a plethora of sophisticated functions, including promoting surface adhesion and aggregation [16], enhancing mechanical rigidity [17], advanced architecture for water retention and uptake of nutrients [18], promoting cell-cell communication [19], and conferring enhanced antibiotic resistance [20]. Thus it is key for microorganisms to have a robust collective strategy for regulating biofilm matrix production and spore generation.Bacillus subtilis is a convenient model bacteria to work with in view of the extensive single-cell molecular analyses focused on investigating the lineage of biofilm formation [21]. In the early stages of the B. subtilis biofilm de- * shmuel@seas.harva...

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Section: Discussionmentioning

confidence: 99%

Matrix production inBacillus subtilisbiofilms is localized to a propagating front

Srinivasan

Vladescu

Koehler

et al. 2017

Preprint

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“…The reporter fusion was then moved into 3610 by transduction (40), generating strain JG156. To construct the dual-reporter, the reporter was introduced to YCN095, which contains a P tapA -mKate2 reporter fusion integrated at sacA (44), generating strain JG157.…”

Section: Methodsmentioning

confidence: 99%

Decreasing Serine Levels During Growth Transition Triggers Biofilm Formation inBacillus subtilis

Greenwich

Reverdy

Gozzi

et al. 2019

Preprint

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25Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number 26 of known signals that trigger biofilm formation do so through the activation of one or more 27 sensory histidine kinases, it was recently discovered that biofilm activation is also coordinated by 28 sensing intracellular metabolic signals, including serine starvation. Serine starvation causes 29 ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR, 30 which encodes a master repressor for biofilm matrix genes, and ultimately biofilm induction. 31 How serine levels change in different growth stages, how B. subtilis regulates intracellular serine 32 levels in response to metabolic status, and how serine starvation triggers ribosomes to pause on 33 selective serine codons remain unknown. Here we show that serine levels decrease as cells enter 34 stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine 35 biosynthesis genes decreases upon the transition into stationary phase. Deletion of the gene for a 36 serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm 37 formation, further supporting the idea that serine levels are a critical intracellular signal for 38 biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are 39 decreased in stationary phase compared to exponential phase. Interestingly, the three 40 isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two 41 that recognize AGC and AGU serine codons. Our findings provide evidence for a link between 42 serine homeostasis and biofilm development in B. subtilis. 43 44 3 IMPORTANCE 45In Bacillus subtilis, biofilm formation is triggered in response to various environmental 46 and cellular signals. It was previously proposed that serine limitation acts as a proxy for nutrient 47 status and triggers biofilm formation at the onset of biofilm entry through a novel signaling 48 mechanism caused by global ribosome pausing on selective serine codons. In this study, we 49 revealed that serine levels decrease at the biofilm entry due to catabolite control and a shunt 50 mechanism. We also show that levels of five serine tRNA isoacceptors are differentially 51 decreased in stationary phase compared to exponential phase; three isoacceptors recognizing 52 UCN serine codons are reduced much greater than the two recognizing AGC and AGU codons. 53This indicates a possible mechanism for selective ribosome pausing. 54 55 4

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“…We propose a potential mechanism for this activation: recent research has indicated that certain cells in a culture will tend to accumulate reactive oxygen species and DNA damage. Those cells will produce Sda (a developmental checkpoint protein), and form a subpopulation separate from those that produce biofilm 35 . The LexA+, biofilmpopulation would no longer be producing EpsE, which catalyzes a step in the biofilm synthesis process and also suppresses swarming 36 .…”

Section: I-modulons Generate Novel Hypotheses I-modulon Activities Cmentioning

confidence: 99%

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

Rychel

Sastry

Kim

2020

Preprint

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The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression.We obtain 83 independently modulated gene sets that explain most of the variance in expression, and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover novel or recently discovered roles for at least 5 regulons, such as a relationship between histidine utilization and quorum sensing.The TRN also facilitates quantification of population-level sporulation states, revealing a putative anaerobic metabolism role for SigG. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis.

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Bacillus subtilis utilizes the DNA damage response to manage multicellular development

Cited by 31 publications

References 43 publications

Matrix production inBacillus subtilisbiofilms is localized to a propagating front

Matrix production inBacillus subtilisbiofilms is localized to a propagating front

Decreasing Serine Levels During Growth Transition Triggers Biofilm Formation inBacillus subtilis

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

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