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1. Dynamic aqueous transformations of lithium cobalt oxide nanoparticle induce distinct oxidative stress responses of B. subtilis

   https://doi.org/10.1039/D0EN01151G  

   Gari, Metti K.; Lemke, Paul; Lu, Kelly H.; Laudadio, Elizabeth D.; Henke, Austin H.; Green, Curtis M.; Pho, Thomas; Hoang, Khoi Nguyen; Murphy, Catherine J.; Hamers, Robert J.; et al (January 2021, Environmental Science: Nano)

   null (Ed.)

   Lithium cobalt oxide (LiCoO 2 ), an example of nanoscale transition metal oxide and a widely commercialized cathode material in lithium ion batteries, has been shown to induce oxidative stress and generate intracellular reactive oxygen species (ROS) in model organisms. In this study, we aimed to understand the time-dependent roles of abiotic ROS generation and Co ions released in aqueous medium by LiCoO 2 NPs, and examined the induced biological responses in model bacterium, B. subtilis upon exposure. We found that the redox-active LiCoO 2 NPs produced abiotic ROS primarily through H 2 O 2 generation when freshly suspended. Subsequently, the freshly-suspended LiCoO 2 NPs induced additional DNA breakage, and changes in expression of oxidative stress genes in B. subtilis that could not be accounted for by the released Co ions alone. Notably, in 48 hour old LiCoO 2 suspensions, H 2 O 2 generation subsided while higher concentrations of Co ions were released. The biological responses in DNA damage and gene expression to the aged LiCoO 2 NPs recapitulated those induced by the released Co ions. Our results demonstrated oxidative stress mechanisms for bacteria exposed to LiCoO 2 NPs were mediated by the generation of distinct biotic and abiotic ROS species, which depended on the aqueous transformation state of the NPs. This study revealed the interdependent and dynamic nature of NP transformation and their biological consequences where the state of NPs resulted in distinct NP-specific mechanisms of oxidative injury. Our work highlights the need to capture the dynamic transformation of NPs that may activate the multiple routes of oxidative stress responses in cells. 

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2. Does Cellular Metabolism from Primary Fibroblasts and Oxidative Stress in Blood Differ between Mammals and Birds? The (Lack-thereof) Scaling of Oxidative Stress

   https://doi.org/10.1093/icb/icz017  

   Jimenez, A G; O’Connor, E S; Tobin, K J; Anderson, K N; Winward, J D; Fleming, A; Winner, C; Chinchilli, E; Maya, A; Carlson, K; et al (April 2019, Integrative and Comparative Biology)

   Abstract As part of mitonuclear communication, retrograde and anterograde signaling helps maintain homeostasis under basal conditions. Basal conditions, however, vary across phylogeny. At the cell-level, some mitonuclear retrograde responses can be quantified by measuring the constitutive components of oxidative stress, the balance between reactive oxygen species (ROS) and antioxidants. ROS are metabolic by-products produced by the mitochondria that can damage macromolecules by structurally altering proteins and inducing mutations in DNA, among other processes. To combat accumulating damage, organisms have evolved endogenous antioxidants and can consume exogenous antioxidants to sequester ROS before they cause cellular damage. ROS are also considered to be regulated through a retrograde signaling cascade from the mitochondria to the nucleus. These cellular pathways may have implications at the whole-animal level as well. For example, birds have higher basal metabolic rates, higher blood glucose concentration, and longer lifespans than similar sized mammals, however, the literature is divergent on whether oxidative stress is higher in birds compared with mammals. Herein, we collected literature values for whole-animal metabolism of birds and mammals. Then, we collected cellular metabolic rate data from primary fibroblast cells isolated from birds and mammals and we collected blood from a phylogenetically diverse group of birds and mammals housed at zoos and measured several parameters of oxidative stress. Additionally, we reviewed the literature on basal-level oxidative stress parameters between mammals and birds. We found that mass-specific metabolic rates were higher in birds compared with mammals. Our laboratory results suggest that cellular basal metabolism, total antioxidant capacity, circulating lipid damage, and catalase activity were significantly lower in birds compared with mammals. We found no body-size correlation on cellular metabolism or oxidative stress. We also found that most oxidative stress parameters significantly correlate with increasing age in mammals, but not in birds; and that correlations with reported maximum lifespans show different results compared with correlations with known aged birds. Our literature review revealed that basal levels of oxidative stress measurements for birds were rare, which made it difficult to draw conclusions. 

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3. A Decrease in Serine Levels during Growth Transition Triggers Biofilm Formation in Bacillus subtilis

   https://doi.org/10.1128/JB.00155-19  

   Greenwich, Jennifer; Reverdy, Alicyn; Gozzi, Kevin; Di Cecco, Grace; Tashjian, Tommy; Godoy-Carter, Veronica; Chai, Yunrong; Henkin, Tina M. (August 2019, Journal of Bacteriology)

   ABSTRACT Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number of known signals that trigger biofilm formation do so through the activation of one or more sensory histidine kinases, it was discovered that biofilm activation is also coordinated by sensing intracellular metabolic signals, including serine starvation. Serine starvation causes ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR , which encodes a master repressor for biofilm matrix genes and ultimately triggers biofilm induction. How serine levels change in different growth stages, how B. subtilis regulates intracellular serine levels, and how serine starvation triggers ribosomes to pause on selective serine codons remain unknown. Here, we show that serine levels decrease as cells enter stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine biosynthesis genes decreases upon the transition into stationary phase. The deletion of the gene for a serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm formation, further supporting the idea that serine levels are a critical intracellular signal for biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are decreased in stationary phase compared with exponential phase. However, the three isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two that recognize AGC and AGU serine codons. Our findings provide evidence for a link between serine homeostasis and biofilm development in B. subtilis . IMPORTANCE In Bacillus subtilis , biofilm formation is triggered in response to environmental and cellular signals. It was proposed that serine limitation acts as a proxy for nutrient status and triggers biofilm formation at the onset of biofilm entry through a novel signaling mechanism caused by global ribosome pausing on selective serine codons. In this study, we reveal that serine levels decrease at the biofilm entry due to catabolite control and a serine shunt mechanism. We also show that levels of five serine tRNA isoacceptors are differentially decreased in stationary phase compared with exponential phase; three isoacceptors recognizing UCN serine codons are reduced much more than the two recognizing AGC and AGU codons. This finding indicates a possible mechanism for selective ribosome pausing. 

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4. Fatty Acid Synthesis Knockdown Promotes Biofilm Wrinkling and Inhibits Sporulation in Bacillus subtilis

   https://doi.org/10.1128/mbio.01388-22  

   Arjes, Heidi A.; Gui, Haiwen; Porter, Rachel; Atolia, Esha; Peters, Jason M.; Gross, Carol; Kearns, Daniel B.; Huang, Kerwyn Casey (September 2022, mBio)

   Parsek, Matthew (Ed.)

   ABSTRACT Many bacterial species typically live in complex three-dimensional biofilms, yet much remains unknown about differences in essential processes between nonbiofilm and biofilm lifestyles. Here, we created a CRISPR interference (CRISPRi) library of knockdown strains covering all known essential genes in the biofilm-forming Bacillus subtilis strain NCIB 3610 and investigated growth, biofilm colony wrinkling, and sporulation phenotypes of the knockdown library. First, we showed that gene essentiality is largely conserved between liquid and surface growth and between two media. Second, we quantified biofilm colony wrinkling using a custom image analysis algorithm and found that fatty acid synthesis and DNA gyrase knockdown strains exhibited increased wrinkling independent of biofilm matrix gene expression. Third, we designed a high-throughput screen to quantify sporulation efficiency after essential gene knockdown; we found that partial knockdowns of essential genes remained competent for sporulation in a sporulation-inducing medium, but knockdown of essential genes involved in fatty acid synthesis exhibited reduced sporulation efficiency in LB, a medium with generally lower levels of sporulation. We conclude that a subset of essential genes are particularly important for biofilm structure and sporulation/germination and suggest a previously unappreciated and multifaceted role for fatty acid synthesis in bacterial lifestyles and developmental processes. IMPORTANCE For many bacteria, life typically involves growth in dense, three-dimensional communities called biofilms that contain cells with differentiated roles held together by extracellular matrix. To examine how essential gene function varies between vegetative growth and the developmental states of biofilm formation and sporulation, we created and screened a comprehensive library of strains using CRISPRi to knockdown expression of each essential gene in the biofilm-capable Bacillus subtilis strain 3610. High-throughput assays and computational algorithms identified a subset of essential genes involved in biofilm wrinkling and sporulation and indicated that fatty acid synthesis plays important and multifaceted roles in bacterial development. 

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5. Heterogeneity in respiratory electron transfer and adaptive iron utilization in a bacterial biofilm

   https://doi.org/10.1038/s41467-019-11681-0  

   Qin, Yuxuan; He, Yinghao; She, Qianxuan; Larese-Casanova, Philip; Li, Pinglan; Chai, Yunrong (August 2019, Nature Communications)

   Abstract InBacillus subtilis, robust biofilm formation requires large quantities of ferric iron. Here we show that this process requires preferential production of a siderophore precursor, 2,3-dihydroxybenzoate, instead of the siderophore bacillibactin. A large proportion of iron is associated extracellularly with the biofilm matrix. The biofilms are conductive, with extracellular iron potentially acting as electron acceptor. A relatively small proportion of ferric iron is internalized and boosts production of iron-containing enzymes involved in respiratory electron transfer and establishing strong membrane potential, which is key to biofilm matrix production. Our study highlights metabolic diversity and versatile energy generation strategies withinB. subtilisbiofilms. 

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