More Like this

1. Quorum sensing in Vibrio controls carbon metabolism to optimize growth in changing environmental conditions

   https://doi.org/10.1371/journal.pbio.3002891  

   Simpson, Chelsea A; Celentano, Zach R; Haas, Nicholas W; McKinlay, James B; Nadell, Carey D; van_Kessel, Julia C (November 2024, PLOS Biology)

   Shou, Wenying (Ed.)

   Bacteria sense population density via the cell–cell communication system called quorum sensing (QS). The evolution of QS and its maintenance or loss in mixed bacterial communities is highly relevant to understanding how cell–cell signaling impacts bacterial fitness and competition, particularly under varying environmental conditions such as nutrient availability. We uncovered a phenomenon in whichVibriocells grown in minimal medium optimize expression of the methionine and tetrahydrofolate (THF) synthesis genes via QS. Strains that are genetically “locked” at high cell density grow slowly in minimal glucose media and suppressor mutants accumulate via inactivating mutations inmetF(methylenetetrahydrofolate reductase) andluxR(the master QS transcriptional regulator). In mixed cultures, QS mutant strains initially coexist with wild-type, but as glucose is depleted, wild-type outcompetes the QS mutants. Thus, QS regulation of methionine/THF synthesis is a fitness benefit that links nutrient availability and cell density, preventing accumulation of QS-defective mutants. 

   more » « less
2. Machine Learning Guided Rational Design of a Non‐Heme Iron‐Based Lysine Dioxygenase Improves its Total Turnover Number

   https://doi.org/10.1002/cbic.202400495  

   Hunter_Wilson, R; Diaz, Daniel J; Damodaran, Anoop R; Bhagi‐Damodaran, Ambika (December 2024, ChemBioChem)

   Abstract Highly selective C−H functionalization remains an ongoing challenge in organic synthetic methodologies. Biocatalysts are robust tools for achieving these difficult chemical transformations. Biocatalyst engineering has often required directed evolution or structure‐based rational design campaigns to improve their activities. In recent years, machine learning has been integrated into these workflows to improve the discovery of beneficial enzyme variants. In this work, we combine a structure‐based self‐supervised machine learning framework, MutComputeX, with classical molecular dynamics simulations to down select mutations for rational design of a non‐heme iron‐dependent lysine dioxygenase, LDO. This approach consistently resulted in functional LDO mutants and circumvents the need for extensive study of mutational activity before‐hand. Our rationally designed single mutants purified with up to 2‐fold higher expression yields than WT and displayed higher total turnover numbers (TTN). Combining five such single mutations into a pentamutant variant, LPNYI LDO, leads to a 40 % improvement in the TTN (218±3) as compared to WT LDO (TTN=160±2). Overall, this work offers a low‐barrier approach for those seeking to synergize machine learning algorithms with pre‐existing protein engineering strategies. 

   more » « less
3. The non-canonical Wnt receptor Ror2 is required for cartilage cell polarity and morphogenesis of the craniofacial skeleton in zebrafish

   https://doi.org/10.1242/dev.201273  

   Dranow, Daniel B.; Le Pabic, Pierre; Schilling, Thomas F. (April 2023, Development)

   ABSTRACT Non-canonical/β-catenin-independent Wnt signaling plays crucial roles in tissue/cell polarity in epithelia, but its functions have been less well studied in mesenchymal tissues, such as the skeleton. Mutations in non-canonical Wnt signaling pathway genes cause human skeletal diseases such as Robinow syndrome and Brachydactyly Type B1, which disrupt bone growth throughout the endochondral skeleton. Ror2 is one of several non-canonical Wnt receptor/co-receptors. Here, we show that ror2−/− mutant zebrafish have craniofacial skeletal defects, including disruptions of chondrocyte polarity. ror1−/− mutants appear to be phenotypically wild type, but loss of both ror1 and ror2 leads to more severe cartilage defects, indicating partial redundancy. Skeletal defects in ror1/2 double mutants resemble those of wnt5b−/− mutants, suggesting that Wnt5b is the primary Ror ligand in zebrafish. Surprisingly, the proline-rich domain of Ror2, but not its kinase domain, is required to rescue its function in mosaic transgenic experiments in ror2−/− mutants. These results suggest that endochondral bone defects in ROR-related human syndromes reflect defects in cartilage polarity and morphogenesis. 

   more » « less
4. A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments

   https://doi.org/10.1038/s41467-022-28045-w  

   Zhao, Boyang; Rao, Yiyun; Leighow, Scott; O’Brien, Edward P.; Gilbert, Luke; Pritchard, Justin R. (February 2022, Nature Communications)

   Abstract A genetic knockout can be lethal to one human cell type while increasing growth rate in another. This context specificity confounds genetic analysis and prevents reproducible genome engineering. Genome-wide CRISPR compendia across most common human cell lines offer the largest opportunity to understand the biology of cell specificity. The prevailing viewpoint, synthetic lethality, occurs when a genetic alteration creates a unique CRISPR dependency. Here, we use machine learning for an unbiased investigation of cell type specificity. Quantifying model accuracy, we find that most cell type specific phenotypes are predicted by the function of related genes of wild-type sequence, not synthetic lethal relationships. These models then identify unexpected sets of 100-300 genes where reduced CRISPR measurements can produce genome-scale loss-of-function predictions across >18,000 genes. Thus, it is possible to reduce in vitro CRISPR libraries by orders of magnitude—with some information loss—when we remove redundant genes and not redundant sgRNAs. 

   more » « less
5. Recent Advancement in Elimination Strategies and Potential Rejuvenation Targets of Senescence

   https://doi.org/10.1002/adbi.202300461  

   Kureel, Sanjay Kumar; Blair, Brandon; Sheetz, Michael P. (October 2023, Advanced Biology)

   Cellular senescence is a state of exiting the cell cycle, resisting apoptosis, and changing phenotype. Senescent cells (SCs) can be identified by large, distorted morphology and irreversible inability to replicate. In early development, senescence has beneficial roles like tissue patterning and wound healing, where SCs are cleared by the immune system. However, there is a steep rise in SC number as organisms age. The issue with SC accumulation stems from the loss of cellular function, alterations of the microenvironment, and secretions of pro‐inflammatory molecules, consisting of cytokines, chemokines, matrix metalloproteinases (MMPs), interleukins, and extracellular matrix (ECM)‐associated molecules. This secreted cocktail is referred to as the senescence‐associated secretory phenotype (SASP), a hallmark of cellular senescence. The SASP promotes inflammation and displays a bystander effect where paracrine signaling turns proliferating cells into senescent states. To alleviate age‐associated diseases, researchers have developed novel methods and techniques to selectively eliminate SCs in aged individuals. Although studies demonstrated that selectively killing SCs improves age‐related disorders, there are drawbacks to SC removal. Considering favorable aspects of senescence in the body, this paper reviews recent advancements in elimination strategies and potential rejuvenation targets of senescence to bring researchers in the field up to date. 

   more » « less