Biology subjects

Silpe, J. E.

Publications and source records attributed to Silpe, J. E..

8 recordsLinked to original sources

bioRxiv2026

A pectin-based formulation protects milk fat globule membranes in stored human milk

During household storage, expressed human milk can develop odor and flavor changes that trigger infant refusal and lead caregivers to discard their saved milk supply. We show that typical refrigeration and freezing conditions disrupt the milk fat globule membrane (MFGM), exposing milk lipids to lipases that catalyze hydrolysis and oxidation. A pectin-based formulation (PBF) maintains MFGM integrity during storage and following lipase challenge, suppressing production of glycerol, free fatty acid, and oxylipin byproducts without broadly affecting milk macronutrients, the proteome, and culturable microbial burden. Across an independent cohort of lactating individuals, lipase activity varied but tracked with maternal milk lipase gene expression, implicating endogenous lipolysis in stored-milk deterioration. In a blinded olfactory panel, PBF-treated, lipase-challenged milk smelled more like fresh milk than untreated controls. Together, these findings show that stabilizing the MFGM can protect stored human milk from lipase-driven deterioration, preserve sensory quality, and support use for infant feeding.

biochemistry↗

bioRxiv2024

Food-Derived Compounds Extend the Shelf-Life of Frozen Human Milk

Breastmilk is known to provide optimal nutrition for infant growth and development. A cross-sectional analysis of nationally representative US data from 2016 to 2021 revealed that >90% of lactating mothers reported using breast pumps to express milk.1 We conducted a survey of n = 1,049 lactating or recently lactating individuals from a US nationally representative population to explore breastmilk storage practices among this group. The data revealed that 83% of respondents store breastmilk in their homes, with 68% using freezers to do so for >1 month. The lowest available temperature in most household freezers is -20 {degrees}C, a temperature that is inadequate to maintain human milks emulsified structure, leading to separation, degradation of fats, loss of key vitamins, and changes in palatability. We developed a first-of-its-kind high-throughput screening platform to identify food-derived compounds and combinations of compounds that, when added to human breastmilk, preserve fat content, retain antioxidant capacity, and reduce production of rancid-associated free fatty acids during extended freezer storage. These formulations represent leads for the development of safe and affordable frozen breastmilk shelf-life extenders for easy at-home use to increase the longevity of stored breastmilk.

molecular biology↗

bioRxiv2022

Natural and synthetic inhibitors of a phage-encoded quorum-sensing receptor affect phage-host dynamics in mixed bacterial communities

Viruses that infect bacteria, called phages, shape the composition of bacterial communities and are important drivers of bacterial evolution. We recently showed that temperate phages, when residing in bacteria (i.e., prophages), are capable of manipulating the bacterial cell-to-cell communication process called quorum sensing (QS). QS relies on the production, release, and population-wide detection of signaling molecules called autoinducers (AI). Gram-negative bacteria commonly employ N-acyl homoserine lactones (HSL) as AIs that are detected by LuxR-type QS receptors. Phage ARM81ld is a prophage of the aquatic bacterium Aeromonas sp. ARM81, and it encodes a homolog of a bacterial LuxR, called LuxRARM81ld. LuxRARM81ld detects host Aeromonas-produced C4-HSL, and in response, activates the phage lytic program, triggering death of its host and release of viral particles. Here, we show that phage LuxRARM81ld activity is modulated by non-cognate HSL ligands and by a synthetic small molecule inhibitor. We determine that HSLs with acyl chain lengths equal to or longer than C8 antagonize LuxRARM81ld. For example, the C8-HSL AI produced by Vibrio fischeri that co-exists with Aeromonads in marine environments, binds to and inhibits LuxRARM81ld, and consequently, protects the host from lysis. Co-culture of V. fischeri with the Aeromonas sp. ARM81 lysogen suppresses phage ARM81ld virion production. We propose that the cell density and species composition of the bacterial community could determine outcomes in bacterial-phage partnerships. SIGNIFICANCEBacteria use the cell-to-cell communication process called quorum sensing to orchestrate group behaviors. Quorum sensing relies on extracellular molecules called autoinducers. Bacteria-infecting viruses (phages) can possess homologs of bacterial quorum-sensing receptors that detect autoinducers to control lysis-lysogeny transitions. We show that a phage LuxR-type quorum-sensing receptor is activated by the autoinducer produced by its host bacterium and is inhibited by non-cognate autoinducers made by bacteria that naturally co-exist with the phages host and by a synthetic quorum-sensing inhibitor. Our findings demonstrate that microbial community composition, mediated through quorum-sensing-communication, influences phage lysis-lysogeny transitions. These results deepen the understanding of host-phage interactions in communities and could inspire new phage-specific, quorum-sensing interventions.

microbiology↗

bioRxiv2022

Small protein modules dictate prophage fates during polylysogeny

DNA-damaging agents are the pervasive inducers of temperate phages in model bacteria. However, most bacteria in the biosphere are predicted to carry multiple prophages, a state called polylysogeny, making it unclear how co-residing prophages compete for host cell resources if they all respond to the identical trigger. We discover regulatory modules encoded on phage genomes that control prophage induction independently of the DNA damage cue. Genes specifying these pathways exist in linear plasmid-like phages at sites essential for phage propagation. The modules lack sequence similarity but display a shared regulatory logic of a transcription factor that activates expression of a neighboring gene encoding a small protein. The small protein inactivates the master repressor of lysis, leading to prophage induction. In some phages, the regulatory unit detects sensory information including quorum-sensing autoinducers, making lysis host-cell-density dependent. Exposure of the polylysogens studied here to different induction scenarios reveals that mixed phage populations emerge following DNA damage, however, induction through the SOS-independent module drives near-exclusive production of the phage sensitive to that specific cue. Considering the lack of potent DNA-damaging agents in natural habitats, we propose that additional phage-encoded sensory pathways that drive lysis play fundamental roles in phage-host biology and inter-prophage competition.

microbiology↗

bioRxiv2021

The gut bacterial natural product colibactin triggers induction of latent viruses in diverse bacteria

Colibactin is a chemically unstable small molecule genotoxin produced by multiple different bacteria, including members of the human gut microbiome.1,2 While the biological activity of colibactin has been extensively investigated in mammalian systems,3 little is known about its effects on other microorganisms. Here, we discover that colibactin targets bacteria carrying prophages, inducing lytic development via the bacterial SOS response. DNA, added exogenously, protects bacteria from colibactin, as does expressing a colibactin resistance protein (ClbS) in non-colibactin-producing cells. The prophage-inducing effects we observe apply broadly across taxonomically diverse phage-bacteria systems. Finally, we identify bacteria that possess colibactin resistance genes but lack colibactin biosynthetic genes. Many of these bacteria are infected with predicted prophages, and we show that the expression of their ClbS homologs provides immunity from colibactin-triggered induction. Our study reveals a mechanism by which colibactin production could impact microbiomes and highlights an underappreciated role for microbial natural products in influencing population-level events such as phage outbreaks.

microbiology↗

bioRxiv2019

Mechanism underlying autoinducer recognition in the Vibrio cholerae DPO-VqmA quorum-sensing pathway

Quorum sensing is a bacterial communication process whereby bacteria produce, release and detect the accumulation of extracellular signaling molecules called autoinducers to coordinate collective behaviors. In Vibrio cholerae, the quorum-sensing autoinducer, DPO (3,5-dimethyl-pyrazin-2-ol), binds the receptor-transcription factor, VqmA. In response, the DPO-VqmA complex activates transcription of the vqmR gene encoding the VqmR small RNA. VqmR represses genes required for biofilm formation and virulence factor production. Here, we show that VqmA has DPO-dependent and DPO-independent activity. We solved the DPO-VqmA crystal structure and compared it to existing structures to understand the conformational changes the protein undergoes upon DNA binding. Analysis of DPO analogs reveals that a hydroxyl or carbonyl group at the 2 position is critical for binding. The proposed DPO precursor, a linear molecule, Ala-AA (N-alanyl-aminoacetone), also binds and activates VqmA. DPO and Ala-AA occupy the same binding site as judged by site-directed mutagenesis and competitive ligand binding analyses.

microbiology↗

bioRxiv2019

Separating Functions of the Phage-Encoded Quorum-Sensing-Activated Antirepressor Qtip

Quorum sensing is a process of chemical communication that bacteria use to track cell density and coordinate gene expression across a population. Bacteria-infecting viruses, called phages, can encode quorum-sensing components that enable them to integrate host cell density information into the lysis-lysogeny decision. Vibriophage VP882 is one such phage, and activation of its quorum-sensing pathway leads to the production of an antirepressor called Qtip. Qtip interferes with the prophage repressor (cIVP882), leading to host-cell lysis. Here, we show that Qtip interacts with the N-terminus of cIVP882, inhibiting both cIVP882 DNA-binding and cIVP882 autoproteolysis. Qtip also sequesters cIVP882, localizing it to the poles. Qtip can localize to the poles independently of cIVP882. Alanine-scanning mutagenesis of Qtip shows that its localization and interference with cIVP882 activities are separable. Comparison of Qtip to a canonical phage antirepressor reveals that, despite both proteins interacting with their partner repressors, only Qtip drives polar localization.

microbiology↗

bioRxiv2019

Phage-Encoded LuxR-Type Receptors Responsive to Host-Produced Bacterial Quorum-Sensing Autoinducers

Quorum sensing (QS) is a process of cell-to-cell communication that bacteria use to orchestrate collective behaviors. QS relies on the cell-density-dependent production, accumulation, and receptor-mediated detection of extracellular signaling molecules called autoinducers (AIs). Gram-negative bacteria commonly use N-acyl homoserine lactones (AHLs) as their AIs and they are detected by LuxR-type receptors. Often, LuxR-type receptors are insoluble when not bound to a cognate AI. In this report, we show that LuxR-type receptors are encoded on phage genomes and, in the cases we tested, the phage LuxR-type receptors bind to and are solubilized specifically by the AHL AI produced by the host bacterium. We do not yet know the viral activities that are controlled by these phage QS receptors, however, our observations, coupled with recent reports, suggest that their occurrence is more widespread than previously appreciated. Using receptor-mediated detection of QS AIs could enable phages to garner information concerning the population density status of their bacterial hosts. We speculate that such information can be exploited by phages to optimize the timing of execution of particular steps in viral infection.\n\nImportanceBacteria communicate with chemical signal molecules to regulate group behaviors in a process called quorum sensing (QS). In this report, we find that genes encoding receptors for Gram-negative bacterial QS communication molecules are present on genomes of viruses that infect these bacteria. These viruses are called phages. We show that two phage-encoded receptors, like their bacterial counterparts, bind to the communication molecule produced by the host bacterium, suggesting that phages can \"listen in\" on their bacterial hosts. Interfering with bacterial QS and using phages to kill pathogenic bacteria represent attractive possibilities for development of new antimicrobials to combat pathogens that are resistant to traditional antibiotics. Our findings of interactions between phages and QS bacteria need consideration as new antimicrobial therapies are developed.

microbiology↗