Biology subjects

Devlin, K. L.

Publications and source records attributed to Devlin, K. L..

7 recordsLinked to original sources

bioRxiv2026

Carbon starvation of Mycobacterium abscessus induces a non-replicating state with extensive proteomic remodeling

Mycobacterium abscessus (Mab) is an opportunistic pathogen that can cause chronic, debilitating lung disease. Mab is intrinsically resistant to most antibiotics, making Mab infections challenging to manage and frequently incurable. During infection, Mab adapts to survive various stresses, including hypoxia and nutrient starvation. In vitro, these conditions drive Mab into a drug-tolerant, non-replicating state. Changes in the Mab proteome that result from entering a non-replicating state have been minimally described despite the clinical importance of this physiological state. Using Mab reference strain ATCC 19977, we collected proteomic data comparing replicating to non-replicating states using a carbon starvation (CS) model of persistence. We identified 2251 proteins overall (46% proteome coverage), and 17% of these proteins were found in only one of the two conditions. A third of identified proteins were significantly changed in abundance, indicating an extensive proteomic response to CS. The response regulator DosR and many DosRS responsive proteins were significantly more abundant under CS, suggesting that the DosRS stress response regulator plays a key role in CS-induced Mab persistence. Many aspects of cell wall biosynthesis were changed, including changes in glycolipid abundance under CS. Proteins involved in other key cellular processes such as secretion, oxidative phosphorylation, and nutrient metabolism were altered under CS. The proteomic analysis presented provides new insights and clarity into how the Mab proteome is regulated during non-replicating persistence, a key consideration for understanding Mab pathophysiology.

microbiology↗

bioRxiv2025

Identification of senescence-associated drivers of tumour growth and progression using a novel microarray platform

Senescence and the senescence associated secretory phenotype (SASP) are implicated in promoting early tumorigenesis but due to the complexity of SASP it has been difficult to identify the responsible factors. We used canonical SASP factors on our microenvironment microarray (MEMA) platform to systematically identify SASP-associated drivers of tumorigenesis in breast and lung cancer cells. We found multiple SASP factors enhanced the proliferation and overall cell numbers for both lung and breast cells grown on the MEMA, and that there was significant overlap in SASP-associated growth-promoting factors between the two different cell types. We validated the ability of several factors, including IL-6, TGF-{beta} and EGF, to drive growth in in vitro assays. Interestingly, these factors were effective in driving growth and survival in cells that were altered (either immortalized or fully transformed) but not in normal cells and impacted breast cells differently depending on the age of the patient. RNAseq identified upregulation of wound-healing and stem-cell programs in SASP factor-treated cells. Many of these same SASP factors were present in conditioned media collected from senescent cells, which enhanced the growth of both lung and breast cancer cells, and inhibitors of the specific SASP factors partially reduced growth. Similarly, targeted inhibition of EGF partially reduced lung tumour growth in xenografts when senescent but not normal fibroblasts were co-implanted. Our findings have identified core SASP drivers of tumorigenesis and suggest that effective tumorigenesis driven by SASP is multifactorial and requires alterations in the target cells to achieve maximal response.

cancer biology↗

bioRxiv2025

Chemoproteomic elucidation of β-lactam drug targets in Mycobacterium abscessus

The pathogen Mycobacterium abscessus (Mab) can cause severe and difficult to treat chronic lung infections. Despite the rising incidence and clinical concern of Mab infections, treatment options are limited and often ineffective. Treatment is complicated by Mabs ability to persist in a non-replicative, drug-resistant state. Several {beta}-lactam antibiotics are potently bactericidal against Mab but are underutilized because their molecular mechanisms of action against Mab are incompletely understood. In the current study, we used {beta}-lactam-derived activity-based probes and chemoproteomics to report the first comprehensive list of enzymes in Mab targeted by {beta}-lactams. We compared {beta}-lactam targets across two Mab subspecies in actively replicating and non-replicative cultures, using a new carbon starvation model of persistence. We identified 17 targets that were active in every condition tested, seven of which were previously unknown to bind {beta}-lactams. Lastly, we characterized the {beta}-lactamase activity and {beta}-lactam inhibition profiles of nine Mab enzymes, demonstrating that imipenem inhibits these targets more effectively than cefoxitin. These findings provide clarity on the mechanisms of action of clinically relevant {beta}-lactams in Mab, a crucial step toward fully realizing their potential for treating infections caused by this opportunistic pathogen.

microbiology↗

bioRxiv2025

Comprehensive identification of β-lactam antibiotic polypharmacology in Mycobacterium tuberculosis

Infections with Mycobacterium tuberculosis (Mtb) cause tuberculosis (TB), which requires at least six months of treatment with multiple antibiotics. There is emergent interest in using {beta}-lactam antibiotics to improve treatment outcomes for patients. These drugs target cell wall biosynthesis, but a comprehensive list of enzymes inhibited by {beta}-lactams in Mtb is lacking. In the current study, we sought to identify and characterize Mtb enzymes inhibited by {beta}-lactam antibiotics using physiological conditions representative of both acute and chronic TB disease. We used new activity-based probes based on the {beta}-lactam antibiotic meropenem due to its approval by the World Health Organization for TB treatment. Activity-based probes label enzymes based on both substrate specificity and catalytic mechanism, enabling precise identification of drug targets. We identified previously undiscovered targets of meropenem in addition to known cell wall biosynthetic enzymes. We validated {beta}-lactam binding and hydrolysis for six newly identified targets: Rv1723, Rv2257c, Rv0309, DapE (Rv1202), MurI (Rv1338), and LipD (Rv1923). Our results demonstrate that there are at least 30 enzymes in Mtb vulnerable to inhibition by meropenem. This is many more {beta}-lactam targets than historically described, suggesting that efficacy in Mtb is a direct result of polypharmacology.

biochemistry↗

bioRxiv2025

Combinations comprising dual β-lactams and a β-lactamase inhibitor achieve optimal synergistic inhibition of Mycobacterium abscessus growth

The historical model, which posits that {beta}-lactams inhibit bacterial growth while {beta}-lactamase inhibitors (BLIs) merely protect {beta}-lactams from enzymatic degradation, fails to fully explain their activity against Mycobacterium abscessus (Mab). This study demonstrates that synergistic effects extend beyond the traditional one {beta}-lactam+one BLI paradigm, refuting the oversimplified mechanistic framework. First, {beta}-lactam-based BLIs such as clavulanic acid, sulbactam, and tazobactam exhibit intrinsic antibacterial activity against Mab. These agents synergized not only with {beta}-lactams but also with one another, undermining their historical classification as mere {beta}-lactamase inhibitors. The data indicate that their activity is not limited to inhibiting {beta}-lactamases but extends to directly targeting critical bacterial processes. Second, dual {beta}-lactam combinations exhibit synergism against Mab even in the absence of BLIs. For example, despite being rapidly hydrolyzed by the native {beta}-lactamase BlaMab, amoxicillin demonstrates strong synergism with {beta}-lactams such as imipenem or ceftaroline. This suggests that the second {beta}-lactam either acts as a functional BLI surrogate or targets complementary pathways. Supporting this, experiments using penicillin- and carbapenem-based probes revealed that {beta}-lactams bind to multiple Mab proteins simultaneously, reinforcing the idea that their synergy arises from targeting complementary essential proteins. Finally, triple combinations comprising dual {beta}-lactam and one BLI, such as amoxicillin + ceftaroline + avibactam, achieved very high synergy, underscoring the complementary roles of dual {beta}-lactams and BLIs. The evidence in this study necessitates a revised model that can more accurately explain the activities of {beta}-lactams and BLIs and underscores the potential for optimizing {beta}-lactam/BLI regimens against Mab. IMPORTANCEThis research challenges old assumptions about how antibiotics fight bacteria, particularly Mycobacterium abscessus (Mab), a tough-to-treat infection. Traditionally, {beta}-lactam antibiotics were thought to stop bacterial growth, while {beta}-lactamase inhibitors (BLIs) just protected them from breakdown. However, this study reveals that BLIs like clavulanic acid can work together with another BLI or {beta}-lactam antibiotics for stronger effects. Surprisingly, even combinations comprising two BLIs can be highly effective, showing they target multiple critical bacterial processes simultaneously. Triple combinations--two {beta}-lactams and one BLI--proved especially powerful. These findings overturn outdated ideas, offering a smarter way to use these drugs to combat difficult infections and save lives.

microbiology↗

bioRxiv2024

Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious-disease related deaths worldwide. TB infections present as a spectrum from active to latent disease. In the human host, Mtb faces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions, Mtb can enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. These dormant Mtb pose a major challenge to curing infections and eradicating TB globally. In the current study, we subjected Mtb to carbon starvation (CS), a culture condition that induces growth stasis and mimics nutrient-starved conditions associated with dormancy in vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or upregulated in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically-distinct state of stasis compared to hypoxia in Mtb.

microbiology↗

bioRxiv2022

A set of orthogonal versatile interacting peptide tags for imaging cellular proteins

Genetic tags are transformative tools for investigating the function, localization, and interactions of cellular proteins. Most studies today are reliant on selective labeling of more than one protein to obtain comprehensive information on a proteins behavior in situ. Some proteins can be analyzed by fusion to protein tag, such as green fluorescent protein, HaloTag, or SNAP-Tag. Other proteins benefit from labeling via small peptide tags, such as the recently reported versatile interacting peptide (VIP) tags. VIP tags enable observations of protein localization and trafficking with bright fluorophores or nanoparticles. Here we expand the VIP toolkit by presenting two new tags: TinyVIPER and PunyVIPER. These two tags were designed for use with MiniVIPER for labeling up to three distinct proteins at once in living cells. Labeling is mediated by the formation of a high affinity, biocompatible heterodimeric coiled coil. Each tag was validated by fluorescence microscopy, including observation of transferrin receptor 1 trafficking in live cells. We verified that labeling via each tag is highly specific, with no cross-reactivity between the three VIP tags under cellular conditions. Lastly, the self-sorting tags were used for simultaneous labeling of three protein targets (i.e., TOMM20, histone 2B, and actin), highlighting their utility for multicolor microscopy. MiniVIPER, TinyVIPER, and PunyVIPER are small and robust peptide tags for selective labeling of cellular proteins.

biochemistry↗