Biology subjects

Malarney, K. P.

Publications and source records attributed to Malarney, K. P..

5 recordsLinked to original sources

bioRxiv2026

A class of metallohydrolases expands bile salt hydrolase activity in the gut

Abstract/Summary ParagraphBile acids are steroidal metabolites produced by host and microbial metabolism that shape gut microbiome ecology and influence host physiology1,2. Bile acid structural diversification requires gut microbial bile salt hydrolase (BSH) activities, which cleave the amide bond of liver-derived bile acid amidates (BAAs)3. Beyond this gatekeeping metabolic function, BSHs expand the bile acid pool via their amine N-acyltransferase activity to produce numerous microbially derived BAAs that signal via host receptors and are further metabolized4,5. To date, all BSH activity has been attributed to a family of N-terminal nucleophile (Ntn) cysteine hydrolases. However, numerous gut anaerobic bacteria possess BSH activity but do not encode bsh genes from the Ntn family. Here, we describe a previously unknown class of metal-dependent BSHs (mBSHs) broadly distributed in the gut microbiome. These metalloenzymes have a distinct active site architecture from the canonical Ntn superfamily of cysteine hydolase BSHs (cBSHs) and are selective for taurine-conjugated BAAs. The discovery of this heretofore unappreciated class of BSHs overturns the paradigm that this important, conserved biochemical activity of the gut microbiota is provided exclusively by canonical cysteine hydrolases, greatly expands the known landscape of bile acid metabolism, and reveals a previously unrecognized link connecting host-microbiota bile acid co-metabolism with microbial taurine utilization pathways.

biochemistry↗

bioRxiv2025

Chemical proteomics reveals regulation of bile salt hydrolases via oxidative post-translational modifications

The gut microbiome is the vast, diverse ecosystem of microorganisms that inhabits the human intestines and provides numerous essential functions for the host. One such key role is the metabolism of primary bile acids that are biosynthesized in the host liver into a plethora of secondary bile acids produced by gut bacteria. These metabolites serve as both antimicrobial and chemical signaling agents within the host. The critical microbial enzyme that plays a gatekeeping role in secondary bile acid metabolism is bile salt hydrolase (BSH), a cysteine hydrolase that is primarily known for its deconjugating and reconjugating activities on bile acid substrates. Despite the crucial nature of these biotransformations, regulation of BSH activity is not well understood. Here, we found that the catalytic cysteine 2 (Cys2) within the BSH active site exists in multiple sulfur oxidation states including sulfenic acid (Cys-SOH). Importantly, we show this reversible oxidative post-translational modification (oxPTM) ablates BSH catalytic activity. We have leveraged this discovery to develop a chemoproteomic platform featuring a sulfenic acid-reactive bile acid probe to profile BSH Cys2 oxPTMs throughout the gut microbiome. Our results reveal that though most gut microbiota-associated BSHs exist in the active Cys2-SH state, some are preferentially and reversibly inactivated in the Cys2-SOH state. This reversible oxidation of Cys2 may serve as a general mechanism to regulate BSH activity in vivo in response to a changing physiological environment.

biochemistry↗

bioRxiv2024

Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases

The gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the hosts overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.

microbiology↗

bioRxiv2023

Electrostatic Interactions Dictate Bile Salt Hydrolase Substrate Preference

The human intestines are colonized by trillions of microbes, comprising the gut microbiota, which produce diverse small molecule metabolites and modify host metabolites, such as bile acids, that regulate host physiology. Biosynthesized in the liver, bile acids are conjugated with glycine or taurine and secreted into the intestines, where gut microbial bile salt hydrolases (BSHs) deconjugate the amino acid to produce unconjugated bile acids that serve as precursors for secondary bile acid metabolites. Among these include a recently discovered class of microbially-conjugated bile acids (MCBAs), wherein alternative amino acids are conjugated onto bile acids. To elucidate the metabolic potential of MCBAs, we performed detailed kinetic studies to investigate the preference of BSHs for host- and microbially-conjugated bile acids. We identified a BSH that exhibits positive cooperativity uniquely for MCBAs containing an aromatic sidechain. Further molecular modeling and phylogenetic analyses indicated that BSH preference for aromatic MCBAs is due to a substrate-specific cation-{rho}{varepsilon} interaction and is predicted to be widespread among human gut microbial BSHs. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/559308v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@11d6764org.highwire.dtl.DTLVardef@16efed0org.highwire.dtl.DTLVardef@1b13a7org.highwire.dtl.DTLVardef@1a7682e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2019

Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds

Metals are essential for the molecular machineries of life, and microbes have evolved a variety of small molecules to acquire, compete for, and utilize metals. Systematic methods for the discovery of metal-small molecule complexes from biological samples are limited. Here we describe a two-step native electrospray ionization mass spectrometry method, in which double-barrel post-column metal-infusion and pH adjustment is combined with ion identity molecular networking, a rule-based informatics workflow. This method can be used to identify metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion features with the same chromatographic profiles. As this native metal metabolomics approach can be easily implemented on any liquid chromatography-based mass spectrometry system, this method has the potential to become a key strategy for elucidating and understanding the role of metal-binding molecules in biology.

biochemistry↗