Biology subjects

Dassama, L. M. K.

Publications and source records attributed to Dassama, L. M. K..

6 recordsLinked to original sources

bioRxiv2026

A cofactor-promiscuous HMGR from the Lyme disease pathogen illuminates diversity in bacterial isoprenoid biosynthesis

The Lyme disease pathogen Borrelia burgdorferi contains a highly reduced genome lacking many primary metabolic pathways. However, B. burgdorferi retains the mevalonate pathway that synthesizes isopentenyl pyrophosphate (IPP), the precursor to the peptidoglycan carrier lipid. While the mevalonate pathway and the enzyme that catalyzes its rate-limiting step (3-hydroxy-3-methyl glutaryl coenzyme A reductase, HMGR) are well studied in vertebrates, little is known about the pathway in B. burgdorferi and many pathogenic bacteria. In this work, we reveal that HMGR is a critical metabolic enzyme in B. burgdorferi. We demonstrate that loss of HMGR causes morphological defects and muted de novo synthesis of peptidoglycan; these defects are ameliorated by exogenous mevalonate and IPP. Biochemical characterization unveiled the HMGR as a highly unusual cofactor-promiscuous oxidoreductase that functions with both nicotinamide cofactors. Bioinformatics and biochemical characterization uncovered examples of similarly promiscuous HMGRs and revealed a previously unrecognized evolutionary link to cofactor choice. Moreover, structures of the enzyme reveal a highly divergent active site architecture. Together, these findings firmly establish HMGR as an opportunity target for the development of antibacterials for a diderm pathogen while highlighting cofactor promiscuity as an evolutionary acquired feature in HMGRs.

biochemistry↗

bioRxiv2026

The NanoBridge system for targeted post-translational modification of challenging proteins

The ability to edit posttranslational modifications (PTMs) of endogenous proteins within cells is essential for precisely delineating the biological roles of PTMs and for developing targeted therapeutics. While the paradigm of chemically induced proximity (CIP) has advanced this field by enabling the recruitment of PTM enzymes to the proximity of proteins of interest (POIs), CIP requires small-molecule binders that are difficult to obtain for proteins without well-defined binding pockets. In principle, the use of biomolecular ligands that target disordered proteins should overcome this limitation. In this work, we developed the NanoBridge as a modular and generalizable platform to enable PTM editing of challenging POIs in live cells. The NanoBridge employs biologic binders to transiently direct the small protein tag FKBP12F36V to unmodified target proteins, thereby enabling multiplex PTM editing upon use of heterobifunctional small molecules that recruit endogenous PTM enzymes. Compared with existing approaches, the NanoBridge offers greater flexibility to induce multiple types of PTMs on the same POI while providing precise temporal control and avoiding the introduction of exogenous PTM writers. Using eight protein binders targeting three structurally diverse and largely unstructured proteins - BCL11A (a hemoglobin regulator), KRAS (a cancer driver), and p53 (a tumor suppressor) - the NanoBridge mediated targeted degradation, phosphorylation, and acetylation in a rapid, reversible, and temporally controlled manner. As such, the NanoBridge represents a versatile strategy for the targeted modulation of endogenous proteins, particularly those lacking accessible small molecule ligands, and presents new opportunities for investigating the physiology of PTMs on challenging proteins.

biochemistry↗

bioRxiv2026

A lipid compendium of a metabolically compromised bacterium provides insights into lipid acquisition, biosynthesis, and metabolism

The Lyme disease agent Borrelia burgdorferi belongs to a class of metabolically compromised bacteria that cannot survive without host-derived lipids. Survival of the agent in tick and vertebrate hosts requires substantial nutrient acquisition and potential cell envelope remodeling. While prior studies identified cholesterol, cholesterol glycolipids, and phosphatidylcholines as membrane lipids in B. burgdorferi, the identity of many other membrane lipids, their origin, and their physiological relevance remain unknown. Here, we used a suite of untargeted and targeted high-resolution mass spectrometry methods to reveal a complex lipid profile of the pathogen and to identify the origin of its lipids. The analysis detected more than 500 lipids in B. burgdorferi, the majority of which are sourced from the environment. However, the bacterium selectively accumulates certain lipids while excluding others, suggesting discriminatory uptake. These include cholesteryl esters and triglycerides that are organized in foci within the pathogen. Intriguingly, the pathogen also synthesizes predominantly eukaryotic lipids such as the lysosomal bis(monoacylglycerol)phosphate and the plant glycolipid sulfoquinovosyl diacylglycerol (SQDG). The biosynthesis of the latter is carried out by enzymes that exhibit structural homology to plant oxidoreductases and galactosyltransferases, yet their closest orthologs are found in bacteria. This hints that the capability of SQDG synthesis is more widespread in spirochaetes and other bacteria. Together, the comprehensive lipid profiling we report here uncovers novel aspects of the physiology of the metabolically challenged B. burgdorferi and highlights lipid acquisition and synthesis pathways as potentially critical for pathogen survival.

biochemistry↗

bioRxiv2024

Rapid proteome-wide prediction of lipid-interacting proteins through ligand-guided structural genomics

Lipids are essential metabolites that play critical roles in multiple cellular pathways. Like many primary metabolites, mutations that disrupt lipid synthesis can be lethal. Proteins involved in lipid synthesis, trafficking, and modification, are targets for therapeutic intervention in infectious disease and metabolic disorders. The ability to rapidly detect these proteins can accelerate their evaluation as targets for deranged lipid pathologies. However, it remains challenging to identify lipid binding motifs in proteins because the rules that govern protein engagement with specific lipids are poorly understood. As such, new bioinformatic tools that reveal conserved features in lipid binding proteins are necessary. Here, we present Structure-based Lipid-interacting Pocket Predictor (SLiPP), an algorithm that leverages machine learning to detect protein cavities capable of binding to lipids in protein structures. SLiPP uses a Random Forest classifier and operates at scale to predict lipid binding pockets with an accuracy of 96.8% and an F1 score of 86.9% when testing against a set of 8,380 pockets embedded within proteins. Our analyses revealed that the algorithm relies on hydrophobicity-related features to distinguish lipid binding pockets from those that bind to other ligands. SLiPP is fast and does not require substantial computational resources. Use of the algorithm to detect lipid binding proteins in various proteomes produced hits annotated or verified as bona fide lipid binding proteins. Additionally, SLiPP identified many new putative lipid binders in well studied proteomes. Because of its ability to identify novel lipid binding proteins, SLiPP can spur the discovery of new and "targetable" lipid-sensitive pathways.

bioinformatics↗

bioRxiv2022

A cell-permeant nanobody-based degrader that induces fetal hemoglobin

Proximity-based strategies to degrade proteins have enormous therapeutic potential in medicine, but the technologies are limited to proteins for which small molecule ligands exist. The identification of such ligands for therapeutically relevant but "undruggable" proteins remains challenging. Herein, we employed yeast surface display of synthetic nanobodies to identify a protein ligand selective for BCL11A, a critical repressor of fetal globin gene transcription. Fusion of the nanobody to a cell-permeant miniature protein and an E3 adaptor creates a degrader that depletes cellular BCL11A in erythroid precursor cells, thereby inducing the expression of fetal hemoglobin, a modifier of clinical severity of sickle cell disease and {beta}-thalassemia. This work establishes a new paradigm for the targeted degradation of previously intractable proteins using cell-permeant nanobody-based degraders. One sentence summaryA cell-permeant, protein-based degrader is used for the induction of fetal hemoglobin.

biochemistry↗

bioRxiv2022

Structural insights into bacterial sterol transport

Sterol lipids are widely present in eukaryotes and play essential roles in signaling and modulating membrane fluidity. Although rare, some bacteria also produce sterols, but their function in bacteria is not known. Moreover, many more species, including pathogens and commensal microbes, acquire or modify sterols from eukaryotic hosts through poorly understood molecular mechanisms. The aerobic methanotroph Methylococcus capsulatus was the first bacterium shown to synthesize sterols, producing a mixture of C-4 methylated sterols that are distinct from those observed in eukaryotes. C-4 methylated sterols are synthesized in the cytosol and localized to the outer membrane, suggesting that a bacterial sterol transport machinery exists. Until now, the identity of such machinery remained a mystery. In this study, we identified three novel proteins that may be the first examples of transporters for bacterial sterol lipids. The proteins, which all belong to well-studied families of bacterial metabolite transporters, are predicted to reside in the inner membrane, periplasm, and outer membrane of M. capsulatus, and may work as a conduit to move modified sterols to the outer membrane. Quantitative analysis of ligand binding revealed their remarkable specificity for 4-methylsterols, and crystallographic structures coupled with docking and molecular dynamics simulations revealed the structural bases for substrate binding by two of the putative transporters. Their striking structural divergence from eukaryotic sterol transporters signals that they form a distinct sterol transport system within the bacterial domain. Finally, bioinformatics revealed the widespread presence of similar transporters in bacterial genomes, including in some pathogens that use host sterol lipids to construct their cell envelopes. The unique folds of these bacterial sterol binding proteins should now guide the discovery of other proteins that handle this essential metabolite.

biochemistry↗