Biology subjects

Baylink, A.

Publications and source records attributed to Baylink, A..

4 recordsLinked to original sources

bioRxiv2026

Structure and signaling mechanism of Helicobacter pylori transducer-like protein D

Chemoreceptors, or methyl-accepting chemotaxis proteins (MCPs), are ancient and widespread prokaryotic sensors that direct taxis in response to stimuli and are attractive targets for therapeutic control of bacteria 1-4. Decades of study have yielded substantial mechanistic insight into chemoreceptor function, but the absence of high-resolution full-length structures containing ligand-binding domains (LBD) has limited understanding of how effector sensing is structurally coupled to long-range signal transduction. Here, we present the intact structure of the chemoreceptor transducer-like protein D (TlpD) from the gastric pathogen Helicobacter pylori, in complex with its ligand Zn2+, determined by X-ray crystallography in two crystal forms at 2.4-3.0 [A]. Three different conformations are captured, revealing how interactions in the ligand-binding site of the chemoreceptor zinc-binding (CZB) domain are interconnected with the distal kinase interface. Small changes at the ligand-binding site coincide with cascades of side-chain rearrangements across the dimer, distortion of the receptor coiled-coil, and conformational and dynamic shifts at the kinase interface over 140 [A] away. These near-atomic resolution structures provide a framework for understanding cooperativity and allosteric communication in chemoreceptors, and establish a representative model for a widespread class of soluble chemoreceptors important in bacterial pathogenesis 2,5.

molecular biology↗

bioRxiv2025

AlphaFold 3 accurately models natural variants of Helicobacter pylori catalase KatA

Subtle changes in protein sequence can equate to large changes in function, such as enabling pathogens to evade the immune system, hindering antibody recognition of antigens, or conferring antibiotic resistance. Even single amino acid substitutions may alter ligand binding affinity, enzymatic activity, and protein stability. Yet, due to limitations in time and resources, proteins closely related in sequence to those already characterized often remain unexamined. AlphaFold has emerged as a promising tool for protein structure prediction, though its utility in modeling single amino acid substitutions remains uncertain. In this study, we assessed AlphaFold 3s accuracy in modeling natural variants of the Helicobacter pylori catalase KatA by comparing its predictions to a novel high-resolution crystal structure of KatA from strain SS1. This variant contains key substitutions at residues 234, 237, 255, and 421 relative to the well-characterized strain 26695. AlphaFold 3 models accurately reproduced the global structure and local conformations of most variant residues, with high fidelity in conservative substitutions but variable accuracy in more flexible or interface-exposed sites. We further explored how user inputs, such as incorrect oligomeric states or sequence modifications, influence prediction quality. While AlphaFold 3 consistently produced high-quality models, deviations at variant sites occurred when incorrect oligomeric states were specified. Our findings highlight both the strengths and limitations of AlphaFold 3 in modeling natural protein variants and underscore the importance of accurate user input for reliable structural predictions. ImportanceExperimental structure determination is rarely performed for natural protein variants possessing only minor amino acid differences from published structures, even though small substitutions can significantly impact structure and function. Here, we present a case study showing that AlphaFold 3 can accurately model the structures of natural protein variants. However, providing an incorrect oligomeric state can reduce model accuracy--an error that non-expert users may easily make.

microbiology↗

bioRxiv2024

Navigating contradictions: Salmonella Typhimurium chemotactic responses to conflicting chemoeffector signals show parity with bacterial growth benefits

Motile bacteria sense and avoid deleterious stimuli in their environment through chemorepulsion, a behavior that helps them locate permissive ecological niches. In the gut, indole is a bacteriostatic compound produced by the microbiota and is thought to act as a chemorepellent for invading pathogens, thereby protecting the host against infection. The principal reservoir of intestinal indole is fecal matter, a complex biological material that contains both attractant and repellent stimuli. Whether indole in its natural context is sufficient for pathogen chemorepulsion or host protection has remained unknown. Using an intestinal explant system, we show that while pure indole indeed suppresses an infection advantage mediated through chemotaxis for the enteric pathogen Salmonella enterica serovar Typhimurium, this effect is abolished in the presence of other chemoeffectors present in feces, including the chemoattractant L-Serine (L-Ser), in a manner dependent on the chemoreceptor Tsr. Live imaging reveals that although S. Typhimurium is repelled by pure indole, the pathogen is actually strongly attracted to human fecal matter despite its high indole content, and that this response is mediated by Tsr, which simultaneously senses both indole and L-Ser. Fecal attraction is conserved across diverse Enterobacteriaceae species that harbor Tsr orthologues, including Escherichia coli, Citrobacter koseri, Enterobacter cloacae, and clinical isolates of non-typhoidal Salmonella. In a defined system of fecal chemoeffectors, we find that L-Ser and other fecal chemoattractants override indole chemorepulsion, but the magnitude of bacterial chemoattraction is controlled by indole levels. Together, these findings suggest that indole in its native context is not protective against enteric infection and that indole taxis actually benefits pathogens during infection by locating niches with low competitor density. Our study highlights the limitations of applying single-effector studies in predicting bacterial behavior in natural environments, where chemotaxis is shaped by the integration of multiple, often opposing, chemical signals.

microbiology↗

bioRxiv2023

Bacterial vampirism mediated through chemotaxis

Bacteria of the family Enterobacteriaceae are associated with gastrointestinal (GI) bleeding and bacteremia and are a leading cause of death, from sepsis, for individuals with inflammatory bowel diseases. The bacterial behaviors and mechanisms underlying why these bacteria are prone to bloodstream entry remains poorly understood. Herein, we report that clinical isolates of non-typhoidal Salmonella enterica serovars, Escherichia coli, and Citrobacter koseri are rapidly attracted toward sources of human serum. To simulate GI bleeding, we utilized a custom injection-based microfluidics device and found that femtoliter volumes of human serum are sufficient to induce the bacterial population to swim toward and aggregate at the serum source. This response is orchestrated through chemotaxis, and a major chemical cue driving chemoattraction is L-serine, an amino acid abundant in serum that is recognized through direct binding by the chemoreceptor Tsr. We report the first crystal structures of Salmonella Typhimurium Tsr in complex with L-serine and identify a conserved amino acid recognition motif for L-serine shared among Tsr orthologues. By mapping the phylogenetic distribution of this chemoreceptor we found Tsr to be widely conserved among Enterobacteriaceae and numerous World Health Organization priority pathogens associated with bloodstream infections. Lastly, we find that Enterobacteriaceae use human serum as a source of nutrients for growth and that chemotaxis and the chemoreceptor Tsr provides a competitive advantage for migration into enterohaemorrhagic lesions. We term this bacterial behavior of taxis toward serum, colonization of hemorrhagic lesions, and the consumption of serum nutrients, as "bacterial vampirism" which may relate to the proclivity of Enterobacteriaceae for bloodstream infections.

microbiology↗