About

Christopher S. Hayes is the Roy and Janet Hardiman Interdisciplinary Chair in Molecular Biology and Department Chair at UC Santa Barbara's Department of Molecular, Cellular, and Developmental Biology (MCDB). He received his B.A. in Biology and M.S. in Applied Immunology from the University of Southern Maine, and his Ph.D. in Molecular Biology & Biochemistry from the University of Connecticut School of Medicine. Following his doctoral studies, he was a Walter Winchell-Damon Runyon Cancer Research Fund postdoctoral fellow at the Massachusetts Institute of Technology. He joined the MCDB faculty in 2004. Dr. Hayes's research focuses on the structure, function, and physiology of specialized secretion systems that mediate inter-bacterial conflict. His work investigates how bacteria transfer growth-inhibitory protein toxins between cells, and how these toxin-immunity protein pairs contribute to self/nonself discrimination in bacteria. His lab is particularly interested in the mechanisms of antibacterial effector delivery systems, which are of interest for developing novel antimicrobial therapies. His contributions include elucidating the molecular mechanisms of contact-dependent growth inhibition, toxin delivery, and bacterial competition, advancing understanding of bacterial intercellular interactions and potential therapeutic targets.

Research topics

• Biology
• Biochemistry
• Genetics
• Cell biology
• Computer Science
• Microbiology
• Computational biology
• Chemistry

Selected publications

• Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization

  Science · 2026-02-19 · 2 citations

  articleSenior authorCorresponding

  Pathogenic Bordetella bacteria use protein adhesins to infect the ciliated respiratory epithelia of vertebrate hosts. In this work, we show that the filamentous hemagglutinin FhaB adhesin of Bordetella carries a C-terminal microtubule-binding domain (FhaB-CT), which is translocated into host cells to promote colonization. FhaB-CT delivery is required to occupy a niche at the base of cilia in airway epithelia, and mutant bacteria lacking this domain are defective for nasal colonization. These observations suggest that FhaB-CT is transferred into motile respiratory cilia to interact with core axonemal microtubules. We propose that Bordetella adheres initially to the tips of cilia and then deploys multiple FhaB adhesins to migrate to the base of the cilia forest, where the bacteria resist removal by the mucociliary “escalator” that normally clears the respiratory tract of microbes.

  PublisherDOI

• Redox regulated auto-processing controls delivery of an antibacterial cysteine peptidase toxin

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-08

  articleOpen access1st authorCorresponding

  Abstract Contact-dependent growth inhibition (CDI) is a mechanism of inter-bacterial competition mediated by CdiA effectors, which deliver polymorphic C-terminal toxins (CT) into neighboring competitors. StbD from Citrobacter rodentium DBS100 is an unusual CdiA-like protein that carries a C-terminal cysteine peptidase toxin. Crystallography reveals that StbD-CT is composed of an N-terminal cytoplasm-entry domain connected to a C39 family peptidase by a flexible linker. The entry domain hijacks membrane-embedded YajC for translocation into the target-cell cytosol where the peptidase inactivates type II topoisomerases. Intoxication leads to a loss of DNA super-helicity, impaired chromosome segregation and cell filamentation. In addition to cleaving topoisomerases, StbD-CT exhibits auto-proteolytic processing under reducing conditions, and this activity is required for target cell intoxication. We propose that StbD-CT remains tethered to the cell periphery via interactions with YajC after delivery. Auto-processing releases the peptidase, enabling the domain to penetrate into the cell interior where it cleaves nucleoid-associated topoisomerases. Together, these findings identify a proteolytic effector that deactivates type II topoisomerases and reveal a redox regulatory strategy that coordinates toxin activation with intercellular delivery.

  PublisherOA PDFDOI

• Elongation Factor Tu Acts as a Chaperone to Activate an Antibacterial <scp>RNase</scp> Toxin

  Molecular Microbiology · 2026-01-20 · 2 citations

  articleOpen accessSenior authorCorresponding

  ABSTRACT Many Gram‐negative bacterial species use contact‐dependent growth inhibition (CDI) systems to deliver toxic proteins into neighboring competitors. CDI + strains deploy CdiA effector proteins, which translocate their C‐terminal toxin (CT) domains into target bacteria through a receptor‐mediated delivery pathway. To protect against auto‐intoxication, CDI + bacteria also produce CdiI immunity proteins that neutralize CT toxin activity. Here, we present the crystal structure of the CT·CdiI O32:H37 complex from Escherichia coli O32:H37. CT O32:H37 adopts the same fold as the tRNase domain of colicin D, and the nucleases share similar catalytic centers. However, unlike colicin D, which cleaves the anticodon loops of tRNA Arg isoacceptors, CT O32:H37 exhibits nonspecific RNase activity. Notably, we find that endogenous elongation factor Tu (EF‐Tu) co‐purifies with the over‐produced CT·CdiI O32:H37 complex. Although EF‐Tu does not bind stably to CT O32:H37 in the absence of CdiI O32:H37 , the translation factor is required for toxic RNase activity in vitro. AlphaFold 3 modeling and site‐directed mutagenesis indicate that CT O32:H37 interacts with the N‐terminal GTPase domain of EF‐Tu. EF‐Tu appears to stabilize residue Trp52 within the hydrophobic core of the toxin, which in turn supports the RNase active site through an unusual hydrogen‐bonding interaction with the catalytic His67 residue. Thus, EF‐Tu is hijacked as an essential co‐factor to organize the toxin's catalytic center.

  PublisherOA PDFDOI

• Advanced glycation end product (AGE) crosslinking of a bacterial protein: Are AGE-modifications going undetected in our studies?

  Structural Dynamics · 2025-05-01 · 2 citations

  articleOpen access

  The small reactive molecules, glyoxal (GO) and methylglyoxal (MGO), are common byproducts of metabolic processes. GO and MGO are known to modify proteins, DNA, and lipids, resulting in advance glycation end products (AGEs). AGEs are linked to numerous human diseases but are found across all three domains of life due to the widespread presence of GO and MGO. Recent structural studies have revealed that an antibacterial phospholipase toxin contains a methylglyoxal-derived imidazolium crosslink (MODIC). Unlike AGEs that are associated with human diseases and protein dysfunction, crosslinking is required for the toxin's enzymatic activity, indicating that MODIC acts as a bona fide post-translational modification to promote function. The MODIC-modified toxin represents the first structure in the protein data bank with an AGE-modification. However, because GO and MGO are present in all cells, AGE-modifications are likely more prevalent than currently reported but have gone undetected. We used the toxin's MODIC structural motif to query the protein data bank for other modified proteins. This search recovered the colicin Ia pore-forming toxin. Using the deposited crystal structure and structural data for colicin Ia, we were able to model glyoxal-derived imidazolium crosslink or MODIC modifications into the electron density map, suggesting that GO/MGO modifications may indeed be more common in bacterial proteins.

  PublisherDOI

• Structural and functional insights into <i>Escherichia coli</i> O32:H37 contact dependent inhibition

  Structural Dynamics · 2025-09-01

  articleOpen access

  Many gram-negative bacteria utilize contact-dependent growth inhibition (CDI) systems to introduce toxic effector proteins into neighboring cells, thereby outcompeting them. In CDI+ strains, CdiA effector proteins, carrying C-terminal toxin (CT) domains, are delivered into target cells through receptor-mediated pathways. To prevent self-intoxication, these bacteria produce CdiI immunity proteins that bind and neutralize the CT domains. Here, we present the crystal structure of the CT•CdiIO32:H37 complex from Escherichia coli O32:H37. Our findings reveal that CTO32:H37 is structurally homologous to the C-terminal tRNase domain of colicin D, and contains similar catalytic centers. However, CTO32:H37 exhibits non- specific RNase activity, unlike colicin D, which targets the anticodon loops of tRNAArg isoacceptors. The CdiIO32:H37 immunity protein features a unique fold coordinating a central Fe3+ ion with cysteine residues. Intriguingly, CT• CdiIO32:H37 complex co-purifies with endogenous elongation factor Tu (EF-Tu), forming a stable ternary complex. Although CTO32:H37 does not stably interact with EF-Tu without CdiIO32:H37, EF-Tu is essential for RNase activity in vitro. AlphaFold3 modeling suggests that CTO32:H37 binds to the GTPase domain of EF-Tu at a site overlapping the EF-Ts binding site. Our data indicate that EF-Tu supports the toxin’s active site, stabilizing a core tryptophan residue that interacts with a catalytic histidine.

  PublisherDOI

• Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-17 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Pathogenic Bordetella bacteria infect the ciliated respiratory epithelia of mammalian and avian hosts. Several bacterial proteins mediate host cell adhesion, but filamentous hemagglutinin (FhaB) is a principal adhesin because mutants lacking this protein exhibit profound colonization defects. Here, we show that FhaB carries a C-terminal microtubule-binding domain (FhaB-CT), which is translocated into the host-cell cytoplasm to promote bacterial colonization. Cryogenic electron microscopy of microtubule-bound FhaB-CT shows that the domain binds primarily to α-tubulin through a network of polar interactions. Live-cell microscopy of infected tracheal explants reveals that FhaB-CT delivery is required for Bordetella to occupy a niche at the base of cilia on airway epithelia. Finally, we demonstrate that the microtubule-binding domain is required for long-term colonization of the mouse nasal cavity by B. pertussis . These observations suggest that the FhaB-CT domain is delivered into motile cilia, where it interacts with axonemal microtubules. We propose that Bordetella initially adhere to the tips of cilia, then deploy multiple FhaB adhesin molecules to migrate to the base of the cilial forest. This mechanism enables Bordetella to resist removal by the mucociliary ‘escalator’ that clears the respiratory tract of microbes and debris.

  PublisherOA PDFDOI

• Advanced glycation end-product crosslinking activates a type VI secretion system phospholipase effector protein

  Nature Communications · 2024-10-11 · 7 citations

  articleOpen accessSenior authorCorresponding

  Advanced glycation end-products (AGE) are a pervasive form of protein damage implicated in the pathogenesis of neurodegenerative disease, atherosclerosis and diabetes mellitus. Glycation is typically mediated by reactive dicarbonyl compounds that accumulate in all cells as toxic byproducts of glucose metabolism. Here, we show that AGE crosslinking is harnessed to activate an antibacterial phospholipase effector protein deployed by the type VI secretion system of Enterobacter cloacae. Endogenous methylglyoxal reacts with a specific arginine-lysine pair to tether the N- and C-terminal α-helices of the phospholipase domain. Substitutions at these positions abrogate both crosslinking and toxic phospholipase activity, but in vitro enzyme function can be restored with an engineered disulfide that covalently links the N- and C-termini. Thus, AGE crosslinking serves as a bona fide post-translation modification to stabilize phospholipase structure. Given the ubiquity of methylglyoxal in prokaryotic and eukaryotic cells, these findings suggest that glycation may be exploited more generally to stabilize other proteins. This alternative strategy to fortify tertiary structure could be particularly advantageous in the cytoplasm, where redox potentials preclude disulfide bond formation.

  PublisherOA PDFDOI

• Abstract 1374 Licensed to kill: Post-translational activation of an antibacterial effector protein

  Journal of Biological Chemistry · 2024-03-01

  articleOpen access1st authorCorresponding

  All bacteria compete for growth niches and other limited resources in the environment. These existential battles are waged at several levels, but one common strategy entails the direct transfer of toxic effector proteins between competing cells. Antibacterial effectors are invariably encoded with immunity proteins, which neutralize the effector to protect the cell from auto-inhibition and intoxication by neighboring siblings. Here, I show that an immunity protein from Enterobacter cloacae is also required to activate its cognate effector prior to delivery into target bacteria. Genetic, biochemical and structural analyses reveal that the toxic effector is subject to a novel post-translational modification when bound to its immunity protein. This modification stabilizes the effector fold and is absolutely required for toxic enzymatic activity in vitro and in vivo. Join us on Tuesday afternoon to learn the identity of this new post-translational modification. This work was supported by grant R01 GM117930 from the National Institutes of Health.

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• Contact-dependent growth inhibition (CDI) systems deploy a large family of polymorphic ionophoric toxins for inter-bacterial competition

  PLoS Genetics · 2024-11-26 · 14 citations

  articleOpen accessSenior authorCorresponding

  Contact-dependent growth inhibition (CDI) is a widespread form of inter-bacterial competition mediated by CdiA effector proteins. CdiA is presented on the inhibitor cell surface and delivers its toxic C-terminal region (CdiA-CT) into neighboring bacteria upon contact. Inhibitor cells also produce CdiI immunity proteins, which neutralize CdiA-CT toxins to prevent auto-inhibition. Here, we describe a diverse group of CDI ionophore toxins that dissipate the transmembrane potential in target bacteria. These CdiA-CT toxins are composed of two distinct domains based on AlphaFold2 modeling. The C-terminal ionophore domains are all predicted to form five-helix bundles capable of spanning the cell membrane. The N-terminal "entry" domains are variable in structure and appear to hijack different integral membrane proteins to promote toxin assembly into the lipid bilayer. The CDI ionophores deployed by E. coli isolates partition into six major groups based on their entry domain structures. Comparative sequence analyses led to the identification of receptor proteins for ionophore toxins from groups 1 & 3 (AcrB), group 2 (SecY) and groups 4 (YciB). Using forward genetic approaches, we identify novel receptors for the group 5 and 6 ionophores. Group 5 exploits homologous putrescine import proteins encoded by puuP and plaP, and group 6 toxins recognize di/tripeptide transporters encoded by paralogous dtpA and dtpB genes. Finally, we find that the ionophore domains exhibit significant intra-group sequence variation, particularly at positions that are predicted to interact with CdiI. Accordingly, the corresponding immunity proteins are also highly polymorphic, typically sharing only ~30% sequence identity with members of the same group. Competition experiments confirm that the immunity proteins are specific for their cognate ionophores and provide no protection against other toxins from the same group. The specificity of this protein interaction network provides a mechanism for self/nonself discrimination between E. coli isolates.

  PublisherDOI

• Paradoxical activation of a type VI secretion system (T6SS) phospholipase effector by its cognate immunity protein

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-03-29

  preprintOpen accessSenior authorCorresponding

  Abstract Type VI secretion systems (T6SS) deliver cytotoxic effector proteins into target bacteria and eukaryotic host cells. Antibacterial effectors are invariably encoded with cognate immunity proteins that protect the producing cell from self-intoxication. Here, we identify transposon insertions that disrupt the tli immunity gene of Enterobacter cloacae and induce auto-permeabilization through unopposed activity of the Tle phospholipase effector. This hyper-permeability phenotype is T6SS-dependent, indicating that the mutants are intoxicated by Tle delivered from neighboring sibling cells rather than by internally produced phospholipase. Unexpectedly, an in-frame deletion of tli does not induce hyper-permeability because Δ tli null mutants fail to deploy active Tle. Instead, the most striking phenotypes are associated with disruption of the tli lipoprotein signal sequence, which prevents immunity protein localization to the periplasm. Immunoblotting reveals that most hyper-permeable mutants still produce Tli, presumably from alternative translation initiation codons downstream of the signal sequence. These observations suggest that cytosolic Tli is required for the activation and/or export of Tle. We show that Tle growth inhibition activity remains Tli-dependent when phospholipase delivery into target bacteria is ensured through fusion to the VgrG β-spike protein. Together, these findings indicate that Tli has distinct functions depending on its subcellular localization. Periplasmic Tli acts as a canonical immunity factor to neutralize incoming effector proteins, while a cytosolic pool of Tli is required to activate the phospholipase domain of Tle prior to T6SS-dependent export.

  PublisherOA PDFDOI

Recent grants

• Molecular Mechanisms of anti-bacterial contact-dependent growth inhibition (CDI)

  NIH · $3.0M · 2016–2026

• Molecular mechanisms of antibacterial CDI toxin activation

  NIH · $1.2M · 2016–2021

• Molecular determinants of A-site mRNA cleavage during ribosome pausing

  NIH · $2.5M · 2006–2016

Frequent coauthors

• David A. Low

  University of California, Santa Barbara

  48 shared

• Fernando Garza‐Sánchez

  University of California, Santa Barbara

  24 shared

• A. Joachimiak

  University of Chicago

  19 shared

• Celia W. Goulding

  University of California, Irvine

  18 shared

• Zachary C. Ruhe

  University of California, Santa Barbara

  17 shared

• K. Michalska

  University of Chicago

  12 shared

• Brian D. Janssen

  University of Iowa

  11 shared

• Christina M. Beck

  Seattle Children's Hospital

  11 shared

Labs

• Hayes LabPI

  Not provided

Education

• B.A., Biology

  University of Southern Maine

• M.S., Applied Immunology

  University of Southern Maine

• Ph.D., Molecular Biology & Biochemistry

  University of Connecticut School of Medicine