About

Tania A. Baker is the E. C. Whitehead Professor of Biology at MIT and an Investigator at the Howard Hughes Medical Institute. Her current research explores mechanisms and regulation of enzyme-catalyzed protein unfolding, ATP-dependent protein degradation, and remodeling of the proteome during cellular stress responses. Her work aims to understand the mechanisms and regulation behind AAA+ unfoldases and macromolecular machines from the 'Clp/Hsp100 family' of protein unfolding enzymes. She employs biochemistry, structural biology, molecular biology, genetics, and single molecule biophysics to study these biological catalysts. Baker has made significant contributions to the understanding of proteolytic machines, including the structural basis of substrate recognition, the activation of enzymes involved in heme biosynthesis, and the mechanochemical basis of protein degradation by AAA+ machines. Her research has advanced knowledge of how these molecular machines function and are regulated within the cell.

Research topics

• Biology
• Chemistry
• Biophysics
• Biochemistry
• Cell biology

Selected publications

• ClpP2 modulates ClpXP assembly to promote multiple pathogenic phenotypes in <i> <i>Pseudomonas aeruginosa</i> </i>

  Proceedings of the National Academy of Sciences · 2026-04-01 · 1 citations

  articleOpen accessSenior authorCorresponding

  In the opportunistic pathogen Pseudomonas aeruginosa ( Pa ), ClpXP proteases selectively degrade key transcriptional regulators (TRs), enabling dynamic control over phenotypes that promote pathogenesis and virulence. Here, we report that a natural Pa variant activates multiple pathogenic phenotypes by modulating ClpXP assembly dynamics through a spontaneous hypomorphic mutation in the canonical peptidase subunit ClpP1 (ClpP1 P6L ) and its synergistic activation by the atypical peptidase subunit ClpP2. Genetics, cell-based reporter assays, and biochemical analyses reveal that ClpP1 P6L impairs ClpXP-complex formation, but that this defect is partially suppressed upon heterooligomerization with ClpP2. Consequently, ClpX, ClpP1 P6L , and ClpP2 combine to catalyze sufficient proteolysis to trigger mucoid conversion, a virulence-associated phenotype characterized by alginate overproduction. Further, ClpP1 P6L also triggers premature rhl quorum sensing, thereby upregulating the expression of additional virulence factors. These findings demonstrate that by encoding two ClpP paralogs (ClpP1 and ClpP2), Pa can adaptively modulate ClpXP assembly dynamics to adjust proteolysis and expand its phenotypic versatility. We propose that organisms that encode multiple ClpP subunits can exert finer control over regulated substrate degradation and thereby optimize their display of pathogenic traits that support opportunistic infections.

  PublisherOA PDFDOI

• Structural insights into the <i>Pseudomonas aeruginosa</i><scp>ClpP1</scp>•<scp>ClpP2</scp> heterocomplex and its interactions with the <scp>AAA</scp>+ <scp>ClpX</scp> unfoldase

  Protein Science · 2025-09-22 · 2 citations

  articleOpen access

  Abstract ClpXP and other AAA+ proteases play central roles in bacterial proteostasis by degrading misfolded and regulatory proteins. In Pseudomonas aeruginosa , ClpXP consists of the ClpX unfoldase and ClpP peptidase, which influence critical adaptive processes contributing to stress resistance. P. aeruginosa Pa ClpP1 and Pa ClpP2 paralogs assemble into homomeric ( Pa ClpP1•ClpP1) and heteromeric ( Pa ClpP1•ClpP2) complexes. Pa ClpP2 is only active in the Pa ClpP1•ClpP2 heterocomplex. Here, we present a cryo‐EM structure of Pa ClpX•ClpP1•ClpP2, revealing how Pa ClpX binds Pa ClpP1, which in turn interacts with Pa ClpP2. Comparison of the active heterocomplex with an inactive Pa ClpP2 crystal structure shows that Pa ClpP1 binding induces conformational changes in Pa ClpP2, stabilizing an active catalytic triad. Differences in Pa ClpP1 and Pa ClpP2 substrate‐binding residues and an unstructured ClpP2 N‐terminal segment that protrudes into the peptidase chamber likely contribute to distinct peptide‐cleavage specificities of Pa ClpX•ClpP1•ClpP2 and Pa ClpX•ClpP1•ClpP1. Given the role of Pa ClpP1•ClpP2 in biofilm formation and virulence, these structural insights may provide a foundation for developing selective inhibitors to combat P. aeruginosa infections.

  PublisherOA PDFDOI

• Regulation of the Essential Transmembrane AAA+ Protease FtsH by HflK/C Oligomeric Assembly

  Structural Dynamics · 2025-03-01 · 1 citations

  articleOpen access

  Membrane-anchored AAA+ proteases, such as FtsH, degrade membrane-bound and soluble substrates to maintain protein homeostasis and regulate cellular functions across a diverse array of organisms and organelles, including eubacteria, chloroplasts, mitochondria, and apicomplexan parasites. FtsH functions as a homohexamer, with each monomer comprising a AAA+ module, a zinc-peptidase, transmembrane helices, and a periplasmic domain. The AAA+ module is responsible for ATP-dependent unfolding of substrates and translocation of the unfolded polypeptide chain into the peptidase chamber for degradation. In E. coli, FtsH interacts with the membrane proteins HflK and HflC, which together form a 1.8-MDa protein assembly within the bacterial inner membrane. However, the intricacies of how this complex assembles and functions, including how it recruits and extracts membrane substrates from the lipid bilayer for degradation, remain unknown. We determined a series of cryo-EM structures of the native FtsH•HflK/C complex from E. coli that contain two FtsH hexamers associated with each asymmetric HflK/C nautilus shell-like assembly. Our structures reveal an opening in the HflKC assembly that we hypothesize aids in recruitment of membrane-protein substrates. To probe for the effect of HflK/C on the degradation of putative substrates, we applied pulse-labeling mass spectrometry to both wild-type and ΔhflK/C strains of E. coli and identified a series of proteins whose rates of degradation depend on the presence of HflK/C. Integrating single-particle cryo-EM, cryo-ET, liposome reconstitution, and proteomic data, we propose a novel model for the FtsH•HflK/C microdomain that posits that the opening within the assembly provides an entryway to the FtsH axial channel. We further suggest that membrane curvature observed in our detergent-free structures may give rise to membrane thinning, facilitating the efficient extraction of FtsH substrates from the lipid bilayer.

  PublisherDOI

• An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins

  The EMBO Journal · 2025-03-13 · 21 citations

  articleOpen access

  The AAA protease FtsH associates with HflK/C subunits to form a megadalton-size complex that spans the inner membrane and extends into the periplasm of E. coli. How this bacterial complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following the overproduction of protein components, recent cryo-EM structures showed symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit the degradation of membrane-embedded substrates. Here, we present structures of native protein complexes, in which HflK/C instead forms an asymmetric nautilus-shaped assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. Membrane curvature in our FtsH•HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.

  PublisherOA PDFDOI

• How the double-ring ClpAP protease motor grips the substrate to unfold and degrade stable proteins

  Journal of Biological Chemistry · 2024-10-05 · 1 citations

  articleOpen accessSenior author

  Loops in the axial channels of ClpAP and other AAA+ proteases bind a short peptide degron connected by a linker to the N- or C-terminal residue of a native protein to initiate degradation. ATP hydrolysis then powers pore-loop movements that translocate these segments through the channel until a native domain is pulled against the narrow channel entrance, creating an unfolding force. Substrate unfolding is thought to depend on strong contacts between pore loops and a subset of amino acids in the unstructured sequence directly preceding the folded domain. Here, we identify such contact sequences that promote grip for ClpAP and use ClpA structures to place these sequences within ClpA's two AAA+ rings. The positions and chemical nature of certain residues within an unstructured segment that are positioned to interact with the D2 ring have major positive effects on substrate unfolding, whereas segments located within the D1 ring have little consequence. Within the D2-bound segment, two short elements are critical for accelerating degradation; one is at the "top" of D2 and consists of at least two properly positioned nonslippery residues. In contrast, the second D2 element, which can be as short as one residue, is positioned to contact pore loops near the "bottom" of this ring. Comparison with similar studies for ClpXP reveals that positioning a well-gripped substrate sequence within the major unfoldase motor is more important than its proximity to the folded domain and that charged, polar, and hydrophobic residues all contribute favorable contacts to substrate grip.

  PublisherOA PDFDOI

• An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-10 · 8 citations

  preprintOpen access

  . How this complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following overproduction of protein components, recent cryo-EM structures reveal symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit degradation of membrane-embedded substrates. Here, we present structures of native complexes in which HflK/C instead forms an asymmetric nautilus-like assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. The membrane curvature in our FtsH•HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid-scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.

  PublisherOA PDFDOI

• The membrane-cytoplasmic linker defines activity of FtsH proteases in Pseudomonas aeruginosa clone C

  Journal of Biological Chemistry · 2024-01-03 · 6 citations

  articleOpen accessCorresponding

  Pandemic Pseudomonas aeruginosa clone C strains encode two inner-membrane associated ATP-dependent FtsH proteases. PaftsH1 is located on the core genome and supports cell growth and intrinsic antibiotic resistance, whereas PaftsH2, a xenolog acquired through horizontal gene transfer from a distantly related species, is unable to functionally replace PaftsH1. We show that purified PaFtsH2 degrades fewer substrates than PaFtsH1. Replacing the 31-amino acid-extended linker region of PaFtsH2 spanning from the C-terminal end of the transmembrane helix-2 to the first seven highly divergent residues of the cytosolic AAA+ ATPase module with the corresponding region of PaFtsH1 improves hybrid-enzyme substrate processing in vitro and enables PaFtsH2 to substitute for PaFtsH1 in vivo. Electron microscopy indicates that the identity of this linker sequence influences FtsH flexibility. We find membrane-cytoplasmic (MC) linker regions of PaFtsH1 characteristically glycine-rich compared to those from FtsH2. Consequently, introducing three glycines into the membrane-proximal end of PaFtsH2's MC linker is sufficient to elevate its activity in vitro and in vivo. Our findings establish that the efficiency of substrate processing by the two PaFtsH isoforms depends on MC linker identity and suggest that greater linker flexibility and/or length allows FtsH to degrade a wider spectrum of substrates. As PaFtsH2 homologs occur across bacterial phyla, we hypothesize that FtsH2 is a latent enzyme but may recognize specific substrates or is activated in specific contexts or biological niches. The identity of such linkers might thus play a more determinative role in the functionality of and physiological impact by FtsH proteases than previously thought.

  PublisherOA PDFDOI

• Lon degrades stable substrates slowly but with enhanced processivity, redefining the attributes of a successful AAA+ protease

  Cell Reports · 2023-09-01 · 6 citations

  articleOpen accessSenior authorCorresponding

  Lon is a widely distributed AAA+ (ATPases associated with diverse cellular activities) protease known for degrading poorly folded and damaged proteins and is often classified as a weak protein unfoldase. Here, using a Lon-degron pair from Mesoplasma florum (MfLon and MfssrA, respectively), we perform ensemble and single-molecule experiments to elucidate the molecular mechanisms underpinning MfLon function. Notably, we find that MfLon unfolds and degrades stably folded substrates and that translocation of these unfolded polypeptides occurs with a ∼6-amino-acid step size. Moreover, the time required to hydrolyze one ATP corresponds to the dwell time between steps, indicating that one step occurs per ATP-hydrolysis-fueled "power stroke." Comparison of MfLon to related AAA+ enzymes now provides strong evidence that HCLR-clade enzymes function using a shared power-stroke mechanism and, surprisingly, that MfLon is more processive than ClpXP and ClpAP. We propose that ample unfoldase strength and substantial processivity are features that contribute to the Lon family's evolutionary success.

  PublisherDOI

• A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation

  Nature Communications · 2023-11-10 · 21 citations

  articleOpen access

  AAA+ proteases degrade intracellular proteins in a highly specific manner. E. coli ClpXP, for example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize proteins, which are then unfolded by ClpX and subsequently translocated through its axial channel and into the degradation chamber of ClpP for proteolysis. Prior cryo-EM structures reveal that the ssrA tag initially binds to a ClpX conformation in which the axial channel is closed by a pore-2 loop. Here, we show that substrate-free ClpXP has a nearly identical closed-channel conformation. We destabilize this closed-channel conformation by deleting residues from the ClpX pore-2 loop. Strikingly, open-channel ClpXP variants degrade non-native proteins lacking degrons faster than the parental enzymes in vitro but degraded GFP-ssrA more slowly. When expressed in E. coli, these open channel variants behave similarly to the wild-type enzyme in assays of filamentation and phage-Mu plating but resulted in reduced growth phenotypes at elevated temperatures or when cells were exposed to sub-lethal antibiotic concentrations. Thus, channel closure is an important determinant of ClpXP degradation specificity.

  PublisherOA PDFDOI

• The membrane-cytoplasmic linker defines activity of FtsH proteases in <i>Pseudomonas aeruginosa</i> clone C

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-06-20

  preprintOpen accessCorresponding

  Abstract Pandemic Pseudomonas aeruginosa clone C strains encode a xenolog of FtsH (PaFtsH2), an inner-membrane associated ATP-dependent protease. FtsH1 supports growth and intrinsic antibiotic resistance but cannot be replaced by ftsH2 . We show that purified PaFtsH2 degrades fewer substrates than PaFtsH1. Swapping residues of a short MC peptide that links transmembrane helix-2 with the cytosolic AAA+ ATPase module from PaFtsH1 into PaFtsH2 improves hybrid-enzyme substrate processing in vitro and enables PaFtsH2 to substitute for PaFtsH1 in vivo . FtsH1 MC peptides are glycine rich. Introducing three glycines into the membrane-proximal end of PaFtsH2’s MC linker is sufficient to elevate activity in vitro and in vivo . Electron microscopy including PaFtsH2 indicates that MC linker identity influences FtsH flexibility. Our findings establish that the efficiency of substrate processing by two PaFtsH isoforms depends on how they are attached to the membrane and suggest that greater linker flexibility/length allows FtsH to degrade a wider spectrum of substrates. As FtsH2 homologs occur across bacterial phyla, we hypothesize that FtsH2 is not a latent enzyme, rather recognizes specific substrates or is activated in specific contexts or biological niches. We hypothesize that such linkers might play a more determinative role in functionality and physiological impact of FtsH proteases than previously thought.

  PublisherOA PDFDOI

Recent grants

• Pre-Doctoral Training in Biological Sciences

  NIH · $64.8M · 1975–2021

• AAA+ proteolytic machines

  NIH · $17.5M · 1980–2024

• Macromolecular interactions controlling the ALA synthases, keystone enzymes that initiate heme biosynthesis

  NIH · $2.1M · 2017–2023

• NIH Grant R01GM049224

  NIH · $5.3M · 2015

Frequent coauthors

• Robert T. Sauer

  Massachusetts Institute of Technology

  268 shared

• Igor Levchenko

  Pirogov Russian National Research Medical University

  61 shared

• Robert A. Grant

  Massachusetts Institute of Technology

  34 shared

• Julia M. Flynn

  University of Massachusetts Chan Medical School

  32 shared

• Andrew R. Nager

  Pfizer (United States)

  27 shared

• Julia R. Kardon

  Brandeis University

  27 shared

• Adrian O. Olivares

  Vanderbilt University

  22 shared

• Kiyoshi Mizuuchi

  Osaka Research Institute of Industrial Science and Technology

  21 shared

Labs

• Tania A. Baker LabPI

Education

• Postdoctoral Fellow

  National Institute of Diabetes and Digestive and Kidney Diseases

  1992

• Postdoctoral Fellow, Biochemistry

  Stanford University School of Medicine

  1989

• PhD, Biochemistry

  Stanford University

  1988

• B.S., Biochemistry

  University of Wisconsin Madison

  1983

Awards & honors

• Margaret MacVicar Faculty Fellow, 2008-2018
• National Academy of Sciences, Member, 2007
• American Academy of Arts and Sciences, Fellow, 2005
• Howard Hughes Medical Institute, HHMI Investigator, 1994