About

Peter Chien is a Professor at the Department of Microbiology at the University of Massachusetts Amherst. The provided page text does not include specific details about his research focus, background, or key contributions. Therefore, a detailed biography cannot be generated from the available information.

Research topics

• Biology
• Cell biology
• Biochemistry
• Physics
• Chemistry
• Genetics
• Optics
• Medicinal chemistry

Selected publications

• Cluster GG Annotation Report

  QUBES · 2026-01-05

  articleOpen access

  <p>This report describes features of actinobacteriophages assigned to Cluster GG.  Additional phages may have been added to the phagesDB database since this report was generated.</p>

  PublisherDOI

• Stress testing reveals selective vulnerabilities in protein homeostasis

  Cell Reports · 2026-01-22

  articleOpen accessSenior author

  Protein quality control (PQC) systems are essential for cellular resilience to proteotoxic stress. Despite intensive study, functional redundancies in the system obscure the contributions of important individual genes. Here, we leverage transposon sequencing (Tn-seq) across bacterial strains lacking key chaperones and proteases to reveal hidden determinants of stress response in protein homeostasis. By profiling fitness under multiple proteotoxic stresses, we uncover stress-specific vulnerabilities and reveal how major players of PQC mask correlations between transcriptomic responses and gene fitness. We identify a heat-specific synthetic lethality between the ClpB disaggregase and DNA polymerase 1 mediated by prolific aggregation of the RecA recombinase and persistent induction of the heat shock regulon, supporting a conclusion that vulnerabilities in PQC are genetic- and environmental-context specific. Overall, our work presents a framework to reveal critical addressable fragilities in stress responses using gene fitness scores adaptable to a variety of systems.

  PublisherDOI

• Abstract 2059 An Investigation into the OxyR A105V Mutant in Caulobacter crescentus

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access

  The Lon protease is an important ATP-dependent protease for protein quality control and helps to maintain cellular homeostasis when the cell is under stress. Deletion of lon in Caulobacter crescentus results in growth defects under oxidative stress, but how the Lon protease is involved in this response remains unclear. In a screen for suppressors of this phenotype we identified a gain-of-function allele of the oxidative stress response regulator OxyR. In this work, we characterize this mutation to understand the mechanism of this suppression.

  PublisherOA PDFDOI

• Lon-dependent proteolysis in oxidative stress responses

  Journal of Bacteriology · 2025-06-06 · 5 citations

  reviewOpen accessSenior author

  Accumulation of reactive oxygen species (ROS) induces oxidative stress, leading to substantial damage to cellular macromolecules, necessitating efficient protein quality control mechanisms. The Lon protease, a highly conserved ATP-dependent protease, is thought to play a central role in mitigating oxidative stress by targeting damaged and misfolded proteins for degradation. This review examines the role of Lon in oxidative stress responses, including its role in degrading oxidized proteins, regulating antioxidant pathways, and modulating heme and Fe-S cluster homeostasis. We highlight cases of substrate recognition through structural changes and describe situations where Lon activity is further regulated by redox conditions. By synthesizing studies across a range of organisms, we find that despite the clear importance of Lon for oxidative stress tolerance, universal rules for Lon degradation of damaged proteins during this response remain unclear.

  PublisherDOI

• Stress testing reveals selective vulnerabilities in protein homeostasis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-16

  preprintOpen accessSenior authorCorresponding

  Protein quality control (PQC) systems are essential for cellular resilience to proteotoxic stress. Despite intensive study for decades, functional redundancies in the system obscure the contributions of the collectively important individual genes. Here, we leverage transposon sequencing across bacteria strains lacking key chaperones and proteases to reveal hidden determinants of stress response in protein homeostasis. By profiling fitness under multiple proteotoxic stresses, we uncover stress-specific vulnerabilities and reveal how major players of PQC mask correlations between transcriptomic responses and gene fitness. As an illustration of unexpected connections, we identify a heat-specific synthetic lethality between the disaggregase ClpB and DNA Polymerase I (PolA) mediated by persistent aggregation of the RecA recombinase and toxic persistence of the heat shock regulon. Our findings reveal that stress-induced aggregation is not broadly toxic. Rather, it becomes lethal in specific genetic or environmental contexts due to the depletion of components only needed in those specific circumstances. This work presents a framework to reveal normally hidden fragility in stress responses using gene fitness scores adaptable to a variety of systems.

  PublisherOA PDFDOI

• Comparison of CcrM-dependent methylation in <i>Caulobacter crescentus</i> and <i>Brucella abortus</i> by nanopore sequencing

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-03

  preprintOpen accessSenior authorCorresponding

  Abstract Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order, Caulobacter crescentus , relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such as Brucella abortus , depend on the same systems. We addressed these questions by first measuring CcrM-dependent DNA methylation in Caulobacter and show excellent correlation between nanopore-based detection and previously published results. We then directly measure the impact of Lon-mediated CcrM degradation on the epigenome, verifying that loss of Lon results in pervasive methylation. We also show that the AlkB demethylase has no global impact on DNA methylation during normal growth. Next, we report on the global DNA methylation in Brucella abortus for the first time and find that CcrM-dependent methylation is reliant on Lon but impacts the two chromosomes differently. Finally, we explore the impact of the MucR transcription factor, known to compete with CcrM methylation, on the Brucella methylome and share the results with a publicly available visualization package. Our work demonstrates the utility of nanopore-based sequencing for epigenome measurements in Alphaproteobacteria and reveals new features of CcrM-dependent methylation in a zoonotic pathogen. Importance DNA methylation plays an important role in bacteria to maintain genome integrity and regulate of gene expression. We used nanopore sequencing to directly measure methylated bases in Caulobacter crescentus and Brucella abortus . In Caulobacter , we showed that stabilization of the CcrM methyltransferase upon loss of the Lon protease results in prolific methylation and discovered that the putative methylase AlkB is unlikely to have a global physiological effect. We measured genome-wide methylation in Brucella for the first time, revealing a similar role for CcrM in cell-cycle methylation but a more complex regulation by the Lon protease than in Caulobacter. Finally, we show how the virulence factor MucR impacts DNA methylation patterns in Brucella .

  PublisherOA PDFDOI

• Proteolytic control of FixT by the Lon protease impacts FixLJ signaling in <i>Caulobacter crescentus</i>

  Journal of Bacteriology · 2024-06-28 · 2 citations

  articleOpen accessSenior author

  ABSTRACT Responding to changes in oxygen levels is critical for aerobic microbes. In Caulobacter crescentus , low oxygen is sensed by the FixL-FixJ two-component system which induces multiple genes, including those involved in heme biosynthesis, to accommodate microaerobic conditions. The FixLJ inhibitor FixT is also induced under low oxygen conditions and is degraded by the Lon protease when the oxygen levels are sufficient, which together provides negative feedback proposed to adjust FixLJ signaling thresholds during changing conditions. Here, we address whether degradation of FixT by the Lon protease contributes to phenotypic defects associated with loss of Lon. We find that ∆ lon strains are deficient in FixLJ-dependent heme biosynthesis, consistent with elevated FixT levels as deletion of fixT suppresses this defect. Transcriptomics validate this result as, along with heme biosynthesis, there is diminished expression of many FixL-activated genes in ∆ lon . However, stabilization of FixT in ∆ lo n strains does not contribute to restoring any known Lon-related fitness defect, such as cell morphology defects or stress sensitivity. In fact, cells lacking both FixT and Lon are compromised in viability during growth in standard aerobic conditions. Our work highlights the complexity of protease-dependent regulation of transcription factors and explains the molecular basis of defective heme accumulation in Lon-deficient Caulobacter . IMPORTANCE The Lon protease shapes protein quality control, signaling pathways, and stress responses in many bacteria species. Loss of Lon often results in multiple phenotypic consequences. In this work, we found a connection between the Lon protease and deficiencies in heme accumulation that then led to our finding of a global change in gene expression due in part to degradation of a regulator of the hypoxic response. However, loss of degradation of this regulator did not explain other phenotypes associated with Lon deficiencies demonstrating the complex and multiple pathways that this highly conserved protease can impact.

  PublisherOA PDFDOI

• Allosteric modulation of the Lon protease by effector binding and local charges

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-06

  preprintOpen accessSenior authorCorresponding

  Abstract The ATPase Associated with diverse cellular Activities (AAA+) family of proteases play crucial roles in cellular proteolysis and stress responses. Like other AAA+ proteases, the Lon protease is known to be allosterically regulated by nucleotide and substrate binding. Although it was originally classified as a DNA binding protein, the impact of DNA binding on Lon activity is unclear. In this study, we characterize the regulation of Lon by single-stranded DNA (ssDNA) binding and serendipitously identify general activation strategies for Lon. Upon binding to ssDNA, Lon’s ATP hydrolysis rate increases due to improved nucleotide binding, leading to enhanced degradation of protein substrates, including physiologically important targets. We demonstrate that mutations in basic residues that are crucial for Lon’s DNA binding not only reduces ssDNA binding but result in charge-specific consequences on Lon activity. Introducing negative charge at these sites induces activation akin to that induced by ssDNA binding, whereas neutralizing the charge reduces Lon’s activity. Based on single molecule measurements we find that this change in activity is correlated with changes in Lon oligomerization. Our study provides insights into the complex regulation of the Lon protease driven by electrostatic contributions from either DNA binding or mutations. Highlights ssDNA binding allosterically activates Lon ATP hydrolysis Negative charge at DNA binding site is sufficient for Lon activation Neutralization of charge at DNA binding site inhibits Lon ATP hydrolysis Lon activity is linked to formation of stable Lon hexamers Significance The energy-dependent protease Lon is integral in both eukaryotic and prokaryotic physiology, contributing to protein quality control, stress management, developmental regulation, and pathogenicity. The ability to precisely regulate protein levels through targeted degradation underscores a need for tunability. We find that single-stranded DNA (ssDNA) acts as an allosteric regulator of Lon, leading to enhanced enzymatic activity. Mutations in basic residues crucial for DNA binding were found to affect Lon activity in a charge-specific manner highlighting the importance of electrostatic interactions regulating Lon’s function. Changes in Lon activity due to ssDNA binding or mutations were correlated with its oligomerization state. Our findings provide insights into the activation strategies of Lon, emphasizing the role of electrostatic contribution that modulate nucleotide affinity, oligomerization and proteolysis to advance our understanding of the complex regulatory mechanisms of the Lon protease.

  PublisherOA PDFDOI

• Comparison of CcrM-dependent methylation in <i>Caulobacter crescentus</i> and <i>Brucella abortus</i> by nanopore sequencing

  Journal of Bacteriology · 2024-05-09 · 3 citations

  articleOpen accessSenior author

  ABSTRACT Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order, Caulobacter crescentus , relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such as Brucella abortus , depend on the same systems. We addressed these questions by first measuring CcrM-dependent DNA methylation in Caulobacter and showing excellent correlation between nanopore-based detection and previously published results. We then directly measure the impact of Lon-mediated CcrM degradation on the epigenome, verifying that loss of Lon results in pervasive methylation. We also show that the AlkB demethylase has no global impact on DNA methylation during normal growth. Next, we report on the global DNA methylation in B. abortus for the first time and find that CcrM-dependent methylation is reliant on Lon but impacts the two chromosomes differently. Finally, we explore the impact of the MucR transcription factor, known to compete with CcrM methylation, on the Brucella methylome and share the results with a publicly available visualization package. Our work demonstrates the utility of nanopore-based sequencing for epigenome measurements in Alphaproteobacteria and reveals new features of CcrM-dependent methylation in a zoonotic pathogen. IMPORTANCE DNA methylation plays an important role in bacteria, maintaining genome integrity and regulating gene expression. We used nanopore sequencing to directly measure methylated bases in Caulobacter crescentus and Brucella abortus . In Caulobacter , we showed that stabilization of the CcrM methyltransferase upon loss of the Lon protease results in prolific methylation and discovered that the putative methylase AlkB is unlikely to have a global physiological effect. We measured genome-wide methylation in Brucella for the first time, revealing a similar role for CcrM in cell-cycle methylation but a more complex regulation by the Lon protease than in Caulobacter. Finally, we show how the virulence factor MucR impacts DNA methylation patterns in Brucella .

  PublisherOA PDFDOI

• Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in <i>Caulobacter</i>

  PNAS Nexus · 2024-03-28 · 1 citations

  articleOpen access

  Abstract In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers guanosine 5′-diphosphate 3′-diphosphate and guanosine 5′-triphosphate 3′-diphosphate (collectively known as (p)ppGpp), which affect transcription by binding RNA polymerase (RNAP) to down-regulate anabolic genes. (p)ppGpp also impacts the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important are unclear. In this study, we show that CdnL is down-regulated posttranslationally during starvation in a manner dependent on SpoT and the ClpXP protease. Artificial stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.

  PublisherOA PDFDOI

Recent grants

• Stress related proteases in Caulobacter crescentus

  NIH · $1.6M · 2014–2019

• NIH Grant K99GM084157

  NIH · $180k · 2010

• Regulated Proteolysis in Bacteria Development and Stress Response

  NIH · $3.4M · 2019–2029

• NIH Grant R00GM084157

  NIH · $742k · 2014

Frequent coauthors

• Rilee Zeinert

  National Institute of General Medical Sciences

  27 shared

• Catarina E. Hioe

  James J. Peters VA Medical Center

  21 shared

• Sandra Cohen

  Université de Montréal

  19 shared

• Michael Tuen

  New York University

  17 shared

• Erin D. Goley

  Johns Hopkins Medicine

  16 shared

• Pei‐de Chen

  VA NY Harbor Healthcare System

  16 shared

• Tania A. Baker

  Massachusetts Institute of Technology

  15 shared

• Jonathan S. Weissman

  Whitehead Institute for Biomedical Research

  14 shared