James Chen, PhD
Assistant Professor
Microbiology and Immunology
School of Medicine

Our laboratory investigates fundamental principles of mycobacterial physiology and host interaction. Focusing on the cell envelope, our research is organized around three aims.

First, we investigate how substrates are synthesized, transported, and incorporated to construct the cell envelope in mycobacteria. Complex lipid and glycan precursors are made within the cell but must traverse multiple layers of the envelope to reach their final sites of assembly. The lab studies the protein complexes involved in modifying and translocating these substrates.

Second, we investigate how the biogenesis of the mAGP complex is spatiotemporally orchestrated. This process must be tightly coordinated with cellular elongation and division. We study how the multi-protein assemblies—the elongasome and divisome—are recruited to sites of active growth, such as the cell poles and the division septum. We also aim to define the regulatory signals that govern these assemblies, ensuring the architectural integrity of the cell envelope throughout growth and division.

Third, we probe how the cell envelope functions as the primary host-pathogen interface. Mycobacteria use dedicated protein secretion systems to translocate proteins that interact with the host. The lab studies how these complex protein machines transport these effector proteins across the cell envelope and how these secreted effectors function in the host cell.

To address these questions, our lab combines bacterial genetics, biochemistry, and structural biology. Through this work, we aim to define the fundamental mechanisms of mycobacterial physiology. Our goal is to reveal new vulnerabilities for the development of novel treatments for this group of bacteria.

• A tale of two inhibitors: diarylquinolines and squaramides.
  The EMBO journal 2023 Chen J, Ekiert DC
• A general mechanism for transcription bubble nucleation in bacteria.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA
• An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R
• Structural basis for substrate selection by the SARS-CoV-2 replicase.
  Nature 2023 Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Götte M, Chait BT, Campbell EA, Darst SA
• Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile.
  Nature 2022 Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA
• Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
  Nature structural & molecular biology 2022 Chen J, Wang Q, Malone B, Llewellyn E, Pechersky Y, Maruthi K, Eng ET, Perry JK, Campbell EA, Shaw DE, Darst SA
• Structural origins of Escherichia coli RNA polymerase open promoter complex stability.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
• Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA
• Structural basis for transcription complex disruption by the Mfd translocase.
  eLife 2021 Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA
• Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM.
  Structure (London, England : 1993) 2020 Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT
• The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Müller R, Mooney R, Landick R, Darst SA, Campbell EA
• Diverse and unified mechanisms of transcription initiation in bacteria.
  Nature reviews. Microbiology 2020 Chen J, Boyaci H, Campbell EA
• Time-resolved cryo-EM using Spotiton.
  Nature methods 2020 Dandey VP, Budell WC, Wei H, Bobe D, Maruthi K, Kopylov M, Eng ET, Kahn PA, Hinshaw JE, Kundu N, Nimigean CM, Fan C, Sukomon N, Darst SA, Saecker RM, Chen J, Malone B, Potter CS, Carragher B
• Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex.
  Cell 2020 Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA, Campbell EA
• Stepwise Promoter Melting by Bacterial RNA Polymerase.
  Molecular cell 2020 Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
• E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation.
  eLife 2019 Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA
• Eliminating effects of particle adsorption to the air/water interface in single-particle cryo-electron microscopy: Bacterial RNA polymerase and CHAPSO.
  Journal of structural biology: X 2019 Chen J, Noble AJ, Kang JY, Darst SA
• Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.
  Nature 2019 Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA
• Structural Basis for NusA Stabilized Transcriptional Pausing.
  Molecular cell 2018 Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A
• Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts.
  eLife 2018 Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA
• 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.
  Molecular cell 2017 Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA
• Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex.
  eLife 2017 Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA
• Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence.
  Journal of bacteriology 2017 Garner AL, Rammohan J, Huynh JP, Onder LM, Chen J, Bae B, Jensen D, Weiss LA, Manzano AR, Darst SA, Campbell EA, Nickels BE, Galburt EA, Stallings CL
• CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
  eLife 2015 Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA
• Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD.
  Nucleic acids research 2014 Davis E, Chen J, Leon K, Darst SA, Campbell EA
• Requirements for catalysis in the Cre recombinase active site.
  Nucleic acids research 2010 Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD