About

Rachel Green received her B.S. in Chemistry at the University of Michigan in 1986. She performed her thesis work in biochemistry in 1993 in the laboratory of Jack Szostak at Harvard University, focusing on structural and functional analysis of catalytic RNAs and the implications of such molecules for the earliest evolution of life. As a postdoctoral fellow at UC Santa Cruz, she began her work on the ribosome with Harry Noller, exploring the diverse functions of rRNA and tRNA in translation. In 1998, she started as an assistant professor in the Department of Molecular Biology and Genetics at The Johns Hopkins University School of Medicine and was promoted to full professor in 2007. Since 2000, her work has been supported by the Howard Hughes Medical Institute (HHMI). Her laboratory focuses on diverse aspects of translation and its regulation in bacteria, yeast, and higher eukaryotic systems, with a recent emphasis on defining the molecular mechanisms that specify the high fidelity of protein synthesis during translation.

Research topics

• Cell biology
• Biology
• Biochemistry
• Genetics

Selected publications

• RIOK3 mediates the degradation of 40S ribosomes

  Molecular Cell · 2025-02-01 · 20 citations

  articleOpen accessCorresponding

  Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces the selective depletion of 40S ribosomes following their ubiquitylation by the E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif, visualized by cryoelectron microscopy (cryo-EM). RIOK3 binding and ubiquitin recognition are essential for 40S ribosome degradation during starvation. RIOK3 induces the degradation of ubiquitylated 40S ribosomes through progressive decay of their 18S rRNA beginning at the 3′ end, as revealed by cryo-EM structures of degradation intermediates. Together, these data define a pathway and mechanism for stress-induced degradation of 40S ribosomes, directly connecting ubiquitylation to regulation of ribosome homeostasis. • Amino acid starvation induces selective degradation of ubiquitylated 40S ribosomes • RIOK3 binds ubiquitylated 40S ribosomes via an unusual ubiquitin-interacting motif • Cryo-EM structures capture 40S ribosome degradation intermediates • RIOK3 binding to 40S ribosomes triggers 18S rRNA decay starting from the 3′ end Huang et al. identify a pathway for stress-induced 40S ribosome degradation: 40S ribosomes ubiquitylated by RNF10 are subsequently bound by the atypical kinase RIOK3, which mediates their degradation by triggering 18S rRNA decay from the 3′ end. Cryo-EM structures capture degradation intermediates, providing insights into the mechanisms of ribosome degradation.

  PublisherDOI

• Single-protein/RNA imaging reveals ZNF598 as a limiting factor in resolving collided ribosomes

  The EMBO Journal · 2025-08-01 · 4 citations

  articleOpen access

  Ribosome-associated protein quality control (RQC) is a surveillance system that identifies and processes aberrant mRNAs with collided ribosomes. ZNF598 plays a key role by ubiquitinating the 40S subunit of collided ribosomes. However, how ZNF598 distinguishes stalled from transient ribosome collisions remains unclear. To address this, we developed a method to visualize the binding of a single protein to a specific mRNA while simultaneously determining its translation status. By endogenously tagging ZNF598 with HaloTag, we observed its strong interaction with RQC reporter mRNAs. We discovered that multiple ZNF598s engage with a single RQC mRNA, suggesting that ZNF598 recognizes more than just the leading collided ribosome in a queue. Overexpressing ZNF598 increased the ribosomal clearance rate, indicating that it is a rate-limiting factor for RQC. Interestingly, a subset of supposedly "normal" mRNAs may be damaged and targeted by ZNF598, underscoring the importance of RQC to maintain the proteome quality even in unstressed conditions. Under global UV-induced RNA damage, ZNF598 recruitment to the reporter RQC mRNA diminished, highlighting its role as a limiting factor in managing widespread ribosome collisions.

  PublisherOA PDFDOI

• HYPK promotes N-terminal protein acetylation through rapid ribosome exchange of NatA

  Molecular Cell · 2025-12-01

  articleOpen access
  PublisherOA PDFDOI

• Homozygous Deletions in AHNAK2 as an Unexpected Genetic Cause of Polyneuropathy (P12-11.019)

  Neurology · 2025-04-07

  article

  To provide a case review of a patient with a rare, genetic cause of polyneuropathy.

  PublisherDOI

• Abstract Wed095: Reduced Hypusination of eIF5A Suppresses Generation of Free Ubiquitin and Protein Ubiquitination Resulting in Heart Failure with Preserved Ejection Fraction

  Circulation Research · 2025-08-01

  article

  Heart failure with preserved ejection fraction (HFpEF) accounts for more than half of all HF, yet effective therapies remain limited. Metabolomics of myocardial biopsies from patients with HFpEF revealed spermidine the most upregulated. Spermidine is critical to ribosomal translation due to its engagement with hypusination of the post-translation modification of eukaryotic translation initiation factor 5A (eIF5A Hyp ). We find eIF5A Hyp to be decreased in HFpEF but not HFrEF, associated with reduced expression of the primary synthetic enzyme deoxy hypusine synthase (DHPS). Accordingly, mice with cardiomyocyte specific conditional knockout of DHPS (cDHPS-KO) were generated and display preserved ejection fraction yet increased E/E’, pulmonary edema, and exercise intolerance. Ribosome profiling and sequencing was performed to assess transcripts with impaired translation, and among those identified, gene ontology highlighted ubiquitin related pathways. CRISPR knock-out of DHPS in neonatal rat cardiomyocytes reduces eIF5A Hyp , total ubiquitinated proteins, and free ubiquitin. Reducing eIF5A Hyp pharmacologically and genetically leads to accumulation of protein aggregates in cardiomyocytes but they are less ubiquitinated. The ubiquitin precursor, UBC encoding 9 ubiquitin monomers, and deubiquitinases, USP7, USP16, and USP9X, are required to generate free ubiquitin, and all have reduced expression in myocytes with reduced eIF5A Hyp , in cDHPS-KO hearts, and human HFpEF myocardium. Transfection of recombinant single ubiquitin suppresses toxicity seen in cardiomyocytes with reduced eIF5A Hyp . In conclusion, we have identified impaired protein quality control that is unique to HFpEF, caused by reduced eIF5A Hyp that in turn impairs translation of UBC and key deubiquitinases required to generate free ubiquitin.

  PublisherDOI

• Advances in the Design of Biomedical Devices for Diabetes Management

  American Journal of Biomedical Engineering · 2025-08-31

  articleOpen access1st authorCorresponding

  Diabetes management has seen remarkable advancements in biomedical engineering, with innovations in device design enabling more effective monitoring, treatment, and overall disease management. This article explores the latest developments in biomedical devices for diabetes management, including continuous glucose monitors (CGMs), insulin pumps, and smart insulin delivery systems. It discusses the role of miniaturization, wireless communication, and personalized treatment strategies in enhancing the management of diabetes, as well as future trends in closed-loop systems and artificial pancreas technologies. Challenges such as device accuracy, patient adherence, and affordability are also addressed.

  PublisherDOI

• 2024 White Paper on Recent Issues in Bioanalysis: Three Way-Cross Validation; Urine Clinical Analysis; Automated Methods; Regulatory Queries on Plasma Protein Binding; Automated Biospecimen Management; ELN Migration; Ultra-Sensitivity Mass Spectrometry ( <u>Part 1A</u> – Recommendations on Advanced Strategies for Mass Spectrometry Assays, Chromatography, Sample Preparation and BMV/Regulated Bioanalysis <u>Part 1B</u> - Regulatory Agencies’ Inputs on Regulated Bioanalysis/BMV)

  Bioanalysis · 2025-01-25 · 5 citations

  articleOpen access

  edition.As in previous years, WRIB continued to gather a wide diversity of international, industry opinion leaders and regulatory authority experts working on both small and large molecules as well as gene, cell therapies and vaccines to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance, and achieving scientific excellence on bioanalytical issues.This 2024 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2024 edition of this comprehensive White Paper has been divided into three parts for editorial reasons.This publication (Part 1) covers in Part 1A the Recommendations on Mass Spectrometry Assays and Regulated Bioanalysis/BMV and in Part 1B the Regulatory Inputs on these topics. Part 3 (Gene Therapy, Cell therapy, Vaccines and Biotherapeutics Immunogenicity) and Part 2 (Biomarkers/BAV, IVD/CDx, LBA and Cell-Based Assays) are published in volume 17 of Bioanalysis, issues 3 and 4 (2025), respectively.

  PublisherOA PDFDOI

• ZAK activation at the collided ribosome

  Nature · 2025-11-19 · 8 citations

  articleOpen access

  . Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.

  PublisherDOI

• CTx001 for geographic atrophy: a gene therapy expressing soluble, truncated complement receptor 1 (mini-CR1)

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-03

  preprintOpen access

  Abstract Over-activation of the complement system is strongly associated with geographic atrophy (GA), a late-stage form of age-related macular degeneration (AMD) and major cause of blindness. Here we report the development of a candidate GA treatment that is a potent complement modifier (mini-CR1) that addresses consequences of complement over-activation including membrane attack complex (MAC) formation. Mini-CR1 acts a potent cofactor for factor I driven proteolysis of C3b leading to iC3b and then C3dg formation; iC3b itself remains a potent opsonin. As well as inhibiting the alternative complement pathway, mini-CR1 acts as a cofactor for C4b degradation thereby inhibiting the classical pathway. Mini-CR1 prevents MAC formation in activated human serum with an IC 50 of 125 nM. Mini-CR1 was shown to cross human Bruch’s membrane ex vivo , implying the ability to cross into the choroidal space. Transduction of RPE cell lines with rAAV2-mini-CR1 (CTx001) resulted in dose-dependent transcription, and both basolateral and apical secretion of mini-CR1 by monolayers of human iPSC derived RPE cells. Mini-CR1 transduction of ARPE19 cells resulted in increased consumption of C3b and iC3b1 in activated culture media and decreased MAC formation on the cell surfaces. Subretinal injection of CTx001 in rats resulted in dose-dependent mini-CR1 production as demonstrated by solid-phase immunoassay. MAC formation following laser induced CNV in a rat model was reduced by 75% in CTx001-treated animals relative to null vector ( p &lt;0.01). This first generation of CTx001 represents a potent single administration complement modifier capable of effectively addressing pathologic complement amplification in the retina/choroid.

  PublisherOA PDFDOI

• Abstract 5506: Inactivation of mTOR is a strategy for tumor resistance to ribosome biogenesis inhibition

  Cancer Research · 2025-04-21

  article

  Abstract Increased ribosome biogenesis supports the need for high translation capacity and is a hallmark of cancer. Targeting this process presents a promising strategy for cancer therapy. We have developed first-in-class inhibitors of RNA polymerase I (Pol I) transcription that block the first and rate-limiting step of ribosome biogenesis, rRNA synthesis. We find that Pol I inhibition by BMH-21 leads to a significant decrease in active ribosomes. We found a broad, but heterogenous efficacy in 18 cancer cell lineages. To identify genes that drive potential resistance to Pol I inhibition, we performed genome-wide CRISPR-Cas9 screens in human colorectal carcinoma cells. These positive selection screens identified high-confidence hits leading to drug resistance and included all key positive regulators of the mTORC1 complex. These findings are striking and counterintuitive given that mTOR is a major driver of ribosome biogenesis and cellular translational programs. The findings were validated using chemical inhibition of mTOR by Torin-1, a catalytic mTOR inhibitor and genetic knockout of an activator of mTOR signaling. Consistently, compromised mTOR activity led to resistance to BMH-21. However, loss of mTOR activity did not abrogate Pol I transcription inhibition by BMH-21. To assess the impact on protein translation, we used polysome profiling and found that BMH-21 treatment caused a severe defect in ribosome biogenesis. Surprisingly, mTOR inactivation partially rescued the translation repressed by Pol I inhibition, suggesting that this rescue could be pivotal for cell survival. To profile translational events, we performed Ribo-seq and RNA-seq in the BMH-21 sensitive and resistant cells. These multi-omics results revealed that mTOR inactivation decreased polysome-based translation on 5’TOP mRNAs encoding ribosomal proteins, suggesting that mTOR inactivation reduces ribosome occupation on ribosomal mRNAs. We propose that mTOR inactivation switches off polysome translation to rearrange active ribosomes for translation of survival-essential mRNAs. We further quantified newly synthesized proteins by AHA-labeling combined with TMT-mass spectrometry. These data show that distinct proteins continue to be translated when both Pol I transcription and mTOR activity are blocked. Next, we will examine preferentially translated proteins in resistant cells, and explore combination therapies to circumvent the drug resistance. In summary, we uncover a new non-genetic model of cancer drug resistance termed as translational fitness that enables cells to survive severe translational repression. These findings reveal an unexpected complication by mTOR inhibitory strategies and have implications for exploring effective drug combinations in cancer therapy. Citation Format: Wenjun Fan, Lijing Yang, Hester Liu, Steffie Pitts, Niladri Sinha, Rajeshkumar N.V., Hariharan Easwaran, Rachel Green, Marikki Laiho. Inactivation of mTOR is a strategy for tumor resistance to ribosome biogenesis inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5506.

  PublisherDOI

Recent grants

• NIH Grant U54GM105816

  NIH · $3.7M · 2019

• NIH Grant R01GM05942506A1

  NIH · $288k · 2009

• NIH Grant R01GM059425

  NIH · $3.4M · 2014

• Biochemistry, Cellular and Molecular Biology Program

  NIH · $32.3M · 1977–2022

• Molecular mechanisms of ribosome pausing and the cellular response

  NIH · $3.5M · 1999–2025

Frequent coauthors

• Boris Zinshteyn

  Johns Hopkins University

  94 shared

• Julie L Brunelle

  Howard Hughes Medical Institute

  91 shared

• Colin Chih‐Chien Wu

  Center for Cancer Research

  78 shared

• Allen R. Buskirk

  Johns Hopkins University

  73 shared

• Niladri K. Sinha

  Johns Hopkins University

  63 shared

• Jamie R Wangen

  Howard Hughes Medical Institute

  50 shared

• Daniel Goldman

  Western University

  48 shared

• Laura N. Lessen

  Howard Hughes Medical Institute

  48 shared

Labs

• The Green Lab @ JHMIPI

Awards & honors

• Supported by Howard Hughes Medical Institute (since 2000)