James R Williamson

James R Williamson
The Scripps Research Institute | scripps · Department of Integrative Structural and Computational Biology

Ph. D.

About

237
Publications
19,400
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17,291
Citations
Additional affiliations
January 2002 - December 2012
The Scripps Research Institute
January 1992 - December 1995
Education
September 1981 - June 1988
Stanford University
Field of study
  • Chemistry

Publications

Publications (237)
Article
Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations into different groups through computational classification. However, there is a dearth of tools for surveying the heterogeneity landscape, quantitativel...
Preprint
Macromolecular complexes are dynamic entities whose function is often intertwined with their many structural configurations. Single particle cryo-electron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct populations into different groups through compu...
Article
Full-text available
Microorganisms adjust metabolic activity to cope with diverse environments. While many studies have provided insights into how individual pathways are regulated, the mechanisms that give rise to coordinated metabolic responses are poorly understood. Here, we identify the regulatory mechanisms that coordinate catabolism and anabolism in Escherichia...
Article
HIV-1 Gag and Gag-Pol are responsible for viral assembly and maturation and represent a major paradigm for enveloped virus assembly. Numerous intracellular Gag-containing complexes (GCCs) have been identified in cellular lysates using sucrose gradient ultracentrifugation. While these complexes are universally present in Gag-expressing cells, their...
Article
Full-text available
The rate of cell growth is crucial for bacterial fitness and drives the allocation of bacterial resources, affecting, for example, the expression levels of proteins dedicated to metabolism and biosynthesis1,2. It is unclear, however, what ultimately determines growth rates in different environmental conditions. Moreover, increasing evidence suggest...
Article
Highlights: • Real-time tracking of transcription, nascent RNA folding, and protein binding • Nascent RNA folding is complicated by native long-range RNA-RNA interactions • Late-binding ribosomal proteins chaperone nascent rRNA folding early in assembly • Protein-RNA binding dynamics cooperatively decrease during ribosome assembly Abstract: Riboso...
Article
Full-text available
Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of...
Preprint
Full-text available
To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it a...
Article
Ribosome assembly is an efficient, but complex and heterogeneous process during which ribosomal proteins assemble on the nascent ribosomal RNA (rRNA) during transcription. Understanding how the interplay between nascent RNA folding and protein binding determines the fate of transcripts remains a major challenge. Here, using single-molecule fluoresc...
Article
Full-text available
Aging impairs the activation of stress signaling pathways (SSPs), preventing the induction of longevity mechanisms late in life. Here, we show that the antibiotic minocycline increases lifespan and reduces protein aggregation even in old, SSP-deficient Caenorhabditis elegans by targeting cytoplasmic ribosomes, preferentially attenuating translation...
Preprint
Full-text available
Aging impairs the activation of Stress Signaling Pathways (SSPs), preventing the induction of longevity mechanisms late in life. Here we show that the antibiotic minocycline increases lifespan and reduces protein aggregation even in old, SSP-deficient C. elegans by targeting cytoplasmic ribosomes, preferentially attenuating translation of highly tr...
Article
In nature, bacteria frequently experience many adverse conditions, including heat, oxidation, acidity, and hyperosmolarity, which all tend to slow down if not outright stop cell growth. Previous work on bacterial stress mainly focused on understanding gene regulatory responses. Much less is known about how stresses compromise protein synthesis, whi...
Article
Full-text available
A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms and they remain a topic of active investigation. Although much is know...
Article
Full-text available
Overflow metabolism in the presence of oxygen occurs at fast growth rates in a wide range of organisms including bacteria, yeast and cancer cells and plays an important role in biotechnology during production of proteins or metabolic compounds. As recently suggested, overflow metabolism can be understood in terms of proteome allocation, since ferme...
Article
We present a strategy for tackling preferred specimen orientation in single-particle cryogenic electron microscopy by employing tilts during data collection. We also describe a tool to quantify the resulting directional resolution using 3D Fourier shell correlation volumes. We applied these methods to determine the structures at near-atomic resolut...
Article
HIV-1 requires a specialized nuclear export pathway to transport unspliced and partially spliced viral transcripts to the cytoplasm. Central to this pathway is the viral protein Rev, which binds to the Rev response element in stem IIB located on unspliced viral transcripts and subsequently oligomerizes in a cooperative manner. Previous work identif...
Article
Full-text available
The HIV-1 Rev protein activates nuclear export of unspliced and partially spliced viral RNA transcripts, which encode the viral genome and the genes encoding viral structural proteins, by binding to and oligomerizing on the Rev Response Element (RRE). The human DEAD-box protein 1 (DDX1) enhances the RNA export activity of Rev through an unknown mec...
Article
Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical, biophysical and structural techniques to understand macromolecular assembly generally. Recent work inspecting the process in vivo has advanced our understanding of the role of ribosome biogene...
Article
Bacteria growing under different conditions experience a broad range of demand on the rate of protein synthesis, which profoundly affects cellular resource allocation. During fast growth, protein synthesis has long been known to be modulated by adjusting the ribosome content, with the vast majority of ribosomes engaged at a near-maximal rate of elo...
Article
The HIV-1 Rev (Regulator of Expression of Virion) protein activates nuclear export of unspliced and partially spliced viral mRNAs, which encode the viral genome and the genes encoding viral structural proteins. Rev interacts with a highly conserved region, the Rev Response Element (RRE), located within the viral mRNA. In order to activate nuclear e...
Article
Full-text available
Nuclear export of partially spliced or unspliced HIV-1 RNA transcripts requires binding of the viral protein Rev. to the Rev. Response Element (RRE) and subsequent oligomerization in a cooperative manner. Cellular DEAD-box helicase DDX1 plays a role in HIV replication, interacting with and affecting Rev.-containing HIV transcripts in vivo, interact...
Article
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein,...
Article
Full-text available
YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumul...
Article
Full-text available
Our understanding regarding the function of YjeQ (also called RsgA), RbfA, RimM and Era in ribosome biogenesis has been derived in part from the study of immature 30S particles that accumulate in null strains lacking one of these factors. However, their mechanistic details are still unknown. Here, we demonstrate that these immature particles are no...
Article
RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a sh...
Article
The splicing factor SYNCRIP (hnRNP Q) is involved in viral replication, neural morphogenesis, modulation of circadian oscillation and the regulation of the cytidine deaminase APOBEC1. It consists of three globular RNA-recognition motifs (RRM) domains flanked by an N-terminal acid-rich acidic sequence segment domain (AcD12-97 ) and an C-terminal dom...
Article
Ribosome assembly has been studied intensively using Förster resonance energy transfer (FRET) with fluorophore-labeled fragments of RNA produced by chemical synthesis. However, these studies are limited by the size of the accessible RNA fragments. We have developed a replicable unnatural base pair (UBP) formed between (d)5SICS and (d)MMO2 or (d)NaM...
Article
Overflow metabolism refers to the seemingly wasteful strategy in which cells use fermentation instead of the more efficient respiration to generate energy, despite the availability of oxygen. Known as the Warburg effect in the context of cancer growth, this phenomenon occurs ubiquitously for fast-growing cells, including bacteria, fungi and mammali...
Article
Full-text available
Caenorhabditis elegans has emerged as a powerful model to study the genetics of feeding, food-related behaviors, and metabolism. Despite the many advantages of C. elegans as a model organism, direct measurement of its bacterial food intake remains challenging. Here, we describe two complementary methods that measure the food intake of C. elegans. T...
Article
Full-text available
A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome...
Article
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Conference Paper
Full-text available
Ribosome biogenesis in prokaryotes involves coordinated assembly of ~55 protein and 3 RNAs. Many different factors participate in this process, among these are a group of GTPases denoted as ribosome assembly GTPases that are essential for ribosome biogenesis in bacteria and eukaryotes. The GTPases that our laboratory focuses on are RbgA, YphC, and...
Article
Full-text available
Author Summary Ribosomes are complex macromolecular machines that carry out the essential function of protein synthesis in the cell. The assembly of ribosomal subunits is a multistep process that involves the accurate and timely assembly of 3 rRNA molecules and>50 ribosomal-proteins. In recent years many ribosome assembly factors have been identifi...
Data
Proteomic data for sucrose gradient fractions from E. coli BW25113 and E. coli BW25113 ΔrimP. Gradient fractions are labeled as in Figure 1B and Figure 5A. Spectral counts for positively identified proteins are reported for each fraction. A brief gene description is given for each protein. DOI: http://dx.doi.org/10.7554/eLife.04491.019
Data
Screen of the E. coli Keio collection.Cold sensitivity factors for each strain were normalized to 1, based on the mean of all cold sensitivity factors calculated.DOI: http://dx.doi.org/10.7554/eLife.03574.004
Data
Related to Figure 5. Temperature-dependent activity of lamotrigine across bacterial species. DOI: http://dx.doi.org/10.7554/eLife.03574.023
Data
Small molecule screen for cold senstivity.OD values were normalized across screening plates to account for plate-to-plate variations.DOI: http://dx.doi.org/10.7554/eLife.03574.007
Data
In vivo r-protein synthesis rates measured using qMS.Synthesis rates are log2 transformed after normalization to the measured synthesis rate of E. coli in the presence of DMSO. Growth rates are reported as 1/doubling time (hr).DOI: http://dx.doi.org/10.7554/eLife.03574.019
Data
Related to Figure 1. Identification of previously reported cold sensitive ribosome biogenesis genes. All genes presented have been reported as cold sensitive. The Comments column describes whether each gene deletion strain displayed cold sensitivity in our screen of the Keio collection. DOI: http://dx.doi.org/10.7554/eLife.03574.022
Data
R-protein occupancy across sucrose gradients, normalized to the maximum value observed.DOI: http://dx.doi.org/10.7554/eLife.03574.013
Article
Post-transcriptional RNA modifications that are introduced during the multi-step ribosome biogenesis process are essential for protein synthesis. The current lack of a comprehensive method for a fast quantitative analysis of ribosomal RNA modifications significantly limits our understanding of how individual modification steps are coordinated durin...
Article
Full-text available
Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate...
Article
Fluorescence Correlation Spectroscopy (FCS) is widely used to quantitate reaction rates and concentrations of molecules in vitro and in vivo. We recently reported Fluorescence Triple Correlation Spectroscopy (F3CS), which correlates three signals together instead of two. F3CS can analyze the stoichiometries of complex mixtures and detect irreversib...
Article
The ribosome is an essential and highly complex biological system in all living cells. A large body of literature is available on the assembly of the ribosome in vitro, but a clear picture of this process inside the cell has yet to emerge. Here, we directly characterized in vivo ribosome assembly intermediates and associated assembly factors from w...
Article
Caenorhabditis elegans CPB-1 (cytoplasmic polyadenylation element binding protein) and FBF (fem-3 mRNA binding factor) are evolutionary conserved regulators of mRNA translation that belong to the CPEB (cytoplasmic polyadenylation element binding) and PUF (Pumilio and FBF) protein families, respectively. In hermaphrodite worms CPB-1 and FBF control...
Article
The Pumilio and FBF (PUF) family of RNA-binding proteins interacts with protein partners to post-transcriptionally regulate mRNAs in eukaryotes. The interaction between PUF family member fem-3binding factor (FBF) and germline development defective-3 protein (GLD-3) promotes spermatogenesis in Caenorhabditis elegans by increasing expression of the f...
Article
The ribosome is an essential organelle responsible for cellular protein synthesis. Until recently, the study of ribosome assembly has been largely limited to in vitro assays, with few attempts to reconcile these results with the more complex ribosome biogenesis process inside the living cell. Here, we characterize the ribosome synthesis and assembl...
Article
Full-text available
Quaking (QkI) is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in posttranscriptional gene regulation by controlling mRNA translation, stability and splicing. QkI-5 has been shown to regulate mRNA expression in the central nervous system, but little is known about its roles in other...