Bio

Honors & Awards


  • NIH NRSA Postdoctoral Fellowship, NIGMS (2012-15)

Professional Education


  • Doctor of Philosophy, Northwestern University (2011)

Stanford Advisors


Research & Scholarship

Current Research and Scholarly Interests


Translational control and bacterial development

Publications

Journal Articles


  • The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle. PLoS genetics Zhou, B., Schrader, J. M., Kalogeraki, V. S., Abeliuk, E., Dinh, C. B., Pham, J. Q., Cui, Z. Z., Dill, D. L., McAdams, H. H., Shapiro, L. 2015; 11 (1)

    Abstract

    Each Caulobacter cell cycle involves differentiation and an asymmetric cell division driven by a cyclical regulatory circuit comprised of four transcription factors (TFs) and a DNA methyltransferase. Using a modified global 5' RACE protocol, we globally mapped transcription start sites (TSSs) at base-pair resolution, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Out of 2726 TSSs, 586 were shown to be cell cycle-regulated and we identified 529 binding sites for the cell cycle master regulators. Twenty-three percent of the cell cycle-regulated promoters were found to be under the combinatorial control of two or more of the global regulators. Previously unknown features of the core cell cycle circuit were identified, including 107 antisense TSSs which exhibit cell cycle-control, and 241 genes with multiple TSSs whose transcription levels often exhibited different cell cycle timing. Cumulatively, this study uncovered novel new layers of transcriptional regulation mediating the bacterial cell cycle.

    View details for DOI 10.1371/journal.pgen.1004831

    View details for PubMedID 25569173

  • The Interface between Escherichia coli Elongation Factor Tu and Aminoacyl-tRNA BIOCHEMISTRY Yikilmaz, E., Chapman, S. J., Schrader, J. M., Uhlenbeck, O. C. 2014; 53 (35): 5710-5720

    View details for DOI 10.1021/bi500533x

    View details for Web of Science ID 000341543300014

  • The Coding and Noncoding Architecture of the Caulobacter crescentus Genome. PLoS genetics Schrader, J. M., Zhou, B., Li, G., Lasker, K., Childers, W. S., Williams, B., Long, T., Crosson, S., McAdams, H. H., Weissman, J. S., Shapiro, L. 2014; 10 (7)

    Abstract

    Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5'-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5'-RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the coding DNA sequence (CDS). These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach, providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division.

    View details for DOI 10.1371/journal.pgen.1004463

    View details for PubMedID 25078267

  • The interface between Escherichia coli Elongation Factor Tu and aminoacyl-tRNA. Biochemistry Yikilmaz, E., Chapman, S. J., Schrader, J. M., Uhlenbeck, O. C. 2014

    Abstract

    Nineteen of the highly conserved residues of Escherichia coli (E. coli) Elongation factor Tu (EF-Tu) that form the binding interface with aa-tRNA were mutated to alanine to better understand how modifying the thermodynamic properties of EF-Tu-tRNA interaction can affect the decoding properties of the ribosome. Comparison of ΔΔGo values for binding EF-Tu to aa-tRNA show that the majority of the interface residues stabilize the ternary complex and their thermodynamic contribution can depend on the tRNA species that is used. Experiments with a very tight binding mutation of tRNATyr indicate that interface amino acids distant from the tRNA mutation can contribute to the specificity. For nearly all of the mutations, the values of ΔΔGo were identical to those previously determined at the orthologous positions of Thermus thermophilus (T. thermophiles) EF-Tu indicating that the thermodynamic properties of the interface were conserved between distantly related bacteria. Measurement of the rate of GTP hydrolysis on encoded ribosomes revealed that nearly all of the interface mutations were able to function in ribosomal decoding. The only interface mutation with greatly impaired GTPase activity was R223A which is the only one that also forms a direct contact with the ribosome. Finally, the ability of the EF-Tu interface mutants to destabilize the EF-Tu-aa-tRNA interaction on the ribosome after GTP hydrolysis were evaluated by their ability to suppress the hyperstable T1 tRNATyr variant where EF-Tu release is sufficiently slow to limit the rate of peptide bond formation (kpep) . In general, interface mutations that destabilize EF-Tu binding are also able to stimulate kpep of T1 tRNATyr, suggesting that the thermodynamic properties of the EF-Tu-aa-tRNA interaction on the ribosome are quite similar to those found in the free ternary complex.

    View details for DOI 10.1021/bi500533x

    View details for PubMedID 25094027

  • Labeled EF-Tus for rapid kinetic studies of pre-translocation complex formation. ACS chemical biology Liu, W., Kavaliauskas, D., Schrader, J. M., Poruri, K., Birkedal, V., Goldman, E., Jakubowski, H., Mandecki, W., Uhlenbeck, O. C., Knudsen, C. R., Goldman, Y. E., Cooperman, B. S. 2014

    Abstract

    The universally conserved translation elongation factor EF-Tu delivers aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary complex (TC) to the ribosome where it binds to the cognate mRNA codon within the ribosomal A-site, leading to formation of a pretranslocation (PRE) complex. Here we describe preparation of QSY9 and Cy5 derivatives of the variant E348C-EF-Tu that are functional in translation elongation. Together with fluorophore derivatives of aa-tRNA and of ribosomal protein L11, located within the GTPase associated center (GAC), these labeled EF-Tus allow development of two new FRET assays that permit the dynamics of distance changes between EF-Tu and both L11 (Tu-L11 assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding process. We use these assays to examine: i) the relative rates of EF-Tu movement away from the GAC and from aa-tRNA during decoding, ii) the effects of the misreading-inducing antibiotics streptomycin and paromomycin on tRNA selection at the A-site and iii) how strengthening the binding of aa-tRNA to EF-Tu affects the rate of EF-Tu movement away from L11 on the ribosome. These FRET assays have the potential to be adapted for high throughput screening of ribosomal antibiotics.

    View details for DOI 10.1021/cb500409y

    View details for PubMedID 25126896

  • Deciphering the Transcriptional Landscape of Caulobacter crescentus at Base Pair Resolution COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY Zhou, B., Schrader, J., Christen, B., McAdams, H., Shapiro, L. 2013; 8130: 247-247
  • Histidine 66 in Escherichia coli Elongation Factor Tu Selectively Stabilizes Aminoacyl-tRNAs JOURNAL OF BIOLOGICAL CHEMISTRY Chapman, S. J., Schrader, J. M., Uhlenbeck, O. C. 2012; 287 (2): 1229-1234

    Abstract

    The universally conserved His-66 of elongation factor Tu (EF-Tu) stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into Escherichia coli EF-Tu, whereas Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of 10 different aminoacyl-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for different esterified amino acids. However, the H66A mutation does not greatly affect the ability of the ternary complex to bind ribosomes, hydrolyze GTP, or form dipeptide, suggesting that this residue does not directly participate in ribosomal decoding. Selective mutation of His-66 may improve the ability of certain unnatural amino acids to be incorporated by the ribosome.

    View details for DOI 10.1074/jbc.M111.294850

    View details for Web of Science ID 000299170300038

    View details for PubMedID 22105070

  • Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria? NUCLEIC ACIDS RESEARCH Schrader, J. M., Uhlenbeck, O. C. 2011; 39 (22): 9746-9758

    Abstract

    Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that predicts the ?G° of any tRNA to EF-Tu using the sequence of its three T-stem base pairs. Despite dramatic differences in T-stem sequences, the predicted ?G° values for the majority of tRNA classes are similar in all bacteria and closely match the ?G° values determined for E. coli tRNAs. Each individual tRNA class has evolved to have a characteristic ?G° value to EF-Tu, but different T-stem sequences are used to achieve this ?G° value in different bacteria. Thus, the compensatory relationship between the affinity of the tRNA body and the affinity of the esterified amino acid is universal among bacteria. Additionally, we predict and validate a small number of aa-tRNAs that bind more weakly to EF-Tu than expected and thus are candidates for acting as activated amino acid donors in processes outside of translation.

    View details for DOI 10.1093/nar/gkr641

    View details for Web of Science ID 000298186000030

    View details for PubMedID 21893586

  • Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Schrader, J. M., Chapman, S. J., Uhlenbeck, O. C. 2011; 108 (13): 5215-5220

    Abstract

    To better understand why aminoacyl-tRNAs (aa-tRNAs) have evolved to bind bacterial elongation factor Tu (EF-Tu) with uniform affinities, mutant tRNAs with differing affinities for EF-Tu were assayed for decoding on Escherichia coli ribosomes. At saturating EF-Tu concentrations, weaker-binding aa-tRNAs decode their cognate codons similarly to wild-type tRNAs. However, tighter-binding aa-tRNAs show reduced rates of peptide bond formation due to slow release from EF-Tu•GDP. Thus, the affinities of aa-tRNAs for EF-Tu are constrained to be uniform by their need to bind tightly enough to form the ternary complex but weakly enough to release from EF-Tu during decoding. Consistent with available crystal structures, the identity of the esterified amino acid and three base pairs in the T stem of tRNA combine to define the affinity of each aa-tRNA for EF-Tu, both off and on the ribosome.

    View details for DOI 10.1073/pnas.1102128108

    View details for Web of Science ID 000288894800020

    View details for PubMedID 21402928

  • Understanding the Sequence Specificity of tRNA Binding to Elongation Factor Tu using tRNA Mutagenesis JOURNAL OF MOLECULAR BIOLOGY Schrader, J. M., Chapman, S. J., Uhlenbeck, O. C. 2009; 386 (5): 1255-1264

    Abstract

    Measuring the binding affinities of 42 single-base-pair mutants in the acceptor and T Psi C stems of Saccharomyces cerevisiae tRNA Phe to Thermus thermophilus elongation factor Tu (EF-Tu) revealed that much of the specificity for tRNA occurs at the 49-65, 50-64, and 51-63 base pairs. Introducing the same mutations at the three positions into Escherichia coli tRNA CAG Leu resulted in similar changes in binding affinity. Swapping the three pairs from several E. coli tRNAs into yeast tRNA Phe resulted in chimeras with EF-Tu binding affinities similar to those for the donor tRNA. Finally, analysis of double- and triple-base-pair mutants of tRNA Phe showed that the thermodynamic contributions at the three sites are additive, permitting reasonably accurate prediction of the EF-Tu binding affinity for all E. coli tRNAs. Thus, it appears that the thermodynamic contributions of three base pairs in the T Psi C stem primarily account for tRNA binding specificity to EF-Tu.

    View details for DOI 10.1016/j.jmb.2009.01.021

    View details for Web of Science ID 000264383500007

    View details for PubMedID 19452597

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