shapiro lab stanford

By combining insights from multiple systems, its possible to identify the detailed molecular basis of many interesting evolutionary differences, including classic traits and diseases that affect millions of people around the world. Colocalization experiments with the genomic replicons of A. tumefaciens revealed that the repABC replicons, although preferentially positioned at the cell pole, colocalize only rarely. The NPI number of this provider is 1114219102 and was assigned on May 2011. Chemical Engineering, Imperial College London Other mutants bearing Tn5 insertions retained cross-reacting MCP activity and were altered only in their methyltransferase and methylesterase activities. Thus, it is the signal transduction pathway mediated by CckA that culminates in CtrA activation, which is temporally regulated and essential for cell cycle progression. Flow cytometry was used to screen a collection of temperature-sensitive mutants for those blocked at discrete points in the cell cycle with respect to the replicative status of the chromosome. The transcript start site in front of flaE was determined and the -10 region conforms to the E. coli sigma 28 promoter consensus sequence. However, these mutants efficiently transported fatty acids and had beta-oxidation enzyme levels comparable with that of the wild type. The 0.2 kb fragment contained a homolog of the bacterial gene encoding 4.5 S RNA. Dingwall, A., Zhuang, W. Y., Quon, K., Shapiro, L. The control of timing and spatial organization during Caulobacter cell differentiation. The second region is adjacent to the hook and is approximately 10 nm in length. Transcription of the fliQR operon is initiated at a specific time in the cell cycle, and deletion analysis revealed that the minimal sequence required for transcriptional activation resides within 59 bp of the start site. In addition, transcription of phiCdl DNA by the E. coli enzyme produced a subset of transcripts not synthesized by the C. crescentus enzyme. Chromosomal deletions that extend beyond the cloned region were not complemented by this plasmid. Asymmetric cell division in Caulobacter crescentus yields daughter cells that have different cell fates. Progression of the Caulobacter cell cycle requires temporal and spatial control of gene expression, culminating in an asymmetric cell division yielding distinct daughter cells. B.S. Ramya Deshpande, SURF Scholar 2019-20 PhD at Harvard B.S. The lower rings were all approximately 21 nm in diameter, although they varied significantly in width. Analysis of mutations in the IHF-binding region of the hook operon demonstrated that an intact IHF-binding site is necessary for transcription in vivo. Mutations that inhibited dynamic PopZ localization inhibited the recruitment of other factors to cell poles. Cell death also occurred when phospholipid synthesis was inhibited by cerulenin. Postdoctoral Scholar, 2016-19 Bacteria which appear not to possess extrachromosomal elements, e.g., Caulobacter crescentus, did not show homology with any insertion sequences tested. The sequential changes in the chromosomal methylation state serve to couple the progression of DNA replication to cell-cycle events regulated by the master transcriptional regulatory cascade, thus providing a ratchet mechanism for robust cell-cycle control. Ptacin, J. L., Gahlmann, A., Bowman, G. R., Perez, A. M., von Diezmann, A. R., Eckart, M. R., Moerner, W. E., Shapiro, L. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. [email protected], x=ecriadoh, Willow Coleman Biol. August, J. T., EOYANG, L., FRANZE DE FERNANDEZ, M. T., Hasegawa, S., Kuo, C. H., RENSING, U., Shapiro, L. Resolution of two factors required in the Q-beta-RNA polymerase reaction. An inducible promoter is a useful tool for the controlled expression of a given gene. Research Technician Overall, the core circuit topology of the Fix network is conserved between the rhizobia and C. crescentus, a free-living aerobe that cannot fix nitrogen, respire anaerobically, or metabolize hydrogen. Ph.D. Student, Bioengineering University of California, San Francisco, Gabrielle Ho Hong, S., Toro, E., Mortensen, K. I., de la Rosa, M. A., Doniach, S., Shapiro, L., Spakowitz, A. J., McAdams, H. H. Chromosome architecture is a key element of bacterial cellular organization, Deciphering the Transcriptional Landscape of Caulobacter crescentus at Base Pair Resolution. Chemistry and Biotechnology, University of Tokyo The acidic phospholipids, phosphatidylglycerol and cardiolipin, comprise approximately 87% of the total phospholipids. Work from several Caulobacter labs has revealed that differentiation requires concerted regulation by several two-component system (TCS) signaling pathways that are differentially positioned at the poles of the predivisional cell (Figure 1). We demonstrate here that each of these genes is also required for the expression of chemotaxis methylation genes known to map elsewhere on the chromosome. The total group of CtrA-regulated genes includes those involved in polar morphogenesis, DNA replication initiation, DNA methylation, cell division, and cell wall metabolism. Nucleoid-associated proteins (NAPs) play a pivotal role in this process, so their detailed characterization is crucial for our understanding of DNA organization into bacterial cells. Rice University, Dr. Hunter Davis The membrane-bound DivJ and PleC histidine kinases, which are asymmetrically localized at the opposite poles of the predivisional cell, control the temporal and spatial localization of DivK. and M.S. Research Technician Shapiro completed postdoctoral research at Stanford University Medical School and was named a Guggenheim Fellow at MITs Center for Cancer Research. However, 27 GANTC sites remained unmethylated throughout the cell cycle, suggesting that these protected sites could participate in epigenetic regulatory functions. Its chromosome replication origin (Cori) may be prototypical of the large and diverse class of alpha-proteobacteria. The mutant strain, AE6000 , was altered in both of these regulatory functions. The dnaA gene is preferentially transcribed from a fully methylated promoter. [email protected]. Degradation of the CtrA response regulator normally coincides with initiation of DNA replication, but in strains lacking SsrA activity there is a 40-min delay between the degradation of CtrA and replication initiation. When ccrM gene expression is placed under control of a constitutive promoter, these chromosomal sites are fully methylated throughout the cell cycle. We find that the CtrA proteolysis adaptor protein PopA assumes distinct oligomeric states at the two cell poles through asymmetrically distributed c-di-GMP: dimeric at the stalked pole and monomeric at the swarmer pole. Previous microarray experiments revealed that several Caulobacter genes are significantly upregulated in response to uranium but not in response to other heavy metals. The bacterial chromosome encodes information at multiple levels. UCSD, Prof. George Lu Ph.D. Student, Bioengineering, Defended 2020 Can we use ultrasound to remote-control the location and motion of specific cells? The region downstream of the dnaX AUG, which is important for efficient translation, exhibits homology with the corresponding region from the Caulobacter hemE gene adjacent to the replication origin. Postdoctoral Scholar, 2014-16 The maintenance of cell shape in Caulobacter crescentus requires the essential gene mreB, which encodes a member of the actin superfamily and the target of the antibiotic, A22. The genes involved in the biogenesis of the flagellum and the chemotaxis machinery are temporally regulated during the Caulobacter crescentus cell cycle. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress. Postdoctoral Scholar The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. View details for Web of Science ID A1995QB30700010, View details for PubMedCentralID PMC176597, View details for Web of Science ID A1995BG35H00001. The time of methyltransferase expression coincides with the time of methylation of these three chromosomal sites and of plasmid DNA in the predivisional cell. Previous studies have implicated two histidine kinases, DivJ and PleC, and the response regulator, DivK, in the regulation of morphogenesis in the dimorphic bacterium Caulobacter crescentus. This is in contrast to a subset of flagellar genes which are transcribed from the chromosome in the incipient swarmer portion of the predivisional cell. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. Isolation of the full-length ccrM genes from the aquatic bacterium C. crescentus, the soil bacterium R. meliloti, and the intracellular pathogen B. abortus showed that this sequence conservation extends over the entire protein. B.S. The CtrA master transcriptional regulator is a central control element in Caulobacter cell cycle progression and polar morphogenesis. In addition, dynamically localized DNA-binding proteins ensure that DNA segregation is coupled to the timing and cellular position of the cytokinetic ring. We have also identified a new structural feature at the flagellated pole and the tip of the stalk: the 10-nm polar particle. Stanford AI Lab Papers and Talks at ICLR 2023. Citation: Roussel, Edelen et al., Physical Review Letters, 5 April 2023 (https://doi.org/10.1103/PhysRevLett.130.145001). Saurabh, S., Perez, A., Comerci, C., Shapiro, L., Moerner, W. A Localized Complex of Two Protein Oligomers Controls the Orientation of Cell Polarity. Postdoctoral Scholar (co-advised with Richard Andersen) The activity of the enzyme shows an unusual sensitivity to salt levels, apparently dissociating more rapidly from methylated DNA product as the salt level is decreased. [email protected] In an effort to understand this developmental control of replication, we employed pulsed-field gel electrophoresis to localize and to isolate the chromosomal origin of replication. The flgH gene, encoding the L-ring protein, is also transcribed from an internal promoter. To define the mechanisms that mediate this temporal and spatial control, fla genes whose products are not known were accessed by the insertion of transposon-carried drug resistance markers. Because regulatory proteins are among those that reside at specific cellular sites, it is now necessary to consider three-dimensional organization when describing the genetic networks that control bacterial cells. Such dynamic protein localization is essential for polar organelle development, establishment of asymmetry, and chromosome replication during the Caulobacter crescentus cell cycle. Here, we show that ATP depletion promotes phase separation in bacterial condensates composed of intrinsically disordered proteins. Evidence that flaE and flaY are transcribed as a polycistronic message includes (1) the polar effect of Tn5 insertions; (2) deletion analysis showing that the flaE promoter is essential for complementation of both flaE and flaY alleles; and (3) nuclease S1 assays showing protection of a transcript spanning both genes. A mutation in the flaD gene results in the assembly of a partial basal body which is missing the outermost P and L rings as well as the external hook and filament (K.M. In addition, increasing the cellular content of sigma32 by introducing a plasmid-encoded copy of rpoH induced DnaK expression in C. crescentus cultures grown at 30 degrees C. The C. crescentus rpoH gene was transcribed from either of two heat shock consensus promoters. Research Technician The effect of cyclic AMP on growth on sugars metabolized by inducible enzymes, as well as on sugars metabolized by constitutive enzymes, may represent a regulatory system common to both types of sugar utilization, since they share features that differ from glucose utilization, namely, temperature-sensitive growth and low intracellular concentrations of cyclic guanosine 3',5'-monophosphate. Menlo Park, Calif. The Department of Energys SLAC National Accelerator Laboratory and Stanford University today announced the launch of a new joint battery center at SLAC. Cell type determinants in stalked progeny promote entry into S phase, whereas swarmer progeny remain in G1 phase. Homologs of GapR, which are ubiquitous among the -proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. To explain the phenotype of both the secA and ffs36 strains, we propose that a cell-cycle checkpoint prevents further progression through the cell-cycle in response to increased intracellular levels of heat shock and misfolded proteins. View details for Web of Science ID 000079706600016, View details for PubMedCentralID PMC93667. View details for Web of Science ID 000260532500013, View details for PubMedCentralID PMC2655310. Teaching staff, Understanding of the cell cycle control logic in Caulobacter has progressed to the point where we now have an integrated view of the operation of an entire bacterial cell cycle system functioning as a state machine. CcrM, an adenine DNA methyltransferase, is essential for viability in Caulobacter crescentus. Postdoctoral Scholar, 2014-17 Evidence suggests that the protein product of some fla and che genes is targeted to the incipient swarmer cell pole. Cell division in Gram-negative organisms requires coordinated invagination of the multilayered cell envelope such that each daughter receives an intact inner membrane, peptidoglycan (PG) layer and outer membrane (OM). The start site of the fliLM operon lies 166 bp from the divergently transcribed flaCBD operon that encodes several basal body genes. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. The expression of the Caulobacter ccrM gene and the activity of its product, the M.Ccr II DNA methyltransferase, are limited to a discrete portion of the cell cycle (G. Zweiger, G. Marczynski, and L. Shapiro, J. Mol. Nateras cell-free DNA tests help inform more personalized health caredecisions. In contrast, PopZ and SpmX cannot be directly identified in CET. We have attempted to develop the studies initiated by Poindexter,Stove and Stanier, and Schmidt and Stanier (16, 17, 20) with the Caulobacter genus so that these bacteria can serve as a model system for prokaryotic differentiation.

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