Harley H McAdams

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Bacterial stalks are nutrient-scavenging antennas
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:11435-6. 2006
  2. pmc System-level design of bacterial cell cycle control
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    FEBS Lett 583:3984-91. 2009
  3. ncbi request reprint A bacterial cell-cycle regulatory network operating in time and space
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, CA 94305, USA
    Science 301:1874-7. 2003
  4. ncbi request reprint The evolution of genetic regulatory systems in bacteria
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, California 94305, USA
    Nat Rev Genet 5:169-78. 2004
  5. ncbi request reprint Oscillating global regulators control the genetic circuit driving a bacterial cell cycle
    Julia Holtzendorff
    Department of Developmental Biology, School of Medicine, Beckman Center, Stanford University, Stanford, CA 94305, USA
    Science 304:983-7. 2004
  6. ncbi request reprint DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus
    Alison K Hottes
    Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
    Mol Microbiol 58:1340-53. 2005
  7. pmc Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease
    Joseph C Chen
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
    EMBO J 25:377-86. 2006
  8. pmc Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function
    Grant R Bowman
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Microbiol 76:173-89. 2010
  9. pmc An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation
    Meng How Tan
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:18985-90. 2010
  10. ncbi request reprint A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator
    Patrick T McGrath
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    Cell 124:535-47. 2006

Collaborators

Detail Information

Publications39

  1. pmc Bacterial stalks are nutrient-scavenging antennas
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:11435-6. 2006
  2. pmc System-level design of bacterial cell cycle control
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    FEBS Lett 583:3984-91. 2009
    ..An essential phospho-signaling system integral to the cell cycle circuitry is central to accomplishing asymmetric cell division...
  3. ncbi request reprint A bacterial cell-cycle regulatory network operating in time and space
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, CA 94305, USA
    Science 301:1874-7. 2003
    ..Modeling the cell cycle probably requires a top-down modeling approach and a hybrid control system modeling paradigm to treat its combined discrete and continuous characteristics...
  4. ncbi request reprint The evolution of genetic regulatory systems in bacteria
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, California 94305, USA
    Nat Rev Genet 5:169-78. 2004
  5. ncbi request reprint Oscillating global regulators control the genetic circuit driving a bacterial cell cycle
    Julia Holtzendorff
    Department of Developmental Biology, School of Medicine, Beckman Center, Stanford University, Stanford, CA 94305, USA
    Science 304:983-7. 2004
    ..CtrA functions as a silencer of the replication origin and GcrA as an activator of components of the replisome and the segregation machinery...
  6. ncbi request reprint DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus
    Alison K Hottes
    Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
    Mol Microbiol 58:1340-53. 2005
    ..This redundant control of gcrA transcription by DnaA (activation) and CtrA (repression) forms a robust switch controlling the decision to proceed through the cell cycle or to remain in the G1 stage...
  7. pmc Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease
    Joseph C Chen
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
    EMBO J 25:377-86. 2006
    ..Thus, temporal activation of the PerP protease and spatial restriction of the polar PodJ(L) substrate cooperatively control the cell cycle-dependent onset of Rip...
  8. pmc Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function
    Grant R Bowman
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Microbiol 76:173-89. 2010
    ..We propose that pole-specific control of PopZ function co-ordinates polar development and cell cycle progression by enabling independent assembly and tethering activities at the two cell poles...
  9. pmc An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation
    Meng How Tan
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:18985-90. 2010
    ..The presence of SciP in the control network enhances the robustness of the cell cycle to varying growth rates...
  10. ncbi request reprint A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator
    Patrick T McGrath
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    Cell 124:535-47. 2006
    ..Thus, a dynamically localized ClpXP proteolysis complex in concert with a cytoplasmic factor provides temporal and spatial specificity to protein degradation during a bacterial cell cycle...
  11. ncbi request reprint High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons
    Patrick T McGrath
    Department of Physics, Stanford University, Varian Physics, 382 Via Pueblo Mall, Stanford, California 94305, USA
    Nat Biotechnol 25:584-92. 2007
    ..Using these motifs, we predict coregulated genes. We verified novel promoter motifs that regulate stress-response genes, including those responding to uranium challenge, a stress-response sigma factor and a stress-response noncoding RNA...
  12. pmc The essential genome of a bacterium
    Beat Christen
    Department of Developmental Biology, Stanford University, Stanford, CA, USA
    Mol Syst Biol 7:528. 2011
    ..The high-resolution strategy used here is applicable to high-throughput, full genome essentiality studies and large-scale genetic perturbation experiments in a broad class of bacterial species...
  13. pmc The caulobacter Tol-Pal complex is essential for outer membrane integrity and the positioning of a polar localization factor
    Yi Chun Yeh
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    J Bacteriol 192:4847-58. 2010
    ..The Caulobacter Tol-Pal complex is thus a key component of cell envelope structure and function, mediating OM constriction at the final step of cell division as well as the positioning of a protein localization factor...
  14. pmc High-throughput identification of protein localization dependency networks
    Beat Christen
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:4681-6. 2010
    ....
  15. pmc Fluorescence bleaching reveals asymmetric compartment formation prior to cell division in Caulobacter
    Ellen M Judd
    Department of Developmental Biology, Stanford University School of Medicine, 300 Beckman Center, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:8235-40. 2003
    ..Monitoring of a fluorescent marker for CtrA showed that the differential degradation of CtrA in the nascent stalk cell compartment occurs only after the cytoplasm is compartmentalized...
  16. pmc Caulobacter requires a dedicated mechanism to initiate chromosome segregation
    Esteban Toro
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 105:15435-40. 2008
    ..Also, a mutation in the ATPase domain of ParA halts segregation without affecting replication initiation. Chromosome segregation in Caulobacter cannot occur unless a dedicated parS guiding mechanism initiates movement...
  17. pmc Assembly of the Caulobacter cell division machine
    Erin D Goley
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Microbiol 80:1680-98. 2011
    ..Our analysis revealed differences in divisome assembly among Caulobacter and other bacteria that establish a framework for identifying aspects of bacterial cytokinesis that are widely conserved from those that are more variable...
  18. pmc Architecture and inherent robustness of a bacterial cell-cycle control system
    Xiling Shen
    Department of Electrical Engineering, 161 Packard Building, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 105:11340-5. 2008
    ....
  19. pmc Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement
    Sun Hae Hong
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:1674-9. 2013
    ..We suggest that the force causing rapid transport of loci remote from the parS centromere to the distal cell pole may arise from the release at the polar region of potential energy within the supercoiled DNA...
  20. pmc A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression
    Antonio A Iniesta
    Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:10935-40. 2006
    ..Dynamic protease localization mediated by a phospho-signaling pathway is a novel mechanism to integrate spatial and temporal control of bacterial cell cycle progression...
  21. doi request reprint Small non-coding RNAs in Caulobacter crescentus
    Stephen G Landt
    Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
    Mol Microbiol 68:600-14. 2008
    ..The probe correlation analysis approach reported here is of general use for large-scale sRNA identification for any sequenced microbial genome...
  22. pmc A DNA methylation ratchet governs progression through a bacterial cell cycle
    Justine Collier
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 104:17111-6. 2007
    ....
  23. pmc Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication
    Patrick H Viollier
    Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:9257-62. 2004
    ....
  24. doi request reprint Three enhancements to the inference of statistical protein-DNA potentials
    Mohammed Alquraishi
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Proteins 81:426-42. 2013
    ..These enhancements are directly applicable to all statistical potentials used in protein-DNA modeling, and we show that they can improve the accuracy of predicted DNA binding sites by up to 21%...
  25. doi request reprint Compaction and transport properties of newly replicated Caulobacter crescentus DNA
    Sun Hae Hong
    Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
    Mol Microbiol 82:1349-58. 2011
    ..While DNA segregation is highly reliable and succeeds in virtually all wild-type cells, the high degree of cell to cell variation in the segregation process is noteworthy...
  26. ncbi request reprint Generating and exploiting polarity in bacteria
    Lucy Shapiro
    Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, CA 94305, USA
    Science 298:1942-6. 2002
    ..Interestingly, M. xanthus, which has nozzles at both poles, can reverse direction by closing one nozzle and opening the other in response to end-to-end interactions between cells...
  27. pmc Conserved modular design of an oxygen sensory/signaling network with species-specific output
    Sean Crosson
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:8018-23. 2005
    ..Thus, the Fix network is a conserved sensory/signaling module whose transcriptional output has been adapted to the unique physiologies of C. crescentus and the nitrogen-fixing rhizobia...
  28. pmc Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle
    Jennifer B Kozdon
    Department of Developmental Biology, Stanford University, Stanford, CA 94305
    Proc Natl Acad Sci U S A 110:E4658-67. 2013
    ..The cognate methyltransferase was identified for one of these motifs as well as for one of two 5-methylcytosine motifs. ..
  29. pmc The architecture and conservation pattern of whole-cell control circuitry
    Harley H McAdams
    Department of Developmental Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
    J Mol Biol 409:28-35. 2011
    ..When sufficient details accumulate, as for Caulobacter cell cycle regulation, the system design has been found to be eminently rational and indeed consistent with good design practices for human-designed asynchronous control systems...
  30. pmc Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle
    Michael T Laub
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, 279 Campus Drive, Palo Alto, CA 94304 5329, USA
    Proc Natl Acad Sci U S A 99:4632-7. 2002
    ..Identification of additional regulatory genes activated by CtrA will serve to directly connect new regulatory modules to the network controlling cell cycle progression...
  31. pmc Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
    Alison K Hottes
    Departments of Electrical Engineering Developmental Biology, Stanford University, Stanford, California 94305, USA
    J Bacteriol 186:1448-61. 2004
    ..crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation...
  32. doi request reprint The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach
    Diego Gonzalez
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, CH 1015, Switzerland, Department of Developmental Biology, Stanford University, CA 94305, USA and Department of Chemistry, Stanford University, CA 94305, USA
    Nucleic Acids Res 42:3720-35. 2014
    ..crescentus and, presumably, of many other Alphaproteobacteria. ..
  33. pmc Codon usage between genomes is constrained by genome-wide mutational processes
    Swaine L Chen
    Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, B300, Stanford, CA 94304, USA
    Proc Natl Acad Sci U S A 101:3480-5. 2004
    ..Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences...
  34. ncbi request reprint Setting the pace: mechanisms tying Caulobacter cell-cycle progression to macroscopic cellular events
    Patrick T McGrath
    Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, CA 94305, USA
    Curr Opin Microbiol 7:192-7. 2004
    ..These mechanisms invoke rapid, precisely timed and even spatially differentiated regulatory responses at important points in the cell cycle...
  35. pmc Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes
    Ellen M Judd
    Department of Applied Physics, Stanford University School of Medicine, 279 Campus Drive, Beckman Center B300, Stanford, CA 94305 5329, USA
    J Bacteriol 187:6874-82. 2005
    ..Here, we also used FLIP experiments to show that both membrane-bound and periplasmic fluorescent proteins diffuse freely through the FtsZ ring during most of the constriction procession...
  36. pmc Direct inference of protein-DNA interactions using compressed sensing methods
    Mohammed Alquraishi
    Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 108:14819-24. 2011
    ..This de novo potential method is directly extendable to other biomolecule interaction domains (enzymes and signaling molecule interactions) and to other classes of molecular interactions...
  37. pmc Graemlin: general and robust alignment of multiple large interaction networks
    Jason Flannick
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 16:1169-81. 2006
    ..We find that Graemlin achieves substantial scalability gains over previous methods while improving sensitivity...
  38. pmc Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
    Ping Hu
    Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A3317, Berkeley, CA 94720, USA
    J Bacteriol 187:8437-49. 2005
    ..Several differentially regulated transcripts from regions previously not known to encode proteins were identified, demonstrating the advantage of evaluating the transcriptome by using whole-genome microarrays...
  39. ncbi request reprint Systems biology of Caulobacter
    Michael T Laub
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Annu Rev Genet 41:429-41. 2007
    ....