Bio

Honors & Awards


  • Postdoctoral Fellowship, National Sciences and Engineering Council of Canada (11/2010-11/2012)
  • SB5.0 International Conference Travel Award, Synthetic Biology 5.0 Conference (2011)
  • Best Presentation at Life Sciences Institute Conference, Sigma-Aldrich (2009)
  • Beverley Green Award for outstanding work in photosynthesis research, Western Photosynthesis Conference (2008)
  • University of BC Graduate Fellowship, The University of British Columbia (2008)
  • The Pacific Century Graduate Scholarship, The University of British Columbia (2008)
  • John Richard Turner Fellowship in Microbiology, The University of British Columbia (2007)
  • University of BC Graduate Fellowship, The University of British Columbia (2006)
  • Postgraduate Scholarship, Natural Sciences & Engineering Research Council (2005)
  • Presentation Award, Canadian Institutes of Health Research (2003)
  • Jason Lang Scholarship, Province of Alberta (2000 and 2002)
  • Summer Studentship, Alberta Heritage Foundation for Medical Research (2002 and 2003)
  • Valedictorian, Peace River High School (1998)

Professional Education


  • B.Sc. (Honors), University of Alberta, Biochemistry (2003)
  • Doctor of Philosophy, University of British Columbia (2010)

Stanford Advisors


Research & Scholarship

Current Research and Scholarly Interests


Design and construction of synthetic genomes should enable powerful new approaches to the field of bioengineering and biotechnology applications, such as constructing new metabolic pathways in bacteria to synthesize medicines. However, due to the overwhelming complexity of biological systems, most designs to date have largely recapitulated natural sequences.

My research focuses on developing new methods of simplifying synthetic genomes. I chose to use a small lytic coliphage called phiX174 for my research. The intricate architecture of the circular 5.4 kb phiX174 genome encodes 11 gene products via highly overlapped protein coding sequences spanning multiple reading frames. The combination of small size and complexity makes the phiX174 genome an excellent test case.

Building synthetic phage genomes has been hampered in the past by the extreme toxicity of these viruses to E. coli. Recently, I developed a method that solves this problem by using yeast as a platform to assemble phiX174 genomes via homologous recombination (Jaschke PR, et al. 2012. Virology, in press). Using this method I have decompressed the phiX174 genome (i.e. separated all gene sequences), and showed that the virus is fully functional without gene overlaps.

My future goal is to pioneer a new method of simplifying synthetic genomes, a process I call 'negative genomics'. I will develop this method by systematically identifying and eliminating all cryptic DNA sequences from the phiX174 genome. Negative genomics will enable the building of more reliable and predictable synthetic genomes. Specifically, my work could facilitate concise engineering of bacteriophage genomes for improved diagnostics, next generation antimicrobials, and attenuated vaccines.

Lab Affiliations


Publications

Journal Articles


  • A fully decompressed synthetic bacteriophage empty setX174 genome assembled and archived in yeast VIROLOGY Jaschke, P. R., Lieberman, E. K., Rodriguez, J., Sierra, A., Endy, D. 2012; 434 (2): 278-284

    Abstract

    The 5386 nucleotide bacteriophage øX174 genome has a complicated architecture that encodes 11 gene products via overlapping protein coding sequences spanning multiple reading frames. We designed a 6302 nucleotide synthetic surrogate, øX174.1, that fully separates all primary phage protein coding sequences along with cognate translation control elements. To specify øX174.1f, a decompressed genome the same length as wild type, we truncated the gene F coding sequence. We synthesized DNA encoding fragments of øX174.1f and used a combination of in vitro- and yeast-based assembly to produce yeast vectors encoding natural or designer bacteriophage genomes. We isolated clonal preparations of yeast plasmid DNA and transfected E. coli C strains. We recovered viable øX174 particles containing the øX174.1f genome from E. coli C strains that independently express full-length gene F. We expect that yeast can serve as a genomic 'drydock' within which to maintain and manipulate clonal lineages of other obligate lytic phage.

    View details for DOI 10.1016/j.virol.2012.09.020

    View details for Web of Science ID 000312509300018

    View details for PubMedID 23079106

  • A bchD (Magnesium Chelatase) Mutant of Rhodobacter sphaeroides Synthesizes Zinc Bacteriochlorophyll through Novel Zinc-containing Intermediates JOURNAL OF BIOLOGICAL CHEMISTRY Jaschke, P. R., Hardjasa, A., Digby, E. L., Hunter, C. N., Beatty, J. T. 2011; 286 (23): 20313-20322

    Abstract

    Heme and bacteriochlorophyll a (BChl) biosyntheses share the same pathway to protoporphyrin IX, which then branches as follows. Fe(2+) chelation into the macrocycle by ferrochelatase results in heme formation, and Mg(2+) addition by Mg-chelatase commits the porphyrin to BChl synthesis. It was recently discovered that a bchD (Mg-chelatase) mutant of Rhodobacter sphaeroides produces an alternative BChl in which Mg(2+) is substituted by Zn(2+). Zn-BChl has been found in only one other organism before, the acidophilic Acidiphilium rubrum. Our objectives in this work on the bchD mutant were to 1) elucidate the Zn-BChl biosynthetic pathway in this organism and 2) understand causes for the low amounts of Zn-BChl produced. The bchD mutant was found to contain a Zn-protoporphyrin IX pool, analogous to the Mg-protoporphyrin IX pool found in the wild type strain. Inhibition of ferrochelatase with N-methylprotoporphyrin IX caused Zn-protoporphyrin IX and Zn-BChl levels to decline by 80-90% in the bchD mutant, whereas in the wild type strain, Mg-protoporphyrin IX and Mg-BChl levels increased by 170-240%. Two early metabolites of the Zn-BChl pathway were isolated from the bchD mutant and identified as Zn-protoporphyrin IX monomethyl ester and divinyl-Zn-protochlorophyllide. Our data support a model in which ferrochelatase synthesizes Zn-protoporphyrin IX, and this metabolite is acted on by enzymes of the BChl pathway to produce Zn-BChl. Finally, the low amounts of Zn-BChl in the bchD mutant may be due, at least in part, to a bottleneck upstream of the step where divinyl-Zn-protochlorophyllide is converted to monovinyl-Zn-protochlorophyllide.

    View details for DOI 10.1074/jbc.M110.212605

    View details for Web of Science ID 000291267600019

    View details for PubMedID 21502322

  • Electron transfer in the Rhodobacter sphaeroides reaction center assembled with zinc bacteriochlorophyll PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lin, S., Jaschke, P. R., Wang, H., Paddock, M., Tufts, A., Allen, J. P., Rosell, F. I., Mauk, A. G., Woodbury, N. W., Beatty, J. T. 2009; 106 (21): 8537-8542

    Abstract

    The cofactor composition and electron-transfer kinetics of the reaction center (RC) from a magnesium chelatase (bchD) mutant of Rhodobacter sphaeroides were characterized. In this RC, the special pair (P) and accessory (B) bacteriochlorophyll (BChl) -binding sites contain Zn-BChl rather than BChl a. Spectroscopic measurements reveal that Zn-BChl also occupies the H sites that are normally occupied by bacteriopheophytin in wild type, and at least 1 of these Zn-BChl molecules is involved in electron transfer in intact Zn-RCs with an efficiency of >95% of the wild-type RC. The absorption spectrum of this Zn-containing RC in the near-infrared region associated with P and B is shifted from 865 to 855 nm and from 802 to 794 nm respectively, compared with wild type. The bands of P and B in the visible region are centered at 600 nm, similar to those of wild type, whereas the H-cofactors have a band at 560 nm, which is a spectral signature of monomeric Zn-BChl in organic solvent. The Zn-BChl H-cofactor spectral differences compared with the P and B positions in the visible region are proposed to be due to a difference in the 5th ligand coordinating the Zn. We suggest that this coordination is a key feature of protein-cofactor interactions, which significantly contributes to the redox midpoint potential of H and the formation of the charge-separated state, and provides a unifying explanation for the properties of the primary acceptor in photosystems I (PS1) and II (PS2).

    View details for DOI 10.1073/pnas.0812719106

    View details for Web of Science ID 000266432700025

    View details for PubMedID 19439660

  • Electron Transfer in Rhodobacter sphaeroides Reaction Centers Containing Zn-Bacteriochlorophylls: A Hole-Burning Study Journal of Physical Chemistry B Neupane B, Jaschke P, Saer R, Beatty JT, Reppert M, Jankowiak R 2012; 116 (10): 3457-3466
  • MODIFICATION OF THE GENOME OF RHODOBACTER SPHAEROIDES AND CONSTRUCTION OF SYNTHETIC OPERONS METHODS IN ENZYMOLOGY, VOL 497: SYNTHETIC BIOLOGY, METHODS FOR PART/DEVICE CHARACTERIZATION AND CHASSIS ENGINEERING, PT A Jaschke, P. R., Saer, R. G., Noll, S., Beatty, J. T. 2011; 497: 519-538

    Abstract

    The ?-proteobacterium Rhodobacter sphaeroides is an exemplary model organism for the creation and study of novel protein expression systems, especially membrane protein complexes that harvest light energy to yield electrical energy. Advantages of this organism include a sequenced genome, tools for genetic engineering, a well-characterized metabolism, and a large membrane surface area when grown under hypoxic or anoxic conditions. This chapter provides a framework for the utilization of R. sphaeroides as a model organism for membrane protein expression, highlighting key advantages and shortcomings. Procedures covered in this chapter include the creation of chromosomal gene deletions, disruptions, and replacements, as well as the construction of a synthetic operon using a model promoter to induce expression of modified photosynthetic reaction center proteins for structural and functional analysis.

    View details for DOI 10.1016/B978-0-12-385075-1.00023-8

    View details for Web of Science ID 000291321200023

    View details for PubMedID 21601102

  • Modification of a French pressure cell to improve microbial cell disruption PHOTOSYNTHESIS RESEARCH Jaschke, P. R., Drake, I., Beatty, J. T. 2009; 102 (1): 95-97

    Abstract

    A procedure for modification of the valve stem of a 40 K French pressure cell is described. The modification should be done by a machinist and requires a metalworking lathe. After modification of the valve stem, a torlon 4203 plastic ball is used between the valve stem and valve seat to control the pressure within the cell. The torlon plastic ball is a key component needed to obtain the high pressures required for efficient disruption of microbial cells.

    View details for DOI 10.1007/s11120-009-9493-4

    View details for Web of Science ID 000270447600010

    View details for PubMedID 19731071

  • The PucC protein of Rhodobacter capsulatus mitigates an inhibitory effect of light-harvesting 2 alpha and beta proteins on light-harvesting complex 1 PHOTOSYNTHESIS RESEARCH Jaschke, P. R., LeBlanc, H. N., Lang, A. S., Beatty, J. T. 2008; 95 (2-3): 279-284

    Abstract

    Rhodobacter capsulatus contains lhaA and pucC genes that have been implicated in light-harvesting complex 1 and 2 (LH1 and LH2) assembly. The proteins encoded by these genes, and homologues in other photosynthetic organisms, have been classified as the bacteriochlorophyll delivery (BCD) family of the major facilitator superfamily. A new BCD family phylogenetic tree reveals that several PucC, LhaA and Orf428-related sequences each form separate clusters, while plant and cyanobacterial homologues cluster more distantly. The PucC protein is encoded in the pucBACDE superoperon which also codes for LH2 alpha (PucA) and beta (PucB) proteins. PucC was previously shown to be necessary for formation of LH2. This article gives evidence indicating that PucC has a shepherding activity that keeps the homologous alpha and beta proteins of LH1 and LH2 apart, allowing LH1 to assemble properly. This shepherding function was indicated by a 62% reduction in LH1 levels in DeltaLHII strains carrying plasmids encoding pucBA along with a C-terminally truncated pucC gene. More severe reductions in LH1 were seen when the truncated pucC gene was co-expressed in the presence of C-terminal PucC::PhoA fusion proteins. It appears that interaction between truncated PucC::PhoA fusion proteins and the truncated PucC protein disrupts LH1 assembly, pointing towards a PucC dimeric or multimeric functional unit.

    View details for DOI 10.1007/s11120-007-9258-x

    View details for Web of Science ID 000252107900022

    View details for PubMedID 17922301

  • The photosystem of Rhodobacter sphaeroides assembles with zinc bacteriochlorophyll in a bchD (Magnesium chelatase) mutant BIOCHEMISTRY Jaschke, P. R., Beatty, J. T. 2007; 46 (43): 12491-12500

    Abstract

    A Rhodobacter sphaeroides bchD (magnesium chelatase) mutant was studied to determine the properties of its photosystem in the absence of bacteriochlorophyll (BChl). Western blots of reaction center H, M, and L (RC H/M/L) proteins from mutant membranes showed levels of 12% RC H, 32% RC L, and 46% RC M relative to those of the wild type. Tricine-SDS-PAGE revealed 52% light-harvesting complex alpha chain and 14% beta chain proteins compared to those of the wild type. Pigment analysis of bchD cells showed the absence of BChl and bacteriopheophytin (BPhe), but zinc bacteriochlorophyll (Zn-BChl) was discovered. Zn-BChl binds to light-harvesting 1 (LH1) and 2 (LH2) complexes in place of BChl in bchD membranes, with a LH2:LH1 ratio resembling that of wild-type cells under BChl-limiting conditions. Furthermore, the RC from the bchD mutant contained Zn-BChl in the special pair and accessory BChl binding sites, as well as carotenoid and quinone, but BPhe was absent. Comparison of the bchD mutant RC absorption spectrum to that of Acidiphilium rubrum, which contains Zn-BChl in the RC, suggests the RC protein environment at L168 contributes to A. rubrum special pair absorption characteristics rather than solely Zn-BChl. We speculate that Zn-BChl is synthesized via the normal BChl biosynthetic pathway, but with ferrochelatase supplying zinc protoporphyrin IX for enzymatic steps following the nonfunctional magnesium chelatase. The absence of BPhe in bchD cells is likely related to Zn2+ stability in the chlorin macrocycle and consequently high resistance of Zn-BChl to pheophytinization (dechelation). Possible agents prevented from dechelating Zn-BChl include the RC itself, a hypothetical dechelatase enzyme, and spontaneous processes.

    View details for DOI 10.1021/bi701407k

    View details for Web of Science ID 000250379900049

    View details for PubMedID 17910480

  • Structural and functional characterization of the human NBC3 sodium/bicarbonate co-transporter carboxyl-terminal cytoplasmic domain MOLECULAR MEMBRANE BIOLOGY Loiselle, F. B., Jaschke, P., Casey, J. R. 2003; 20 (4): 307-317

    Abstract

    The sodium bicarbonate co-transporter, NBC3, is expressed in a range of tissues including heart, skeletal muscle and kidney, where it modulates intracellular pH and bicarbonate levels. NBC3 has a three-domain structure: 67 kDa N-terminal cytoplasmic domain, 57 kDa membrane domain and an 11 kDa C-terminal cytoplasmic domain (NBC3Ct). The role of C-terminal domains as important regulatory regions is an emerging theme in bicarbonate transporter physiology. This study determined the functional role of human NBC3Ct and characterized its structure using biochemical techniques. The NBC3 C-terminal domain deletion mutant (NBC3DeltaCt) had only 12 +/- 5% of wild-type transport activity. This low activity is attributable to low steady-state levels of NBC3DeltaCt and almost complete retention inside the cell, as assessed by immunoblots and confocal microscopy, suggesting a role of NBC3Ct in cell surface processing. To characterize the structure of NBC3Ct, amino acids 1127-1214 of NBC3 were expressed as a GST fusion protein (GST.NBC3Ct). GST.NBC3Ct was cleaved with PreScission Protease and native NBC3Ct could be purified to 94% homogeneity. Gel permeation chromatography and sedimentation velocity ultracentrifugation of NBC3Ct indicated a Stokes radius of 26 and 30 angstroms, respectively. Shape modelling revealed NBC3Ct as a prolate shape with long and short axes of 19 and 2 nm, respectively. The circular dichroism spectra of NBC3Ct did not change over the pH 6.2-7.8 range, which rules out a large change of secondary structure as a component of pH sensor function. Proteolysis with trypsin and chymotrypsin identified two proteolytically sensitive regions, R1129 and K1183-K1186, which could form protein interaction sites.

    View details for DOI 10.1080/0968768031000122520

    View details for Web of Science ID 000185918200004

    View details for PubMedID 14578046

Stanford Medicine Resources: