Research Summary

Our laboratory’s research activities are centered on the general areas of bacterial molecular biology, physiology and genetics, with an emphasis on the regulation of gene expression, and protein structure and function. Some of the techniques used are molecular cloning, gene fusions, site-directed mutagenesis, RNA analyses, and purification of proteins.

Gene Regulation
One area of research in our laboratory is on gene structure and expression in photosynthetic bacteria. We study changes in transcription initiation, mRNA processing and protein-protein interactions in response to environmental factors such as oxygen concentration and light intensity, and a newly discovered quorum sensing pathway. The genomes of several species of purple photosynthetic bacteria are being sequenced, with complete or nearly complete sequences available at this time. We are using these and other DNA sequences to discover new genes, to investigate their regulation of expression, and the function of their protein products.

Gene Transfer Agent
We are also studying a novel bacteriophage-like genetic exchange element called the “gene transfer agent”, or GTA. The production of GTA is controlled by changes in environmental conditions that are sensed by a cellular signal transduction system, which produces a burst of GTA production in the stationary phase of laboratory cultures. The nature of the signal(s), and the identities and activities of regulatory factors are of great interest to us.

Photosynthetic Reaction Center
The crystal structures of several purple bacterial photosynthetic reaction centers and light-harvesting complexes have been solved and shown to be highly conserved. We are using this structural information to design and interpret site-directed mutagenesis experiments to address questions about how individual proteins bind to each other and to cofactors, and pathways of charge transfer within and between protein complexes. We are working collaboratively with John. D. Madden’s group in the Department of Electrical and Computer Engineering on the design and fabrication of hybrid protein/synthetic solar energy devices.

Funding Sources
Research in the Beatty group is supported by funding from the Canadian Institutes of Health Research (CIHR), Genome BC, and the Natural Sciences and Engineering Research Council (NSERC). Daniel Jun is supported by an NSERC PGS D scholarship.

Bio

Ph.D. Indiana University, Microbiology (1980)
Postdoctoral, Stanford University School of Medicine (1983)

Publications

2016

      1. Pan J, Saer RG, Lin S, Guo Z, Beatty JT, and NW Woodbury (2016). Electron transfer in bacterial reaction centers with the photoactive bacteriopheophytin replaced by a
        bacteriochlorophyll through coordinating ligand substitution. Biochemistry 55:4909−4918 PMID: 27478991.
      2. Jankowiak, R, O Rancova, J Chen, A Kell, RG Saer, JT Beatty, and D Abramavicius (2016). Mutation-induced changes in the protein environment and site energies in the
        (M)L214G mutant of the Rhodobacter sphaeroides bacterial reaction center. J Phys Chem B, 120:7859-7871; PMID: 27458891 DOI: 10.1021/acs.jpcb.6b06151.
      3. Kuchinski K, CA Brimacombe, AB Westbye, H Ding , JT Beatty (2016). The SOS response master regulator LexA regulates the gene transfer agent of Rhodobacter capsulatus
        and represses transcription of the signal transduction protein CckA. J Bacteriol 198:1137–1148.
      4. Westbye, AB, K Kuchinski, CK Yip, JT Beatty (2016). The gene transfer agent RcGTA contains head spikes needed for binding to the Rhodobacter capsulatus polysaccharide
        cell capsule. J Mol Biol 428:477–491.

2015

      1. Brimacombe, CA, H Ding, JA Johnson, JT Beatty (2015). Homologues of genetic transformation DNA import genes are required for Rhodobacter capsulatus gene transfer
        agent recipient capability regulated by the response regulator CtrA. J. Bacteriol 197: 2653-2663.
      2. Yaghoubi, H, Lafalce, E, Jun, D, Jiang, X, Beatty, JT, Takshi, A (2015). Large photocurrent response and external quantum efficiency in bio-photoelectrochemical cells
        incorporating reaction center plus light harvesting complexes. Biomacromolecules 16:1112-1118.

2014

      1. Cedric A. Brimacombe, Hao Ding and J. Thomas Beatty (2014). Rhodobacter capsulatus DprA is essential for RecA-mediated Gene Transfer Agent (RcGTA) recipient capability regulated by quorum-sensing and the CtrA response regulator. Molec Microbiol, accepted manuscript online | DOI: 10.1111/mmi.12628
      2. Seyed M. Mirvakili, Joanna E. Slota, Ashwin R. Usgaocar, Ali Mahmoudzadeh, Daniel Jun, Mehr Negar Mirvakili, J. Thomas Beatty and John D. W. Madden (2014). Photoactive Electrodes Incorporating Electrosprayed Bacterial Reaction Centers. Advanced Funct published online: DOI: 10.1002/adfm.201400350
      3. Dutta PK, Lin S, Loskutov A, Levenberg S, Jun D, Saer R, Beatty JT, Liu Y, Yan H, Woodbury NW. (2014). Reengineering the optical absorption cross-section of photosynthetic reaction centers. J Am Chem Soc. 4599-604 dx.doi.org/10.1021/ja411843k.
      4. Ding H, Moksa MM, Hirst M, Beatty JT (2014). Draft Genome Sequences of Six Rhodobacter capsulatus Strains, YW1, YW2, B6, Y262, R121, and DE442. Genome Announc. 2. pii: e00050-14. doi: 10.1128/genomeA.00050-14.
      5. Fixen, K. R., A. W. Baker, E. A. Stojković, J. T. Beatty, and C. S. Harwood (2014). Apo-bacteriophytochromes modulate bacterial photosynthesis in response to low light. Proc. Natl. Acad. Sci. USA 111:E237-44. doi: 10.1073/pnas.1322410111.
      6. Saer, RG, Pan J, Hardjassa, A., Lin S., F.I. Rosell, A.G. Mauk, N.W. Woodbury, M.E. Murphy, and J.T. Beatty (2014). Structural and kinetic properties of Rhodobacter sphaeroides photosynthetic reaction centers containing exclusively Zn-coordinated bacteriochlorophyll as bacteriochlorin cofactors. Biochim Biophys Acta, 1837:366–374
      7. Jun, D., Saer, R.G., Madden, J.D., and J.T. Beatty (2014). Use of new strains of Rhodobacter sphaeroides and a modified simple culture medium to increase yield and facilitate purification of the reaction centre. Photosynth Res 120:197-205.

2013

      1. Westbye, A.B., Leung, M.M., Florizone, S., Taylor, T.A., Johnson, J.A., Fogg P.C., Beatty, J.T. (2013). Phosphate concentration and the putative sensor kinase protein CckA modulate cell lysis and release of the Rhodobacter capsulatus gene transfer agent. J Bacteriol 195:5025-5040.
      2. Pan J, Saer RG, Lin S, Guo Z, Beatty JT, and NW Woodbury (2013). The protein environment of the bacteriopheophytin anion modulates charge separation and charge recombination in bacterial reaction centers. J Phys Chem B. 117:7179–7189.
      3. Brimacombe CA, Stevens A, Jun D, Mercer R, Lang AS, and JT Beatty. (2013) Quorum-sensing regulation of a capsular polysaccharide receptor for the Rhodobacter capsulatus gene transfer agent (RcGTA). Mol Microbiol. 87:802-817.
      4. Saer, RG, A. Hardjasa, F.I. Rosell, A.G. Mauk, M.E. Murphy, J.T. Beatty (2013). Role of Rhodobacter sphaeroides photosynthetic reaction center residue M214 in the composition, absorbance properties, and conformations of HA and BA cofactors. Biochemistry 52:2206-2217.
      5. Vasilev, Cvetelin, Amanda A. Brindley, John D. Olsen, Rafael G. Saer, J. T. Beatty, and C. N. Hunter (2013). Nano-mechanical mapping of the interactions between surface-bound RC-LH1-PufX core complexes and cytochrome c2 attached to an AFM probe. Photosynth. Res. Published online 29 Mar.
      6. Leung, M.M., C.A. Brimacombe, and J. T. Beatty (2013). Transcriptional regulation of the Rhodobacter capsulatus response regulator ctrA gene. Microbiology 159:96-106

2012

      1. Yaghoubi H, Li Z, Jun D, Saer R, Slota JE, Beerbom M, Schlaf R, Madden JD, Beatty JT, and Takshi A. 2012. The role of gold-adsorbed photosynthetic reaction centers and redox mediators in the charge transfer and photocurrent generation in a bio-electrochemical cell. J. Phys. Chem. C. 116(47): 24868-77. http://pubs.acs.org/doi/abs/10.1021/jp306798p
      2. Neupane B, Jaschke P, Saer R, Beatty JT, Reppert M, and Jankowiak R. 2012. Electron transfer in Rhodobacter sphaeroides reaction centers containing Zn-bacteriochlorophylls: a hole-burning study. J. Phys. Chem. B. 116(10): 3457-66 http://pubs.acs.org/doi/abs/10.1021/jp300304r
      3. Leung, M.M., C.A. Brimacombe, and J. . Beatty (2012). Transcriptional regulation of the Rhodobacter capsulatus response regulator ctrA gene. In press, Microbiology
      4. Lang, A.S., O. Zhaxybayeva, and J.T. Beatty (2012). Prokaryotic gene transfer agents. Nature Rev. Microbiol. 10:472-482.
      5. Fogg, P.C.M., A. B. Westbye, and J.T. Beatty (2012). One for all or all for one: Heterogeneous expression and host cell lysis are key to gene transfer agent activity in Rhodobacter capsulatus. PLoS One, 7(8): e43772. doi:10.1371/journal.pone.0043772.
      6. Mercer, R.G., M. Quinlan, A.R. Rose, S. Noll, J.T.Beatty and A.S. Lang (2012). Regulatory systems controlling motility and gene transfer agent production and release in Rhodobacter capsulatus. FEMS Microbiol Lett 331:53-62.
      7. Zheng, Q., R. Zhang P.C.M. Fogg, J.T. Beatty and N. Jiao (2012). Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes. PLoS One 7(4): e35790. doi:10.1371/journal.pone.0035790.
      8. Leung, M.M., C.A. Brimacombe, G. B. Spiegelman and J.T. Beatty (2012).The GtaR protein negatively regulates transcription of the gtaRI operon and modulates gene transfer agent (RcGTA) expression in Rhodobacter capsulatus. Molec. Microbiol. 83:759-774.

2011

      1. Mahmoudzadeh A, Saer R, Jun D, Mirvakili SM, Takshi A, Iranpour B Oullet E, Lagally ET, Madden JDW, and Beatty JT. 2011. Photocurrent generation by direct electron transfer using photosynthetic reaction centres. Smart Mater. Struct. 20: 094019 http://iopscience.iop.org/0964-1726/20/9/094019
      2. Fogg, P.C.M, A.P. Hynes, E. Digby; A.S. Lang; J.T. Beatty (2011). Characterization of a newly discovered Mu-like bacteriophage, RcapMu, in Rhodobacter capsulatus strain SB1003. Virology 421: 211–221.
      3. Halsey,C.M, J. Xiong, O.O. Oshokoya, J.A. Johnson, S. Shinde, J.T. Beatty, G. Ghirlanda, R.D. JiJi, and J.W. Cooley (2011). Simultaneous observation of peptide backbone lipid solvation and a-helical structure by deep-UV resonance Raman spectroscopy. ChemBioChem 12:2125-2128.
      4. Jaschke, P.R., A. Hardjasa, E.L. Digby, C.N. Hunter and J.T. Beatty. (2011) A BchD (Mg-chelatase) mutant of Rhodobacter sphaeroides synthesizes zinc-bacteriochlorophyll through novel zinc-containing intermediates. J. Biol. Chem. 286: 20313–20322.
      5. Mahmoudzadeh, A. , R. Saer, D. Jun, S.M. Mirvakili, A. Takshi, B. Iranpour, J.D.W. Madden and J.T. Beatty (2011). Direct electron transfer in photosynthetic reaction center-based photovoltaic devices. Smart Material Struct. 20:094019.
      6. Jaschke, P.R., R.G. Saer, S. Noll and J.T. Beatty (2011). Modification of the genome of Rhodobacter sphaeroides and construction of synthetic operons. Meth. Enzymol. 497:519-538.
      7. Shelswell, K. and J.T. Beatty (2011). Coordinated, long-range, solid-substrate movement of the purple photosynthetic bacterium Rhodobacter capsulatus. PLoS ONE 6:e19646.2010.
      8. Takshi A, Madden JDW, Mahmoudzadeh A, Saer R, and Beatty JT. 2010. A photovoltaic device using an electrolyte containing photosynthetic reaction centers. Energies 3(11): 1721-7 http://www.mdpi.com/1996-1073/3/11/1721
      9. Takshi, A., J.D.W. Madden, A. Mahmoudzadeh, R. Saer and J.T. Beatty (2010). A photovoltaic device using an electrolyte containing photosynthetic reaction centers. Energies 3:1721-1727.
      10. Mercer, R.G., S.J. Callister, M.S. Lipton, L. Pasa-Tolic, H. Strnad, V. Paces, J.T Beatty and A.S. Lang (2010). Loss of the response regulator CtrA causes pleiotropic effects on gene expression in Rhodobacter capsulatus but does not affect growth phase regulation. J. Bacteriol. 192: 2701-2710.
      11. Lang, A.S., C. Harwood, and J.T. Beatty (2010). Evolutionary relationships among antenna proteins of purple phototrophic bacteria. In “Functional genomics and evolution of photosynthetic systems”; Burnap, R. and Vermaas, W. (eds), Springer, in press.
      12. Leung, M.M., S.M. Florizone, T.A. Taylor, A.S. Lang and J.T. Beatty (2010). The gene transfer agent of Rhodobacter capsulatus. In “Recent Advances in Phototrophic Prokaryotes”; P.C. Hallenbeck (ed), Springer.
      13. Lang, A.S. and J.T. Beatty (2010). Gene transfer agents and defective bacteriophages as sources of extracellular prokaryotic DNA. In “Extracellular Nucleic Acids”; Y. Kikuchi and E. Rykova (eds), Springer.
      14. Li, M., S. Noll and J.T. Beatty (2010). Bacteriophytochrome-dependent regulation of light-harvesting complexes in Rhodopseudomonas palustris anaerobic cultures. Curr. Microbiol. 61: 429-434.

2009

      1. Lin, S., P.R. Jaschke, H. Wang, M. Paddock, A. Tufts, J.P. Allen, F.I. Rosell, G.A. Mauk, M. Okamura, N.W. Woodbury, and J.T. Beatty (2009). Electron transfer in the Rhodobacter sphaeroides reaction center assembled with zinc bacteriochlorophyll. Proc. Natl. Acad. Sci. USA. 106:8537-8542.
      2. Jaschke, P.R., I. Drake and J.T. Beatty (2009). Modification of a French pressure cell to improve microbial cell disruption. Photosynth. Res. 102:95-97.
      3. Hunter, C.N., F. Daldal, M. Thurnauer and J.T. Beatty (2009). Preface. In “The Purple Phototrophic Bacteria”; C.N. Hunter, F. Daldal, M. Thurnauer and J.T. Beatty (eds), Springer
      4. Takshi, A., J.D. Madden and J.T. Beatty (2009). Diffusion model for charge transfer from a photosynthetic reaction center to an electrode in a photovoltaic device. Electrochim. Acta 54:3806-3811.

2008

      1. Oda, Y., F.W. Larimer, P.S.G. Chain, S. Malfatti, M.V. Shin, L.M. Vergez, L.Hauser, M.L. Land, S. Braatsch, J.T. Beatty, D.A. Pelletier, A.L. Schaefer and C.S. Harwood (2008). Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proc. Natl. Acad. Sci. USA 105:18543–18548.
      2. Rathgeber, C., M. Lince, J. Alric, A.S. Lang, E. Humphrey, R.E. Blankenship, A. Verméglio, F.G. Plumley, C.L. Van Dover, J.T. Beatty, and V. Yurkov (2008). Vertical distribution and characterization of aerobic phototrophic bacteria at the Juan de Fuca Ridge in the Pacific Ocean. Photosynth. Res. 97:235-244.

2007

      1. Jaschke, P. R., and J. T. Beatty (2007). The photosystem of Rhodobacter sphaeroides assembles with zinc-bacteriochlorophyll in a bchD (magnesium-chelatase) mutant. Biochemistry, 46:12491-12500.
      2. Jaschke, P. R., H. N. LeBlanc, A. S. Lang, and J. T. Beatty (2007). The PucC protein of Rhodobacter capsulatus mitigates an inhibitory effect of light-harvesting 2 a and b proteins on light-harvesting complex 1. Photosynth. Res. 95:279-284.
      3. Rathgeber, C., N. Yurkova, E. Stackebrandt, P. Schumann, E. Humphrey, J.T. Beatty, and V. Yurkov (2007). Porphyrobacter meromictus sp. nov., an appendaged bacterium that produces bacteriochlorophyll a. Curr Microbiol. 55:356-361.
      4. Braatsch, S., J.A. Johnson, K. Noll, and J.T. Beatty (2007). The O2-responsive repressor PpsR2 but not PpsR1 transduces a light signal sensed by the BphP1 phytochrome in Rhodopseudomonas palustris CGA009. FEMS Microbiol. Lett. 272:60-64.
      5. Lang, A.S., and J.T. Beatty (2007). Importance of widespread gene transfer agent genes in the a-proteobacteria. Trends Microbiol. 15:54-62.
      6. Swingley, W.D, G. Sumedha, S.D. Mastrian, H.J.. Matthies, Ji. Hao, H. Ramos, C.R. Acharya, A.L. Conrad, H.L. Taylor, L.C. Dejesa, M.K. Shah, M.E. O’Huallachain, M.T. Lince, R.E. Blankenship, J.T. Beatty, and J.W. Touchman (2007). The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic as opposed to photosynthetic metabolism. J. Bacteriol. 189:683-690.

2006

      1. Rathgeber, C., N. Yurkova, E. Stackebrandt, E. Humphrey, J.T. Beatty, and V. Yurkov (2006). Metalloid reducing bacteria isolated from deep ocean hydrothermal vents of the Juan de Fuca Ridge, Pseudoalteromonas telluritireducens sp. nov. and Pseudoalteromonas spiralis sp. nov. Current Microbiol. 53:449-456.
      2. Aklujkar, M., R.C. Prince, and J.T. Beatty (2006). The photosynthetic deficiency due to puhC gene deletion in Rhodobacter capsulatus suggests a PuhC protein-dependent process of RC/LH1/PufX complex reorganization. Arch. Biochem. Biophys. 454:59-71.
      3. Braatsch, S., J. Bernstein, F. Lessner, J. Morgan, J. Liao, C. Harwood, and J.T. Beatty (2006). Rhodopseudomonas palustris CGA009 has two functional ppsR genes that each encodes a repressor of photosynthesis gene expression. Biochemistry 45:14441-14451.
      4. VerBerkmoes, N. C., M. B. Shah, P. K. Lankford, D. A. Pelletier, M. B. Strader, D. L., Tabb, W. H. McDonald, J. W. Barton, G. B. Hurst, L. Hauser, B . H. Davison, J. T. Beatty, C. S. Harwood, F. R. Tabita, R. L. Hettich, and F. W. Larimer (2006). Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J. Proteome Res. 5:287-298.
      5. Aklujkar, M., and J.T. Beatty (2006). Investigation of Rhodobacter capsulatus PufX interactions in the core complex of the photosynthetic apparatus. Photosynth. Res. 88:159-171.
      6. Beatty, J.T. (2006). On the natural selection and evolution of the aerobic phototrophic bacteria. In “Discoveries in Photosynthesis”; Govindjee, J.T. Beatty, H. Gest, and J.F. Allen (eds.), Springer Publishers.
      7. Gest, H., Beatty, J.T., J.F. Allen, and Govindjee (2006). The encyclopedia of photosynthesis research. In “Discoveries in Photosynthesis”; Govindjee, H. Gest, J.T. Beatty, and J.F. Allen (eds.), Springer Publishers.

2005

      1. Beatty, J.T., Overmann, J., Lince, M.T., Manske, A.K., Lang, A.S., Blankenship, R.E., Van Dover, C.L., Martinson, T.A., and G.F. Plumley (2005). An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proc. Natl. Acad. Sci. USA 102: 9306-9310.
      2. Aklujkar, M., and J.T. Beatty (2005). The PufX protein of Rhodobacter capsulatus affects the properties of bacteriochlorophyll a and carotenoid pigments of light-harvesting complex 1. Arch Biochem. Biophys. 443:21-32.
      3. Tuschak, C., M.M. Leung, J.T. Beatty, and J. Overmann (2005). The puf operon of the purple sulfur bacterium Amoebobacter purpureus: structure, transcription and phylogenetic analysis. Arch. Microbiol. 183:431–443.
      4. Abresch, E.C., H.L.A. Axelrod, J.T. Beatty, J.A. Johnson, R. Nechushtai, and M.L. Paddock (2005). Characterization of a highly purified, fully active, crystallizable RC-LH1-PufX core complex from Rhodobacter sphaeroides. Photosyn. Res. 86:61–70.
      5. Shelswell, K.J, T.A. Taylor, and J.T. Beatty (2005). Photoresponsive flagellum-independent motility of the purple phototrophic bacterium Rhodobacter capsulatus. J. Bacteriol. 187:5040-5043.
      6. Aklujkar, M., R.C. Prince, and J.T. Beatty (2005). The puhE gene of Rhodobacter capsulatus is needed for optimal transition from aerobic to photosynthetic growth and encodes a putative negative modulator of bacteriochlorophyll production. Arch. Biochem. Biophys 437:186-198.
      7. Rathgeber, C., N. Yurkova, E. Stackebrandt, P. Schumann, J.T. Beatty, and V. Yurkov (2005). Roseicyclus mahoneyensis gen. nov., sp nov., an aerobic phototrophic bacterium isolated from a meromictic lake. Int. J. Syst. Evol. Biol. 55:1597-1603.
      8. Aklujkar, M., R.C. Prince, and J.T. Beatty (2005). The PuhB protein of Rhodobacter capsulatus functions in photosynthetic reaction center assembly with a secondary effect on light-harvesting complex 1. J. Bacteriol. 182:5440-5447.

2004

      1. Rathgeber, C., Beatty, J.T., and V. Yurkov (2004). Aerobic phototrophic bacteria: new evidence for the diversity, ecological importance and applied potential of this previously overlooked group. Photosyn. Res. 81:113–128.
      2. Tuschak, C., Beatty, J.T., and J. Overmann (2004). Photosynthesis genes and LH1 proteins of Roseospirillum parvum 930I, a purple non-sulfur bacterium with unusual spectral properties. Photosyn. Res. 81:181 – 199.
      3. Larimer, F., P. Chain, L. Hauser, J. Lamerdin, S. Malfatti, L. Do, M.L. Land, D.A. Pelletier, J.T. Beatty, A.S. Lang, F. R. Tabita, J.L. Gibson, T.E. Hanson, C. Bobst, J. Torres y Torres, C. Peres, F. Harrison, J. Gibson, and C. S. Harwood (2004). Complete genome sequence of the metabolically versatile phototrophic bacterium Rhodopseudomonas palustris. Nature Biotechnol. 22:55-61.
      4. Tehrani, A., and J.T. Beatty (2004). Effects of precise deletions in Rhodobacter sphaeroides reaction center genes on steady-state levels of reaction center proteins: A revised model for reaction center assembly. Photosyn. Res. 79:101-108.
      5. Govindjee, Allen, J.F., and J.T. Beatty (2004). Celebrating the millennium: historical highlights of photosynthesis research. Photosyn. Res. 80:1-13
      6. Abresch, E.C., Axelrod, H.L.A., Beatty, J.T., Johnson, J.A., Okamura, M.Y., Feher, G., and R. Nechustai (2004) Isolation and characterization of an active RCLH1 complex from Rhodobacter sphaeroides. Biophys. J. .86:146a.
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