Caltech Logo

Special Seminar

Tuesday, March 5, 2019
4:00pm to 5:00pm
Add to Cal
Noyes 147 (J. Holmes Sturdivant Lecture Hall)
"How a soil bacterium responds to light"
Tilman Lamparter, Botanical institute, Karlsruhe Institute of Technology,

Agrobacterium fabrum C58 is a soil bacterium that can transfer genes into plants. The transferred genes result in tumor growth and in the production of opines the plant tissue, that are metabolized by Agrobacterium. Because the bacteria live in the soil, it has long been suggested that the cells do not respond to sunlight. Our group has uncovered four light responsive proteins in Agrobacterium, two phytochromes termed Agp1 and Agp2 (1) and two photolyases (2-4) termed PhrA and PhrB. We established recombinant expression for these proteins and used them as models for biophysical studies and X-ray crystallography. Phytochromes are photoreceptors with a bilin chromophore that were first identified in plants and later discovered in cyanobacteria, other bacteria and fungi. We found that in Agrobacterium, Agp1 and Agp2 regulate growth and swimming, DNA transfer from cell to cell and DNA transfer from bacterium to plant. How are phytochromes activated or inactivated by light? Several detailed steps from chromophore isomerization to gross protein conformational changes are meanwhile established. The contribution of Agp1 and Agp2 crystal structures (5, 6) will be discussed.

Photolyases are repair enzymes for UV-damaged DNA. We have shown that PhrB serves as a so called (6-4) photolyase, the first prokaryotic of this kind (2). The phylogenetic group of PhrB is probably the most ancient group of photolyases and cryptochromes. A number of central changes that occurred in the early evolution were uncovered by studies on PhrB. The DMRL antenna chromophore of PhrB was replaced by MTHF or other antenna chromophores. PhrB has an iron-sulfur cluster, photolyase and cryptochrome members or other groups have no iron sulfur cluster. The so called photoreduction switched from Trp-Trp-Tyr in PhrB to (non homologous) Trp-Trp-Trp in the other groups. And finally, the repair activity of PhrB is drastically increased by Mg2+ or other divalent cations that are bound next to the DNA lesion site. In other groups this dependency on Mg2+ was lost.

Thus, a number of previously unexpected light responses were discovered in Agrobacterium fabrum. These studies contribute to the understanding of phytochrome and photolyase function and evolution.

  1. Lamparter T, Michael N, Mittmann F, Esteban B. Phytochrome from Agrobacterium tumefaciens has unusual spectral properties and reveals an N-terminal chromophore attachment site. Proc Natl Acad Sci U S A. 2002;99:11628-33.
  2. Zhang F, Scheerer P, Oberpichler I, Lamparter T, Krauss N. Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore. Proc Natl Acad Sci U S A. 2013;110(18):7217-22.
  3. Scheerer P, Zhang F, Kalms J, von Stetten D, Krauss N, Oberpichler I, et al. The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways. J Biol Chem. 2015;290(18):11504-14.
  4. Oberpichler I, Pierik AJ, Wesslowski J, Pokorny R, Rosen R, Vugman M, et al. A photolyase-like protein from Agrobacterium tumefaciens with an iron-sulfur cluster. Plos One. 2011;6(10):e26775.
  5. Schmidt A, Sauthof L, Szczepek M, Lopez MF, Escobar FV, Qureshi BM, et al. Structural snapshot of a bacterial phytochrome in its functional intermediate state. Nature Communications. 2018;9(1):4912.
  6. Nagano S, Scheerer P, Zubow K, Michael N, Inomata K, Lamparter T, et al. The crystal structures of the N-terminal photosensory core module of Agrobacterium phytochrome Agp1 as parallel and anti-parallel dimers. J Biol Chem. 2016;291(39):20674-91.


Nirit Kantor Uriel,

Faculty Host:

Jackie Barton

John G. Kirkwood and Arthur A. Noyes Professor of Chemistry;

Norman Davidson Leadership Chair, Division of Chemistry and Chemical Engineering