Bathy Phytochromes in Rhizobial Soil Bacteria

Abstract

Phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. Prototypical phytochromes have a Pr ground state that absorbs in the red spectral range and is converted by light into the Pfr form, which absorbs longer-wavelength, far-red light. Recently, some bacterial phytochromes have been described that undergo dark conversion of Pr to Pfr and thus have a Pfr ground state. We show here that such so-called bathy phytochromes are widely distributed among bacteria that belong to the order Rhizobiales. We measured in vivo spectral properties and the direction of dark conversion for species which have either one or two phytochrome genes. Agrobacterium tumefaciens C58 contains one bathy phytochrome and a second phytochrome which undergoes dark conversion of Pfr to Pr in vivo. The related species Agrobacterium vitis S4 contains also one bathy phytochrome and another phytochrome with novel spectral properties. Rhizobium leguminosarum 3841, Rhizobium etli CIAT652, and Azorhizobium caulinodans ORS571 contain a single phytochrome of the bathy type, whereas Xanthobacter autotrophicus Py2 contains a single phytochrome with dark conversion of Pfr to Pr. We propose that bathy phytochromes are adaptations to the light regime in the soil. Most bacterial phytochromes are light-regulated histidine kinases, some of which have a C-terminal response regulator subunit on the same protein. According to our phylogenetic studies, the group of phytochromes with this domain arrangement has evolved from a bathy phytochrome progenitor.

Unusual Spectral Properties of Bacteriophytochrome Agp2 Result from a Deprotonation of the Chromophore in the Red-absorbing Form Pr

“…In particular, 3 increases, and 2 decreases. The value of 4 , the time constant characterizing the dark reaction within the first 4 s (after switching off the pre-illumination at 785 nm), is almost doubled between pH 6 and 9.…”

“…Spectral properties of six members of this group (Agp2, Avp1, Avp2, and phytochromes of Rhizobium leguminosarum, Rhizobium etli, and Azorhizobium caulinodans) have been characterized by in vivo photometry and studies on recombinant proteins (3). All of these phytochromes with the exception of Avp1, which displays unusual spectral properties, are bathy phytochromes.…”

“…In a recent study, 15 phytochromes with an Agp2-like domain arrangement have been identified in the order Rhizobiales (3). Spectral properties of six members of this group (Agp2, Avp1, Avp2, and phytochromes of Rhizobium leguminosarum, Rhizobium etli, and Azorhizobium caulinodans) have been characterized by in vivo photometry and studies on recombinant proteins (3).…”

Fluorescence of Phytochrome Adducts with Synthetic Locked Chromophores

“…2 To whom correspondence may be addressed. (17) as well as other rhizobial species (18). Early studies on plant phytochromes have shown that the fluorescence quantum yield of Pr is low at ambient temperature but is increased significantly under cryoconditions where photoconversion is blocked (19).…”

Structure of the Biliverdin Cofactor in the Pfr State of Bathy and Prototypical Phytochromes

“…This different stability of the parent states is most probably the reason why three-dimensional structures so far have been mainly obtained for the Pr state of protypical phytochromes and the Pfr state of bathy phytochromes (13)(14)(15)(16)(17)(18)(19)(20). Although the gross chromophore structures in the respective parent states are likely to be similar in prototypical and bathy phytochromes, it appears to be premature to consider the available three-dimensional structures of the Pr states of the prototypical phytochrome and the yet only available three-dimensional structure of the Pfr state of bathy phytochrome from Pseudomonas aeruginosa (PaBphP) as representative structures for the respective parent states in both classes of phytochromes (12).…”