Reconstructing the deep-branching relationships of the papilionoid legumes

Resolving the phylogenetic relationships of the deep nodes of papilionoid legumes (Papilionoideae) is essential to understanding the evolutionary history and diversification of this economically and ecologically important legume subfamily. The early-branching papilionoids include mostly Neotropical trees traditionally circumscribed in the tribes Sophoreae and Swartzieae. They are more highly diverse in floral morphology than other groups of Papilionoideae. For many years, phylogenetic analyses of the Papilionoideae could not clearly resolve the relation- ships of the early-branching lineages due to limited sampling. In the eight years since the publication of Legumes of the World, we have seen an extraordinary wealth of new molecular data for the study of Papilionoideae phylogeny, enabling increasingly greater resolution and many surprises. This study draws on recent molecular phylogenetic studies and a new comprehensive Bayesian phylogenetic analysis of 668 plastid matK sequences. The present matK phylogeny resolves the deep-branching relationships of the papilionoids with increased support for many clades, and suggests that taxonomic realignments of some genera and of numerous tribes are necessary. The potentially earliest-branching papilionoids fall within an ADA clade, which includes the recircumscribed monophyletic tribes Angylocalyceae, Dipterygeae, and Amburanae. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade. The quinolizidine-alkaloid-accumulating Genistoid s.l. clade is expanded to include Dermatophyllum and a strongly supported and newly circumscribed tribe Ormosieae. Sophoreae and Swartzieae are dramatically reorganized so as to comprise mono-phyletic groups within the Core Genistoid clade and outside the 50-kb inversion clade, respectively. Acosmium is excluded from the Genistoids s.l. and strongly resolved within the newly circumscribed tribe Dalbergieae. By providing a better resolved phylogeny of the earliest-branching papilionoids, this study, in combination with other recent evidence, will lead to a more stable phylogenetic classification of the Papilionoideae.Web of Scienc

Electron paramagnetic resonance studies of zinc-substituted reaction centers from Rhodopseudomonas viridis

The primary quinone acceptor radical anion Q(A)· (a menaquinone-9) is studied in reaction centers (RCs) of Rhodopseudomonas viridis in which the high-spin non-heme Fe is replaced by diamagnetic Zn. The procedure for the iron substitution, which follows the work of Debus et al. [Debus, R. J., Feher, G., and Okamura, M. Y. (1986) Biochemistry 25, 2276-2287], is described. In Rps. viridis an exchange rate of the iron of ~50% ± 10% is achieved. Time-resolved optical spectroscopy shows that the ZnRCs are fully competent in charge separation and that the charge recombination times are similar to those of native RCs. The g tensor of Q(A)· in the ZnRCs is determined by a simulation of the EPR at 34 GHz yielding g(x) = 2.00597 (5), g(y) = 2.00492 (5), and g(z) = 2.00216 (5). Comparison with a menaquinone anion radical (MQ·) dissolved in 2-propanol identifies Q(A)· as a naphthoquinone and shows that only one tensor component (g(x)) is predominantly changed in the RC. This is attributed to interaction with the protein environment. Electron-nuclear double resonance (ENDOR) experiments at 9 GHz reveal a shift of the spin density distribution of Q(A)· in the RC as compared with MQ· in alcoholic solution. This is ascribed to an asymmetry of the Q(A) binding site. Furthermore, a hyperfine coupling constant from an exchangeable proton is deduced and assigned to a proton in a hydrogen bond between the quinone oxygen and surrounding amino acid residues. By electron spin-echo envelope modulation (ESEEM) techniques performed on Q(A)· in the ZnRCs, two N nuclear quadrupole tensors are determined that arise from the surrounding amino acids. One nitrogen coupling is assigned to a N(δ(1))-H of a histidine and the other to a polypeptide backbone N-H by comparison with the nuclear quadrupole couplings of respective model systems. Inspection of the X-ray structure of Rps. viridis RCs shows that His(M217) and Ala(M258) are likely candidates for the respective amino acids. The quinone should therefore be bound by two H bonds to the protein that could, however, be of different strength. An asymmetric H-bond situation has also been found for Q(A)· in the RC of Rhodobacter sphaeroides. Time-resolved electron paramagnetic resonance (EPR) experiments are performed on the radical pair state P·Q(A)· in ZnRCs of Rps. viridis that were treated with o-phenanthroline to block electron transfer to Q(B). The orientations of the two radicals in the radical pair obtained from transient EPR and their distance deduced from pulsed EPR (out-of-phase ESEEM) are very similar to the geometry observed for the ground state PQ(A) in the X-ray structure [Lancaster, R., Michel, H. (1997) Structure 5, 1339]

A High-Field EPR Study of P700+• in Wild-Type and Mutant Photosystem I from Chlamydomonas reinhardtii

High-frequency, high-field EPR at 330 GHz was used to study the photo-oxidized primary donor of photosystem I (P700(+.)) in wild-type and mutant forms of photosystem I in the green alga Chlamydomonas reinhardtii. The main focus was the substitution of the axial ligand of the chlorophyll a and chlorophyll a' molecules that form the P-700 heterodimer. Specifically, we examined PsaA-H676Q, in which the histidine axial ligand of the A-side chlorophyll a' (P-A) is replaced with glutamine, and PsaB-H656Q, with a similar replacement of the axial ligand of the B-side chlorophyll a (P-B), as well as the double mutant (PsaA-H676Q/PsaB-H656Q), in which both axial ligands were replaced. We also examined the PsaA-T739A mutant, which replaces a threonine residue hydrogen-bonded to the 13(1)-keto group Of PA with an alanine residue. The principal g-tensor components of the P700(+.) radical determined in these mutants and in wild-type photosystem I were compared with each other, with the monomeric chlorophyll cation radical (Chl(z)(+.)) in photosystem II, and with recent theoretical calculations for different model structures of the chlorophyll a(+) cation radical. In mutants with a modified P-B axial ligand, the g(zz) component of P-700(+.) was shifted down by up to 2 x 10(-4), while mutations near P-A had no significant effect. We discuss the shift of the gzz component in terms of a model with a highly asymmetric distribution of unpaired electron spin in the P-700(+.) radical cation, mostly localized on PB, and a deviation of the PB chlorophyll structure from planarity due to the axial ligand