Brenda S.J. Winkel

Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1.

In plants, Glycoside Hydrolase (GH) Family 1 β-glycosidases are believed to play important roles in many diverse processes including chemical defense against herbivory, lignification, hydrolysis of cell wall-derived oligosaccharides during germination, and control of active phytohormone levels. Completion of the Arabidopsis thalianagenome sequencing project has enabled us, for the first time, to determine the total number of Family 1 members in a higher plant. Reiterative database searches revealed a multigene family of 48 members that includes eight probable pseudogenes. Manual reannotation and analysis of the entire family were undertaken to rectify existing misannotations and identify phylogenetic relationships among family members. Forty-seven members (designated BGLU1 through BGLU47) share a common evolutionary origin and were subdivided into approximately 10 subfamilies based on phylogenetic analysis and consideration of intron–exon organizations. The forty-eighth member of this family (At3g06510; sfr2) is a β-glucosidase-like gene that belongs to a distinct lineage. Information pertaining to expression patterns and potential functions of Arabidopsis GH Family 1 members is presented. To determine the biological function of all family members, we intend to investigate the substrate specificity of each mature hydrolase after its heterologous expression in the Pichia pastoris expression system. To test the validity of this approach, the BGLU44-encoded hydrolase was expressed in P. pastoris and purified to homogeneity. When tested against a wide range of natural and synthetic substrates, this enzyme showed a preference for β-mannosides including 1,4-β-D-mannooligosaccharides, suggesting that it may be involved in A. thaliana in degradation of mannans, galactomannans, or glucogalactomannans. Supporting this notion, BGLU44 shared high sequence identity and similar gene organization with tomato endosperm β-mannosidase and barley seed β-glucosidase/β-mannosidase BGQ60.

Nuclear Localization of Flavonoid Enzymes in Arabidopsis

Flavonoids represent one of the oldest, largest, and most diverse families of plant secondary metabolites. These compounds serve a wide range of functions in plants, from pigmentation and UV protection to the regulation of hormone transport. Flavonoids also have interesting pharmacological activities in animals that are increasingly being characterized in terms of effects on specific proteins or other macromolecules. Although flavonoids are found in many different locations both inside and outside the cell, biosynthesis has long been believed to take place exclusively in the cytoplasm. Recent reports from a number of different plant species have documented the presence of flavonoids in nuclei, raising the possibility of novel mechanisms of action for these compounds. Here we present evidence that not only flavonoids, but also at least two of the biosynthetic enzymes, are located in the nucleus in several cell types in Arabidopsis. This is the first indication that differential targeting of the biosynthetic machinery may be used to regulate the deposition of plant secondary products at diverse sites of action within the cell.

Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks

Auxin and ethylene are key regulators of plant growth and development, and thus the transcriptional networks that mediate responses to these hormones have been the subject of intense research. This study dissected the hormonal cross talk regulating the synthesis of flavonols and examined their impact on root growth and development. We analyzed the effects of auxin and an ethylene precursor on roots of wild-type and hormone-insensitive Arabidopsis (Arabidopsis thaliana) mutants at the transcript, protein, and metabolite levels at high spatial and temporal resolution. Indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) differentially increased flavonol pathway transcripts and flavonol accumulation, altering the relative abundance of quercetin and kaempferol. The IAA, but not ACC, response is lost in the transport inhibitor response1 (tir1) auxin receptor mutant, while ACC responses, but not IAA responses, are lost in ethylene insensitive2 (ein2) and ethylene resistant1 (etr1) ethylene signaling mutants. A kinetic analysis identified increases in transcripts encoding the transcriptional regulators MYB12, Transparent Testa Glabra1, and Production of Anthocyanin Pigment after hormone treatments, which preceded increases in transcripts encoding flavonoid biosynthetic enzymes. In addition, myb12 mutants were insensitive to the effects of auxin and ethylene on flavonol metabolism. The equivalent phenotypes for transparent testa4 (tt4), which makes no flavonols, and tt7, which makes kaempferol but not quercetin, showed that quercetin derivatives are the inhibitors of basipetal root auxin transport, gravitropism, and elongation growth. Collectively, these experiments demonstrate that auxin and ethylene regulate flavonol biosynthesis through distinct signaling networks involving TIR1 and EIN2/ETR1, respectively, both of which converge on MYB12. This study also provides new evidence that quercetin is the flavonol that modulates basipetal auxin transport.

Functional Analysis of a Predicted Flavonol Synthase Gene Family in Arabidopsis

The genome of Arabidopsis (Arabidopsis thaliana) contains five sequences with high similarity to FLAVONOL SYNTHASE1 (AtFLS1), a previously characterized flavonol synthase gene that plays a central role in flavonoid metabolism. This apparent redundancy suggests the possibility that Arabidopsis uses multiple isoforms of FLS with different substrate specificities to mediate the production of the flavonols, quercetin and kaempferol, in a tissue-specific and inducible manner. However, biochemical and genetic analysis of the six AtFLS sequences indicates that, although several of the members are expressed, only AtFLS1 encodes a catalytically competent protein. AtFLS1 also appears to be the only member of this group that influences flavonoid levels and the root gravitropic response in seedlings under nonstressed conditions. This study showed that the other expressed AtFLS sequences have tissue- and cell type-specific promoter activities that overlap with those of AtFLS1 and encode proteins that interact with other flavonoid enzymes in yeast two-hybrid assays. Thus, it is possible that these “pseudogenes” have alternative, noncatalytic functions that have not yet been uncovered.

Redox, spectroscopic, and photophysical properties of Ru-Pt mixed-metal complexes incorporating 4,7-diphenyl-1,10-phenanthroline as efficient DNA binding and photocleaving agents.

The redox, spectroscopic, and photophysical properties as well as DNA interactions of the new bimetallic complexes [(Ph2phen)2Ru(BL)PtCl2](2+) (Ph2phen = 4,7-diphenyl-1,10-phenanthroline, and BL (bridging ligand) = dpp = 2,3-bis(2-pyridyl)pyrazine, or dpq = 2,3-bis(2-pyridyl)quinoxaline) were investigated. These Ru-polyazine chromophores with Ph2phen TLs (terminal ligands) and polyazine BLs are efficient light absorbers. The [(Ph2phen)2Ru(BL)PtCl2](2+) complexes display reversible Ru(II/III) oxidations at 1.57 (dpp) and 1.58 (dpq) V vs SCE (saturated calomel electrode) with an irreversible Pt(II/IV) oxidation occurring prior at 1.47 V vs SCE. Four, reversible ligand reductions occur at -0.50 dpp(0/-), -1.06 dpp(-/2-), -1.37 Ph2phen(0/-), and -1.56 V vs SCE Ph2phen(0/-). For the [(Ph2phen)2Ru(dpq)PtCl2](2+) complex, the first two reductions shift to more positive potentials at -0.23 and -0.96 V vs SCE. The electronic absorption spectroscopy is dominated in the UV region by π → π* ligand transitions and in the visible region by metal-to-ligand charge transfer (MLCT) transitions at 517 nm for [(Ph2phen)2Ru(dpp)PtCl2](2+) and 600 nm for [(Ph2phen)2Ru(dpq)PtCl2](2+). Emission spectroscopy shows that upon attaching Pt to the Ru monometallic precursor the λmax(em) shifts from 664 nm for [(Ph2phen)2Ru(dpp)](2+) to 740 nm for [(Ph2phen)2Ru(dpp)PtCl2](2+). The cis-Pt(II)Cl2 bioactive site offers the potential of targeting DNA by covalently binding the mixed-metal complex to DNA bases. The multifunctional interactions with DNA were assayed using both linear and circular plasmid pUC18 DNA gel shift assays. Both title complexes can bind to and photocleave DNA with dramatically enhanced efficiency relative to previously reported systems. The impact of the Ph2phen TL on photophysics and bioreactivity is somewhat surprising given the Ru → BL charge transfer (CT) nature of the photoreactive state in the complexes.

Förster resonance energy transfer demonstrates a flavonoid metabolon in living plant cells that displays competitive interactions between enzymes

FLS1 physically interacts with CHS and DFR by competition binding (View interaction)

Functional analysis of Arabidopsis genes involved in mitochondrial iron–sulfur cluster assembly

Machinery for the assembly of the iron–sulfur ([Fe–S]) clusters that function as cofactors in a wide variety of proteins has been identified in microbes, insects, and animals. Homologs of the genes involved in [Fe–S] cluster biogenesis have recently been found in plants, as well, and point to the existence of two distinct systems in these organisms, one located in plastids and one in mitochondria. Here we present the first biochemical confirmation of the activity of two components of the mitochondrial machinery in Arabidopsis, AtNFS1 and AtISU1. Analysis of the expression patterns of the corresponding genes, as well as AtISU2 and AtISU3, and the phenotypes of plants in which these genes are up or down-regulated are consistent with a role for the mitochondrial [Fe–S] assembly system in the maturation of proteins required for normal plant development.

A new Os,Rh bimetallic with O2 independent DNA cleavage and DNA photobinding with red therapeutic light excitation

Many Ru and Os systems display photoactive (3)MLCT states. Systems activated by therapeutic window light in the absence of O(2) remain elusive. [(bpy)(2)Os(dpp)RhCl(2)(phen)](3+) photobinds and photocleaves DNA under red light in an oxygen independent manner, due to molecular design involving one Os chromophore coupled to a photoactive cis-Rh(III)Cl(2) moiety.

Comparative characterization of the Arabidopsis subfamily a1 β-galactosidases

The Arabidopsis genome contains 17 predicted beta-galactosidase genes, all of which belong to glycosyl hydrolase (GH) Family 35. These genes have been further grouped into seven subfamilies based on sequence similarity. The largest of these, subfamily a1, consists of six genes, Gal-1 (At3g13750), Gal-2 (At3g52840), Gal-3 (At4g36360), Gal-4 (At5g56870), Gal-5 (At1g45130), and Gal-12 (At4g26140), some of which were characterized in previous studies. We report here the purification and biochemical characterization of recombinant Gal-1, Gal-3, Gal-4 and Gal-12 from Pichiapastoris, completing the analysis of all six recombinant proteins, as well as the isolation and characterization of the native Gal-2 protein from Arabidopsis leaves. Comparison of the relative expression levels of the subfamily a1 beta-galactosidases at the mRNA and protein levels uncovered evidence of differential regulation, which may involve post-transcriptional and post-translational processes. In addition, this study provides further support for the proposed function of the subfamily a1 beta-galactosidases in cell wall modification based on analysis of the organ-specific expression and subcellular localization of Gal-1 and Gal-12. Our study suggests that, despite some differences in individual biochemical characteristics and expression patterns, each member of the family has the potential to contribute to the dynamics of the Arabidopsis plant cell wall.

Red-light-induced inhibition of DNA replication and amplification by PCR with an Os/Rh supramolecule.

The search for efficient antitumor drugs with low toxicity has sparked interest in transition metal complexes for photodynamic therapy (PDT). Current PDT uses reactive species to induce damage to biomolecules. Photofrin photochemically generates O2 leading to tumor cell death. [3] Excitation by light in the phototherapeutic window (600–900 nm) is needed for tissue penetration. A new PDT drug, [(bpy)2Os(dpp)RhCl2(phen)] 3+ (bpy = 2,2’-bipyridine, phen = 1,10-phenanthroline, dpp = 2,3-bis(2-pyridyl)pyrazine), photocleaves and photobinds DNA (i.e., it binds to DNA upon exposure to light) through an oxygen-independent mechanism when using light in the therapeutic window. Herein it is demonstrated that this complex functions at low concentrations and inhibits DNA replication and amplification by PCR. DNA is often the target for metal-based drugs. Ru or Os polyazine complexes related to the classic [Ru(bpy)3] 2+ and [Os(bpy)3] 2+ are suggested as prototypes for future drugs. The long-lived triplet metal-to-ligand charge transfer (MLCT) state of [Ru(bpy)3] 2+ can photocleave pBR322 DNA with visible light (lirr> 450 nm) through singlet-oxygen generation by energy transfer. Very few metal complexes function for DNA modification by using red light in the therapeutic window, thus presenting a barrier to their implementation. Turro and co-workers reported that [(bpy)2Os(dppn)] 2+