Plasma membrane H+-ATPases sustain pollen tube growth and fertilization

Pollen tubes are highly polarized tip-growing cells that depend on cytosolic pH gradients for signaling and growth. Autoinhibited plasma membrane proton (H+) ATPases (AHAs) have been proposed to energize pollen tube growth and underlie cell polarity, however, mechanistic evidence for this is lacking. Here we report that the combined loss of AHA6, AHA8, and AHA9 in Arabidopsis thaliana delays pollen germination and causes pollen tube growth defects, leading to drastically reduced fertility. Pollen tubes of aha mutants had reduced extracellular proton (H+) and anion fluxes, reduced cytosolic pH, reduced tip-to-shank proton gradients, and defects in actin organization. Furthermore, mutant pollen tubes had less negative membrane potentials, substantiating a mechanistic role for AHAs in pollen tube growth through plasma membrane hyperpolarization. Our findings define AHAs as energy transducers that sustain the ionic circuit defining the spatial and temporal profiles of cytosolic pH, thereby controlling downstream pH-dependent mechanisms essential for pollen tube elongation, and thus plant fertility.

Roles of plasma membrane proton ATPases AHA2 and AHA7 in normal growth of roots and root hairs in Arabidopsis thaliana

Plasma membrane H⁺ -ATPase pumps build up the electrochemical H⁺ gradients that energize most other transport processes into and out of plant cells through channel proteins and secondary active carriers. In Arabidopsis thaliana, the AUTOINHIBITED PLASMA MEMBRANE H⁺ -ATPases AHA1, AHA2 and AHA7 are predominant in root epidermal cells. In contrast to other H⁺ -ATPases, we find that AHA7 is autoinhibited by a sequence present in the extracellular loop between transmembrane segments 7 and 8. Autoinhibition of pump activity was regulated by extracellular pH, suggesting negative feedback regulation of AHA7 during establishment of an H⁺ gradient. Due to genetic redundancy, it has proven difficult to test the role of AHA2 and AHA7, and mutant phenotypes have previously only been observed under nutrient stress conditions. Here, we investigated root and root hair growth under normal conditions in single and double mutants of AHA2 and AHA7. We find that AHA2 drives root cell expansion during growth but that, unexpectedly, restriction of root hair elongation is dependent on AHA2 and AHA7, with each having different roles in this process.

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana

Background

Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown.

Results

Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3′ untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses.

Conclusions

Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2803-2) contains supplementary material, which is available to authorized users.

Mother-plant-mediated pumping of zinc into the developing seed

Insufficient intake of zinc and iron from a cereal-based diet is one of the causes of 'hidden hunger' (micronutrient deficiency), which affects some two billion people(1,2). Identifying a limiting factor in the molecular mechanism of zinc loading into seeds is an important step towards determining the genetic basis for variation of grain micronutrient content and developing breeding strategies to improve this trait(3). Nutrients are translocated to developing seeds at a rate that is regulated by transport processes in source leaves, in the phloem vascular pathway, and at seed sinks. Nutrients are released from a symplasmic maternal seed domain into the seed apoplasm surrounding the endosperm and embryo by poorly understood membrane transport processes(4-6). Plants are unique among eukaryotes in having specific P1B-ATPase pumps for the cellular export of zinc(7). In Arabidopsis, we show that two zinc transporting P1B-ATPases actively export zinc from the mother plant to the filial tissues. Mutant plants that lack both zinc pumps accumulate zinc in the seed coat and consequently have vastly reduced amounts of zinc inside the seed. Blockage of zinc transport was observed at both high and low external zinc supplies. The phenotype was determined by the mother plant and is thus due to a lack of zinc pump activity in the seed coat and not in the filial tissues. The finding that P1B-ATPases are one of the limiting factors controlling the amount of zinc inside a seed is an important step towards combating nutritional zinc deficiency worldwide.

Epigenetic repression of male gametophyte-specific genes in the Arabidopsis sporophyte

Tissue formation, the identity of cells, and the functions they fulfill, are results of gene regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several hundred genes expressed in pollen are not expressed in the sporophyte. How pollen-specific genes are down-regulated in the sporophyte has yet to be established. In this study, we have performed a bioinformatics analysis of publicly available genome-wide epigenetics data of several sporophytic tissues. By combining this analysis with DNase I footprinting data, we assessed means by which the repression of pollen-specific genes in the Arabidopsis sporophyte is conferred. Our findings show that, in seedlings, the majority of pollen-specific genes are associated with histone-3 marked by mono- or trimethylation of Lys-27 (H3K27me1/H3K27me3), both of which are repressive markers for gene expression in the sporophyte. Analysis of DNase footprint profiles of pollen-specific genes in the sporophyte displayed closed chromatin proximal to the start codon. We describe a model of two-staged gene regulation in which a lack of nucleosome-free regions in promoters and histone modifications in open reading frames repress pollen-specific genes in the sporophyte.

A new 1 --> infinity [Ni7] cluster in LaNi7In6 and distorted bcc indium cubes in LaNiIn4

LaNiIn4 and LaNi7In, were prepared by reaction of the elements in an arc melting furnace and subsequent annealing at 870 K for five weeks. Both compounds were investigated by X-ray diffraction on powders and single crystals and the structures were refined from single-crystal data: Cmcm, a = 448.2(1), b = 1689.5(4). c = 722.1(1) pm, wR2 = 0.0340, 472 F2 values, 24 variables for LaNiIn4, and Ibam, a = 806.6(2). b = 924.8(2). c = 1246.5(2) pm. wR2 = 0.0681. 726 F2 values and 40 variables for LaNi7In,. LaNiIn4 adopts the YNiAl4-type structure. The nickel and indium atoms form a three-dimensional infinite [NiIn4] polyanion in which the lanthanum atoms fill distorted hexagonal channels. No Ni-Ni contacts occur. The indium substructure consists of distorted bcc-like indium cubes. LaNi7In6 crystallizes with a peculiar new structure type. The nickel atoms build a 1 --> infinity [Ni7] cluster unit with Ni-Ni distances ranging from 249 to 269 pm. The cluster units are enveloped by indium atoms. These larger units show an orthorhombic rod packing with the lanthanum atoms filling the space between the rods. Several nickel clusters in ternary rare earth metal nickel indides and the structural relations of the LaNi7In6 structure with the cubic NaZn13 type are discussed.

Virtual screening: an effective tool for lead structure discovery?

Different methods of virtual screening as a tool for lead structure discovery are described. They range from structure based docking procedures to ligand based methods such as the chemical features based pharmacophore hypothesis approach. A review on several successful applications of virtual screening is given. Different approaches have been described to derive pharmacophore models, which were subsequently used for 3D database searching. The studies so far published cover a wide range of pharmacological applications. The results hereby obtained clearly indicate that focused assessment of corporate databases by virtual screening using well validated pharmacophore models yield to a significant improvement in lead structure determination compared to high throughput screening.

Orthonitridoborate ions [BN3]6- in oxonitridosilicate cages: synthesis, crystal structure, and magnetic properties of Ba4Pr7[Si12N23O][BN3], Ba4Nd7[Si12N23O][BN3], and Ba4Sm7[Si12N23O][BN3]

The isotypic title compounds Ba4Pr7[Si12N23O][BN3], Ba4Nd7[Si12N23O][BN3], and Ba4Sm7[Si12N23O][BN3] were prepared by reaction of Pr, Nd, or Sm, with barium, BaCO3, Si(NH)2, and poly(boron amide imide) in nitrogen atmosphere in tungsten crucibles using a radiofrequency furnace at temperatures up to 1650 C. They were obtained as main products (approximately 70%) embedded in a very hard glass matrix in the form of intense dark green (Pr), orange-brown (Sm), or dark red (Nd) large single crystals, respectively. The stoichiometric composition of Ba4Sm7[Si12N23O][BN3] was verified by a quantitative elemental analysis. According to the single-crystal X-ray structure determinations (Ba4Ln7[Si12N23][BN3], Z= , P6 with Ln = Pr: a = 1225.7(1), c = 544.83(9) pm, R1 = 0.013, wR2 = 0.030; Ln = Nd: a = 1222.6(1), c = 544.6(1) pm, R1 = 0.017, wR2 = .039; Ln = Sm: a = 1215.97(5), c = 542.80(5) pm, R1 = 0.047, wR2 = 0.099) all three compounds are built up by a framework structure [Si12N23O]23- of corner-sharing SiX4 tetrahedrons (X = O, N). The oxygen atoms are randomly distributed over the X positions. The trigonal-planar orthonitridoborate ions [BN3]6- and also the Ln(3)3+ are situated in hexagonal cages of the framework (bond lengths Si-(N/O) 169-179 pm for Ln=Pr). The remaining Ba2+ and Ln3- ions are positioned in channels of the large-pored network. The trigonal-planar [BN3]6- ions have a B-N distance of 147.1(6) pm (for Ln = Pr). Temperature-dependent susceptibility measurements for Ba4Nd7[Si12N23O][BN3] revealed Curie-Weiss behavior above 60 K with an experimental magnetic moment of muexp = 3.36(5) microB/Nd. The deviation from Curie-Weiss behavior below 60 K may be attributed to crystal field splitting of the J = 9/2 ground state of the Nd3+ ions. No magnetic ordering is evident down to 4.2 K.

Structure-Based Focusing Using Pharmacophores Derived from the Active Site of 17beta-Hydroxysteroid Dehydrogenase

Structure-based focusing constitutes a powerful approach to design libraries of compounds with a given biological profile. Computers with special software can be used to analyse the large amount of data usually available for the compounds. Pharmacophores can be used to identify new compounds that present a specific arrangement of features responsible for a certain type of activity. When available, information about the 3D structure of a biological target can also be included in the building of pharmacophore models. These pharmacophores can then be used as queries to search and/or focus large compound libraries. Multiple pharmacophores were generated from the 3D structure 17beta-hydroxystreoid dehydrogenase type1 complexed with different inhibitors. The validity of these pharmacophores was assessed against a test database containing known active and inactive 17beta-hydroxystreoid dehydrogenase type1 inhibitors. The most selective models were then used to search commercial databases for new structural lead molecules. This approach has allowed us to identify a few new compounds possessing structural features common to flavonoids, a structural class of compounds known to contain good inhibitors of 17beta-hydroxystreoid dehydrogenase type1 enzyme. A structure-based focusing approach is demonstrated to be a meaningful and powerful technique for identifying new lead candidates, which can be taken into the lead optimization process.

Two-dimensional [TIn2] polyanions in BaTIn2 (T=Rh, Pd, Ir, Pt)--the collapse of the three-dimensional indium polyanion of BaIn2

The title compounds were prepared from the elements by reactions in sealed tantalum tubes in a high-frequency furnace. The four compounds were investigated by X-ray diffraction both on powders and single crystals, and the structures of the rhodium and platinum compounds were refined from single-crystal data: Cmcm, a = 447.68(8), b = 1131.1(2), c = 805.6(2) pm, wR2 = 0.0561, 354 F2 values for BaRhIn2; a = 452.06(8), b = 1162.4(2). c = 801.5(1) pm, wR2 = 0.1427, 362 F2 values, for BaPtIn2: with 16 variables for each refinement. The structures are isopointal to MgCuAl2 and can be considered to be a transition metal (T) filled CaIn2 type, in which the indium atoms form a distorted network like hexagonal diamond (lonsdaleite). The indium substructure is cut apart in BaTIn2 and resembles together with the transition metal atoms a two-dimensional polyanion rather than a three-dimensional polyanion as found in the compounds CaTIn2, CaTSn2, and SrTIn2. Semiempirical band structure calculations support the assumption of a two-dimensional polyanion in which the strongest interactions are found for the T-In contacts.

Distorted bcc indium cubes as structural motifs in Ca

The title compounds were prepared from the elements by reactions in water-cooled glassy carbon crucibles under an argon atmosphere in a high-frequency furnace. CaPdIn4 crystallizes with the YNiAl4-type structure: Cmcm, a=446.7(3), b=1665(1), c=754.3(5) pm, wR2=0.0465 with 646 F2 values and 24 variables. The structure is built up from a complex three-dimensional [PdIn4] polyanion in which the calcium atoms occupy distorted pentagonal tubes formed by indium and palladium atoms. CaRhIn4 and CaIrIn4 adopt the LaCoAl4-type structure: Pmma, a=867.6(1), b=422.91(8), c=745.2(1) pm, wR2=0.0583 with 468 F2 values and 24 variables for CaRhIn4; a=869.5(1), b=424.11(6), c=746.4(1) pm, wR2= 0.0614 471 F2 values with 24 variables for CaIrIn4. This structure type, too, has a three-dimensional [RhIn4] polyanion which is related to the structure of binary RhIn3. The calcium atoms fill distorted pentagonal prismatic channels formed by indium atoms. Semi-empirical band structure calculations for Ca-RhIn4 and CaPdIn4 reveal strongly bonding In-In, Rh-In and Pd-In interactions but weaker Ca-Rh, Ca-Pd and Ca-In interactions. CaRhIn4 and Ca-PdIn4 are compared with other indium-rich compounds such as YCoIn5 and Y2CoIn8, and with elemental indium. Common structural motifs of the indium-rich compounds are distorted bcc-like indium cubes.