Structural implications of mutations in the pea SYM8 symbiosis gene, the DMI1 ortholog, encoding a predicted ion channel

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceThe Pisum sativum SYM8 gene plays an essential part in both rhizobial and mycorrhizal symbioses. Mutation of sym8 in the original type line R25 blocks nodulation, mycorrhization, and Nod-factor-induced calcium spiking, an early component of the nodulation signaling pathway. We describe four new sym8 alleles of pea, which fall into the same complementation group as R25. The sym8 mutants are phenotypically similar to Medicago truncatula dmi1 mutants and map to a syntenic location. We used sequence homology to isolate the pea ortholog of M. truncatula DMI1 and have shown that the cloned pea ortholog can complement a M. truncatula dmi1 mutant for nodulation. Each of the five pea sym8 mutants carries a mutation in the DMI1 ortholog, confirming that the pea SYM8 is the DMI1 ortholog. Based on predicted structural similarities with an archaebacterial ion channel, we propose that SYM8 forms a tetrameric calcium-gated channel of a predicted structure similar to the archaebacterial potassium channel but containing a filter region that is different. The predicted structure identifies four aspartate residues (one from each subunit) forming the channel opening. We made a mutation changing the aspartate to valine and identified a missense mutation (changing alanine to valine adjacent to the aspartate residues) in this predicted filter region; both mutations caused a loss of function. We also identified a loss-of-function missense mutation (changing arginine to isoleucine) in a domain proposed to link the predicted channel and the gating ring domains, indicating that this mutation may block function by preventing a protein conformational change being transmitted from the gating-ring domain to the pore domain

Analysis of the nitric oxide-sensing non-heme iron center in the NorR regulatory protein

The NorR regulatory protein senses nitric oxide ( NO) to activate genes required for NO detoxification under anaerobic and microaerobic conditions in Escherichia coli. NorR belongs to the sigma(54)-dependent family of transcriptional activators and contains an N-terminal regulatory GAF (c (G) under bar MP phosphodiesterase, adenylate cyclase, (F) under bar hlA) domain that controls the ATPase activity of the central AAA+ domain to regulate productive interactions with sigma(54). Binding of NO to a non-heme iron center in the GAF domain results in the formation of a mononitrosyl-iron complex and releases intramolecular repression of the AAA+ domain to enable activation of transcription. In this study, we have further characterized NorR spectroscopically and substituted conserved residues in the GAF domain. This analysis, in combination with structural modeling of the GAF domain, has identified five candidate ligands to the non-heme iron and suggests a model in which the metal ion is coordinated in a pseudo-octahedral environment by three aspartate residues, an arginine, and a cysteine

Polyhedral metallathiaborane chemistry. Synthesis and characterisation of metallathiaboranes based on the twelve-vertex icosahedral closo-{MSB10H10} unit, where M is Rh or Ir

The reaction of [nido-7-SB10H12] with [RhCl(PPh3)3] in the presence of N,N,N′N′-tetramethylnaphthalene-1,8-diamine (tmnd) in CH2Cl2 gives twelve-vertex [2,2-(PPh3)2-2-H-closo-2,1-RhSB10H10] (1) and eleven-vertex [8,8-(PPh3)2-nido-8,7-RhSB9H10] (2), as major products, plus the dimeric species [{(PPh3)-closo-RhSB10H10}2] (3) as a minor product. Reaction of 1 with PMe2Ph in CH2Cl2 results in phosphine exchange and hydride substitution, affording the chloro analogue of 1, [2,2-(PMe2Ph)2-2-Cl-closo-2,1-RhSB10H10] (4). By contrast, reaction between [IrCl(PPh3)3] and [nido-7-SB10H12] in CH2Cl2 with tmnd affords only one product, twelve-vertex [2,2-(PPh3)2-2-H-closo-2,1-IrSB10H10] (5). [RhCl2(η5-C5Me5)]2 with [nido-7-SB10H12] under the same conditions gives twelve-vertex [2-(η5-C5Me5)-closo-2,1-RhSB10H10] (6). All the compounds are characterised by NMR spectroscopy, and by mass spectrometry, and the molecular structure of [2,2-(PMe2Ph)2-2-Cl-closo-2,1-RhSB10H10] (4) was established by single-crystal X-ray diffraction analysis. This last rhodathiaborane 4 is fluxional in solution through a process that involves a reversible partial rotation of the {RhCl(PMe2Ph)2} unit above the {SB4} pentagonal face of the {SB10H10} fragment.Contribution No. 113 from the Leeds-Řež Anglo-Czech Polyhedron Collaboration (ACPC). R.M. thanks the Basque Government for a scholarship, and the Ministry of Education and Science of Spain for support within the framework of the “Ramón y Cajal” program. We thank the Ministry of Education of the Czech Republic (project no. LC 523) for support and the UK EPSRC for equipment grants (J/56929, L/49505, M/83360 and R/61949). We also thank the Royal Society (London) and the Czech Academy of Sciences, together with the Royal Society of Chemistry Overseas Author’s fund, for support and assistance with reciprocal visits.Peer reviewe

An SNF2 Protein Associated with Nuclear RNA Silencing and the Spread of a Silencing Signal between Cells in Arabidopsis[W][OA]

The silencing phenotype in Arabidopsis thaliana lines with an inverted repeat transgene under the control of a phloem-specific promoter was manifested in regions around veins due to a mobile signal of silencing. Genetic analysis implicates RNA-DEPENDENT RNA POLYMERASE2 (RDR2) and an RNA polymerase IVa subunit gene (NRPD1a) in the signaling mechanism. We also identified an SNF2 domain–containing protein (CLASSY1) that acts together with RDR2 and NRPD1a in the spread of transgene silencing and in the production of endogenous 24-nucleotide short interfering RNAs (siRNAs). Cytochemical analysis indicates that CLASSY1 may act in the nucleus with NRPD1a and RDR2 in the upstream part of RNA silencing pathways that generate a double-stranded RNA substrate for Dicer-like (DCL) nucleases. DCL3 and ARGONAUTE4 act in a downstream part of the pathway, leading to endogenous 24-nucleotide siRNA production, but are not required for intercellular signaling. From genetic analysis, we conclude that another downstream part of the pathway associated with intercellular signaling requires DCL4 and at least one other protein required for 21-nucleotide trans-acting siRNAs. We interpret the effect of polymerase IVa and trans-acting siRNA pathway mutations in terms of a modular property of RNA silencing pathways

An SNF2 Protein Associated with Nuclear RNA Silencing and the Spread of a Silencing Signal between Cells in Arabidopsis[W][OA]

The silencing phenotype in Arabidopsis thaliana lines with an inverted repeat transgene under the control of a phloem-specific promoter was manifested in regions around veins due to a mobile signal of silencing. Genetic analysis implicates RNA-DEPENDENT RNA POLYMERASE2 (RDR2) and an RNA polymerase IVa subunit gene (NRPD1a) in the signaling mechanism. We also identified an SNF2 domain–containing protein (CLASSY1) that acts together with RDR2 and NRPD1a in the spread of transgene silencing and in the production of endogenous 24-nucleotide short interfering RNAs (siRNAs). Cytochemical analysis indicates that CLASSY1 may act in the nucleus with NRPD1a and RDR2 in the upstream part of RNA silencing pathways that generate a double-stranded RNA substrate for Dicer-like (DCL) nucleases. DCL3 and ARGONAUTE4 act in a downstream part of the pathway, leading to endogenous 24-nucleotide siRNA production, but are not required for intercellular signaling. From genetic analysis, we conclude that another downstream part of the pathway associated with intercellular signaling requires DCL4 and at least one other protein required for 21-nucleotide trans-acting siRNAs. We interpret the effect of polymerase IVa and trans-acting siRNA pathway mutations in terms of a modular property of RNA silencing pathways