Plant peptidoglycan precursor biosynthesis: Conservation between moss chloroplasts and Gram negative bacteria

An accumulation of evidence suggests that peptidoglycan, consistent with a bacterial cell wall, is synthesised around the chloroplasts of many photosynthetic eukaryotes, from glaucophyte algae to land plants at least as evolved as pteridophyte ferns, but the biosynthetic pathway has not been demonstrated. We employed mass spectrometry and enzymology in a two fold approach to characterize the synthesis of peptidoglycan in chloroplasts of the moss Physcomitrium (Physcomitrella) patens. To drive the accumulation of peptidoglycan pathway intermediates, P.patens was cultured with the antibiotics phosphomycin, D-cycloserine and carbenicillin, which inhibit key peptidoglycan pathway proteins in bacteria. Mass spectrometry of the TCA-extracted moss metabolome revealed elevated levels of five of the predicted intermediates from UDP-GlcNAc through to the UDP-MurNAc-D,L-diaminopimelate (DAP)-pentapeptide. Most Gram negative bacteria, including cyanobacteria, incorporate meso-diaminopimelate (D,L-DAP) into the third residue of the stem peptide of peptidoglycan, as opposed to L-Lysine, typical of most Gram positive bacteria. To establish the specificity of D,L-DAP incorporation into the P.patens precursors, we analysed the recombinant protein that appends the third stem peptide amino acid, UDP-MurNAc-tripeptide ligase (MurE), from both P.patens and the cyanobacterium Anabaena sp. strain PCC 7120. Both ligases incorporated D,L-DAP in almost complete preference to L-Lys, consistent with the mass spectrophotometric data, with catalytic efficiencies similar to previously documented Gram negative bacterial MurE ligases. We discuss how these data accord with the conservation of active site residues common to DL-DAP-incorporating bacterial MurE ligases and of the probability of a horizontal gene transfer event within the plant peptidoglycan pathway.

Ultrafast Proton Transfer Reaction in Phenol–(Ammonia)n Clusters: An Ab-Initio Molecular Dynamics Investigation.

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer process, the phenol molecule must be embedded in a cluster consisting of at least eight ammonia molecules, even though several local minima with proton transferred can be observed for clusters consisting of 5-7 ammonia molecules. Further, phenol solvated in large clusters of ammonia, the proton transfer is spontaneous with the proton transfer event being instantaneous (about 20-120 fs). These simulations indicate that the rate-determining step for the proton transfer process is the reorganization of the solvent around the OH group and the proton transfer process in phenol-(ammonia)n clusters. The fluctuations in the solvent occur until a particular set of configurations projects the field in excess of critical electric field along the O–H bond which drives the proton transfer process with a respone time of about 70 fs. Further, the proton transfer process follows a curvilinear path which includes the O–H bond elongation and out-of-plane movement of the proton and can be referred to as a “Bend-to-Break” process.

MESSENGER observations of planetary ion enhancements at Mercury’s northern magnetospheric cusp during Flux Transfer Event Showers

At Mercury, several processes can release ions and neutrals out of the planet’s surface. Here we present enhancements of dayside planetary ions in the solar wind entry layer during flux transfer event (FTE) “showers” near Mercury’s northern magnetospheric cusp. In this entry layer, solar wind ions are accelerated and move downward (i.e. planetward) toward the cusps, which sputter upward-moving planetary ions within 1 minute. The precipitation rate is enhanced by an order of magnitude during FTE showers and the neutral density of the exosphere can vary by >10% due to this FTE-driven sputtering. These in situ observations of enhanced planetary ions in the entry layer likely correspond to an escape channel of Mercury’s planetary ions, and the large-scale variations of the exosphere observed on minute-timescales by ground-based telescopes. Comprehensive, future multi-point measurements made by BepiColombo will greatly enhance our understanding of the processes contributing to Mercury’s dynamic exosphere and magnetosphere.

Review of Mercury’s dynamic magnetosphere: Post-MESSENGER era and comparative magnetospheres

This review paper summarizes the research of Mercury’s magnetosphere in the Post-MESSENGER era and compares its dynamics to those in other planetary magnetospheres, especially to those in Earth’s magnetosphere. This review starts by introducing the planet Mercury, including its interplanetary environment, magnetosphere, exosphere, and conducting core. The frequent and intense magnetic reconnection on the dayside magnetopause, which is represented by the flux transfer event “shower”, is reviewed on how they depend on magnetosheath plasma β and magnetic shear angle across the magnetopause, following by how it contributes to the flux circulation and magnetosphere-surface-exosphere coupling. In the next, Mercury’s magnetosphere under extreme solar events, including the core induction and the reconnection erosion on the dayside magnetosphere, the responses of the nightside magnetosphere, are reviewed. Then, the dawn-dusk properties of the plasma sheet, including the features of the ions, the structure of the current sheet, and the dynamics of magnetic reconnection, are summarized. The last topic is devoted to the particle energization in Mercury’s magnetosphere, which includes the energization of the Kelvin-Helmholtz waves on the magnetopause boundaries, reconnection-generated magnetic structures, and the cross-tail electric field. In each chapter, the last section discusses the open questions related to each topic, which can be considered by the simulations and the future spacecraft mission. We end this paper by summarizing the future BepiColombo opportunities, which is a joint mission of ESA and JAXA and is en route to Mercury.

Ultrafast Proton Transfer Reaction in Phenol–(Ammonia)n Clusters: An Ab-Initio Molecular Dynamics Investigation.

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer process, the phenol molecule must be embedded in a cluster consisting of at least eight ammonia molecules, even though several local minima with proton transferred can be observed for clusters consisting of 5-7 ammonia molecules. Further, phenol solvated in large clusters of ammonia, the proton transfer is spontaneous with the proton transfer event being instantaneous (about 20-120 fs). These simulations indicate that the rate-determining step for the proton transfer process is the organization of the solvent around the OH group and the proton transfer process in phenol-(ammonia)n clusters follows a curvilinear path which includes the O–H bond elongation and out-of-plane movement of the proton and can be referred to as a “Bend-to-Break” process.

Dayside magnetopause reconnection and flux transfer events: BepiColombo earth-Flyby observations

This study analyzes the flux transfer event (FTE)-type flux ropes and magnetic reconnection around the dayside magnetopause during BepiColombo’s Earth flyby. The magnetosheath corresponds to a high plasma β (~ 8) and the IMF has a significant radial component. Six flux ropes are identified. The motion of flux rope together with the maximum magnetic shear model suggests that the reconnection X-line swipes BepiColombo near the magnetic equator due to an increase of the radial IMF. The flux rope with the highest flux content contains a clear coalescence signature, i.e., two smaller flux ropes merging, supporting theoretical predictions the flux content of flux ropes can grow through coalescence. The secondary reconnection associated with coalescence exhibits a large normalized guide field and a reconnection rate comparable to the reconnection rate measured at the magnetopause (~ 0.1).

Horizontal transfer of the n-TASE gene cluster in Burkholderia seminalis TC3.4.2R3 inferred from phylogenetic and molecular methods

This study describes the n-TASE cluster in Burkholderia seminalis TC3.4.2R3, which was present in B. contaminans (CP046609.1), but absent in other related Burkholderia species. Phylogeny, comparative genomics and molecular analysis indicated it is not common to B. seminalis species, presenting similarity with homologous genes presents Aquamicrobium sp. SK-2 and B. contaminans LMG23361, probably acquired by an HGT (Horizontal Gene Transfer) event. It was not possible to determine which was the most likely donor strain of the n-TASE cluster. The HGT event did not occur in all strains of the Bcc group, nor in the B. seminalis, but it did occur punctually in the strain B. seminalis TC34.2R3. It has a correlation in biotechnological applications related processes. Aiming at understanding the involvement of the n-TASE cluster in the interaction of this bacterium in the environment, genes in this cluster will be inactivated, next.

Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages

Duplication-Transfer-Loss (DTL) reconciliation is a widely used computational technique for understanding gene family evolution and inferring horizontal gene transfer (transfer for short) in microbes. However, most existing models and implementations of DTL reconciliation cannot account for the effect of unsampled or extinct species lineages on the evolution of gene families, likely affecting their accuracy. Accounting for the presence and possible impact of any unsampled species lineages, including those that are extinct, is especially important for inferring and studying horizontal transfer since many genes in the species lineages represented in the reconciliation analysis are likely to have been acquired through horizontal transfer from unsampled lineages. While models of DTL reconciliation that account for transfer from unsampled lineages have already been proposed, they use a relatively simple framework for transfer from unsampled lineages and cannot explicitly infer the location on the species tree of each unsampled or extinct lineage associated with an identified transfer event. Furthermore, there does not yet exist any systematic studies to assess the impact of accounting for unsampled lineages on the accuracy of DTL reconciliation. In this work, we address these deficiencies by (i) introducing an extended DTL reconciliation model, called the DTLx reconciliation model, that accounts for unsampled and extinct species lineages in a new, more functional manner compared to existing models, (ii) showing that optimal reconciliations under the new DTLx reconciliation model can be computed just as efficiently as under the fastest DTL reconciliation model, (iii) providing an efficient algorithm for sampling optimal DTLx reconciliations uniformly at random, (iv) performing the first systematic simulation study to assess the impact of accounting for unsampled lineages on the accuracy of DTL reconciliation, and (v) comparing the accuracies of inferring transfers from unsampled lineages under our new model and the only other previously proposed parsimony-based model for this problem.

Biochemical and Phylogenetic Characterization of a Novel NADP+-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum

Isocitrate dehydrogenase (IDH) family of proteins is classified into three subfamilies, namely, types I, II, and III. Although IDHs are widely distributed in bacteria, archaea, and eukaryotes, all type III IDHs reported to date are found only in prokaryotes. Herein, a novel type III IDH subfamily member from the marine microalga Phaeodactylum tricornutum (PtIDH2) was overexpressed, purified, and characterized in detail for the first time. Relatively few eukaryotic genomes encode this type of IDH and PtIDH2 shares the highest homology with marine bacterial monomeric IDHs, suggesting that PtIDH2 originated through a horizontal gene transfer event between a marine alga and a bacterium. Size-exclusion chromatography revealed that the native PtIDH2 is a homotetramer (∼320 kDa) in solution, comprising four monomeric IDH-like subunits (80 kDa each). Enzymatic characterization showed that PtIDH2 is a bivalent metal ion-dependent enzyme and Mn2+ is the optimal activator. The recombinant PtIDH2 protein exhibited maximal activity at 35°C and pH 8.0 in the presence of Mn2+. Heat-inactivation analysis revealed that PtIDH2 is a cold-adapted enzyme. Kinetic analysis demonstrated that PtIDH2 is a completely NADP+-specific IDH with no detectable NAD+-associated catalytic activity. The three putative key NADP+-binding residues (His604, Arg615, and Arg664) in PtIDH2 were also evaluated by site-directed mutagenesis. The H604L/R615D/R664S triple mutant showed a 3.25-fold preference for NAD+ over NADP+, implying that the coenzyme specificity of PtIDH2 can be converted from NADP+ to NAD+ through rational engineering approaches. Additionally, the roles of the conserved residues Ala718 and Leu742 in the thermostability of PtIDH2 were also explored by site-directed mutagenesis. We found that the L742F mutant displayed higher thermostability than wild-type PtIDH2. This study expands the phylogeny of the IDH family and provides new insights into the evolution of IDHs.

Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees

Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least one horizontal transfer event. As a natural generalization, we consider symmetrized Fitch maps, that is, symmetric maps $\varepsilon$ that assign a subset of colors to each pair of vertices in $X$ and that can be explained by a tree $T$ with edges that are labeled with subsets of colors in the sense that the color $m$ appears in $\varepsilon(x,y)$ if and only if $m$ appears in a label along the unique path between $x$ and $y$ in $T$. We first give an alternative characterization of the monochromatic case and then give a characterization of symmetrized Fitch maps in terms of compatibility of a certain set of quartets. We show that recognition of symmetrized Fitch maps is NP-complete. In the restricted case where $|\varepsilon(x,y)|\leq 1$ the problem becomes polynomial, since such maps coincide with class of monochromatic Fitch maps whose graph-representations form precisely the class of complete multi-partite graphs.