Predicted Functional Shifts Due to Type of Soil Microbiome and Watering of Two Wild Plants in Western Region of Saudi Arabia

The present study aimed to predict differential enrichment of pathways and compounds in the rhizosphere microbiomes of the two wild plants (Abutilon fruticosum and Nitrosalsola vermiculata) and to predict functional shifts in microbiomes due to water. Amplicon sequencing of 16S rRNA region V3–V4 was done and gene-based microbial compositions were enrolled in PICRUSt to predict enriched pathways and compounds. The results indicated that “ABC transporters” and “Quorum sensing” pathways are among the highest enriched pathways in rhizosphere microbiomes of the two wild plants compared with those of the bulk soil microbiomes. The highest enriched compounds in soil microbiomes of the two wild plants included five proteins and three enzymes participating in one or more KEGG pathways. Six of these eight compounds showed higher predicted enrichment in rhizosphere soil microbiomes, while only one, namely phosphate transport system substrate-binding protein, showed higher enrichment in the surrounding bulk soil microbiomes. In terms of differentially enriched compounds due to watering, only the dual-specific aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln) amidotransferase subunit A showed higher enrichment in rhizosphere soil of the two wild plants after 24 h of watering. Two of the highly enriched compounds namely branched-chain amino acid transport system ATP-binding protein and branched-chain amino acid transport system substrate-binding protein, are encoded by genes stimulated by the plant’s GABA that participates in conferring biotic and abiotic stresses in plants and improves the plant’s growth performance. The 3-Oxoacyl-[ACP] reductase, a member of the short-chain alcohol dehydrogenase/ reductase (SDR) superfamily, participates in fatty acids elongation cycles and contributes to plant-microbe symbiotic relationships, while enoyl-CoA hydratase has a reverse action as it participates in “Fatty acid degradation” pathway. The methyl-accepting chemotaxis protein is an environmental signal that sense “Bacterial chemotaxis” pathway to help establishing symbiosis with plant roots by recruiting/colonizing of microbial partners (symbionts) to plant rhizosphere. This information justifies the high enrichment of compounds in plant rhizosphere. The dual-specific aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln) amidotransferase subunit A contributes to the plant ability to respond to watering as it participates in attaching the correct amino acid during translation to its cognate tRNA species, while hydrolyzing incorrectly attached amino acid. These two actions reduce the influence of oxidative stress in generating misfolded proteins and in reducing fidelity of translation.     

A hybrid of the transhydrogenases from Rhodospirillum rubrum and Mycobacterium tuberculosis catalyses rapid hydride transfer but not the complete, proton-translocating reaction

All transhydrogenases appear to have three components: dI, which binds NAD(H), and dIII, which binds NADP(H), protrude from the membrane, and dII spans the membrane. However, the polypeptide composition of the enzymes varies amongst species. The transhydrogenases of Mycobacterium tuberculosis and of Rhodospirillum rubrum have three polypeptides. Sequence analysis indicates that an ancestral three-polypeptide enzyme evolved into transhydrogenases with either two polypeptides (such as the Escherichia coli enzyme) or one polypeptide (such as the mitochondrial enzyme). The fusion steps in each case probably led to the development of an additional transmembrane helix. A hybrid transhydrogenase was constructed from the dI component of the M. tuberculosis enzyme and the dII and dIII components of the R. rubrum enzyme. The hybrid catalyses cyclic transhydrogenation but not the proton-translocating, reverse reaction. This shows that nucleotide-binding/release at the NAD(H) site, and hydride transfer, are fully functional but that events associated with NADP(H) binding/release are compromised. It is concluded that sequence mismatch in the hybrid prevents a conformational change between dI and dIII which is essential for the step accompanying proton translocation.     

Characterization of MARCKS (Myristoylated alanine-rich C kinase substrate) identified by a monoclonal antibody generated against chick embryo neural retina

To identify molecular markers of cell differentiation in developing nervous tissue, monoclonal antibodies against chick embryo neural retina were made. One of them, 3C3mAb, recognized a developmentally regulated antigen present in several organs of the CNS. Data from MALDI-TOF mass spectrometry and peptide sequencing of the immuno-affinity purified protein indicated identity of the antigen with MARCKS. The immunoreactive material was always found as a unique polypeptide (Mr 71 kDa) in SDS-PAGE, however isoelectrofocusing revealed the existence of several bands (pI ranging from 4.0 to 4.5). Interestingly some retinal cell types, as photoreceptors, exhibited an extremely significant decrease in the intensity of the immunoreactive material during the final phases of terminal differentiation while others, as some retinal neurons, maintained the immunoreactivity when fully differentiated. Taken together these results indicate that MARCKS, a protein susceptible of several posttranslational modifications as myristoylation and phosphorylation at variable extent, may act differently in neural retina cell types.     

Membrane lipids composition and metabolism during early embryonic development. Phospholipid subcellular distribution and 32P labeling

Phospholipid composition and 32P metabolism were studied in oocytes and early developing embryos of the toad, Bufo arenarum, Hensel. The content and distribution of phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, phosphatidic acid, sphingomyelin, phosphatidylserine, and diphosphatidylglycerol in embryos, whole oocytes, and the subcellular fractions of both were determined. Phosphatidylcholine and phosphatidylethanolamine were the major constituents of yolk platelet. Diphosphatidylglycerol was confined to the mitochondrial fraction, where it represented about 7% of the total phosphoacylglycerols. Relatively large amounts of sphingomyelin were found in microsomal and postmicrosomal supernatants. After in vivo labeling with 32P, the early development of individual phospholipids in subcellular fractions and in whole eggs was followed. The greatest uptake was found in mitochondrial and yolk platelet fractions. A steady increase in the amount of 32P present in phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol was seen in the whole embryo from oocyte to late gastrula stage and in all subcellular fractions. Phosphatidic acid exhibited a slight decrease in specific activity, except in the yolk platelet fraction. This high 32P incorporation would indicate a rapid and uneven polar headgroup turnover determined by phospholipid class and subcellular fraction. At the same time, the phospholipid content of the subcellular fractions studied remained unchanged during early embryogenesis. Moreover, 32P was actively incorporated into the individual phospholipids in the absence of measurable net synthesis.     

Rananos expression pattern during oogenesis and early embryonic development in Rhynchosciara americana

The Dipteran Rhynchosciara americana, a native Brazilian insect that has become a valuable model system for developmental biology research because it provides an interesting opportunity to study a different type of insect oogenesis. Sequences from a cDNA library that was constructed with poly A+RNA from the ovaries of R. americana larvae at different ages were analyzed. Molecular characterization confirmed interesting findings, such as the presence of Rananos. The nanos gene encodes a conserved RNA-binding protein that is required during early development for the maintenance and division of the primordial germ cells of Diptera. nanos plays an important role in specifying the posterior regions of insect embryos and is important for abdomen formation. In the present work, we showed the spatial and temporal expression profiles of this important gene, which is involved in oogenesis and early development. Data mining techniques were used to obtain the complete sequence of Rananos. Bioinformatic tools were used to determine the following: (1) the secondary structure of the 3'-untranslated region of the Rananos mRNA, (2) the encoded protein of the isolated Rananos gene, (3) the conserved zinc-finger domains of the RaNanos protein, and (4) phylogenetic analyses. Furthermore, RNA in situ hybridization and immunolocalization were used to determine mRNA and protein expression in the tissues that were studied and to define Rananos as a germ cell molecular marker.     

Insights into the regulation of the core clock component TOC1 in the green picoeukaryote Ostreococcus

Living organisms such as plants and animals have evolved endogenous clocks in order to anticipate the environmental changes associated with the earth’s rotation and to orchestrate biological processes in the course of the 24 hour daily cycle. We have recently identified clock components in the primitive green picoalga Ostreococcus tauri, a promising minimal cellular and genomic model for systems biology approaches. A homologue of the Arabidopsis core clock gene Time of CAB expression-1 (TOC1) was shown to play a central role in Ostreococcus heralding an early emergence of clock components in the green lineage. Here we report the regulation of TOC1 at dusk in response to light and dark cues.Key words: Ostreococcus, circadian, clock, plants, microalgaeThe circadian clock is an autonomous timer, which provides for living organisms a means to measure time internally. As such the clock has two fundamental properties: (1) it allows the organism to anticipate daily predictable environmental changes such as light and temperature cycles; (2) it coordinates key physiological processes during the 24 hour daily cycle. As a result, internal time given by the clock and external time given by the photoperiod exhibit a stable phase relationship for a wide range of photoperiods during the course of the year. The clock is therefore also involved in regulating annual rhythms such as flowering (also called photoperiodism) and many clock mutants have been identified on the basis of abnormalities in the timing of flowering. Other clock genes, such as TOC1 were identified through screens for defects in the rhythmic expression of circadian-regulated genes such as the Light-harvesting complex (LHCB/CAB) gene.²In plants, the clock appears as a complex circuit relying on interconnected feedback loops, which are being studied through a combination of experimental and modelling approaches.³ However, circadian studies are complicated by cell-autonomous and tissue specific clockworks in multicellular plants. We have recently implemented tools for gene function, analysis in the very simple green cell Ostreococcus tauri.⁴ Amongst known core clock genes we identified two homologues of the plant clock genes TOC1 and CCA1 (Circadian Clock Associated 1). Furthermore we found that a conserved CCA1 binding site was required for the circadian expression of TOC1. TOC1 appears to play a more central role than CCA1 in the Ostreococcus clock since only TOC1 knock-down abolishes circadian function in constant light.⁴ In plants the dark-dependent degradation of TOC1 relies on the F box protein ZEITLUPE which is stabilized by GIGANTEA in blue light.^5,6 We identified no ZEITLUPE AND GIGANTEA homologues in Ostreococcus. We chose, therefore to investigate the regulation of TOC1 in Ostreococcus at dusk since there are similarities between TOC1 functions and patterns of expression in Ostreococcus and Arabidopsis.     

Signaling of Pigment-Dispersing Factor (PDF) in the Madeira Cockroach Rhyparobia maderae

The insect neuropeptide pigment-dispersing factor (PDF) is a functional ortholog of vasoactive intestinal polypeptide, the coupling factor of the mammalian circadian pacemaker. Despite of PDF''s importance for synchronized circadian locomotor activity rhythms its signaling is not well understood. We studied PDF signaling in primary cell cultures of the accessory medulla, the circadian pacemaker of the Madeira cockroach. In Ca²⁺ imaging studies four types of PDF-responses were distinguished. In regularly bursting type 1 pacemakers PDF application resulted in dose-dependent long-lasting increases in Ca²⁺ baseline concentration and frequency of oscillating Ca²⁺ transients. Adenylyl cyclase antagonists prevented PDF-responses in type 1 cells, indicating that PDF signaled via elevation of intracellular cAMP levels. In contrast, in type 2 pacemakers PDF transiently raised intracellular Ca²⁺ levels even after blocking adenylyl cyclase activity. In patch clamp experiments the previously characterized types 1–4 could not be identified. Instead, PDF-responses were categorized according to ion channels affected. Application of PDF inhibited outward potassium or inward sodium currents, sometimes in the same neuron. In a comparison of Ca²⁺ imaging and patch clamp experiments we hypothesized that in type 1 cells PDF-dependent rises in cAMP concentrations block primarily outward K⁺ currents. Possibly, this PDF-dependent depolarization underlies PDF-dependent phase advances of pacemakers. Finally, we propose that PDF-dependent concomitant modulation of K⁺ and Na⁺ channels in coupled pacemakers causes ultradian membrane potential oscillations as prerequisite to efficient synchronization via resonance.     

Evidence that the low-affinity K+ transport system of Rhodobacter capsulatus is a uniporter. The effects of ammonium on the transporter

Comparison of the rate of accumulation of ⁸⁶Rb⁺ by intact cells of Rhodobacter capsulatus during short periods of illumination with the Rb⁺-dependent membrane ionic current measured by electrochromism supports the view that both activities reflect the operation of a low-affinity K⁺ transport system. In experiments performed under similar conditions the ratio of ⁸⁶Rb⁺ uptake to charge uptake was approx. 1.0, suggesting that the transport system operates as a uniporter. The addition of NH _inf4 ^sup+ to a cell suspension led to an increase in membrane ionic current but failed to inhibit the accumulation of ⁸⁶Rb⁺ during illumination. The presence of K⁺ and NH _inf4 ^sup+ inhibited the increase in cellular ATP levels at the onset of illumination. This effect was prevented by Cs⁺. The results are considered within the context of the hypothesis (Golby et al. Eur J Biochem 187: 589–597) that NH _inf4 ^sup+ can be transported by the K⁺ carrier and in the context of an alternative hypothesis that NH _inf4 ^sup+ increases the affinity of the K⁺ transport system for its natural substrate and for Rb⁺.Abbreviations pH pH difference across the cytoplasmic membrane - electrical potential difference across the cytoplasmic membrane