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Identification of three urease accessory proteins that are required for urease activation in Arabidopsis.

Urease is a nickel-containing urea hydrolase involved in nitrogen recycling from ureide, purine, and arginine catabolism in plants. The process of urease activation by incorporation of nickel into the active site is a prime example of chaperone-mediated metal transfer to an enzyme. Four urease accessory proteins are required for activation in Klebsiella aerogenes. In plants urease accessory proteins have so far been only partially defined. Using reverse genetic tools we identified four genes that are necessary for urease activity in Arabidopsis (Arabidopsis thaliana; ecotypes Columbia and Nössen). Plants bearing T-DNA or Ds element insertions in either the structural gene for urease or in any of the three putative urease accessory genes AtureD, AtureF, and AtureG lacked the corresponding mRNAs and were defective in urease activity. In contrast to wild-type plants, the mutant lines were not able to support growth with urea as the sole nitrogen source. To investigate whether the identified accessory proteins would be sufficient to support eukaryotic urease activation, the corresponding cDNAs were introduced into urease-negative Escherichia coli. In these bacteria, urease activity was observed only when all three plant accessory genes were coexpressed together with the plant urease gene. Remarkably, plant urease activation occurred as well in cell-free E. coli extracts, but only in extracts from cells that had expressed all three accessory proteins. The future molecular dissection of the plant urease activation process may therefore be performed in vitro, providing a powerful tool to further our understanding of the biochemistry of chaperone-mediated metal transfer processes in plants.

Arabidopsis↗

Maternal, Single-Gene Regulation of Assimilate Partitioning in Pea.

Assimilate partitioning has been identified as a key process in the control of yield. Although the role of reproductive structures in this process has received intensive study, our understanding of the role of the maternal plant is limited. We suggest that the Sn gene of pea (Pisum sativum L.) is a potentially valuable genetic tool for studying maternal regulation of partitioning. In this study, nearly isogenic lines differing at the Sn locus were compared with respect to seed-filling characteristics and carbon assimilation. Lines with the Sn gene had a slower rate and shorter duration of seed growth than the line recessive for this gene, and these traits could not be ascribed to reduced carbon assimilation. Flowers of the two nearly isogenic lines were manually pollinated to control the genotype of the developing embryo independently of the maternal genotype. The final dry weight of the seed was determined by the genotype of the maternal plant and not by the genotype of the embryo, supporting the hypothesis that the Sn gene acts in the vegetative plant to regulate the partitioning of assimilates between vegetative and reproductive growth. Although the Sn gene has been noted for delaying apical senescence, it also delayed leaf senescence in this study; leaves of the Sn line continued to photosynthesize long past the time that leaves of the recessive line had senesced and after the seeds and pods were dry.

Journal Article↗

Arabidopsis genes encoding components of the chloroplastic protein import apparatus.

The process of protein import into plastids has been studied extensively using isolated pea (Pisum sativum) chloroplasts. As a consequence, virtually all of the known components of the proteinaceous apparatus that mediates import were originally cloned from pea. With the recent completion of the Arabidopsis genome sequencing project, it is now possible to identify putative homologs of the import components in this species. Our analysis has revealed that Arabidopsis homologs with high sequence similarity exist for all of the pea import complex subunits, making Arabidopsis a valid model for further study of this system. Multiple homologs can be identified for over one-half of the components. In all but one case it is known that more than one of the putative isoforms for a particular subunit are expressed. Thus, it is possible that multiple types of import complexes are present within the same cell, each having a unique affinity for different chloroplastic precursor proteins, depending upon the exact mix of isoforms it contains. Sequence analysis of the putative Arabidopsis homologs for the chloroplast protein import apparatus has revealed many questions concerning subunit function and evolution. It should now be possible to use the genetic tools available in Arabidopsis, including the generation of knockout mutants and antisense technology, to address these questions and learn more about the molecular functions of each of the components during the import process.

Amino Acid Sequence↗

Ovule Development in Wild-Type Arabidopsis and Two Female-Sterile Mutants.

Ovules are complex structures that are present in all seed bearing plants and are contained within the carpels in flowering plants. Ovules are the site of megasporogenesis and megagametogenesis and, following fertilization, develop into seeds. We combined genetic methods with anatomical and morphological analyses to dissect ovule development. Here, we present a detailed description of the morphological development of Arabidopsis ovules and report on the isolation of two chemically induced mutants, bell (bel1) and short integuments (sin1), with altered ovule development. Phenotypic analyses indicated that bel1 mutants initiate a single integument-like structure that develops aberrantly, sin1 mutants initiate two integuments, but growth of the integuments is disrupted such that cell division continues without normal cell elongation. Both mutants can differentiate archesporial cells, but neither forms a normal embryo sac. Genetic analyses indicated that bel1 segregates as a single recessive mutation, and complementation tests showed that the two mutants are not allelic. The phenotypes of the mutants indicate that normal morphological development of the integuments and proper embryo sac formation are interdependent or are governed in part by common pathways. The ovule mutants that we describe in Arabidopsis represent novel genetic tools for the study of this stage of reproductive development.

Journal Article↗

An integrative approach for the identification of quantitative trait loci.

The genetic dissection of complex traits is one of the most difficult and most important challenges facing science today. We discuss here an integrative approach to quantitative trait loci (QTL) mapping in mice. This approach makes use of the wealth of genetic tools available in mice, as well as the recent advances in genome sequence data already available for a number of inbred mouse strains. We have developed mapping strategies that allow a stepwise narrowing of a QTL mapping interval, prioritizing candidate genes for further analysis with the potential of identifying the most probable candidate gene for the given trait. This approach integrates traditional mapping tools, fine mapping tools, sequence-based analysis, bioinformatics and gene expression.

Animals↗

Linear chromosomal physical and genetic map of Borrelia burgdorferi, the Lyme disease agent.

A physical map of the 952 kbp chromosome of Borrelia burgdorferi Sh-2-82 has been constructed. Eighty-three intervals on the chromosome, defined by the cleavage sites of 15 restriction enzymes, are delineated. The intervals vary in size from 96 kbp to a few hundred bp, with an average size of 11.5 kbp. A striking feature of the map is its linearity; no other bacterial groups are known to have linear chromosomes. The two ends of the chromosome do not hybridize with one another, indicating that there are no large common terminal regions. The chromosome of this strain was found to be stable in culture; passage 6, 165 and 320 cultures have identical chromosomal restriction maps. We have positioned all previously known Borrelia burgdorferi chromosomal genes and several newly identified ones on this map. These include the gyrA/gyrB/dnaA/dnaN gene cluster, the rRNA gene cluster, fla, flgE, groEL (hsp60), recA, the rho/hip cluster, the dnaK (hsp70)/dnaJ/grpE cluster, the pheT/pheS cluster, and the genes which encode the potent immunogen proteins p22A, p39 and p83. Our electrophoretic analysis detects five linear and at least two circular plasmids in B. burgdorferi Sh-2-82. We have constructed a physical map of the 53 kbp linear plasmid and located the operon that encodes the two major outer surface proteins ospA and ospB on this plasmid. Because of the absence of functional genetic tools for this organism, these maps will serve as a basis for future mapping, cloning and sequencing studies of B. burgdorferi.

Blotting, Southern↗

Endocytosis, membrane recycling and sorting of GPI-anchored proteins: Trypanosoma brucei as a model system.

In the flagellated protozoon Trypanosoma brucei, endo- and exocytosis are restricted to a small area of the plasma membrane, the flagellar pocket. All endosomal compartments and the single Golgi complex are located within the posterior part of the cell between the flagellar pocket and the nucleus. The use of reverse genetic tools, including RNA interference, in combination with quantitative 3D-fluorescence and electron microscopic techniques has provided an insight into endosomal membrane traffic, which occurs at a very high rate and appears to exhibit a lower level of complexity than in mammalian cells. The flagellate is an excellent model system for studies on endocytosis, sorting and recycling of glycosylphosphatidylinositol-anchored glycoproteins, because 10(7) molecules of the variant surface glycoprotein form a dense coat at the cell's surface. Because the endocytic rate varies widely at different stages in the parasite's life cycle, trypanosomes may be used for investigating developmental aspects of their endocytic system.

Animals↗

Apoptosis in yeast--mechanisms and benefits to a unicellular organism.

Initial observations that the budding yeast Saccharomyces cerevisiae can be induced to undergo a form of cell death exhibiting typical markers of apoptosis has led to the emergence of a thriving new field of research. Since this discovery, a number of conserved pro- and antiapoptotic proteins have been identified in yeast. Indeed, early experiments have successfully validated yeasts as a powerful genetic tool with which to investigate mechanisms of apoptosis. However, we still have little understanding as to why programmes of cell suicide exist in unicellular organisms and how they may be benefit such organisms. Recent research has begun to elucidate pathways that regulate yeast apoptosis in response to environmental stimuli. These reports strengthen the idea that physiologically relevant mechanisms of programmed cell death are present, and that these function as important regulators of yeast cell populations.

Apoptosis↗

Managing the genome: microRNAs in Drosophila.

MicroRNAs (miRNAs) represent a growing class of short non-coding RNAs that regulate gene expression by post-transcriptional mechanisms. By binding to target mRNAs via stretches of sequence complementarity, microRNAs inhibit the production of target proteins or induce degradation of mRNAs. Several hundred miRNAs have recently been predicted and cloned from eukaryotic organisms as diverse as plants, invertebrates, and vertebrates. Some miRNAs were shown to be widely conserved across phyla. However, except in a few described cases, rather little is known about their endogenous target genes and the physiological pathways they impinge on. Invertebrate model organisms such as C. elegans and Drosophila have been instrumental to develop methods and to dissect biological roles of miRNAs. In this review, we will focus on recent progress in characterizing miRNAs and steps toward identification of target genes in Drosophila. Many of these recent experiments provide evidence that a systematic target discovery is feasible and that the biology of miRNAs can be functionally explored using forward and reverse genetic tools.

Animals↗

Trade-offs between longevity and pathogen resistance in Drosophila melanogaster are mediated by NFkappaB signaling.

The innate immune response protects numerous organisms, including humans, from the universe of pathogenic molecules, viruses and micro-organisms. Despite its role in promoting pathogen resistance, inappropriate activation and expression of NFkappaB and other immunity-related effector molecules can lead to cancer, inflammation, and other diseases of aging. Understanding the mechanisms leading to immune system activation as well as the short- and long-term consequences of such activation on health and lifespan is therefore critical for the development of beneficial immuno-modulating and longevity-promoting interventions. Mechanisms of innate immunity are highly conserved across species, and we take advantage of genetic tools in the model organism, Drosophila melanogaster, to study the effects of acute and chronic activation of immunity pathways on pathogen resistance and general fitness of adult flies. Our findings indicate that fat body specific overexpression of a putative pathogen recognition molecule, peptidoglycan recognition protein (PGRP-LE), is sufficient for constitutive up-regulation of the immune response and for enhanced pathogen resistance. Primary components of fitness are unaffected by acute activation, but chronic activation leads to an inflammatory state and reduced lifespan. These phenotypes are dependent on the NFkappaB-related transcriptional factor, Relish, and they establish a mechanistic basis for a link between immunity, inflammation, and longevity.

Animals↗

Genetic and other contributions to alcohol intake in rhesus macaques (Macaca mulatta).

BACKGROUND: The etiology of alcoholism and alcohol abuse, like many other complex diseases, is heterogeneous and multifactorial. Numerous studies demonstrate a genetic contribution to variation in the expression of alcohol-related disorders in humans. Over the past decade, nonhuman primates have emerged as a valuable model for some aspects of human alcohol abuse because of their phylogenetic proximity to humans. Long-term, longitudinal studies of rhesus macaques (Macaca mulatta) have provided much insight into environmental influences, especially early life experiences, on alcohol consumption and behavior patterns that characterize alcohol intake later in life. It is not known, however, whether there is a genetic component as well to the variation seen in alcohol consumption in rhesus macaques. A significant genetic component to variation in alcohol consumption in rhesus macaques would show for the first time that like humans, for nonhuman primates additive genetic influences are important. Moreover, their use as a model for alcohol-related disorders in humans would have even greater relevance and utility for designing experiments incorporating the expanding molecular genetics field, and allow researchers to investigate the interaction among the known environmental influences and various genotypes. METHODS: In this study, we investigate factors contributing to variation in alcohol consumption of 156 rhesus macaques collected over 10 years when subjects were adolescent in age, belonging to a single extended pedigree, with each cohort receiving identical early rearing backgrounds and subsequent treatments. To measure alcohol consumption each animal was provided unfettered simultaneous access both to an aspartame-sweetened 8.4% (v/v) alcohol-water solution, the aspartame-sweetened vehicle, and to water for 1 hour each day during the early afternoon between 13:00 and 15:00 in their home cages for a period of 5 to 7 weeks. We use multiple regression to identify factors that significantly affect alcohol consumption among these animals and a maximum likelihood program (ASReml) that, controlling for the significant factors, estimates the genetic contribution to the variance in alcohol consumption. RESULTS: Multiple regression analysis identified test cohort and rearing environment as contributing to 57 and 2%, respectively, of the total variance in alcohol consumption. Of the remaining 41% of the variance about half (19.8%) was attributable to additive genetic effects using a maximum likelihood program. CONCLUSION: This study demonstrates that, as in humans, there are additive genetic factors that contribute to variation in alcohol consumption in rhesus macaques, with other nongenetic factors accounting for substantial portions of the variance in alcohol consumption, Our findings show the presence of an additive genetic component and suggest the potential utility of the nonhuman primate as a molecular genetics tool for understanding alcohol abuse and alcoholism.

Alcohol Drinking↗

Transposon induced mutation in Gluconobacter oxydans with special reference to its direct-glucose oxidation metabolism.

Transposons are important genetic tools for mutation studies and for location of genes in prokaryotes. However, very little published work is available on transposon mutagenesis in Gluconobacter oxydans. We report here Tn5-induced mutation in a keto acid-producing strain of G. oxydans ATCC 9937 with special reference to the direct-glucose oxidation pathway operative in this organism. In this study, a mutant deficient in glucose dehydrogenase (GDH) activity has been developed by Tn5 mutagenesis. The data of plasmid profiles in the wild-type and the GDH- mutant are indicative of transposition in the first instance on one of the three plasmids (pVJ1) harboured by the organism, resulting in rearrangement of the plasmid and finally stable transposition of Tn5 on the main genome. The final location of Tn5 on the genome has been established by DNA hybridisation studies.

Acetobacteraceae↗

Sequence and characterization of an Ehrlichia chaffeensis gene encoding 314 amino acids highly homologous to the NAD A enzyme.

DNA sequence analysis of the nadA gene of Ehrlichia chaffeensis revealed a 942 bp open reading frame with the capacity to encode 314 amino acids. The amino acid sequence of the E. chaffeensis quinolinate synthetase A (NAD/A) has 53.6% identity and 82% similarity to the NAD A of the cyanelle of Cyanophora paradoxa. Portions of the homologous genes of E. canis and E. muris were also sequenced. The amino acid sequences of the NAD A of E. canis and E. muris have 89.2% and 93.2% homology, respectively, to the NAD A of E. chaffeensis. We propose that the nadA gene may be an excellent candidate for a genetic tool for the phylogenetic study of ehrlichiae.

Bacterial Proteins↗

Molecular genetics and the initiation of solventogenesis in Clostridium beijerinckii (formerly Clostridium acetobutylicum) NCIMB 8052.

A physical map of the Clostridium beijerinckii (formerly Clostridium acetobutylicum) NCIMB 8052 chromosome has been constructed, encompassing about 90 rare restriction sites. The 14 rrn operons together with about 40 genes have been assigned positions on the map. Genetic analysis and gene transfer have been developed in this organism to enable in vivo analysis of the roles of cloned genes using marker replacement technology. Experiments using the available genetic tools have shown that spo0A plays a cardinal role in controlling several aspects of the transition from exponential growth to stationary phase in C. beijerinckii. These include initiation of sporulation, accumulation of the storage polysaccharide, granulose, and production of acetone and butanol. Several C. beijerinckii and C. acetobutylicum genes concerned with fermentative metabolism, whose expression is modulated at the onset of solventogenesis, contain sequence motifs resembling 0A boxes in their 5' regulatory regions. This invites the speculation that they are under the direct control of Spo0A, and additional data are now required to test this prediction.

Base Sequence↗

Themes and variations in prokaryotic cell division.

Perhaps the biggest single task facing a bacterial cell is to divide into daughter cells that contain the normal complement of chromosomes. Recent technical and conceptual breakthroughs in bacterial cell biology, combined with the flood of genome sequence information and the excellent genetic tools in several model systems, have shed new light on the mechanism of prokaryotic cell division. There is good evidence that in most species, a molecular machine, organized by the tubulin-like FtsZ protein, assembles at the site of division and orchestrates the splitting of the cell. The determinants that target the machine to the right place at the right time are beginning to be understood in the model systems, but it is still a mystery how the machine actually generates the constrictive force necessary for cytokinesis. Moreover, although some cell division determinants such as FtsZ are present in a broad spectrum of prokaryotic species, the lack of FtsZ in some species and different profiles of cell division proteins in different families suggests that there are diverse mechanisms for regulating cell division.

Archaea↗

Ion currents in Drosophila flight muscles.

1. The dorsal longitudinal flight muscles of Drosophila melanogaster contain three voltage-activated ion currents, two distinct potassium currents and a calcium current. The currents can be isolated from each other by exploiting the developmental properties of the system and genetic tools, as well as conventional pharmacology.2. The fast transient potassium current (I(A)) is the first channel to appear in the developing muscle membrane. It can be studied in isolation between 60 and 70 hr of pupal development. The channels can be observed to carry both outward and inward currents depending on the external potassium concentration. I(A) is blocked by both tetraethylammonium ion (TEA) and 3- or 4-aminopyridine. The inactivation and recovery properties of I(A) are responsible for a facilitating effect on membrane excitability.3. The delayed outward current (I(K)) develops after maturation of the I(A) system. I(K) can be isolated from I(A) by use of a mutation that removes I(A) from the membrane current response and can be studied before the development of Ca(2+) channels. I(K) shows no inactivation. The channels are more sensitive to blockage by TEA than I(A) channels, but are not substantially blocked by 3- or 4-aminopyridine.4. The calcium current (I(Ca)) is the last of the major currents to develop and must be isolated pharmacologically with potassium-blocking agents. I(Ca) shows inactivation when Ca(2+) is present but not when Ba(2+) is the sole current carrier. When Ca(2+) is the current carrier, the addition of Na(+) or Li(+) retards the inactivation of the net inward current. When the membrane voltage is not clamped, Ba(2+) alone, or Ca(2+) with Na(+) (or Li(+)), produces a plateau response of extended duration.5. The synaptic current (I(J)) evoked by motoneurone stimulation is the fastest and largest of the current systems. It has a reversal potential of approximately -5 mV, indicating roughly equal permeabilities of Na(+) and K(+). During a nerve-driven muscle spike, I(J) is the major inward current, causing a very rapid depolarization away from resting potential. An exceptionally large synaptic current is necessary to rapidly discharge the high membrane capacitance (0.03 muF/cell) in these large (0.05 x 0.1 x 0.8 mm) isopotential cells.

Aminopyridines↗

Selective knock-down of P2X7 ATP receptor function by dominant-negative subunits.

Among the family of P2X ATP-gated cation channels, the P2X7 receptor is a homomeric subtype highly expressed in immune cells of the monocyte-macrophage lineage. We report here that the WC167-168AA mutation in the ectodomain of P2X7 produced nonfunctional subunits with strong dominant-negative effect on wild-type P2X7 receptors (77% inhibition with cotransfection of wild-type and mutant DNA at a ratio of 3:1). The C168A single mutant was also very effective in suppressing P2X7 receptor function (72% reduction at a DNA ratio of 3:1), indicating the major role played by the C168A mutation in this inhibition. The dominant-negative effect is selective; the mutant subunit did not suppress the function of other receptor-channel subtypes. The reduced current responses in cells coexpressing wild-type and dominant-negative subunits display wild-type characteristics in both agonist affinity and ionic selectivity, strongly suggesting that the heteromeric channels are functionally impaired. The mutant subunits also suppressed the P2X7-dependent pore formation as assessed by uptake of the propidium dye YO-PRO-1 (Molecular Probes, Eugene, OR) in response to 2',3'-O-(4-benzoyl)-benzoyl-ATP (BzATP) in transfected human embryonic kidney 293 cells. Native responses to BzATP as well as ATP-induced ethidium dye uptake were significantly knocked down (31 +/- 9% and 25 +/- 7% of control, respectively) in mouse macrophage cell line RAW264.7 transfected with the mutant subunits. Therefore, these dominant-negative subunits provide selective genetic tools to investigate the functional roles of native P2X7 receptors.

Animals↗

Casting a genetic light on the evolution of eyes.

Light has been exploited for information by organisms through the evolution of photoreceptors and, ultimately, eyes in animals. Only a handful of eye types exist because the physics of light constrains photodetection. In the past few years, genetic tools have revealed several parallel pathways through which light guides behavior and have provided insights into the convergent evolution of eyes. The gene encoding opsin (the primary phototransduction protein) and some developmental genes had very early origins and were recruited repeatedly during eye evolution. Eye lens proteins arose separately and make up a diverse group, many of which were co-opted from other functions. A major challenge now is understanding how newly discovered pathways for processing light evolved and how they collaborate with eyes to harvest information from light.

Animals↗