Academic literature on the topic 'S-RNase gene'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'S-RNase gene.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "S-RNase gene"
1
Hugot, Karine, Michel Ponchet, Antoine Marais, Pierre Ricci, and Eric Galiana. "A Tobacco S-like RNase Inhibits Hyphal Elongation of Plant Pathogens." Molecular Plant-Microbe Interactions® 15, no. 3 (March 2002): 243–50. http://dx.doi.org/10.1094/mpmi.2002.15.3.243.
Full textAbstract:
Ribonuclease (RNase) NE gene expression is induced in tobacco leaves in response to Phytophthora parasitica. Using antibodies directed against RNase NE, we demonstrate that RNase NE is extracellular at the early steps of the interaction, while the fungal tip growth is initiated in the apoplas-tic compartment. After production in Pichia pastoris and biochemical purification, we show that the S-like RNase NE inhibits hyphal growth from P. parasitica zoospores and from Fusarium oxysporum conidia in vitro. Conversion into an enzymatically inactive form after mutagenesis of the active site-histidine 97 residue to phenylalanine leads to the suppression of this activity, suggesting that RNase NE inhibits the elongation of germ tubes by degradation of microbial RNAs. Exogenous application of RNase NE in the extracellular space of leaves inhibits the development of P. parasitica. Based on its induction by inoculation, its localization, and its activity against two plant pathogens, we propose that RNase NE participates in tobacco defense mechanisms by a direct action on hyphal development in the extracellular space. The RNase activity-dependent antimicrobial activity of the S-like RNase NE shares similarities with the only other biological activity demonstrated for plant RNases, the inhibition of elongation of pollen tubes by the S-RNase in gametophytic self-incompatibility, suggesting a functional link between self and nonself interactions in plants.
2
Shu, H. H., C. A. Wise, G. D. Clark-Walker, and N. C. Martin. "A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA." Molecular and Cellular Biology 11, no. 3 (March 1991): 1662–67. http://dx.doi.org/10.1128/mcb.11.3.1662-1667.1991.
Full textAbstract:
We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.
3
Shu, H. H., C. A. Wise, G. D. Clark-Walker, and N. C. Martin. "A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA." Molecular and Cellular Biology 11, no. 3 (March 1991): 1662–67. http://dx.doi.org/10.1128/mcb.11.3.1662.
Full textAbstract:
We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.
4
Li, Yu-Ze, Jia-Wei Zhu, Wei Lin, Mo-Ying Lan, Cong Luo, Li-Ming Xia, Yi-Li Zhang, et al. "Genome-Wide Analysis of the RNase T2 Family and Identification of Interacting Proteins of Four ClS-RNase Genes in ‘XiangShui’ Lemon." International Journal of Molecular Sciences 23, no. 18 (September 9, 2022): 10431. http://dx.doi.org/10.3390/ijms231810431.
Full textAbstract:
S-RNase plays vital roles in the process of self-incompatibility (SI) in Rutaceae plants. Data have shown that the rejection phenomenon during self-pollination is due to the degradation of pollen tube RNA by S-RNase. The cytoskeleton microfilaments of pollen tubes are destroyed, and other components cannot extend downwards from the stigma and, ultimately, cannot reach the ovary to complete fertilisation. In this study, four S-RNase gene sequences were identified from the ‘XiangShui’ lemon genome and ubiquitome. Sequence analysis revealed that the conserved RNase T2 domains within S-RNases in ‘XiangShui’ lemon are the same as those within other species. Expression pattern analysis revealed that S3-RNase and S4-RNase are specifically expressed in the pistils, and spatiotemporal expression analysis showed that the S3-RNase expression levels in the stigmas, styles and ovaries were significantly higher after self-pollination than after cross-pollination. Subcellular localisation analysis showed that the S1-RNase, S2-RNase, S3-RNase and S4-RNase were found to be expressed in the nucleus according to laser confocal microscopy. In addition, yeast two-hybrid (Y2H) assays showed that S3-RNase interacted with F-box, Bifunctional fucokinase/fucose pyrophosphorylase (FKGP), aspartic proteinase A1, RRP46, pectinesterase/pectinesterase inhibitor 51 (PME51), phospholipid:diacylglycerol acyltransferase 1 (PDAT1), gibberellin receptor GID1B, GDT1-like protein 4, putative invertase inhibitor, tRNA ligase, PAP15, PAE8, TIM14-2, PGIP1 and p24beta2. Moreover, S3-RNase interacted with TOPP4. Therefore, S3-RNase may play an important role in the SI of ‘XiangShui’ lemon.
5
Sanzol, Javier, and Timothy P. Robbins. "Combined Analysis of S-Alleles in European Pear by Pollinations and PCR-based S-Genotyping; Correlation between S-Phenotypes and S-RNase Genotypes." Journal of the American Society for Horticultural Science 133, no. 2 (March 2008): 213–24. http://dx.doi.org/10.21273/jashs.133.2.213.
Full textAbstract:
Pollen–pistil incompatibility in european pear (Pyrus communis L.) compromises adequate orchard pollination and fruit set and restricts cross-fertility between cultivars suitable as parents in breeding programs. Genetic control is simple, with a single locus expressed gametophytically in pollen controlling the rejection of the pollen tube in the style. Semicompatible pollination arises when only one allele of a pollen parent matches the pistil. Semicompatible test-crosses using partially S-genotyped european pear cultivars allowed the discrimination of 14 S-alleles (S1 to S14) at the phenotypic level and the assignment of 33 cultivars to 13 incompatibility groups. Partial genomic sequences of the S-RNase gene, spanning between the C1 and C5 conserved regions, were obtained for each new S-allele identified (S6 to S14). These sequences and those reported previously for the S1 to S5 RNases allowed a set of consensus primers amplifying all 14 S-RNase alleles to be designed. Allele-specific PCR allowed discrimination between those S-RNases giving amplification products of similar size with consensus primers. These two approaches provided a method for the molecular identification of all 14 S-alleles in european pear. With this methodology, we demonstrate that the S-RNase genotypes inferred from PCR exactly matches the S-phenotypes deduced from test-crosses. Comparison of the sequences obtained with those of S-RNases already published allowed us to relate S-alleles between studies. This will allow the prediction of cross-incompatibility among an even larger number of european pear cultivars.
6
Niska, Reut, Martin Goldway, and Doron Schneider. "S6-RNase Is a Marker for Self-compatibility in Loquat (Eriobotrya japonica Lindl.)." HortScience 45, no. 8 (August 2010): 1146–49. http://dx.doi.org/10.21273/hortsci.45.8.1146.
Full textAbstract:
Loquat (Eriobotrya japonica Lindl.), a member of the Rosaceae, carries the RNase-dependent gametophytic self-incompatibility fertilization system. Analysis of S-RNase-allele content in the commercial loquat cultivars Avri, Yehuda, and Akko 1 revealed that each of them contains one different S-RNase allele—S2, S3, and S4, respectively, and one that they all share, S6. Although all four S-alleles were isolated in this work, only S6 was found to be novel. Amino acid similarity between the partial sequence of S6-RNase and other known loquat RNases (S1 to S4) ranged between 62% and 65% with highest similarity (83%) to the S110-allele of European pear (Pyrus communis). Determination of S-RNase-allele content in progeny of ‘Avri’, ‘Yehuda’, and ‘Akko 1’, obtained in an open-pollinated, mixed-cultivar orchard, revealed that all of the progeny derived from self-fertilization contained the S6 haplotype, indicating that a mutation in the S6 locus is responsible for the self-fertilization. However, sequencing of most of the S6-RNase gene (from C1 to C5) did not reveal any mutation and the alignment of the deduced amino acid sequence showed that it has the expected S-RNase primary and tertiary structural organization. Nonetheless, because it is apparent that the S6-RNase allele is linked to the self-compatibility trait, it could serve as a marker for early selection of self-compatible loquat cultivars.
7
Marcellán, Olga N., Alberto Acevedo, and Elsa L. Camadro. "S16, a novel S-RNase allele in the diploid species Solanum chacoense." Genome 49, no. 8 (August 1, 2006): 1052–54. http://dx.doi.org/10.1139/g06-058.
Full textAbstract:
Wild potato species have a gametophytic self-incompatibility system controlled by a single multiallelic S locus. In the style, the S-RNase gene codes for an allele-specific ribonuclease that is involved in the rejection of pollen that carries the same S haplotype. This gene has 5 conserved regions (C1–C5) and highly variable regions outside of these areas that play a role in S-RNase allele specificity. In this work, PCR-mediated amplification of genomic DNA from 2 Solanum chacoense accessions was performed using primers designed on the basis of the C1 and C4 conserved regions. By sequencing the PCR products, a new S-RNase allele (S16) was identified in 1 plant of the QBCM argentinian accession. Comparison of the partial sequence (from C2 to C3) of S16 RNase with those of 11 S-RNase genes of other Solanaceae species showed the highest and the lowest similarity scores within the same plant species (respectively, 71% with the S11 and S13 RNase and 35% with the S2 RNase). Differences at the nucleotide level between S16 and S11 RNase alleles are discussed.Key words: gametophytic self-incompatibility, Solanum chacoense, S16 RNase allele, nucleotide and amino acid sequence variability.
8
Uyenoyama, Marcy K., Yu Zhang, and Ed Newbigin. "On the Origin of Self-Incompatibility Haplotypes: Transition Through Self-Compatible Intermediates." Genetics 157, no. 4 (April 1, 2001): 1805–17. http://dx.doi.org/10.1093/genetics/157.4.1805.
Full textAbstract:
AbstractSelf-incompatibility (SI) in flowering plants entails the inhibition of fertilization by pollen that express specificities in common with the pistil. In species of the Solanaceae, Rosaceae, and Scrophulariaceae, the inhibiting factor is an extracellular ribonuclease (S-RNase) secreted by stylar tissue. A distinct but as yet unknown gene (provisionally called pollen-S) appears to determine the specific S-RNase from which a pollen tube accepts inhibition. The S-RNase gene and pollen-S segregate with the classically defined S-locus. The origin of a new specificity appears to require, at minimum, mutations in both genes. We explore the conditions under which new specificities may arise from an intermediate state of loss of self-recognition. Our evolutionary analysis of mutations that affect either pistil or pollen specificity indicates that natural selection favors mutations in pollen-S that reduce the set of pistils from which the pollen accepts inhibition and disfavors mutations in the S-RNase gene that cause the nonreciprocal acceptance of pollen specificities. We describe the range of parameters (rate of receipt of self-pollen and relative viability of inbred offspring) that permits the generation of a succession of new specificities. This evolutionary pathway begins with the partial breakdown of SI upon the appearance of a mutation in pollen-S that frees pollen from inhibition by any S-RNase presently in the population and ends with the restoration of SI by a mutation in the S-RNase gene that enables pistils to reject the new pollen type.
9
Broothaerts, W., J. Keulemans, and I. Van Nerum. "Self-fertile apple resulting from S-RNase gene silencing." Plant Cell Reports 22, no. 7 (October 15, 2003): 497–501. http://dx.doi.org/10.1007/s00299-003-0716-4.
Full text
10
Sapir, Gal, Raphael A. Stern, Martin Goldway, and Sharoni Shafir. "SFBs of Japanese Plum (Prunus salicina): Cloning Seven Alleles and Determining Their Linkage to the S-RNase Gene." HortScience 42, no. 7 (December 2007): 1509–12. http://dx.doi.org/10.21273/hortsci.42.7.1509.
Full textAbstract:
Japanese plum (Prunus salicina Lindl.), a species of the Rosaceae family, carries the S-RNase-mediated gametophytic self-incompatibility system. Self-incompatibility is manifested if the S-haplotype of the pollen is carried also by the pollinated flower. Thus, for fertilization to occur, the cultivars have to be genetically compatible. The haplotype is conferred by an S-locus, which contains the style-specific expressed S-RNase and the pollen-specific expressed F-box genes (SFB). Since both the S-RNase and the SFB genes are multiallelic and are characteristic of each of the S-haplotypes, they are ideal markers for molecular S-typing. In this work, seven SFBs, from eight japanese plum cultivars, were cloned and sequenced. Five of the alleles were published recently and two SFBg and SFBk are new. The physical linkage of SFBb and SFBc to their adjacent S-RNase was determined; it is 544 base pairs (bp) and 404 bp for the Sb and Sc loci, respectively.
Dissertations / Theses on the topic "S-RNase gene"
1
Morimoto, Takuya. "Insights into the evolution and establishment of the Prunus-specific self-incompatibility recognition mechanism." 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225645.
Full text
2
Nunes, Vanessa Catarina Ribeiro. "Characterization of the genes determining pollen specificity in self-incompatibility mechanism of Malus x domestica." Master's thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/15402.
Full textAbstract:
Mestrado em Biologia Molecular e CelularTo understand the molecular basis of the S-RNase-based gametophytic selfincompability system of subtribe Pyrinae from Rosaceae family, in this work, Malus x domestica species was used to determine the genes involved in pollen S-specificity. Previously 18 F-box genes, similar to the S-locus F-box brothers (SFBBs), were identified by conventional polymerase chain reaction techniques and with the pollen transcriptome analysis of nine M. domestica cultivars. However, not all 10 S-haplotypes, covered by the nine M. domestica cultivars used, have been characterized for all SFBB genes, and 12 SFBB sequences found, align as highly divergent sequences in 12 SFBB genes. Thus, in this work, by cloning and sequencing analysis of two highly diverged alleles, namely, SFBBGu8 and SFBBN3 of SFBB5 and SFBB1 genes, respectively, was concluded that SFBBGu8 sequence represent the S1- and S24- diverged alleles of SFBB5 gene, while SFBBN3 sequence represent the S28- diverged allele of SFBB1 gene. Additionally, for SFBB5 gene there is no SFBB copy number variation. This pattern was also observed for other 12 SFBB genes. For 15 of the 18 SFBB genes identified, linkage with the S-RNase gene (gene involved in pistil S-specificity) was established by segregation analysis of the F1 progeny from the cross of Fuji (S1, S9) with Honeycrisp (S2, S24), previously genotyped. As result, for SFBB2, SFBB3, SFBB4, SFBB6, SFBB7, SFBB8, SFBB9, SFBB10, SFBB11, SFBB12, SFBB13, SFBB14 and SFBB16 genes, linkage with at least one S-RNase allele was established. Thus, since these 13 SFBB genes also present pollen-specific expression and S-haplotypespecific polymorphism, these genes are pollen S-genes. In conclusion, consistent features with the collaborative non-self recognition model, were identified in M. domestica species, such as, large number of SFBB genes and the presence of highly diverged SFBB alleles, that may be conserved in other S-haplotypes, and thus, involved in the recognition of a particular non-self S-RNase. However, in M. domestica species, it was not verified SFBB copy number variation within the different S-haplotypes, as observed in Petunia. The characterization of the S-pollen genes involved in the self-incompatibility mechanism in M. domestica species is the first step to characterize self-pollen rejection mechanism in Pyrinae subtribe.
Para compreender a base molecular do sistema de auto-incompatibilidade gametofítica baseada em S-RNases da subtribo Pyrinae da família Rosaceae, neste trabalho, a espécie Malus x domestica foi utilizada para determinar os genes envolvidos na especificidade S do pólen. Previamente 18 genes F-box, semelhantes aos “S-locus F-box brothers” (SFBBs), foram identificados por uma abordagem baseada em técnicas convencionais de reação em cadeia da polimerase e por análise de transcriptomas do pólen de nove cultivares de M. domestica. Contudo, nem todos os 10 haplótipos S, cobertos pelos nove cultivares de M. domestica utilizados, foram caracterizados para todos os genes SFBB, e 12 sequências SFBB encontradas, alinham como sequências altamente divergentes em 12 genes SFBB. Assim, neste trabalho, por clonagem e sequenciação de dois alelos altamente divergentes, nomeadamente, SFBBGu8 e SFBBN3 dos genes SFBB5 e SFBB1, respectivamente, concluiu-se que a sequência SFBBGu8 representa os alelos divergentes S1- e S24- do gene SFBB5, enquanto que a sequência SFBBN3 representa o alelo divergente S28- do gene SFBB1. Adicionalmente, para o gene SFBB5 não existe variação do número de cópias dos SFBBs. Este padrão foi também observado para outros 12 genes SFBB. Para 15 dos 18 genes SFBB identificados, foi determinada associação com o gene da SRNase (gene envolvido na especificidade S do pistilo) através de análises de segregação da progenia F1 resultante do cruzamento de Fuji (S1, S9) com Honeycrisp (S2, S24), previamente genotipada. Como resultado, para os genes SFBB2, SFBB3, SFBB4, SFBB6, SFBB7, SFBB8, SFBB9, SFBB10, SFBB11, SFBB12, SFBB13, SFBB14 e SFBB16, foi estabelecida associação com pelo menos um alelo da S-RNase. Assim, dado que estes 13 genes SFBB também apresentam expressão exclusiva no pólen e polimorfismo específico para cada haplótipo S, estes genes são genes S do pólen. Em conclusão, foram identificadas características consistentes com o modelo “collaborative non-self-recognition” em M. domestica, tais como, um grande número de genes SFBB e a presença de alelos SFBB altamente divergentes, que podem ser conservados noutros haplótipos S e assim, estar envolvidos no reconhecimento de uma S-RNase não-própria. Contudo, em M. domestica, não ser verificou variação do número de cópias dos SFBBs nos diferentes haplótipos S, como observado em Petunia. A caraterização dos genes S do pólen envolvidos no mecanismo de auto-incompatibilidade em M. domestica é o primeiro passo para caracterizar o mecanismo de rejeição do pólen do próprio, na subtribo Pyrinae.
3
Escalera-Maurer, Andres. "Regulation of virulence related genes by RNA and RNA-interacting proteins in bacteria." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/20748.
Full textAbstract:
Ziel der Arbeit war es, die regulatorischen Mechanismen von Virulenz-assoziierten Genen in den Pathogenen Francisella novicida und Streptococcus pyogenes zu untersuchen. Kapitel eins befasst sich mit der Regulation des Virulenzfaktors Streptolysin S (SLS) von S. pyogenes. Wir untersuchten die Rolle der Ribonuklease (RNase) Y in der transkriptionellen und posttranstrikptionellen Regulation des Gens sagA. RNase Y begünstigte die Produktion einer kleinen RNA (sRNA) vom sagA Transkript, war jedoch nicht an der posttranskriptionellen Regulierung der sagA RNA beteiligt. Dennoch förderte RNase Y die Transkription von sagA indirekt. Wir konnten weiterhin zeigen, dass die 5′- untranslatierte Region (UTR) der sgaA RNA eine Sekundärstruktur besitzt, die möglicherweise einen Liganden bindet und damit die Zugänglichkeit der ribosomalen Bindungsstelle beeinflusst. Die Deletion einzelner Abschnitte der 5′ UTR hat einen negativen Effekt auf die sagA Expression. Wir haben eine Methode entwickelt um die Aktivität von Riboswitches, (u.a. die sagA 5‘ UTR) zu analysieren und konnten damit drei putative Riboswitches in S. pyogenes validieren.
In Kapitel zwei charakterisierten wir den Mechanismus mit dem CRISPR-Cas9 aus F. novicida (FnoCas9) die Expression bakterieller Lipoproteine (BLPs) unterdrückt, um dem Immunsystem des Wirtes zu entgehen. Wir zeigen, dass FnoCas9 eine duale Funktion besitzt, die es dem Protein ermöglicht nicht nur DNA zu schneiden, sondern auch Transkription zu regulieren. In dieser erstmals beschriebenen Aktivität bindet FnoCas9 an den tracrRNA:scaRNA Duplex, wodurch der Protein-RNA Komplex an einen DNA Abschnitt hinter dem Promoter der blp Gene bindet und somit deren Transkription verhindert. Diese Bindungsstelle besitzt ein protospacer-adjacent motif (PAM) und eine scaRNA-komplementäre Sequenz, an die der FnoCas9-RNA Komplex bindet, allerdings nicht schneidet. Dieses System könnte in Zukunft das Repertoire an CRISPR-basierten Anwendungsmöglichkeiten erweitern.The aim of this thesis was to study regulatory mechanisms of virulence-related genes in the bacterial pathogens Francicella novicida and Streptococcus pyogenes. Chapter one focuses on the regulation of the virulence factor streptolysin S (SLS) in S. pyogenes. First, we investigated the role of the ribonuclease (RNase) Y in the transcriptional and post-transcriptional regulation of SLS-coding gene, sagA. We found that RNase Y promotes the production of a small RNA (sRNA) from the sagA transcript but we observed no regulation at the post-transcriptional level. Yet, RNase Y promotes sagA transcription indirectly and affects hemolysis levels. We next showed that the sagA 5′ untranslated region (UTR) contains a secondary structure that is is possibly modulated by direct binding to a ligand and may affect the accessibility to the ribosomal binding site (RBS). Our results indicate that removing fragments of the 5′ UTR has a negative effect on sagA expression. We developed a method for testing the activity of putative riboswitches, including sagA 5′ UTR. Using this method, we validated three predicted riboswitches in S. pyogenes. In chapter two, we characterized the mechanism by which F. novicida CRISPR-Cas9 (FnoCas9) represses the expression of bacterial lipoproteins (BLPs), allowing evasion of the host immune system. We show that FnoCas9 is a dual-function protein that, in addition to its canonical DNA nuclease activity, evolved the ability to regulate transcription. In this newly-described mechanism, the non-canonical RNA duplex tracrRNA:scaRNA guides FnoCas9 to the DNA target located downstream of the promoter of the BLP-coding genes, causing transcriptional interference. The endogenous targets contain a protospacer-adjacent motif (PAM) and a sequence that is complementary to scaRNA, promoting FnoCas9 binding but not DNA cleavage. Engineering this system expands the toolbox of CRISPR applications by allowing repressing other genes of interest.
4
Goonetilleke, Wasala Adikari Shashiprabha Nilupuli Sridevi Tennakoon. "Genetic analysis of reproductive and nut traits in almond [Prunus dulcis (Mill.) D.A. Webb]." Thesis, 2017. http://hdl.handle.net/2440/107579.
Full textAbstract:
Almond is a perennial tree crop with a gametophytic self-incompatibility (SI) system. The SI system of almond is controlled by a multi-allelic locus, S, which is about 70,000 bp long. A nearly complete sequence for the entire S locus sequence has been available only for the S₇ haplotype. In this research, next-generation sequencing technology was implemented to sequence the entire S locus simultaneously from 15 haplotypes. The results confirmed the accuracy of available S₇ haplotype sequence, generated the entire S locus sequences for the Sf [f subscript], S₁ and S₈ haplotypes and generated partial S locus sequences for 11 other haplotypes (S₃, S₅, S₆, S₉, S₁₃, S₁₄, S₁₉, S₂₂, S₂₃, S₂₅ and S₂₇). Comparisons among haplotype sequences revealed higher polymorphism in the region where the S-RNase and SFB genes are located and considerable differences in the number and locations of long terminal repeat retrotransposons. There are about 50 known S alleles, of which one confers self-fertility. For some of these, complete or partial S-RNase and SFB sequences are available. Here, more complete sequences were generated for several alleles of the S-RNase gene (S₃, S₆, S₉, S₁₃, S₁₉, S₂₂ and S₂₅) and the SFB gene (S₉, S₂₃ and S₂₇). In almond breeding, SI limits the parental combinations that can be used for crossing. Detection of S alleles prior to crossing would be beneficial. Until now, molecular detection of the S alleles has relied on detection of length polymorphisms in the S-RNase gene. Here, single nucleotide polymorphisms (SNPs) in the S-RNase and SFB genes were used in designing assays to distinguish among S alleles. This thesis also reports on the construction of linkage maps for Nonpareil and Lauranne based on genotyping-by-sequencing (GBS) and on the design of uniplex assays for detection of SNPs detected by GBS. These assays were applied to additional Nonpareil × Lauranne progeny and to progeny from three other Nonpareil crosses (Nonpareil × Constantί, Nonpareil × Tarraco and Nonpareil × Vairo). Data from all four populations were used to generate a composite map for Nonpareil. Comparisons of marker positions detected for Nonpareil and Lauranne with positions in the peach genome confirmed high collinearity between the almond and peach genomes. Quantitative trait loci analysis detected 23 genomic regions as affecting nut and/or kernel traits in Nonpareil × Lauranne. Nine and 14 QTLs were detected for Nonpareil and Lauranne, respectively. Of the kernel and nut traits mapped here, shell weight, kernel shape, tocopherol concentration, fatty acid concentration and oleic/linoleic ratio were mapped for the first time in almond. For shell hardness and oleic/linoleic ratio, markers were identified that could be useful for marker-assisted selection. Some of the QTLs related to fatty acid and tocopherol concentration were closely located to the genes that are known to be involved in the synthesis of fatty acids and/or tocopherols. Some of the sequence information generated here may be useful for designing primers to amplify these genes (or components of these genes) for resequencing from multiple almond genotypes.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Agriculture, Food and Wine, 2017.
5
Σταματοπούλου, Βασιλική. "Μελέτες επί της μιτοχονδριακής ριβονουκλεάσης Ρ από το σχιζοσακχαρομύκητα S. pombe." Thesis, 2006. http://nemertes.lis.upatras.gr/jspui/handle/10889/1393.
Full textAbstract:
Η ριβονουκλεάση Ρ (RNase P) είναι μια πανταχού παρούσα ενδονουκλεάση, και σε πολλές περιπτώσεις αποτελεί ένα ριβοένζυμο, η οποία συμμετέχει στον μηχανισμό ωρίμανσης των πρόδρομων tRNAs. Στην πλειοψηφία των περιπτώσεων είναι ένα ριβονουκλεοπρωτεϊνικό σύμπλοκο που αποτελείται από μια RNA υπομονάδα και τουλάχιστον μια πρωτεϊνική υπομονάδα. Όσον αφορά τα ευκαρυωτικά κύτταρα, πιστεύεται πως υπάρχουν δυο διακριτές μορφές του ολοενζύμου, μια πυρηνική και μια μιτοχονδριακή. Στο Saccharomyces cerevisiae η μιτοχονδριακή RNase P διαθέτει μια RNA και μια πρωτεϊνική υπομονάδα που κωδικοποιούνται από ένα μιτοχονδριακό (rnpB) και ένα πυρηνικό γονίδιο, αντίστοιχα. Σε αυτήν την εργασία απομονώσαμε και μερικώς καθαρίσαμε την μιτοχονδριακή RNase P από τον Schizosaccharomyces pombe. Κλωνοποιήθηκε, επίσης, το γονίδιο που κωδικοποιεί την RNA υπομονάδα της μιτοχονδριακής RNase P. Αυτό το ένζυμο παρουσιάζει διαφορετική εξειδίκευση για τα υποστρώματα SupS1 (pre-tRNASer) και pre-tRNATyr και δεν απενεργοποιείται από την μικροκοκκική νουκλεάση.Ribonuclease P is a universally conserved ribozyme that it is involved in the 5΄ maturation of precursors tRNAs. It is in most cases a ribonucleoprotein complex which comprises an RNA subunit and at least one protein subunit. Concerning the eukaruotic cells, it is expected that distinctive nuclear and mitochondrial RNase P activities exist. In Saccharomyces cerevisiae the mitochondrial RNase P consists of an RNA and a protein subunit encoded by a mitochondrial (rnpB) and a nuclear gene, respectively. In the present study we isolated and partially purified mitochondrial RNase P from Schizosaccharomyces pombe and we cloned the gene that encodes the mitochondrial RNase P RNA subunit. This enzyme exhibits different specificity on SupS1 and pre-tRNATyr substrates and is not inactivated by micrococcal nuclease.
Book chapters on the topic "S-RNase gene"
1
Dillon, Lawrence S. "The 5 S Ribosomal and Other Small RNAs." In The Gene, 93–143. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4899-2007-2_3.
Full text
2
XUE, YONGBIAO, HAIYANG CUI, ZHAO LAI, WENSHI MA, LIZHI LIANG, HUIJUN YANG, and YANSHENG ZHANG. "S RNASES AND SELF AND NON-SELF POLLEN RECOGNITION IN FLOWERING PLANTS." In Gene Families, 149–55. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812810557_0014.
Full text
3
Sorkheh, Karim. "Evolutionary Analysis of Basic RNase Genes from Rosaceous Species — S-RNase and Non-SRNase Genes." In Plants for the Future. InTech, 2015. http://dx.doi.org/10.5772/61439.
Full text
4
Basu, Anamika, Piyali Basak, and Anasua Sarkar. "Molecular-Docking-Based Anti-Allergic Drug Design." In Advances in Medical Technologies and Clinical Practice, 232–48. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0362-0.ch009.
Full textAbstract:
Allergens are foreign proteins that when come in contact of part(s) of human body stimulate the production of immunoglobulin types of proteins (antibodies). These allergens react with antibodies (immunoglobulin type E or IgE) produces allergic reactions, also known as immediate-type hypersensitivity reactions. As much as 20% of the general population may be affected by grass pollen as a major cause of allergic disease. EXPB class of proteins are known in the immunological literature as group-1 grass pollen allergens Molecular docking method can be used to identify the predicated the interaction of pollen allergen EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize with IgE molecules of human. The World Health Organization recognised allergen immunotherapy, as therapeutics for allergic diseases. RNA Interference (RNAi) is a biological process in which RNA molecules e.g. Small Interfering RNAs (siRNAs) inhibit gene expression, by cleavage and destruction of specific mRNA molecules. Use of Small Interfering RNA (siRNA) is a novel method in the induction of RNA Interference (RNAi), which is a potent method for therapeutics of allergic reactions. Due to various effects of STAT 6 proteins during hypersensitivity reactions caused by pollen allergens, mRNA of STAT6 gene is selected as target gene for allergy therapeutics via Post-Transcriptional Gene Silencing (PTGS). Using molecular docking study a specific sense siRNA is identified as anti allergic drug to treat allergic asthma during immediate type of hypersensitivity reaction, caused by Zea m 1 pollen allergen.
5
Basu, Anamika, Piyali Basak, and Anasua Sarkar. "Molecular-Docking-Based Anti-Allergic Drug Design." In Pharmaceutical Sciences, 711–26. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch027.
Full textAbstract:
Allergens are foreign proteins that when come in contact of part(s) of human body stimulate the production of immunoglobulin types of proteins (antibodies). These allergens react with antibodies (immunoglobulin type E or IgE) produces allergic reactions, also known as immediate-type hypersensitivity reactions. As much as 20% of the general population may be affected by grass pollen as a major cause of allergic disease. EXPB class of proteins are known in the immunological literature as group-1 grass pollen allergens Molecular docking method can be used to identify the predicated the interaction of pollen allergen EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize with IgE molecules of human. The World Health Organization recognised allergen immunotherapy, as therapeutics for allergic diseases. RNA Interference (RNAi) is a biological process in which RNA molecules e.g. Small Interfering RNAs (siRNAs) inhibit gene expression, by cleavage and destruction of specific mRNA molecules. Use of Small Interfering RNA (siRNA) is a novel method in the induction of RNA Interference (RNAi), which is a potent method for therapeutics of allergic reactions. Due to various effects of STAT 6 proteins during hypersensitivity reactions caused by pollen allergens, mRNA of STAT6 gene is selected as target gene for allergy therapeutics via Post-Transcriptional Gene Silencing (PTGS). Using molecular docking study a specific sense siRNA is identified as anti allergic drug to treat allergic asthma during immediate type of hypersensitivity reaction, caused by Zea m 1 pollen allergen.
Conference papers on the topic "S-RNase gene"
1
Zhang, Lin, Jiao Hu, Xiaofeng Tan, Hongxu Long, Deyi Yuan, and Xiugen Li. "Identification of a Novel S-RNase Gene and S-Genotypes of Four Pear (Pyrus pyrifolia) Cultivars." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2010). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5516677.
Full text
2
Lin, Zhang, Tan Xiaofeng, He Gongxiu, Hu Jiao, Long Hongxu, and Cao Yufen. "Clone the S-RNase gene to clarify the compatibility between pear cultivars vulnerable to environmental impacts." In 2010 International Conference on Mechanic Automation and Control Engineering (MACE). IEEE, 2010. http://dx.doi.org/10.1109/mace.2010.5536449.
Full text
3
Duan, Jing-Hua, Fang-Dong Li, and Hong-Yan Du. "Identification and Sequence Analysis of Four S-RNase Genes in Plumcot (Prunus simonii Carr.)." In 2009 3rd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2009). IEEE, 2009. http://dx.doi.org/10.1109/icbbe.2009.5162918.
Full text
4
Shikata, Tetsuo, Toshihiko Shiraishi, Kumiko Tanaka, Shin Morishita, and Ryohei Takeuchi. "Effects of Acceleration Amplitude and Frequency of Mechanical Vibration on Osteoblast-Like Cells." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-41797.
Full textAbstract:
Bone formation is subject in vivo to mechanical stimulation. Although many researches for bone cells of osteoblastic lineage sensing and responding to mechanical stimulation have been reported mainly in the biochemical field, effects of mechanical stimulation on bone cells are not well understood. In this study, in order to clarify effects of acceleration amplitude and frequency of mechanical stimulation on MC3T3-E1, which is an osteoblast-like cell line derived from mouse calvaria, in the sense of mechanical vibrations, their cell proliferation, cell morphology, bone matrix generation and gene expression of alkaline phosphatase (ALP) were investigated when sinusoidal inertia force was applied to the cells. After the cells were cultured in culture plates in a CO2 incubator for one day and adhered on the cultured plane, vibrating groups of the culture plates were set on an aluminum plate attached to a exciter and cultured under sinusoidal excitation in another incubator separated from non-vibrating groups of the culture plates. Acceleration amplitude and frequency were set to several kinds of conditions. The time evolution of cell density was obtained by counting the number of cells with a hemocytometer. The cell morphology was observed with a phase contrast microscope. Calcium salts generated by the cells were observed by being stained with alizarin red S solution and their images were captured with a CCD camera. The vibrating groups for the cell proliferation and the calcium salts staining were sinusoidally excited for 24 hours a day during 28-day cultivation. Gene expression of ALP was measured by a real-time reverse transcription polymerase chain reaction (real-time RT-PCR) method. After the vibrating groups for the PCR were excited for 7 days, the total RNAs were extracted. After reverse transcription, real-time RT-PCR was performed. Gene expression for ALP and a housekeeping gene were determined simultaneously for each sample. ALP gene level in each sample was normalized to the measured housekeeping gene level. The results to be obtained are as follows. In the range from 12.5 to 200 Hz, saturation cell density for the cell proliferation shows tendency of increase as frequency decreases and ALP gene expression shows a peak to frequency at 50 Hz. Among 0, 0.25 and 0.5 G, saturation cell density and ALP gene expression show tendency of increase as acceleration amplitude increases.
5
Shikata, Tetsuo, Toshihiko Shiraishi, Kumiko Tanaka, Shin Morishita, and Ryohei Takeuchi. "Effects of Amplitude and Frequency of Vibration Stimulation on Cultured Osteoblasts." In ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-34949.
Full textAbstract:
Mechanical stimulation to bones affects osteogenesis such as decrease of bone mass of astronauts under zero gravity, walking rehabilitation to bone fracture and fracture repair with ultrasound devices. Bone cells have been reported to sense and response to mechanical stimulation at cellular level morphologically and metabolically. In the view of mechanical vibrations, bone cells are deformed according to mechanical stimulation and their mechanical characteristics. Recently, it was reported that viscoelasticity of cells was measured using tensile and creep tests and that there was likely natural frequency and nonlinearity of cells in the sense of structural dynamics. It suggests that there is effective frequency and amplitude of mechanical stimulation on osteogenesis by bone cells. In this study, sinusoidal inertia force was applied to cultured osteoblasts, MC3T3-E1, and effects of frequency and acceleration amplitude of mechanical vibration on the cells were investigated in respect of cell proliferation, cell morphology, bone matrix generation and alkaline phosphatase (ALP) gene expression. After the cells were cultured in culture plates in a CO2 incubator for one day and adhered on the cultured plane, vibrating groups of the culture plates were set on an aluminum plate attached to a exciter and cultured under sinusoidal excitation in another incubator separated from non-vibrating groups of the culture plates. Acceleration amplitude and frequency were set to several kinds of conditions. The time evolution of cell density was obtained by counting the number of cells with a hemocytometer. The cell morphology was observed with a phase contrast microscope. Calcium salts generated by the cells were observed by being stained with alizarin red S solution and their images were captured with a CCD camera. The vibrating groups for the cell proliferation and the calcium salts staining were sinusoidally excited for 24 hours a day during 28-day cultivation. Gene expression of ALP was measured by a real-time RT-PCR method. After the vibrating groups for the PCR were excited for 6 hours, the total RNAs were extracted. After reverse transcription, real-time RT-PCR was performed. Gene expression for ALP and a housekeeping gene were determined simultaneously for each sample. Gene levels in each sample were normalized to the measured housekeeping gene levels. As a result, it is shown that saturate cell density becomes high and bone matrix generation is promoted by applying mechanical vibration and that there may be some peaks to frequency and a certain threshold value to acceleration amplitude of mechanical vibration for saturation cell density and bone matrix generation.
6
Shikata, Tetsuo, Toshihiko Shiraishi, Shin Morishita, and Ryohei Takeuchi. "Effects of Acceleration Amplitude and Frequency of Mechanical Vibration on Cultured Osteoblasts." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-67221.
Full textAbstract:
This paper describes the effects of the frequency and acceleration amplitude of mechanical vibration on osteoblasts, the bone cells that generate the bone matrix. Their cell proliferation and bone matrix generation were investigated when sinusoidal inertia force was applied to the cells. Bone formation is subject in vivo to mechanical stimulation. Although many researches for bone cells of osteoblastic lineage sensing and responding to mechanical stimulation have been reported mainly in the biochemical field, effects of mechanical stimulation on bone cells are not well understood. After the cells were cultured in culture plates in a CO2 incubator for one day and adhered on the cultured plane, vibrating groups of the culture plates were set on an aluminum plate attached to a exciter and cultured under sinusoidal excitation in another incubator separated from non-vibrating groups of the culture plates. Acceleration amplitude and frequency were set to several kinds of conditions. The time evolution of cell density was obtained by counting the number of cells with a hemocytometer. Calcium salts generated by the cells were observed by being stained with alizarin red S solution and their images were captured with a CCD camera. The vibrating groups for the cell proliferation and the calcium salts staining were sinusoidally excited for 24 hours a day during 28 days of culture. Gene expression of alkaline phosphatase (ALP) and runt-related gene 2 (Runx2) was measured by a real-time reverse transcription polymerase chain reaction (real-time RT-PCR) method. After the vibrating groups for the PCR were excited for 4 days, the total RNAs were extracted. After reverse transcription, real-time RT-PCR was performed. Gene expression for ALP, Runx2, and a housekeeping gene were determined simultaneously for each sample. ALP and Runx2 gene level in each sample was normalized to the measured housekeeping gene level. The following experimental results of sinusoidal excitation of osteoblasts have been shown: (a) Cell density decreased at 0.5 G with increasing frequency in the range from 12.5 to 1000 Hz and increased at 25 Hz with increasing acceleration amplitude from 0 to 0.5 G at 14 days of culture. (b) No calcium salts were observed in the non-vibrating group and the areas of calcium salts observed in the 0.5 G vibration group were larger than those in the 0.25 G group at 25 Hz at 21 days of culture. (c) The mRNA level of ALP at 0.5 G showed the peak at 50 Hz in the range from 12.5 to 1000 Hz and that at 50 Hz showed the peak at 0.5 G in the range from 0.25 to 1 G at 4 days of culture. In the case of Runx2, the same tendency was found. It has been shown that it is important to consider mechanical vibration as well as biochemical aspects in studies of the functional adaptation of cells to mechanical stimulation.
Reports on the topic "S-RNase gene"
1
Shoseyov, Oded, Steven A. Weinbaum, Raphael Goren, and Abhaya M. Dandekar. Biological Thinning of Fruit Set by RNAase in Deciduous Fruit Trees. United States Department of Agriculture, August 1993. http://dx.doi.org/10.32747/1993.7568110.bard.
Full textAbstract:
Fruit thinning is a common and necessary practice for commercial fruit production in many deciduous tree fruit species. Fruit thinning in apple may be accomplished with a variety of chemical thinning agents, but the use of these chemicals is a subject of environmental concern. It has been shown recently that RNase enzyme, secreted from the stigma and the style, inhibits pollen germination and pollen tube elongation. In this study we have been able to show that Aspergillus niger B-1 RNase can effectively inhibit peach and apple pollen germination, and tube elongation in-vitro, as well as thin fruit in peach and apple, and reduce the number of seeds in citrus. The objectives of the research were to detrmine the conditions for effective thinning of (USA and Israel), develop fermentation process for cost effective production of RNase from A. niger. (Israel), and clone apple S-RNase cDNA (USA). All the objectives of the research were addressed. We have determined the optimal fermentation conditions for cost effective production of the A. niger at a 20,000 liters scale. TheA. niger B1 RNase was isolated to homogeneity and its kinetic and biochemical properties including its N-terminal sequence were fully characterized. The field test results both in Israel and California have shown variability in effectiveness and more work is needed to define the RNase concentration necessary to completely inhibit pollen development. Plant transformation vectors expressing anti-sense apple S-RNase genes were constructed (USA) with an attempt to produce self compatible transgenic apple trees. Bovine S-Protein cDNA was cloned and successfully expressed in E. coli (Israel). Plant transformation vector expressing the S-Protein gene was constructed (USA) with an attempt to produce transgenic plants expressing S-protein in the style. Exogenous application of S-peptide to these plants will result in active RNase and consequently prevention of fertilization.
2
Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.
Full textAbstract:
Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
3
Eyal, Yoram, and Sheila McCormick. Molecular Mechanisms of Pollen-Pistil Interactions in Interspecific Crossing Barriers in the Tomato Family. United States Department of Agriculture, May 2000. http://dx.doi.org/10.32747/2000.7573076.bard.
Full textAbstract:
During the evolutionary process of speciation in plants, naturally occurring barriers to reproduction have developed that affect the transfer of genes within and between related species. These barriers can occur at several different levels beginning with pollination-barriers and ending with hybrid-breakdown. The interaction between pollen and pistils presents one of the major barriers to intra- and inter-specific crosses and is the focus of this research project. Our long-term goal in this research proposal was defined to resolve questions on recognition and communication during pollen-pistil interactions in the extended tomato family. In this context, this work was initiated and planned to study the potential involvement of tomato pollen-specific receptor-like kinases (RLK's) in the interaction between pollen and pistils. By special permission from BARD the objectives of this research were extended to include studies on pollen-pistil interactions and pollination barriers in horticultural crops with an emphasis on citrus. Functional characterization of 2 pollen-specific RLK's from tomato was carried out. The data shows that both encode functional kinases that were active as recombinant proteins. One of the kinases was shown to accumulate mainly after pollen germination and to be phosphorylated in-vitro in pollen membranes as well as in-vivo. The presence of style extract resulted in dephosphorylation of the RLK, although no species specificity was observed. This data implies a role for at least one RLK in pollination events following pollen germination. However, a transgenic plant analysis of the RLK's comprising overexpression, dominant-negative and anti-sense constructs failed to provide answers on their role in pollination. While genetic effects on some of the plants were observed in both the Israeli and American labs, no clear functional answers were obtained. An alternative approach to addressing function was pursued by screening for an artificial ligand for the receptor domain using a peptide phage display library. An enriched peptide sequence was obtained and will be used to design a peptide-ligand to be tested for its effect o pollen germination and tube growth. Self-incompatibility (SI) in citrus was studied on 3 varieties of pummelo. SI was observed using fluorescence microscopy in each of the 3 varieties and compatibility relations between varieties was determined. An initial screen for an S-RNase SI mechanism yielded only a cDNA homologous to the group of S-like RNases, suggesting that SI results from an as yet unknown mechanism. 2D gel electrophoresis was applied to compare pollen and style profiles of different compatibility groups. A "polymorphic" protein band from style extracts was observed, isolated and micro-sequenced. Degenerate primers designed based on the peptide sequence date will be used to isolate the relevant genes i order to study their potential involvement in SI. A study on SI in the apple cultivar Top red was initiated. SI was found, as previously shown, to be complete thus requiring a compatible pollinator variety. A new S-RNase allele was discovered fro Top red styles and was found to be highly homologous to pear S-RNases, suggesting that evolution of these genes pre-dated speciation into apples and pears but not to other Rosaceae species. The new allele provides molecular-genetic tools to determine potential pollinators for the variety Top red as well as a tool to break-down SI in this important variety.
4
Prusky, Dov, Nancy P. Keller, and Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600012.bard.
Full textAbstract:
Background to the topic- Penicilliumas a postharvest pathogen and producer of the mycotoxin PAT. Penicilliumspp. are destructive phytopathogens, capable of causing decay in many deciduous fruits, during postharvest handling and storage; and the resulting losses can amount to 10% of the stored produce and the accumulation of large amounts of the mycotoxinpatulin. The overall goal of this proposal is to identify critical host and pathogen factors that modulate P. expansummycotoxin genes and pathways which are required for PAT production and virulence. Our preliminary results indicated that gluconic acid are strongly affecting patulin accumulation during colonization. P. expansumacidifies apple fruit tissue during colonization in part through secretion of gluconic acid (GLA). Several publications suggested that GLA accumulation is an essential factor in P. expansumpathogenicity. Furthermore, down regulation of GOX2 significantly reduced PAT accumulation and pathogenicity. PAT is a polyketide and its biosynthesis pathway includes a 15-gene cluster. LaeA is a global regulator of mycotoxin synthesis. It is now known that patulin synthesis might be subjected to LaeA and sometimes by environmental sensing global regulatory factors including the carbon catabolite repressor CreA as well as the pH regulator factor PacC and nitrogen regulator AreA. The mechanisms by which LaeA regulates patulin synthesis was not fully known and was part of our work. Furthermore, the regulatory system that controls gene expression in accordance with ambient pH was also included in our work. PacC protein is in an inactive conformation and is unable to bind to the promoter sites of the target genes; however, under alkaline growth conditions activated PacC acts as both an activator of alkaline-expressed genes and a repressor of acid-expressed genes. The aims of the project- This project aims to provide new insights on the roles of LaeA and PacC and their signaling pathways that lead to GLA and PAT biosynthesis and pathogenicity on the host. Specifically, our specific aims were: i) To elucidate the mechanism of pH-controlled regulation of GLA and PAT, and their contribution to pathogenesis of P. expansum. We are interested to understanding how pH and/or GLA impact/s under PacC regulation affect PAT production and pathogenesis. ii) To characterize the role of LaeA, the global regulator of mycotoxin production, and its effect on PAT and PacC activity. iii) To identify the signaling pathways leading to GLA and PAT synthesis. Using state- of-the-art RNAseq technologies, we will interrogate the transcriptomes of laeAand pacCmutants, to identify the common signaling pathways regulating synthesis of both GLA and PAT. Major conclusions, solutions, achievements- In our first Aim our results demonstrated that ammonia secreted at the leading edge of the fungal colony induced transcript activation of the global pH modulator PacC and PAT accumulation in the presence of GLA. We assessed these parameters by: (i) direct exogenous treatment of P. expansumgrowing on solid medium; (ii) direct exogenous treatment on colonized apple tissue; (iii) growth under self-ammonia production conditions with limited carbon; and (iv) analysis of the transcriptional response to ammonia of the PAT biosynthesis cluster. Ammonia induced PAT accumulation concurrently with the transcript activation of pacCand PAT biosynthesis cluster genes, indicating the regulatory effect of ammonia on pacCtranscript expression under acidic conditions. Transcriptomic analysis of pH regulated processes showed that important genes and BARD Report - Project 4773 Page 2 of 10 functionalities of P. expansumwere controlled by environmental pH. The differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Concerning the second and third Aims, we demonstrated that LaeA regulates several secondary metabolite genes, including the PAT gene cluster and concomitant PAT synthesis invitro. Virulence studies of ΔlaeAmutants of two geographically distant P. expansumisolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit ranging from no reduction for Ch-Pe-T01 strains in immature fruit to 15–25% reduction for both strains in mature fruit, with the ΔlaeAstrains of Is-Pe-21 always showing a greater loss in virulence. Results suggest the importance of LaeA regulation of PAT and other secondary metabolites on pathogenicity. Our work also characterized for the first time the role of sucrose, a key nutritional factor present in apple fruit, as a negative regulator of laeAexpression and consequent PAT production in vitro. This is the first report of sugar regulation of laeAexpression, suggesting that its expression may be subject to catabolite repression by CreA. Some, but not all of the 54 secondary metabolite backbone genes in the P. expansumgenome, including the PAT polyketide backbone gene, were found to be regulated by LaeA. Together, these findings enable for the first time a straight analysis of a host factor that potentially activates laeAand subsequent PAT synthesis.
5
Bennett, Alan B., Arthur A. Schaffer, Ilan Levin, Marina Petreikov, and Adi Doron-Faigenboim. Manipulating fruit chloroplasts as a strategy to improve fruit quality. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598148.bard.
Full textAbstract:
The Original Objectives were modified and two were eliminated to reflect the experimental results: Objective 1 - Identify additional genetic variability in SlGLK2 and IPin wild, traditional and heirloom tomato varieties Objective 2 - Determine carbon balance and horticultural characteristics of isogenic lines expressing functional and non-functional alleles of GLKsand IP Background: The goal of the research was to understand the unique aspects of chloroplasts and photosynthesis in green fruit and the consequences of increasing the chloroplast capacity of green fruit for ripe fruit sugars, yield, flavor and nutrient qualities. By focusing on the regulation of chloroplast formation and development solely in fruit, our integrated knowledge of photosynthetic structures/organs could be broadened and the results of the work could impact the design of manipulations to optimize quality outputs for the agricultural fruit with enhanced sugars, nutrients and flavors. The project was based on the hypothesis that photosynthetic and non-photosynthetic plastid metabolism in green tomato fruit is controlled at a basal level by light for minimal energy requirements but fruit-specific genes regulate further development of robust chloroplasts in this organ. Our BARD project goals were to characterize and quantitate the photosynthesis and chloroplast derived products impacted by expression of a tomato Golden 2- like 2 transcription factor (US activities) in a diverse set of 31 heirloom tomato lines and examine the role of another potential regulator, the product of the Intense Pigment gene (IP activities). Using tomato Golden 2-like 2 and Intense Pigment, which was an undefined locus that leads to enhanced chloroplast development in green fruit, we sought to determine the benefits and costs of extensive chloroplast development in fruit prior to ripening. Major conclusions, solutions, achievements: Single nucleotide polymorphisms in the promoter, coding and intronicSlGLK2 sequences of 20 heirloom tomato lines were identified and three SlGLK2 promoter lineages were identified; two lineages also had striped fruit variants. Lines with striped fruit but no shoulders were not identified. Green fruit chlorophyll and ripe fruit soluble sugar levels were measured in 31 heirloom varieties and fruit size correlates with ripe fruit sugars but dark shoulders does not. A combination of fine mapping, recombinant generation, RNAseq expression and SNP calling all indicated that the proposed localization of a single locus IP on chr 10 was incorrect. Rather, the IP line harbored 11 separate introgressions from the S. chmielewskiparent, scattered throughout the genome. These introgressions harbored ~3% of the wild species genome and no recombinant consistently recovered the IP parental phenotype. The 11 introgressions were dissected into small combinations in segregating recombinant populations. Based on these analyses two QTL for Brix content were identified, accounting for the effect of increased Brix in the IP line. Scientific and agricultural implications: SlGLK2 sequence variation in heirloom tomato varieties has been identified and can be used to breed for differences in SlGLK2 expression and possibly in the green striped fruit phenotype. Two QTL for Brix content have been identified in the S. chmielewskiparental line and these can be used for increasing soluble solids contents in breeding programs.
6
Bar-Joseph, Moshe, William O. Dawson, and Munir Mawassi. Role of Defective RNAs in Citrus Tristeza Virus Diseases. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575279.bard.
Full textAbstract:
This program focused on citrus tristeza virus (CTV), the largest and one of the most complex RNA-plant-viruses. The economic importance of this virus to the US and Israeli citrus industries, its uniqueness among RNA viruses and the possibility to tame the virus and eventually turn it into a useful tool for the protection and genetic improvement of citrus trees justify these continued efforts. Although the overall goal of this project was to study the role(s) of CTV associated defective (d)-RNAs in CTV-induced diseases, considerable research efforts had to be devoted to the engineering of the helper virus which provides the machinery to allow dRNA replication. Considerable progress was made through three main lines of complementary studies. For the first time, the generation of an engineered CTV genetic system that is capable of infecting citrus plants with in vitro modified virus was achieved. Considering that this RNA virus consists of a 20 kb genome, much larger than any other previously developed similar genetic system, completing this goal was an extremely difficult task that was accomplished by the effective collaboration and complementarity of both partners. Other full-length genomic CTV isolates were sequenced and populations examined, resulting in a new level of understanding of population complexities and dynamics in the US and Israel. In addition, this project has now considerably advanced our understanding and ability to manipulate dRNAs, a new class of genetic elements of closteroviruses, which were first found in the Israeli VT isolate and later shown to be omnipresent in CTV populations. We have characterized additional natural dRNAs and have shown that production of subgenomic mRNAs can be involved in the generation of dRNAs. We have molecularly cloned natural dRNAs and directly inoculated citrus plants with 35S-cDNA constructs and have shown that specific dRNAs are correlated with specific disease symptoms. Systems to examine dRNA replication in protoplasts were developed and the requirements for dRNA replication were defined. Several artificial dRNAs that replicate efficiently with a helper virus were created from infectious full-genomic cDNAs. Elements that allow the specific replication of dRNAs by heterologous helper viruses also were defined. The T36-derived dRNAs were replicated efficiently by a range of different wild CTV isolates and hybrid dRNAs with heterologous termini are efficiently replicated with T36 as helper. In addition we found: 1) All CTV genes except of the p6 gene product from the conserved signature block of the Closteroviridae are obligate for assembly, infectivity, and serial protoplast passage; 2) The p20 protein is a major component of the amorphous inclusion bodies of infected cells; and 3) Novel 5'-Co-terminal RNAs in CTV infected cells were characterized. These results have considerably advanced our basic understanding of the molecular biology of CTV and CTV-dRNAs and form the platform for the future manipulation of this complicated virus. As a result of these developments, the way is now open to turn constructs of this viral plant pathogen into new tools for protecting citrus against severe CTV terms and development of virus-based expression vectors for other citrus improvement needs. In conclusion, this research program has accomplished two main interconnected missions, the collection of basic information on the molecular and biological characteristics of the virus and its associated dRNAs toward development of management strategies against severe diseases caused by the virus and building of novel research tools to improve citrus varieties. Reaching these goals will allow us to advance this project to a new phase of turning the virus from a pathogen to an ally.
7
Ostersetzer-Biran, Oren, and Alice Barkan. Nuclear Encoded RNA Splicing Factors in Plant Mitochondria. United States Department of Agriculture, February 2009. http://dx.doi.org/10.32747/2009.7592111.bard.
Full textAbstract:
Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for a small number of genes required in organellar genome expression and respiration. Yet, the vast majority of the organellar proteins are encoded by nuclear genes, thus necessitating complex mechanisms to coordinate the expression and accumulation of proteins encoded by the two remote genomes. Many organellar genes are interrupted by intervening sequences (introns), which are removed from the primary presequences via splicing. According to conserved features of their sequences these introns are all classified as “group-II”. Their splicing is necessary for organellar activity and is dependent upon nuclear-encoded RNA-binding cofactors. However, to-date, only a tiny fraction of the proteins expected to be involved in these activities have been identified. Accordingly, this project aimed to identify nuclear-encoded proteins required for mitochondrial RNA splicing in plants, and to analyze their specific roles in the splicing of group-II intron RNAs. In non-plant systems, group-II intron splicing is mediated by proteins encoded within the introns themselves, known as maturases, which act specifically in the splicing of the introns in which they are encoded. Only one mitochondrial intron in plants has retained its maturaseORF (matR), but its roles in organellar intron splicing are unknown. Clues to other proteins required for organellar intron splicing are scarce, but these are likely encoded in the nucleus as there are no other obvious candidates among the remaining ORFs within the mtDNA. Through genetic screens in maize, the Barkan lab identified numerous nuclear genes that are required for the splicing of many of the introns within the plastid genome. Several of these genes are related to one another (i.e. crs1, caf1, caf2, and cfm2) in that they share a previously uncharacterized domain of archaeal origin, the CRM domain. The Arabidopsis genome contains 16 CRM-related genes, which contain between one and four repeats of the domain. Several of these are predicted to the mitochondria and are thus postulated to act in the splicing of group-II introns in the organelle(s) to which they are localized. In addition, plant genomes also harbor several genes that are closely related to group-II intron-encoded maturases (nMats), which exist in the nucleus as 'self-standing' ORFs, out of the context of their cognate "host" group-II introns and are predicted to reside within the mitochondria. The similarity with known group-II intron splicing factors identified in other systems and their predicted localization to mitochondria in plants suggest that nuclear-encoded CRM and nMat related proteins may function in the splicing of mitochondrial-encoded introns. In this proposal we proposed to (i) establish the intracellular locations of several CRM and nMat proteins; (ii) to test whether mutations in their genes impairs the splicing of mitochondrial introns; and to (iii) determine whether these proteins are bound to the mitochondrial introns in vivo.