Статті в журналах: "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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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11

McCubbin, Andrew G., Xi Wang, and Teh-hui Kao. "Identification of self-incompatibility (S-) locus linked pollen cDNA markers in Petunia inflata." Genome 43, no. 4 (August 1, 2000): 619–27. http://dx.doi.org/10.1139/g00-019.

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Solanaceous type self-incompatibility (SI) is controlled by a single polymorphic locus, termed the S-locus. The only gene at the S-locus that has been characterized thus far is the S-RNase gene, which controls pistil function, but not pollen function, in SI interactions between pistil and pollen. One approach to identifying additional genes (including the pollen S-gene, which controls pollen function in SI) at the S-locus and to study the structural organization of the S-locus is chromosome walking from the S-RNase gene. However, the presence of highly repetitive sequences in its flanking regions has made this approach difficult so far. Here, we used RNA differential display to identify pollen cDNAs of Petunia inflata, a self-incompatible solanaceous species, which exhibited restriction fragment length polymorphism (RFLP) for at least one of the three S-haplotypes (S1, S2, and S3) examined. We found that the genes corresponding to 10 groups of pollen cDNAs are genetically tightly linked to the S-RNase gene. These cDNA markers will expedite the mapping and cloning of the chromosomal region of the Solanaceae S-locus by providing multiple starting points.Key words: Petunia inflata, pollen cDNAs, self-incompatibility, S-linked cDNA markers, S-locus.

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12

Yu, Jie, Baoan Wang, Wenqi Fan, Songbo Fan, Ya Xu, Chunsheng Liu, Tianxing Lv, et al. "Polyamines Involved in Regulating Self-Incompatibility in Apple." Genes 12, no. 11 (November 15, 2021): 1797. http://dx.doi.org/10.3390/genes12111797.

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Apple exhibits typical gametophytic self-incompatibility, in which self-S-RNase can arrest pollen tube growth, leading to failure of fertilization. To date, there have been few studies on how to resist the toxicity of self-S-RNase. In this study, pollen tube polyamines were found to respond to self-S-RNase and help pollen tubes defend against self-S-RNase. In particular, the contents of putrescine, spermidine, and spermine in the pollen tube treated with self-S-RNase were substantially lower than those treated with non-self-S-RNase. Further analysis of gene expression of key enzymes in the synthesis and degradation pathways of polyamines found that the expression of DIAMINE OXIDASE 4 (MdDAO4) as well as several polyamine oxidases such as POLYAMINE OXIDASES 3 (MdPAO3), POLYAMINE OXIDASES 4 (MdPAO4), and POLYAMINE OXIDASES 6 (MdPAO6) were significantly up-regulated under self-S-RNase treatment, resulting in the reduction of polyamines. Silencing MdPAO6 in pollen tubes alleviates the inhibitory effect of self-S-RNase on pollen tube growth. In addition, exogenous polyamines also enhance pollen tube resistance to self-S-RNase. Transcriptome sequencing data found that polyamines may communicate with S-RNase through the calcium signal pathway, thereby regulating the growth of the pollen tubes. To summarize, our results suggested that polyamines responded to the self-incompatibility reaction and could enhance pollen tube tolerance to S-RNase, thus providing a potential way to break self-incompatibility in apple.

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13

Ushijima, Koichiro, Hidenori Sassa, Mihoko Tamura, Makoto Kusaba, Ryutaro Tao, Thomas M. Gradziel, Abhaya M. Dandekar, and Hisashi Hirano. "Characterization of the S-Locus Region of Almond (Prunus dulcis): Analysis of a Somaclonal Mutant and a Cosmid Contig for an S Haplotype." Genetics 158, no. 1 (May 1, 2001): 379–86. http://dx.doi.org/10.1093/genetics/158.1.379.

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Abstract Almond has a self-incompatibility system that is controlled by an S locus consisting of the S-RNase gene and an unidentified “pollen S gene.” An almond cultivar “Jeffries,” a somaclonal mutant of “Nonpareil” (ScSd), has a dysfunctional Sc haplotype both in pistil and pollen. Immunoblot and genomic Southern blot analyses detected no Sc haplotype-specific signal in Jeffries. Southern blot showed that Jeffries has an extra copy of the Sd haplotype. These results indicate that at least two mutations had occurred to generate Jeffries: (1) deletion of the Sc haplotype and (2) duplication of the Sd haplotype. To analyze the extent of the deletion in Jeffries and gain insight into the physical limit of the S locus region, ∼200 kbp of a cosmid contig for the Sc haplotype was constructed. Genomic Southern blot analyses showed that the deletion in Jeffries extends beyond the region covered by the contig. Most cosmid end probes, except those near the Sc-RNase gene, cross-hybridized with DNA fragments from different S haplotypes. This suggests that regions away from the Sc-RNase gene can recombine between different S haplotypes, implying that the cosmid contig extends to the borders of the S locus.

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14

McCubbin, Andrew G., Carmen Zuniga, and Teh-hui Kao. "Construction of a binary bacterial artificial chromosome library of Petunia inflata and the isolation of large genomic fragments linked to the self-incompatibility (S-) locus." Genome 43, no. 5 (October 1, 2000): 820–26. http://dx.doi.org/10.1139/g00-057.

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The Solanaceae family of flowering plants possesses a type of self-incompatibility mechanism that enables the pistil to reject self pollen but accept non-self pollen for fertilization. The pistil function in this system has been shown to be controlled by a polymorphic gene at the S-locus, termed the S-RNase gene. The pollen function is believed to be controlled by another as yet unidentified polymorphic gene at the S-locus, termed the pollen S-gene. As a first step in using a functional genomic approach to identify the pollen S-gene, a genomic BAC (bacterial artificial chromosome) library of the S2S2 genotype of Petunia inflata, a self-incompatible solanaceous species, was constructed using a Ti-plasmid based BAC vector, BIBAC2. The average insert size was 136.4 kb and the entire library represented a 7.5-fold genome coverage. Screening of the library using cDNAs for the S2-RNase gene and 13 pollen-expressed genes that are linked to the S-locus yielded 51 positive clones, with at least one positive clone for each gene. Collectively, at least 2 Mb of the chromosomal region was spanned by these clones. Together, three clones that contained the S2-RNase gene spanned ~263 kb. How this BAC library and the clones identified could be used to identify the pollen S-gene and to study other aspects of self-incompatibility is discussed.Key words: bacterial artificial chromosome, Petunia inflata, pollen-pistil interactions, self-incompatibility, S-locus.

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15

Kardile, Hemant Balasaheb, Solomon Yilma, and Vidyasagar Sathuvalli. "Molecular Approaches to Overcome Self-Incompatibility in Diploid Potatoes." Plants 11, no. 10 (May 17, 2022): 1328. http://dx.doi.org/10.3390/plants11101328.

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There has been an increased interest in true potato seeds (TPS) as planting material because of their advantages over seed tubers. TPS produced from a tetraploid heterozygous bi-parental population produces non-uniform segregating progenies, which have had limited uniformity in yield and quality in commercial cultivation, and, thus, limited success. Inbreeding depression and self-incompatibility hamper the development of inbred lines in both tetraploid and diploid potatoes, impeding hybrid development efforts. Diploid potatoes have gametophytic self-incompatibility (SI) controlled by S-locus, harboring the male-dependent S-locus F-box (SLF/SFB) and female-dependent Stylar-RNase (S-RNase). Manipulation of these genes using biotechnological tools may lead to loss of self-incompatibility. Self-compatibility can also be achieved by the introgression of S-locus inhibitor (Sli) found in the self-compatible (SC) natural mutants of Solanum chacoense. The introgression of Sli through conventional breeding methods has gained much success. Recently, the Sli gene has been cloned from diverse SC diploid potato lines. It is expressed gametophytically and can overcome the SI in different diploid potato genotypes through conventional breeding or transgenic approaches. Interestingly, it has a 533 bp insertion in its promoter elements, a MITE transposon, making it a SC allele. Sli gene encodes an F-box protein PP2-B10, which consists of an F-box domain linked to a lectin domain. Interaction studies have revealed that the C-terminal region of Sli interacts with most of the StS-RNases, except StS-RNase 3, 9, 10, and 13, while full-length Sli cannot interact with StS-RNase 3, 9, 11, 13, and 14. Thus, Sli may play an essential role in mediating the interactions between pollen and stigma and function like SLFs to interact with and detoxify the S-RNases during pollen tube elongation to confer SC to SI lines. These advancements have opened new avenues in the diploid potato hybrid.

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16

Luu, Doan-Trung, Xike Qin, Geneviève Laublin, Qing Yang, David Morse, and Mario Cappadocia. "Rejection of S-Heteroallelic Pollen by a Dual-Specific S-RNase in Solanum chacoense Predicts a Multimeric SI Pollen Component." Genetics 159, no. 1 (September 1, 2001): 329–35. http://dx.doi.org/10.1093/genetics/159.1.329.

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Abstract S-heteroallelic pollen (HAP) grains are usually diploid and contain two different S-alleles. Curiously, HAP produced by tetraploids derived from self-incompatible diploids are typically self-compatible. The two different hypotheses previously advanced to explain the compatibility of HAP are the lack of pollen-S expression and the “competition effect” between two pollen-S gene products expressed in a single pollen grain. To distinguish between these two possibilities, we used a previously described dual-specific S11/13-RNase, termed HVapb-RNase, which can reject two phenotypically distinct pollen (P11 and P13). Since the HVapb-RNase does not distinguish between the two pollen types (it recognizes both), P11P13 HAP should be incompatible with the HVapb-RNase in spite of the competition effect. We show here that P11P13 HAP is accepted by S11S13 styles, but is rejected by the S11/13-RNase, which demonstrates that the pollen-S genes must be expressed in HAP. A model involving tetrameric pollen-S is proposed to explain both the compatibility of P11P13 HAP on S11S13-containing styles and the incompatibility of P11P13 HAP on styles containing the HVapb-RNase.

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17

Dodds, Peter N., Ingrid Bonig, He Du, Joakim Rodin, Marilyn A. Anderson, Ed Newbigin, and Adrienne E. Clarke. "S-RNase Gene of Nicotiana alata Is Expressed in Developing Pollen." Plant Cell 5, no. 12 (December 1993): 1771. http://dx.doi.org/10.2307/3869693.

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18

Dodds, P. N., I. Bönig, H. Du, J. Rödin, M. A. Anderson, E. Newbigin, and A. E. Clarke. "S-RNase gene of Nicotiana alata is expressed in developing pollen." Plant Cell 5, no. 12 (December 1993): 1771–82. http://dx.doi.org/10.1105/tpc.5.12.1771.

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19

Zhang, Cheng-Cai, Li-Qiang Tan, Li-Yuan Wang, Kang Wei, Li-Yun Wu, Fen Zhang, Hao Cheng, and De-Jiang Ni. "Cloning and characterization of an S-RNase gene in Camellia sinensis." Scientia Horticulturae 207 (August 2016): 218–24. http://dx.doi.org/10.1016/j.scienta.2016.06.002.

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20

Entani, T., M. Iwano, H. Shiba, S. Takayama, K. Fukui, and A. Isogai. "Centromeric localization of an S-RNase gene in Petunia hybrida Vilm." Theoretical and Applied Genetics 99, no. 3-4 (August 1999): 391–97. http://dx.doi.org/10.1007/s001220051249.

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21

Price, Brenda, Trifon Adamidis, Renqui Kong, and Wendy Champness. "A Streptomyces coelicolor Antibiotic Regulatory Gene, absB, Encodes an RNase III Homolog." Journal of Bacteriology 181, no. 19 (October 1, 1999): 6142–51. http://dx.doi.org/10.1128/jb.181.19.6142-6151.1999.

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ABSTRACT Streptomyces coelicolor produces four genetically and structurally distinct antibiotics in a growth-phase-dependent manner.S. coelicolor mutants globally deficient in antibiotic production (Abs− phenotype) have previously been isolated, and some of these were found to define the absB locus. In this study, we isolated absB-complementing DNA and show that it encodes the S. coelicolor homolog of RNase III (rnc). Several lines of evidence indicate that theabsB mutant global defect in antibiotic synthesis is due to a deficiency in RNase III. In marker exchange experiments, the S. coelicolor rnc gene rescued absB mutants, restoring antibiotic production. Sequencing the DNA of absB mutants confirmed that the absB mutations lay in thernc open reading frame. Constructed disruptions ofrnc in both S. coelicolor 1501 andStreptomyces lividans 1326 caused an Abs−phenotype. An absB mutation caused accumulation of 30S rRNA precursors, as had previously been reported for E. coli rncmutants. The absB gene is widely conserved in streptomycetes. We speculate on why an RNase III deficiency could globally affect the synthesis of antibiotics.

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22

Lei, L., B. Zhang, M. Mao, H. Chen, S. Wu, Y. Deng, Y. Yang, H. Zhou, and T. Hu. "Carbohydrate Metabolism Regulated by Antisense vicR RNA in Cariogenicity." Journal of Dental Research 99, no. 2 (December 10, 2019): 204–13. http://dx.doi.org/10.1177/0022034519890570.

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Streptococcus mutans is a major cariogenic pathogen that resides in multispecies oral microbial biofilms. The VicRK 2-component system is crucial for bacterial adaptation, virulence, and biofilm organization and contains a global and vital response regulator, VicR. Notably, we identified an antisense vicR RNA (AS vicR) associated with an adjacent RNase III–encoding ( rnc) gene that was relevant to microRNA-size small RNAs (msRNAs). Here, we report that ASvicR overexpression significantly impeded bacterial growth, biofilm exopolysaccharide synthesis, and cariogenicity in vivo. Transcriptome analysis revealed that the AS vicR RNA mainly regulated carbohydrate metabolism. In particular, overproducing AS vicR demonstrated a reduction in galactose and glucose metabolism by monosaccharide composition analysis. The results of high-performance gel permeation chromatography revealed that the water-insoluble glucans isolated from AS vicR presented much lower molecular weights. Furthermore, direct evidence showed that total RNAs were disrupted by rnc-encoded RNase III. With the coexpression of T4 RNA ligase, putative msRNA1657, which is an rnc-related messenger RNA, was verified to bind to the 5′-UTR regions of the vicR gene. Furthermore, AS vicR regulation revealed a sponge regulatory-mediated network for msRNA associated with adjacent RNase III–encoding genes. There was an increase in AS vicR transcript levels in clinical S. mutans strains from caries-free children, while the expression of AS vicR was decreased in early childhood caries patients; this outcome may be explored as a potential strategy contributing to the management of dental caries. Taken together, our findings suggest an important role of AS vicR-mediated sponge regulation in S. mutans, indicating the characterization of lactose metabolism by a vital response regulator in cariogenicity. These findings have a number of implications and have reshaped our understanding of bacterial gene regulation from its transcriptional conception to the key roles of regulatory RNAs.

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23

Hegedüs, Attila, Zoltán Szabó, József Nyéki, Júlia Halász, and Andrzej Pedryc. "Molecular Analysis of S-haplotypes in Peach, a Self-compatible Prunus Species." Journal of the American Society for Horticultural Science 131, no. 6 (November 2006): 738–43. http://dx.doi.org/10.21273/jashs.131.6.738.

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The most commercially grown peach [Prunus persica (L.) Batsch.] cultivars do not require cross-pollination for reasonable fruit set; however, self-incompatibility is a well-known feature within the Prunoideae subfamily. Isoelectric focusing and native polyacrylamide gel electrophoresis of S-ribonucleases; PCR analyses of S-RNase and S-haplotype-specific F-box genes as well as DNA sequencing were carried out to survey the self-(in)compatibility allele pool and to uncover the nature of self-compatibility in peach. From 25 cultivars and hybrids with considerable diversity in phenotype and origin, only two S-haplotypes were detected. Allele identity could be checked by exact length determination of the PCR-amplified fragments and/or partial sequencing of the peach S1-, S2-, and Prunus davidiana (Carr.) Franch. S1-RNases. S-RNases of peach were detected to possess ribonuclease activity, and a single nucleotide polymorphism in the S1-RNase was shown, which represents a synonymous substitution and does not change the amino acid present at the position in the protein. A 700-bp fragment of the peach SFB gene was PCR-amplified, which is similar to the fragment size of functional Prunus L. SFBs. All data obtained in this study may support the contribution of genes outside the S-locus to the self-compatible phenotype of peaches.

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24

Ma, R. C., and M. M. Oliveira. "The RNase PD2 gene of almond (Prunus dulcis) represents an evolutionarily distinct class of S-like RNase genes." Molecular and General Genetics MGG 263, no. 6 (August 2000): 925–33. http://dx.doi.org/10.1007/s004380000258.

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25

Qin, Xiaoqiong, and Roger T. Chetelat. "Ornithine decarboxylase genes contribute to S-RNase-independent pollen rejection." Plant Physiology 186, no. 1 (February 11, 2021): 452–68. http://dx.doi.org/10.1093/plphys/kiab062.

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Abstract Unilateral incompatibility (UI) manifests as pollen rejection in the pistil, typically when self-incompatible (SI) species are pollinated by self-compatible (SC) relatives. In the Solanaceae, UI occurs when pollen lack resistance to stylar S-RNases, but other, S-RNase-independent mechanisms exist. Pistils of the wild tomato Solanum pennellii LA0716 (SC) lack S-RNase yet reject cultivated tomato (Solanum lycopersicum, SC) pollen. In this cross, UI results from low pollen expression of a farnesyl pyrophosphate synthase gene (FPS2) in S. lycopersicum. Using pollen from fps2−/− loss-of-function mutants in S. pennellii, we identified a pistil factor locus, ui3.1, required for FPS2-based pollen rejection. We mapped ui3.1 to an interval containing 108 genes situated on the IL 3-3 introgression. This region includes a cluster of ornithine decarboxylase (ODC2) genes, with four copies in S. pennellii, versus one in S. lycopersicum. Expression of ODC2 transcript was 1,034-fold higher in S. pennellii than in S. lycopersicum styles. Pistils of odc2−/− knockout mutants in IL 3-3 or S. pennellii fail to reject fps2 pollen and abolish transmission ratio distortion (TRD) associated with FPS2. Pollen of S. lycopersicum express low levels of FPS2 and are compatible on IL 3-3 pistils, but incompatible on IL 12-3 × IL 3-3 hybrids, which express both ODC2 and ui12.1, a locus thought to encode the SI proteins HT-A and HT-B. TRD observed in F2 IL 12-3 × IL 3-3 points to additional ODC2-interacting pollen factors on both chromosomes. Thus, ODC2 genes contribute to S-RNase independent UI and interact genetically with ui12.1 to strengthen pollen rejection.

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26

Bralley, Patricia, Bertolt Gust, Samantha Chang, Keith F. Chater, and George H. Jones. "RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase." Microbiology 152, no. 3 (March 1, 2006): 627–36. http://dx.doi.org/10.1099/mic.0.28363-0.

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As in other bacteria, 3′-tails are added post-transcriptionally to Streptomyces coelicolor RNA. These tails are heteropolymeric, and although there are several candidates, the enzyme responsible for their synthesis has not been definitively identified. This paper reports on three candidates for this role. First, it is confirmed that the product of S. coelicolor gene SCO3896, although it bears significant sequence similarity to Escherichia coli poly(A) polymerase I, is a tRNA nucleotidyltransferase, not a poly(A) polymerase. It is further shown that SCO2904 encodes an RNase PH homologue that possesses the polymerization and phosphorolysis activities expected for enzymes of that family. S. coelicolor RNase PH can add poly(A) tails to a model RNA transcript in vitro. However, disruption of the RNase PH gene has no effect on RNA 3′-tail length or composition in S. coelicolor; thus, RNase PH does not function as the RNA 3′-polyribonucleotide polymerase [poly(A) polymerase] in that organism. These results strongly suggest that the enzyme responsible for RNA 3′-tail synthesis in S. coelicolor and other streptomycetes is polynucleotide phosphorylase (PNPase). Moreover, this study shows that both PNPase and the product of SCO3896 are essential. It is possible that the dual functions of PNPase in the synthesis and degradation of RNA 3′-tails make it indispensable in Streptomyces.

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27

Ren, Yi, Qingzhu Hua, Jiayan Pan, Zhike Zhang, Jietang Zhao, Xinhua He, Yonghua Qin, and Guibing Hu. "SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen." PeerJ 8 (December 22, 2020): e10578. http://dx.doi.org/10.7717/peerj.10578.

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S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’.

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Liang, Lizhi, Zhao Lai, Wenshi Ma, Yansheng Zhang, and Yongbiao Xue. "AhSL28, a senescence- and phosphate starvation-induced S-like RNase gene in Antirrhinum." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1579, no. 1 (November 2002): 64–71. http://dx.doi.org/10.1016/s0167-4781(02)00507-9.

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29

Keulemans, J., W. Broothaerts, M. M. Oliveira, I. Van Nerum, and A. C. Certal. "PD1 , an S-like RNase gene from a self-incompatible cultivar of almond." Plant Cell Reports 19, no. 11 (November 14, 2000): 1108–14. http://dx.doi.org/10.1007/s002990000235.

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30

Ivanovych, Ya I., N. V. Tryapitsyna, K. M. Udovychenko, and R. A. Volkov. "Self-incompatibility allele identification in Ukrainian sweet cherry (Prunus avium L.) cultivars." Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv 15, no. 2 (February 28, 2018): 150–58. http://dx.doi.org/10.7124/visnyk.utgis.15.2.873.

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Aim. Ukrainian breeders have created a large number of sweet cherry cultivars, which still remain almost unexplored at the molecular level. The aim of our study was to identify the self-incompatibility alleles (S-alleles) in Ukrainian sweet cherry cultivars and landraces, and to elucidate, to which cross-incompatibility group the cultivars belong. Methods. The PCR was conducted using consensus primers to the first and second introns of S-RNAse gene and to the single intron of SFB gene. The electrophoretic analysis of the PCR products of the second intron of S-RNAse was carried out in agarose gel, whereas detection of fluorescently labeled DNA fragments of the first S-RNAse intron and the SFB intron was performed using a genetic analyzer. Results. The S-alleles of 25 Ukrainian sweet cherry cultivars and 10 landraces were identified. The S-alleles frequencies and affiliation of cultivars and landraces to the groups of cross-incompatibility were determined. The obtained data can be used in breeding programs and by planning of industrial plantings. Conclusions. In the study, 12 different S-alleles and 79 S-haplotypes were identified. The S1, S3, S4, S5, S6 and S9 alleles are the most widespread among Ukrainian sweet cherry cultivars and landraces. The high frequencies of S5 and especially of S9 alleles are characteristic for the Ukrainian cultivars and distinguish them from other European ones. For the Ukrainian sweet cherry cultivars, the XXXVII (S5S9) cross-incompatibility group appeared to be the most numerous.Keywords: Ukrainian sweet cherry cultivars, S-locus, Sgenotypes, self- and cross-incompatibility, Prunus avium.

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31

Wencker, Freya D. R., Gabriella Marincola, Sonja M. K. Schoenfelder, Sandra Maaß, Dörte Becher, and Wilma Ziebuhr. "Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay." Nucleic Acids Research 49, no. 4 (January 15, 2021): 2192–212. http://dx.doi.org/10.1093/nar/gkaa1277.

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Abstract In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5′ untranslated region (met leader RNA) of the S. aureus metICFE-mdh operon controls downstream gene transcription upon interaction with uncharged methionyl-tRNA. met leader and metICFE-mdh (m)RNAs undergo RNase-mediated degradation in a process whose molecular details are poorly understood. Here we determined the secondary structure of the met leader RNA and found the element to harbor, beyond other conserved T-box riboswitch structural features, a terminator helix which is target for RNase III endoribonucleolytic cleavage. As the terminator is a thermodynamically highly stable structure, it also forms posttranscriptionally in met leader/ metICFE-mdh read-through transcripts. Cleavage by RNase III releases the met leader from metICFE-mdh mRNA and initiates RNase J-mediated degradation of the mRNA from the 5′-end. Of note, metICFE-mdh mRNA stability varies over the length of the transcript with a longer lifespan towards the 3′-end. The obtained data suggest that coordinated RNA decay represents another checkpoint in a complex regulatory network that adjusts costly methionine biosynthesis to current metabolic requirements.

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32

Yamane, H., R. Tao, A. Sugiura, N. Hauck, and A. Iezzoni. "483 Identification of S-RNase in Tetraploid Sour Cherry." HortScience 35, no. 3 (June 2000): 477D—477. http://dx.doi.org/10.21273/hortsci.35.3.477d.

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Most fruit tree species of Prunus exhibit gametophytic self-incompatibility, which is controlled by a single locus with multiple alleles (S-alleles). One interesting aspect of gametophytic self-incompatibility is that it commonly “breaks down” as a result of polyploidy, resulting in self-compatible individuals. This phenomenon is exhibited in the diploid sweet cherry (P. avium) and the tetraploid sour cherry (P. cerasus), in which most cultivars are self-compatible. Recently, S-gene products in pistil of Prunus species were shown to be S-RNases. As sour cherry is one Prunus species, it is likely to possess S-alleles encoding pistil S-RNases. To confirm this, we surveyed stylar extracts of 11 sour cherry cultivars, including six self-compatible and five self-incompatible cultivars, by 2D-PAGE. As expected, all 11 cultivars tested yielded glycoprotein spots similar to S-RNases of other Prunus species in terms of Mr, immunological characteristics, and N-terminal sequences. A cDNA clone encoding one of these glycoproteins was cloned from the cDNA library constructed from styles with stigmas of a self-compatible cultivar, `Erdi Botermo'. Deduced amino acid sequence from the cDNA clone contained two active sites of T2/S type RNases and five conserved regions of rosaceous S-RNases. In order to determine the inheritance of self-incompatibility and S-allele diversity in sour cherry, we conducted genomic DNA blot analysis for sour cherry germplasm collections and mapping populations in MSU using the cDNA as a probe. To date, it appears as if self-compatibility in sour cherry is not simply controlled by a self-fertile allele as demonstrated in other Prunus species.

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33

Bai, C., and P. P. Tolias. "Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc finger protein." Molecular and Cellular Biology 16, no. 12 (December 1996): 6661–67. http://dx.doi.org/10.1128/mcb.16.12.6661.

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Control of RNA turnover is a major, but poorly understood, aspect of gene regulation. In multicellular organisms, progress toward dissecting RNA turnover pathways has been made by defining some cis-acting sequences that function as either regulatory or cleavage targets (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993). However, the identification of genes encoding proteins that regulate or cleave target RNAs has been elusive (C. A. Beelman and R. Parker, Cell 81:79-183, 1995); this gap in knowledge has made it difficult to identify additional components of RNA turnover pathways. We have utilized a modified expression cloning strategy to identify a developmentally regulated gene from Drosophila melanogaster that encodes a RNase that we refer to as Clipper (CLP). Significant sequence matches to open reading frames encoding unknown functions identified from the Caenorhabditis elegans and Saccharomyces cerevisiae genome sequencing projects suggest that all three proteins are members of a new protein family conserved from lower eukaryotes to invertebrates. We demonstrate that a member of this new protein family specifically cleaves RNA hairpins and that this activity resides in a region containing five copies of a previously uncharacterized CCCH zinc finger motif. CLP's endoribonucleolytic activity is distinct from that associated with RNase A (P. Blackburn and S. Moore, p. 317-433, in P. D. Boyer, ed., The Enzymes, vol. XV, part B, 1982) and is unrelated to RNase III processing of rRNAs and tRNAs (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993, and S. A. Elela, H. Igel, and M. Ares, Cell 85:115-124, 1995). Our results suggest that CLP may function directly in RNA metabolism.

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34

Good-Avila, S. V., D. Majumder, H. Amos, and A. G. Stephenson. "Characterization of self-incompatibility in Campanula rapunculoides (Campanulaceae) through genetic analyses and microscopy." Botany 86, no. 1 (January 2008): 1–13. http://dx.doi.org/10.1139/b07-100.

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In this paper, we seek to identify the genetic basis of self-incompatibility (SI) in Campanula rapunculoides L. through diallel analysis of full siblings; to characterize the growth of pollen tubes in vivo after incompatible and compatible pollination; and to determine whether the SI system is based on pistil S-RNases. Pollinations were performed among individuals from five diallel crosses and scored for both fruit set and pollen-tube growth to determine the genetic basis of SI. On a subset of these individuals with known cross-(in)compatibility relationships, additional crosses were performed and pistils collected 1, 3, 6, 12, and 24 h after pollination to assess both the percentage of pollen grains that had germinated on the stigma, and the number of pollen tubes that had grown 20%, 40% 60%, 80%, and 100% of the distance down the pistil over five time intervals. Finally, total pistillate proteins were extracted and subjected to isoelectric focusing and RNase activity staining to find evidence of a highly basic S-RNases associated with SI in the Solanaceae. We found evidence that the SI system was based on the haplotype of the male gametophyte, and was not sporophytic. Protein analyses showed that SI was not based on a pistillate S-RNase. The existence of modifiers of SI and possible polyploidy at the S-locus complicated the expression of SI in this species, and single-gene inheritance could not be determined. This represents the first published characterization of incompatibility in the family Campanulaceae.

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35

Bralley, Patricia, and George H. Jones. "Organization and Expression of the Polynucleotide Phosphorylase Gene (pnp) of Streptomyces: Processing of pnp Transcripts in Streptomyces antibioticus." Journal of Bacteriology 186, no. 10 (May 15, 2004): 3160–72. http://dx.doi.org/10.1128/jb.186.10.3160-3172.2004.

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ABSTRACT We have examined the expression of pnp encoding the 3′-5′-exoribonuclease, polynucleotide phosphorylase, in Streptomyces antibioticus. We show that the rpsO-pnp operon is transcribed from at least two promoters, the first producing a readthrough transcript that includes both pnp and the gene for ribosomal protein S15 (rpsO) and a second, Ppnp, located in the rpsO-pnp intergenic region. Unlike the situation in Escherichia coli, where observation of the readthrough transcript requires mutants lacking RNase III, we detect readthrough transcripts in wild-type S. antibioticus mycelia. The Ppnp transcriptional start point was mapped by primer extension and confirmed by RNA ligase-mediated reverse transcription-PCR, a technique which discriminates between 5′ ends created by transcription initiation and those produced by posttranscriptional processing. Promoter probe analysis demonstrated the presence of a functional promoter in the intergenic region. The Ppnp sequence is similar to a group of promoters recognized by the extracytoplasmic function sigma factors, sigma-R and sigma-E. We note a number of other differences in rspO-pnp structure and function between S. antibioticus and E. coli. In E. coli, pnp autoregulation and cold shock adaptation are dependent upon RNase III cleavage of an rpsO-pnp intergenic hairpin. Computer modeling of the secondary structure of the S. antibioticus readthrough transcript predicts a stem-loop structure analogous to that in E. coli. However, our analysis suggests that while the readthrough transcript observed in S. antibioticus may be processed by an RNase III-like activity, transcripts originating from Ppnp are not. Furthermore, the S. antibioticus rpsO-pnp intergenic region contains two open reading frames. The larger of these, orfA, may be a pseudogene. The smaller open reading frame, orfX, also observed in Streptomyces coelicolor and Streptomyces avermitilis, may be translationally coupled to pnp and the gene downstream from pnp, a putative protease.

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36

Yaegaki, H., T. Shimada, H. Hayaman, T. Haji, and M. Yamaguchi. "087 Determining S-genotype of Japanese Apricot (Prunus mume) Cultivar." HortScience 35, no. 3 (June 2000): 403E—403. http://dx.doi.org/10.21273/hortsci.35.3.403e.

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Japanese apricot (Prunus mume) originated in south-eastern China and is one of the major fruit trees in Japan. The major cultivars of Japanese apricot are self-incompatible. Self-incompatibility of Japanese apricot is gametophytic, the same as other Prunus species. Since S-genotype of every cultivar remained unclear until now, we examined molecular markers to determine S-genotype which was explored based on the information about S-RNase of other Prunus spiecies. Total DNA isolated from six cultivars was PCR-amplified by oligonucleotide primers designed from conserved region of Prunus S-RNase Every six cultivars yielded two amplified bands. In total, seven kind of polymorphism in molecular size were determined among those six cultivar, controlled pollination tests were carried out among cultivars that showed same band pattern, and these cross-combinations indicated cross-incompatibility. So, we were made clear that S-genotype of Japanese apricot could effectively and easily be determined by PCR method, and that there exists seven S-gene at least.

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37

Sekido, Keiko, Yusaku Hayashi, Kunio Yamada, Katsuhiro Shiratake, Shogo Matsumoto, Tsutomu Maejima, and Hiromitsu Komatsu. "Efficient Breeding System for Red-fleshed Apple Based on Linkage with S3-RNase Allele in ‘Pink Pearl’." HortScience 45, no. 4 (April 2010): 534–37. http://dx.doi.org/10.21273/hortsci.45.4.534.

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We have used a red-fleshed apple cultivar, Malus ×domestica Pink Pearl, and its progeny, ‘JPP 35’, as paternal parents for producing new red-fleshed cultivars suitable for fresh use or processing such as pie fillings, dried apple, apple juice, or cider. In this process, we found that the S3-RNase allele of ‘Pink Pearl’ was linked to its red flesh trait. It was suggested that this trait might be controlled by a new gene apart from the MYB10 (MdMYB10) gene. Using ‘JPP 35’ (S-RNase allele genotype; S3S7) produced by ‘Jonathan’ (S7S9) × ‘Pink Pearl’ (S3Sx) as a paternal parent, we developed a system for producing red-fleshed progenies suitable for fresh use. That is, 96% and 86% of progenies from ‘Shinano Sweet’ (S1S7) × ‘JPP35’ (S3S7) and ‘Orin’ (S2S7) × ‘JPP35’ (S3S7) containing the S3-RNase allele, respectively, showed the red flesh trait. Similarly, red-fleshed progenies suitable for apple pie or natural red juice could be produced by ‘Jonathan’ (S7S9) × ‘JPP35’ (S3S7).

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38

Mahieux, R., P. F. Lambert, E. Agbottah, M. A. Halanski, L. Deng, F. Kashanchi, and J. N. Brady. "Cell Cycle Regulation of Human Interleukin-8 Gene Expression by the Human Immunodeficiency Virus Type 1 Tat Protein." Journal of Virology 75, no. 4 (February 15, 2001): 1736–43. http://dx.doi.org/10.1128/jvi.75.4.1736-1743.2001.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) Tat protein has been reported to transactivate several cellular genes, including the potent chemotactic factor interleukin-8 (IL-8). Consistent with these in vitro assays, elevated levels of IL-8 protein are found in the serum of HIV-infected individuals. We now extend these observations by demonstrating that Tat induction of IL-8 is linked to the cell cycle. Cells that constitutively express the Tat(1–86) protein (eTat) and control cells (pCEP) were reversibly blocked at the G1/S border with hydroxyurea or thymidine. The cells were subsequently released, and IL-8 expression was monitored by RNase protection assays and enzyme-linked immunosorbent assay (ELISA). RNase protection assays demonstrated that IL-8 mRNA expression is transiently induced, approximately fourfold, as the Tat-expressing cells enter S phase. Consistent with the RNase protection assay, an increase in IL-8 protein was observed in the cell supernatant using an IL-8 ELISA. Similar experiments were performed following a reversible block at the G2/M border with nocodazole and release into G1. Using the RNase protection assay and ELISA, little or no increase in IL-8 expression was observed during G1. Using gel shift as well as an immobilized DNA binding assay, we demonstrate that the increase in IL-8 gene expression correlates with a specific increase in p65 NF-κB binding activity only in the nucleus of the Tat-expressing cells. Moreover, the CREB-binding protein coactivator is present in the complex in the Tat cell line. Finally, we demonstrate that the presence of the proteasome inhibitor MG-132 inhibits the induction of NF-κB binding, as well as IL-8 expression, supporting the role of NF-κB.

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Miao, Hong-xia, Yong-hua Qin, Jaime A. Teixeira da Silva, Zi-xing Ye, and Gui-bing Hu. "Cloning and expression analysis of S-RNase homologous gene in Citrus reticulata Blanco cv. Wuzishatangju." Plant Science 180, no. 2 (February 2011): 358–67. http://dx.doi.org/10.1016/j.plantsci.2010.10.012.

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40

Liu, Xue-ying, Ta-na Wuyun, and Hong-yan Zeng. "Cloning, characterization and promoter analysis of S-RNase gene promoter from Chinese pear (Pyrus pyrifolia)." Gene 505, no. 2 (September 2012): 246–53. http://dx.doi.org/10.1016/j.gene.2012.06.017.

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41

Gordillo-Romero, Milton, Lisa Correa-Baus, Verónica Baquero-Méndez, María de Lourdes Torres, Carlos Vintimilla, Jose Tobar, and Andrés F. Torres. "Gametophytic self-incompatibility in Andean capuli (Prunus serotina subsp. capuli): allelic diversity at the S-RNase locus influences normal pollen-tube formation during fertilization." PeerJ 8 (August 31, 2020): e9597. http://dx.doi.org/10.7717/peerj.9597.

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Capuli (Prunus serotina subsp. capuli) is a tree species that is widely distributed in the northern Andes. In Prunus, fruit set and productivity appears to be limited by gametophytic self-incompatibility (GSI) which is controlled by the S-Locus. For the first time, this research reveals the molecular structure of the capuli S-RNase (a proxy for S-Locus diversity) and documents how S-Locus diversity influences GSI in the species. To this end, the capuli S-RNase gene was amplified and sequenced in order to design a CAPS (Cleaved Amplified Polymorphic Sequence) marker system that could unequivocally detect S-alleles by targeting the highly polymorphic C2–C3 S-RNase intra-genic region. The devised system proved highly effective. When used to assess S-Locus diversity in 15 P. serotina accessions, it could identify 18 S-alleles; 7 more than when using standard methodologies for the identification of S-alleles in Prunus species. CAPS marker information was subsequently used to formulate experimental crosses between compatible and incompatible individuals (as defined by their S-allelic identity). Crosses between heterozygote individuals with contrasting S-alleles resulted in normal pollen tube formation and growth. In crosses between individuals with exactly similar S-allele identities, pollen tubes often showed morphological alterations and arrested development, but for some (suspected) incompatible crosses, pollen tubes could reach the ovary. The latter indicates the possibility of a genotype-specific breakdown of GSI in the species. Overall, this supports the notion that S-Locus diversity influences the reproductive patterns of Andean capuli and that it should be considered in the design of orchards and the production of basic propagation materials.

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42

Ciurkot, Klaudia, Thomas E. Gorochowski, Johannes A. Roubos, and René Verwaal. "Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a." Nucleic Acids Research 49, no. 13 (July 1, 2021): 7775–90. http://dx.doi.org/10.1093/nar/gkab529.

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Abstract CRISPR Cas12a is an RNA-programmable endonuclease particularly suitable for gene regulation. This is due to its preference for T-rich PAMs that allows it to more easily target AT-rich promoter sequences, and built-in RNase activity which can process a single CRISPR RNA array encoding multiple spacers into individual guide RNAs (gRNAs), thereby simplifying multiplexed gene regulation. Here, we develop a flexible dCas12a-based CRISPRi system for Saccharomyces cerevisiae and systematically evaluate its design features. This includes the role of the NLS position, use of repression domains, and the position of the gRNA target. Our optimal system is comprised of dCas12a E925A with a single C-terminal NLS and a Mxi1 or a MIG1 repression domain, which enables up to 97% downregulation of a reporter gene. We also extend this system to allow for inducible regulation via an RNAP II-controlled promoter, demonstrate position-dependent effects in crRNA arrays, and use multiplexed regulation to stringently control a heterologous β-carotene pathway. Together these findings offer valuable insights into the design constraints of dCas12a-based CRISPRi and enable new avenues for flexible and efficient gene regulation in S. cerevisiae.

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43

Pinar, Hasan, Mustafa Unlu, Sezai Ercisli, Aydin Uzun, Mustafa Bircan, and Kadir Ugurtan-Yilmaz. "Determination of self-(in)compatibility in some Turkish cultivated and wild apricots." Genetika 47, no. 3 (2015): 777–84. http://dx.doi.org/10.2298/gensr1503777p.

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In this study, self-(in) compatibility of 34 wild apricot genotypes, called as Sakit apricots, sampled from Sakit valley located in east Mediterranean region of Turkey and 9 well known Turkish apricot cultivars were determined by using molecular methods. Genomic PCR with S-RNase and SFB-specific primers was conducted using the degenerate primers EM-PC2consFD and EM-PC3consRD for the amplification of the second intron region of the S-RNase gene. To amplify the first intron, the fluorescently labelled (JOE) forward primer SRc-F was used in combination with the reverse primer SRc-R. According to the results, Sc (self-compatible) allele is not present in all wild and cultivated materials. All wild genotypes had same S allele (S6S19) composition indicating they do not carry the SC-haplotype. These wild materials previously reported self-compatible by fruit set studies on field. Mutations rendering the S-locus non-functional in these genotypes can be supposed and checked in the future. The most important dried apricot cultivars of Turkey such as Hacihaliloglu, Kabaasi, and Cataloglu were observed to be self-incompatible cultivars.

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Okamoto, Susumu, Alexander Lezhava, Takeshi Hosaka, Yoshiko Okamoto-Hosoya, and Kozo Ochi. "Enhanced Expression of S-Adenosylmethionine Synthetase Causes Overproduction of Actinorhodin in Streptomyces coelicolor A3(2)." Journal of Bacteriology 185, no. 2 (January 15, 2003): 601–9. http://dx.doi.org/10.1128/jb.185.2.601-609.2003.

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ABSTRACT We found that a 46-kDa protein is highly expressed in an actinorhodin-overproducing Streptomyces coelicolor A3(2) mutant (KO-179), which exhibited a low-level resistance to streptomycin. The protein was identified as S-adenosylmethionine (SAM) synthetase, which is a product of the metK gene. Enzyme assay revealed that SAM synthetase activity in strain KO-179 was 5- to 10-fold higher than in wild-type cells. The elevation of SAM synthetase activity was found to be associated with an increase in the level of intracellular SAM. RNase protection assay revealed that the metK gene was transcribed from two distinct promoters (p1 and p2) and that enhanced expression of the MetK protein in the mutant strain KO-179 was attributed to elevated transcription from metKp2. Strikingly, the introduction of a high-copy-number plasmid containing the metK gene into wild-type cells resulted in a precocious hyperproduction of actinorhodin. Furthermore, the addition of SAM to the culture medium induced Act biosynthesis in wild-type cells. Overexpression of metK stimulated the expression of the pathway-specific regulatory gene actII-ORF4, as demonstrated by the RNase protection assay. The addition of SAM also caused hyperproduction of streptomycin in Streptomyces griseus. These findings implicate the significant involvement of intracellular SAM in initiating the onset of secondary metabolism in Streptomyces.

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45

Muñoz-Sanz, Juan Vicente, Alejandro Tovar-Méndez, Lu Lu, Ru Dai, and Bruce McClure. "A Cysteine-Rich Protein, SpDIR1L, Implicated in S-RNase-Independent Pollen Rejection in the Tomato (Solanum Section Lycopersicon) Clade." International Journal of Molecular Sciences 22, no. 23 (December 2, 2021): 13067. http://dx.doi.org/10.3390/ijms222313067.

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Tomato clade species (Solanum sect. Lycopersicon) display multiple interspecific reproductive barriers (IRBs). Some IRBs conform to the SI x SC rule, which describes unilateral incompatibility (UI) where pollen from SC species is rejected on SI species’ pistils, but reciprocal pollinations are successful. However, SC x SC UI also exists, offering opportunities to identify factors that contribute to S-RNase-independent IRBs. For instance, SC Solanum pennellii LA0716 pistils only permit SC Solanum lycopersicum pollen tubes to penetrate to the top third of the pistil, while S. pennellii pollen penetrates to S. lycopersicum ovaries. We identified candidate S. pennellii LA0716 pistil barrier genes based on expression profiles and published results. CRISPR/Cas9 mutants were created in eight candidate genes, and mutants were assessed for changes in S. lycopersicum pollen tube growth. Mutants in a gene designated Defective in Induced Resistance 1-like (SpDIR1L), which encodes a small cysteine-rich protein, permitted S. lycopersicum pollen tubes to grow to the bottom third of the style. We show that SpDIR1L protein accumulation correlates with IRB strength and that species with weak or no IRBs toward S. lycopersicum pollen share a 150 bp deletion in the upstream region of SpDIR1L. These results suggest that SpDIR1L contributes to an S-RNase-independent IRB.

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46

Agapito-Tenfen, Sarah Zanon, Adriana Cibele de Mesquita Dantas, Frederico Denardi, and Rubens Onofre Nodari. "Identification of the Er1 resistence gene and RNase S-alleles in Malus prunifolia var. ringo rootstock." Scientia Agricola 72, no. 1 (February 2015): 62–68. http://dx.doi.org/10.1590/0103-9016-2013-0210.

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47

Li, Jun-cheng, Yulin Wang, Hong-fen Dai, and Qingming Sun. "Global transcriptome dissection of pollen–pistil interactions induced self-incompatibility in dragon fruit (Selenicereus spp.)." PeerJ 10 (November 1, 2022): e14165. http://dx.doi.org/10.7717/peerj.14165.

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Self-incompatibility (SI) is a major issue in dragon fruit (Selenicereus spp.) breeding and production. Therefore, a better understanding of the dragon fruit SI mechanism is needed to improve breeding efficiency and ultimate production costs. To reveal the underlying mechanisms of SI in dragon fruit, plant anatomy, de novo RNA sequencing-based transcriptomic analysis, and multiple bioinformatic approaches were used to analyze gene expression in the pistils of the self-pollinated and cross-pollinated dragon fruit flowers at different intervals of time after pollination. Using fluorescence microscopy, we observed that the pollen of ‘Hongshuijing’, a self-incompatible dragon fruit variety (S. monacanthus), germinated on its own stigma. However, the pollen tube elongation has ceased at 1/2 of the style, confirming that dragon fruit experiences gametophyte self-incompatibility (GSI). We found that the pollen tube elongation in vitro was inhibited by self-style glycoproteins in the SI variety, indicating that glycoproteins were involved in SI. That is to say the female S factor should be homologous of S-RNase or PrsS (P. rhoeas stigma S factor), both of which are glycoproteins and are the female S factors of the two known GSI mechanism respectively. Bioinformatics analyses indicated that among the 43,954 assembled unigenes from pistil, there were six S-RNase genes, while 158 F-box genes were identified from a pollen transcriptomic dataset. There were no P. rhoeas type S genes discovered. Thus, the identified S-RNase and F-box represent the candidate female and male S genes, respectively. Analysis of differentially expressed genes (DEGs) between the self and cross-pollinated pistils at different time intervals led to the identification of 6,353 genes. We then used a weighted gene co-expression network analysis (WGCNA) to find some non-S locus genes in SI responses in dragon fruit. Additionally, 13 transcription factors (TFs) (YABBY4, ANL2, ERF43, ARF2, BLH7, KNAT6, PIF3, two OBF1, two HY5 and two LHY/CCA) were identified to be involved in dragon fruit GSI. Thus, we uncovered candidate S and non-S genes and predicted more SI-related genes for a more detailed investigation of the molecular mechanism of dragon fruit SI. Our findings suggest that dragon fruit possesses a GSI system and involves some unique regulators. This study lays the groundwork for future research into SI mechanisms in dragon fruit and other plant species.

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48

Lécrivain, Anne-Laure, Anaïs Le Rhun, Thibaud T. Renault, Rina Ahmed-Begrich, Karin Hahnke, and Emmanuelle Charpentier. "In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes." Proceedings of the National Academy of Sciences 115, no. 46 (October 31, 2018): 11814–19. http://dx.doi.org/10.1073/pnas.1809663115.

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mRNA decay plays an essential role in the control of gene expression in bacteria. Exoribonucleases (exoRNases), which trim transcripts starting from the 5′ or 3′ end, are particularly important to fully degrade unwanted transcripts and renew the pool of nucleotides available in the cell. While recent techniques have allowed genome-wide identification of ribonuclease (RNase) targets in bacteria in vivo, none of the 3′-to-5′ exoRNase targetomes (i.e., global processing sites) have been studied so far. Here, we report the targetomes of YhaM, polynucleotide phosphorylase (PNPase), and RNase R of the human pathogen Streptococcus pyogenes. We determined that YhaM is an unspecific enzyme that trims a few nucleotides and targets the majority of transcript ends, generated either by transcription termination or by endonucleolytic activity. The molecular determinants for YhaM-limited processivity are yet to be deciphered. We showed that PNPase clears the cell from mRNA decay fragments produced by endoribonucleases (endoRNases) and is the major 3′-to-5′ exoRNase for RNA turnover in S. pyogenes. In particular, PNPase is responsible for the degradation of regulatory elements from 5′ untranslated regions. However, we observed little RNase R activity in standard culture conditions. Overall, our study sheds light on the very distinct features of S. pyogenes 3′-to-5′ exoRNases.

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49

Békefi, Z., S. Vaughan, and K. Tobutt. "Determination of incompatibility (S) genotypes of sweet cherries in the Hungarian gene-bank by a PCR-based method." Acta Agronomica Hungarica 58, no. 4 (December 1, 2010): 377–84. http://dx.doi.org/10.1556/aagr.58.2010.4.6.

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The sweet cherry (Prunus avium L.) gene-bank collection in Hungary comprises mainly local cultivars. The incompatibility (S) genotypes of 48 accessions from the central region of Hungary were investigated by PCR amplification of the intron regions of the SRNase and SFB genes responsible for compatibility relationships in sweet cherry. The Sgenotypes of 38 accessions were completely determined; they showed various pairs of nine alleles and could be assigned to 15 of the existing incompatibility groups or, in the case of three accessions having the novel genotype S6S13, to the new incompatibility group XLII. For 10 accessions only one S-allele could be identified, as a single S-RNase product was generated and the intron region of the SFB gene of the second allele could not be amplified.

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50

Feng, Jianrong, Xuesen Chen, Yan Wu, Wen Liu, Qing Liang, and Lijie Zhang. "Detection and transcript expression of S-RNase gene associated with self-incompatibility in apricot (Prunus armeniaca L.)." Molecular Biology Reports 33, no. 3 (September 2006): 215–21. http://dx.doi.org/10.1007/s11033-006-0011-x.

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