Mycoplasma, solely culturable bacteria with the smallest genome, is an important organism to understand the minimal form of life. Mutagenesis using mutagens is a useful methodology for understanding the essential regions of genomic information. Ultraviolet light and trimethyl psoralen are mutagens known to induce various mutations; the latter is reported to specifically induce deletions in nematodes. However, their mutagenic effects on mycoplasma are not known. Here, we exposed Metamycoplasma salivarium to ultraviolet (UV) light or trimethyl psoralen and UV as mutagens, and analyzed the mutational pattern after several rounds of serial cultivation ranging from 34 to 56 for different lineages. Our results showed that more deletions, but fewer point mutations, were induced with TMP and UV-A than with UV alone, indicating the usefulness of TMP in inducing deletions. In addition, we compared our results with mutational data from other studies, which suggested that both TMP-UVA and UV exposure induced point mutations that were highly biased toward C to T and G to A transitions. These data provide useful basic knowledge for mutational studies on M. salivarium.
支原体是基因组最小的唯一可培养细菌,是了解生命最小形式的重要生物。使用诱变剂进行诱变是了解基因组信息重要区域的有效方法。紫外线和三甲基补骨脂素是已知可诱导各种突变的诱变剂;据报道,后者可特异性地诱导线虫体内的缺失。然而,它们对支原体的诱变作用尚不清楚。在此,我们将唾液支原体暴露于紫外线(UV)或三甲基补骨脂素和紫外线作为诱变剂,并分析了不同品系经过 34 至 56 轮连续培养后的突变模式。我们的结果表明,与单独使用紫外线相比,使用 TMP 和 UV-A 诱导的缺失更多,但点突变更少,这表明 TMP 有助于诱导缺失。此外,我们还将我们的结果与其他研究的突变数据进行了比较,结果表明 TMP-UVA 和紫外线照射诱导的点突变高度偏向于 C 到 T 和 G 到 A 的转变。这些数据为唾液腺霉菌的突变研究提供了有用的基础知识。
{"title":"Mutagenic effect of ultraviolet radiation and trimethyl psoralen in Mycoplasma towards minimal genome.","authors":"Kaito Seo, Kensei Okada, Norikazu Ichihashi","doi":"10.1266/ggs.24-00061","DOIUrl":"https://doi.org/10.1266/ggs.24-00061","url":null,"abstract":"<p><p>Mycoplasma, solely culturable bacteria with the smallest genome, is an important organism to understand the minimal form of life. Mutagenesis using mutagens is a useful methodology for understanding the essential regions of genomic information. Ultraviolet light and trimethyl psoralen are mutagens known to induce various mutations; the latter is reported to specifically induce deletions in nematodes. However, their mutagenic effects on mycoplasma are not known. Here, we exposed Metamycoplasma salivarium to ultraviolet (UV) light or trimethyl psoralen and UV as mutagens, and analyzed the mutational pattern after several rounds of serial cultivation ranging from 34 to 56 for different lineages. Our results showed that more deletions, but fewer point mutations, were induced with TMP and UV-A than with UV alone, indicating the usefulness of TMP in inducing deletions. In addition, we compared our results with mutational data from other studies, which suggested that both TMP-UVA and UV exposure induced point mutations that were highly biased toward C to T and G to A transitions. These data provide useful basic knowledge for mutational studies on M. salivarium.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We investigated the variation and geographical distribution of the Pseudo-regulator response 37 (Setaria italica PRR37; SiPRR37) gene, which is involved in heading time (photoperiodism) in foxtail millet. An allele of the SiPRR37 gene, in which an approximately 4.9-kb transposable element (designated TE1) is inserted (a loss-of-function or reduction-of-function type), is distributed sporadically in East Asia and broadly in Southeast Asia and South Asia, implying that this gene is important in latitudinal adaptation. In addition, we found a new allele of SiPRR37 with an insertion of a 360-bp TE (TE2) at this locus and investigated the geographical distribution of this new type. This SiPRR37 allele with TE2 is distributed in Japan, Korea, Nepal, Iran and Turkey. Both TE1 and TE2 are useful markers for tracing foxtail millet dispersal pathways in Asia.
{"title":"Latitudinal adaptation and dispersal pathway of foxtail millet suggested by geographical distribution of transposable elements inserted in the SiPRR37 gene.","authors":"Kenji Fukunaga, Akira Abe, Kazue Ito, Kaori Oikawa, Masaya Tsuji, Makoto Kawase","doi":"10.1266/ggs.24-00023","DOIUrl":"10.1266/ggs.24-00023","url":null,"abstract":"<p><p>We investigated the variation and geographical distribution of the Pseudo-regulator response 37 (Setaria italica PRR37; SiPRR37) gene, which is involved in heading time (photoperiodism) in foxtail millet. An allele of the SiPRR37 gene, in which an approximately 4.9-kb transposable element (designated TE1) is inserted (a loss-of-function or reduction-of-function type), is distributed sporadically in East Asia and broadly in Southeast Asia and South Asia, implying that this gene is important in latitudinal adaptation. In addition, we found a new allele of SiPRR37 with an insertion of a 360-bp TE (TE2) at this locus and investigated the geographical distribution of this new type. This SiPRR37 allele with TE2 is distributed in Japan, Korea, Nepal, Iran and Turkey. Both TE1 and TE2 are useful markers for tracing foxtail millet dispersal pathways in Asia.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shunta Sakamoto, Takanori Yoshikawa, Yutaka Sato, Naoki Mori
Intraspecific variations in specialized metabolites play a crucial role in the adaptive response to diverse environments. Two major subspecies, japonica and indica, are observed in Asian cultivated rice (Oryza sativa L.). Previously, we identified (3R)-β-tyrosine, a novel nonproteinogenic β-amino acid in plants, along with the enzyme tyrosine aminomutase (TAM1), required for β-tyrosine biosynthesis, in the japonica cultivar Nipponbare. Notably, TAM1 and β-tyrosine preferentially distributed in japonica cultivars compared with indica cultivars. Considering its phytotoxicity and antimicrobial activity, intraspecific variations in β-tyrosine may contribute to defensive potentials of japonica rice. Investigation of the evolutionary trajectory of TAM1 and β-tyrosine should enhance our understanding of evolution of rice defense. However, their distribution patterns in Oryza rufipogon, the direct ancestor of O. sativa, remain unclear. Therefore, in this study, we extensively examined TAM1 presence/absence and β-tyrosine contents involving 110 genetically and geographically diverse O. rufipogon and revealed that they are characteristically observed in the ancestral subpopulation of japonica rice, while being absent or slightly accumulated in other subpopulations. Thus, we conclude that TAM1 and β-tyrosine in japonica rice are likely derived from its ancestral subpopulation. Furthermore, the high and low TAM1 possession rates and β-tyrosine contents in japonica and indica rice, respectively, could be attributed to distribution patterns of TAM1 and β-tyrosine in their ancestral subpopulations. This study provides fundamental insights into evolution of rice defense.
{"title":"β-Tyrosine and its biosynthetic enzyme TAM1 are predominantly distributed in the ancestral subpopulation of japonica rice in Oryza rufipogon.","authors":"Shunta Sakamoto, Takanori Yoshikawa, Yutaka Sato, Naoki Mori","doi":"10.1266/ggs.24-00017","DOIUrl":"https://doi.org/10.1266/ggs.24-00017","url":null,"abstract":"<p><p>Intraspecific variations in specialized metabolites play a crucial role in the adaptive response to diverse environments. Two major subspecies, japonica and indica, are observed in Asian cultivated rice (Oryza sativa L.). Previously, we identified (3R)-β-tyrosine, a novel nonproteinogenic β-amino acid in plants, along with the enzyme tyrosine aminomutase (TAM1), required for β-tyrosine biosynthesis, in the japonica cultivar Nipponbare. Notably, TAM1 and β-tyrosine preferentially distributed in japonica cultivars compared with indica cultivars. Considering its phytotoxicity and antimicrobial activity, intraspecific variations in β-tyrosine may contribute to defensive potentials of japonica rice. Investigation of the evolutionary trajectory of TAM1 and β-tyrosine should enhance our understanding of evolution of rice defense. However, their distribution patterns in Oryza rufipogon, the direct ancestor of O. sativa, remain unclear. Therefore, in this study, we extensively examined TAM1 presence/absence and β-tyrosine contents involving 110 genetically and geographically diverse O. rufipogon and revealed that they are characteristically observed in the ancestral subpopulation of japonica rice, while being absent or slightly accumulated in other subpopulations. Thus, we conclude that TAM1 and β-tyrosine in japonica rice are likely derived from its ancestral subpopulation. Furthermore, the high and low TAM1 possession rates and β-tyrosine contents in japonica and indica rice, respectively, could be attributed to distribution patterns of TAM1 and β-tyrosine in their ancestral subpopulations. This study provides fundamental insights into evolution of rice defense.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Response regulators (RRs), which are implicated in various developmental processes as well as environmental responses by acting as either positive or negative regulators, are crucial components of cytokinin signaling in plants. We characterized 36 RRs using in silico and computational analyses of publicly available data. A comprehensive analysis of OsRR family members was performed covering their physicochemical properties, chromosomal distribution, subcellular localization, phylogeny, gene structure, distribution of conserved motifs and domains, and gene duplication events. Gene Ontology analysis results indicate that 22 OsRR genes contribute mainly to the cytokinin-response and signal transduction. Predicted cis-elements in RRs promoter sequences related to phytohormones and abiotic stresses indicate that RRs are involved in hormonal and environmental responses as described in previous studies. MicroRNA (miRNA) target analysis showed that 148 miRNAs target 29 OsRR genes. In some cases, those RRs are targets of the same miRNA group, and may be controlled by common stimulus responses. Based on the analysis of publicly available gene expression data, OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, OsPRR73, and OsPRR95 were found to be involved in response to abiotic stresses. Using quantitative reverse transcription polymerase chain reaction (qPCR) we confirmed that those RRs, namely OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, and OsPRR73, are involved in the response to salinity, osmotic, alkaline and wounding stresses, and can potentially be used as models to understand molecular mechanisms underlying stress responsiveness.
{"title":"Identification of abiotic stress responsive genes: A genome wide analysis of the cytokinin response regulator gene family in rice.","authors":"Setu Rani Saha, S M Shahinul Islam, Kimiko Itoh","doi":"10.1266/ggs.24-00068","DOIUrl":"https://doi.org/10.1266/ggs.24-00068","url":null,"abstract":"<p><p>Response regulators (RRs), which are implicated in various developmental processes as well as environmental responses by acting as either positive or negative regulators, are crucial components of cytokinin signaling in plants. We characterized 36 RRs using in silico and computational analyses of publicly available data. A comprehensive analysis of OsRR family members was performed covering their physicochemical properties, chromosomal distribution, subcellular localization, phylogeny, gene structure, distribution of conserved motifs and domains, and gene duplication events. Gene Ontology analysis results indicate that 22 OsRR genes contribute mainly to the cytokinin-response and signal transduction. Predicted cis-elements in RRs promoter sequences related to phytohormones and abiotic stresses indicate that RRs are involved in hormonal and environmental responses as described in previous studies. MicroRNA (miRNA) target analysis showed that 148 miRNAs target 29 OsRR genes. In some cases, those RRs are targets of the same miRNA group, and may be controlled by common stimulus responses. Based on the analysis of publicly available gene expression data, OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, OsPRR73, and OsPRR95 were found to be involved in response to abiotic stresses. Using quantitative reverse transcription polymerase chain reaction (qPCR) we confirmed that those RRs, namely OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, and OsPRR73, are involved in the response to salinity, osmotic, alkaline and wounding stresses, and can potentially be used as models to understand molecular mechanisms underlying stress responsiveness.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.
{"title":"Development of polymorphic microsatellite markers for distylous-homostylous Primula secundiflora (Primulaceae) using HiSeq sequencing.","authors":"Hua-Ying Sun, Wen-Ping Zhang, Wei Zhou, Zhi-Kun Wu, Lan-Ping Zheng","doi":"10.1266/ggs.23-00340","DOIUrl":"10.1266/ggs.23-00340","url":null,"abstract":"<p><p>Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140331648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-10Epub Date: 2024-04-18DOI: 10.1266/ggs.23-00320
Jing Qu, Shuai Dang, Yuan-Yuan Sun, Tao Zhang, Hai Jiang, Hong-Zhao Lu
Homeostasis is essential for muscle repair and regeneration after skeletal muscle exercise. This study investigated the role of methyltransferase-like 21C (METTL21C) in skeletal muscle of mice after exercise and the potential mechanism. First, muscle samples were collected at 2, 4 and 6 weeks after exercise, and liver glycogen, muscle glycogen, blood lactic acid and triglyceride were assessed. Moreover, the expression levels of autophagy markers and METTL21C in skeletal muscle were analyzed. The results showed that the expression levels of METTL21C and MYH7 in the gastrocnemius muscle of mice in the exercise group were significantly higher after exercise than those in the control group, which suggested that long-term exercise promoted the formation of slow-twitch muscle fibers in mouse skeletal muscle. Likewise, the autophagy capacity was enhanced with the prolongation of exercise in muscles. The findings were confirmed in mouse C2C12 cells. We discovered that knockdown of Mettl21c reduced the expression of MYH7 and the autophagy level in mouse myoblasts. These findings indicate that METTL21C promotes skeletal muscle homeostasis after exercise by enhancing autophagy, and also contributes to myogenic differentiation and the formation of slow muscle fibers.
{"title":"METTL21C mediates autophagy and formation of slow-twitch muscle fibers in mice after exercise.","authors":"Jing Qu, Shuai Dang, Yuan-Yuan Sun, Tao Zhang, Hai Jiang, Hong-Zhao Lu","doi":"10.1266/ggs.23-00320","DOIUrl":"10.1266/ggs.23-00320","url":null,"abstract":"<p><p>Homeostasis is essential for muscle repair and regeneration after skeletal muscle exercise. This study investigated the role of methyltransferase-like 21C (METTL21C) in skeletal muscle of mice after exercise and the potential mechanism. First, muscle samples were collected at 2, 4 and 6 weeks after exercise, and liver glycogen, muscle glycogen, blood lactic acid and triglyceride were assessed. Moreover, the expression levels of autophagy markers and METTL21C in skeletal muscle were analyzed. The results showed that the expression levels of METTL21C and MYH7 in the gastrocnemius muscle of mice in the exercise group were significantly higher after exercise than those in the control group, which suggested that long-term exercise promoted the formation of slow-twitch muscle fibers in mouse skeletal muscle. Likewise, the autophagy capacity was enhanced with the prolongation of exercise in muscles. The findings were confirmed in mouse C2C12 cells. We discovered that knockdown of Mettl21c reduced the expression of MYH7 and the autophagy level in mouse myoblasts. These findings indicate that METTL21C promotes skeletal muscle homeostasis after exercise by enhancing autophagy, and also contributes to myogenic differentiation and the formation of slow muscle fibers.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying chromatin regulation with high-resolution genome-wide analyses. Since newly generated genome-wide data are often compared with publicly available datasets, expanding our dataset repertoire will be beneficial for the field. Information on transcription start sites (TSSs) determined at base pair resolution is essential for elucidating mechanisms of transcription and related chromatin regulation, yet no datasets that cover two different cell types are available. Here, we present a CAGE (cap analysis of gene expression) dataset for a-cells and α-cells grown in defined and rich media. Cell type-specific genes were differentially expressed as expected, ensuring the reliability of the data. Some of the differentially expressed TSSs were medium-specific or detected due to unrecognized chromosome rearrangement. By comparing the CAGE data with a high-resolution nucleosome map, major TSSs were primarily found in +1 nucleosomes, with a peak approximately 30 bp from the promoter-proximal end of the nucleosome. The dataset is available at DDBJ/GEA.
{"title":"A budding yeast CAGE dataset comprising two cell types.","authors":"Kei Kawakami, Shin-Ichi Maeda, Yoshiko Tanimoto, Mitsuhiro Shimizu, Hiroaki Kato","doi":"10.1266/ggs.24-00020","DOIUrl":"10.1266/ggs.24-00020","url":null,"abstract":"<p><p>The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying chromatin regulation with high-resolution genome-wide analyses. Since newly generated genome-wide data are often compared with publicly available datasets, expanding our dataset repertoire will be beneficial for the field. Information on transcription start sites (TSSs) determined at base pair resolution is essential for elucidating mechanisms of transcription and related chromatin regulation, yet no datasets that cover two different cell types are available. Here, we present a CAGE (cap analysis of gene expression) dataset for a-cells and α-cells grown in defined and rich media. Cell type-specific genes were differentially expressed as expected, ensuring the reliability of the data. Some of the differentially expressed TSSs were medium-specific or detected due to unrecognized chromosome rearrangement. By comparing the CAGE data with a high-resolution nucleosome map, major TSSs were primarily found in +1 nucleosomes, with a peak approximately 30 bp from the promoter-proximal end of the nucleosome. The dataset is available at DDBJ/GEA.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140049242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-29Epub Date: 2024-02-21DOI: 10.1266/ggs.23-00287
Takayuki Suzuki
The developmental mechanisms of limb buds have been studied in developmental biology as an excellent model of pattern formation. Chick embryos have contributed to the discovery of new principles in developmental biology, as it is easy to observe live embryos and manipulate embryonic tissues. Herein, I outline recent findings and future issues over the next decade regarding three themes, based on my research: limb positioning, proximal-distal limb elongation and digit identity determination. First, how hindlimb position is determined at the molecular level is described, with a focus on the transforming growth factor-β signaling molecule GDF11. Second, I explain how the cell population in the limb bud deforms with developmental progress, shaping the limb bud with elongation along the proximal-distal axis. Finally, I describe the developmental mechanisms that determine digit identity through the interdigits.
{"title":"Current research on mechanisms of limb bud development, and challenges for the next decade.","authors":"Takayuki Suzuki","doi":"10.1266/ggs.23-00287","DOIUrl":"10.1266/ggs.23-00287","url":null,"abstract":"<p><p>The developmental mechanisms of limb buds have been studied in developmental biology as an excellent model of pattern formation. Chick embryos have contributed to the discovery of new principles in developmental biology, as it is easy to observe live embryos and manipulate embryonic tissues. Herein, I outline recent findings and future issues over the next decade regarding three themes, based on my research: limb positioning, proximal-distal limb elongation and digit identity determination. First, how hindlimb position is determined at the molecular level is described, with a focus on the transforming growth factor-β signaling molecule GDF11. Second, I explain how the cell population in the limb bud deforms with developmental progress, shaping the limb bud with elongation along the proximal-distal axis. Finally, I describe the developmental mechanisms that determine digit identity through the interdigits.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139930833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lack of pigmentation in seed coats of soybean is caused by natural RNA silencing of chalcone synthase (CHS) genes. This phenomenon is an evolutionary consequence of structural changes in DNA that resulted in the production of double-stranded RNAs (dsRNAs) that trigger RNA degradation. Here we determined that a mutant with pigmented seed coats derived from a cultivar that lacked the pigmentation had a deletion between DNA regions ICHS1 and a cytochrome P450 gene; the deletion included GmIRCHS, a candidate gene that triggers CHS RNA silencing via production of CHS dsRNAs. We also characterized CHS short interfering RNAs (siRNAs) produced in the wild-type seed coats that had CHS RNA silencing. Phased 21-nt CHS siRNAs were detected in all 21 phases and were widely distributed in exon 2 of CHS7, which indicates commonality in the pattern of RNA degradation in natural CHS RNA silencing between distantly related species. These results with the similarities in the rearrangements found in spontaneous mutants suggest that the structural organization that generates dsRNAs that trigger phased siRNA production is vulnerable to further structural changes, which eventually abolish the induction of RNA silencing.
{"title":"Pigmentation of soybean seed coats via a mutation that abolishes production of multiple-phased siRNAs of chalcone synthase genes.","authors":"Mashiro Yuhazu, Shun Mikuriya, Ayumi Mori, Maria Stefanie Dwiyanti, Mineo Senda, Akira Kanazawa","doi":"10.1266/ggs.23-00260","DOIUrl":"10.1266/ggs.23-00260","url":null,"abstract":"<p><p>Lack of pigmentation in seed coats of soybean is caused by natural RNA silencing of chalcone synthase (CHS) genes. This phenomenon is an evolutionary consequence of structural changes in DNA that resulted in the production of double-stranded RNAs (dsRNAs) that trigger RNA degradation. Here we determined that a mutant with pigmented seed coats derived from a cultivar that lacked the pigmentation had a deletion between DNA regions ICHS1 and a cytochrome P450 gene; the deletion included GmIRCHS, a candidate gene that triggers CHS RNA silencing via production of CHS dsRNAs. We also characterized CHS short interfering RNAs (siRNAs) produced in the wild-type seed coats that had CHS RNA silencing. Phased 21-nt CHS siRNAs were detected in all 21 phases and were widely distributed in exon 2 of CHS7, which indicates commonality in the pattern of RNA degradation in natural CHS RNA silencing between distantly related species. These results with the similarities in the rearrangements found in spontaneous mutants suggest that the structural organization that generates dsRNAs that trigger phased siRNA production is vulnerable to further structural changes, which eventually abolish the induction of RNA silencing.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139930835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The freezing-thawing (F/T) method for fusing giant unilamellar vesicles (GUVs) can provide substrates, enzymes and membrane material simultaneously and repetitively, and is useful for constructing a recursive model of an artificial cell. However, enzymatic efficiency after F/T is reduced due to rupture of the GUVs and leakage of the inner solution during F/T. Previously, liposomes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and a negatively charged lipid, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), showed lower rupture and leakage rates during F/T. In this study, we investigated the effect of POPG on the supply of components required for T7 RNA polymerase reactions via F/T by flow cytometry analysis. We found that the addition of POPG to liposome preparations reduced the efficiency of RNA synthesis. In addition, DNA was concentrated during F/T and RNA synthesis occurred after F/T in liposomes composed of POPC and POPG. Our results provide new insights for more efficient supply of substrates and enzymes by the F/T method, thereby increasing the utility of the F/T method for the construction of recursive bioreactors.
{"title":"RNA synthesis in liposomes with negatively charged lipids after fusion via freezing-thawing.","authors":"Gakushi Tsuji, Ayu Shimomura, Shota Fukuoka, Masaya Oki","doi":"10.1266/ggs.23-00297","DOIUrl":"10.1266/ggs.23-00297","url":null,"abstract":"<p><p>The freezing-thawing (F/T) method for fusing giant unilamellar vesicles (GUVs) can provide substrates, enzymes and membrane material simultaneously and repetitively, and is useful for constructing a recursive model of an artificial cell. However, enzymatic efficiency after F/T is reduced due to rupture of the GUVs and leakage of the inner solution during F/T. Previously, liposomes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and a negatively charged lipid, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), showed lower rupture and leakage rates during F/T. In this study, we investigated the effect of POPG on the supply of components required for T7 RNA polymerase reactions via F/T by flow cytometry analysis. We found that the addition of POPG to liposome preparations reduced the efficiency of RNA synthesis. In addition, DNA was concentrated during F/T and RNA synthesis occurred after F/T in liposomes composed of POPC and POPG. Our results provide new insights for more efficient supply of substrates and enzymes by the F/T method, thereby increasing the utility of the F/T method for the construction of recursive bioreactors.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139930836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}