Functional Analysis of the Promoter of a Female-Specific Cucumber CsACS1G Gene
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The basic underlying problem in reverse engineering of gene regulatory networks from gene expression data is that the expression of a gene encoding the regulator provides only limited information about its protein activity. The proteins, which result from translation, are subject to stringent posttranscriptional control and modification. Often, it is only the modified version of the protein that is capable of activating or repressing its regulatory targets. At present there exists no reliable high-throughput technology to measure the protein activity levels in real-time, and therefore they are, so-to-say, lost in translation. However, these activity levels can be recovered by studying the gene expression of their targets. Here, we describe a computational approach to predict temporal regulator activity levels from the gene expression of its transcriptional targets in a network motif with one regulator and many targets. We consider an example of an SOS repair system, and computationally infer the regulator activity of its master repressor, LexA. The reconstructed activity profile of LexA exhibits a behavior that is similar to the experimentally measured profile of this repressor: after UV irradiation, the amount of LexA substantially decreases within a few minutes, followed by a recovery to its normal level. Our approach can easily be applied to known single-input motifs in other organisms.
Repressor lexA
YY1
GATAD2B
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Thellungiella salsuginea (先前 T。halophila ) ，种仔细与 Arabidopsis (Arabidopsis thaliana ) 有关，是容忍的不仅高腌层次，而且到寒心，结冰，并且臭氧。这里，我们报导那 T。salsuginea 也比 Arabidopsis 显示出更大的热忍耐。我们识别了 T。作为基因，那能授与的 salsuginea HsfA1d (TsHsfA1d ) 在 Arabidopsis 上标记热忍耐。TsHsfA1d 经由全身的 cDNA 被识别从许多 heat-stress-related T 之中狩猎的过去表示的基因(狐狸) 。salsuginea cDNAs。转基因的 Arabidopsis overexpressing TsHsfA1d 在正常生长温度下面在 Arabidopsis AtHsfA1 regulon 显示出许多基因的组成的起来规定。在 Arabidopsis 叶肉原物， TsHsfA1d 在原子核和细胞质是局部性的。TsHsfA1d 也与 AtHSP90 交往了，它否定地由在细胞质形成 HsfA1HSP90 建筑群调整 AtHsfA1s。TsHsfA1d 的部分原子本地化在正常温度在转基因的植物导致了 AtHsfA1d regulon 的表示，是可能的。我们也发现转基因的 Arabidopsis 植物 overexpressing AtHsfA1d 比野类型的植物更热容忍、起来调整 HsfA1d regulon 的表示在 TsHsfA1d-overexpressing 植物被观察。我们建议 TsHsfA1d 和 AtHsfA1d 的产品作为 Arabidopsis 热压力反应的积极管理者工作并且将为在另外的植物的热压力忍耐的改进有用。
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The basic underlying problem in reverse engineering of gene regulatory networks from gene expression data is that the expression of a gene encoding the regulator provides only limited information about its protein activity. The proteins, which result from translation, are subject to stringent posttranscriptional control and modification. Often, it is only the modified version of the protein that is capable of activating or repressing its regulatory targets. At present there exists no reliable high-throughput technology to measure the protein activity levels in real-time, and therefore they are, so-to-say, lost in translation. However, these activity levels can be recovered by studying the gene expression of their targets. Here, we describe a computational approach to predict temporal regulator activity levels from the gene expression of its transcriptional targets in a network motif with one regulator and many targets. We consider an example of an SOS repair system, and computationally infer the regulator activity of its master repressor, LexA. The reconstructed activity profile of LexA exhibits a behavior that is similar to the experimentally measured profile of this repressor: after UV irradiation, the amount of LexA substantially decreases within a few minutes, followed by a recovery to its normal level. Our approach can easily be applied to known single-input motifs in other organisms.
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YY1
GATAD2B
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Pathogen perception by plants is mediated by plasma membrane-localized immune receptors that have varied extracellular domains. Lectin receptor kinases (LecRKs) are among these receptors and are subdivided into 3 classes, C-type LecRKs (C-LecRKs), L-type LecRKs (L-LecRKs) and G-type LecRKs (G-LecRKs). While C-LecRKs are represented by one or two members in all plant species investigated and have unknown functions, L-LecRKs have been characterized in a few plant species and have been shown to play roles in plant defense against pathogens. Whereas Arabidopsis G-LecRKs have been characterized, this family of LecRKs has not been studied in tomato.This investigation updates the current characterization of Arabidopsis G-LecRKs and characterizes the tomato G-LecRKs, using LecRKs from the monocot rice and the basal eudicot columbine to establish a basis for comparisons between the two core eudicots. Additionally, revisiting parameters established for Arabidopsis nomenclature for LecRKs is suggested for both Arabidopsis and tomato. Moreover, using phylogenetic analysis, we show the relationship among and between members of G-LecRKs from all three eudicot plant species. Furthermore, investigating presence of motifs in G-LecRKs we identified conserved motifs among members of G-LecRKs in tomato and Arabidopsis, with five present in at least 30 of the 38 Arabidopsis members and in at least 45 of the 73 tomato members.This work characterized tomato G-LecRKs and added members to the currently characterized Arabidopsis G-LecRKs. Additionally, protein sequence analysis showed an expansion of this family in tomato as compared to Arabidopsis, and the existence of conserved common motifs in the two plant species as well as conserved species-specific motifs.
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A phenotype-based screening of the T1 transgenic Arabidopsis population transformed by overexpression constructs of the entire poplar MYB transcription factor family found that overexpression of a poplar MYB transcription factor, PtrMYB012, in Arabidopsis resulted in upwardly curled rosette leaves, dwarfism and male sterility. Sequence analysis identified that PtrMYB012 is homologous to the Arabidopsis GAMYB genes (e.g., AtMYB65 and AtMYB33). Gene expression analysis revealed that PtrMYB012 is specifically expressed in floral tissues, especially in male catkins, similar to AtMYB65. It was well known that Arabidopsis GAMYBs are negatively regulated by microRNA159 (miR159) during vegetative growth; thus, the typical phenotypes of upwardly curled leaves, dwarfism and male sterility were only shown in overexpression of GAMYBs with mutations in the miR159 target sequence. To confirm our phenotypic consequences, we independently re-produced transgenic Arabidopsis plants overexpressing PtrMYB012 without mutations in the miR159 target sequence. The resulting 35 S::PtrMYB012 Arabidopsis plants phenocopied the previous transgenic Arabidopsis plants, suggesting that PtrMYB012 is probably not a target of Arabidopsis miR159 despite containing the conserved miR159 target sequence. To gain further insight, we produced transgenic poplars overexpressing the intact PtrMYB012. As a result, no conspicuous phenotype was found in 35 S::PtrMYB012 poplar plants. These results suggest that PtrMYB012 transcripts are down-regulated by miR159 in poplar but not in Arabidopsis. Indeed, subsequent 5'-RACE analysis confirmed that PtrMYB012 transcripts are completely degraded in poplar, probably by miR159, but not in Arabidopsis. These results suggest that species-specific family members of miR159 are important for the regulation of normal growth and development in plants.
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In Arabidopsis thaliana (Arabidopsis), nonhost resistance (NHR) is influenced by both leaf age and the moment of inoculation. While the circadian clock and photoperiod have been linked to the time-dependent regulation of NHR in Arabidopsis, the mechanism underlying leaf age-dependent NHR remains unclear. In this study, we investigated leaf age-dependent NHR to Pyricularia oryzae in Arabidopsis. Our findings revealed that this NHR type is regulated by both miR156-dependent and miR156-independent pathways. To identify the key players, we utilized rice-FOX Arabidopsis lines and identified the rice HD-Zip I OsHOX6 gene. Notably, OsHOX6 expression confers robust NHR to P. oryzae and Colletotrichum nymphaeae in Arabidopsis, with its effect being contingent upon leaf age. Moreover, we explored the role of AtHB7 and AtHB12, the Arabidopsis closest homologues of OsHOX6, by studying mutants and overexpressors in Arabidopsis-C. higginsianum interaction. AtHB7 and AtHB12 were found to contribute to both penetration resistance and post-penetration resistance to C. higginsianum in a leaf age- and time-dependent manner. These findings highlight the involvement of HD-Zip I AtHB7 and AtHB12, well-known regulators of development and abiotic stress responses, in biotic stress responses in Arabidopsis.
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在 Arabidopsis 的南船座基因在控制植物机关尺寸起一个关键作用。决定它的功能是在米饭的 ortholog，从米饭纸巾的通常认为的南船座 orthologous 基因被孤立并且指定了为 OsARGOS。这基因在米饭染色体有仅仅一个拷贝。OsARGOS 抄本在大多数米饭纸巾被检测，特别地在年轻纸巾，并且它的表示被植物生长素或细胞激动素的申请在米饭幼苗导致。表示 OsARGOS 的 Arabidopsis 植物导致了更大的机关，例如叶子和 siliques，与野类型的植物相比。有趣地，根生长也在这些转基因的 Arabidopsis 植物被提高。因此，转基因的植物的生物资源显著地被增加。进一步的分析揭示了那，与在 Arabidopsis 的 ARGOS 和像南船座的基因不同， OsARGOS 基因由房间数字和房间尺寸的增加扩大了机关。另外，抄本调整细胞分割或细胞生长的联系尺寸的基因在上面的几个器官铺平在转基因的 Arabidopsis 植物调整了。我们也转了到米饭的 OsARGOS 基因，而是转基因的植物没与控制植物相比在机关尺寸显示出任何变化。在机关尺寸控制的 OsARGOS 的功能在米饭取决于另外的尺寸管理者，是可能的。在 Arabidopsis 的 OsARGOS 的表达式可以激活在植物生长和开发的功课期间控制房间增长和房间扩大的发信号的小径。自从 OsARGOS 原因机关增大的表示，通过遗传工程的这基因的潜在的申请可以显著地在农业实践改进生物资源的生产。
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SUMMARY The leap from simple unicellularity to complex multicellularity remains one of life's major enigmas. The origins of metazoan developmental gene regulatory mechanisms are sought by analyzing gene regulation in extant eumetazoans, sponges, and unicellular organisms. The main hypothesis of this manuscript is that, developmental enhancers evolved from unicellular inducible promoters that diversified the expression of regulatory genes during metazoan evolution. Promoters and enhancers are functionally similar; both can regulate the transcription of distal promoters and both direct local transcription. Additionally, enhancers have experimentally characterized structural features that reveal their origin from inducible promoters. The distal co‐operative regulation among promoters identified in unicellular opisthokonts possibly represents the precursor of distal regulation of promoters by enhancers. During metazoan evolution, constitutive‐type promoters of regulatory genes would have acquired novel receptivity to distal regulatory inputs from promoters of inducible genes that eventually specialized as enhancers. The novel regulatory interactions would have caused constitutively expressed genes controlling differential gene expression in unicellular organisms to become themselves differentially expressed. The consequence of the novel regulatory interactions was that regulatory pathways of unicellular organisms became interlaced and ultimately evolved into the intricate developmental gene regulatory networks (GRNs) of extant metazoans.
Multicellular organism
Gene regulatory network
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During sporulation, Bacillus thuringiensis produces intracellular, crystalline inclusions comprised of a mixture of protoxins active on insect larvae. A major class of these protoxin genes, designated cry1, is transcribed from two overlapping promoters (BtI and BtII) utilizing RNA polymerase containing sporulation sigma factors sigma(E) and sigma(K), respectively. Fusions of these promoters to lacZ were constructed in order to analyze transcription patterns. Mutations within the -10 region of the BtII promoter (within the spacer region of the BtI promoter) which departed from the consensus -10 sequence for either sigma(E) or sigma(K) resulted in inactivation of transcription from BtII and a fivefold stimulation of transcription from BtI. In contrast, transcription from both promoters was inhibited with a change to the sigma(E) consensus. One of the "promoter-up" mutations was fused to the cry1Ac1 gene, and enhanced transcription was confirmed by Northern blotting. There was an increase in the accumulation of Cry1Ac antigen at early but not later times in sporulation in the mutant. This shift was due to the rapid turnover of much of the excessively accumulated protoxin at the early times as measured by pulse-chase labeling. As a result of the turnover and the inactivation of the BtII promoter, the mutant produced smaller inclusions which contained two- to threefold-less protoxin than inclusions from the wild type. Promoter overlap is a mechanism for modulating protoxin synthesis, thus ensuring the efficient packaging of these protoxins into inclusions.
Bacillus thuringiensis
Bacillus (shape)
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