scholarly journals Molecular mechanisms for the plant promoter efficiency correction

Author(s):  
R. A. Komakhin ◽  
L. N. Efremova ◽  
S. R. Strelnikova

The mutations determining functional differences between two highly identical promoters from the chickweed plant were identified. These mutations lead to the formation of hypoosmolarity-responsive cis-element within core promoter and its specific positioning relative to the other cis-elements.

2020 ◽  
Author(s):  
Fumiko Matsukawa Usami ◽  
Masaki Arata ◽  
Dongbo Shi ◽  
Sanae Oka ◽  
Yoko Higuchi ◽  
...  

SummaryThe molecular mechanisms by which cilia orientation is coordinated within and between multiciliated cells (MCCs) is not fully understood. By observing the orientation of basal bodies (BB) in MCCs of mouse oviducts, here, we show that Celsr1, a planar cell polarity (PCP) factor involved in tissue polarity regulation, is dispensable for determining BB orientation in individual cells, whereas CAMSAP3, a microtubule minus-end regulator, is critical for this process but not for PCP. MCCs exhibit a characteristic BB orientation and microtubule gradient along the tissue axis, and these intracellular polarities were maintained in the cells lacking Celsr1, although the intercellular coordination of the polarities was partly disrupted. On the other hand, CAMSAP3 regulated the assembly of microtubules interconnecting BBs by localizing at the BBs, and its mutation led to disruption of intracellular coordination of BB orientation, but not affecting PCP factor localization. Thus, both Celsr1 and CAMSAP3 are responsible for BB orientation but in distinct ways; and therefore, their cooperation should be critical for generating functional multiciliated tissues.


Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 291 ◽  
Author(s):  
Hannah A. Nicolas ◽  
Marie-Andrée Akimenko ◽  
Frédérique Tesson

The lamin A/C (LMNA) gene codes for nuclear intermediate filaments constitutive of the nuclear lamina. LMNA has 12 exons and alternative splicing of exon 10 results in two major isoforms—lamins A and C. Mutations found throughout the LMNA gene cause a group of diseases collectively known as laminopathies, of which the type, diversity, penetrance and severity of phenotypes can vary from one individual to the other, even between individuals carrying the same mutation. The majority of the laminopathies affect cardiac and/or skeletal muscles. The underlying molecular mechanisms contributing to such tissue-specific phenotypes caused by mutations in a ubiquitously expressed gene are not yet well elucidated. This review will explore the different phenotypes observed in established models of striated muscle laminopathies and their respective contributions to advancing our understanding of cardiac and skeletal muscle-related laminopathies. Potential future directions for developing effective treatments for patients with lamin A/C mutation-associated cardiac and/or skeletal muscle conditions will be discussed.


1995 ◽  
Vol 269 (6) ◽  
pp. C1433-C1449 ◽  
Author(s):  
P. A. Piepenhagen ◽  
W. J. Nelson

Structural and functional differences among epithelial cells of kidney nephrons may be regulated by variations in cell-to-cell (cell-cell) and cell-to-substratum (cell-substratum) junctions. Using immunofluorescence microscopy, we demonstrate that the cadherin-associated proteins alpha- and beta-catenin are localized to basolateral membranes of cells in all nephron segments, whereas plakoglobin, a protein associated with both classical and desmosomal cadherins, is localized to noninterdigitated lateral membranes in the distal half of the nephron where it colocalizes with desmoplakin and cytokeratin K8. Plakoglobin is also present in capillary endothelial cells where staining for the other catenins and desmosomal proteins is not observed. Immunofluorescence for laminin A and alpha 6-integrin, proteins that mediate cell-substratum contacts, reveal no correlations with the other staining patterns observed. These data indicate that plakoglobin and beta-catenin subserve distinct functions in cell-cell adhesion and suggest that E-cadherin-mediated contacts generate a basal level of cell-cell adhesion, whereas desmosomal junctions provide additional strength to cell-cell contacts in the distal nephron.


2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Yan Chen ◽  
Ying Wang ◽  
Ming Liu ◽  
Junze Qu ◽  
Mingdong Yao ◽  
...  

ABSTRACTSaccharomyces cerevisiaeis an established cell factory for production of terpenoid pharmaceuticals and chemicals. Numerous studies have demonstrated that deletion or overexpression of off-pathway genes in yeast can improve terpenoid production. The deletion ofYPL062WinS. cerevisiae, in particular, has benefitted carotenoid production by channeling carbon toward carotenoid precursors acetyl coenzyme A (acetyl-CoA) and mevalonate. The genetic function ofYPL062Wand the molecular mechanisms for these benefits are unknown. In this study, we systematically examined this gene deletion to uncover the gene function and its molecular mechanism. RNA sequencing (RNA-seq) analysis uncovered thatYPL062Wdeletion upregulated the pyruvate dehydrogenase bypass, the mevalonate pathway, heterologous expression of galactose (GAL) promoter-regulated genes, energy metabolism, and membrane composition synthesis. Bioinformatics analysis and serial promoter deletion assay revealed thatYPL062Wfunctions as a core promoter forALD6and that the expression level ofALD6is negatively correlated to terpenoid productivity. We demonstrate that ΔYPL062Wincreases the production of all major terpenoid classes (C10, C15, C20, C30, and C40). Our study not only elucidated the biological function ofYPL062Wbut also provided a detailed methodology for understanding the mechanistic aspects of strain improvement.IMPORTANCEAlthough computational and reverse metabolic engineering approaches often lead to improved gene deletion mutants for cell factory engineering, the systems level effects of such gene deletions on the production phenotypes have not been extensively studied. Understanding the genetic and molecular function of such gene alterations on production strains will minimize the risk inherent in the development of large-scale fermentation processes, which is a daunting challenge in the field of industrial biotechnology. Therefore, we established a detailed experimental and systems biology approach to uncover the molecular mechanisms ofYPL062Wdeletion inS. cerevisiae, which is shown to improve the production of all terpenoid classes. This study redefines the genetic function ofYPL062W, demonstrates a strong correlation betweenYPL062Wand terpenoid production, and provides a useful modification for the creation of terpenoid production platform strains. Further, this study underscores the benefits of detailed and systematic characterization of the metabolic effects of genetic alterations on engineered biosynthetic factories.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Aaron B. Bogutz ◽  
Julie Brind’Amour ◽  
Hisato Kobayashi ◽  
Kristoffer N. Jensen ◽  
Kazuhiko Nakabayashi ◽  
...  

AbstractImprinted genes are expressed from a single parental allele, with the other allele often silenced by DNA methylation (DNAme) established in the germline. While species-specific imprinted orthologues have been documented, the molecular mechanisms underlying the evolutionary switch from biallelic to imprinted expression are unknown. During mouse oogenesis, gametic differentially methylated regions (gDMRs) acquire DNAme in a transcription-guided manner. Here we show that oocyte transcription initiating in lineage-specific endogenous retroviruses (ERVs) is likely responsible for DNAme establishment at 4/6 mouse-specific and 17/110 human-specific imprinted gDMRs. The latter are divided into Catarrhini- or Hominoidea-specific gDMRs embedded within transcripts initiating in ERVs specific to these primate lineages. Strikingly, imprinting of the maternally methylated genes Impact and Slc38a4 was lost in the offspring of female mice harboring deletions of the relevant murine-specific ERVs upstream of these genes. Our work reveals an evolutionary mechanism whereby maternally silenced genes arise from biallelically expressed progenitors.


Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1407
Author(s):  
Larisa N. Efremova ◽  
Svetlana R. Strelnikova ◽  
Guzel R. Gazizova ◽  
Elena A. Minkina ◽  
Roman A. Komakhin

Synthetic promoters are vital for genetic engineering-based strategies for crop improvement, but effective methodologies for their creation and systematic testing are lacking. We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap analysis of gene expression method, we detected no differences in the structure of the transcription start sites for either promoter in transgenic plants. For both promoters, we used fine-scale deletion analysis to identify 160 bp-long sequences that retain the unique properties of each promoter. With the use of chimeric promoters and directed mutagenesis, we demonstrated that the superiority of the pro-SmAMP1 promoter for Agrobacterium-mediated infiltration is caused by the proline-inducible ACTCAT cis-element strictly positioned relative to the TATA box in the core promoter. Surprisingly, the ACTCAT cis-element not only activated but also suppressed the efficiency of the pro-SmAMP1 promoter under proline stress. The absence of the ACTCAT cis-element and CAANNNNATC motif (negative regulator) in the pro-SmAMP2 promoter provided a more constitutive gene expression profile and better selection of transgenic cells on selective medium. We created a new synthetic promoter that enjoys high effectiveness both in transient expression and in selection of transgenic cells. Intact promoters with differing properties and high degrees of sequence identity may thus be used as a basis for the creation of new synthetic promoters for precise and coordinated gene expression.


2016 ◽  
Vol 60 (3) ◽  
pp. 1702-1707 ◽  
Author(s):  
Parham Sendi ◽  
Martina Furitsch ◽  
Stefanie Mauerer ◽  
Carlos Florindo ◽  
Barbara C. Kahl ◽  
...  

Streptococcus agalactiae(group BStreptococcus[GBS]) is a leading cause of sepsis in neonates. The rate of invasive GBS disease in nonpregnant adults also continues to climb. Aminoglycosides alone have little or no effect on GBS, but synergistic killing with penicillin has been shownin vitro. High-level gentamicin resistance (HLGR) in GBS isolates, however, leads to the loss of a synergistic effect. We therefore performed a multicenter study to determine the frequency of HLGR GBS isolates and to elucidate the molecular mechanisms leading to gentamicin resistance. From eight centers in four countries, 1,128 invasive and colonizing GBS isolates were pooled and investigated for the presence of HLGR. We identified two strains that displayed HLGR (BSU1203 and BSU452), both of which carried theaacA-aphDgene, typically conferring HLGR. However, only one strain (BSU1203) also carried the previously described chromosomal gentamicin resistance transposon designated Tn3706. For the other strain (BSU452), plasmid purification and subsequent DNA sequencing resulted in the detection of plasmid pIP501 carrying a remnant of a Tn3family transposon. Its ability to confer HLGR was proven by transfer into anEnterococcus faecalisisolate. Conversely, loss of HLGR was documented after curing both GBS BSU452 and the transformedE. faecalisstrain from the plasmid. This is the first report showing plasmid-mediated HLGR in GBS. Thus, in our clinical GBS isolates, HLGR is mediated both chromosomally and extrachromosomally.


1991 ◽  
Vol 6 (4) ◽  
pp. 293-301 ◽  
Author(s):  
Craig W. Hawryshyn

AbstractThe light-adaptation properties of goldfish photoreceptor mechanisms were examined using Stiles' two-color threshold technique. Threshold vs. background intensity (TVI) curves were determined for isolated cone and rod mechanisms using the heart-rate conditioning technique. The principal aim of this study was to compare the light-adaptation properties of the ultraviolet (UV)-sensitive cone mechanism to the other receptor mechanisms of goldfish. This examination revealed several striking functional differences: (1) The UV-sensitive cone mechanism threshold vs. background intensity (TVI) exhibited a slope of 0.65 (compared to the approximate 1.0 for the other cone mechanisms on a log/log plot) and thus was not in accordance with Weber's law. This may in part be related to the intrusion of the blue-sensitive mechanism at the upper radiance range. (2) The operation of the UV-sensitive cone mechanism was limited to intermediate intensities (i.e. not very dim or bright). (3) The UV-sensitive cone mechanism exhibited a Weber fraction or luminance contrast threshold of 0.316 that was approximately six times larger than the other cone mechanisms but comparable to the rod mechanism. This indicates that the UV-sensitive cone mechanism performs relatively poorly in terms of brightness contrast detection.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 5227-5227
Author(s):  
Matilde Y Follo ◽  
Carlo Finelli ◽  
Cristina Clissa ◽  
Sara Mongiorgi ◽  
Carmen Baldazzi ◽  
...  

Abstract Lenalidomide is an immunomodulating drug currently used in the treatment of del(5q) low-risk MDS patients, where it can suppress the del(5q) clone and restore a normal erythropoiesis. The exact molecular mechanisms underlying the effect of Lenalidomide in del(5q) MDS are not completely clear, although Akt phosphorylation is inhibited in Lenalidomide-sensitive del(5q) cell lines (Gandhi et al, 2006). On the other hand, the activation of the Akt/mTOR pathway has been demonstrated in CD34+ cells from high-risk MDS (Follo et al, 2007), which show alterations on stem cell proliferation, differentiation and apoptosis. These processes are important also in low-risk MDS, that usually show a stable disease but can evolve towards a worse clinical status, characterized by an increased cell proliferation. In this study we firstly investigated the effect of Lenalidomide in 6 patients with del(5q) MDS (IPSS: Low or Int-1). Given the limited number of cells, we analyzed bone marrow total mononuclear cells. As for Akt phosphorylation, we analyzed its localization along with RPS14, in order to specifically detect the del(5q) clone. On the other hand, by Real-Time PCR analyses, we assessed the expression of Globin genes, to evaluate the effect of the drug on erythropoiesis. In addition, we analyzed the effect of Lenalidomide on two cell lines with a different 5q status, one bearing a normal 5q chromosome and one showing the 5q deletion, to further investigate the effect of this drug on cell cycle, erythroid differentiation and inositide signalling pathways. Clinically, 4/6 del(5q) MDS patients showed a favourable response to Lenalidomide. At a molecular level, these cases showed an activation of erythropoiesis, in that Beta-Globin levels increased, as compared with baseline. Moreover, these subjects also displayed a specific phosphorylation of Akt. Interestingly, Akt resulted to be specifically activated in cells not showing the 5q deletion, whereas it was down-regulated in del(5q) cells. The two non responder patients early discontinued Lenalidomide for adverse events, and for these patients neither a clinical assessment of Lenalidomide effect, nor a molecular analysis, were possible. As for cell lines, ongoing analyses are showing that Lenalidomide specifically inhibits the growth of the del(5q) clone, blocking cells in G1 phase. On the other hand, Akt phosphorylation specifically increases in cells with a normal 5q chromosome. Taken together, our data show a specific activation of erythropoiesis in del(5q) low-risk MDS patients responding to Lenalidomide. In addition, our results indicate that Akt is specifically phosphorylated in normal cells without the del(5q), leading to hypothesize that Lenalidomide has a double effect: it can induce apoptosis in clonal del(5q) cells, but it also supports the proliferation and erythroid differentiation of normal cells, as also described in non-del(5q) MDS (Ebert et al, 2008). Therefore, our findings might contribute to elucidate the molecular mechanisms of Lenalidomide and possibly pave the way for the development of innovative therapeutic targeted strategies in MDS. Disclosures: No relevant conflicts of interest to declare.


1993 ◽  
Vol 48 (9-10) ◽  
pp. 673-688 ◽  
Author(s):  
Günter Strittmatter ◽  
Dorothee Wegener

Abstract Rapid progress in gene technology has allowed, on the one hand, insight to be gained into the complex molecular mechanisms of plant/pathogen recognition and the natural defence strategies of host plants. On the other hand, this technology can also be used for the controlled and efficient generation of genetic variability and for the identification of desirable genotypes, far beyond the possibilities of classical breeding. The first successful attempts have been made to improve resistance against pathogenic viruses, bacteria, fungi and insects by engineering transgenic plants. The majority of these strategies were based on constitutively expressing single proteins that are either toxic to the pathogen/pest, or interfere with its reproductive cycle. More refined strategies, which are at the stage of testing, try to mimic and modify naturally-evolved defence reactions of plants and, thereby, will potentially confer a more durable resistance to a broad range of pathogens


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