Smoke-water-induced changes of expression pattern in Grand Rapids lettuce achenes

AbstractAerosol smoke and smoke-water can break dormancy and promote seed germination of many plant species. In this study we investigated changes in gene expression after imbibition of light-sensitive Lactuca sativa L. cv. ‘Grand Rapids’ achenes with dilute smoke-water compared to water control samples kept in the dark or continuous light, using the fluorescent differential display technique. Although no difference was detected in the smoke-water versus water control samples germinated in light, smoke-water treatment resulted in the differential display of several expressed sequence tags (ESTs) when compared to water control samples kept in the dark. The most pronounced fragments isolated correspond to known genes related to germination, with functions in cell wall expansion, regulation of translation, the cell division cycle, carbohydrate metabolism and abscisic acid (ABA) regulation. Real-time polymerase chain reaction (PCR) validation revealed that the transcript abundance of the genes, HVA22, short-chain dehydrogenase/reductase and late embryogenesis abundant protein, are upregulated after smoke treatment when compared to control achenes kept in the light. The results indicate that smoke has a dual effect. On the one hand, the smoke can induce genes that may be linked to ABA action, whereas, on the other hand, it elicits a faster germination rate by inducing a similar pattern in gene expression as light treatment. Smoke effects could be manifested mainly through the induction of the cell division cycle, cell wall extension and storage mobilization.

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A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes

Molecular Biology of the Cell ◽

10.1091/mbc.e11-11-0961 ◽

2012 ◽

Vol 23 (10) ◽

pp. 1986-1997 ◽

Cited By ~ 30

Author(s):

Nikolai Slavov ◽

Edoardo M. Airoldi ◽

Alexander van Oudenaarden ◽

David Botstein

Keyword(s):

Gene Expression ◽

Growth Rate ◽

Oxygen Consumption ◽

Heat Stress ◽

Cell Division ◽

Environmental Stress ◽

Fission Yeast ◽

Budding Yeast ◽

Cell Division Cycle ◽

Metabolic Cycle

The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases that are most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is associated with the periodic expression of thousands of genes, producing oscillating patterns of gene expression found in synchronized cultures and in single cells of slowly growing unsynchronized cultures. Systematic variation in the durations of the HOC and LOC phases can account quantitatively for well-studied transcriptional responses to growth rate differences. Here we show that a similar mechanism—transitions from the HOC phase to the LOC phase—can account for much of the common environmental stress response (ESR) and for the cross-protection by a preliminary heat stress (or slow growth rate) to subsequent lethal heat stress. Similar to the budding yeast metabolic cycle, we suggest that a metabolic cycle, coupled in a similar way to the ESR, in the distantly related fission yeast, Schizosaccharomyces pombe, and in humans can explain gene expression and respiratory patterns observed in these eukaryotes. Although metabolic cycling is associated with the G0/G1 phase of the cell division cycle of slowly growing budding yeast, transcriptional cycling was detected in the G2 phase of the division cycle in fission yeast, consistent with the idea that respiratory metabolic cycling occurs during the phases of the cell division cycle associated with mass accumulation in these divergent eukaryotes.

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Gene Expression Changes and Anti-proliferative Effect of Noni (Morinda Citrifolia) Fruit Extract Analysed by Real Time-PCR

Molekul ◽

10.20884/1.jm.2017.12.1.333 ◽

2017 ◽

Vol 12 (1) ◽

pp. 37

Author(s):

Hermansyah Hermansyah ◽

Susilawati Susilawati

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Cell Cycle ◽

Cell Division ◽

Real Time ◽

Cell Division Cycle ◽

Morinda Citrifolia ◽

Transcriptional Analysis ◽

Fruit Extract ◽

Proliferative Effect

To elucidate the anti-proliferative effect of noni (Morinda citrifolia) fruit extract for a Saccharomyces cerevisiae model organism, analysis of gene expression changes related to cell cycle associated with inhibition effect of noni fruit extract was carried out. Anti-proliferative of noni fruit extract was analyzed using gene expression changes of Saccharomyces cerevisiae (strains FY833 and BY4741).Â Transcriptional analysis of genes that play a role in cell cycle was conducted by growing cells on YPDAde broth medium containing 1% (w/v) noni fruit extract, and then subjected using quantitative real-time polymerase chain reaction (RT-PCR).Â Transcriptional level of genes CDC6 (Cell Division Cycle-6), CDC20 (Cell Division Cycle-20), FAR1 (Factor ARrest-1), FUS3 (FUSsion-3), SIC1 (Substrate/Subunit Inhibitor of Cyclin-dependent protein kinase-1), WHI5 (WHIskey-5), YOX1 (Yeast homeobOX-1) and YHP1 (Yeast Homeo-Protein-1) increased, oppositely genes expression of DBF4 (DumbBell Forming), MCM1 (Mini Chromosome Maintenance-1) and TAH11 (Topo-A Hypersensitive-11) decreased, while the expression level of genes CDC7 (Cell Division Cycle-7), MBP1 (MIul-box Binding Protein-1) and SWI6 (SWItching deficient-6) relatively unchanged. These results indicated that gene expression changes might associate with anti-proliferative effect from noni fruit extract. These gene expressions changes lead to the growth inhibition of S.cerevisiae cell because of cell cycle defect.

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Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes

Open Biology ◽

10.1098/rsob.120033 ◽

2012 ◽

Vol 2 (4) ◽

pp. 120033 ◽

Cited By ~ 35

Author(s):

S. Kelly ◽

S. Kramer ◽

A. Schwede ◽

P. K. Maini ◽

K. Gull ◽

...

Keyword(s):

Gene Expression ◽

Cell Division ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Expression Patterns ◽

Cell Division Cycle ◽

Control Of Gene Expression ◽

Polycistronic Transcription ◽

A Genome ◽

Gene Expression Control

The trypanosome genome is characterized by RNA polymerase II-driven polycistronic transcription of protein-coding genes. Ten to hundreds of genes are co-transcribed from a single promoter; thus, selective regulation of individual genes via initiation is impossible. However, selective responses to external stimuli occur and post-transcriptional mechanisms are thought to account for all temporal gene expression patterns. We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant. We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect. Analysis of gene ontology annotations reveals that positional bias is not restricted to stress–response genes and that there is a genome-wide organization based on proximity to transcription initiation sites. Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites. This work provides evidence that the genome in trypanosomes is organized to facilitate co-coordinated temporal control of gene expression in the absence of selective promoters.

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Molecular cloning and cold-inducible gene expression of the cell division cycle gene CDC48 in zebrafish cells

Fisheries Science ◽

10.2331/fishsci.68.sup2_1291 ◽

2002 ◽

Vol 68 (sup2) ◽

pp. 1291-1292 ◽

Cited By ~ 1

Author(s):

SHINTARO IMAMURA ◽

NOBUHIKO OJIMA ◽

MICHIAKI YAMASHITA

Keyword(s):

Gene Expression ◽

Cell Division ◽

Molecular Cloning ◽

Cell Division Cycle ◽

Inducible Gene Expression ◽

Inducible Gene

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Identification of cell division cycle 20 as a candidate biomarker and potential therapeutic target in bladder cancer using bioinformatics analysis

Bioscience Reports ◽

10.1042/bsr20194429 ◽

2020 ◽

Vol 40 (7) ◽

Cited By ~ 1

Author(s):

Peilin Shen ◽

Xuejun He ◽

Lin Lan ◽

Yingkai Hong ◽

Mingen Lin

Keyword(s):

Gene Expression ◽

Bladder Cancer ◽

Cell Division ◽

Mrna Expression ◽

Therapeutic Target ◽

Gene Expression Omnibus ◽

Cell Division Cycle ◽

Hub Genes ◽

Potential Therapeutic Target ◽

Protein Protein Interaction

Abstract Purpose: As bladder cancer (BC) is very heterogeneous and complicated in the genetic level, exploring genes to serve as biomarkers and therapeutic targets is practical. Materials and methods: We searched Gene Expression Omnibus (GEO) and downloaded the eligible microarray datasets. After intersection analysis for identified differentially expressed genes (DEGs) of included datasets, overlapped DEGs were identified and subsequently analyzed with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein–Protein Interaction (PPI) and hub genes identification. Hub genes were further analyzed with mRNA expression comparation in Oncomine and Gene Expression Profiling Interactive Analysis (GEPIA) database, proteomics-based validation in The Human Protein Atlas (THPA) and survival analysis in GEO and Oncolnc database. Results: We analyzed five eligible GEO datasets and identified 76 overlapped DEGs mapped into PPI network with 459 edges which were mainly enriched in cell cycle pathway and related terms in GO and KEGG analysis. Among five identified hub genes, which are Cyclin-Dependent Kinase 1 (CDK1), Ubiquitin-Conjugating Enzyme E2 C (UBE2C), Cell Division Cycle 20 (CDC20), Microtubule Nucleation Factor (TPX2) and Cell Division Cycle Associated 8 (CDCA8); CDC20 and CDCA8 were confirmed as significant in mRNA expression comparation and proteomics-based validation. However, only CDC20 was considered prognostically significant in both GEO and Oncolnc database. Conclusions: CDC20 and CDCA8 were identified as candidate diagnostic biomarkers for BC in the present study; however, only CDC20 was validated as prognostically valuable and may possibly serve as a candidate prognostic biomarker and potential therapeutic target. Still, further validation studies are essential and indispensable.

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The Forkhead Transcription Factor Fkh2 Regulates the Cell Division Cycle of Schizosaccharomyces pombe

Eukaryotic Cell ◽

10.1128/ec.3.4.944-954.2004 ◽

2004 ◽

Vol 3 (4) ◽

pp. 944-954 ◽

Cited By ~ 35

Author(s):

Richard Bulmer ◽

Aline Pic-Taylor ◽

Simon K. Whitehall ◽

Kate A. Martin ◽

Jonathan B. A. Millar ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Transcription Factor ◽

Cell Division ◽

Schizosaccharomyces Pombe ◽

Regulation Of Gene Expression ◽

Cell Division Cycle ◽

Specific Gene ◽

Dependent Manner ◽

Forkhead Transcription Factor

ABSTRACT In eukaryotes the regulation of gene expression plays a key role in controlling cell cycle progression. Here, we demonstrate that a forkhead transcription factor, Fkh2, regulates the periodic expression of cdc15 + and spo12 + in the M and G1 phases of the cell division cycle in the fission yeast Schizosaccharomyces pombe. We also show that Fkh2 is important for several cell cycle processes, including cell morphology and cell separation, nuclear structure and migration, and mitotic spindle function. We find that the expression of fkh2 + is itself regulated in a cell cycle-dependent manner in G1 coincident with the expression of cdc18 +, a Cdc10-regulated gene. However, fkh2 + expression is independent of Cdc10 function. Fkh2 was found to be phosphorylated during the cell division cycle, with a timing that suggests that this posttranslational modification is important for cdc15 + and spo12 + expression. Related forkhead proteins regulate G2 and M phase-specific gene expression in the evolutionarily distant Saccharomyces cerevisiae, suggesting that these proteins play conserved roles in regulating cell cycle processes in eukaryotes.

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Mechanisms of polar growth in the alphaproteobacterial order rhizobiales

10.32469/10355/79574 ◽

2019 ◽

Author(s):

◽

Michelle A. Williams

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Cell Division ◽

Molecular Mechanisms ◽

Cell Wall Composition ◽

Wall Material ◽

Polar Growth ◽

Cell Wall Synthesis ◽

Type Vi Secretion System ◽

Atypical Form

All bacteria elongate and divide to faithfully reproduce their cell shape. Understanding the mechanisms that drive bacterial morphology requires an intimate knowledge of how the cell wall is synthesized. During cell division, most bacteria synthesize new cell wall at mid-cell and the mechanism underlying this process is highly conserved. In contrast, there is a high degree of diversity in bacterial growth patterning during elongation. Bacteria in the Rhizobiales exhibit an atypical form of unipolar elongation, and the molecular mechanisms of how new cell wall is synthesized during growth and division currently remains unexplored. Using microfluidics and fluorescent cell wall probes we first investigated whether polar growth is conserved in a morphologically complex bacterium, Prosthecomicrobium hirschii. We showed that P. hirschii has a dimorphic lifestyle and can switch between a long-stalked, non-motile form and a short-stalked, motile form. Furthermore, we found that all morphotypes of P. hirschii elongate using polar growth, suggesting the polar elongation is a widespread feature of bacteria in this order. Next, we used the rod-shaped bacterium Agrobacterium tumefaciens as a model to investigate the precise mechanisms that drive polar elongation. We characterized a comprehensive set of cell wall synthesis enzymes in A. tumefaciens and identified penicillin-binding protein 3a (PBP3a) and PBP3b as a synthetic lethal pair that function during cell division, and PBP1a as an essential enzyme required for polar growth and maintenance of rod shape. Compositional analysis of the PBP1a depletion, suggested that LD-transpeptidase (LDT) enzymes may play an important role in polar growth. We identified three LDTs that likely function in polar growth. We also observed subpolar localization of LDTs, suggesting bacteria in the Rhizobiales may insert or remodel cell wall material in a subpolar zone during growth. Finally, we used RNA-seq to explore changes in gene expression during PBP1a depletion, revealing that that loss of PBP1a induces a lifestyle switch which mimics the switch from a free-living bacterium into a plant-associated state. The change in lifestyle is characterized by increased exopolysaccharide production and Type VI Secretion System activity and a decrease in flagella-mediated motility. This finding indicates that bacteria have a mechanism to sense changes in cell wall composition or integrity due to the loss of PBP1a and respond through changes in gene expression that impact physiology and behavior. This finding opens the door to future studies on the link between changes in cell wall composition and complex bacterial behaviors and lifestyles. Overall, this research provides mechanistic insights about the roles of cell wall synthesis during cell growth and division in the A. tumefaciens, which are conserved in other Rhizobiales, including agriculturally and medically species such as Sinorhizobium and Brucella.

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Transcriptome analysis reveals the differences between cellular response to ribosomal stress and translational stress

10.1101/203356 ◽

2017 ◽

Author(s):

Md Shamsuzzaman ◽

Brian Gregory ◽

Vincent Bruno ◽

Lasse Lindahl

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Cell Wall ◽

Cell Division ◽

Cell Growth ◽

Cell Membrane ◽

Ribosomal Protein ◽

Ribosome Biogenesis ◽

Responsive Gene ◽

Ribosomal Stress

AbstractRibosome biogenesis is an essential metabolic process of a growing cell. Cells need to continuously synthesize new ribosomes in order to make new proteins than can support building biomass and cell division. It is obvious that in the absence of ribosome biogenesis, cell growth will stop and cell division will stall. However, it is not clear whether cell growth stops due to reduced protein synthesis capacity (translational stress) or due to activation of signaling specific to ribosome biogenesis abnormalities (ribosomal stress). To understand the signaling pathways leading to cell cycle arrest under ribosomal and translational stress conditions, we performed time series RNA-seq experiments of cells at different time of ribosomal and translational stress. We found that expression of ribosomal protein genes follow different course over the time of these two stress types. In addition, ribosomal stress is sensed early in the cell, as early as 2hr. Up-regulation of genes responsive to oxidative stress and over representation of mRNAs for transcription factors responsive to stress was detected in cell at 2hr of ribosomal protein depletion. Even though, we detected phenotypic similarities in terms of cell separation and accumulation in G1 phase cells during inhibition of ribosome formation and ribosome function, different gene expression patterns underlie these phenotypes, indicating a difference in causalities of these phenotypes. Both ribosomal and translational stress show common increased expression of stress responsive gene expression, like Crz1 target gene expression, signature of oxidative stress response and finally membrane or cell wall instability. We speculate that cell membrane and cell wall acts as major stress sensor in the cell and adjust cellular metabolism accordingly. Any change in membrane lipid composition, or membrane protein oxidation, or decrease or increase in intracellular turgor pressure causes stress in cell membrane. Cell membrane or cell wall stress activates and/or inactivates specific signaling pathway which triggers stress responsive gene expression and adaptation of cellular behavior accordingly.

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Coherent Gene Assemblies: Example, Yeast Cell Division Cycle, CDC

10.1101/2021.09.05.459023 ◽

2021 ◽

Author(s):

Lawrence Sirovich

Keyword(s):

Gene Expression ◽

Cell Division ◽

Yeast Cell ◽

Dimensional Space ◽

Cell Division Cycle ◽

Dynamic Mode Decomposition ◽

Dynamic Mode ◽

Sampled Data ◽

Mode Decomposition ◽

Mother And Daughter

A fresh approach to the dynamics of gene assemblies is presented. Central to the exposition are the concepts of: high value genes; correlated activity; and the orderly unfolding of gene dynamics; and especially dynamic mode decomposition, DMD, a remarkable new tool for dissecting dynamics. This program is carried out, in detail, for the Orlando et al yeast database (Orlando et al. 2008). It is shown that the yeast cell division cycle, CDC, requires no more than a six dimensional space, formed by three complex temporal modal pairs, each associated with characteristic aspects of the cell cycle: (1) A mother cell cohort that follows a fast clock; (2) A daughter cell cohort that follows a slower clock; (3) inherent gene expression, unrelated to the CDC. A derived set of sixty high-value genes serves as a model for the correlated unfolding of gene activity. Confirmation of our results comes from an independent database, and other considerations. The present analysis, leads naturally, to a Fourier description, for the sparsely sampled data. From this, resolved peak times of gene expression are obtained. This in turn leads to prediction of precise times of expression in the unfolding of the CDC genes. The activation of each gene appears as uncoupled dynamics from the mother and daughter cohorts, of different durations. These deliberations lead to detailed estimates of the fraction of mother and daughter cells, specific estimates of their maturation periods, and specific estimates of the number of genes in these cells. An algorithmic framework for yeast modeling is proposed, and based on the new analyses, a range of theoretical ideas and new experiments are suggested.

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