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

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.

Transcriptome profiling of aSaccharomyces cerevisiaemutant with a constitutively activated Ras/cAMP pathway

2003 ◽  
Vol 16 (1) ◽  
pp. 107-118 ◽  
Author(s):  
D. L. Jones ◽  
J. Petty ◽  
D. C. Hoyle ◽  
A. Hayes ◽  
E. Ragni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Microarray Analysis ◽  
Cellular Response ◽  
Ribosome Biogenesis ◽  
Biological Significance ◽  
Altered Expression ◽  
Wall Functions ◽  
Constitutive Activation ◽  
Camp Pathway

Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2Δ mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of ∼11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway.

scholarly journals The Antituberculosis Drug Ethambutol Selectively Blocks Apical Growth in CMN Group Bacteria

mBio ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Karin Schubert ◽  
Boris Sieger ◽  
Fabian Meyer ◽  
Giacomo Giacomelli ◽  
Kati Böhm ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Division ◽  
Cell Growth ◽  
Antibiotic Treatment ◽  
Bacterial Infections ◽  
Apical Cell ◽  
Combined Treatment ◽  
Mycolic Acid ◽  
Cell Wall Synthesis ◽  
Beta Lactam

ABSTRACT Members of the genus Mycobacterium are the most prevalent cause of infectious diseases. Mycobacteria have a complex cell envelope containing a peptidoglycan layer and an additional arabinogalactan polymer to which a mycolic acid bilayer is linked; this complex, multilayered cell wall composition (mAGP) is conserved among all CMN group bacteria. The arabinogalactan and mycolic acid synthesis pathways constitute effective drug targets for tuberculosis treatment. Ethambutol (EMB), a classical antituberculosis drug, inhibits the synthesis of the arabinose polymer. Although EMB acts bacteriostatically, its underlying molecular mechanism remains unclear. Here, we used Corynebacterium glutamicum and Mycobacterium phlei as model organisms to study the effects of EMB at the single-cell level. Our results demonstrate that EMB specifically blocks apical cell wall synthesis, but not cell division, explaining the bacteriostatic effect of EMB. Furthermore, the data suggest that members of the family Corynebacterineae have two dedicated machineries for cell elongation (elongasome) and cytokinesis (divisome). IMPORTANCE Antibiotic treatment of bacterial pathogens has contributed enormously to the increase in human health. Despite the apparent importance of antibiotic treatment of bacterial infections, surprisingly little is known about the molecular functions of antibiotic actions in the bacterial cell. Here, we analyzed the molecular effects of ethambutol, a first-line antibiotic against infections caused by members of the genus Mycobacterium. We find that this drug selectively blocks apical cell growth but still allows for effective cytokinesis. As a consequence, cells survive ethambutol treatment and adopt a pneumococcal cell growth mode with cell wall synthesis only at the site of cell division. However, combined treatment of ethambutol and beta-lactam antibiotics acts synergistically and effectively stops cell proliferation. IMPORTANCE Antibiotic treatment of bacterial pathogens has contributed enormously to the increase in human health. Despite the apparent importance of antibiotic treatment of bacterial infections, surprisingly little is known about the molecular functions of antibiotic actions in the bacterial cell. Here, we analyzed the molecular effects of ethambutol, a first-line antibiotic against infections caused by members of the genus Mycobacterium. We find that this drug selectively blocks apical cell growth but still allows for effective cytokinesis. As a consequence, cells survive ethambutol treatment and adopt a pneumococcal cell growth mode with cell wall synthesis only at the site of cell division. However, combined treatment of ethambutol and beta-lactam antibiotics acts synergistically and effectively stops cell proliferation.

scholarly journals Tol-Pal System and Rgs Proteins Interact to Promote Unipolar Growth and Cell Division in Sinorhizobium meliloti

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Elizaveta Krol ◽  
Hamish C. L. Yau ◽  
Marcus Lechner ◽  
Simon Schäper ◽  
Gert Bange ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Division ◽  
Cell Growth ◽  
Cell Elongation ◽  
Sinorhizobium Meliloti ◽  
Rgs Proteins ◽  
Polar Growth ◽  
Content Type ◽  
Cell Pole ◽  
Growing Cell

ABSTRACT Sinorhizobium meliloti is an alphaproteobacterium belonging to the Rhizobiales. Bacteria from this order elongate their cell wall at the new cell pole, generated by cell division. Screening for protein interaction partners of the previously characterized polar growth factors RgsP and RgsM, we identified the inner membrane components of the Tol-Pal system (TolQ and TolR) and novel Rgs (rhizobial growth and septation) proteins with unknown functions. TolQ, Pal, and all Rgs proteins, except for RgsE, were indispensable for S. meliloti cell growth. Six of the Rgs proteins, TolQ, and Pal localized to the growing cell pole in the cell elongation phase and to the septum in predivisional cells, and three Rgs proteins localized to the growing cell pole only. The putative FtsN-like protein RgsS contains a conserved SPOR domain and is indispensable at the early stages of cell division. The components of the Tol-Pal system were required at the late stages of cell division. RgsE, a homolog of the Agrobacterium tumefaciens growth pole ring protein GPR, has an important role in maintaining the normal growth rate and rod cell shape. RgsD is a periplasmic protein with the ability to bind peptidoglycan. Analysis of the phylogenetic distribution of the Rgs proteins showed that they are conserved in Rhizobiales and mostly absent from other alphaproteobacterial orders, suggesting a conserved role of these proteins in polar growth. IMPORTANCE Bacterial cell proliferation involves cell growth and septum formation followed by cell division. For cell growth, bacteria have evolved different complex mechanisms. The most prevalent growth mode of rod-shaped bacteria is cell elongation by incorporating new peptidoglycans in a dispersed manner along the sidewall. A small share of rod-shaped bacteria, including the alphaproteobacterial Rhizobiales, grow unipolarly. Here, we identified and initially characterized a set of Rgs (rhizobial growth and septation) proteins, which are involved in cell division and unipolar growth of Sinorhizobium meliloti and highly conserved in Rhizobiales. Our data expand the knowledge of components of the polarly localized machinery driving cell wall growth and suggest a complex of Rgs proteins with components of the divisome, differing in composition between the polar cell elongation zone and the septum.

scholarly journals Novel Stress-responsive Genes EMG1 and NOP14 Encode Conserved, Interacting Proteins Required for 40S Ribosome Biogenesis

2001 ◽  
Vol 12 (11) ◽  
pp. 3644-3657 ◽  
Author(s):  
Phillip C. C. Liu ◽  
Dennis J. Thiele
Keyword(s):  
Gene Expression ◽  
Ribosome Biogenesis ◽  
Expression Patterns ◽  
Ribosomal Subunit ◽  
Temperature Sensitive ◽  
Physical Interaction ◽  
Ribosomal Protein Genes ◽  
Yeast Saccharomyces Cerevisiae ◽  
40S Ribosomal Subunit ◽  
Responsive Gene

Under stressful conditions organisms adjust the synthesis, processing, and trafficking of molecules to allow survival from and recovery after stress. In baker's yeast Saccharomyces cerevisiae, the cellular production of ribosomes is tightly matched with environmental conditions and nutrient availability through coordinate transcriptional regulation of genes involved in ribosome biogenesis. On the basis of stress-responsive gene expression and functional studies, we have identified a novel, evolutionarily conserved gene, EMG1, that has similar stress-responsive gene expression patterns as ribosomal protein genes and is required for the biogenesis of the 40S ribosomal subunit. The Emg1 protein is distributed throughout the cell; however, its nuclear localization depends on physical interaction with a newly characterized nucleolar protein, Nop14. Yeast depleted of Nop14 or harboring a temperature-sensitive allele of emg1 have selectively reduced levels of the 20S pre-rRNA and mature18S rRNA and diminished cellular levels of the 40S ribosomal subunit. Neither Emg1 nor Nop14 contain any characterized functional motifs; however, isolation and functional analyses of mammalian orthologues of Emg1 and Nop14 suggest that these proteins are functionally conserved among eukaryotes. We conclude that Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production.

scholarly journals Physiological and Transcriptional Responses of Candida parapsilosis to Exogenous Tyrosol

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Ágnes Jakab ◽  
Zoltán Tóth ◽  
Fruzsina Nagy ◽  
Dániel Nemes ◽  
Ildikó Bácskay ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Stress Response ◽  
Ethanol Fermentation ◽  
Ribosome Biogenesis ◽  
Candida Parapsilosis ◽  
Efflux Pump ◽  
Oxidative Stress Response ◽  
Antifungal Effect ◽  
Content Type

ABSTRACT Tyrosol plays a key role in fungal morphogenesis and biofilm development. Also, it has a remarkable antifungal effect at supraphysiological concentrations. However, the background of the antifungal effect remains unknown, especially in the case of non-albicans Candida species such as Candida parapsilosis. We examined the effect of tyrosol on growth, adhesion, redox homeostasis, virulence, as well as fluconazole susceptibility. To gain further insights into the physiological consequences of tyrosol treatment, we also determined genome-wide gene expression changes using transcriptome sequencing (RNA-Seq). A concentration of 15 mM tyrosol caused significant growth inhibition within 2 h of the addition of tyrosol, while the adhesion of yeast cells was not affected. Tyrosol increased the production of reactive oxygen species remarkably, as revealed by a dichlorofluorescein test, and it was associated with elevated superoxide dismutase, glutathione peroxidase, and catalase activities. The interaction between fluconazole and tyrosol was antagonistic. Tyrosol exposure resulted in 261 and 181 differentially expressed genes with at least a 1.5-fold increase or decrease in expression, respectively, which were selected for further study. Genes involved in ribosome biogenesis showed downregulation, while genes related to the oxidative stress response and ethanol fermentation were upregulated. In addition, tyrosol treatment upregulated the expression of efflux pump genes, including MDR1 and CDR1, and downregulated the expression of the FAD2 and FAD3 virulence genes involved in desaturated fatty acid formation. Our data demonstrate that exogenous tyrosol significantly affects the physiology and gene expression of C. parapsilosis, which could contribute to the development of treatments targeting quorum sensing in the future. IMPORTANCE Candida-secreted quorum-sensing molecules (i.e., farnesol and tyrosol) are key regulators in fungal physiology, which induce phenotypic adaptations, including morphological changes, altered biofilm formation, and synchronized expression of virulence factors. Moreover, they have a remarkable antifungal activity at supraphysiological concentrations. Limited data are available concerning the tyrosol-induced molecular and physiological effects on non-albicans Candida species such as C. parapsilosis. In addition, the background of the previously observed antifungal effect caused by tyrosol remains unknown. This study reveals that tyrosol exposure enhanced the oxidative stress response and the expression of efflux pump genes, while it inhibited growth and ribosome biogenesis as well as several virulence-related genes. Metabolism was changed toward glycolysis and ethanol fermentation. Furthermore, the initial adherence was not influenced significantly in the presence of tyrosol. Our results provide several potential explanations for the previously observed antifungal effect.

scholarly journals Tol-Pal system and Rgs proteins interact to promote unipolar growth and cell division in Sinorhizobium meliloti

2020 ◽  
Author(s):  
Elizaveta Krol ◽  
Hamish C. L. Yau ◽  
Marcus Lechner ◽  
Simon Schäper ◽  
Gert Bange ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Division ◽  
Cell Growth ◽  
Cell Elongation ◽  
Sinorhizobium Meliloti ◽  
Normal Growth ◽  
Rgs Proteins ◽  
Polar Growth ◽  
Cell Pole ◽  
Growing Cell

ABSTRACTSinorhizobium meliloti is an α-proteobacterium belonging to the Rhizobiales. Bacteria from this order elongate their cell wall at the new cell pole, generated by cell division. Screening for protein interaction partners of the previously characterized polar growth factors RgsP and RgsM, we identified the inner membrane components of the Tol-Pal system (TolQ and TolR) and novel Rgs (rhizobial growth and septation) proteins with unknown functions. TolQ, Pal and all Rgs proteins, except for RgsE, were indispensable for S. meliloti cell growth. Six of the Rgs proteins, TolQ and Pal localized to the growing cell pole in the cell elongation phase and to the septum in pre-divisional cells, and three Rgs proteins localized to growing cell pole only. The FtsN-like protein RgsS contains a conserved SPOR domain and is indispensable at the early stages of cell division. The components of the Tol-Pal system were required at the late stages of cell division. RgsE, a homolog of the Agrobacterium tumefaciens growth pole ring protein GPR, has an important role in maintaining the normal growth rate and rod cell shape. RgsD is a novel periplasmic protein with the ability to bind peptidoglycan. Analysis of the phylogenetic distribution of novel Rgs proteins showed that they are conserved in Rhizobiales and mostly absent from other α-proteobacterial orders, suggesting a conserved role of these proteins in polar growth.IMPORTANCEBacterial cell proliferation involves cell growth and septum formation followed by cell division. For cell growth, bacteria have evolved different complex mechanisms. The most prevalent growth mode of rod shaped bacteria is cell elongation by incorporating new peptidoglycan in a dispersed manner along the sidewall. A small share of rod-shaped bacteria, including the α-proteobacterial Rhizobiales, grow unipolarly. Here, we identified and initially characterized a set of Rgs (rhizobial growth and septation) proteins, which are involved in cell division and unipolar growth of Sinorhizobium meliloti and highly conserved in Rhizobiales. Our data expand the knowledge of components of the polarly localized machinery driving cell wall growth and suggest a complex of Rgs proteins with components of the divisome, differing in composition between the polar cell elongation zone and the septum.

scholarly journals OBSERVATIONS ON CELL GROWTH, MITOSIS, AND DIVISION IN THE FUNGUS BASIDIOBOLUS RANARUM

1963 ◽  
Vol 17 (1) ◽  
pp. 123-152 ◽  
Author(s):  
C. F. Robinow
Keyword(s):  
Cell Wall ◽  
Cell Division ◽  
Cell Growth ◽  
Mitotic Spindle ◽  
Phase Contrast ◽  
Phase Contrast Microscopy ◽  
Large Nucleus ◽  
Slowing Down ◽  
Contrast Microscopy ◽  
Duplication Cycle

The paper describes the forward streaming, growth, and division of the vegetative cell of Basidiobolus ranarum. The cell is several hundred microns long and has a single large nucleus. Mitosis is invariably followed by cell division. Both processes have been studied in the living cell by ordinary and phase contrast microscopy. Mitosis is accompanied by a temporary coarsening of the organisation of the cytoplasm and a considerable slowing down of the rate of growth of the cell wall tube. Fixed and stained preparations have shown that there is a large number of small chromosomes and that the mitotic spindle is formed from the nucleolus. Basidiobolus appears suitable for observations on the cell duplication cycle and the physiology of mitosis.

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

2009 ◽  
Vol 19 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Vilmos Soós ◽  
Angela Juhász ◽  
Marnie E. Light ◽  
Johannes Van Staden ◽  
Ervin Balázs
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Cell Division ◽  
Differential Display ◽  
Continuous Light ◽  
Cell Division Cycle ◽  
Water Control ◽  
Grand Rapids ◽  
Smoke Water ◽  
Control Samples

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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