Unusual Phosphoenolpyruvate (PEP) Synthetase-Like Protein Crucial to Enhancement of Polyhydroxyalkanoate Accumulation in Haloferax mediterranei Revealed by Dissection of PEP-Pyruvate Interconversion Mechanism

ABSTRACT Phosphoenolpyruvate (PEP)/pyruvate interconversion is a major metabolic point in glycolysis and gluconeogenesis and is catalyzed by various sets of enzymes in different Archaea groups. In this study, we report the key enzymes that catalyze the anabolic and catabolic directions of the PEP/pyruvate interconversion in Haloferax mediterranei. The in silico analysis showed the presence of a potassium-dependent pyruvate kinase (PYKHm [HFX_0773]) and two phosphoenol pyruvate synthetase (PPS) candidates (PPSHm [HFX_0782] and a PPS homolog protein named PPS-like [HFX_2676]) in this strain. Expression of the pykHm gene and ppsHm was induced by glycerol and pyruvate, respectively; whereas the pps-like gene was not induced at all. Similarly, genetic analysis and enzyme activities of purified proteins showed that PYKHm catalyzed the conversion from PEP to pyruvate and that PPSHm catalyzed the reverse reaction, while PPS-like protein displayed no function in PEP/pyruvate interconversion. Interestingly, knockout of the pps-like gene led to a 70.46% increase in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) production. The transcriptome sequencing (RNA-Seq) and quantitative reverse transcription-PCR (qRT-PCR) results showed that many genes responsible for PHBV monomer supply and for PHBV synthesis were upregulated in a pps-like gene deletion strain and thereby improved PHBV accumulation. Additionally, our phylogenetic evidence suggested that PPS-like protein diverged from PPS enzyme and evolved as a distinct protein with novel function in haloarchaea. Our findings attempt to fill the gaps in central metabolism of Archaea by providing comprehensive information about key enzymes involved in the haloarchaeal PEP/pyruvate interconversion, and we also report a high-yielding PHBV strain with great future potentials. IMPORTANCE Archaea, the third domain of life, have evolved diversified metabolic pathways to cope with their extreme habitats. Phosphoenol pyruvate (PEP)/pyruvate interconversion during carbohydrate metabolism is one such important metabolic process that is highly differentiated among Archaea. However, this process is still uncharacterized in the haloarchaeal group. Haloferax mediterranei is a well-studied haloarchaeon that has the ability to produce polyhydroxyalkanoates (PHAs) under unbalanced nutritional conditions. In this study, we identified the key enzymes involved in this interconversion and discussed their differences with their counterparts from other members of the Archaea and Bacteria domains. Notably, we found a novel protein, phosphoenolpyruvate synthetase-like (PPS-like), which exhibited high homology to PPS enzyme. However, PPS-like protein has evolved some distinct sequence features and functions, and strikingly the corresponding gene deletion helped to enhance poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) synthesis significantly. Overall, we have filled the gap in knowledge about PEP/pyruvate interconversion in haloarchaea and reported an efficient strategy for improving PHBV production in H. mediterranei.

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Transcriptomic and Physiological Insights into the Robustness of Long Filamentous Cells of Methanosaeta harundinacea, Prevalent in Upflow Anaerobic Sludge Blanket Granules

Applied and Environmental Microbiology ◽

10.1128/aem.03092-14 ◽

2014 ◽

Vol 81 (3) ◽

pp. 831-839 ◽

Cited By ~ 11

Author(s):

Liguang Zhou ◽

Haiying Yu ◽

Guomin Ai ◽

Bo Zhang ◽

Songnian Hu ◽

...

Keyword(s):

Cell Envelope ◽

Upflow Anaerobic Sludge Blanket ◽

Anaerobic Sludge ◽

Natural Environments ◽

Rna Seq ◽

Content Type ◽

Anaerobic Reactors ◽

Reverse Transcription Pcr ◽

Aceticlastic Methanogenesis ◽

Anaerobic Sludge Blanket

ABSTRACTMethanosaetaspp. are widely distributed in natural environments, and their filamentous cells contribute significantly to sludge granulation and the good performance of anaerobic reactors. A previous study indicated thatMethanosaeta harundinacea6Ac displays a quorum sensing-regulated morphological transition from short to long filaments, and more acetate is channeled into methane production in long filaments, whereas more is channeled into biomass synthesis in short filaments. Here, we performed transcriptomic and physiological analysis to gain insights into active methanogenesis in long filaments ofM. harundinacea6Ac. Both RNA sequencing (RNA-seq) and quantitative reverse transcription-PCR indicated that transcription of the genes involved in aceticlastic methanogenesis and energy metabolism was upregulated 1.2- to 10.3-fold in long filaments, while transcription of the genes for the methyl oxidative shunt was upregulated in short filaments. [2-13C]acetate trace experiments demonstrated that a relatively higher portion of the acetate methyl group was oxidized to CO2in short filaments than in long filaments. The long filaments exhibited higher catalase activity and oxygen tolerance than the short ones, which is consistent with increased transcription of the oxidant-scavenging genes. Moreover, transcription of genes for cell surface structures was upregulated in the long filaments, and transmission electron microscopy revealed a thicker cell envelope in the filaments. RNA-seq determined a >2-fold upregulation of a variety of antistress genes in short filaments, like those encoding chaperones and DNA repair systems, which implies that the short filaments can be stressed. This study reveals the genetic basis for the prevalence of the long filamentous morphology ofM. harundinaceacells in upflow anaerobic sludge blanket granules.

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Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica

Applied and Environmental Microbiology ◽

10.1128/aem.02079-13 ◽

2013 ◽

Vol 79 (23) ◽

pp. 7360-7370 ◽

Cited By ~ 54

Author(s):

John Seip ◽

Raymond Jackson ◽

Hongxian He ◽

Quinn Zhu ◽

Seung-Pyo Hong

Keyword(s):

Yarrowia Lipolytica ◽

Lipid Accumulation ◽

Oleaginous Yeast ◽

De Novo ◽

Lipid Synthesis ◽

Omega 3 ◽

Wild Type ◽

Content Type ◽

Reverse Transcription Pcr ◽

Dry Cell Weight

ABSTRACTIn the oleaginous yeastYarrowia lipolytica,de novolipid synthesis and accumulation are induced under conditions of nitrogen limitation (or a high carbon-to-nitrogen ratio). The regulatory pathway responsible for this induction has not been identified. Here we report that the SNF1 pathway plays a key role in the transition from the growth phase to the oleaginous phase inY. lipolytica. Strains with aY. lipolyticasnf1(Ylsnf1) deletion accumulated fatty acids constitutively at levels up to 2.6-fold higher than those of the wild type. When introduced into aY. lipolyticastrain engineered to produce omega-3 eicosapentaenoic acid (EPA),Ylsnf1deletion led to a 52% increase in EPA titers (7.6% of dry cell weight) over the control. Other components of theY. lipolyticaSNF1 pathway were also identified, and their function in limiting fatty acid accumulation is suggested by gene deletion analyses. Deletion of the gene encoding YlSnf4, YlGal83, or YlSak1 significantly increased lipid accumulation in both growth and oleaginous phases compared to the wild type. Furthermore, microarray and quantitative reverse transcription-PCR (qRT-PCR) analyses of theYlsnf1mutant identified significantly differentially expressed genes duringde novolipid synthesis and accumulation inY. lipolytica. Gene ontology analysis found that these genes were highly enriched with genes involved in lipid metabolism. This work presents a new role for Snf1/AMP-activated protein kinase (AMPK) pathways in lipid accumulation in this oleaginous yeast.

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Decreased Vancomycin Susceptibility in Staphylococcus aureus Caused by IS256Tempering of WalKR Expression

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00279-13 ◽

2013 ◽

Vol 57 (7) ◽

pp. 3240-3249 ◽

Cited By ~ 34

Author(s):

Christopher R. E. McEvoy ◽

Brian Tsuji ◽

Wei Gao ◽

Torsten Seemann ◽

Jessica L. Porter ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Fluorescent Protein ◽

Site Directed Mutagenesis ◽

Infection Model ◽

Content Type ◽

Reverse Transcription Pcr ◽

Phenotype Analysis ◽

Dosing Regimens ◽

Mrsa Strains ◽

Green Fluorescent

ABSTRACTVancomycin-intermediateStaphylococcus aureus(VISA) strains often arise by mutations in the essential two-component regulatorwalKR; however their impact onwalKRfunction has not been definitively established. Here, we investigated 10 MRSA strains recovered serially after exposure of vancomycin-susceptibleS. aureus(VSSA) JKD6009 to simulated human vancomycin dosing regimens (500 mg to 4,000 mg every 12 h) using a 10-day hollow fiber infection model. After continued exposure to the vancomycin regimens, two isolates displayed reduced susceptibility to both vancomycin and daptomycin, developing independent IS256insertions in thewalKR5′ untranslated region (5′ UTR). Quantitative reverse transcription-PCR (RT-PCR) revealed a 50% reduction inwalKRgene expression in the IS256mutants compared to the VSSA parent. Green fluorescent protein (GFP) reporter analysis, promoter mapping, and site-directed mutagenesis confirmed these findings and showed that the IS256insertions had replaced two SigA-likewalKRpromoters with weaker, hybrid promoters. Removal of IS256reverted the phenotype to VSSA, showing that reduced expression of WalKR did induce the VISA phenotype. Analysis of selected WalKR-regulated autolysins revealed upregulation ofssaAbut no change in expression ofsakandsceDin both IS256mutants. Whole-genome sequencing of the two mutants revealed an additional IS256insertion withinagrCfor one mutant, and we confirmed that this mutation abolishedagrfunction. These data provide the first substantial analysis ofwalKRpromoter function and show that prolonged vancomycin exposure can result in VISA through an IS256-mediated reduction inwalKRexpression; however, the mechanisms by which this occurs remain to be determined.

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Target (MexB)- and Efflux-Based Mechanisms Decreasing the Effectiveness of the Efflux Pump Inhibitor D13-9001 in Pseudomonas aeruginosa PAO1: Uncovering a New Role for MexMN-OprM in Efflux of β-Lactams and a Novel Regulatory Circuit (MmnRS) Controlling MexMN Expression

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01718-18 ◽

2018 ◽

Vol 63 (2) ◽

pp. e01718-18 ◽

Cited By ~ 1

Author(s):

Srijan Ranjitkar ◽

Adriana K. Jones ◽

Mina Mostafavi ◽

Zachary Zwirko ◽

Oleg Iartchouk ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Efflux Pump ◽

Response Regulator ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Rna Seq ◽

Efflux Pump Inhibitor ◽

Content Type ◽

Regulatory Circuit ◽

Outer Membrane Channel

ABSTRACT Efflux pumps contribute to antibiotic resistance in Gram-negative pathogens. Correspondingly, efflux pump inhibitors (EPIs) may reverse this resistance. D13-9001 specifically inhibits MexAB-OprM in Pseudomonas aeruginosa. Mutants with decreased susceptibility to MexAB-OprM inhibition by D13-9001 were identified, and these fell into two categories: those with alterations in the target MexB (F628L and ΔV177) and those with an alteration in a putative sensor kinase of unknown function, PA1438 (L172P). The alterations in MexB were consistent with reported structural studies of the D13-9001 interaction with MexB. The PA1438L172P alteration mediated a >150-fold upregulation of MexMN pump gene expression and a >50-fold upregulation of PA1438 and the neighboring response regulator gene, PA1437. We propose that these be renamed mmnR and mmnS for MexMN regulator and MexMN sensor, respectively. MexMN was shown to partner with the outer membrane channel protein OprM and to pump several β-lactams, monobactams, and tazobactam. Upregulated MexMN functionally replaced MexAB-OprM to efflux these compounds but was insusceptible to inhibition by D13-9001. MmnSL172P also mediated a decrease in susceptibility to imipenem and biapenem that was independent of MexMN-OprM. Expression of oprD, encoding the uptake channel for these compounds, was downregulated, suggesting that this channel is also part of the MmnSR regulon. Transcriptome sequencing (RNA-seq) of cells encoding MmnSL172P revealed, among other things, an interrelationship between the regulation of mexMN and genes involved in heavy metal resistance.

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RNA Sequencing-Based Transcriptional Overview of Xerotolerance inCronobacter sakazakiiSP291

Applied and Environmental Microbiology ◽

10.1128/aem.01993-18 ◽

2018 ◽

Vol 85 (3) ◽

Cited By ~ 6

Author(s):

Shabarinath Srikumar ◽

Yu Cao ◽

Qiongqiong Yan ◽

Koenraad Van Hoorde ◽

Scott Nguyen ◽

...

Keyword(s):

Infant Formula ◽

Mortality Rates ◽

Secondary Response ◽

Ecological Niches ◽

Infant Food ◽

Powdered Infant Formula ◽

Cronobacter Sakazakii ◽

Rna Seq ◽

Production Environment ◽

Content Type

ABSTRACTCronobacter sakazakiiis a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often resulting in high mortality rates. Here, we used transcriptome sequencing (RNA-seq) to provide transcriptional insights into the survival ofC. sakazakiiin desiccated conditions. Our RNA-seq data show that about 22% of the totalC. sakazakiigenes were significantly upregulated and 9% were downregulated during desiccation survival. When reverse transcription-quantitative PCR (qRT-PCR) was used to validate the RNA-seq data, we found that the primary desiccation response was gradually downregulated during the tested 4 hours of desiccation, while the secondary response remained constitutively upregulated. The 4-hour desiccation tolerance ofC. sakazakiiwas dependent on the immediate microenvironment surrounding the bacterial cell. The removal of Trypticase soy broth (TSB) salts and the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival ofC. sakazakiiSP291. The trehalose biosynthetic pathway encoded byotsAandotsB, a prominent secondary bacterial desiccation response, was highly upregulated in desiccatedC. sakazakii.C. sakazakiiSP291 ΔotsABwas significantly inhibited compared with the isogenic wild type in an 8-hour desiccation survival assay, confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq-based transcriptional overview along with confirmation of the phenotypic importance of trehalose metabolism inCronobacter sakazakiiduring desiccation.IMPORTANCECronobacter sakazakiiis a pathogen of importance to neonatal health and is known to persist in dry food matrices, such as powdered infant formula (PIF) and its associated production environment. When infections are reported in neonates, mortality rates can be high. The success of this bacterium in surviving these low-moisture environments suggests thatCronobacterspecies can respond to a variety of environmental signals. Therefore, understanding those signals that aid the persistence of this pathogen in these ecological niches is an important step toward the development of strategies to reduce the risk of contamination of PIF. This research led to the identification of candidate genes that play a role in the persistence of this pathogen in desiccated conditions and, thereby, serve as a model target to design future strategies to mitigate PIF-associated survival ofC. sakazakii.

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Role of metAB in Methionine Metabolism and Optimal Chicken Colonization in Campylobacter jejuni

Infection and Immunity ◽

10.1128/iai.00542-20 ◽

2020 ◽

Vol 89 (1) ◽

pp. e00542-20

Author(s):

Brandon Ruddell ◽

Alan Hassall ◽

Orhan Sahin ◽

Qijing Zhang ◽

Paul J. Plummer ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Differential Distribution ◽

Time Resolved ◽

Content Type ◽

Reverse Transcription Pcr ◽

Adenosyl Methionine ◽

Strain Type

ABSTRACTCampylobacter jejuni is a zoonotic pathogen and is one of the leading causes of human gastroenteritis worldwide. C. jejuni IA3902 (representative of the sheep abortion clone) is genetically similar to C. jejuni W7 (representative of strain type NCTC 11168); however, there are significant differences in the ability of luxS mutants of these strains to colonize chickens. LuxS is essential for the activated methyl cycle and generates homocysteine for conversion to l-methionine. Comparative genomics identified differential distribution of the genes metA and metB, which function to convert homoserine for downstream production of l-methionine, between IA3902 and W7, which could enable a secondary pathway for l-methionine biosynthesis in a W7 ΔluxS but not in an IA3902 ΔluxS strain. To test the hypothesis that the genes metA and metB contribute to l-methionine production and chicken colonization by Campylobacter, we constructed two mutants for phenotypic comparison, the W7 ΔmetAB ΔluxS and IA3902 ΔluxS::metAB mutants. Quantitative reverse transcription-PCR and tandem mass spectrometry protein analysis were used to validate MetAB transcription and translation as present in the IA3902 ΔluxS::metAB mutant and absent in the W7 ΔmetAB ΔluxS mutant. Time-resolved fluorescence resonance energy transfer fluorescence assays demonstrated that l-methionine and S-adenosyl methionine concentrations decreased in the W7 ΔmetAB ΔluxS mutant and increased in the IA3902 ΔluxS::metAB mutant. Assessment of chicken colonization revealed that the IA3902 ΔluxS::metAB strain partially rescued the colonization defect of the IA3902 ΔluxS strain, while the W7 ΔmetAB ΔluxS strain showed significantly decreased colonization compared to that of the wild-type and the W7 ΔluxS strain. These results indicate that the ability to maintain l-methionine production in vivo, conferred by metA and metB in the absence of luxS, is critical for normal chicken colonization by C. jejuni.

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Toxoplasma gondii Extends the Life Span of Infected Human Neutrophils by Inducing Cytosolic PCNA and Blocking Activation of Apoptotic Caspases

mBio ◽

10.1128/mbio.02031-20 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Tatiane S. Lima ◽

Sharmila Mallya ◽

Allen Jankeel ◽

Ilhem Messaoudi ◽

Melissa B. Lodoen

Keyword(s):

Cell Death ◽

Toxoplasma Gondii ◽

Life Span ◽

Peripheral Blood ◽

Productive Infection ◽

Human Neutrophils ◽

Serum Starvation ◽

Rna Seq ◽

Content Type ◽

Blood Neutrophils

ABSTRACT Toxoplasma gondii is an intracellular protozoan parasite that has the remarkable ability to infect and replicate in neutrophils, immune cells with an arsenal of antimicrobial effector mechanisms. We report that T. gondii infection extends the life span of primary human peripheral blood neutrophils by delaying spontaneous apoptosis, serum starvation-induced apoptosis, and tumor necrosis alpha (TNF-α)-mediated apoptosis. T. gondii blockade of apoptosis was associated with an inhibition of processing and activation of the apoptotic caspases caspase-8 and -3, decreased phosphatidylserine exposure on the plasma membrane, and reduced cell death. We performed a global transcriptome analysis of T. gondii-infected peripheral blood neutrophils using RNA sequencing (RNA-Seq) and identified gene expression changes associated with DNA replication and DNA repair pathways, which in mature neutrophils are indicative of changes in regulators of cell survival. Consistent with the RNA-Seq data, T. gondii infection upregulated transcript and protein expression of PCNA, which is found in the cytosol of human neutrophils, where it functions as a key inhibitor of apoptotic pro-caspases. Infection of neutrophils resulted in increased interaction of PCNA with pro-caspase-3. Inhibition of this interaction with an AlkB homologue 2 PCNA-interacting motif (APIM) peptide reversed the infection-induced delay in cell death. Taken together, these findings indicate a novel strategy by which T. gondii manipulates cell life span in primary human neutrophils, which may allow the parasite to maintain an intracellular replicative niche and avoid immune clearance. IMPORTANCE Toxoplasma gondii is an obligate intracellular parasite that can cause life-threatening disease in immunocompromised individuals and in the developing fetus. Interestingly, T. gondii has evolved strategies to successfully manipulate the host immune system to establish a productive infection and evade host defense mechanisms. Although it is well documented that neutrophils are mobilized during acute T. gondii infection and infiltrate the site of infection, these cells can also be actively infected by T. gondii and serve as a replicative niche for the parasite. However, there is a limited understanding of the molecular processes occurring within T. gondii-infected neutrophils. This study reveals that T. gondii extends the life span of human neutrophils by inducing the expression of PCNA, which prevents activation of apoptotic caspases, thus delaying apoptosis. This strategy may allow the parasite to preserve its replicative intracellular niche.

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Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships

mSystems ◽

10.1128/msystems.00980-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Kumari Sonal Choudhary ◽

Julia A. Kleinmanns ◽

Katherine Decker ◽

Anand V. Sastry ◽

Ye Gao ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Target Gene ◽

Target Genes ◽

Rna Seq ◽

Content Type ◽

E Coli ◽

Component Systems ◽

Two Component ◽

Two Component Systems

ABSTRACT Escherichia coli uses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data were used to validate condition-specific target gene binding sites. Based on these data, we do the following: (i) identify the target genes for each TCS; (ii) show how the target genes are transcribed in response to stimulus; and (iii) reveal novel relationships between TCSs, which indicate noncognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded. IMPORTANCE E. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli’s two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in E. coli and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.

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Photobiomodulation of inflamed dental pulp stem cells under different nutritional conditions

Regenerative Medicine ◽

10.2217/rme-2021-0056 ◽

2021 ◽

Author(s):

Seyedeh Sareh Hendi ◽

Leila Gholami ◽

Massoud Saidijam ◽

Roghayeh Mahmoudi ◽

Ali Asghar Arkian ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Cell Proliferation ◽

Laser Irradiation ◽

Dental Pulp ◽

Culture Conditions ◽

Dental Pulp Stem Cells ◽

Reverse Transcription Pcr ◽

Nutritional Conditions ◽

Proliferation And Differentiation

Aim: The present study aimed to investigate photobiomodulation's (PBM) effect on inflamed dental pulp stem cells (IDPSCs) under different nutritional conditions. Methods: Cell proliferation and odontogenic differentiation were evaluated using the MTT assay and real-time quantitative reverse transcription PCR, respectively after laser PBM of cells in 5 or 10% fetal bovine serum (FBS) culture conditions. Results: A significant positive effect of laser irradiation on cell proliferation under both nutritional conditions after 24 and 48 h was observed. DMP-1 gene expression increased in the groups with laser irradiation and 5% FBS. Comparison of gene expression levels in the four groups revealed no statistically significant stimulatory effect. The highest gene expression was observed in the non-laser group with 5% FBS. Conclusion: Further studies are required to obtain an irradiation setup to ideally improve inflamed dental pulp stem cells' proliferation and differentiation.

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The CtrA Regulon of Rhodobacter sphaeroides Favors Adaptation to a Particular Lifestyle

Journal of Bacteriology ◽

10.1128/jb.00678-19 ◽

2020 ◽

Vol 202 (7) ◽

Author(s):

José Hernández-Valle ◽

Alejandro Sanchez-Flores ◽

Sebastian Poggio ◽

Georges Dreyfus ◽

Laura Camarena

Keyword(s):

Rhodobacter Sphaeroides ◽

Stress Responses ◽

Transcriptome Sequencing ◽

Growth Conditions ◽

Fine Tuning ◽

Rna Seq ◽

Two Component System ◽

Component System ◽

Content Type ◽

Two Component

ABSTRACT Activation of the two-component system formed by CckA, ChpT, and CtrA (kinase, phosphotransferase, and response regulator, respectively) in Rhodobacter sphaeroides does not occur under the growth conditions commonly used in the laboratory. However, it is possible to isolate a gain-of-function mutant in CckA that turns the system on. Using massive parallel transcriptome sequencing (RNA-seq), we identified 321 genes that are differentially regulated by CtrA. From these genes, 239 were positively controlled and 82 were negatively regulated. Genes encoding the Fla2 polar flagella and gas vesicle proteins are strongly activated by CtrA. Genes involved in stress responses as well as several transcriptional factors are also positively controlled, whereas the photosynthetic and CO2 fixation genes are repressed. Potential CtrA-binding sites were bioinformatically identified, leading to the proposal that at least 81 genes comprise the direct regulon. Based on our results, we ponder that the transcriptional response orchestrated by CtrA enables a lifestyle in which R. sphaeroides will effectively populate the surface layer of a water body enabled by gas vesicles and will remain responsive to chemotactic stimuli using the chemosensoring system that controls the Fla2 flagellum. Simultaneously, fine-tuning of photosynthesis and stress responses will reduce the damage caused by heat and high light intensity in this water stratum. In summary, in this bacterium CtrA has evolved to control physiological responses that allow its adaptation to a particular lifestyle instead of controlling the cell cycle as occurs in other species. IMPORTANCE Cell motility in Alphaproteobacteria is frequently controlled by the CckA, ChpT, and CtrA two-component system. Under the growth conditions commonly used in the laboratory, ctrA is transcriptionally inactive in Rhodobacter sphaeroides, and motility depends on the Fla1 flagellar system that was acquired by a horizontal transfer event. Likely, the incorporation of this flagellar system released CtrA from the strong selective pressure of being the main motility regulator, allowing this two-component system to specialize and respond to some specific conditions. Identifying the genes that are directly regulated by CtrA could help us understand the conditions in which the products of this regulon are required. Massive parallel transcriptome sequencing (RNA-seq) revealed that CtrA orchestrates an adaptive response that contributes to the colonization of a particular environmental niche.

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