scholarly journals Modulation of the ComA-Dependent Quorum Response in Bacillus subtilis by Multiple Rap Proteins and Phr Peptides

2006 ◽  
Vol 188 (14) ◽  
pp. 5273-5285 ◽  
Author(s):  
Jennifer M. Auchtung ◽  
Catherine A. Lee ◽  
Alan D. Grossman
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Dna Microarrays ◽  
Response Regulator ◽  
Biological Processes ◽  
Expression Of Genes ◽  
Signaling Peptides ◽  
Number Of Genes ◽  
Signaling Modules ◽  
Different Levels

ABSTRACT In Bacillus subtilis, extracellular peptide signaling regulates several biological processes. Secreted Phr signaling peptides are imported into the cell and act intracellularly to antagonize the activity of regulators known as Rap proteins. B. subtilis encodes several Rap proteins and Phr peptides, and the processes regulated by many of these Rap proteins and Phr peptides are unknown. We used DNA microarrays to characterize the roles that several rap-phr signaling modules play in regulating gene expression. We found that rapK-phrK regulates the expression of a number of genes activated by the response regulator ComA. ComA activates expression of genes involved in competence development and the production of several secreted products. Two Phr peptides, PhrC and PhrF, were previously known to stimulate the activity of ComA. We assayed the roles that PhrC, PhrF, and PhrK play in regulating gene expression and found that these three peptides stimulate ComA-dependent gene expression to different levels and are all required for full expression of genes activated by ComA. The involvement of multiple Rap proteins and Phr peptides allows multiple physiological cues to be integrated into a regulatory network that modulates the timing and magnitude of the ComA response.

scholarly journals Extracellular Phosphate Alters Cementoblast Gene Expression

2006 ◽  
Vol 85 (6) ◽  
pp. 505-509 ◽  
Author(s):  
R.B. Rutherford ◽  
B.L. Foster ◽  
T. Bammler ◽  
R.P. Beyer ◽  
S. Sato ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Mouse Genome ◽  
Genetic Data ◽  
Phosphate Concentration ◽  
Transcription Factor Activity ◽  
Expression Of Genes ◽  
Time Period ◽  
Global Patterns ◽  
Genome Analyses

Genetic data from humans and mice reveal that the formation of cementum is sensitive to intra- and extracellular phosphate/pyrophosphate distribution. The intracellular molecular pathways whereby altered levels of extracellular phosphate concentration may affect cementum formation have not been elucidated. To initiate inquiry, we have studied the temporal effects of extracellular phosphate on global patterns of gene expression in a line of immortalized mouse cementoblasts. Total RNA from cultured cementoblasts treated with 5 mM inorganic phosphate over a designated time period, from 1–48 hrs, was analyzed for global patterns of gene expression by means of DNA microarrays representing the complete mouse genome. Analyses of significant hybridization signals indicated that 5 mM extracellular phosphate alters the expression of genes comprising several gene ontology (GO) groups, including transcription factor activity and Wnt signaling.

Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays

2001 ◽  
Vol 5 (4) ◽  
pp. 161-170 ◽  
Author(s):  
DAVID GERHOLD ◽  
MEIQING LU ◽  
JIAN XU ◽  
CHRISTOPHER AUSTIN ◽  
C. THOMAS CASKEY ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Metabolism ◽  
Stress Responses ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Metabolic Effects ◽  
Microarray Technology ◽  
Drug Candidates ◽  
Expression Of Genes

Oligonucleotide DNA microarrays were investigated for utility in measuring global expression profiles of drug metabolism genes. This study was performed to investigate the feasibility of using microarray technology to minimize the long, expensive process of testing drug candidates for safety in animals. In an evaluation of hybridization specificity, microarray technology from Affymetrix distinguished genes up to a threshold of ∼90% DNA identity. Oligonucleotides representing human cytochrome P-450 gene CYP3A5 showed heterologous hybridization to CYP3A4 and CYP3A7 RNAs. These genes could be clearly distinguished by selecting a subset of oligonucleotides that hybridized selectively to CYP3A5. Further validation of the technology was performed by measuring gene expression profiles in livers of rats treated with vehicle, 3-methylcholanthrene (3MC), phenobarbital, dexamethasone, or clofibrate and by confirming data for six genes using quantitative RT-PCR. Responses of drug metabolism genes, including CYPs, epoxide hydrolases ( EHs), UDP-glucuronosyl transferases ( UGTs), glutathione sulfotransferases ( GSTs), sulfotransferases ( STs), drug transporter genes, and peroxisomal genes, to these well-studied compounds agreed well with, and extended, published observations. Additional gene regulatory responses were noted that characterize metabolic effects or stress responses to these compounds. Thus microarray technology can provide a facile overview of gene expression responses relevant to drug metabolism and toxicology.

scholarly journals stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics

2021 ◽  
Author(s):  
Shengquan Chen ◽  
Boheng Zhang ◽  
Xiaoyang Chen ◽  
Xuegong Zhang ◽  
Rui Jiang
Keyword(s):  
Gene Expression ◽  
Spatial Organization ◽  
Correlation Coefficients ◽  
Detection Sensitivity ◽  
Gene Detection ◽  
Spatially Resolved ◽  
Expression Of Genes ◽  
Number Of Genes ◽  
Joint Embedding ◽  
Spatial Cell

Motivation: Single-cell RNA sequencing (scRNA-seq) techniques have revolutionized the investigation of transcriptomic landscape in individual cells. Recent advancements in spatial transcriptomic technologies further enable gene expression profiling and spatial organization mapping of cells simultaneously. Among the technologies, imaging-based methods can offer higher spatial resolutions, while they are limited by either the small number of genes imaged or the low gene detection sensitivity. Although several methods have been proposed for enhancing spatially resolved transcriptomics, inadequate accuracy of gene expression prediction and insufficient ability of cell-population identification still impede the applications of these methods. Results: We propose stPlus, a reference-based method that leverages information in scRNA-seq data to enhance spatial transcriptomics. Based on an auto-encoder with a carefully tailored loss function, stPlus performs joint embedding and predicts spatial gene expression via a weighted k-NN. stPlus outperforms baseline methods with higher gene-wise and cell-wise Spearman correlation coefficients. We also introduce a clustering-based approach to assess the enhancement performance systematically. Using the data enhanced by stPlus, cell populations can be better identified than using the measured data. The predicted expression of genes unique to scRNA-seq data can also well characterize spatial cell heterogeneity. Besides, stPlus is robust and scalable to datasets of diverse gene detection sensitivity levels, sample sizes, and number of spatially measured genes. We anticipate stPlus will facilitate the analysis of spatial transcriptomics. Availability: stPlus with detailed documents is freely accessible at http://health.tsinghua.edu.cn/software/stPlus/ and the source code is openly available on https://github.com/xy-chen16/stPlus.

scholarly journals Dynamic Clustering of Gene Expression

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lingling An ◽  
R. W. Doerge
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Optimal Number ◽  
Sequential Data ◽  
Dynamic Clustering ◽  
Biological Processes ◽  
Time Frequency ◽  
Expression Of Genes

It is well accepted that genes are simultaneously involved in multiple biological processes and that genes are coordinated over the duration of such events. Unfortunately, clustering methodologies that group genes for the purpose of novel gene discovery fail to acknowledge the dynamic nature of biological processes and provide static clusters, even when the expression of genes is assessed across time or developmental stages. By taking advantage of techniques and theories from time frequency analysis, periodic gene expression profiles are dynamically clustered based on the assumption that different spectral frequencies characterize different biological processes. A two-step cluster validation approach is proposed to statistically estimate both the optimal number of clusters and to distinguish significant clusters from noise. The resulting clusters reveal coordinated coexpressed genes. This novel dynamic clustering approach has broad applicability to a vast range of sequential data scenarios where the order of the series is of interest.

scholarly journals An Autoregulatory Circuit Affecting Peptide Signaling in Bacillus subtilis

1999 ◽  
Vol 181 (17) ◽  
pp. 5193-5200 ◽  
Author(s):  
Beth A. Lazazzera ◽  
Iren G. Kurtser ◽  
Ryan S. McQuade ◽  
Alan D. Grossman
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Bacillus Subtilis ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Exponential Phase ◽  
Peptide Signaling ◽  
Expression Of Genes ◽  
Low Concentrations ◽  
Competence And Sporulation Factor

ABSTRACT The competence and sporulation factor (CSF) of Bacillus subtilis is an extracellular pentapeptide produced from the product of phrC. CSF has at least three activities: (i) at low concentrations, it stimulates expression of genes activated by the transcription factor ComA; at higher concentrations, it (ii) inhibits expression of those same genes and (iii) stimulates sporulation. Because the activities of CSF are concentration dependent, we measured the amount of extracellular CSF produced by cells. We found that by mid-exponential phase, CSF accumulated to concentrations (1 to 5 nM) that stimulate ComA-dependent gene expression. Upon entry into stationary phase, CSF reached 50 to 100 nM, concentrations that stimulate sporulation and inhibit ComA-dependent gene expression. Transcription of phrC was found to be controlled by two promoters: P1, which precedes rapC, the gene upstream ofphrC; and P2, which directs transcription ofphrC only. Both RapC and CSF were found to be part of autoregulatory loops that affect transcription from P1, which we show is activated by ComA∼P. RapC negatively regulates its own expression, presumably due to its ability to inhibit accumulation of ComA∼P. CSF positively regulates its own expression, presumably due to its ability to inhibit RapC activity. Transcription from P2, which is controlled by the alternate sigma factor ςH, increased as cells entered stationary phase, contributing to the increase in extracellular CSF at this time. In addition to controlling transcription ofphrC, ςH appears to control expression of at least one other gene required for production of CSF.

The graft response to transplantation: a gene expression profile analysis

2003 ◽  
Vol 15 (1) ◽  
pp. 52-64 ◽  
Author(s):  
Kenneth Christopher ◽  
Thomas F. Mueller ◽  
Rachel DeFina ◽  
Yurong Liang ◽  
Jianhua Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Constitutive Expression ◽  
Biological Processes ◽  
Heart Transplants ◽  
Self Organizing Maps ◽  
Gene Ontology Database ◽  
Expression Profile Analysis

Little is known regarding the graft response to transplantation injury. This study investigates the posttransplantation response of genes that are constitutively expressed in the heart. Constitutive heart and lymph node tissue-restricted gene expression was first analyzed with DNA microarrays. To demonstrate changes following transplantation in genes constitutively expressed in the heart, we performed vascularized murine heart transplants in allogeneic (BALB/c to B6), syngeneic (B6 to B6), and alymphoid (BALB/c-RAG2−/− to B6-RAG1−/−) experimental groups. Temporal induction of genes posttransplant relative to constitutive expression was evaluated with DNA microarrays. Dendrograms and self-organizing maps were generated to determine the dissimilarity between the experimental groups and to identify subsets of differentially expressed genes within the groups, respectively. Expression patterns of selected genes were confirmed by real-time PCR. Biological processes were assigned to genes induced posttransplant using the AnnBuilder package via the Gene Ontology Database. Post-transplant, a shift was noted in genes classified as defense, communication, and metabolism. Our results identify novel components of the graft response to transplantation injury and rejection.

Comparison of gene expression at the feto–maternal interface between normal and recurrent pregnancy loss patients

2002 ◽  
Vol 14 (4) ◽  
pp. 235 ◽  
Author(s):  
Kwang-Hyun Baek ◽  
Bum Chae Choi ◽  
Jin-Hie Lee ◽  
Hee-Kyung Choi ◽  
Sook-Hwan Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pregnancy Loss ◽  
Recurrent Pregnancy Loss ◽  
Expression Patterns ◽  
Subtractive Hybridization ◽  
Normal Pregnancy ◽  
Chorionic Villi ◽  
Expression Of Genes ◽  
Different Levels ◽  
In Pregnancy

—Normal pregnancy requires a series of immunological, metabolic, vascular and endocrine regulating processes. However, the specific genes and proteins involved in these processes are not well defined. Aberration of these processes may lead to problems in pregnancy. One of these problems may be recurrent pregnancy loss (RPL). Little information is available on the level of expression of genes that may play a role in normal pregnancy. Therefore, this study determined whether different levels of gene expression at the feto-maternal interface could be associated with factors for RPL. The expression patterns of genes isolated from subtractive hybridization analysis performed with chorionic villi from normal and abnormal pregnancies were investigated. Eight genes classified into groups, including immunosuppression-related, embryo attachment-related and angiogenesis-related, were isolated.

scholarly journals SOS Induction in a Subpopulation of Structural Maintenance of Chromosome (Smc) Mutant Cells in Bacillus subtilis

2007 ◽  
Vol 189 (12) ◽  
pp. 4359-4366 ◽  
Author(s):  
Robert A. Britton ◽  
Elke Küster-Schöck ◽  
Thomas A. Auchtung ◽  
Alan D. Grossman
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Topoisomerase I ◽  
Dna Microarrays ◽  
Single Cells ◽  
Sos Response ◽  
Dna Supercoiling ◽  
Phage Gene ◽  
Chromosome Partitioning ◽  
Structural Maintenance Of Chromosome

ABSTRACT The structural maintenance of chromosome (Smc) protein is highly conserved and involved in chromosome compaction, cohesion, and other DNA-related processes. In Bacillus subtilis, smc null mutations cause defects in DNA supercoiling, chromosome compaction, and chromosome partitioning. We investigated the effects of smc mutations on global gene expression in B. subtilis using DNA microarrays. We found that an smc null mutation caused partial induction of the SOS response, including induction of the defective prophage PBSX. Analysis of SOS and phage gene expression in single cells indicated that approximately 1% of smc mutants have fully induced SOS and PBSX gene expression while the other 99% of cells appear to have little or no expression. We found that induction of PBSX was not responsible for the chromosome partitioning or compaction defects of smc mutants. Similar inductions of the SOS response and PBSX were observed in cells depleted of topoisomerase I, an enzyme that relaxes negatively supercoiled DNA.

scholarly journals The Two-Component Regulatory System senX3-regX3 Regulates Phosphate-Dependent Gene Expression in Mycobacterium smegmatis

2007 ◽  
Vol 189 (15) ◽  
pp. 5495-5503 ◽  
Author(s):  
Robert T. Glover ◽  
Jordan Kriakov ◽  
Scott J. Garforth ◽  
Anthony D. Baughn ◽  
William R. Jacobs
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Mycobacterium Smegmatis ◽  
Transcriptional Control ◽  
Response Regulator ◽  
Transcriptional Start Site ◽  
Regulatory System ◽  
Expression Of Genes ◽  
Two Component ◽  
Regulated Gene Expression

ABSTRACT Phosphate import is required for the growth of mycobacteria and is regulated by environmental inorganic phosphate (Pi) concentrations, although the mechanism of this regulation has not been characterized. The expression of genes involved in Pi acquisition is frequently regulated by two-component regulatory systems (2CRs) consisting of a sensor histidine kinase and a DNA-binding response regulator. In this work, we have identified the senX3-regX3 2CR as a Pi-dependent regulator of genes involved in phosphate acquisition in Mycobacterium smegmatis. Characterization of senX3 mutants with different PhoA phenotypes suggests a dual role for SenX3 as a phosphatase or a phosphodonor for the response regulator RegX3, depending upon Pi availability. Expression of PhoA activity required phosphorylation of RegX3, consistent with a role for phosphorylated RegX3 (RegX3∼P) as a transcriptional activator of phoA. Furthermore, purified RegX3∼P bound to promoter sequences from phoA, senX3, and the high-affinity phosphate transporter component pstS, demonstrating direct transcriptional control of all three genes. DNase I footprinting and primer extension analyses have further defined the DNA-binding region and transcriptional start site within the phoA promoter. A DNA motif consisting of an inverted repeat was identified in each of the promoters bound by RegX3∼P. Based upon our findings, we propose a model for Pi-regulated gene expression mediated by SenX3-RegX3 in mycobacteria.

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