scholarly journals Spatial organization of different sigma factor activities and c-di-GMP signalling within the three-dimensional landscape of a bacterial biofilm

Open Biology ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. 180066 ◽  
Author(s):  
Gisela Klauck ◽  
Diego O. Serra ◽  
Alexandra Possling ◽  
Regine Hengge
Keyword(s):  
Gene Expression ◽  
Extracellular Matrix ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Spatial Organization ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Biomechanical Properties ◽  
Ribosomal Gene ◽  
Bacterial Biofilm

Bacterial biofilms are large aggregates of cells embedded in an extracellular matrix of self-produced polymers. In macrocolony biofilms of Escherichia coli , this matrix is generated in the upper biofilm layer only and shows a surprisingly complex supracellular architecture. Stratified matrix production follows the vertical nutrient gradient and requires the stationary phase σ S (RpoS) subunit of RNA polymerase and the second messenger c-di-GMP. By visualizing global gene expression patterns with a newly designed fingerprint set of Gfp reporter fusions, our study reveals the spatial order of differential sigma factor activities, stringent control of ribosomal gene expression and c-di-GMP signalling in vertically cryosectioned macrocolony biofilms. Long-range physiological stratification shows a duplication of the growth-to-stationary phase pattern that integrates nutrient and oxygen gradients. In addition, distinct short-range heterogeneity occurs within specific biofilm strata and correlates with visually different zones of the refined matrix architecture. These results introduce a new conceptual framework for the control of biofilm formation and demonstrate that the intriguing extracellular matrix architecture, which determines the emergent physiological and biomechanical properties of biofilms, results from the spatial interplay of global gene regulation and microenvironmental conditions. Overall, mature bacterial macrocolony biofilms thus resemble the highly organized tissues of multicellular organisms.

scholarly journals The environmental stress response causes ribosome loss in aneuploid yeast cells

2020 ◽  
Vol 117 (29) ◽  
pp. 17031-17040 ◽  
Author(s):  
Allegra Terhorst ◽  
Arzu Sandikci ◽  
Abigail Keller ◽  
Charles A. Whittaker ◽  
Maitreya J. Dunham ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Response ◽  
Stationary Phase ◽  
Environmental Stress ◽  
Budding Yeast ◽  
Expression Patterns ◽  
Yeast Cells ◽  
Specific Gene ◽  
Environmental Stress Response ◽  
Cellular Stresses

Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene-expression patterns have been reported: the “environmental stress response” (ESR) and the “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. Here, we investigate this controversy. We show that the CAGE signature is not an aneuploidy-specific gene-expression signature but the result of normalizing the gene-expression profile of actively proliferating aneuploid cells to that of euploid cells grown into stationary phase. Because growth into stationary phase is among the strongest inducers of the ESR, the ESR in aneuploid cells was masked when stationary phase euploid cells were used for normalization in transcriptomic studies. When exponentially growing euploid cells are used in gene-expression comparisons with aneuploid cells, the CAGE signature is no longer evident in aneuploid cells. Instead, aneuploid cells exhibit the ESR. We further show that the ESR causes selective ribosome loss in aneuploid cells, providing an explanation for the decreased cellular density of aneuploid cells. We conclude that aneuploid budding yeast cells mount the ESR, rather than the CAGE signature, in response to aneuploidy-induced cellular stresses, resulting in selective ribosome loss. We propose that the ESR serves two purposes in aneuploid cells: protecting cells from aneuploidy-induced cellular stresses and preventing excessive cellular enlargement during slowed cell cycles by down-regulating translation capacity.

scholarly journals Global Analysis of Cell Type-Specific Gene Expression

2003 ◽  
Vol 4 (2) ◽  
pp. 208-215 ◽  
Author(s):  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Global Analysis ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
Cell Types ◽  
Reasonable Assumption ◽  
Specific Gene ◽  
Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

scholarly journals Three-dimensional migration of macrophages requires Hck for podosome organization and extracellular matrix proteolysis

Blood ◽  
2010 ◽  
Vol 115 (7) ◽  
pp. 1444-1452 ◽  
Author(s):  
Céline Cougoule ◽  
Véronique Le Cabec ◽  
Renaud Poincloux ◽  
Talal Al Saati ◽  
Jean-Louis Mège ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Spatial Organization ◽  
Ectopic Expression ◽  
Three Dimensional ◽  
Matrix Metalloproteases ◽  
3 Dimensional ◽  
Normal Expression ◽  
Migration Of Macrophages

Abstract Tissue infiltration of phagocytes exacerbates several human pathologies including chronic inflammations or cancers. However, the mechanisms involved in macrophage migration through interstitial tissues are poorly understood. We investigated the role of Hck, a Src-family kinase involved in the organization of matrix adhesion and degradation structures called podosomes. In Hck−/− mice submitted to peritonitis, we found that macrophages accumulated in interstitial tissues and barely reached the peritoneal cavity. In vitro, 3-dimensional (3D) migration and matrix degradation abilities, 2 protease-dependent properties of bone marrow–derived macrophages (BMDMs), were affected in Hck−/− BMDMs. These macrophages formed few and undersized podosome rosettes and, consequently, had reduced matrix proteolysis operating underneath despite normal expression and activity of matrix metalloproteases. Finally, in fibroblasts unable to infiltrate matrix, ectopic expression of Hck provided the gain–of–3D migration function, which correlated positively with formation of podosome rosettes. In conclusion, spatial organization of podosomes as large rosettes, proteolytic degradation of extracellular matrix, and 3D migration appeared to be functionally linked and regulated by Hck in macrophages. Hck, as the first protein combining a phagocyte-limited expression with a role in 3D migration, could be a target for new anti-inflammatory and antitumor molecules.

scholarly journals Intranuclear trafficking of transcription factors: implications for biological control

2000 ◽  
Vol 113 (14) ◽  
pp. 2527-2533 ◽  
Author(s):  
G.S. Stein ◽  
A.J. van Wijnen ◽  
J.L. Stein ◽  
J.B. Lian ◽  
M. Montecino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Myelogenous Leukemia ◽  
Regulatory Factors ◽  
Acute Myelogenous ◽  
Gene Transcripts ◽  
Targeting Signals ◽  
Discrete Domains

The subnuclear organization of nucleic acids and cognate regulatory factors suggests that there are functional interrelationships between nuclear structure and gene expression. Nuclear proteins that are localized in discrete domains within the nucleus include the leukemia-associated acute myelogenous leukemia (AML) and promyelocytic leukemia (PML) factors, the SC-35 RNA-processing factors, nucleolar proteins and components of both transcriptional and DNA replication complexes. Mechanisms that control the spatial distribution of transcription factors within the three-dimensional context of the nucleus may involve the sorting of regulatory information, as well as contribute to the assembly and activity of sites that support gene expression. Molecular, cellular, genetic and biochemical approaches have identified distinct protein segments, termed intranuclear-targeting signals, that are responsible for directing regulatory factors to specific subnuclear sites. Gene rearrangements that remove or alter intranuclear-targeting signals are prevalent in leukemias and have been linked to altered localization of regulatory factors within the nucleus. These modifications in the intranuclear targeting of transcription factors might abrogate fidelity of gene expression in tumor cells by influencing the spatial organization and/or assembly of machineries involved in the synthesis and processing of gene transcripts.

scholarly journals Investigating the dynamics of microbial consortia in spatially structured environments

2020 ◽  
Author(s):  
Sonali Gupta ◽  
Tyler D. Ross ◽  
Marcella M. Gomez ◽  
Job L. Grant ◽  
Philip A. Romero ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spatial Organization ◽  
Expression Patterns ◽  
Interaction Network ◽  
Spatial Separation ◽  
Microbial Consortia ◽  
Ecosystem Functions ◽  
Pass Filter ◽  
Low Pass Filter ◽  
Microfluidic Platform

ABSTRACTThe spatial organization of microbial communities arises from a complex interplay of biotic and abiotic interactions and is a major determinant of ecosystem functions. We design a microfluidic platform to investigate how the spatial arrangement of microbes impacts gene expression and growth. We elucidate key biochemical parameters that dictate the mapping between spatial positioning and gene expression patterns. We show that distance can establish a low-pass filter to periodic inputs, and can enhance the fidelity of information processing. Positive and negative feedback can play disparate roles in the synchronization and robustness of a genetic oscillator distributed between two strains to spatial separation. Quantification of growth and metabolite release in an amino-acid auxotroph community demonstrates that the interaction network and stability of the community are highly sensitive to temporal perturbations and spatial arrangements. In sum, our microfluidic platform can quantify spatiotemporal parameters influencing diffusion-mediated interactions in microbial consortia.

scholarly journals Regulation of Proteolysis of the Stationary-Phase Sigma Factor RpoS

1998 ◽  
Vol 180 (5) ◽  
pp. 1154-1158 ◽  
Author(s):  
Yanning Zhou ◽  
Susan Gottesman
Keyword(s):  
Gene Expression ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Exponential Phase ◽  
Specific Substrate ◽  
Response Regulators ◽  
Rapid Degradation ◽  
The Family ◽  
Regulation Of Activity ◽  
Sigma Factor Rpos

ABSTRACT RpoS, the stationary-phase sigma factor of Escherichia coli, is responsible for increased transcription of an array of genes when cells enter stationary phase and under certain stress conditions. RpoS is rapidly degraded during exponential phase and much more slowly during stationary phase; the resulting changes in RpoS accumulation play an important role in providing differential expression of RpoS-dependent gene expression. It has previously been shown that rapid degradation of RpoS during exponential growth depends on RssB (also called SprE and MviA), a protein with homology to the family of response regulators, and on the ClpXP protease. We find that RssB regulation of proteolysis does not extend to another ClpXP substrate, bacteriophage lambda O protein, suggesting that RssB acts on the specific substrate RpoS rather than on the protease. In addition, the activity of RpoS is down-regulated by RssB when degradation is blocked. In cells blocked for RpoS degradation by a mutation inclpP, cells devoid of RssB show a four- to fivefold-higher activity of an RpoS-dependent reporter fusion than cells overproducing RssB. Therefore, RssB allows specific environmental regulation of RpoS accumulation and may also modulate activity. The regulation of degradation provides an irreversible switch, while the regulation of activity may provide a second, presumably reversible level of control.

scholarly journals Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences

2021 ◽  
Vol 118 (18) ◽  
pp. e2020125118
Author(s):  
Yoshiaki Kita ◽  
Hirozumi Nishibe ◽  
Yan Wang ◽  
Tsutomu Hashikawa ◽  
Satomi S. Kikuchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Neural Circuit ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Control Of Gene Expression ◽  
Cellular Resolution

Precise spatiotemporal control of gene expression in the developing brain is critical for neural circuit formation, and comprehensive expression mapping in the developing primate brain is crucial to understand brain function in health and disease. Here, we developed an unbiased, automated, large-scale, cellular-resolution in situ hybridization (ISH)–based gene expression profiling system (GePS) and companion analysis to reveal gene expression patterns in the neonatal New World marmoset cortex, thalamus, and striatum that are distinct from those in mice. Gene-ontology analysis of marmoset-specific genes revealed associations with catalytic activity in the visual cortex and neuropsychiatric disorders in the thalamus. Cortically expressed genes with clear area boundaries were used in a three-dimensional cortical surface mapping algorithm to delineate higher-order cortical areas not evident in two-dimensional ISH data. GePS provides a powerful platform to elucidate the molecular mechanisms underlying primate neurobiology and developmental psychiatric and neurological disorders.

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.

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