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Nla18/DK1622

ABSTRACT: NtrC-like activators regulate transcription of a wide variety of adaptive genes in bacteria. Previously we demonstrated that a mutation in the NtrC-like activator gene nla18 severely inhibits M. xanthus fruiting body development and vegetative growth. In this study, we found that inactivation of nla18 has dramatic effects on gene expression patterns during development and vegetative growth. Gene expression in nla18 cells is altered in the early stages of fruiting body development. In addition, nla18 cells are defective for two of the earliest events in development, production of the intracellular starvation signal ppGpp and production of A-signal. Taken together, these results indicate that the developmental program in nla18 cells goes awry very early. Inactivation nla18 also causes a dramatic decrease in the vegetative growth rate of M. xanthus cells. When the vegetative gene expression profiles of nla18 cells were compared to their wild type counterparts using DNA microarrays, we found that more than 700 genes have altered expression patterns. Furthermore, inactivation of nla18 seems to have a profound effect on expression of genes that code for putative membrane and membrane-associated proteins. This idea is supported by our finding that the profiles of membrane proteins isolated from nla18 cells during vegetative growth are noticeably different from the profiles of wild type M. xanthus cells. These results demonstrate that Nla18 is an important regulator of gene expression during both vegetative growth and fruiting body development. Keywords: vegetative analysis

ORGANISM(S): Myxococcus xanthus

PROVIDER: GSE3323 | GEO | 2005/09/20

SECONDARY ACCESSION(S): PRJNA93361

REPOSITORIES: GEO

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Nla18/DK1622

Project description:NtrC-like activators regulate transcription of a wide variety of adaptive genes in bacteria. Previously we demonstrated that a mutation in the NtrC-like activator gene nla18 severely inhibits M. xanthus fruiting body development and vegetative growth. In this study, we found that inactivation of nla18 has dramatic effects on gene expression patterns during development and vegetative growth. Gene expression in nla18 cells is altered in the early stages of fruiting body development. In addition, nla18 cells are defective for two of the earliest events in development, production of the intracellular starvation signal ppGpp and production of A-signal. Taken together, these results indicate that the developmental program in nla18 cells goes awry very early. Inactivation nla18 also causes a dramatic decrease in the vegetative growth rate of M. xanthus cells. When the vegetative gene expression profiles of nla18 cells were compared to their wild type counterparts using DNA microarrays, we found that more than 700 genes have altered expression patterns. Furthermore, inactivation of nla18 seems to have a profound effect on expression of genes that code for putative membrane and membrane-associated proteins. This idea is supported by our finding that the profiles of membrane proteins isolated from nla18 cells during vegetative growth are noticeably different from the profiles of wild type M. xanthus cells. These results demonstrate that Nla18 is an important regulator of gene expression during both vegetative growth and fruiting body development. 5 biological replicates, normalized ratios to Cy3

2010-06-30 | E-GEOD-3323 | biostudies-arrayexpress

Global profiling of developmental gene expression in Myxococcus xanthus

Project description:In response to starvation, Myxococcus xanthus initiates a developmental program that results in the formation of spore-filled multicellular fruiting bodies. Here we have used cDNA microarray analysis to determine changes in the global gene expression at different time points of the developmental process. The expression of nearly 900 genes was found to be altered at least two-fold during development as compared to vegetative cells. Genes encoding proteins with typical vegetative functions such as protein synthesis and energy metabolism were transcriptionally down-regulated in the early stages of development. Among the 430 genes transcriptionally up-regulated during development genes with regulatory functions were overrepresented; underlining that fruiting body formation relies on a complex signalling network. Notably, almost 40% of all genes with increased expression at different stages of development encoded hypothetical proteins indicating a large unexplored potential of proteins important for fruiting body formation. Keywords: Time course of development with 9 time points 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

2008-01-31 | E-GEOD-9477 | biostudies-arrayexpress

RNA-seq analysis of Myxococcus xanthus at various developmental time points

Project description:Myxococcus xanthus is a model organism for studying social behaviors and cell differentiation in bacteria. Upon nutrient depletion, M. xanthus cells initiate a developmental program that culminates in formation of spore-filled fruiting bodies and peripheral rods outside of fruiting bodies. Completion of this developmental program depends on fine-tuned spatial and temporal regulation of gene expression, intercellular communication, signaling by nucleotide-based second messengers, and motility. In order to understand stage-specific gene expression during growth and development, we extracted total RNA from vegetative cells (referred as 0 h of development) and from cells developed for 6, 12, 18 and 24 h under submerged conditions in two replicates.

2021-10-20 | E-MTAB-11043 | biostudies-arrayexpress

Global profiling of developmental gene expression in Myxococcus xanthus

2008-02-01 | GSE9477 | GEO

Cappable-seq analysis of Myxococcus xanthus at various developmental time points

Project description:Myxococcus xanthus is a model organism for studying social behaviors and cell differentiation in bacteria. Upon nutrient depletion, M. xanthus cells initiate a developmental program that culminates in formation of spore-filled fruiting bodies and peripheral rods outside of fruiting bodies. Completion of this developmental program depends on fine-tuned spatial and temporal regulation of gene expression, intercellular communication, signaling by nucleotide-based second messengers, and motility. In order to understand regulation of gene expression during growth and development, transcription start sites were identified using Cappable-seq. To this end, we extracted total RNA from vegetative cells (referred as 0 h of development) and from cells developed for 6, 12, 18 and 24 h under submerged conditions in two replicates.

2021-10-20 | E-MTAB-11042 | biostudies-arrayexpress

Global profiling of gene expression during glycerol-induced spore formation in Myxococcus xanthus

Project description:Myxococcus xanthus is a gram negative rod-shaped delta proteobacterium that differentiates into environmentally resistant spores in response to starvation. Little is known about the sporulation mechanism in part because sporulation occurs in a subpopulation of cells undergoing a lenghtly complex multicellular developmental program. This developmental program requires a solid surface, motility, a minimum population density and a sophisticated network of inter and intra-cellular signals which direct some cells first to aggregate into multicellular fruiting bodies and then to sporulate exclusively within these fruiting bodies. However, it has previously been demonstrated that synchronous conversion of vegetative cells into myxospores can also be triggered in nutrient-rich liquid medium by addition of glycerol to 0.5 M. Here, we took advantage of the glycerol-induced sporulation process to gain information about the core M. xanthus sprorulation mechanism. We determined changes in the global gene expression at 0.5, 1, 2, and 4 hours after glycerol induction compared to vegetative cells (wild-type DK1622). The expression of nearly 1,500 genes was found to be significantly altered at least two-fold within four hours of glycerol-induced development. Most of the known core sporulation marker genes were up-regulated, whereas most genes required for proper aggregation and fruiting body formation were not significantly regulated. Keywords: Time course of glycerol-induced (0.5 M final conc.) development with 4 time points referenced to vegetative cells 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy3

2010-05-06 | E-GEOD-17912 | biostudies-arrayexpress

Global profiling of gene expression during glycerol-induced spore formation in Myxococcus xanthus

2010-05-06 | GSE17912 | GEO

Global profiling of gene expression in A signal mutants of Myxococcus xanthus

Project description:In response to starvation Myxococcus xanthus initiates a developmental program that culminates in the formation of fruiting bodies inside which the rod-shaped cells differentiate to spores. Fruiting body formation depends on intercellular communication and two intercellular signals are known, the A-signal and the C-signal. Five genes have been identified which are required for A-signal synthesis. To begin to understand the function of the genes required for A-signal synthesis, we have analysed gene expression in the asgA and the asgB mutant. Keywords: Vegetative cells of WT (DK1622) and AsgA mutant (DK5057) and AsgB mutant (DK4398) 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

2012-05-17 | E-GEOD-18029 | biostudies-arrayexpress

Global profiling of gene expression in A signal mutants of Myxococcus xanthus

2012-05-18 | GSE18029 | GEO

5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

Project description:Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. We evaluated the expression of >3,000 genes in the two respective growth stages and demonstrated that almost one-third of these genes were preferentially expressed in either stage, which implicated a significant transcriptomic switch during fruiting body initiation. We annotated >34,000 and >45,000 transcription start sites (TSSs) in the transcriptomes of Myc and S1-Pri respectively. We identified a wealth of potential URGs related to early fruiting events, although their functions and roles are not exactly known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea. 5'-SAGE analysis of the transcriptomes of vegetative mycelium and primordium of C. cinerea by 454 GS20 high-throughput pyrosequencer

2013-01-10 | E-GEOD-40722 | biostudies-arrayexpress

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