scholarly journals Analysis of Temporal Gene Expression during Bacillus subtilis Spore Germination and Outgrowth

2007 ◽  
Vol 189 (9) ◽  
pp. 3624-3634 ◽  
Author(s):  
Bart J. F. Keijser ◽  
Alex Ter Beek ◽  
Han Rauwerda ◽  
Frank Schuren ◽  
Roy Montijn ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Spore Germination ◽  
Dependent Manner ◽  
Temporal Gene Expression ◽  
Bacillus Subtilis Spore ◽  
Physiological Processes ◽  
Genome Wide ◽  
Extracellular Metabolites ◽  
A Genome ◽  
Spore Outgrowth

ABSTRACT Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites, and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, the results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30% of the B. subtilis genome.

scholarly journals Genome-Wide Analysis of the Stationary-Phase Sigma Factor (Sigma-H) Regulon of Bacillus subtilis

2002 ◽  
Vol 184 (17) ◽  
pp. 4881-4890 ◽  
Author(s):  
Robert A. Britton ◽  
Patrick Eichenberger ◽  
Jose Eduardo Gonzalez-Pastor ◽  
Paul Fawcett ◽  
Rita Monson ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Transcriptional Profiling ◽  
Open Reading Frames ◽  
Nutrient Sources ◽  
Genome Wide ◽  
A Genome ◽  
Sigma H

ABSTRACT Sigma-H is an alternative RNA polymerase sigma factor that directs the transcription of many genes that function at the transition from exponential growth to stationary phase in Bacillus subtilis. Twenty-three promoters, which drive transcription of 33 genes, are known to be recognized by sigma-H-containing RNA polymerase. To identify additional genes under the control of sigma-H on a genome-wide basis, we carried out transcriptional profiling experiments using a DNA microarray containing >99% of the annotated B. subtilis open reading frames. In addition, we used a bioinformatics-based approach aimed at the identification of promoters recognized by RNA polymerase containing sigma-H. This combination of approaches was successful in confirming most of the previously described sigma-H-controlled genes. In addition, we identified 26 putative promoters that drive expression of 54 genes not previously known to be under the direct control of sigma-H. Based on the known or inferred function of most of these genes, we conclude that, in addition to its previously known roles in sporulation and competence, sigma-H controls genes involved in many physiological processes associated with the transition to stationary phase, including cytochrome biogenesis, generation of potential nutrient sources, transport, and cell wall metabolism.

scholarly journals Genome-wide CRISPR screen identifies ELP5 as a determinant of gemcitabine sensitivity in gallbladder cancer

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Sunwang Xu ◽  
Ming Zhan ◽  
Cen Jiang ◽  
Min He ◽  
Linhua Yang ◽  
...  
Keyword(s):  
Gallbladder Cancer ◽  
Locally Advanced ◽  
Internal Ribosomal Entry Site ◽  
Dependent Manner ◽  
Entry Site ◽  
P53 Expression ◽  
Elongator Complex ◽  
Genome Wide ◽  
A Genome ◽  
Crispr Screen

AbstractGemcitabine is the first-line treatment for locally advanced and metastatic gallbladder cancer (GBC), but poor gemcitabine response is universal. Here, we utilize a genome-wide CRISPR screen to identify that loss of ELP5 reduces the gemcitabine-induced apoptosis in GBC cells in a P53-dependent manner through the Elongator complex and other uridine 34 (U34) tRNA-modifying enzymes. Mechanistically, loss of ELP5 impairs the integrity and stability of the Elongator complex to abrogate wobble U34 tRNA modification, and directly impedes the wobble U34 modification-dependent translation of hnRNPQ mRNA, a validated P53 internal ribosomal entry site (IRES) trans-acting factor. Downregulated hnRNPQ is unable to drive P53 IRES-dependent translation, but rescuing a U34 modification-independent hnRNPQ mutant could restore P53 translation and gemcitabine sensitivity in ELP5-depleted GBC cells. GBC patients with lower ELP5, hnRNPQ, or P53 expression have poor survival outcomes after gemcitabine chemotherapy. These results indicate that the Elongator/hnRNPQ/P53 axis controls gemcitabine sensitivity in GBC cells.

scholarly journals Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper (Piper nigrum L.)

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1740
Author(s):  
Jing Li ◽  
Rui Fan ◽  
Baoduo Wu ◽  
Xunzhi Ji ◽  
Chaoyun Hao
Keyword(s):  
Gene Family ◽  
Purifying Selection ◽  
Tissue Expression ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Tissue Expression Analysis ◽  
Physiological Processes ◽  
Genome Wide ◽  
Go Enrichment ◽  
A Genome

Black pepper (Piper nigrum L.), is dubbed “the King of Spices”. However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes.

scholarly journals Sulfate-Dependent Repression of Genes That Function in Organosulfur Metabolism in Bacillus subtilis Requires Spx

2005 ◽  
Vol 187 (12) ◽  
pp. 4042-4049 ◽  
Author(s):  
Kyle N. Erwin ◽  
Shunji Nakano ◽  
Peter Zuber
Keyword(s):  
Oxidative Stress ◽  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Transcriptional Control ◽  
Sulfur Metabolism ◽  
Growth Conditions ◽  
Sulfur Source ◽  
Dependent Manner ◽  
Α Subunit ◽  
A Genome

ABSTRACT Oxidative stress in Bacillus subtilis results in the accumulation of Spx protein, which exerts both positive and negative transcriptional control over a genome-wide scale through its interaction with the RNA polymerase α subunit. Previous microarray transcriptome studies uncovered a unique class of genes that are controlled by Spx-RNA polymerase interaction under normal growth conditions that do not promote Spx overproduction. These genes were repressed by Spx when sulfate was present as a sole sulfur source. The genes include those of the ytmI, yxeI, and ssu operons, which encode products resembling proteins that function in the uptake and desulfurization of organic sulfur compounds. Primer extension and analysis of operon-lacZ fusion expression revealed that the operons are repressed by sulfate and cysteine; however, Spx functioned only in sulfate-dependent repression. Both the ytmI operon and the divergently transcribed ytlI, encoding a LysR-type regulator that positively controls ytmI operon transcription, are repressed by Spx in sulfate-containing media. The CXXC motif of Spx, which is necessary for redox sensitive control of Spx activity in response to oxidative stress, is not required for sulfate-dependent repression. The yxeL-lacZ and ssu-lacZ fusions were also repressed in an Spx-dependent manner in media containing sulfate as the sole sulfur source. This work uncovers a new role for Spx in the control of sulfur metabolism in a gram-positive bacterium under nonstressful growth conditions.

scholarly journals Analysis of Nucleoid Morphology during Germination and Outgrowth of Spores of Bacillus Species

2000 ◽  
Vol 182 (19) ◽  
pp. 5556-5562 ◽  
Author(s):  
Katerina Ragkousi ◽  
Ann E. Cowan ◽  
Margery A. Ross ◽  
Peter Setlow
Keyword(s):  
Bacillus Subtilis ◽  
Dna Binding ◽  
Bacillus Megaterium ◽  
Spore Germination ◽  
Great Majority ◽  
Dna Binding Proteins ◽  
Soluble Proteins ◽  
Bacillus Species ◽  
Chromosomal Protein ◽  
Spore Outgrowth

ABSTRACT After a few minutes of germination, nucleoids in the great majority of spores of Bacillus subtilis and Bacillus megaterium were ring shaped. The major spore DNA binding proteins, the α/β-type small, acid-soluble proteins (SASP), colocalized to these nucleoid rings early in spore germination, as did the B. megaterium homolog of the major B. subtilis chromosomal protein HBsu. The percentage of ring-shaped nucleoids was decreased in germinated spores with lower levels of α/β-type SASP. As spore outgrowth proceeded, the ring-shaped nucleoids disappeared and the nucleoid became more compact. This change took place after degradation of most of the spores' pool of major α/β-type SASP and was delayed when α/β-type SASP degradation was delayed. Later in spore outgrowth, the shape of the nucleoid reverted to the diffuse lobular shape seen in growing cells.

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