scholarly journals Advances in bacterial transcriptome understanding: From overlapping transcription to the excludon concept

2020 ◽  
Vol 113 (3) ◽  
pp. 593-602 ◽  
Author(s):  
Alejandro Toledo‐Arana ◽  
Iñigo Lasa
Keyword(s):  
Overlapping Transcription ◽  
Bacterial Transcriptome

scholarly journals Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling

2020 ◽  
Vol 64 (3) ◽  
Author(s):  
Aubrie O’Rourke ◽  
Sinem Beyhan ◽  
Yongwook Choi ◽  
Pavel Morales ◽  
Agnes P. Chan ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Public Health Problem ◽  
Transcriptome Profiling ◽  
Health Crisis ◽  
Rapid Spread ◽  
Pure Compounds ◽  
Bacterial Transcriptome ◽  
Antibiotic Discovery

ABSTRACT Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread of drug-resistant bacterial pathogens is causing a global health crisis. To facilitate the drug discovery processes, we present a large-scale study of reference antibiotic challenge bacterial transcriptome profiles, which included 37 antibiotics across 6 mechanisms of actions (MOAs) and provide an economical approach to aid in antimicrobial dereplication in the discovery process. We demonstrate that classical MOAs can be sorted based upon the magnitude of gene expression profiles despite some overlap in the secondary effects of antibiotic exposures across MOAs. Additionally, using gene subsets, we were able to subdivide broad MOA classes into subMOAs. Furthermore, we provide a biomarker gene set that can be used to classify most antimicrobial challenges according to their canonical MOA. We also demonstrate the ability of this rapid MOA diagnostic tool to predict and classify the expression profiles of pure compounds and crude extracts to their expression profile-associated MOA class.

scholarly journals Bacterial transcriptome reorganization in thermal adaptive evolution

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Bei-Wen Ying ◽  
Yuki Matsumoto ◽  
Kazuki Kitahara ◽  
Shingo Suzuki ◽  
Naoaki Ono ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Bacterial Transcriptome

Overlapping transcription of the nifA regulatory gene in Rhizobium meliloti

Gene ◽  
1986 ◽  
Vol 50 (1-3) ◽  
pp. 141-148 ◽  
Author(s):  
Choong-Hyun Kim ◽  
Donald R. Helinski ◽  
Gary Ditta
Keyword(s):  
Rhizobium Meliloti ◽  
Regulatory Gene ◽  
Overlapping Transcription

scholarly journals Structure and Complexity of a Bacterial Transcriptome

2009 ◽  
Vol 191 (10) ◽  
pp. 3203-3211 ◽  
Author(s):  
Karla D. Passalacqua ◽  
Anjana Varadarajan ◽  
Brian D. Ondov ◽  
David T. Okou ◽  
Michael E. Zwick ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacterial Cell ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Transcript Abundance ◽  
Growth Conditions ◽  
A Genome ◽  
Nucleotide Resolution ◽  
Bacterial Transcriptome

ABSTRACT Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on absolute abundance all provide valuable insights into gene function and regulation, but none has ever been determined on a genome-wide scale for any bacterium. Indeed, these aspects of the prokaryotic transcriptome have been explored on a large scale in only a few instances, and consequently little is known about the absolute composition of the mRNA population within a bacterial cell. Here we report the use of a high-throughput sequencing-based approach in assembling the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome under a variety of growth conditions and showed that the data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the sequence data identified previously nonannotated regions with significant transcriptional activity and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance and suggest that there is significant transcriptional heterogeneity within a clonal, synchronized bacterial population. Overall, our results offer an unprecedented view of gene expression and regulation in a bacterial cell.

scholarly journals Author response: Spatial organization shapes the turnover of a bacterial transcriptome

2016 ◽  
Author(s):  
Jeffrey R Moffitt ◽  
Shristi Pandey ◽  
Alistair N Boettiger ◽  
Siyuan Wang ◽  
Xiaowei Zhuang
Keyword(s):  
Spatial Organization ◽  
Author Response ◽  
Bacterial Transcriptome

Overlapping transcription structure of human cytomegalovirus UL140 and UL141 genes

2013 ◽  
Vol 38 (1) ◽  
pp. 35-44 ◽  
Author(s):  
Yanping Ma ◽  
Mali Li ◽  
Bo Zheng ◽  
Ning Wang ◽  
Shuang Gao ◽  
...  
Keyword(s):  
Human Cytomegalovirus ◽  
Overlapping Transcription

Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing

2011 ◽  
Vol 29 (11) ◽  
pp. 586-594 ◽  
Author(s):  
Melanie Febrer ◽  
Kirsten McLay ◽  
Mario Caccamo ◽  
Kate B. Twomey ◽  
Robert P. Ryan
Keyword(s):  
Second Generation ◽  
Insertion Site ◽  
Transposon Insertion ◽  
Second Generation Sequencing ◽  
Bacterial Transcriptome ◽  
Generation Sequencing
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