The Life-Cycle of Operons [PDF]
PLoS Genetics, 2006 Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood. To elucidate the life-cycle of operons, we compared gene order between Escherichia coli K12 and its relatives and identified the ...
Eric J. Alm, Morgan N Price, Adam Arkin
exaly +7 more sources
Operon Prediction Model Based on Markov Clustering Algorithm [PDF]
International Journal Bioautomation, 2019 There are many operon prediction models, but few methods can be applied to the operon prediction of new sequencing species effectively. In this paper, an operon prediction model based on Markov clustering algorithm is proposed.
Zhenmei Zhang, Yongquan Liang
doaj +3 more sources
Data Mining of Groundwater Genomes for Metagenome-Assembled Genomes (MAGs) Containing Monooxygenase Operons Associated with Contaminant Biodegradation [PDF]
BiologyThis study examined freely available whole genome sequencing (WGS) data for genes associated with contaminant biodegradation. Thirteen WGS datasets (>600 individual samples) involving more than 12,000 Gbases from multiple countries were examined.
Alison M. Cupples +2 more
doaj +2 more sources
Validation of a model of regulation in the tryptophan operon against multiple experiment data using global optimisation [PDF]
, 2009 This paper is concerned with validating a mathematical model of regulation in the tryptophan operon using global optimization. Although a number of models for this biochemical network are proposed, in many cases only qualitative agreement between the ...
Kim, Jung-Su +9 more
core +8 more sources
Co-Directional Chromosomal Clustering of Metabolic Pathway Genes as a Layout Prior for Synthetic Construct Design [PDF]
BioTechMetabolic pathway design tools largely address reaction routes and enzyme choice, whereas a complementary set of questions—how pathway genes are arranged on bacterial chromosomes and whether co-directional neighborhoods can inform multi-gene construct ...
Xiaowei Han +3 more
doaj +2 more sources
microRNAs and the Operon paper
Journal of Molecular Biology, 2011 The "Operon paper" by F. Jacob and J. Monod started 50 years of research into understanding how the expression of genes is regulated on a molecular level. Ten years ago, microRNAs emerged as major regulators of eukaryotic gene expression.
Nikolaus Rajewsky, Rajewsky, N.
core +3 more sources
eLife, 2021 Prokaryotes utilize polycistronic messages (operons) to co-translate proteins involved in the same biological processes. Whether eukaryotes achieve similar regulation by selectively assembling and translating monocistronic messages derived from different
Rohini R Nair +7 more
doaj +1 more source
Reporter Gene-Based qRT-PCR Assay for Rho-Dependent Termination In Vivo
Cells, 2023 In bacteria, the Rho protein mediates Rho-dependent termination (RDT) by identifying a non-specific cytosine-rich Rho utilization site on the newly synthesized RNA. As a result of RDT, downstream RNA transcription is reduced.
Monford Paul Abishek N +3 more
doaj +1 more source
Operon-SEQer ensemble tested against new data sets.
, 2022 Recall (blue) and specificity (red) of the Operon-SEQer ensemble with algorithm agreement cutoffs of 1–6 for operon pair calls for the new data set from (A) B. subtilis, (B) P. syringiae, and (C) M. tuberculosis. (TIF)
Raga Krishnakumar (11909990) +1 more
core +2 more sources
Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT
Frontiers in Microbiology, 2022 Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors.
Lorenzo Cimmino +3 more
doaj +1 more source