ArticleGenome research2011
Parallel evolution of transcriptome architecture during genome reorganization.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 57 citations in OpenAlex.
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- Study of Fe-S Cluster Proteins in Methanococcus maripaludis , a Model Archaeal Organism.Methods in molecular biology (Clifton, N.J.) · 2021Article
- The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances.Microorganisms · 2020Article
- Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754MicrobiologyOpen · 2020Article
- Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.Journal of molecular biology · 2019Review
- Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of theFrontiers in microbiology · 2019Article
- Role of free DNA ends and protospacer adjacent motifs for CRISPR DNA uptake in Pyrococcus furiosus.Nucleic acids research · 2017Article
- Ethanol production by the hyperthermophilic archaeon Pyrococcus furiosus by expression of bacterial bifunctional alcohol dehydrogenases.Microbial biotechnology · 2017Article
- Genomic and transcriptomic landscape of Escherichia coli BL21(DE3).Nucleic acids research · 2017Article
- A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.Nucleic acids research · 2017Article
- A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea.Journal of bacteriology · 2017Article
- Detecting differential growth of microbial populations with Gaussian process regression.Genome research · 2017Article
- Ancillary contributions of heterologous biotin protein ligase and carbonic anhydrase for COBiotechnology and bioengineering · 2016Article
- Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus.BMC genomics · 2016Article
- Heterologous Production of an Energy-Conserving Carbon Monoxide Dehydrogenase Complex in the Hyperthermophile Pyrococcus furiosus.Frontiers in microbiology · 2016Article
- Overlapping genes: a new strategy of thermophilic stress tolerance in prokaryotes.Extremophiles : life under extreme conditions · 2015Article
- Recombinant expression library of Pyrococcus furiosus constructed by high-throughput cloning: a useful tool for functional and structural genomics.Frontiers in microbiology · 2015Article
- PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.Nucleic acids research · 2015Article
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Authors and funding
15 authors at 4 institutions in 2 countries.
Funding
Abstract
Assembly of genes into operons is generally viewed as an important process during the continual adaptation of microbes to changing environmental challenges. However, the genome reorganization events that drive this process are also the roots of instability for existing operons. We have determined that there exists a statistically significant trend that correlates the proportion of genes encoded in operons in archaea to their phylogenetic lineage. We have further characterized how microbes deal with operon instability by mapping and comparing transcriptome architectures of four phylogenetically diverse extremophiles that span the range of operon stabilities observed across archaeal lineages: a photoheterotrophic halophile (Halobacterium salinarum NRC-1), a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and an anaerobic hyperthermophile (Pyrococcus furiosus DSM 3638). We demonstrate how the evolution of transcriptional elements (promoters and terminators) generates new operons, restores the coordinated regulation of translocated, inverted, and newly acquired genes, and introduces completely novel regulation for even some of the most conserved operonic genes such as those encoding subunits of the ribosome. The inverse correlation (r=-0.92) between the proportion of operons with such internally located transcriptional elements and the fraction of conserved operons in each of the four archaea reveals an unprecedented view into varying stages of operon evolution. Importantly, our integrated analysis has revealed that organisms adapted to higher growth temperatures have lower tolerance for genome reorganization events that disrupt operon structures.
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