ArticleProceedings of the National Academy of Sciences of the United States of America2005
Predicted highly expressed genes in archaeal genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 60 citations in OpenAlex.
- Article
- Recent Advances in Archaeal Translation Initiation.Frontiers in microbiology · 2020Review
- Codon usage pattern and predicted gene expression inGene: X · 2019Article
- Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1.RNA biology · 2019Article
- Article
- Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis.Molecular biology and evolution · 2018Article
- Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis.Nucleic acids research · 2017Article
- Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes.Genomics & informatics · 2017Article
- Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins.Journal of genetics · 2016Article
- Origin and Functional Evolution of the Cdc48/p97/VCP AAA+ Protein Unfolding and Remodeling Machine.Journal of molecular biology · 2016Review
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
- Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.PloS one · 2015Article
- Nucleotides Flanking the Start Codon in hsp70 mRNAs with Very Short 5'-UTRs Greatly Affect Gene Expression in Haloarchaea.PloS one · 2015Article
- Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization.Molecular biology reports · 2014Article
- A new vector for identification of prokaryotes and their variable-size genomes.Current microbiology · 2013Article
- Article
- Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis.Biology letters · 2011Article
- Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression.Journal of bacteriology · 2010Article
- Translational selection is ubiquitous in prokaryotes.PLoS genetics · 2010Article
- Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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4 authors at 1 institution in 1 country.
Funding
Abstract
Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and Euryarchaea. Archaea generally thrive in extreme environments as assessed by temperature, pH, and salinity. For many prokaryotic organisms, ribosomal proteins (RP), transcription/translation factors, and chaperone genes tend to be highly expressed. A gene is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage of at least one of the RP, transcription/translation factors, and chaperone gene classes and deviates strongly from the average gene of the genome. The thermosome (Ths) chaperonin family represents the most salient PHX genes among Archaea. The chaperones Trigger factor and HSP70 have overlapping functions in the folding process, but both of these proteins are lacking in most archaea where they may be substituted by the chaperone prefoldin. Other distinctive PHX proteins of Archaea, absent from Bacteria, include the proliferating cell nuclear antigen PCNA, a replication auxiliary factor responsible for tethering the catalytic unit of DNA polymerase to DNA during high-speed replication, and the acidic RP P0, which helps to initiate mRNA translation at the ribosome. Other PHX genes feature Cell division control protein 48 (Cdc48), whereas the bacterial septation proteins FtsZ and minD are lacking in Crenarchaea. RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea.
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