title: Genome Sequence and Analysis of Escherichia coli MRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI.
abstract: Escherichia coli strain MRE600 was originally identified for its low RNase I activity and has therefore been widely adopted by the biomedical research community as a preferred source for the expression and purification of transfer RNAs and ribosomes. Despite its widespread use, surprisingly little information about its genome or genetic content exists. Here, we present the first de novo assembly and description of the MRE600 genome and epigenome. To provide context to these studies of MRE600, we include comparative analyses with E. coli K-12 MG1655 (K12). Pacific Biosciences Single Molecule, Real-Time sequencing reads were assembled into one large chromosome (4.83 Mb) and three smaller plasmids (89.1, 56.9, and 7.1 kb). Interestingly, the 7.1-kb plasmid possesses genes encoding a colicin E1 protein and its associated immunity protein. The MRE600 genome has a G + C content of 50.8% and contains a total of 5,181 genes, including 4,913 protein-encoding genes and 268 RNA genes. We identified 41,469 modified DNA bases (0.83% of total) and found that MRE600 lacks the gene for type I methyltransferase, EcoKI. Phylogenetic, taxonomic, and genetic analyses demonstrate that MRE600 is a divergent E. coli strain that displays features of the closely related genus, Shigella. Nevertheless, comparative analyses between MRE600 and E. coli K12 show that these two strains exhibit nearly identical ribosomal proteins, ribosomal RNAs, and highly homologous tRNA species. Substantiating prior suggestions that MRE600 lacks RNase I activity, the RNase I-encoding gene, rna, contains a single premature stop codon early in its open-reading frame.
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
authors.forename: Chad M
authors.initials: CM
authors.lastname: Kurylo
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York The Feil Family Brain and Mind Institute, Weill Cornell Medical College, New York, New York.
authors.forename: Noah
authors.initials: N
authors.lastname: Alexander
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Randall A
authors.initials: RA
authors.lastname: Dass
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Parks
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Altman
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: C Theresa
authors.initials: CT
authors.lastname: Vincent
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York The Feil Family Brain and Mind Institute, Weill Cornell Medical College, New York, New York.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York scb2005@med.cornell.edu.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Blanchard
mesh_terms: D057890:Epigenomics; D048168:Escherichia coli K12 / Q000201:enzymology / Q000235:genetics*; D014644:Genetic Variation; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D012259:Ribonuclease, Pancreatic / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics; D012760:Shigella / Q000235:genetics; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000235:genetics*
chemical_list: D012269:Ribosomal Proteins; C093244:DNA modification methylase EcoKI; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); D012259:Ribonuclease, Pancreatic
keywords: Escherichia coli; MRE600; Shigella; colicin; epigenetics; ribonuclease I