Using shotgun sequence data to find active restriction enzyme genes

Whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a biological experiment. It determines which segments of the genome can be cloned into Escherichia coli and which cannot. By analyzing the complete set of sequences from such an experiment, it is possible to identify genes lethal to E. coli. Among this set are genes encoding restriction enzymes which, when active in E. coli, lead to cell death by cleaving the E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence data sets we show that this is a reliable method to detect active restriction enzyme genes in newly sequenced genomes, thereby facilitating functional annotation. Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus.

[1]  P. L. Deininger,et al.  DNA sequence and expression of the B95-8 Epstein—Barr virus genome , 1984, Nature.

[2]  H. Smith,et al.  A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. , 1970, Journal of molecular biology.

[3]  H. Smith,et al.  A restriction enzyme from Hemophilus influenzae. II. , 1970, Journal of molecular biology.

[4]  Shuang-yong Xu,et al.  Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI. , 2004, Journal of molecular biology.

[5]  Anders F. Andersson,et al.  Functional Analysis of the M.HpyAIV DNA Methyltransferase of Helicobacter pylori , 2007, Journal of bacteriology.

[6]  W. D. de Vos,et al.  Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene. , 1992, Nucleic acids research.

[7]  Peer Bork,et al.  Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer , 2007, Science.

[8]  R J Roberts,et al.  Comparative genomics of the restriction-modification systems in Helicobacter pylori , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[9]  K. Murray,et al.  Recognition sequence of restriction endonuclease III from Hemophilus influenzae. , 1975, Journal of molecular biology.

[10]  D. Mccormick Sequence the Human Genome , 1986, Bio/Technology.

[11]  G. Wilson,et al.  Cloning the DdeI restriction-modification system using a two-step method. , 1986, Nucleic acids research.

[12]  R J Roberts,et al.  Predictive motifs derived from cytosine methyltransferases. , 1989, Nucleic acids research.

[13]  R. Roberts,et al.  Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. , 2000, Nucleic acids research.

[14]  Richard J. Roberts,et al.  REBASE—enzymes and genes for DNA restriction and modification , 2007, Nucleic Acids Res..

[15]  A. Janulaitis,et al.  Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases. , 1989, Nucleic acids research.

[16]  D. Hughes,et al.  The Epstein–Barr Virus Genome , 2009 .

[17]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[18]  B. Slatko,et al.  Cloning, analysis and expression of the HindIII R-M-encoding genes. , 1994, Gene.

[19]  Katherine H. Kang,et al.  Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath) , 2004, PLoS biology.

[20]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[21]  M. Marinus,et al.  Isolation of Deoxyribonucleic Acid Methylase Mutants of Escherichia coli K-12 , 1973, Journal of bacteriology.

[22]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[23]  Hamilton O. Smith,et al.  A restriction enzyme from Hemophilus influenzae: II. Base sequence of the recognition site , 1970 .

[24]  H. Kong,et al.  Characterization of a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities. , 1993, The Journal of biological chemistry.

[25]  Hirokazu Kotani,et al.  Cloning, nucleotide sequence, and expression of the HincII restriction- modification system , 1990, Nucleic Acids Res..

[26]  J Messing,et al.  A system for shotgun DNA sequencing. , 1981, Nucleic acids research.

[27]  A. Bhagwat,et al.  A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene , 1990, Journal of bacteriology.

[28]  David A Rasko,et al.  The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. , 2004, Nucleic acids research.

[29]  Stepwise cloning and molecular characterization of the HgiDI restriction-modification system from Herpetosiphon giganteus Hpa2. , 1991, Nucleic acids research.

[30]  H. Fritz,et al.  The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease , 1991, Nature.

[31]  K. Lunnen,et al.  Cloning type-II restriction and modification genes. , 1988, Gene.