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Are Restriction Enzymes Recognition Sites Underrepresented in the Organisms That Host Them?

Mansour Aly, Dina Gamaleldin (2016) BINP30 20161
Degree Projects in Bioinformatics
Abstract
The restriction modification enzyme system is a vital bacterial defense system against invading phages. Restriction modification system consists of a restriction enzyme and a methyltransferase enzyme that work in a complementary fashion to cut foreign DNA and at the same time methylates and protects host DNA. Recognition site sequence is usually specific for each restriction enzyme. Restriction Recognition Site Representation (RRSR) principally calculates the observed frequency of occurrence of each restriction enzyme recognition site and its expected frequency of occurrence based on the abundance of the four nucleotides in the host’s whole genome sequence. A catalogue of restriction enzymes, their properties and annotation was created.... (More)
The restriction modification enzyme system is a vital bacterial defense system against invading phages. Restriction modification system consists of a restriction enzyme and a methyltransferase enzyme that work in a complementary fashion to cut foreign DNA and at the same time methylates and protects host DNA. Recognition site sequence is usually specific for each restriction enzyme. Restriction Recognition Site Representation (RRSR) principally calculates the observed frequency of occurrence of each restriction enzyme recognition site and its expected frequency of occurrence based on the abundance of the four nucleotides in the host’s whole genome sequence. A catalogue of restriction enzymes, their properties and annotation was created. The result from RRSR was statistically tested in R using Chi square goodness of fit test and the results showed that many restriction enzymes had their recognition sites underrepresented in their host genome. Adaptive bacterial ada regulon system, a system that protects bacterial genome against exogenous DNA methylation by environmental mutagens interacted with the restriction modification system and may have accounted for the bacterial restriction recognition sites underrepresentation. The dimerization state of the enzyme subunits and their gene expression, as well as the net cellular concentration for methyltransferase enzyme and cofactors; S-adenosyl-methionine, ATP and magnesium ions are vital to determine to achieve a conclusive decision about the efficiency of the restriction modification system in the host. RSRR in phage genome supported the fact that phages are bacterial specific paving a way for using phages as targeted bactericidal agents. RRSR confirmed the co-evolution of phages and bacteria. (Less)
Popular Abstract
Do host DNA cutters cut their own DNA?

The restriction-modification enzyme system is a vital bacterial defense system against invading phages. Restriction-modification system consists of a restriction enzyme and a methyltransferase enzyme that works in a complementary fashion to cut foreign DNA and at the same time methylates and protects host DNA. Recognition site sequence is usually specific for each restriction enzyme. There are four types of restriction modification systems.


The aim of the project is to test the hypothesis whether host DNA cutters cut their own DNA. Restriction enzyme Recognition Site Representation is a method designed to compare the observed frequency of each restriction enzyme recognition site and its... (More)
Do host DNA cutters cut their own DNA?

The restriction-modification enzyme system is a vital bacterial defense system against invading phages. Restriction-modification system consists of a restriction enzyme and a methyltransferase enzyme that works in a complementary fashion to cut foreign DNA and at the same time methylates and protects host DNA. Recognition site sequence is usually specific for each restriction enzyme. There are four types of restriction modification systems.


The aim of the project is to test the hypothesis whether host DNA cutters cut their own DNA. Restriction enzyme Recognition Site Representation is a method designed to compare the observed frequency of each restriction enzyme recognition site and its expected frequency based on the restriction recognition site nucleotide sequence. A Restriction Enzyme Catalogue was created for all bacterial genomes, their restriction enzymes name and restriction modification system type and restriction recognition site sequence.

Frequency calculator Perl program is designed to search for each restriction recognition site and its reverse complement in each host bacteria genome based on information about the host bacteria from the Restriction Enzyme Catalogue. The frequency calculator outputs a frequency file of the observed and expected frequency for each restriction recognition site for each hosting bacterial genome. The frequency files of all bacteria genomes were merged in bacteria frequency file. The bacteria frequency file was statistically analyzed by chi-square goodness of fit test in R. The output of R analysis is a single file of the bacteria restriction recognition site representation (RRSR).
The same method of frequency calculation and statistical analysis was applied to plasmid genomes and phage genomes. A restriction enzyme database was created in SQL that can be accessed by web interface. The web interface is user friendly and gives information about RRSR in bacteria, gene cloning, recombinant DNA and phage therapy.

Results.
RRSR in bacteria showed that many restriction enzymes had their recognition sites underrepresented in their host genome highlighting the efficiency of the restriction-modification system is not complete. However, the dimerization state of the enzyme subunits and their gene expression, as well as the net cellular concentration for methyltransferase enzyme and cofactors; S-adenosyl-methionine, ATP and magnesium ions are vital to determine to achieve a conclusive decision about the efficiency of the restriction-modification system in the host. RSRR in phage genome supported the fact that phages are bacteria-specific paving a way for using phages as targeted bactericidal agents. RRSR confirmed the co-evolution of phages and bacteria.
Master’s Degree Project in Bioinformatics 30 credits 2016

Supervisor: Björn Canbäck.
Master's Degree Project 30 credits in Bioinformatics, 2016
Department of Biology, Lund University, Lund, Sweden. (Less)
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author
Mansour Aly, Dina Gamaleldin
supervisor
organization
course
BINP30 20161
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8891395
date added to LUP
2016-09-12 09:32:57
date last changed
2016-09-12 09:32:57
@misc{8891395,
  abstract     = {The restriction modification enzyme system is a vital bacterial defense system against invading phages. Restriction modification system consists of a restriction enzyme and a methyltransferase enzyme that work in a complementary fashion to cut foreign DNA and at the same time methylates and protects host DNA. Recognition site sequence is usually specific for each restriction enzyme. Restriction Recognition Site Representation (RRSR) principally calculates the observed frequency of occurrence of each restriction enzyme recognition site and its expected frequency of occurrence based on the abundance of the four nucleotides in the host’s whole genome sequence. A catalogue of restriction enzymes, their properties and annotation was created. The result from RRSR was statistically tested in R using Chi square goodness of fit test and the results showed that many restriction enzymes had their recognition sites underrepresented in their host genome. Adaptive bacterial ada regulon system, a system that protects bacterial genome against exogenous DNA methylation by environmental mutagens interacted with the restriction modification system and may have accounted for the bacterial restriction recognition sites underrepresentation. The dimerization state of the enzyme subunits and their gene expression, as well as the net cellular concentration for methyltransferase enzyme and cofactors; S-adenosyl-methionine, ATP and magnesium ions are vital to determine to achieve a conclusive decision about the efficiency of the restriction modification system in the host. RSRR in phage genome supported the fact that phages are bacterial specific paving a way for using phages as targeted bactericidal agents. RRSR confirmed the co-evolution of phages and bacteria.},
  author       = {Mansour Aly, Dina Gamaleldin},
  language     = {eng},
  note         = {Student Paper},
  title        = {Are Restriction Enzymes Recognition Sites Underrepresented in the Organisms That Host Them?},
  year         = {2016},
}