This project takes advantage of a DNA sequencing technology newly developed by Pacific Biosciences called SMRT sequencing. In addition to providing the DNA base sequence, this approach also allows the detection of modified bases. DNA methyltransferases have traditionally been rather difficult to characterize and as a result, we do not currently know the accurate DNA recognition specificity of any DNA methyltransferases. In the case of those that form part of restriction-modification systems, it has always been assumed that they will have the same recognition specificity as the restriction enzyme. However, in some systems preliminary results indicated that this might not be so, and we now in a position to test that explicitly. A knowledge of the specificity will be key on many fronts. Firstly, in some cases it will allow these methyltransferases to become valuable commercial reagents. Secondly, we expect to discover novel DNA methyltransferases with properties that would make them suitable for specific applications. One such enzyme discovered very recently, is M.EcoGI, which appears to recognize all A residues in a sequence and convert them at very high efficiency to N6- methyladenine. The results of this project will also greatly enhance the value of the cloned restriction-modification systems that we have at New England Biolabs and will also help considerably in the functional annotation of newly determined DNA sequences. It is an ideal blend of academic and commercial research and therefore is especially suited for New England Biolabs.

Public Health Relevance

This project will characterize a large number of DNA methyltransferase genes in terms of their DNA recognition sequences as well as the specific base modified. These methyltransferases, once characterized, can serve as useful research reagents and their characterization will also help to improve genome annotation, which can be especially important for bacterial pathogens.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Small Business Innovation Research Grants (SBIR) - Phase II (R44)
Project #
4R44GM105125-02
Application #
8581665
Study Section
Special Emphasis Panel (ZRG1-IMST-J (15))
Program Officer
Maas, Stefan
Project Start
2012-09-28
Project End
2015-02-28
Budget Start
2013-03-28
Budget End
2014-02-28
Support Year
2
Fiscal Year
2013
Total Cost
$501,060
Indirect Cost
Name
New England Biolabs, Inc.
Department
Type
DUNS #
066605403
City
Ipswich
State
MA
Country
United States
Zip Code
01938
Ee, Robson; Lim, Yan-Lue; Yin, Wai-Fong et al. (2016) Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. Front Microbiol 7:1362
Yao, Kuan; Muruvanda, Tim; Roberts, Richard J et al. (2016) Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar Sloterdijk (ATCC 15791). Genome Announc 4:
Yao, Kuan; Muruvanda, Tim; Roberts, Richard J et al. (2016) Complete Genome and Methylome Sequences of Two Salmonella enterica spp. Genome Announc 4:
Fomenkov, Alexey; Vincze, Tamas; Grabovich, Margarita et al. (2016) Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring. Genome Announc 4:
Blow, Matthew J; Clark, Tyson A; Daum, Chris G et al. (2016) The Epigenomic Landscape of Prokaryotes. PLoS Genet 12:e1005854
Hoffmann, Maria; Payne, Justin; Roberts, Richard J et al. (2015) Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Agona 460004 2-1, Associated with a Multistate Outbreak in the United States. Genome Announc 3:
Fomenkov, Alexey; Vincze, Tamas; Grabovich, Margarita Y et al. (2015) Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T. Genome Announc 3:
Pirone-Davies, Cary; Hoffmann, Maria; Roberts, Richard J et al. (2015) Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars. PLoS One 10:e0123639
Lee, Woon Ching; Anton, Brian P; Wang, Susana et al. (2015) The complete methylome of Helicobacter pylori UM032. BMC Genomics 16:424
Pettengill, Emily A; Hoffmann, Maria; Binet, Rachel et al. (2015) Complete Genome Sequence of Enteroinvasive Escherichia coli O96:H19 Associated with a Severe Foodborne Outbreak. Genome Announc 3:

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