Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: We examine a type of genetic element that can move within host genomes called a transposon. These elements very frequently encode resistance to antibiotics and/or other attributes that are useful to the host organism. The specific elements we study appear to direct their movement into DNA that is undergoing specific forms of DNA replication and repair thereby providing information about these processes. We are dissecting transposons in diverse bacteria in hope of establishing a new paradigm for gene transport by selective transposition. PARTICIPANTS: Kayla Valdes (Undergraduate Researcher), Spencer Zhang (Undergraduate Researcher), Seo In Kim (Undergraduate Researcher), Zaoping Li (Graduate Researcher), and Qiaojuan Shi (Postdoctoral Researcher) TARGET AUDIENCES: Researches interested in molecular mechanisms of DNA replication, DNA recombination, or DNA repair are the target audience. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
We are determining molecular mechanisms that affect the maintenance of genetic information in bacteria. This work provides information on how bacteria evolve new functions, like novel degradation pathways and pathogenicity functions. Work in this bacterial system also provides insight into how genetic information is maintained in higher organisms, including humans, and is relevant to cancer. More specifically we examine a genetic element that can move within host genomes called a transposon. The transposon that we focus on was originally isolated in a calf, but is commonly found worldwide in hospital settings. We find that this same element has dispersed between a remarkable number of highly diverse bacteria in disparate environments. We continue to probe how this genetic element can be so widely dispersed. We have evidence that there is a functional interaction between the host DNA polymerase and the transposon proteins. In the past year we have continued to amass a great amount of biochemical information indicating that these proteins physically interact. The same mechanism used by the transposon to recognize DNA replication is also used by the host to switch between various DNA polymerases, a property that is important in all organisms to allow for DNA repair. We have established the process using purified proteins to better understand the mechanism.
Publications
- Shi, Q. J. C. Huguet-Tapia and J. E. Peters (2009) Tn917 targets the region where DNA replication terminates in B. subtilis highlighting a difference in chromosome processing in the Firmicutes. Journal of Bacteriology 191:7623-7627
- Parks, A. R., Z. Li, Q. Shi, R. Owens, M. Jin and J. E. Peters (2009) Transposition into replicating DNA occurs thought interaction with the processivity factor. Cell 138:685-695
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Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: We examine a type of genetic element that can move within host genomes called a transposon. These elements very frequently encode resistance to antibiotics and/or other attributes that are useful to the host organism. The specific elements we study appear to direct their movement into DNA that is undergoing specific forms of DNA replication and repair thereby providing information about these processes. We are dissecting transposons in diverse bacteria in hope of establishing a new paradigm for gene transport by selective transposition. We are determining molecular mechanisms that affect the maintenance of genetic information in bacteria. This work provides information on how bacteria evolve new functions, like novel degradation pathways and pathogenicity functions. Work in this bacterial system also provides insight into how genetic information is maintained in higher organisms, including humans, and is relevant to cancer. More specifically we examine a genetic element that can move within host genomes called a transposon. The transposon that we focus on was originally isolated in a calf, but is commonly found worldwide in hospital settings. We find that this same element has dispersed between a remarkable number of highly diverse bacteria in disparate environments. We continue to probe how this genetic element can be so widely dispersed. We have evidence that there is a functional interaction between the host DNA polymerase and the transposon proteins. In the past year we have continued to amass a great amount of biochemical information indicating that these proteins physically interact. The same mechanism used by the transposon to recognize DNA replication is also used by the host to switch between various DNA polymerases, a property that is important in all organisms to allow for DNA repair. We are trying to establish the process using purified proteins to better understand the mechanism. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Our work indicates new ways that genetic information can spread to different environments. This is because the ability to target bacterial viruses would greatly maximize the distribution of the transposon. We also show for the first time that transposons can form genomic islands. We now have evidence of a physical interaction between transposon proteins and the 'processivity factor' used during DNA replication. Many repair proteins involved in DNA repair and replication will interact with the processivity factor to recognize the site where they are needed. Our work provides insight into how and when these repair processes operate. We published three publications last year. Two of these articles were solely from our lab. The third article was a collaborative project with another laboratory in the Department of Microbiology.
Publications
- Parks, A. R. and J. E. Peters (2009) Tn7 elements: Engendering diversity from chromosomes to episomes. Plasmid 61:1-14 (published electronically November 1st 2008).
- Shi, Q., A. R. Parks, B. Potter, I. J. Safir, Y. Luo, B. M. Forster and J. E. Peters (2008) DNA damage differentially activates regional chromosomal loci for Tn7 transposition. Genetics 179:1237-1250.
- Bordi, C., B. Butcher, B., A. B. Hachmann, Q. Shi, J. E. Peters, and J. D. Helmann (2008) In vitro mutagenesis of Bacillus subtilis using a modified Tn7 with an outward facing inducible promoter. Applied and Environmental Microbiology 74:3419-3425.
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Progress 10/01/06 to 09/30/07
Outputs
We examine a type of genetic element that can move within host genomes called a transposon. These elements very frequently encode resistance to antibiotics and/or other attributes that are useful to the host organism. The specific elements we study appear to direct their movement into DNA that is undergoing specific forms of DNA replication and repair thereby providing information about these processes. We are dissecting transposons in diverse bacteria in hope of establishing a new paradigm for gene transport by selective transposition. We are determining molecular mechanisms that affect the maintenance of genetic information in bacteria. This work provides information on how bacteria evolve new functions, like novel degradation pathways and pathogenicity functions. Work in this bacterial system also provides insight into how genetic information is maintained in higher organisms, including humans, and is relevant to cancer. More specifically we examine a genetic
element that can move within host genomes called a transposon. The transposon that we focus on was originally isolated in a calf, but is commonly found worldwide in hospital settings. We find that this same element has dispersed between a remarkable number of highly diverse bacteria in disparate environments. We continue to probe how this genetic element can be so widely dispersed. We have evidence that there is a functional interaction between the host DNA polymerase and the transposon proteins. In the past year we have also amassed a great amount of biochemical information that these proteins physically interact. Our work indicates that this ability to recognize certain forms of DNA replication allows the transposon to move to new bacteria using viruses found in bacteria. The same mechanism used by the transposon to recognize DNA replication is also used by the host to switch between various DNA polymerases, a property that is important in all organisms to allow for DNA repair. We
are trying to establish the process using purified proteins to better understand the mechanism.
Impacts
Our work indicates new ways that genetic information can spread to different environments. This is because the ability to target bacterial viruses would greatly maximize the distribution of the transposon. We also show for the first time that transposons can form genomic islands. We now have evidence of a physical interaction between transposon proteins and the 'processivity factor' used during DNA replication. Many repair proteins involved in DNA repair and replication will interact with the processivity factor to recognize the site where they are needed. Our work provides insight into how and when these repair processes operate. We published four publications last year. Two of these were primary literature articles solely from our lab. I also published two book chapters. One was on transposons and other forms of mobile DNA for a molecular biology textbook. The other chapter was on methods in bacterial genetics for a text from the American Society of Microbiology.
Publications
- Peters, J. E. 2007. Gene transfer in gram-negative bacteria, Chapter 31. In C. A. Reddy, T. J. Beveridge, J. A. Breznak, G. A. Marzluf, T. M. Schmidt, and L. R. Snyder (eds.), Methods for General and Molecular Microbiology, 3rd ed. ASM Press, Washington, D.C.
- Finn, J. A., A. R. Parks, and J. E. Peters. 2007. Tn7 Directs Transposition into the Genome of Filamentous Bacteriophage M13 Using the Element-Encoded TnsE Protein. Journal of Bacteriology 189:9122-9125
- Parks, A. R., and Peters J. E. 2007. Transposon Tn7 is Widespread in Diverse Bacteria and Forms Genomic Islands. Journal of Bacteriology 189:2170-2173
- Peters, J. E. 2007. Transposons and Other Mobile Elements in Molecular Biology: Genes to Proteins, Third Edition by Burton E. Tropp pp. 504-551 Jones and Bartlett Publishing
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Progress 01/01/06 to 12/31/06
Outputs
We are determining molecular mechanisms that affect the maintenance of genetic information in bacteria. This work provides information on how bacteria evolve new functions, like novel degradation pathways and pathogenicity functions. Work in this bacterial system also provides insight into how genetic information is maintained in higher organisms, including humans, and is relevant to cancer. More specifically we examine a genetic element that can move within host genomes called a transposon. The transposon that we focus on was originally isolated in a calf, but is commonly found worldwide in hospital settings. We find that this same element has dispersed between a remarkable number of highly diverse bacteria in disparate environments. We continue to probe how this genetic element can be so widely dispersed. We have evidence that there is a functional interaction between the host DNA polymerase and the transposon proteins. In the past year we have also amassed a great
amount of biochemical information that these proteins physically interact. Our work indicates that this ability to recognize certain forms of DNA replication allows the transposon to move to new bacteria using viruses found in bacteria. The same mechanism used by the transposon to recognize DNA replication is also used by the host to switch between various DNA polymerases, a property that is important in all organisms to allow for DNA repair. We are trying to establish the process using purified proteins to better understand the mechanism.
Impacts
Our work indicates new ways that genetic information can spread to different environments. This is because the ability to target bacterial viruses would greatly maximize the distribution of the transposon. We also show for the first time that transposons can for genomic islands. We now have evidence of a physical interaction between transposon proteins and the 'processivity factor' used during DNA replication. Many repair proteins involved in DNA repair and replication will interact with the processivity factor to recognize the site where they are needed. Our work provides insight into how and when these repair processes operate. We published one collaborative publication last year. We have other articles in press, in revision, and in preparation. I also completed a chapter on transposons and other forms of mobile DNA for a molecular biology textbook.
Publications
- Junker, L. M., J. E. Peters, and A. G. Hay. 2006. Global analysis of candidate genes important for fitness in a competitive biofilm using DNA-array-based transposon mapping. Microbiology. 152:2233-2245
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Progress 01/01/05 to 12/31/05
Outputs
We are determining molecular mechanisms that affect the maintenance of genetic information in bacteria. This work provides information on how bacteria evolve new functions, like novel degradation pathways and pathogenicity functions. Work in this bacterial system also provides insight into how genetic information is maintained in higher organisms, including humans, and is relevant to cancer. More specifically we examine a genetic element that can move within host genomes called a transposon. The transposon that we focus on was originally isolated in a calf, but is commonly found worldwide in hospital settings. We find that this same element has dispersed between a remarkable number of highly diverse bacteria in disparate environments. We continue to probe how this genetic element can be so widely dispersed. We now have evidence that there is a functional interaction between the host DNA polymerase and the transposon proteins. Our work indicates that this ability to
recognize certain forms of DNA replication allows the transposon to move to new bacteria using viruses found in bacteria. The same mechanism used by the transposon to recognize DNA replication is also used by the host to switch between various DNA polymerases, a property that is important in all organisms to allow for DNA repair. We are trying to establish the process using purified proteins to better understand the mechanism.
Impacts
Our work indicates new ways that genetic information can spread to different environments. This is because the ability to target bacterial viruses would greatly maximize the distribution of the transposon. This work is in the process of revision for publication. We now have evidence of a functional interaction between transposon proteins and the 'processivity factor' used during DNA replication. Many repair proteins involved in DNA repair and replication will interact with the processivity factor to recognize the site where they are needed. Our work provides insight into how and when these repair processes operate. We are currently working on three manuscripts that should be submitted for publication in the coming months. Last year I also completed a chapter for an upcoming methods book for microbiology that is currently 'in press'.
Publications
- No publications reported this period
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Progress 01/01/04 to 12/31/04
Outputs
We are determining molecular mechanisms that affect the maintenance of genetic information in bacteria. This work provides information on how bacteria evolve new functions, like novel degradation pathways and pathogenicity functions. Work in this bacterial system also provides insight into how genetic information is maintained in higher organisms, including humans, and is relevant to cancer. More specifically we examine a genetic element that can move within host genomes called a transposon in the bacterium Escherichia coli. This element specifically inserts into DNA that is undergoing DNA repair thereby providing information about DNA repair. We are also examining gene acquisition in the bacterium Enterococcus faecalis. Enterococcus faecalis is an important pathogen, but also seems to handle mobile DNA in an unusual way. E. faecalis has more mobile DNA than any other bacterium that has been sequenced to date. Its ability to accumulate DNA seems to be of key value in
being a pathogen. Surprisingly we are finding common themes for how very different mobile genetic elements are able to recognize features of DNA replication to allow sharing of genetic information. The same system that is used in the gram-negative bacterium E. coli seems to operate in gram-positive bacterium E. faecalis. In addition we find the same system of transfer may be operating in diverse aquatic environments based on DNA sequence information. This work suggests that the information we gather in our system will be broadly applicable in describing gene transfer throughout nature. We also have preliminary evidence that mobile DNA may be interacting with the host DNA polymerase machine. Specifically, by analyzing the sequences shared between the many new homologs of our mobile element we find a sequence that is known to be used by some proteins to interact with DNA polymerase holoenzyme. Consistent with this idea we find that when we mutate individual amino acids in this sequence
we see a loss of most or all activity for the mobile element.
Impacts
We expect that our work will lead to a new paradigm for how drug resistance moves between bacteria. This will have a great impact on the way we look at drug resistance in both agricultural and medical settings. These findings will be extendable to diverse environments because of the homologs we identified in multiple aquatic environments. Our work will likely impact the field of DNA repair and cancer. We have strong preliminary evidence that our mobile element can interact with a protein called the 'processivity factor' used during DNA replication. Many repair proteins involved in DNA repair and replication will interact with the processivity factor to recognize the site where they are needed. Our work will provide insight into how and when these repair processes operate. We are currently working on three manuscripts that should be submitted for publication in the coming months.
Publications
- Garsin, D.A., Urbach, J., Huguet-Tapia, J.C., Peters, J.E., and Ausubel, F.M. 2004. Construction of an Enterococcus faecalis Tn917-mediated gene disruption library offers insight into Tn917 insertion patterns. Journal of Bacteriology 186:7280-7289.
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