@article {2372,
	title = {Cell cycle localization dynamics of mitochondrial DNA polymerase IC in African trypanosomes.},
	journal = {Mol Biol Cell},
	volume = {29},
	year = {2018},
	month = {10/2018},
	pages = {2540-2552},
	abstract = {<p>Trypanosoma brucei has a unique catenated mitochondrial DNA (mtDNA) network called kinetoplast DNA (kDNA). Replication of kDNA occurs once per cell cycle in near synchrony with nuclear S phase and requires the coordination of many proteins. Among these are three essential DNA polymerases (TbPOLIB, IC, and ID). Localization dynamics of these proteins with respect to kDNA replication stages and how they coordinate their functions during replication are not well understood. We previously demonstrated that TbPOLID undergoes dynamic localization changes that are coupled to kDNA replication events. Here, we report the localization of TbPOLIC, a second essential DNA polymerase, and demonstrate the accumulation of TbPOLIC foci at active kDNA replication sites (antipodal sites) during stage II of the kDNA duplication cycle. While TbPOLIC was undetectable by immunofluorescence during other cell cycle stages, steady-state protein levels measured by Western blot remained constant. TbPOLIC foci colocalized with the fraction of TbPOLID that localized to the antipodal sites. However, the partial colocalization of the two essential DNA polymerases suggests a highly dynamic environment at the antipodal sites to coordinate the trafficking of replication proteins during kDNA synthesis. These data indicate that cell cycle-dependent localization is a major regulatory mechanism for essential mtDNA polymerases during kDNA replication.</p>
},
	keywords = {Cell Cycle, DNA Replication, DNA, Kinetoplast, DNA-Directed DNA Polymerase, Gene Knockdown Techniques, Gene Silencing, Mitochondria, Protozoan Proteins, S Phase, Trypanosoma brucei brucei},
	issn = {1939-4586},
	doi = {10.1091/mbc.E18-02-0127},
	author = {Concepci{\'o}n-Acevedo, Jeniffer and Miller, Jonathan C and Boucher, Michael J and Klingbeil, Michele M}
}
@article {2374,
	title = {Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA.},
	journal = {PLoS One},
	volume = {10},
	year = {2015},
	month = {2015},
	pages = {e0130998},
	abstract = {<p>Kinetoplast DNA (kDNA), a unique mitochondrial structure common to trypanosomatid parasites, contains thousands of DNA minicircles that are densely packed and can be topologically linked into a chain mail-like network. Experimental data indicate that every minicircle in the network is, on average, singly linked to three other minicircles (i.e., has mean valence 3) before replication and to six minicircles in the late stages of replication. The biophysical factors that determine the topology of the network and its changes during the cell cycle remain unknown. Using a mathematical modeling approach, we previously showed that volume confinement alone can drive the formation of the network and that it induces a linear relationship between mean valence and minicircle density. Our modeling also predicted a minicircle valence two orders of magnitude greater than that observed in kDNA. To determine the factors that contribute to this discrepancy we systematically analyzed the relationship between the topological properties of the network (i.e., minicircle density and mean valence) and its biophysical properties such as DNA bending, electrostatic repulsion, and minicircle relative position and orientation. Significantly, our results showed that most of the discrepancy between the theoretical and experimental observations can be accounted for by the orientation of the minicircles with volume exclusion due to electrostatic interactions and DNA bending playing smaller roles. Our results are in agreement with the three dimensional kDNA organization model, initially proposed by Delain and Riou, in which minicircles are oriented almost perpendicular to the horizontal plane of the kDNA disk. We suggest that while minicircle confinement drives the formation of kDNA networks, it is minicircle orientation that regulates the topological complexity of the network.</p>
},
	keywords = {Cell Cycle, Crithidia fasciculata, DNA Replication, DNA, Kinetoplast, DNA, Mitochondrial},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0130998},
	author = {Diao, Yuanan and Rodriguez, Victor and Klingbeil, Michele and Arsuaga, Javier}
}
@article {380,
	title = {Three mitochondrial DNA polymerases are essential for kinetoplast DNA replication and survival of bloodstream form Trypanosoma brucei.},
	journal = {Eukaryot Cell},
	volume = {10},
	year = {2011},
	month = {2011 Jun},
	pages = {734-43},
	abstract = {Trypanosoma brucei, the causative agent of human African trypanosomiasis, has a complex life cycle that includes multiple life cycle stages and metabolic changes as the parasite switches between insect vector and mammalian host. The parasite{\textquoteright}s single mitochondrion contains a unique catenated mitochondrial DNA network called kinetoplast DNA (kDNA) that is composed of minicircles and maxicircles. Long-standing uncertainty about the requirement of kDNA in bloodstream form (BF) T. brucei has recently eroded, with reports of posttranscriptional editing and subsequent translation of kDNA-encoded transcripts as essential processes for BF parasites. These studies suggest that kDNA and its faithful replication are indispensable for this life cycle stage. Here we demonstrate that three kDNA replication proteins (mitochondrial DNA polymerases IB, IC, and ID) are required for BF parasite viability. Silencing of each polymerase was lethal, resulting in kDNA loss, persistence of prereplication DNA monomers, and collapse of the mitochondrial membrane potential. These data demonstrate that kDNA replication is indeed crucial for BF T. brucei. The contributions of mitochondrial DNA polymerases IB, IC, and ID to BF parasite viability suggest that these and other kDNA replication proteins warrant further investigation as a new class of targets for the development of antitrypanosomal drugs.},
	keywords = {Cell Survival, Cells, Cultured, DNA Replication, DNA, Kinetoplast, DNA-Directed DNA Polymerase, Humans, Membrane Potential, Mitochondrial, Mitochondria, Parasitemia, RNA Interference, Trypanosoma brucei brucei, Trypanosomiasis, African},
	issn = {1535-9786},
	doi = {10.1128/EC.05008-11},
	author = {Bruhn, David F and Sammartino, Mark P and Klingbeil, Michele M}
}
@article {382,
	title = {Mitochondrial DNA polymerase POLIB is essential for minicircle DNA replication in African trypanosomes.},
	journal = {Mol Microbiol},
	volume = {75},
	year = {2010},
	month = {2010 Mar},
	pages = {1414-25},
	abstract = {The unique mitochondrial DNA of trypanosomes is a catenated network of minicircles and maxicircles called kinetoplast DNA (kDNA). The network is essential for survival, and requires an elaborate topoisomerase-mediated release and reattachment mechanism for minicircle theta structure replication. At least seven DNA polymerases (pols) are involved in kDNA transactions, including three essential proteins related to bacterial DNA pol I (POLIB, POLIC and POLID). How Trypanosoma brucei utilizes multiple DNA pols to complete the topologically complex task of kDNA replication is unknown. To fill this gap in knowledge we investigated the cellular role of POLIB using RNA interference (RNAi). POLIB silencing resulted in growth inhibition and progressive loss of kDNA networks. Additionally, unreplicated covalently closed precursors become the most abundant minicircle replication intermediate as minicircle copy number declines. Leading and lagging strand minicircle progeny similarly declined during POLIB silencing, indicating POLIB had no apparent strand preference. Interestingly, POLIB RNAi led to the accumulation of a novel population of free minicircles that is composed mainly of covalently closed minicircle dimers. Based on these data, we propose that POLIB performs an essential role at the core of the minicircle replication machinery.},
	keywords = {DNA Polymerase beta, DNA Replication, DNA, Kinetoplast, Gene Silencing, Protozoan Proteins, Trypanosoma brucei brucei},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2010.07061.x},
	author = {Bruhn, David F and Mozeleski, Brian and Falkin, Laurie and Klingbeil, Michele M}
}
@article {383,
	title = {Unraveling the secrets of regulating mitochondrial DNA replication.},
	journal = {Mol Cell},
	volume = {35},
	year = {2009},
	month = {2009 Aug 28},
	pages = {398-400},
	abstract = {In this issue, Liu et al. (2009) report that maxicircle DNA copy number in trypanosomes is regulated by proteolysis of a helicase; the complex kinetoplast DNA system yields a clear view of how mitochondrial DNA replication can be regulated.},
	keywords = {Animals, DNA Helicases, DNA Replication, DNA, Kinetoplast, DNA, Mitochondrial, DNA, Protozoan, Gene Expression Regulation, Mutation, Peptide Hydrolases, Protozoan Proteins, Time Factors, Trypanosoma brucei brucei},
	issn = {1097-4164},
	doi = {10.1016/j.molcel.2009.08.007},
	author = {Klingbeil, Michele M and Shapiro, Theresa A}
}
@article {384,
	title = {Stem-loop silencing reveals that a third mitochondrial DNA polymerase, POLID, is required for kinetoplast DNA replication in trypanosomes.},
	journal = {Eukaryot Cell},
	volume = {7},
	year = {2008},
	month = {2008 Dec},
	pages = {2141-6},
	abstract = {Kinetoplast DNA (kDNA), the mitochondrial genome of trypanosomes, is a catenated network containing thousands of minicircles and tens of maxicircles. The topological complexity dictates some unusual features including a topoisomerase-mediated release-and-reattachment mechanism for minicircle replication and at least six mitochondrial DNA polymerases (Pols) for kDNA transactions. Previously, we identified four family A DNA Pols from Trypanosoma brucei with similarity to bacterial DNA Pol I and demonstrated that two (POLIB and POLIC) were essential for maintaining the kDNA network, while POLIA was not. Here, we used RNA interference to investigate the function of POLID in procyclic T. brucei. Stem-loop silencing of POLID resulted in growth arrest and the progressive loss of the kDNA network. Additional defects in kDNA replication included a rapid decline in minicircle and maxicircle abundance and a transient accumulation of minicircle replication intermediates before loss of the kDNA network. These results demonstrate that POLID is a third essential DNA Pol required for kDNA replication. While other eukaryotes utilize a single DNA Pol (Pol gamma) for replication of mitochondrial DNA, T. brucei requires at least three to maintain the complex kDNA network.},
	keywords = {Animals, DNA Replication, DNA, Kinetoplast, DNA-Directed DNA Polymerase, Mitochondria, Mitochondrial Proteins, Protozoan Proteins, RNA Interference, RNA, Double-Stranded, Trypanosoma brucei brucei},
	issn = {1535-9786},
	doi = {10.1128/EC.00199-08},
	author = {Chandler, Julian and Vandoros, Anthula V and Mozeleski, Brian and Klingbeil, Michele M}
}
@article {385,
	title = {Closing the gaps in kinetoplast DNA network replication.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {101},
	year = {2004},
	month = {2004 Mar 30},
	pages = {4333-4},
	keywords = {Animals, Crithidia fasciculata, DNA Ligases, DNA Replication, DNA, Kinetoplast, DNA, Mitochondrial, Microscopy, Electron, Trypanosoma brucei brucei},
	issn = {0027-8424},
	doi = {10.1073/pnas.0401400101},
	author = {Klingbeil, Michele M and Englund, Paul T}
}
@article {388,
	title = {Multiple mitochondrial DNA polymerases in Trypanosoma brucei.},
	journal = {Mol Cell},
	volume = {10},
	year = {2002},
	month = {2002 Jul},
	pages = {175-86},
	abstract = {Kinetoplast DNA (kDNA), the unusual mitochondrial DNA of Trypanosoma brucei, is a network containing thousands of catenated circles. Database searching for a kDNA replicative polymerase (pol) revealed no mitochondrial pol gamma homolog. Instead, we identified four proteins (TbPOLIA, IB, IC, and ID) related to bacterial pol I. Remarkably, all four localized to the mitochondrion. TbPOLIB and TbPOLIC localized beside the kDNA where replication occurs, and their knockdown by RNA interference caused kDNA network shrinkage. Furthermore, silencing of TbPOLIC caused loss of both minicircles and maxicircles and accumulation of minicircle replication intermediates, consistent with a role in replication. While typical mitochondria contain one DNA polymerase, pol gamma, trypanosome mitochondria contain five such enzymes, including the previously characterized pol beta.},
	keywords = {Amino Acid Sequence, Animals, DNA, Kinetoplast, DNA-Directed DNA Polymerase, Mitochondria, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, Protein Transport, RNA, Double-Stranded, RNA, Messenger, Sequence Homology, Amino Acid, Trypanosoma brucei brucei},
	issn = {1097-2765},
	author = {Klingbeil, Michele M and Motyka, Shawn A and Englund, Paul T}
}
@article {389,
	title = {Replication of kinetoplast DNA: an update for the new millennium.},
	journal = {Int J Parasitol},
	volume = {31},
	year = {2001},
	month = {2001 May 1},
	pages = {453-8},
	abstract = {In this review we will describe the replication of kinetoplast DNA, a subject that our lab has studied for many years. Our knowledge of kinetoplast DNA replication has depended mostly upon the investigation of the biochemical properties and intramitochondrial localisation of replication proteins and enzymes as well as a study of the structure and dynamics of kinetoplast DNA replication intermediates. We will first review the properties of the characterised kinetoplast DNA replication proteins and then describe our current model for kinetoplast DNA replication.},
	keywords = {Animals, Crithidia fasciculata, DNA Replication, DNA, Kinetoplast, Forecasting},
	issn = {0020-7519},
	author = {Morris, J C and Drew, M E and Klingbeil, M M and Motyka, S A and Saxowsky, T T and Wang, Z and Englund, P T}
}
@article {387,
	title = {Unlocking the secrets of trypanosome kinetoplast DNA network replication.},
	journal = {Protist},
	volume = {152},
	year = {2001},
	month = {2001 Dec},
	pages = {255-62},
	keywords = {Animals, DNA Replication, DNA, Kinetoplast, Protozoan Proteins, Trypanosoma brucei brucei},
	issn = {1434-4610},
	author = {Klingbeil, M M and Drew, M E and Liu, Y and Morris, J C and Motyka, S A and Saxowsky, T T and Wang, Z and Englund, P T}
}
