Interactions of a Replication Initiator with Histone H1-like Proteins Remodel the Condensed Mitochondrial Genome

Kapeller, Irit; Milman, Neta; Yaffe, Nurit; Shlomai, Joseph

doi:10.1074/jbc.m111.270322

Cited by 12 publications

(24 citation statements)

References 48 publications

(46 reference statements)

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“…However, protein-protein interactions between CfKAP3 and CfUMSBP can decondense these networks and restore topo IImediated decatenation (14). This indicates that trypanosomatid KAP proteins could have different roles in different species, especially when they have limited homology, such as between CfKAP3 and TbKAP6.…”

Section: Discussionmentioning

confidence: 98%

“…The major protein to be involved in minicircle release must be a type II topoisomerase (12,13). More recently, in vitro studies have demonstrated that Crithidia fasciculata universal minicircle sequence-binding protein (CfUMSBP) can decondense CfkDNA networks that had been condensed by CfKAP3 or CfKAP4 (14). CfUMSBP is well known to bind the origin sequence (universal minicircle sequence [UMS]), but CfUMSBPmediated decondensation depends upon interactions between two proteins and not the DNA.…”

mentioning

confidence: 99%

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TbKAP6, a Mitochondrial HMG Box-Containing Protein in Trypanosoma brucei, Is the First Trypanosomatid Kinetoplast-Associated Protein Essential for Kinetoplast DNA Replication and Maintenance

et al. 2014

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Kinetoplast DNA (kDNA), the mitochondrial genome of trypanosomatids, is a giant planar network of catenated minicircles and maxicircles. In vivo kDNA is organized as a highly condensed nucleoprotein disk. So far, in Trypanosoma brucei, proteins involved in the maintenance of the kDNA condensed structure remain poorly characterized. In Crithidia fasciculata, some small basic histone H1-like kinetoplast-associated proteins (CfKAP) have been shown to condense isolated kDNA networks in vitro. High-mobility group (HMG) box-containing proteins, such as mitochondrial transcription factor A (TFAM) in mammalian cells and Abf2 in the budding yeast, have been shown essential for the packaging of mitochondrial DNA (mtDNA) into mitochondrial nucleoids, remodeling of mitochondrial nucleoids, gene expression, and maintenance of mtDNA. Here, we report that TbKAP6, a mitochondrial HMG box-containing protein, is essential for parasite cell viability and involved in kDNA replication and maintenance. The RNA interference (RNAi) depletion of TbKAP6 stopped cell growth. Replication of both minicircles and maxicircles was inhibited. RNAi or overexpression of TbKAP6 resulted in the disorganization, shrinkage, and loss of kDNA. Minicircle release, the first step in kDNA replication, was inhibited immediately after induction of RNAi, but it quickly increased 3-fold upon overexpression of TbKAP6. Since the release of covalently closed minicircles is mediated by a type II topoisomerase (topo II), we examined the potential interactions between TbKAP6 and topo II. Recombinant TbKAP6 (rTbKAP6) promotes the topo II-mediated decatenation of kDNA. rTbKAP6 can condense isolated kDNA networks in vitro. These results indicate that TbKAP6 is involved in the replication and maintenance of kDNA.T rypanosoma brucei is a unicellular eukaryotic parasite that causes human African trypanosomiasis (HAT) and nagana in livestock in sub-Saharan Africa. The high toxicity of most current chemotherapies and the emergence of drug-resistant parasites are stimulating efforts to identify promising molecular targets and develop next-generation therapeutics (1, 2). These efforts require better understanding of trypanosome basic biology, which differs markedly from that of its host. For instance, trypanosome mitochondrial DNA is organized as a massive chain mail-like network, known as kinetoplast DNA (kDNA). kDNA consists of several thousand minicircles (1 kb) catenated with a few dozen maxicircles (23 kb). This giant planar network is condensed into a disk within the mitochondrial matrix and connected to the flagellar basal body by a transmembrane filament system named the tripartite attachment complex (see the review in reference 3). The lack of a similar DNA network in mammalian cells suggests that kDNA and proteins involved in its metabolism could be appealing therapeutic targets. Indeed, kDNA replication is the primary therapeutic target for ethidium bromide, a drug still used to treat nagana in livestock (4).Trypanosome kDNA replication is unusual in comparison wi...

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Section: Discussionmentioning

confidence: 98%

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confidence: 99%

TbKAP6, a Mitochondrial HMG Box-Containing Protein in Trypanosoma brucei, Is the First Trypanosomatid Kinetoplast-Associated Protein Essential for Kinetoplast DNA Replication and Maintenance

et al. 2014

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“…Thus, UMSBP apparently has much broader actions than originally thought. Yossi's laboratory has recently shown that UMSBP binds to kDNA networks in another way when the basic DNA-binding proteins CfKAP3 and CfKAP4 are present (68). UMSBP binds to the KAP protein via protein-protein interactions and then binds the DNA to make it more susceptible to topo II.…”

Section: Homologs Is Essential For Growth But Its Function Is Not Ymentioning

confidence: 99%

“…Presumably, it is by the same enzyme that attaches them because this is the only mitochondrial topo II encoded in the nuclear genome. The release mechanism could be related to the interaction of UMSBP and CfKAP3 or CfKAP4, mentioned previously (68).…”

Section: Rna Interferencementioning

confidence: 99%

A Passion for Parasites

Englund

2014

Journal of Biological Chemistry

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I knew nothing and had thought nothing about parasites until 1971. In fact, if you had asked me before then, I might have commented that parasites were rather disgusting. I had been at the Johns Hopkins School of Medicine for three years, and I was on the lookout for a new project. In 1971, I came across a paper in the Journal of Molecular Biology by Larry Simpson, a classmate of mine in graduate school. Larry's paper described a remarkable DNA structure known as kinetoplast DNA (kDNA), isolated from a parasite. kDNA, the mitochondrial genome of trypanosomatids, is a DNA network composed of several thousand interlocked DNA rings. Almost nothing was known about it. I was looking for a project on DNA replication, and I wanted it to be both challenging and important. I had no doubt that working with kDNA would be a challenge, as I would be exploring uncharted territory. I was also sure that the project would be important when I learned that parasites with kDNA threaten huge populations in underdeveloped tropical countries. Looking again at Larry's paper, I found the electron micrographs of the kDNA networks to be rather beautiful. I decided to take a chance on kDNA. Little did I know then that I would devote the next forty years of my life to studying kDNA replication.

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“…In fact, mutations to proteins of this complex [ 53 , 54 ] show enlarged and potentially more complicated networks. Histone-like kinetoplast associated proteins (KAP) may also be involved in the positioning of minicircles since they are implicated in condensing the kDNA network [ 55 – 58 ] and in the remodeling of the kDNA structure during different life cycle phases [ 59 ]. Recent experimental works show that these proteins decrease the excluded volume effects of the minicircles and that interaction of KAP3 and KAP4 with the initiator protein, universal minicircle sequence-binding protein, results in decondensation of the kDNA network and increasing accessibility to topoisomerase II.…”

Section: Discussionmentioning

confidence: 99%

Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA

et al. 2015

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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.

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Interactions of a Replication Initiator with Histone H1-like Proteins Remodel the Condensed Mitochondrial Genome

Cited by 12 publications

References 48 publications

TbKAP6, a Mitochondrial HMG Box-Containing Protein in Trypanosoma brucei, Is the First Trypanosomatid Kinetoplast-Associated Protein Essential for Kinetoplast DNA Replication and Maintenance

TbKAP6, a Mitochondrial HMG Box-Containing Protein in Trypanosoma brucei, Is the First Trypanosomatid Kinetoplast-Associated Protein Essential for Kinetoplast DNA Replication and Maintenance

A Passion for Parasites

Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA

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