A nicked form of kinetoplast DNA in Leishmania tarentolae

Evolutionary, structural and functional insights in nuclear organisation and nucleocytoplasmic transport in trypanosomes

One of the remarkable features of eukaryotes is the nucleus, delimited by the nuclear envelope (NE), a complex structure and home to the nuclear lamina and nuclear pore complex (NPC). For decades, these structures were believed to be mainly architectural elements and, in the case of the NPC, simply facilitating nucleocytoplasmic trafficking. More recently, the critical roles of the lamina, NPC and other NE constituents in genome organisation, maintaining chromosomal domains and regulating gene expression have been recognised. Importantly, mutations in genes encoding lamina and NPC components lead to pathogenesis in humans, while pathogenic protozoa disrupt the progression of normal development and expression of pathogenesis-related genes. Here, we review features of the lamina and NPC across eukaryotes and discuss how these elements are structured in trypanosomes, protozoa of high medical and veterinary importance, highlighting lineage-specific and conserved aspects of nuclear organisation.

A passion for parasites

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.

AFM characterization of single strand-specific endonuclease activity on linear DNA

The specificity of nucleases for nicked and un-nicked double-stranded DNA has been characterized using atomic force microscopy (AFM). We have found that AFM has advantages over the usual macroscopic analyses, such as sucrose gradient centrifugation or electrophoresis, in characterizing nuclease digestion. In particular, short DNA fragments resulting from non-specific digestion were detected and, thus, the true length distribution of digested DNA was revealed. A simple numerical method is proposed to estimate the number of nicked sites per DNA molecule based on AFM images.

Universal minicircle sequence-binding protein, a sequence-specific DNA-binding protein that recognizes the two replication origins of the kinetoplast DNA minicircle

Replication of the kinetoplast DNA minicircle lagging (heavy (H))-strand initiates at, or near, a unique hexameric sequence (5'-ACGCCC-3') that is conserved in the minicircles of trypanosomatid species. A protein from the trypanosomatid Crithidia fasciculata binds specifically a 14-mer sequence, consisting of the complementary strand hexamer and eight flanking nucleotides at the H-strand replication origin. This protein was identified as the previously described universal minicircle sequence (UMS)-binding protein (UMSBP) (Tzfati, Y., Abeliovich, H., Avrahami, D., and Shlomai, J. (1995) J. Biol. Chem. 270, 21339-21345). This CCHC-type zinc finger protein binds the single-stranded form of both the 12-mer (UMS) and 14-mer sequences, at the replication origins of the minicircle L-strand and H-strand, respectively. The attribution of the two different DNA binding activities to the same protein relies on their co-purification from C. fasciculata cell extracts and on the high affinity of recombinant UMSBP to the two origin-associated sequences. Both the conserved H-strand hexamer and its flanking nucleotides at the replication origin are required for binding. Neither the hexameric sequence per se nor this sequence flanked by different sequences could support the generation of specific nucleoprotein complexes. Stoichiometry analysis indicates that each UMSBP molecule binds either of the two origin-associated sequences in the nucleoprotein complex but not both simultaneously.

Cleavable complex formation in Leishmania chagasi treated with anilinoacridines

Anilinoacridines have recently been found to possess antiparasitic activity toward Leishmania, Trypanosoma, and Plasmodium species. These compounds have been examined for their ability to generate cleavable complex, the protein-associated DNA lesion characteristic of topoisomerase II involvement, in intact L. chagasi promastigotes. At cytotoxic concentrations, anilinoacridine compounds give cleavable complex in a whole cell assay which suggests that the drugs affect a nuclear topoisomerase II in the parasite. Linearization of kinetoplast DNA minicircles also occurs in parasites treated with anilinoacridines at similar concentrations. Exonuclease digestions reveal that the linearized minicircles are blocked at the 5' end but not at the 3' end, further implicating a kinetoplast topoisomerase II in the cleavage process. Interestingly, cytotoxic alkylaminoacridines did not stimulate the production of cleaved DNA in the same experiments. DNA binding experiments showed no apparent correlation between the affinity of the compounds for DNA and antileishmanial activity. Although multiple cytotoxic mechanisms are likely at work, these experiments suggest that topoisomerase II enzyme(s) are affected by antileishmanial anilinoacridines.

A unique ATP-dependent DNA topoisomerase from trypanosomatids

Crithidia fasciculata DNA topoisomerase (22) has been purified to near homogeneity from trypanosomatid cell extracts. The purified enzyme catalyzes the reversible interconversion of monomeric duplex DNA circles and catenanes in an ATP dependent reaction. Reversible catenane formation is affected by the ionic strength and is dependent upon the action of a crithidial DNA binding protein, which could be substituted for the polyamine spermidine. Covalently sealed DNA circles are specifically used as substrates for decatenation. Nicking, but not relaxation per se, inhibits network decatenation and has little or no effect on catenane formation. The catalytic properties of this enzyme and its potential role in the prereplication release and post replication reattachment of kDNA minicircles are discussed.