[Fe-S] containing enzymes

[Fe-S] containing enzymes

Many processes associated with DNA synthesis and repair, involve metal-containing cofactors, and misregulation of these processes can lead to carcinogenesis. However, because of the paucity of biochemical and structural information, knowledge of their modi operandi or the molecular linkage between integrity of the metallocofactor and pathological events remain largely unknown. A particularly important class of metal cofactors is that of iron-sulfur [Fe-S] clusters, perhaps the most ubiquitous prosthetic groups in nature. Their abundance is likely the consequence of their structural and redox plasticity, thereby making them versatile and tunable cofactors for mediating electron transfer. However, [Fe-S]-cluster containing proteins are much more functionally versatile than that originally thought; they mediate and participate in a variety of cellular processes, such as DNA maintenance, amino acid and nucleotide metabolism, ribosome function and tRNA modification. [Fe-S] clusters participate in enzyme catalysis and bind substrates, regulate gene expression, act as sensors of small molecules (i.e. O2, NO), store iron, serve as sulfur donors during synthesis of lipoic acid and biotin, etc. Thus, despite the simplicity of their chemical ‘make-up’, their chemical and functional diversity is both astounding and complex.

The HBV protein X harbors an unprecedented [Fe-S] cluster

Chronic infection by Hepatitis B viruses (HBVs) is associated with liver disease and hepatocellular carcinoma (HCC). HCC is the third most common cause of cancer mortality and the fifth most common cancer worldwide. HBx is the smallest gene product of HBV and the main etiological agent of virus-mediated liver oncogenesis. Although there are innumerable reported HBx functions and protein binding partners, the molecular mechanisms by which HBx promotes tumorigenesis are still unclear. Despite the multi-decade studies, hardly any biochemical or structural information is known about HBx, which has been the major obstacle for linking its structure and activity to the cascade of cellular processes it modulates.

We have shown that HBx harbors a non-classical, redox-dependent [Fe-S] cofactor that can switch between a [2Fe] and [4Fe] form. It was previously impossible to identify the [Fe-S] cluster based on sequence, because there are no recognizable binding motifs. The redox-induced conversion of the metallocofactor raises a question about whether the protein ligands stem from one or more polypeptides, a fact that would have a consequence for the oligomeric state of the protein. We hypothesize that the metallocofactor is not solely a structural element, but has an active redox and structural role in the biological activity of HBx.

HBx has multiple functions; it acts as a transactivator by interacting with many cellular factors, it has a reactive oxygen species (ROS) generating potential and exhibits ATPase activity. We propose that the novel [Fe-S] cluster is the missing link in elucidating HBx function, both on its own and in the context of target proteins. We have generated highly soluble HBx constructs that permit its structural and biophysical characterization, which was previously hardly accessible. By structurally and biochemically characterizing HBx and the [Fe-S] cluster, we aim to shed the first light on the oncogenic potential of HBx.

HBx is a potential target for the development of anti-cancer drugs; therefore determining the chemical nature of the metallocofactor and the structure/function relationships supporting its role in viral-induced pathogenesis are of great importance. Discovery of an unusual [Fe-S] cluster in HBx sets new grounds for delineating its structure and function, which was previously inaccessible. Our cofactor reconstituted HBx will allow to resolve its purported, and often controversial, roles in oncogenesis, ultimately yielding new insights for antiviral therapies.

[Fe-S]-containing DNA helicases

Helicases play multiple roles in virtually all aspects of nucleic acid metabolism, including replication, DNA damage repair, transcription, chromosome segregation, and telomere maintenance. They are motor proteins that use ATP to fuel their biochemical activities. Some helicases process either DNA or RNA, while some act on both. They also catalytically disrupt a variety of DNA structures such as triplex, G-quadruplex, etc. Coupling of ATP hydrolysis to translocation is achieved by a set of so- called helicase signature motifs that define the motor core of the protein. Whereas motor cores are structurally and mechanistically similar, DNA helicases exhibit remarkable functional diversity. Based on their amino acid sequences they are classified into two large superfamilies, SF1 and SF2, both of which contain representatives with [Fe-S] clusters. The [Fe-S] cluster is indispensable for helicase activity; in XPD (or Rad3), a prototypical SF2 helicase part of the TFIIH transcription complex, loss of the [Fe-S] cluster results in loss of activity. But why these metalloclusters are necessary for function is largely unknown.

FANCJ

Our analyses show that SF2 of [Fe- S]-containing helicases can be segregated according to sequence similarity into clusters that consist of isofunctional ensembles The enzymes of particular interest are three eukaryotic helicases - FANCJ (ovarian/breast cancer and Fanconi anemia - FA), CHL1 (chromosomal stability and fertility), RTEL1 (telomere maintenance) – and three archeal/bacterial helicases - XPD (component of the TFIIH complex involved in transcription initiation and nucleotide excision repair - NER), DinG (recombinational DNA repair), YoaA (DinG paralog related to DNA replication/repair). Our group is currently focused on the study of the human FANCJ helicase. The FANCJ DNA helicase is mutated in hereditary breast and ovarian cancer as well as the progressive bone marrow failure disorder Fanconi anemia. In addition, FANCJ can collaborate with a number of DNA metabolizing proteins implicated in DNA damage detection and repair. We aim to successfully express and isolate the protein with the intact metallocofactor, so that we can resolve its three dimensional structure and establish the role of clinical mutations in the vicinity of the [Fe-S] cluster to the development of the different diseases. The specific questions that we are interested in addressing are:

- What are the functions of the [Fe-S] cofactors in SF2 helicases? Are they structural, allosteric, regulatory or redox (or a combination)? The presence of 4 Cys is diagnostic of the [Fe-S]-cofactor; why is there such a strong variation in the binding motifs and how do these affect the redox/structural properties of the cluster? Considering the chemical diversity of SF2 helicases with respect to their activities and (D/R)NA substrates, what is the link (if any) between the physicochemical properties of the cluster and specific activities?

- How do clinically relevant mutations in the vicinity of cluster-binding ligands affect [Fe-S] integrity and function? In particular, in FANCJ the mutation M299I adjacent to Cys298, is linked to breast cancer and double-stranded break repair, whereas the A349P mutation adjacent to Cys350, is linked to FA. These two mutations show that the [Fe-S] cluster can fine tune activity and impair ability to couple ATP hydrolysis to unwinding of nucleic acids or displacing DNA-bound proteins, but in ways that are poorly understood.

- Overall, is there a common theme for the presence of [Fe-S] clusters in SF2 helicases? Or are the helicase chemical diversity and substrate specificity contingent on the (redox/structural) properties of the cluster? Our hypothesis is that the [Fe-S] cluster serves different roles for different helicases, which in the most cases is redox and sensory, though mutations such as A349P in FANCJ are most likely to impose structural and conformational changes and inability to assemble an intact [Fe-S] cofactor.