The macro domain protein family: structure, functions, and their potential therapeutic implications

Abstract

Macro domains are ancient, highly evolutionarily conserved domains that are widely distributed throughout all kingdoms of life. The 'macro fold' is roughly 25kDa in size and is composed of a mixed α-β fold with similarity to the P loop-containing nucleotide triphosphate hydrolases. They function as binding modules for metabolites of NAD(+), including poly(ADP-ribose) (PAR), which is synthesized by PAR polymerases (PARPs). Although there is a high degree of sequence similarity within this family, particularly for residues that might be involved in catalysis or substrates binding, it is likely that the sequence variation that does exist among macro domains is responsible for the specificity of function of individual proteins. Recent findings have indicated that macro domain proteins are functionally promiscuous and are implicated in the regulation of diverse biological functions, such as DNA repair, chromatin remodeling and transcriptional regulation. Significant advances in the field of macro domain have occurred in the past few years, including biological insights and the discovery of novel signaling pathways. To provide a framework for understanding these recent findings, this review will provide a comprehensive overview of the known and proposed biochemical, cellular and physiological roles of the macro domain family. Recent data that indicate a critical role of macro domain regulation for the proper progression of cellular differentiation programs will be discussed. In addition, the effect of dysregulated expression of macro domain proteins will be considered in the processes of tumorigenesis and bacterial pathogenesis. Finally, a series of observations will be highlighted that should be addressed in future efforts to develop macro domains as effective therapeutic targets.

Fig. 1

The macro domain family. The structures of the macro domain proteins are depicted, showing the conserved macro domains, as well as other domains found in selected members of the family, such as the histone H2A domain; Lys-rich domain; Glu-rich domain; SEC14 domain, a lipid-binding domain found in SEC14p and other proteins; SNF2 domain, the SNF2 helicase-like domain; PARP domain, poly(ADP-ribose)polymerase domain; WWE domain, a protein–protein interaction domain containing conserved Trp and Glu residues; HLH domain, helix–loop–helix DNA binding domain; ZnF domain, ubiquitin-binding zinc finger domain. Please note that several members of the macroPARPs (PARP-9/BAL1; PARP-14/BAL2/CoaSt6; PARP-15/BAL3) display splicing variants, but for simplicity, only one variant is illustrated. Human macro domain proteins are presented on the left and homologues from other organisms are shown on the right, including macro domain proteins from Escherichia coli (E.c), Drosophila melanogaster (D), Xenopus laevis (X), viruses (V), Archaeoglobus fulgidus (A.F), Arabidopsis thaliana (A.t) and Oryza sativa (O.s). Numbers refer to amino acid positions in the proteins.

Fig. 2

Macro domains are highly conserved structural domains that bind ADPR. (A) X-ray crystal structures of the macro domains from Archaeoglobus fulgidus (archaeal) Af1521 protein (Protein Data Bank (PDB) accession code 2BFQ) and human macroH2A1.1 bound to ADP-ribose (PDB accession code 3IID). The two views are rotated 90° relative to each other. (B) Schematic illustration of the proposed 2′ OH PAR capping function of macro domains, some amino-acids in conserved residues of macro domain proteins can serve as PAR acceptors, such as Asp, Glu. The square (orange) represents a mono-ADP-ribose. (C) Multiple amino acid sequence alignment of macro domain-containing proteins derived from SARS-CoV, SFV, Escherichia coli, Arabidopsis thaliana, and Archaeoglobus fulgidus with human macroH2A, MACROD1, MACROD2, GDAP2, PARP-9, PARP-14, and ALC1. The protein name is followed by the species abbreviation. Uniprot codes: AF1521 (Archaeoglobus fulgidus, O28751); AT2G44980 (Arabidopsis thaliana, Q3E6Q7); ymdB (Escherichia coli, C4ZRY6); ALC1 (human, Q86WJ1); GDAP2 (human, Q9NXN4); MACROD1 (human, Q9BQ69); MACROD2 (human, A1Z1Q3); PARP-9 (human, Q8IXQ6); PARP-14 (human, Q460N5); macroH2A1.1 and macroH2A1.2 (human, O75367); macroH2A (human, Q9P0M6). Conserved residues are colored according to their chemical properties. The black square represents the conserved motif (GDI/VT) among these different macro domain proteins. The bottle green diamond on top of the sequence indicates the amino acid that was mutated in AF1521 and ALC1, and red diamonds indicate the amino acids that were mutated in SARS-CoV. The blue diamond indicates the amino acid that was mutated in macroH2A1.1, and yellow diamonds indicate the amino acids that were mutated both in SFV and in MACROD1.

Fig. 3

Metabolism of poly(ADP-ribose). PARPs hydrolyze NAD⁺, releasing nicotinamide (Nam) and one proton (H⁺), and catalyze the successive transfer of the ADP-ribose moiety to nuclear protein acceptors. The reaction is initiated by the formation of an ester bond between the amino-acid acceptor (Glu, Asp or COOH-Lys) and the first ADP-ribose. Polymer elongation involves the catalysis of a 2′–1′′ glycosidic bond. PAR is heterogeneous in size and complexity, as indicated by the shade labels (x, y, z labels) that represent values from 0 to more than 200. PARG and ARH3 can both hydrolyze PAR at the indicated positions. Activators and functions of PAR synthesis are indicated. Ade, adenine; PAR, poly(ADP-ribose); PARG, poly(ADP-ribose) glycohydrolase; ARH3, ADP-ribosyl hydrolase-3; PARP, poly(ADP-ribose) polymerase; P, phosphate; Rib, ribose.

Fig. 4

Macro domain proteins and the DNA damage response. DNA damage results in the recruitment and activation of PARP-1. Subsequently, PARP-1 catalyzes the synthesis of PAR on itself and other proteins. These polymers serve as molecular bridges for proteins that contain PAR-binding domains (such as macro domain proteins, PBZ proteins, and other proteins), and thereby contribute to chromatin remodeling and DNA repair, when the DNA has been repaired, these components are disengaged from the nucleosomes.

Fig. 5

Differential cellular roles of macro domain proteins. Some examples of the participation of macro domain proteins in cellular pathways linked to cell proliferation and cell death. Collectively, macro domain family proteins are involved in the inactivation of chromosomes and transcriptional repression. See main text for details, the red arrows represent repression and black arrows represent activation.

Fig. 6

Presumed targeting macro domain in cancer therapy. Schematic illustration of possibly machinery involved in resistance to cancer radiotherapy and chemotherapy and the potential application of small molecular analogues of ADP-ribose in combination with PARP inhibitors in cancer therapy.