Actions of iron-dependent dioxygenases

Essential cellular processes including protein modification, DNA damage repair and epigenetic regulation require the activity of α-ketoglutarate (2-oxoglutarate or 2OG) and other iron-dependent oxygenases. The eighth of the Journal of Biological Chemistry’s thematic series on metals in biology features key topics related to this class of oxygenases. The editor of the series, F. Peter Guengerich from Vanderbilt University, highlights recent advances in four key areas of Fe(II)- and 2OG-dependent oxygenase biology: the chemical mechanisms of catalysis; posttranslational protein modifications; epigenetic regulation by the activity of the ten-eleven translocation, or Tet, dioxygenases; and the role of the AlkB family of oxygenases in damaged DNA and RNA repair.

The Fe(II)- and 2OG-dependent enzymes aid in overcoming kinetic barriers involved in biochemical reactions. The first review by Salette Martinez and Robert P. Hausinger at Michigan State University details mechanisms that require Fe(II)- and 2OG-dependent oxygenases to catalyze hydroxylation, halogenation, ring formation and desaturation reactions. Each of these four catalytic reactions is discussed in detail, with examples from human biology and commentary on key enzymatic intermediates. This first minireview is central to understanding the fundamental mechanisms underlying the posttranslational modifications, epigenetic regulations, and DNA and RNA repair processes covered in the subsequent minireviews.

The roles of Fe(II)- and 2OG-dependent oxygenases in posttranslational modifications are presented in the second minireview from Suzana Markolovic, Sarah E. Wilkins, and Christopher J. Schofield at the University of Oxford. Structural studies and reaction mechanisms featured in this review pointedly illustrate the contributions of Fe(II)- and 2OG-dependent oxygenases on enzymatic activity and changes to macromolecular structure. In particular, posttranslational hydroxylation of macromolecules, such as pro-collagen and hypoxia-inducible factors, are regulated by Fe(II)- and 2OG-dependent oxygenases. In addition, N-demethylation of histones catalyzed by these oxygenases affects transcription and posttranscriptional events. This review covers the importance of Fe(II)- and 2OG-dependent oxygenases in regulating protein–protein interactions in addition to regulatory roles in gene expression via histone methylation and demethylation reactions.

The epigenetic roles of 2OG-dependent oxygenases are detailed further in the third minireview from Hideharu Hashimoto, Xing Zhang, Paula Vertino and Xiaodong Cheng at Emory University. Iterative oxidations of the DNA base cytosine are performed by DNA methyltransferases, which convert cytosine to 5-methylcytosisine, or 5meC; 5-hydroxymethylcytosine, or 5hmC; 5-formylcytosine, or 5fmC; and 5-carboxylcytosine, or 5caC. Cytosine modifications do not affect base pairing but may affect epigenetic functions by changing macromolecular interactions and controlling gene expression. A subset of 5meC further is oxidized into 5hmC, 5fmC and 5caC by the activity of Tet dioxygenases, a type of 2OG-dependent oxygenase. This review discusses the downstream implications of Tet enzyme activity on transcription factor binding and base excision repair by DNA glycosylases.

In the fourth minireview, Bogdan Fedeles and colleagues at the Massachusetts Institute of Technology focus on nucleic acid damage repair, highlighting the AlkB family of oxygenases. Studies have shown that the bacterial AlkB oxygenases remove methyl groups and lesions from DNA as a protective mechanism for maintaining genome integrity. While precise functions remain unknown, humans have nine AlkB homologs, two of which repair damaged DNA while the remaining homologs demethylate RNA and proteins. This comprehensive review provides details on AlkB structure, mechanism, substrate specificity and methodologies for studying AlkB activity in vitro and in vivo.

Significant achievements in understanding the Fe(II)- and 2OG-dependent oxygenases featured in this minireview demonstrate the exciting potential in developing diagnostic tools to identify, investigate and treat human diseases.

Christine C. Lee Christine C. Lee is a doctoral candidate in the Department of Biochemistry and Molecular Biology at the Johns Hopkins Bloomberg School of Public Health.