Regulation of DNA-Dependent Activities by the Functional Motifs of the High-Mobility-Group Chromosomal Proteins

Abstract

HMG FUNCTIONAL MOTIFS The orderly progression of most DNA-related activities such as transcription, replication, recombination, and repair involves changes in the structure of the DNA and in the organization of the chromatin fiber. Some of these structural changes are facilitated by a family of ubiquitous and abundant nonhistone nuclear proteins known as the high-mobility-group (HMG) proteins. In the narrowest traditional sense, the HMG protein family consists of six proteins and is subdivided into three subfamilies: the HMG-1/-2 subfamily, the HMG-I/Y subfamily and the HMG-14/-17 subfamily. These three HMG subfamilies are similar in several physical characteristics (detailed reviews on these proteins are found in references 10, 12, 14, 28, and 54); however, each of the subfamilies has a unique protein signature and a characteristic functional sequence motif. These functional sequence motifs are the main site of interaction between the HMG proteins and the DNA or chromatin targets. The HMG-1 domain (often referred to as the HMG-1 box) is the functional motif of the largest HMG subfamily, the HMG-1/-2 proteins; the AT hook is the functional motif of the HMG-I/Y group, and the nucleosomal binding domain is the functional motif of the HMG-14/-17 subfamily. Significantly, all of these functional motifs bind to specific structures in DNA or in chromatin, with little if any specificity for the target DNA sequence. All the HMG proteins are considered to function as architectural elements that modify the structure of DNA and chromatin to generate a conformation that facilitates and enhances various DNA-dependent activities. The functional motifs characteristic of the HMG-1 (8, 10, 45, 61, 63) and HMG-I/Y (3, 51) subfamilies have been identified in numerous nuclear proteins that interact with DNA and chromatin. However, it is important to clearly distinguish the archetypal, or canonical, HMG proteins from the proteins containing these HMG motifs embedded in their primary sequence. The former are ubiquitous in all the cells of higher eukaryotes, are relatively abundant, and bind to DNA in a sequence-independent fashion, while the latter are cell-type specific, are not abundant, bind to DNA in a sequence-specific fashion, and frequently contain additional, distinct non-HMG functional motifs. In considering the biological importance of the HMG motifs, it is important to take into account their relative abundance in the nucleus. The cellular levels of HMG fluctuate; however, on the average, the amount of HMG-1/-2 in a cell is about 10-fold lower than that of a histone, the amount of HMG-14/-17 is 10-fold-lower than that of HMG-1/-2, and the amount of HMG-I/Y is 10-fold lower than that of HMG-14/-17 (54). The amount of HMG-14/-17 in the average cell, about 10 5 molecules, is sufficient to bind to 1% of the nucleosomes, i.e., to approximately 100,000 nucleosomes. Thus, even small fluctuations in the cellular levels of these abundant proteins may have significant biological consequences, since the expression of certain genes can be affected by structural changes in a single nucleosome (118, 119).