New paradigm of functional regulation by DNA mimic proteins: Recent updates

Abstract

For many, “DNA mimic protein” (DMP) remains an unfamiliar term. The key feature of these proteins is their DNA‐like shape and charge distribution, and they affect the activity of DNA‐binding proteins by occupying their DNA‐binding domains. Functionally, DMPs regulate mechanisms such as gene expression, restriction, and DNA repair as well as the nucleosome package. Although a few DMPs, such as phage uracil DNA glycosylase inhibitor (UGI) and overcome classical restriction (Ocr), were reported about 20 years ago, only a small number of DMPs have been studied to date. In 2014, we reviewed the functional and structural features of 16 DMPs that were known at the time. Now, seven new DMPs, namely anti‐CRISPR suppressors AcrF2, AcrF10 and AcrIIA4, human immunodeficiency virus essential factor VPR, multi‐functional inhibitor anti‐restriction nuclease (Arn), translational regulator AbbA, and putative Z‐DNA mimic MBD3, have been reported. In addition, further study of two previously known DMPs, DMP19 and SAUGI, increased our knowledge of their importance and function. Here, we discuss these updated results and address how several characteristics of the structure/sequence of DMPs (e.g. the DNA‐like charge distribution and structural D/E‐rich repeats) might someday be used to identify new DMPs using bioinformatic approach. © 2018 IUBMB Life, 71(5):539–548, 2019

Cytoskeletal regulation of a transcription factor by DNA mimicry

“…The Kif7-CC is characterized by a highly negatively charged rod-like structure that competes for the same binding sites on Gli2-ZF as DNA. Thus, the properties of Kif7-CC are consistent with that of a DNAmimicking protein [45][46][47][48] . The zinc-finger domain of Gli2 binds DNA in the nucleus and is repurposed for Kif7-mediated cytoplasmic localization through the same structural design principle (Fig.…”

Characterization of the Chimeric PriB-SSBc Protein

“…The negative-charged subdomain 1.1 in σ 70 can regulate the binding ability to the promoter DNA during the RNA transcription initiation stage. Many DNA mimic proteins and peptides function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA [ 92 , 93 , 94 , 95 ]. For SSB, SSB-Ct is probably in the case as a kind of DNA mimic [ 13 ].…”

The root‐knot nematode effector MiEFF18 interacts with the plant core spliceosomal protein SmD1 required for giant cell formation

“…The K‐rich C‐terminal part of the effector, carrying nuclear localization signals (NLS) and one nucleolar localization signal (NoLS), undoubtedly mediates import into the nucleus, and the N‐terminal part of the molecule carries D/E repeats, which often are found in DNA/RNA mimic proteins (Chou & Wang, 2015). These proteins regulate the activity of various DNA/RNA‐binding proteins involved in diverse nuclear processes, such as chromatin assembly, DNA repair or transcriptional regulation (Chou & Wang, 2015; Wang et al ., 2019). Further studies of this effector–target pair and associated RNAs would improve our understanding of the role and regulation of the spliceosome machinery in plants and might lead to the development of applications in new control strategies based on the loss of a susceptibility gene essential for development of the disease.…”