Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence

HMGs as rheostats of chromosomal structure and cell proliferation

High mobility group proteins (HMGs) are the most abundant nuclear proteins next to histones and are robustly expressed across tissues and organs. HMGs can uniquely bend or bind distorted DNA, and are central to such processes as transcription, recombination, and DNA repair. However, their dynamic association with chromatin renders capturing HMGs on chromosomes challenging. Recent work has changed this and now implicates these factors in spatial genome organization. Here, I revisit older and review recent literature to describe how HMGs rewire spatial chromatin interactions to sustain homeostasis or promote cellular aging. I propose a 'rheostat' model to explain how HMG-box proteins (HMGBs), and to some extent HMG A proteins (HMGAs), may control cellular aging and, likely, cancer progression.

Global Dynamics in Protein Disorder during Maize Seed Development

Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.

Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription

Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.

Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA

Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content

Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins’ preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications.

We investigated the chromosomal location of a group of highly abundant nuclear proteins. Our genome-wide results for Hmga1 and Hmga2 reveal a unique binding modality indicating preference for DNA rich in A or T bases in vivo. Importantly this preferential binding to AT-rich sequences occurs throughout the genome irrespectively of other local chromatin features. Genomic location and loss of function experiments challenge the view that Hmga proteins act as local modulators of transcriptional regulation but rather argue for a role as structural components of chromatin.

Nano-biomimetic carriers are implicated in mechanistic evaluation of intracellular gene delivery

Several tissue specific non-viral carriers have been developed for gene delivery purposes. However, the inability to escape endosomes, undermines the efficacy of these carriers. Researchers inspired by HIV and influenza virus, have randomly used Gp41 and H5WYG fusogenic peptides in several gene delivery systems without any rational preference. Here for the first time, we have genetically engineered two Nano-biomimetic carriers composed of either HWYG (HNH) or Gp41 (GNH) that precisely provide identical conditions for the study and evaluation of these fusogenic peptides. The luciferase assay demonstrated a two-fold higher transfection efficiency of HNH compared to GNH. These nanocarriers also displayed equivalent properties in terms of DNA binding ability and DNA protection against serum nucleases and formed similar nanoparticles in terms of surface charge and size. Interestingly, hemolysis and cellular analysis demonstrated both of nanoparticles internalized into cells in similar rate and escaped from endosome with different efficiency. Furthermore, the structural analysis revealed the mechanisms responsible for the superior endosomal escaping capability of H5WYG. In conclusion, this study describes the rationale for using H5WYG peptide to deliver nucleic acids and suggests that using nano-biomimetic carriers to screen different endosomal release peptides, improves gene delivery significantly.

Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties

OsMADS1 controls rice (Oryza sativa) floral fate and organ development. Yet, its genome-wide targets and the mechanisms underlying its role as a transcription regulator controlling developmental gene expression are unknown. We identify 3112 gene-associated OsMADS1-bound sites in the floret genome. These occur in the vicinity of transcription start sites, within gene bodies, and in intergenic regions. Majority of the bound DNA contained CArG motif variants or, in several cases, only A-tracts. Sequences flanking the binding peak had a higher AT nucleotide content, implying that broader DNA structural features may define in planta binding. Sequences for binding by other transcription factor families like MYC, AP2/ERF, bZIP, etc. are enriched in OsMADS1-bound DNAs. Target genes implicated in transcription, chromatin remodeling, cellular processes, and hormone metabolism were enriched. Combining expression data from OsMADS1 knockdown florets with these DNA binding data, a snapshot of a gene regulatory network was deduced where targets, such as AP2/ERF and bHLH transcription factors and chromatin remodelers form nodes. We show that the expression status of these nodal factors can be altered by inducing the OsMADS1-GR fusion protein and present a model for a regulatory cascade where the direct targets of OsMADS1, OsbHLH108/SPT, OsERF034, and OsHSF24, in turn control genes such as OsMADS32 and OsYABBY5 This cascade, with other similar relationships, cumulatively contributes to floral organ development. Overall, OsMADS1 binds to several regulatory genes and, probably in combination with other factors, controls a gene regulatory network that ensures rice floret development.

Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility

Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacing neutral N-terminal residues of the HMGB2 protein with cationic sequences from Nhp6Ap. Surprisingly, HMGB proteins constrain DNA winding, and this torsional constraint is released over short timescales. These measurements reveal the microscopic dissociation rates of HMGB from DNA. Separate microscopic and macroscopic (or local and non-local) unbinding rates have been previously proposed, but never independently observed. Microscopic dissociation rates for the chimeric mutants (∼10 s⁻¹) are higher than those observed for wild-type proteins (∼0.1–1.0 s⁻¹), reflecting their reduced ability to bend DNA through short-range interactions, despite their increased DNA-binding affinity. Therefore, transient local HMGB–DNA contacts dominate the DNA-bending mechanism used by these important architectural proteins to increase DNA flexibility.

Molecular basis for the inhibition of HMGA1 proteins by distamycin A

The molecular mechanism for the displacement of HMGA1 proteins from DNA is integral to disrupting their cellular function, which is linked to many metastatic cancers. Chemical shift and NOESY NMR experiments provide structural evidence for the displacement of an AT hook peptide (DNA binding motif of HMGA1 proteins) by both monomeric and dimeric distamycin. However, the displaced AT hook alters distamycin binding by weakening the distamycin:DNA complex, while slowing monomeric distamycin dissociation when AT hook is in excess. The central role of the AT hook was evaluated by monitoring full-length HMGA1a protein binding using fluorescence anisotropy. HMGA1a was effectively displaced by distamycin, but the cooperative binding exhibited by distamycin was eliminated by displaced HMGA1a. Additionally, these studies indicate that HMGA1a is displaced from the DNA by 1 equiv of distamycin, suggesting the ability to develop therapeutics that take advantage of the positively cooperative nature of HMGA1a binding.

A Mass Spectrometric Study on the in Vitro Methylation of HMGA1a and HMGA1b Proteins by PRMTs: Methylation Specificity, the Effect of Binding to AT-Rich Duplex DNA, and the Effect of C-Terminal Phosphorylation

HMGA1a and HMGA1b are members of one subfamily of non-histone chromosomal high-mobility group (HMG) proteins. They bind to various DNA-related substrates, including the minor groove of AT-rich duplex DNA sequences, and have been postulated to be architectural transcription factors functioning in a wide variety of cellular processes. Post-translational modifications of HMGA1 proteins, such as phosphorylation, acetylation, and methylation, are widely observed in tumor cells in vivo and correlated with the modulation of protein function. Here, we investigated the in vitro methylation of recombinant human HMGA1a and HMGA1b proteins by three members of the protein arginine methyltransferase (PRMT) family: PRMT1, PRMT3, and PRMT6. PRMT1 and PRMT3 showed a preference for methylating arginine residues in the first AT-hook of HMGA1 proteins, whereas PRMT6 methylated mainly residues in the second AT-hook. The initial sites of methylation catalyzed by PRMT1 and PRMT3 were mapped by tandem mass spectrometry to be Arg25 and Arg23, respectively, while we confirmed that the initial sites of methylation catalyzed by PRMT6 were at Arg57 and Arg59. Our results also revealed that binding of HMGA1 proteins to AT-rich duplex DNA, but not GC-rich duplex DNA, significantly inhibited the methylation efficiency of all of the PRMTs toward HMGA1 proteins. Moreover, C-terminal constitutive phosphorylation of HMGA1 proteins induced by protein kinase CK2 did not have any appreciable effect on the in vitro methylation of HMGA1. Our results suggest that PRMT1 might be involved in the previously reported methylation of Arg25 in HMGA1a in vivo.

Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide

The functions of DNA satellites of centric heterochromatin are difficult to assess with classical molecular biology tools. Using a chemical approach, we demonstrate that synthetic polyamides that specifically target AT-rich satellite repeats of Drosophila melanogaster can be used to study the function of these sequences. The P9 polyamide, which binds the X-chromosome 1.688 g/cm3 satellite III (SAT III), displaces the D1 protein. This displacement in turn results in a selective loss of HP1 and topoisomerase II from SAT III, while these proteins remain bound to the adjacent rDNA repeats and to other regions not targeted by P9. Conversely, targeting of (AAGAG)n satellite V repeats by the P31 polyamide results in the displacement of HP1 from these sequences, indicating that HP1 interactions with chromatin are sensitive to DNA-binding ligands. P9 fed to larvae suppresses the position-effect variegation phenotype of white-mottled adult flies. We propose that this effect is due to displacement of the heterochromatin proteins D1, HP1 and topoisomerase II from SAT III, hence resulting in stochastic chromatin opening and desilencing of the nearby white gene.

Protein arginine methyltransferase 6 specifically methylates the nonhistone chromatin protein HMGA1a

The HMGA family proteins HMGA1a and HMGA1b are nuclear nonhistone species implicated in a wide range of cellular processes including inducible gene transcription, modulation of chromosome structure through nucleosome and chromosome remodeling, and neoplastic transformation. HMGA proteins are highly modified, and changes in their phosphorylation states have been correlated with the phase of the cell cycle and changes in their transcriptional activity. HMGA1a is also methylated in the first DNA-binding AT-hook at Arg25 and other sites, although the enzyme or enzymes responsible have not been identified. We demonstrate here that a GST fusion of protein arginine methyltransferase 6 (PRMT6) specifically methylates full-length recombinant HMGA1a protein in vitro. Although GST fusions of PRMT1 and PRMT3 were also capable of methylating the full-length HMGA1a polypeptide, they recognize its proteolytic degradation products much better. GST fusions of PRMT4 or PRMT7 were unable to methylate the full-length protein or its degradation products. We conclude that PRMT6 is a good candidate for the endogenous enzyme responsible for HGMA1a methylation.

Structural and transcriptional features of Bombus terrestris satellite DNA and their potential involvement in the differentiation process

A unique satellite DNA family was characterized in the genome of the bumble bee, Bombus terrestris. Sequence analysis revealed that it contains two wide palindromes of about 160 and 190 bp, respectively, that span 75% of the repeated unit. One feature of this satellite DNA is that it accounts for different amounts of genomic DNA in males and females. The DNA curvature and bendability were determined by migration on PAGE and by computer analysis. It has been correlated with the presence of dA/dT stretches repeated in phase with the helix turn and with the presence of the deformable dinucleotide CA-TG embedded in some of these A-T-rich regions. Transcription of the satellite DNA was also analyzed by Northern blot hybridization and RT-PCR. Multimeric transcripts spanning several satellite DNA units were found in RNA samples from males, workers, and queens. These transcripts resulted from a specific transcription occurring on one DNA strand in the embryos or on both DNA strands in imagoes. The involvement of DNA curvature in the organization of the satellite DNA and the function of the satellite transcripts is discussed.

Molecular biology of HMGA proteins: hubs of nuclear function

Members of the HMGA (a.k.a. HMGI/Y) family of 'high mobility group' (HMG) proteins participate in a wide variety of nuclear processes ranging from chromosome and chromatin mechanics to acting as architectural transcription factors that regulate the expression of numerous genes in vivo. As a consequence, they function in the cell as highly connected 'nodes' of protein-DNA and protein-protein interactions that influence a diverse array of normal biological processes including growth, proliferation, differentiation and death. The HMGA proteins, likewise, participate in pathological processes by, for example, acting as regulators of viral gene transcription and by serving as host-supplied proteins that facilitate retroviral integration. HMGA genes are bona fide proto-oncogenes that promote tumor progression and metastasis when overexpressed in cells. High constitutive HMGA protein levels are among the most consistent feature observed in all types of cancers with increasing concentrations being correlated with increasing malignancy. The intrinsic attributes that endow the HMGA proteins with these remarkable abilities are a combination of structural, biochemical and biological characteristics that are unique to these proteins. HMGA proteins have little, if any, secondary structure while free in solution but undergo disordered-to-ordered structural transitions when bound to substrates such as DNA or other proteins. Each protein contains three copies of a conserved DNA-binding peptide motif called the 'AT-hook' that preferentially binds to the minor groove of stretches of AT-rich sequence. In vivo HMGA proteins specifically interact with a large number of other proteins, most of which are transcription factors. They are also subject to many types of in vivo biochemical modifications that markedly influence their ability to interact with DNA substrates, other proteins and chromatin. And, most importantly, both the transcription of HMGA genes and the biochemical modifications of HMGA proteins are direct downstream targets of numerous signal transduction pathways making them exquisitely responsive to various environmental influences. This review covers recent advances that have contributed to our understanding of how this constellation of structural and biological features allows the HMGA proteins to serve as central 'hubs' of nuclear function.

Consecutive steps of phosphorylation affect conformation and DNA binding of the chironomus high mobility group A protein

The high mobility group (HMG) proteins of the AT-hook family (HMGA) lie downstream in regulatory networks with protein kinase C, Cdc2 kinase, MAP kinase, and casein kinase 2 (CK2) as final effectors. In the cells of the midge Chironomus, almost all of the HMGA protein (cHMGA) is phosphorylated by CK2 at two adjacent sites. 40% of the protein population is additionally modified by MAP kinase. Using spectroscopic and protein footprinting techniques, we analyzed how individual and consecutive steps of phosphorylation change the conformation of an HMGA protein and affect its contacts with poly(dA-dT).poly(dA-dT) and a fragment of the interferon-beta promoter. We demonstrate that phosphorylation of cHMGA by CK2 alters its conformation and modulates its DNA binding properties such that a subsequent phosphorylation by Cdc2 kinase changes the organization of the protein-DNA complex. In contrast, consecutive phosphorylation by MAP kinase, which results in a dramatic change in cHMGA conformation, has no direct effect on the complex. Because the phosphorylation of the HMGA proteins attenuates binding affinity and reduces the extent of contacts between the DNA and protein, it is likely that this process mirrors the dynamics and diversity of regulatory processes in chromatin.

HMGI/Y proteins: flexible regulators of transcription and chromatin structure

The mammalian HMGI/Y (HMGA) non-histone proteins participate in a wide variety of cellular processes including regulation of inducible gene transcription, integration of retroviruses into chromosomes and the induction of neoplastic transformation and promotion of metastatic progression of cancer cells. Recent advances have contributed greatly to our understanding of how the HMGI/Y proteins participate in the molecular mechanisms underlying these biological events. All members of the HMGI/Y family of 'high mobility group' proteins are characterized by the presence of multiple copies of a conserved DNA-binding peptide motif called the 'AT hook' that preferentially binds to the narrow minor groove of stretches of AT-rich sequence. The mammalian HMGI/Y proteins have little, if any, secondary structure in solution but assume distinct conformations when bound to substrates such as DNA or other proteins. Their intrinsic flexibility allows the HMGI/Y proteins to participate in specific protein-DNA and protein-protein interactions that induce both structural changes in chromatin substrates and the formation of stereospecific complexes called 'enhanceosomes' on the promoter/enhancer regions of genes whose transcription they regulate. The formation of such regulatory complexes is characterized by reciprocal inductions of conformational changes in both the HMGI/Y proteins themselves and in their interacting substrates. It may well be that the inherent flexibility of the HMGI/Y proteins, combined with their ability to undergo reversible disordered-to-ordered structural transitions, has been a significant factor in the evolutionary selection of these proteins for their functional role(s) in cells.

Recent advances in FRET: distance determination in protein-DNA complexes

Fluorescence resonance energy transfer (FRET) provides information on the distance between a donor and an acceptor dye in the range 10 to 100 A. Knowledge of the exact positions of some dyes with respect to nucleic acids now enables us to translate these data into precise structural information using molecular modeling. Advances in the preparation of dye-labeled nucleic acid molecules and in new techniques, such as the measurement of FRET in polyacrylamide gels or in vivo, will lead to an increasingly important role of FRET in structural and molecular biology.