Biomedical subjects

Imma Ponte

Publications and source records attributed to Imma Ponte.

5 recordsLinked to original sources

PubMed2005

DNA-induced secondary structure of the carboxyl-terminal domain of histone H1.

We have studied the secondary structure of the carboxyl-terminal domains of linker histone H1 subtypes H1(0) (C-H1(0)) and H1t (C-H1t), free in solution and bound to DNA, by IR spectroscopy. The carboxyl-terminal domain has little structure in aqueous solution but becomes extensively folded upon interaction with DNA. The secondary structure elements present in the bound carboxyl-terminal domain include the alpha-helix, beta-structure, turns, and open loops. The structure of the bound domain shows a significant dependence on salt concentration. In low salt (10 mm NaCl), there is a residual amount of random coil, 7% in C-H1(0) and 12% in C-H1t. In physiological salt concentrations (140 mm NaCl), the carboxyl termini become fully structured. Under these conditions, C-H1(0) contained 24% alpha-helix, 25% beta-structure, 17% open loops, and 33% turns. The latter component could include a substantial proportion of the 3(10) helix. Despite their low sequence identity (approximately 30%), the representation of the different structural motifs in C-H1t was similar to that in C-H1(0). Examination of the changes in the amide I components in the 20-80 degrees C temperature interval showed that the secondary structure of the DNA-bound C-H1t is for the most part extremely stable. The H1 carboxyl-terminal domain appears to belong to the so-called disordered proteins, undergoing coupled binding and folding.

Amino Acid Motifs↗

PubMed2004

The preferential binding of histone H1 to DNA scaffold-associated regions is determined by its C-terminal domain.

Histone H1 preferentially binds and aggregates scaffold-associated regions (SARs) via the numerous homopolymeric oligo(dA).oligo(dT) tracts present within these sequences. Here we show that the mammalian somatic subtypes H1a,b,c,d,e and H1 degrees and the male germline-specific subtype H1t, all preferentially bind to the Drosophila histone SAR. Experiments with the isolated domains show that whilst the C-terminal domain maintains strong and preferential binding, the N-terminal and globular domains show weak binding and poor specificity for the SAR. The preferential binding of SAR by the H1 molecule thus appears to be determined by its highly basic C-terminal domain. Salmine, a typical fish protamine, which could have its evolutionary origin in histone H1, also shows preferential binding to the SAR. The interaction of distamycin, a minor groove binder with high affinity for homopolymeric oligo(dA).oligo(dT) tracts, abolishes preferential binding of the C-terminal domain of histone H1 and protamine to the SAR, suggesting the involvement of the DNA minor groove in the interaction.

Amino Acid Sequence↗

PubMed2003

Sequence complexity of histone H1 subtypes.

H1 subtypes are involved in chromatin higher-order structure and gene regulation. H1 has a characteristic three-domain structure. We studied the length variation of the available H1 subtypes and showed that the length of the N-terminal and C-terminal domains was more variable than that of the central domain. The N-terminal and C-terminal domains were of low sequence complexity both at the nucleotide and at the amino acid level, whereas the globular domain was of high complexity. In most subtypes, low complexity was due only to cryptic simplicity, which reflects the clustering of a number of short and often imperfect sequence motifs. However, a subset of subtypes from eubacteria, plants, and invertebrates contained tandem repeats of short amino acid motifs (four to 12 residues), which could amount to a large proportion of the terminal domains. In addition, some other subtypes, such as those of Drosophila and mammalian H1t, were only marginally simple. The coexistence of these three kinds of subtypes suggests that the terminal domains could have originated in the amplification of short sequence motifs, which would then have evolved by point mutation and further slippage.

Animals↗

PubMed2002

Sequence and analysis of the 5' flanking and 5' untranslated regions of the rat N-methyl-D-aspartate receptor 2A gene.

The 5' flanking region and the 5'untranslated region (5' UTR) of the rat N-methyl-D-aspartate receptor subunit 2A were cloned and sequenced using polymerase chain reaction-mediated chromosome walking. The complementary DNA (cDNA) was obtained by rapid amplification of 5'cDNA ends (5'RACE). The comparison of the cDNA and the genomic sequences showed that the 5'UTR contained two introns and three exons, the third exon overlapping the beginning of the coding region. Transcriptional initiation sites were identified by 5'RACE and RNA-protection assays, using total rat brain RNA. The main start sites were found at -591, -577, -560 and -541 nucleotides 5' of the AUG. The promoter region lacked TATA and CAAT positioning elements. A CpG island of about 700 bp overlapped the 5' flanking sequences and the 5' UTR. The CpG island was inside a wider GC-rich region (66% GC) spanning the entire 5' UTR. Comparison of the rat sequences with the human sequences from the Human Genome Data Bank revealed that the 5' UTR exon 2 was extremely conserved with 95.8% sequence identity, as were the initial 640 bp of 5' flanking sequences, with 78% sequence identity. Beyond this point, sequence identity dropped abruptly to 44%. Putative recognition sequences for the transcription factors S8, Sp1, GATA, AML1 and NF-kappaB were identified in both the rat and human promoter sequences.

5' Flanking Region↗

PubMed2002

An inducible helix-Gly-Gly-helix motif in the N-terminal domain of histone H1e: a CD and NMR study.

Knowledge of the structural properties of linker histones is important to the understanding of their role in higher-order chromatin structure and gene regulation. Here we study the conformational properties of the peptide Ac-EKTPVKKKARKAAGGAKRKTSG-NH(2) (NE-1) by circular dichroism and (1)H-NMR. This peptide corresponds to the positively charged region of the N-terminal domain, adjacent to the globular domain, of mouse histone H1e (residues 15-36). This is the most abundant H1 subtype in many kinds of mammalian somatic cells. NE-1 is mainly unstructured in aqueous solution, but in the presence of the secondary-structure stabilizer trifluoroethanol (TFE) it acquires an alpha-helical structure. In 90% TFE solution the alpha-helical population is approximately 40%. In these conditions, NE-1 is structured in two alpha-helices that comprise almost all the peptide, namely, from Thr17 to Ala27 and from Gly29 to Thr34. Both helical regions are highly amphipathic, with the basic residues on one face of the helix and the apolar ones on the other. The two helical elements are separated by a Gly-Gly motif. Gly-Gly motifs at equivalent positions are found in many vertebrate H1 subtypes. Structure calculations show that the Gly-Gly motif behaves as a flexible linker between the helical regions. The wide range of relative orientations of the helical axes allowed by the Gly-Gly motif may facilitate the tracking of the phosphate backbone by the helical elements or the simultaneous binding of two nonconsecutive DNA segments in chromatin.

Amino Acid Motifs↗