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PubMed2026

Control of foreign DNA: emerging roles of xenogeneic silencers.

Bacteria continuously acquire foreign DNA through horizontal gene transfer, yet its successful integration depends on regulatory mechanisms that balance genome protection with evolutionary innovation. Xenogeneic silencers are central to this process: they preferentially bind AT-rich DNA, a common feature of many horizontally acquired genetic elements, and repress its transcription. Recent studies, however, reveal a much broader regulatory repertoire. Beyond transcriptional repression, these proteins contribute to chromosome organization by forming higher-order nucleoprotein complexes and phase-separated condensates that shape bacterial nucleoid architecture. Furthermore, they play roles in regulating bacteriophage infection cycles, including mechanisms by which phages hijack host silencing activities for their own benefit. Their extensive regulatory reach, spanning virulence genes, biofilm formation, specialized metabolite production, and mobile genetic elements (MGEs), underscores their central role in connecting environmental signals, including fluctuations in the second messenger c-di-GMP, with gene expression, and genome organization. The diversification of xenogeneic silencers across bacterial chromosomes, plasmids, phages, and other MGEs highlights their evolutionary significance. Together, these recent findings position xenogeneic silencers as dynamic regulatory modules that shape the fate of foreign DNA across the horizontal gene transfer network.

Gene Transfer, Horizontal↗

PubMed2004

Telomere dysfunction in genome instability syndromes.

Telomeres are nucleoprotein complexes located at the end of eukaryotic chromosomes. They have essential roles in preventing terminal fusions, protecting chromosome ends from degradation, and in chromosome positioning in the nucleus. These terminal structures consist of a tandemly repeated DNA sequence (TTAGGG in vertebrates) that varies in length from 5 to 15 kb in humans. Several proteins are attached to this telomeric DNA, some of which are also involved in different DNA damage response pathways, including Ku80, Mre11, NBS and BLM, among others. Mutations in the genes encoding these proteins cause a number of rare genetic syndromes characterized by chromosome and/or genetic instability and cancer predisposition. Deletions or mutations in any of these genes may also cause a telomere defect resulting in accelerated telomere shortening, lack of end-capping function, and/or end-to-end chromosome fusions. This telomere phenotype is also known to promote chromosomal instability and carcinogenesis. Therefore, it is essential to understand the interplay between telomere biology and genome stability. This review is focused in the dual role of chromosome fragility proteins in telomere maintenance.

Animals↗

PubMed2007

DNA damage responses in neural cells: Focus on the telomere.

Postmitotic neurons must survive for the entire life of the organism and be able to respond adaptively to adverse conditions of oxidative and genotoxic stress. Unrepaired DNA damage can trigger apoptosis of neurons which is typically mediated by the ataxia telangiectasia mutated (ATM)-p53 pathway. As in all mammalian cells, telomeres in neurons consist of TTAGGG DNA repeats and several associated proteins that form a nucleoprotein complex that prevents chromosome ends from being recognized as double strand breaks. Proteins that stabilize telomeres include TRF1 and TRF2, and proteins known to play important roles in DNA damage responses and DNA repair including ATM, Werner and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs). We have been performing studies of developing and adult neurons aimed at understanding the effects of global and telomere-directed DNA damage responses in neuronal plasticity and survival in the contexts of aging and neurodegenerative disorders. Deficits in specific DNA repair proteins, including DNA-PKcs and uracil DNA glycosylase (UDG), render neurons vulnerable to adverse conditions of relevance to the pathogenesis of neurodegenerative disorders such as Alzheimer's disease and stroke. Similarly, early postmitotic neurons with reduced telomerase activity exhibit accentuated responses to DNA damage and are prone to apoptosis demonstrating a pivotal role for telomere maintenance in both mitotic cells and postmitotic neurons. Our recent findings suggest key roles for TRF2 in regulating the differentiation and survival of neurons. TRF2 affects cell survival and differentiation by modulating DNA damage pathways, and gene expression. A better understanding of the molecular mechanisms by which neurons respond to global and telomere-specific DNA damage may reveal novel strategies for prevention and treatment of neurodegenerative disorders. Indeed, work in this and other laboratories has shown that dietary folic acid can protect neurons against Alzheimer's disease by keeping homocysteine levels low and thereby minimizing the misincorporation of uracil into DNA in neurons.

Animals↗

PubMed2003

The csgD promoter, a control unit for biofilm formation in Salmonella typhimurium.

Expression of cellulose and curli fimbriae in Salmonella typhimurium is dependent on the transcriptional regulator CsgD. Transcription of csgD itself is influenced by a variety of regulatory stimuli. Complex nucleoprotein arrangements modulate the transcriptional activity of csgD and trigger the transition between the planktonic status and biofilm formation.

Bacterial Proteins↗

PubMed2004

Chromatin modifiers and carcinogenesis.

Access of gene regulatory factors to the eukaryotic genome is modulated by chromatin. The organization of this nucleoprotein complex is highly dynamic and tightly regulated. The control of wide-ranging nuclear processes through the configuration of chromatin is achieved by the concerted actions of ATP-dependent chromatin-remodeling complexes and histone-modifying enzymes, and by the incorporation of specialized histone variants. It is becoming clear that perturbation of these chromatin modifiers can lead to cancer. Recent findings illustrate the mechanisms by which chromatin influences cancer development, and aid understanding of the regulation of chromatin organization, cellular transformation and the connections between tumor suppressor and oncogene function.

Animals↗

PubMed2005

Viral stop-and-go along microtubules: taking a ride with dynein and kinesins.

Incoming viral particles move from the cell surface to sites of viral transcription and replication. By contrast, during assembly and egress, subviral nucleoprotein complexes and virions travel back to the plasma membrane. Because diffusion of large molecules is severely restricted in the cytoplasm, viruses use ATP-hydrolyzing molecular motors of the host for propelling along the microtubules, which are the intracellular highways. Recent studies have revealed that, besides travelling inside endocytic or exocytic vesicles, viral proteins interact directly with dynein or kinesin motors. Understanding the molecular mechanisms of cytoplasmic viral transport will aid in the construction of viral vectors for human gene therapy and the search for new antiviral targets.

Dyneins↗

PubMed2006

Unraveling androgen receptor interactomes by an array-based method: discovery of proto-oncoprotein c-Rel as a negative regulator of androgen receptor.

The androgen receptor (AR) plays a key role in the development and function of male reproductive organs. Using a high-throughput transcription factor-transcription factor (TF-TF) interaction array method, we captured the AR interactomes in androgen-responsive LNCaP cells. Several known and unknown partners of AR, including AP-2, Pax 3/5 (BSAP), c-Rel, RREB-1, LIII BP, and NPAS2 were identified. We investigated one unreported AR-associated transcription factor, the proto-oncoprotein c-Rel, in detail. C-Rel belongs to the NF-kB/Rel families and is persistently active in a number of diseases, including cancer. The presence of c-Rel transcript, protein, and its in vitro and in vivo association with AR was determined. Co-localization of c-Rel with AR both in cytoplasm and nucleus was confirmed by indirect immunofluorescence analysis. Chromatin immunoprecipitation data indicated that c-Rel, like AR, is a part of the nucleoprotein complex regulating the androgen-responsive prostate-specific antigen (PSA) promoter. Overexpression of c-Rel downregulated the promoter activity of both PSA and GRE4-TATA-Luc plasmids in LNCaP and COS cells. Analysis of AR and c-Rel protein levels indicated that the promoter downregulation was not due to reciprocal decrease in the amounts of AR or c-Rel. In summary, we have identified several new partners of AR by using the TF-TF array method and have provided the first evidence of a functional role for c-Rel in androgen-responsive human prostate cancer cells.

Base Sequence↗

PubMed2004

Mechanism of DNA compaction by yeast mitochondrial protein Abf2p.

We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At a high concentration of Abf2p DNA collapses into a tight nucleoprotein complex. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of Abf2p. We also derived a polymer statistical mechanics model that provides a quantitative description of compaction observed in our experiments. This model shows that sharp bends in the DNA backbone are often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for Abf2p. These studies indicate that Abf2p compacts DNA through a simple mechanism that involves bending of the DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance and organization.

Binding Sites↗

PubMed2001

About the possible origin and mechanism of circulating DNA apoptosis and active DNA release.

BACKGROUND: In addition to cell lysis, apoptosis has been advanced as the origin of circulating DNA on the basis of several observations. Plasma or serum DNA often presents a ladder pattern reminiscent of that displayed by apoptotic cells when subjected to electrophoresis. However, the phenomenon of active release of DNA from cells might also be expected to result in a ladder pattern on electrophoresis. Non-dividing cells, such as lymphocytes, frog auricles and cultured cell lines including HL-60, spontaneously release a nucleoprotein complex within a homeostatic system in which newly synthesized DNA is preferentially released. CONCLUSION: In relation to DNA synthesis, the phenomenon of extracellular DNA in different culture conditions favors apoptosis or spontaneous active DNA release.

Apoptosis↗

PubMed1997

Changes in protamine 1 distribution in human sperm nucleus during in vitro sperm-oocyte interaction: an immunoelectron microscopic study.

OBJECTIVE: To determine whether the process of sperm nuclear destabilization would begin before sperm-oocyte fusion in humans. DESIGN: Changes in the distribution of human protamine 1 were investigated in human spermatozoa from the ejaculate, in spermatozoa selected by swim-up or Percoll techniques, and in spermatozoa bound to zona pellucida (ZP) from oocytes that failed to fertilize in an IVF program. SETTING: Center for Infertility and Assisted Reproductive Technology, and university departments. PATIENT(S): Fifteen couples undergoing an IVF program. INTERVENTION(S): Women underwent a similar superovulation induction protocol that consisted of GnRH agonist associated with hMG. MAIN OUTCOME MEASURE(S): Comparative immunoelectron microscopic study of sperm nucleus labeling with an anti-human protamine 1 specific protamine monoclonal antibody. RESULT(S): After selection by swim-up or by Percoll, spermatozoa show a significantly lower nuclear labeling than in the ejaculate. After binding to the ZP, labeling increases, more in spermatozoa selected by swim-up than by Percoll, but, after Percoll selection, labeling in zona-bound spermatozoa is lower than in the ejaculate. CONCLUSION(S): In humans sperm binding to the ZP induces differences in the accessibility of the anti-human protamine 1 antibody, which are consistent with structural rearrangements of the DNA-nucleoproteins complex. These modifications must be a prelude to sperm decondensation, protamines replacement by histones, and subsequent reactivation of the sperm genome in the oocyte.

Cell Nucleus↗

PubMed2002

Human catalytic RNA- and DNA-hydrolyzing antibodies.

In patients with autoimmune diseases, anti-idiotypic antibodies directed to nucleoprotein complexes, DNA, and enzymes that participate in nucleic acid metabolism may be induced spontaneously by primary antigens and can have characteristics of the primary antigen, including catalytic activity. The first natural catalytic antibody, now termed abzyme, which hydrolyzes intestinal vasoactive peptide, was discovered by Paul et al. [Science 244 (1989) 1158]. Subsequently, other abzymes able to hydrolyze proteins, DNA, RNA, or polysaccharides have been found in the sera of patients with autoimmune and also viral pathologies. Further, we have discovered in the milk of healthy human mothers antibodies that catalyze the hydrolysis of RNA, DNA, nucleotides, and the phosphorylation of lipids and proteins. The phenomenon of catalysis by autoantibodies is extremely interesting and can potentially be applied to many different objectives including new types of efficient catalysts, evaluation of the functional roles of abzymes in innate and adaptive immunity, and understanding of certain aspects of self-tolerance and of the destructive responses in autoimmune diseases. In this review, we collate methods for purifying and characterizing natural abzymes especially those catalyzing DNA and RNA hydrolysis. We also describe new methods that we have developed to provide rigorous criteria that catalytic activity is an intrinsic property of some antibodies. Some major current themes are discussed as well as potential applications of abzymes in scientific, medical, and biotechnological fields.

Antibodies, Catalytic↗

PubMed2003

Analysis of NCp7-dependent activation of HIV-1 cDNA integration and its conservation among retroviral nucleocapsid proteins.

HIV-1 nucleocapsid protein NCp7 is a small basic protein with two zinc fingers, found in the virion core where several hundred molecules coat the genomic RNA. NCp7 has nucleic acid chaperone properties that guide reverse transcriptase (RT) to synthesize the proviral DNA flanked by the long terminal repeats (LTR). In vitro, NCp7 can strongly activate magnesium-dependent LTR-DNA strand transfer by integrase (IN). Here we show that IN activation relies on both the basic residues and the zinc fingers of NCp7. NCp7 lacking the zinc fingers binds DNA but moderately stimulates strand transfer by IN. The NCp7 zinc-finger domain binds DNA poorly and does not efficiently stimulate IN activity. However, the NC zinc-finger domain can complement DNA binding to restore full activation of strand transfer by IN. We propose that the basic residues and the zinc fingers function together to stabilize IN at the LTR ends and promote the formation of a nucleoprotein complex competent for integration. We also show that these properties of HIV-1 NCp7 are remarkably conserved among nucleocapsid proteins of retrotransposon and retrovirus origins.

Amino Acid Sequence↗

PubMed1996

Immunofluorescent analysis of the organization of telomeric DNA sequences and their involvement in chromosomal aberrations in hamster cells.

We have investigated the organization of telomeric TTAGGG)n repeats in the extended DNA loops of chromatin of human and hamster cells by immunofluorescent technique. In humans, telomeric repeats which are predominantly localized at the termini of all the chromosomes, have been found associated with nuclear matrix. This distribution pattern did not alter, even after the removal of 90% of the DNA from the nuclear halos by EcoRI digestion. This suggests that the telomeric sequences are tightly associated with nuclear matrix and hence cannot be solubilized by nucleases. In contrast, in Chinese hamster cells (CHO B11), a major proportion of interstitial telomeric repeats are found in the loop regions, like beads on a string, with attachments to the periphery of the nuclear matrix. Unlike in human cells, EcoRI digestion removed most of the telomeric repeats from the loop regions of Chinese hamster cells. This indicates that intrachromosomal sequences are not associated with nuclear matrix, and this finding has been further substantiated by Southern hybridization of matrix associated and loop DNA fractions of hamster cells with the (TTAGGG)n probe. The organizational differences in the telomeric repeat sequences of Chinese hamster and human cells might be due to their chromosomal location as well as their interaction with nucleoprotein complexes specific for the termini of the eukaryotic chromosomes. Furthermore, the interstitial (TTAGGG)n sequences were found to be more frequently involved in the chromosomal aberrations induced by restriction enzymes. This suggests that the intrachromosomal sites of telomeric sequences behave as hot spots for DNA damage.

Animals↗

PubMed2001

The regulation of pap and type 1 fimbriation in Escherichia coli.

The ability of bacterial pathogens to bind to the host mucosa is a critical step in the pathogenesis of many bacterial infections and, for Escherichia coli, a large number of different fimbrial adhesins have been implicated as virulence factors. In this chapter, our current understanding of the regulatory mechanisms that control the expression of two of the best characterized fimbrial adhesins, pyelonephritis-associated pilus (encoded by pap) and the type 1 fimbria (encoded by fim), will be described. The expression of both fimbrial adhesins is controlled by phase variation (the reversible and apparently random switching between expressing ('on') and non-expressing ('off') states), and is regulated in response to environmental conditions. The phase variation of pap (and of some other fimbriae in Escherichia coli) is determined by the formation of alternative nucleoprotein complexes that either activate (phase 'on') or suppress (phase 'off') transcription of the fimbria genes. Formation of each complex protects a single Dam methylation site (5' GATC) from modification (GATCdist in phase 'on' cells and GATCprox in phase 'off' cells). Furthermore, complex formation is inhibited by methylation of the two 5' GATC sites. Both the phase variation of pap and the transcription of the pap genes in phase 'on' cells, are regulated and expression is subject to both positive and negative feedback control. In contrast to pap, the phase variation of fim is determined by the site-specific inversion of a short element of DNA (the fim switch). In phase 'on' cells, a promoter within the invertible element directs the transcription of the fim structural genes, whereas in phase 'off' cells transcription of the fimbrial genes is silenced. Despite the very different molecular mechanisms controlling the expression of pap and fim, the two systems share many features in common and have probably evolved to fulfill the same function. In addition to details about the molecular mechanisms that control pap and fim, the possible physiological significance of the observed regulation will be discussed.

Adhesins, Escherichia coli↗

PubMed2000

Interleukin-1beta induction of the chemokine RANTES promoter in the human astrocytoma line CH235 requires both constitutive and inducible transcription factors.

The chemokine RANTES is an important mediator of inflammatory processes. In this report, we describe the DNA sequence and transcription factor requirements for interleukin-1beta (IL-1beta) induction of the RANTES promoter in the human astrocytoma line CH235. RANTES promoter sequences between -278 and +55 are sufficient for IL-1beta-inducibility. In vitro DNA binding assays demonstrate constitutive binding of Sp1, HMG, Ets domain, and bZIP family members to their cognate sites in the RANTES promoter, whereas NF-kappaB and IRF-1 bind in an IL-1beta-inducible manner. IL-1beta-inducibility of the RANTES promoter requires both constitutive and inducible transcription factors. The formation of a higher order nucleoprotein complex, or 'enhanceosome', may be critical for IL-1beta induction of the RANTES promoter.

Astrocytoma↗

PubMed1997

TRF1, a mammalian telomeric protein.

Telomerase adds TTAGGG repeats onto mammalian chromosome ends, replenishing the terminal sequence loss incurred during DNA replication. This maintenance of telomeric DNA preserves binding sites for telomeric proteins, which form a protective nucleoprotein complex at chromosome ends. The recent isolation of TRF1, the mammalian telomeric-repeat binding factor, should now allow the structure and function of the telomeric complex to be examined in detail.

Amino Acid Sequence↗

PubMedDate not supplied

Inactivation of Escherichia coli DnaA protein by DNA polymerase III and negative regulations for initiation of chromosomal replication.

Genetic and biochemical evidence indicates that initiation of chromosomal replication in Escherichia coli occurs in a nucleoprotein complex at the replication origin (oriC) formed with DnaA protein. The frequency of initiation at oriC is tightly regulated to only once per chromosome per cell cycle. To prevent untimely, extra initiations, negative control for initiation is indispensable. Recently, we found that the function of the initiator protein, DnaA, is controlled by DNA polymerase III holoenzyme, the replicase of the chromosome. The ATP-bound form of DnaA protein, an active form for initiation, is efficiently converted to the ADP bound form, an inactive form, since a subunit of the polymerase loaded on DNA (beta subunit sliding clamp) stimulates hydrolysis of ATP bound to DnaA protein. Comparison of this system, RIDA (regulatory inactivation of DnaA), with other systems for negative regulation of initiation is included in this review, and the roles of these systems for concerted control for initiation during the cell cycle are discussed.

Adenosine Diphosphate↗

PubMed2003

Transcriptional regulation of the human Runx2/Cbfa1 gene promoter by bone morphogenetic protein-7.

It is well established that core binding factor Runx2/Cbfa1 is required for osteoblast recruitment and differentiation from mesenchymal stem cells. Transcriptional regulation of the Runx2/Cbfa1 gene by osteogenic factors such as bone morphogenetic proteins (BMPs) plays an important role in the stimulation of bone formation by these cytokines. BMP7 (also termed OP-1) is a member of the transforming growth factor beta (TGF-beta) superfamily and induces osteoblast differentiation from mesenchymal precursor stem cells in vitro as well as bone formation in vivo. This study examines the effects of BMP7 on markers of osteoblast differentiation and specifically on human Runx2/Cbfa1 gene transcription in a mouse C2C12 myoblast cell line where it induces expression of both alkaline phosphatase (ALP) and endogenous Runx2/Cbfa1. To further understand the mechanisms of human Runx2/Cbfa1 transcriptional regulation by BMP7, we cloned 3.0 kb of the human Runx2/Cbfa1 gene 5'-upstream flanking region and created a series of promoter deletions cloned into luciferase-based reporter vectors (Runx2/Cbfa1/Luc). Sequence data revealed six copies of the osteoblastic cis-acting element (OSE2) in the proximal promoter region. In C2C12 cells transiently transfected with Runx2/Cbfa1/Luc deletion constructs, transcriptional activity of Runx2/Cbfa1 was upregulated up to 2-fold after 24 h of BMP7 treatment. Mutational analysis demonstrated that the minimal responsive promoter region for BMP7-regulated transcription maps to a proximal -74 OSE2 site. Electromobility shift assays with C2C12 cellular extracts indicate that BMP7 increases binding of OSE2 promoter sequences, and supershift assays with anti-Runx2/Cbfa1 antibodies demonstrate that Runx2/Cbfa1 is part of the nucleoprotein complex binding OSE2. Together, these data indicate BMP7 can upregulate Runx2/Cbfa1 gene expression in C2C12 myoblast cells, and suggest that Runx2/Cbfa1 may bind to OSE2 elements within its own promoter to autoregulate gene transcription in differentiating osteoblasts.

Alkaline Phosphatase↗