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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↗
PubMed2005

TPX or not TPX?

An Aurora A regulatory module has been identified in two different proteins: TPX2 in Xenopus laevis and TPXL-1 in C. elegans. The diverse roles of these two proteins in spindle assembly leave us to beckon the true C. elegans TPX2 ortholog to center stage.

Animals↗
PubMed2004

Identification of an Sp factor-dependent promoter in GCET, a gene expressed at high levels in germinal center B cells.

Antigen-stimulated B lymphocytes undergo genetic and phenotypic changes in germinal centers (GCs), including affinity maturation of immunoglobulin (Ig) genes and Ig heavy chain isotype switching. Expression of the Germinal Center Expressed Transcript (GCET) gene is up-regulated in murine GC B cells. The human homolog of GCET, HGAL/GCET2, is an important prognostic marker for staging lymphomas derived from GCs. To identify mechanisms that control cell type-specific transcription of GCET, we localized promoter sequences using S1 nuclease protection and functional assays. Sequences comprising a TATA-less promoter were localized to a short region upstream of multiple mRNA start sites. In functional assays, the promoter is active in cells irrespectively of endogenous GCET gene expression. In vitro binding assays identified a non-consensus binding site for Sp factors near sites of transcriptional initiation. The site binds Spl and Sp3 in nuclear extracts and recombinant Spl in vitro, and is required for full promoter function in transient promoter assays. Activation of the promoter by Spl or Sp3 in Spl/3-deficient cells was largely dependent on the Sp site. Together, these data provide the first analysis of regulatory modules necessary for GCET expression, a model for GC B cell-specific transcription.

Animals↗
PubMed2026

Small GTPase RAN-driven PNET2 oligomerization and phase separation at the nuclear lamina promote nuclear envelope integrity in plants.

The nuclear envelope is a fundamental organizer of eukaryotic cells, yet how plants regulate its architecture and integrity remains poorly understood. In this study, we identified the plant inner nuclear membrane protein PLANT NUCLEAR ENVELOPE TRANSMEMBRANE 2 (PNET2) as a scaffold that maintains nuclear envelope integrity and genome stability. Loss of PNET2 function compromises nuclear membrane structure and sensitizes cells to DNA damage, whereas overexpression drives aberrant nuclear membrane expansion. Biochemically, PNET2 cooperates with the nuclear lamin protein KAKU4 and CROWDED NUCLEI 1 within the nuclear lamina to promote nuclear membrane remodeling, a process driven by biomolecular condensate formation via their intrinsically disordered regions. We further uncovered a direct interaction between PNET2 and the small GTPase RAN. Structural modeling and biochemical analyses revealed that its active GTP-bound form stimulates PNET2 oligomerization, potentially promoting its phase separation to drive membrane expansion. Genetic analyses showed that PNET2 and RAN function in a shared pathway essential for nuclear membrane integrity. Together, our findings define a regulatory module that orchestrates GTPase signaling to sustain nuclear membrane homeostasis in plants, positioning PNET2 as a nexus linking membrane dynamics, nuclear lamina organization, and genome protection.

PNET2↗
PubMed2026

A cis-regulatory allele of ZmNPR1I spatially uncouples flowering from stalk-rot resistance in maize.

Pleiotropic effects of adaptive genes frequently constrain crop improvement by coupling beneficial traits with unfavorable trade-offs. In maize, ZmCCT10 confers strong stalk-rot resistance but causes delayed flowering under long-day conditions, limiting its deployment in temperate breeding. Here, we identify qPss3 as a cis-regulatory locus that governs its downstream target gene, ZmNPR1I. The ZmNPR1I protein represses ZmCCT10 transcription and, together with ZmNPR1-3, facilitates ZmCCT10 protein degradation. The favorable qPss3A5 allele reduces ZmNPR1I expression in leaves, relieving repression of ZmCCT10, ZmSPL32, and ID1, which collectively enhance ZCN8 expression to accelerate flowering. In roots, however, pathogen-induced activation of the resistant ZmCCT10H5 allele largely bypasses qPss3 regulation, thereby preserving stalk-rot resistance. Introgression of qPss3A5 into ZmCCT10H5-containing maize germplasm restores flowering adaptation without compromising disease resistance, improving yield stability under disease pressure. Our work reveals a tissue-specific qPss3A5-ZmNPR1I regulatory module that uncouples the developmental and immune functions of a pleiotropic adaptive gene, providing a general strategy for optimizing beneficial alleles in crop breeding.

flowering time↗
PubMed2005

A rat 8 kb dentin sialoprotein-phosphophoryn (DSP-PP) promoter directs spatial and temporal LacZ activity in mouse tissues.

Dentin sialoprotein (DSP) and phosphophoryn (PP) are two major dentin noncollagenous proteins that are encoded on a single DSP-PP transcript whose expression is tightly regulated during tooth dentinogenesis. The recent identification of this gene transcript in other tissues, including inner ear and jaw tissue, suggests that DSP and PP may have pleiotropic effects on other organs besides teeth. To identify candidate regulatory elements that control DSP-PP temporal and spatial expression, we constructed a -5 kb upstream region rat DSP-PP promoter into the beta-galactosidase expression vector pnLacF plasmid and used this construct to prepare DSP-PP-LacZ transgenic mice. Multiple mouse tissues including teeth, bone, and kidney obtained from the six resulting transgenic mouse lines displayed strong LacZ activity. This spatial distribution was confirmed in several of these tissues by in situ hybridization studies. LacZ activity was transiently expressed in preameloblasts and continuously expressed in odontoblasts demonstrating that this -5 kb rat promoter-dependent LacZ expression mimics reported DSP-PP mRNA expression patterns. Interestingly, this -5 kb rat promoter construct drives LacZ expression according to the rat developmental clock. Based on identified transcription factors present in this -5 kb promoter region, we have identified several probable cis-regulatory modules whose interaction with one another could account for the spatial and temporal distribution of DSP-PP transcripts in developing tissues.

Animals↗
PubMed2006

Identification of cis-regulatory elements from the C. elegans Hox gene lin-39 required for embryonic expression and for regulation by the transcription factors LIN-1, LIN-31 and LIN-39.

Expression of the Caenorhabditis elegans Hox gene lin-39 begins in the embryo and continues in multiple larval cells, including the P cell lineages that generate ventral cord neurons (VCNs) and vulval precursor cells (VPCs). lin-39 is regulated by several factors and by Wnt and Ras signaling pathways; however, no cis-acting sites mediating lin-39 regulation have been identified. Here, we describe three elements controlling lin-39 expression: a 338-bp upstream fragment that directs embryonic expression in P5-P8 and their descendants in the larva, a 247-bp intronic region sufficient for VCN expression, and a 1.3-kb upstream cis-regulatory module that drives expression in the VPC P6.p in a Ras-dependent manner. Three trans-acting factors regulate expression via the 1.3-kb element. A single binding site for the ETS factor LIN-1 mediates repression in VPCs other than P6.p; however, loss of LIN-1 decreases expression in P6.p. Therefore, LIN-1 acts both negatively and positively on lin-39 in different VPCs. The Forkhead domain protein LIN-31 also acts positively on lin-39 in P6.p via this module. Finally, LIN-39 itself binds to this element, suggesting that LIN-39 autoregulates its expression in P6.p. Therefore, we have begun to unravel the cis-acting sites regulating lin-39 Hox gene expression and have shown that lin-39 is a direct target of the Ras pathway acting via LIN-1 and LIN-31.

Animals↗
PubMed2006

Transcriptional network dynamics in macrophage activation.

Transcriptional regulatory networks govern cell differentiation and the cellular response to external stimuli. However, mammalian model systems have not yet been accessible for network analysis. Here, we present a genome-wide network analysis of the transcriptional regulation underlying the mouse macrophage response to bacterial lipopolysaccharide (LPS). Key to uncovering the network structure is our combination of time-series cap analysis of gene expression with in silico prediction of transcription factor binding sites. By integrating microarray and qPCR time-series expression data with a promoter analysis, we find dynamic subnetworks that describe how signaling pathways change dynamically during the progress of the macrophage LPS response, thus defining regulatory modules characteristic of the inflammatory response. In particular, our integrative analysis enabled us to suggest novel roles for the transcription factors ATF-3 and NRF-2 during the inflammatory response. We believe that our system approach presented here is applicable to understanding cellular differentiation in higher eukaryotes.

Algorithms↗
PubMed2004

A nonlinear discrete dynamical model for transcriptional regulation: construction and properties.

Transcriptional regulation is a fundamental mechanism of living cells, which allows them to determine their actions and properties, by selectively choosing which proteins to express and by dynamically controlling the amounts of those proteins. In this article, we revisit the problem of mathematically modeling transcriptional regulation. First, we adopt a biologically motivated continuous model for gene transcription and mRNA translation, based on first-order rate equations, coupled with a set of nonlinear equations that model cis-regulation. Then, we view the processes of transcription and translation as being discrete, which, together with the need to use computational techniques for large-scale analysis and simulation, motivates us to model transcriptional regulation by means of a nonlinear discrete dynamical system. Classical arguments from chemical kinetics allow us to specify the nonlinearities underlying cis-regulation and to include both activators and repressors as well as the notion of regulatory modules in our formulation. We show that the steady-state behavior of the proposed discrete dynamical system is identical to that of the continuous model. We discuss several aspects of our model, related to homeostatic and epigenetic regulation as well as to Boolean networks, and elaborate on their significance. Simulations of transcriptional regulation of a hypothetical metabolic pathway illustrate several properties of our model, and demonstrate that a nonlinear discrete dynamical system may be effectively used to model transcriptional regulation in a biologically relevant way.

Algorithms↗
PubMed1986

Neonatal developmental pattern of superoxide dismutase and aniline hydroxylase in rat lung.

The developmental biology of superoxide dismutase and aniline hydroxylase was followed in rat lungs from prenatal stage to 3 months old. Total superoxide dismutase activity as determined by spectrophotometry as well as electrophoresis was high in the prenatal rat lung, decreased in the first 24 hr postpartum, increased within 7 days, and then decreased gradually to adult levels. On polyacrylamide gel electrophoresis only two isozymic forms of superoxide dismutase were located as achromatic zones in the fetal lung. In the adult rat lung, there were three molecular forms of superoxide dismutase, two in the postmitochondrial supernatant and one in the mitochondrial fraction. Unlike superoxide dismutase, aniline hydroxylase was detectable only after 5 days of age and the activity exhibited a gradual increase afterward up to 1 month of age. The developmental pattern of superoxide dismutase and aniline hydroxylase activities in lung may be significant in understanding the mechanism of body defenses and their regulatory modulations in response to toxic air pollutants and environmental stress.

Aniline Hydroxylase↗
PubMed2001

Cloning and expression of novel mosaic serine proteases with and without a transmembrane domain from human lung.

Two cDNAs encoding novel mosaic proteins with a serine protease domain and potential regulatory modules, consisting of a protein kinase substrate and a low-density lipoprotein receptor, were cloned from a human lung cDNA library by PCR. One with a transmembrane domain (MSPL) and the other without one (MSPS) comprise 581 and 537 amino acids, respectively. Except for the C-terminal ends, the two isoforms had an identical serine protease domain exhibiting 42, 39 and 43% identity with those of plasma kallikrein, hepsin and transmembrane protease serine 2, respectively. Both genes were predominantly expressed in human lung, placenta, pancreas and prostate.

Amino Acid Sequence↗
PubMed1997

An Acanthamoeba polyubiquitin gene and application of its promoter to the establishment of a transient transfection system.

We have isolated and sequenced a 2388 bp polyubiquitin encoding genomic DNA from Acanthamoeba encompassing two complete and one incomplete ubiquitin units. Codon usage frequency shows extreme bias. The deduced amino acid sequences of each unit are identical to each other and the same as that deduced from a previously sequenced Acanthamoeba castellanii cDNA. The upstream region of this gene, which contained some putative regulatory modules, was recovered by PCR (polymerase chain reaction) amplification and subcloning. This upstream fragment was ligated to the CAT (chloramphenicol acetyltransferase) gene in a eukaryotic expression plasmid and successfully applied to the establishment of an Acanthamoeba transient transfection system. Transfection was performed by electroporation and the optimal voltage was 4500 volts/cm at capacitance 25 microF. DEAE-dextran (25 microg/ml) added into the electroporation buffer increased the transfection efficiency by about 45%. The CAT activity was proportional to the amount of DNA transfected and reached the peak level 48 h after transfection. CAT assays showed that the polyubiquitin gene upstream fragment contains a functional promoter which is about 2.5 times as strong as a viral RSV-LTR promoter when driving CAT expression in Acanthamoeba.

Acanthamoeba↗
PubMed1999

Functional roles of S100 proteins, calcium-binding proteins of the EF-hand type.

A multigenic family of Ca2+-binding proteins of the EF-hand type known as S100 comprises 19 members that are differentially expressed in a large number of cell types. Members of this protein family have been implicated in the Ca2+-dependent (and, in some cases, Zn2+- or Cu2+-dependent) regulation of a variety of intracellular activities such as protein phosphorylation, enzyme activities, cell proliferation (including neoplastic transformation) and differentiation, the dynamics of cytoskeleton constituents, the structural organization of membranes, intracellular Ca2+ homeostasis, inflammation, and in protection from oxidative cell damage. Some S100 members are released or secreted into the extracellular space and exert trophic or toxic effects depending on their concentration, act as chemoattractants for leukocytes, modulate cell proliferation, or regulate macrophage activation. Structural data suggest that many S100 members exist within cells as dimers in which the two monomers are related by a two-fold axis of rotation and that Ca2+ binding induces in individual monomers the exposure of a binding surface with which S100 dimers are believed to interact with their target proteins. Thus, any S100 dimer is suggested to expose two binding surfaces on opposite sides, which renders homodimeric S100 proteins ideal for crossbridging two homologous or heterologous target proteins. Although in some cases different S100 proteins share their target proteins, in most cases a high degree of target specificity has been described, suggesting that individual S100 members might be implicated in the regulation of specific activities. On the other hand, the relatively large number of target proteins identified for a single S100 protein might depend on the specific role played by the individual regions that in an S100 molecule contribute to the formation of the binding surface. The pleiotropic roles played by S100 members, the identification of S100 target proteins, the analysis of functional correlates of S100-target protein interactions, and the elucidation of the three-dimensional structure of some S100 members have greatly increased the interest in S100 proteins and our knowledge of S100 protein biology in the last few years. S100 proteins probably are an example of calcium-modulated, regulatory proteins that intervene in the fine tuning of a relatively large number of specific intracellular and (in the case of some members) extracellular activities. Systems, including knock-out animal models, should be now used with the aim of defining the correspondence between the in vitro regulatory role(s) attributed to individual members of this protein family and the in vivo function(s) of each S100 protein.

Animals↗
PubMed1999

The modularity of biological regulatory networks.

A useful approach to complex regulatory networks consists of modeling their elements and interactions by Boolean equations. In this context, feedback circuits (i.e. circular sequences of interactions) have been shown to play key dynamical roles: whereas positive circuits are able to generate multistationarity, negative circuits may generate oscillatory behavior. In this paper, we principally focus on the case of gene networks. These are represented by fully connected Boolean networks where each element interacts with all elements including itself. Flexibility in network design is introduced by the use of Boolean parameters, one associated with each interaction or group of interactions affecting a given element. Within this formalism, a feedback circuit will generate its typical dynamical behavior (i.e. multistationarity or oscillations) only for appropriate values of some of the logical parameters. Whenever it does, we say that the circuit is 'functional'. More interestingly, this formalism allows the computation of the constraints on the logical parameters to have any feedback circuit functional in a network. Using this methodology, we found that the fraction of the total number of consistent combinations of parameter values that make a circuit functional decreases geometrically with the circuit length. From a biological point of view, this suggests that regulatory networks could be decomposed into small and relatively independent feedback circuits or 'regulatory modules'.

Feedback↗
PubMed2002

Role of cyclic nucleotide signaling in oocyte maturation.

The development of the ovarian follicle, oocyte maturation, and ovulation require a complex set of endocrine, paracrine, and autocrine inputs that are translated into the regulation of cyclic nucleotide levels. Changes in intracellular cAMP mediate the gonadotropin regulation of granulosa and theca cell functions. Likewise, a decrease in cAMP concentration in the oocyte has been associated with the resumption of meiosis. Using pharmacological and molecular approaches, we determined that the expression of cyclic nucleotide phosphodiesterases (PDEs), the enzymes that degrade and inactivate cAMP, is compartmentalized in the ovarian follicle of all species studied, with PDE3 present in the oocytes and PDE4s in granulosa cells. The PDE3 expressed in the mouse oocyte was cloned, and the protein expressed in a heterologous system had properties similar to those of a PDE3A derived from somatic cells. Inhibition of the oocyte PDE3 completely blocked oocyte maturation in vitro and in vivo, demonstrating that the activity of this enzyme is essential for oocyte maturation. Heterologous expression of PDE3A in Xenopus oocyte causes morphological changes distinctive of resumption of meiosis (GVBD), as well as activation of mos translation and MAPK phosphorylation. Using mRNA and antibody microinjection in the Xenopus eggs, we have shown that PDE3 is downstream from the kinase PKB/Akt in the pathway that mediates IGF-1 but not progesterone-induced meiotic resumption. The presence of a similar regulatory module in mammalian oocytes is inferred by pharmacological studies with PDE3 inhibitors and measurement of PDE activity. Thus, PDE3 plays an essential role in the signaling pathway that controls resumption of meiosis in amphibians and mammals. Understanding the regulation of this enzyme may shed some light on the signals that trigger oocyte maturation.

Animals↗
PubMed2003

Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships.

Serine proteases (SPs) and serine protease homologs (SPHs) constitute the second largest family of genes in the Drosophila melanogaster genome. Eighty-four SPs comprise less than 300 amino acid residues, and a significant portion of them are probably digestive enzymes. Some larger SPs may contain one or more regions important for protein-protein interactions, including clip domains, low-density lipoprotein receptor class A repeats, and scavenger receptor cysteine-rich domains. We identified 37 clusters of SP or SPH genes, which probably evolved from relatively recent gene duplication and sequence divergence. A majority of the SPs may be trypsin-like and activated by cleavage after a specific arginine or lysine residue. Among the 147 SPs and 57 SPHs studied, 24 SPs and 13 SPHs contain at least one regulatory clip domain. A multiple sequence alignment of the clip domains provided further information on structural conservation of these regulatory modules. Detailed sequence comparison led to an improved classification system for SPs containing clip domains. These analyses have established a framework of information about evolutionary relationships among the Drosophila SPs and SPHs, which may facilitate research on these proteins as well as homologous molecules from other invertebrate species.

Amino Acid Sequence↗
PubMed1997

Regulation of protein kinase C.

Protein kinase C has been in the spotlight since the discovery two decades ago that it is activated by the lipid second messenger diacylglycerol. Despite protein kinase C's enduring stage presence, the regulation and specific roles of its isozymes in defined cellular processes are still under intense investigation. Elucidation of the structures of protein kinase C's regulatory modules, the discovery that phosphorylation regulates the enzyme, and the identification of targeting mechanisms have made the past year a significant one for unveiling how this ubiquitous class of enzymes operates.

Animals↗