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PubMed2004

The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: structural elements of specificity.

The Escherichia coli protein HU functions as an architectural DNA-binding protein by facilitating DNA looping or bending to form multiprotein complexes. Although HU does not recognize a specific DNA sequence, site-specific binding to a number of discontinuous, looped, or bent DNA substrates has been observed. In this study UV resonance Raman (UVRR) spectroscopy is used to identify structural elements associated with low- and high-affinity binding by examining three different HU-DNA complexes. UVRR spectra obtained with an excitation wavelength of 210 nm, which preferentially enhances protein backbone amide vibrations, indicate that HU secondary structure content increases and the protein structure becomes more rigid upon binding to DNA. The increase in alpha-helical content is attributed to the C-terminal helix, which interacts with the DNA and may play a role in binding affinity and specificity. UVRR spectra obtained with a 215 nm excitation wavelength demonstrate that Pro mode intensity at 1455 cm(-1) decreases upon complex formation. This intensity decrease is attributed to the intercalation of Pro residues between DNA base pairs to induce a bend in the DNA, as has been observed previously in the IHF-DNA and HU-DNA cocrystal structures. DNA vibrational modes are also indicative of significant base unstacking and opening of the minor groove upon protein binding, consistent with bending and distortion of the DNA. In all three complexes, A-DNA conformational features are indicated by deoxyribose-phosphate backbone modes. These and other results suggest that protein-induced bending plays an important role in HU site-specific binding and supports a model of a mutually induced fit.

Binding Sites↗

PubMed2004

Adaptation of the photosynthetic electron transport chain in cyanobacteria to iron deficiency: The function of IdiA and IsiA.

In this review we give an overview on the adaptational responses of photosystem (PS) II and PSI in cyanobacteria to iron starvation, mainly summarizing our results with the mesophilic Synechococcus elongatus PCC 7942. We also discuss this process with respect to the strong interrelationship between iron limitation and oxidative stress that exists in cyanobacteria as oxygenic photosynthetic organisms. The adaptation of the multiprotein complexes PSII and PSI to iron starvation is a sequential process, which is characterized by the enhanced expression of two major iron-regulated proteins, IdiA (iron deficiency induced protein A) and IsiA (iron stress induced protein A). Our results suggest that IdiA protects the acceptor side of PSII against oxidative stress under conditions of mild iron limitation in a currently unclear way, whereas prolonged iron deficiency leads to the synthesis of a chlorophyll a antenna around PSI-trimers consisting of IsiA molecules. The physiological consequences of these alterations under prolonged iron starvation, as shown by acridine yellow fluorescence measurements, are a reduction of linear electron transport activity through PSII and an increase of cyclic electron flow around PSI as well as an increase in respiratory activity. IdiA and IsiA expression are mediated by two distinct helix-turn-helix transcriptional regulators of the Crp/Fnr family. IdiB positively regulates expression of idiA under iron starvation, and Fur represses transcription of isiA under iron-sufficient conditions. Although both transcriptional regulators seem to operate independently of each other, our results indicate that a cross-talk between the signal transduction pathways exists. Moreover, IdiA as well as IsiA expression are affected by hydrogen peroxide. We suggest that due to the interdependence of iron limitation and the formation of reactive oxygen species, peroxide stress might be the superior trigger that leads to expression of these proteins under iron starvation. The modifications of PSII and PSI under iron starvation influence the redox state of redox-sensitive components of the electron transport chain, and thus the activity of metabolic pathways being regulated in dependence of the redox state of these components.

Journal Article↗

PubMed2004

Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter.

Expression from the Escherichia coli nir promoter is co-dependent on both the FNR protein (an anaerobically triggered transcription activator) and NarL or NarP proteins (transcription activators triggered by nitrite and nitrate). We found previously that FNR binds to a site centred at position - 41.5 at the nir promoter, but that FNR-dependent activation is repressed by IHF binding to a site centred at position -88 (IHF I) and Fis binding to sites centred at positions -142 (Fis I) and +23 (Fis II). Here, we have studied the binding of purified IHF, Fis and FNR to the nir promoter in vitro. Our results show that the nir promoter contains a second IHF site at position -115 (IHF II) and a third Fis site at position -97 (Fis III), and that IHF, Fis and FNR can bind together to form multiprotein complexes. Surprisingly, IHF binding at the IHF II site increases FNR-dependent activation by decreasing the repression mediated by IHF and Fis binding at the other sites. In previous work, we found that NarL or NarP activates the nir promoter by binding to a site centred at position -69.5 and counteracting the repressive effects of IHF and Fis. We now show that NarL can displace IHF bound at the IHF I site, but IHF is unable to displace bound NarL. We suggest that NarL interferes with IHF binding at the nir promoter by distorting the minor groove at its target site, and we argue that the resulting activation by NarL results from remodelling of the local nucleoprotein structure to facilitate FNR-dependent transcription.

DNA-Binding Proteins↗

PubMed2004

Euroconference on the Biology of Type IV Secretion Processes: bacterial gates into the outer world.

Type IV secretion systems (T4SSs) mediate both protein and ssDNA secretion from a wide range of bacteria into virtually any cell type or into the milieu. It is this versatility that confers on them the ability to participate in many processes of bacterial life that imply communication with their environment. Type IV secretion systems are involved in horizontal DNA transfer to other bacteria and to plant cells, in DNA uptake from the milieu, in toxin secretion into the milieu, and in the injection of virulence factors into the eukaryotic host cell in a number of mammalian and plant pathogens. Recently, a EuroConference addressed the different aspects of the biology of these transmembrane multiprotein complexes, from the crystal structure of the individual components to the modification that the secreted substrates induce in the recipient cell. Significant progress has been made in the understanding of the molecular architecture and mechanism of secretion. The analysis of protein-protein interactions confirms the role of coupling proteins as substrate recruiters for the transporter. The VirB10 component of the complex has come up as a strong candidate for signal transducer. The wide range of effects on the recipient suggests that many effector proteins are secreted. New effector proteins are being identified for both plant and animal pathogens, as are their targets within the host cells. New T4SS members are being identified that perform novel roles, beyond DNA transfer and virulence, such as establishment of symbiotic processes. Our current knowledge of the Biology of Type IV Secretion Processes increases our ability to exploit them as biotechnological tools or to use them as new targets for inhibitors that could constitute a new generation of antimicrobials in the near future.

Animals↗

PubMed2004

The C-terminal domains of the gingipain K polyprotein are necessary for assembly of the active enzyme and expression of associated activities.

The Porphyromonas gingivalis lysine-specific cysteine protease (gingipain K, Kgp) is expressed as a large precursor protein consisting of a leader sequence, a pro-fragment, a catalytic domain with a C-terminal IgG-like subdomain (IgSF) and a large haemagglutinin/adhesion (HA) domain. In order to directly study the role of these non-catalytic domains in pro-Kgp processing and maturation in P. gingivalis, the wild-type form of the gene was replaced with deletion variants encoding C-terminally truncated proteins, including KgpDeltaHA3/4 (Delta1292-1732 aa), KgpDeltaHA2-4 (Delta1157-1732 aa), KgpDeltaHA1-4 (Delta738-1732 aa), KgpDeltaC-term/HA (Delta681-1732 aa) and KgpDeltaIg/C-term/HA (602-1732 aa). Northern blot and reverse transcription polymerase chain reaction (RT-PCR) analysis revealed that all truncated variants of the kgp gene were transcribed in P. gingivalis. Despite high levels of kgpDeltaC-term/HA and kgpDeltaIg/C-term/HA transcripts, no Kgp-specific antigen was detected in cultures of these mutants as determined by Western blot analysis with monoclonal antibodies specific for the Kgp catalytic domain. Furthermore, only barely measurable amounts of Kgp-specific activity were detected in these two mutants. The remaining mutants expressed significant Kgp activity, however, at lower levels when compared with the parental strain. The decreased activity most probably resulted from altered folding and/or hindered secretion of the protein. The kgp gene truncation was also demonstrated to alter the distribution of the gingipain protein between membrane-associated and -secreted forms. While both gingipain K activity and the protein were cell membrane-associated in the parental strain, the mutants released significant amounts of both protein and activity into the media. Taken together, these results suggest that the C-terminal HA domains of Kgp are not only essential for full expression of gingipain activity, but also for proper processing of the multiprotein complex assembly on the P. gingivalis outer membrane. Moreover, our results indicate that the immunoglobulin-like subdomain is indispensable for proper folding and expression of the gingipains.

Adhesins, Bacterial↗

PubMed2005

IcmS-dependent translocation of SdeA into macrophages by the Legionella pneumophila type IV secretion system.

Legionella pneumophila replicates inside alveolar macrophages and causes an acute, potentially fatal pneumonia called Legionnaires' disease. The ability of this bacterium to grow inside of macrophages is dependent on the presence of a functional dot/icm type IV secretion system (T4SS). Proteins secreted by the Dot/Icm T4SS are presumed to alter the host endocytic pathway, allowing L. pneumophila to establish a replicative niche within the host cell. Here we show that a member of the SidE family of proteins interacts with IcmS and is required for full virulence in the protozoan host Acanthamoeba castellanii. Using immunofluorescence microscopy and adenylate cyclase fusions, we show that SdeA is secreted into host cells by L. pneumophila in an IcmS-dependent manner. The SidE-like proteins are secreted very early during macrophage infection, suggesting that they are important in the initial formation of the replicative phagosome. Secreted SidE family members show a similar localization to other Dot/Icm substrates, specifically, to the poles of the replicative phagosome. This common localization of secreted substrates of the Dot/Icm system may indicate the formation of a multiprotein complex on the cytoplasmic face of the replicative phagosome.

Acanthamoeba castellanii↗

PubMed2006

The functional repertoire of prokaryote cellulosomes includes the serpin superfamily of serine proteinase inhibitors.

Many of the Firmicutes bacteria responsible for plant polysaccharide degradation in Nature produce a multiprotein complex called a cellulosome, which co-ordinates glycoside hydrolase assembly, bacterial adhesion to substrate and polysaccharide hydrolysis. Cellulosomal proteins possess a dockerin module, which mediates their attachment to the scaffoldin protein via its interaction with cohesin modules, and only glycoside hydrolases and other carbohydrate active enzymes were known to reside within the cellulosome. We show here with Clostridium thermocellum ATCC 27405 that members of the serpin superfamily of serine proteinase inhibitors, which are best recognized for their conformational flexibility and co-ordination of key regulatory functions in multicellular eukaryotes, also reside within the cellulosome. These studies are the first to expand the cellulosome paradigm of protein complex assembly beyond glycoside hydrolase and carbohydrate active enzymes, and to include a newly identified functionality in the Firmicutes.

Amino Acid Sequence↗

PubMed2004

Mutants for photosystem I subunit D of Arabidopsis thaliana: effects on photosynthesis, photosystem I stability and expression of nuclear genes for chloroplast functions.

In Arabidopsis thaliana, the D-subunit of photosystem I (PSI-D) is encoded by two functional genes, PsaD1 and PsaD2, which are highly homologous. Knock-out alleles for each of the loci have been identified by a combination of forward and reverse genetics. The double mutant psad1-1 psad2-1 is seedling-lethal, high-chlorophyll-fluorescent and deficient for all tested PSI subunits, indicating that PSI-D is essential for photosynthesis. In addition, psad1-1 psad2-1 plants show a defect in the accumulation of thylakoid multiprotein complexes other than PSI. Of the single-gene mutations, psad2 plants behave like wild-type (WT) plants, whereas psad1-1 markedly affects the accumulation of PsaD mRNA and protein, and photosynthetic electron flow. Additional effects of the psad1-1 mutation include a decrease in growth rate under greenhouse conditions and downregulation of the mRNA expression of most genes involved in the light phase of photosynthesis. In the same mutant, a marked decrease in the levels of PSI and PSII polypeptides is evident, as well as a light-green leaf coloration and increased photosensitivity. Increased dosage of PsaD2 in the psad1-1 background restores the WT phenotype, indicating that PSI-D1 and PSI-D2 have redundant functions.

Alleles↗

PubMed2007

The modular nature of genetic diseases.

Evidence from many sources suggests that similar phenotypes are begotten by functionally related genes. This is most obvious in the case of genetically heterogeneous diseases such as Fanconi anemia, Bardet-Biedl or Usher syndrome, where the various genes work together in a single biological module. Such modules can be a multiprotein complex, a pathway, or a single cellular or subcellular organelle. This observation suggests a number of hypotheses about the human phenome that are now beginning to be explored. First, there is now good evidence from bioinformatic analyses that human genetic diseases can be clustered on the basis of their phenotypic similarities and that such a clustering represents true biological relationships of the genes involved. Second, one may use such phenotypic similarity to predict and then test for the contribution of apparently unrelated genes to the same functional module. This concept is now being systematically tested for several diseases. Most recently, a systematic yeast two-hybrid screen of all known genes for inherited ataxias indicated that they all form part of a single extended protein-protein interaction network. Third, one can use bioinformatics to make predictions about new genes for diseases that form part of the same phenotype cluster. This is done by starting from the known disease genes and then searching for genes that share one or more functional attributes such as gene expression pattern, coevolution, or gene ontology. Ultimately, one may expect that a modular view of disease genes should help the rapid identification of additional disease genes for multifactorial diseases once the first few contributing genes (or environmental factors) have been reliably identified.

Computational Biology↗

PubMed2006

Vacuolar adenosine triphosphatase and pancreatic acinar cell function.

The pathologic activation of proteases within the pancreatic acinar cell is a key initiating event in acute pancreatitis. Past studies have suggested that the generation of a low-pH environment is critical to this process. Vacuolar adenosine triphosphatase (vATPase) is a multiprotein complex that transports protons across cellular membranes. Activation of the vATPase requires assembly of the soluble (V(1)) subunits on the membrane subunits (V(0)). It is found that conditions that cause protease activation in the acinar cell also cause assembly of V(1) on V(0). Further, inhibitors of vATPase block this protease activation. Ethanol and butanol sensitize the acinar cell to cholecystokinin-induced zymogen activation; vATPase inhibitors also blocked this activation. Activation of the vATPase may be central to the pathologic activation of proteases in the acinar cell and may also modulate the sensitizing effects of alcohols.

Acute Disease↗

PubMed2004

Potentiation of myelin proteolipid protein (Plp) gene expression is mediated through AP-1-like binding sites.

The myelin proteolipid protein (Plp) gene is expressed in oligodendrocytes and encodes the most abundant protein found in mature CNS myelin. Expression of the gene is dynamic and peaks during the active myelination period of CNS development. The surge in Plp gene activity during this period has been purported to be mediated by a positive regulatory region located within the first intron. This region, designated ASE for antisilencer/enhancer, is located approximately 1 kb downstream of exon 1 sequences and encompasses nearly 100 bp. However, neither the critical nucleotides within this region, nor the associated DNA-binding proteins have been identified. In the present study, DNase I footprinting analysis demonstrated widespread protection of the region on both the coding and non-coding strands suggesting that multiple transcription factors are likely involved. Targeting of putative DNA-protein binding sites contained within the ASE by gel shift, transfection and mutagenesis studies revealed the importance of several AP-1-like binding sites in governing high levels of Plp gene expression in oligodendrocytes. Our results suggest that factors, which bind to these sites, form the core of a multiprotein complex that assembles on the ASE and ultimately affects the temporal regulation of the gene in oligodendrocytes.

Animals↗

PubMed2004

A role for semaphorin 3A signaling in the degeneration of hippocampal neurons during Alzheimer's disease.

Among the earliest invariant neuropathological changes in Alzheimer's disease (AD) is the degeneration of vulnerable hippocampal CA1 and subicular pyramidal neurons. Semaphorin 3A (Sema3A) is a secreted protein that functions in signaling growth cone collapse, chemorepulsion and neuronal apoptosis during early development of the central nervous system. In this report we show that accumulation of an internalized form of Sema3A is associated with degeneration of neurons in vulnerable fields of the hippocampus during AD. Accumulation of Sema3A overlaps the appearance of phosphorylated MAP1B and tau in many neurons, suggesting that Sema3A signaling at some level may be coupled to these previously identified cytoskeletal markers of neurodegeneration. Consistent with this, we isolated and partially characterized a multiprotein complex from the hippocampus of patients with AD that contains phosphorylated MAP1B, collapsin-response mediator protein 2 (CRMP-2), Plexins A1 and A2, and a processed form of Sema3A. A model is presented in which aberrant release of Sema3A from expressing neurons in the subiculum during AD results in the internalization and transport of Sema3A from this field to CA1. Within the context of the myriad of potential insults that contribute to Alzheimer's and other neurodegenerative diseases, the bioactivity of Sema3A may contribute either directly to neurodegeneration by inducing neuronal collapse, or indirectly by abrogating the recovery capabilities of adult neurons faced with these insults.

Aged↗

PubMed2005

Secrets to a healthy Sox life: lessons for melanocytes.

Sox proteins are transcriptional regulators with a high-mobility-group domain as sequence-specific DNA-binding domain. For function, they generally require other transcription factors as partner proteins. Sox proteins furthermore affect DNA topology and may shape the conformation of enhancer-bound multiprotein complexes as architectural proteins. Recent studies suggest that Sox proteins are tightly regulated in their expression by many signalling pathways, and that their transcriptional activity is subject to post-translational modification and sequestration mechanisms. Sox proteins are thus ideally suited to perform their many different functions as transcriptional regulators throughout mammalian development. Their unique properties also cause Sox proteins to escape detection in many standard transcription assays. In melanocytes, studies have so far focused on the Sox10 protein which functions both during melanocyte specification and at later times in the melanocyte lineage. During specification, Sox10 activates the Mitf gene as the key regulator of melanocyte development. At later stages, it ensures cell-type specific expression of melanocyte genes such as Dopachrome tautomerase. Both activities require cooperation with transcriptional partner proteins such as Pax-3, CREB and eventually Mitf. If predictions can be made from other cell lineages, further functions of Sox proteins in melanocytes may still lie ahead.

Animals↗

PubMed2005

Biochemical and crystallographic studies reveal a specific interaction between TRAPP subunits Trs33p and Bet3p.

Transport protein particle (TRAPP) comprises a family of two highly related multiprotein complexes, with seven common subunits, that serve to target different classes of transport vesicles to their appropriate compartments. Defining the architecture of the complexes will advance our understanding of the functional differences between these highly related molecular machines. Genetic analyses in yeast suggested a specific interaction between the TRAPP subunits Bet3p and Trs33p. A mammalian bet3-trs33 complex was crystallized, and the structure was solved to 2.2 angstroms resolution. Intriguingly, the overall fold of the bet3 and trs33 monomers was similar, although the proteins had little overall sequence identity. In vitro experiments using yeast TRAPP subunits indicated that Bet3p binding to Trs33p facilitates the interaction between Bet3p and another TRAPP subunit, Bet5p. Mutational analysis suggests that yeast Trs33p facilitates other Bet3p protein-protein interactions. Furthermore, we show that Trs33p can increase the Golgi-localized pool of a mutated Bet3 protein normally found in the cytosol. We propose that one of the roles of Trs33p is to facilitate the incorporation of the Bet3p subunit into assembling TRAPP complexes.

Amino Acid Sequence↗

PubMed2006

Recognition and delivery of effector proteins into eukaryotic cells by bacterial secretion systems.

The direct transport of virulence proteins from bacterium to host has emerged as a common strategy employed by Gram-negative pathogens to establish infections. Specialized secretion systems function to facilitate this process. The delivery of 'effector' proteins by these secretion systems is currently confined to two functionally similar but mechanistically distinct pathways, termed type III and type IV secretion. The type III secretion pathway is ancestrally related to the multiprotein complexes that assemble flagella, whereas the type IV mechanism probably emerged from the protein complexes that support conjugal transfer of DNA. Although both pathways serve to transport proteins from the bacterium to host, the recognition of the effector protein substrates and the secretion information contained in these proteins appear highly distinct. Here, we review the mechanisms involved in the selection of substrates by each of these transport systems and secretion signal information required for substrate transport.

Amino Acid Sequence↗

PubMed2006

Cholinergic cells in the nucleus basalis of mice express the N-methyl-D-aspartate-receptor subunit NR2C and its replacement by the NR2B subunit enhances frontal and amygdaloid acetylcholine levels.

It is known that glutamatergic and cholinergic systems interact functionally at the level of the cholinergic basal forebrain. The N-methyl-d-aspartate receptor (NMDA-R) is a multiprotein complex composed of NR1, NR2 and/or NR3 subunits. The subunit composition of NMDA-R of cholinergic cells in the nucleus basalis has not yet been investigated. Here, by means of choline acetyl transferase and NR2B or NR2C double staining, we demonstrate that mice express both the NR2C and NR2B subunits in nucleus basalis cholinergic cells. We generated NR2C-2B mutant mice in which an insertion of NR2B cDNA into the gene locus of the NR2C gene replaced NR2C by NR2B expression throughout the brain. This NR2C-2B mutant was used to examine whether a subunit exchange in cholinergic neurons would affect acetylcholine (ACh) content in several brain structures. We found increased ACh levels in the frontal cortex and amygdala in the brains of NR2C-2B mutant mice. Brain ACh has been implicated in neuroplasticity, novelty-induced arousal and encoding of novel stimuli. We therefore assessed behavioral habituation to novel environments and objects as well as object recognition in NR2C-2B subunit exchange mice. The behavioral analysis did not indicate any gross behavioral alteration in the mutant mice compared with the wildtype mice. Our results show that the NR2C by NR2B subunit exchange in mice affects ACh content in two target areas of the nucleus basalis.

Acetylcholine↗

PubMed2006

NR2C by NR2B subunit exchange in juvenile mice affects emotionality and 5-HT in the frontal cortex.

The N-methyl-D-aspartate receptor (NMDA-R) has been inter alia implicated in synaptic plasticity, brain development and emotional processes. The NMDA-R is a multiprotein complex composed of NR1, NR2 and/or NR3 subunits. We generated NR2C-2B mutant mice in which an insertion of NR2B cDNA into the gene locus of the NR2C gene replaced NR2C by NR2B expression throughout the brain. This NR2C-2B mutant was used to examine whether an NMDA-R subunit exchange in juvenile mice would affect emotional behaviors and acetylcholine (ACh), dopamine (DA) and serotonin (5-HT) content in the frontal cortex (FC) and brain structures, which are part of the brain defense system, such as the periaqueductal grey matter (PAG). Juvenile, 1-month-old NR2C-2B mice showed increased open arm avoidance in the elevated plus-maze and increased fear-induced immobility. In terms of brain neurochemistry, NR2C-2B mice showed an increase in 5-HT levels in the FC at the age of 2 months. A correlational analysis revealed that mice with low open arms avoidance had high levels of ACh in the PAG but reduced 5-HT levels in the FC. Animals which showed high levels of fear-induced immobility also had high levels of 5-HT in the FC. These results suggest that the replacement of subunit NR2C by NR2B in juvenile mice increases anxiety- and fear-related behaviors possibly due to changes in FC-5-HT and PAG-ACh levels.

Acetylcholine↗

PubMed2003

Mitochondria as a target for neurotoxins and neuroprotective agents.

Mitochondrial permeability transition pores represent a multiprotein complex that includes components of both inner and outer membrane. The pores regulate transport of ions and peptides in and out of mitochondria, and their regulation is associated with a general mechanism for maintaining Ca(2+) homeostasis in the cell and apoptosis. Various pathologic factors may induce a pathologic activation of the permeability transition and an irreversible opening of mitochondria pores. This event is a major step in the development of neurotoxicity and neurodegeneration. This paper explores the effect of MPP(+) and beta-amyloid fragment 25-35, neurotoxins that are known to generate Parkinson's-like syndrome and Alzheimer's disease, on the regulation of the mitochondrial pores. Both neurotoxins induce opening of mitochondrial pores, which is prevented by cyclosporin A, a specific inhibitor of the permeability transition. The effect of MPP(+) and beta-amyloid may be also prevented by an endogenous precursor of melatonin, N-acetylserotonin, by an anti-Alzheimer's medication tacrine, and by dimebon, which is in development as an agent for the therapy of Alzheimer's disease and other types of dementia. The paper illustrates that the effect on mitochondrial pores is an important aspect of the mechanism of neurotoxicity. Substances that may prevent opening of mitochondrial pores induced by neurotoxins may preserve the mitochondrial function and, thus, may have potential as neuroprotective agents.

1-Methyl-4-phenylpyridinium↗