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At least 37 records · Page 2Linked to original sources
PubMed2023

Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses.

Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.

Humans↗
PubMed2026

Bacillus thuringiensis pathogenicity islands encode regulatory circuits controlling insecticidal Cry toxin expression during vegetative growth.

Bacillus thuringiensis (Bt) produces insecticidal toxins, including Cry and Vip3 proteins, that are widely used for biological pest control. Cry proteins are classically expressed during sporulation under the control of sporulation-specific σ factors, whereas Vip3 is produced during vegetative growth, suggesting distinct regulatory pathways. Notably, many cry and vip3A genes are clustered within pathogenicity islands (PAIs), such as BtPAI-1. However, whether these PAIs also encode regulatory mechanisms coordinating toxin expression remains unclear. Here, we identify VipR, a BtPAI-1-encoded transcriptional regulator, as an activator of insecticidal gene expression during the vegetative phase in Bt strains HD-1 and CT-43. In these strains, VipR promotes the transcription of BtPAI-1 associated insecticidal genes, including vip3A and selected cry genes, resulting in premature Cry protein accumulation and increased insecticidal activity. In addition, VipR contributes to the vegetative-phase expression of the non-BtPAI-1 cry9Aa genes in strain BGSC 4AE1. Phylogenetic analysis revealed that vipR is widely distributed in one-third of Bt strains, and is strongly associated with PAIs. Futhermore, heterologous expression of vipR in BGSC 4J5 and HD-73 was sufficient to activate vegetative-phase transcription of some cry independently of sporulation-specific σ factor cascade. These results support a role for VipR in coordinating vegetative-phase expression of insecticidal genes in the Bt strains examined and suggest that BtPAI-1 can encode both insecticidal determinants and regulatory functions that influence their expression. These findings provide new insights into the regulatory architecture of Bt pathogenicity islands and may facilitate the engineering of strains with enhanced insecticidal activity.

Bacillus thuringiensis↗
PubMed2026

Phage-encoded sRNA counteracts xenogeneic silencing in pathogenic E. coli.

Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogeneic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet their expression must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA that is enriched in the locus of enterocyte effacement (LEE⁺) E. coli strains and present in up to nine copies in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes. HnrS base-pairs with the hha ribosome-binding site to inhibit translation, thereby modulating Hha-H-NS repression of virulence loci including the LEE type III secretion system. Loss of HnrS alters motility, T3SS expression, and a subset of Hha-regulated genes. These findings reveal an RNA-based counter-silencing strategy encoded by prophage to relieve xenogenic silencing.

Escherichia coli Proteins↗
PubMed2023

Non-coding regions of nuclear-DNA-encoded mitochondrial genes and intergenic sequences are targeted by autoantibodies in breast cancer.

Autoantibodies against mitochondrial-derived antigens play a key role in chronic tissue inflammation in autoimmune disorders and cancers. Here, we identify autoreactive nuclear genomic DNA (nDNA)-encoded mitochondrial gene products (GAPDH, PKM2, GSTP1, SPATA5, MFF, TSPOAP1, PHB2, COA4, and HAGH) recognized by breast cancer (BC) patients' sera as nonself, supporting a direct relationship of mitochondrial autoimmunity to breast carcinogenesis. Autoreactivity of multiple nDNA-encoded mitochondrial gene products was mapped to protein-coding regions, 3' untranslated regions (UTRs), as well as introns. In addition, autoantibodies in BC sera targeted intergenic sequences that may be parts of long non-coding RNA (lncRNA) genes, including LINC02381 and other putative lncRNA neighbors of the protein-coding genes ERCC4, CXCL13, SOX3, PCDH1, EDDM3B, and GRB2. Increasing evidence indicates that lncRNAs play a key role in carcinogenesis. Consistent with this, our findings suggest that lncRNAs, as well as mRNAs of nDNA-encoded mitochondrial genes, mechanistically contribute to BC progression. This work supports a new paradigm of breast carcinogenesis based on a globally dysfunctional genome with altered function of multiple mitochondrial and non-mitochondrial oncogenic pathways caused by the effects of autoreactivity-induced dysregulation of multiple genes and their products. This autoimmunity-based model of carcinogenesis will open novel avenues for BC treatment.

autoimmunity↗
PubMed1979

Spoken words and manual signs as encoding categories in short-term memory for mentally retarded children.

The release from proactive inhibition paradigm was used to test differential encoding of manual signs and spoken words by six severely retarded children. Scores for shift conditions were significantly different from scores for nonshift conditions on the last trial, indicating that manual signs were encoded differently from spoken words for short-term memory storage. Implications of separate encoding categories for the investigation of language processes were discussed.

Adolescent↗
PubMed1978

[Frequency domain analysis of the dynamic properties of the encoder in the slowly adapting crayfish stretch receptor neuron].

The transfer properties of the slowly adapting stretch receptor neuron can be suitably described in the frequency domain. The measurements are carried out by means of sinusoidally varying intracellular currents. The frequency response at low stimulation frequencies has been calculated from responses to current steps. At very low input frequencies the amplitude-frequency characteristic in the Bode diagram is nearly parallel to the abscissa. With increasing stimulation frequency the gain becomes larger and has a maximum at 1--3 Hz (stimulation frequency/carrier frequency (f/fo approximately 0.2). The amplitude-frequency characteristic decreases then, at first slowly then more rapidly, and reaches in the range of carrier frequency (f/fo approximately 1) small values. The phase-frequency characteristic shows at low input frequencies a small positive magnitude of 8--10(0). With higher stimulation frequencies the phase angle decreases and reaches negative values. In the range of carrier frequency the phase shift runs to -180 degrees. The present findings demonstrate also that the transfer function of the encoder depends on the carrier frequency of the receptor neuron. Larger carrier frequencies cause a decrease of the gain but the peak remains. This maximum shifts with increasing fo in direction to higher stimulation frequencies. The elimination of the encoder adaptation by means of a suitable model results in the frequency response of the real encoder. The above statements hold for higher stimulation frequencies too, but the typical differential behaviour at low frequencies disappears.

Animals↗
PubMed1977

Categorical encoding in short-term memory by retarded and nonretarded children.

The use of consonants and digits as encoding categories in short-term memory by 32 EMR children and 32 nonretarded children of the same CA was investigated. The task employed was a modification of the release from proactive inhibition technique similar to that used by Wickens, Born, and Allen (1963). Results indicated that digits and consonants are significant categories used for encoding in short-term memory by 10- to 12-year-old EMR and nonretarded children but that nonretarded children more effectively utilize consonant material as an encoding dimension than do CA-matched EMR children.

Child↗
PubMed2026

Male and Female Mice Show Similar Fear Memory Performance Despite Hippocampal Immediate Early Gene Expression Differences During Encoding and Consolidation.

Accurate and efficient memory processing is essential for survival. A body of ongoing work in both human subjects and animal models suggests that memory processing may differ substantially between males and females. In mice, contextual fear memory (CFM) encoding, consolidation, and recall have been well studied, and the mouse hippocampus and amygdala have been implicated in these processes. The present pilot study addresses whether the activation of these brain regions differs substantially between male and female mice at each stage of CFM processing. We find that male and female mice show no differences in sleep behavior, which is essential for CFM consolidation, following single-trial contextual fear conditioning (CFC). We also find no significant differences in CFM recall performance between male and female mice. However, females show a trend for larger increases in CA1 cFos expression, relative to males, during CFM encoding. On the other hand, only males-but not females-show an apparent increase in cFos expression among dentate gyrus (DG) granule cells during CFM consolidation. Males also show a trend for a larger apparent reduction in cFos in CA1 and CA3 during CFM consolidation, relative to females. These preliminary findings highlight the idea that the neurobiological underpinnings of memory processing may differ between males and females, even when performance during recall is identical.

Animals↗
PubMed1979

Constitutive expression in Escherichia coli of the Neurospora crassa structural gene encoding the inducible enzyme catabolic dehydroquinase.

In Neurospora crassa the qa-2 gene, which encodes catabolic dehydroquinase, is under positive control exerted by the inducer quinic acid and an activator protein encoded in the closely linked qa-1 gene. In order to determine if this regulatory mechanism is maintained when the qa-2 gene is cloned on a recombinant plasmid and expressed in Escherichia coli, molecular cloning experiments have been performed using DNA isolated from a qa-1+ (inducible), a qa-1C (constitutive) and two qa-1 (non-inducible) strains of N. crassa. The results demonstrate that the level of expression of the qa-2 gene in E. coli is completely independent of the mutational state of the qa-1 gene. Moreover, the level of expression of the cloned qa-2 gene was unaffected by either an intracellularly produced inducer of catabolic dehydroquinase or by the general procaryotic positive effector, the CAP factor. The weight of evidence thus supports the conclusion that transcription of the N. crassa qa-2 gene in E. coli does not require the qa-1 activator protein and thus is not controlled by the same mecahnism which functions in N. crassa.

Centrifugation, Density Gradient↗
PubMed1978

Genetics and ontogeny of aldehyde dehydrogenase isozymes in the mouse: localization of Ahd-1 encoding the mitochondrial isozyme on chromosome 4.

Electrophoretic variants for the mitochondrial isozyme of aldehyde dehydrogenase (AHD) have been observed in inbred strains and in Harwell linkage testing stocks of Mus musculus. F1 (LVC X C57BL/Go) mice showed a codominant allele three-bounded phenotype, which suggests a dimeric subunit structure (designated AHD-A2). The anodal-migrating supernatant isozyme of AHD was electrophoretically invariant among the 23 inbred strains and stocks examined. The genetic locus encoding AHD-A2 (suggested name Ahd-1) is localized on chromosome 4 and was mapped close to je (jerker) and Gpd-1 (encoding the liver and kidney isoenzyme of glucose-6-phosphate dehydrogenase). Ontogenetic analyses demonstrated that both AHD isozymes exhibited low activity in late fetal and early neonatal liver and kidney extracts, and reached adult levels within 3 weeks of birth.

Aldehyde Oxidoreductases↗
PubMed1979

An optical scan system for encoding and tabulation of visually scored sleep data.

A system for computer-assisted encoding, tabulation and analysis of visually scored sleep data is presented. The main features of the system are: (1) The use of computer-readable optical scan sheets for direct encoding of the sleep data. This eliminates the need for a separate transcription and/or key-punching operation. (2) The development of a visually scored data base, organized by NREM and REM periods, which contains all items of visually scored data indexed by time and/or page of occurrence in the sleep record. The advantages of this new system are: (a) the low cost per night of operation; (b) the facilitation of analysis of cycle phenomena and testing of new hypotheses that would usually involve retabulation of the data; and (c) the facilitation of analysis of real-time correlates of visually scored sleep stages.

Computers↗
PubMed2025

Identification of IDH3G, encoding the gamma subunit of mitochondrial isocitrate dehydrogenase, as a novel candidate gene for X-linked retinitis pigmentosa.

PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous group of retinal degenerative disorders characterized by the loss of rod and cone photoreceptors, leading to visual impairment and blindness. To date, to our knowledge, X-linked RP has been associated with variants in 3 genes (RPGR, RP2, and OFD1), whereas genetic defects at 3 loci (RP6, RP24, and RP34) are yet unidentified. The aim of this study was to identify a novel candidate gene underlying X-linked RP. METHODS: Participants were identified from cohorts of genetically unsolved male individuals affected by RP, who underwent genome sequencing, exome sequencing, or candidate gene screening via direct Sanger sequencing at 3 referral centers. Specifically, 2 probands were identified at the National Reference Centre for Rare Retinal Diseases (Paris, France), 2 at the Massachusetts Eye and Ear Hospital (Boston, MA), and 1 at the National Reference Centre for Inherited Sensory Diseases (Montpellier, France). The pathogenicity of the identified variants was assessed using bioinformatic predictions, protein expression analyses, and mitochondrial function assays. RESULTS: We identified 4 rare single-nucleotide variants in IDH3G (HGNC:5386), located at the RP34 locus on the X chromosome, and a complete gene deletion, in 5 unrelated male individuals affected with nonsyndromic RP. The variants segregated with the phenotype in all available family members. In all cases, the disease severity was intermediate. None had high myopia. IDH3G encodes the γ subunit of mitochondrial isocitrate dehydrogenase (IDH3), an enzyme involved in the citric acid cycle, which is expressed in the inner segments of photoreceptors. Variants in IDH3A and IDH3B, encoding the other subunits of IDH3, have already been associated with nonsyndromic autosomal recessive RP. Bioinformatic predictions and functional assays support a pathogenic role for the variants identified in this study, possibly through partial loss of enzymatic activity and mitochondrial function. CONCLUSION: Our findings suggest that variants in IDH3G are a novel cause of X-linked RP.

Humans↗
PubMed2026

Surface shaving proteomics reveals a parasite-encoded protein embedded in the spore filaments of Ameson portunus.

The surfaces of microsporidian spores are frequently adorned with filamentous appendages of unknown origin and function. Although some studies suggest that these structures may be host-acquired, the absence of identified parasite-encoded components has hindered our understanding of their biogenesis and role in infection. Here, we applied surface shaving proteomics to profile the surface-exposed proteins of Ameson portunus -a microsporidian pathogen causing severe myopathy in portunid crabs. Our analysis identified 120 candidate surface proteins. Nineteen of these were highly enriched by both direct shaving and SDS-assisted methods, representing a high-confidence surfome. Among these, a previously uncharacterized protein, designated 8-2.11, was confirmed via immunofluorescence assay and immunoelectron microscopy. It was expressed early in development stage and specifically localized to the spore wall and hair-like projections (HLPs) of microsporidia. Notably, polyclonal antibodies against recombinant 8-2.11 recognized a native protein in spores, specifically labeled the HLP structures, and showed no cross-reactivity with host cells. Our results provide the first evidence of a parasite-encoded protein that is integral to HLP formation, challenging the prevailing hypothesis that these surface filaments are solely host-derived. This study establishes surface shaving as a powerful tool for microsporidian research and highlights 8-2.11 as a promising candidate for future functional studies on spore surface biology and host-parasite interactions.

Animals↗
PubMed1979

Framing pictures: the role of knowledge in automatized encoding and memory for gist.

In general, frame theories are theories about the representation and use of knowledge for pattern recognition. In the present article, the general properties of frame theories are discussed with regard to their implications for psychological processes, and an experiment is presented which tests whether this approach yields viable predictions about the manner in which people comprehend and remember pictures of real-world scenes. Normative ratings were used to construct six target pictures, each of which contained both expected and unexpected objects. Eye movements were then recorded as subjects who anticipated a difficult recognition test viewed the targets for 30 sec each. Then, the subjects were asked to discriminate the target pictures from distractors in which either expected or unexpected objects had been changed. One consequence of the embeddedness of frame systems is that global frames may function as "semantic pattern detectors," so that the perceptual knowledge in them could be used for relatively automatic pattern recognition and comprehension. Thus, subjects might be able to identify expected objects by using automatized encoding procedures that operate on global physical features. In contrast, identification of unexpected objects (i.e., objects not represented in the currently active frame) should generally require more analysis of local visual details. These hypotheses were confirmed with the fixation duration data: First fixations to the unexpected objects were approximately twice as long as first fixations to the expected objects. On the recognition test, subjects generally noticed only the changes that had been made to the unexpected objects, despite the fact that the proportions of correct rejections were made conditional on whether the target objects had been fixated. These data are again consistent with the idea that local visual details of objects represented in the frame are not neccesary for identification and are thus not generally encoded. Further, since subjects usually did not notice when expected objects were deleted or replaced with different expected objects, it was concluded that if two events instantiate the same frame, they may often be indistinguishable, as long as any differences between them are represented as arguments in the frame. Thus, for the most part, the only information about an event that is episodically "tagged" is information which distinguishes that particular event from others of the same general class. The data reinforce the utility of a frame theory approach to perception and memory.

Discrimination Learning↗
PubMed1979

The E. coli gene encoding heat stable toxin is a bacterial transposon flanked by inverted repeats of IS1.

Restriction endonuclease subclones of the Escherichia coli gene encoding the heat stable (ST) toxin exhibit a stem and loop structure similar to those seen in many procaryotic transposons. An EcoRI DNA fragment encoding tetracycline (Tc) resistance but no transposition functions was spliced into the ST gene in one of these subclones. By monitoring Tcr, we were able to show that the ST gene transposes. Restriction and DNA sequence data strongly suggest that the ST transposon, Tn 1681, is flanked by inverted repeats of IS1.

Bacterial Toxins↗
PubMedDate not supplied

Identification of the protein encoded by the transposable element Tn3 which is required for its transposition.

Protein products have now been identified which account for the entire coding capacity of the transposable element Tn3. Mutations in Tn3 have allowed us to map the genes encoding each of these peptides and to identify their role in transposition. We have found that only a single Tn3-encoded peptide is required for transposition. Expression of this peptide is repressed by the product of a second gene, which is itself autogenously regulated.

Bacterial Proteins↗
PubMed2024

N6-methyladenosine modification of a parvovirus-encoded small noncoding RNA facilitates viral DNA replication through recruiting Y-family DNA polymerases.

Human bocavirus 1 (HBoV1) is a human parvovirus that causes lower respiratory tract infections in young children. It contains a single-stranded (ss) DNA genome of ~5.5 kb that encodes a small noncoding RNA of 140 nucleotides known as bocavirus-encoded small RNA (BocaSR), in addition to viral proteins. Here, we determined the secondary structure of BocaSR in vivo by using DMS-MaPseq. Our findings reveal that BocaSR undergoes N6-methyladenosine (m6A) modification at multiple sites, which is critical for viral DNA replication in both dividing HEK293 cells and nondividing cells of the human airway epithelium. Mechanistically, we found that m6A-modified BocaSR serves as a mediator for recruiting Y-family DNA repair DNA polymerase (Pol) η and Pol κ likely through a direct interaction between BocaSR and the viral DNA replication origin at the right terminus of the viral genome. Thus, this report represents direct involvement of a viral small noncoding RNA in viral DNA replication through m6A modification.

Humans↗
PubMed1977

Structure of a large segment of the genome of simian virus 40 that does not encode known proteins.

The nucleotide sequence of the region of DNA of simian virus 40 extending from 0.595 to 0.790 map unit has been derived. The sequence includes the DNA complementary to the 5' end of early mRNA and to the 5' end of some of the forms of late RNA. Because there are termination codons in all three phases in early and late RNA, there is a sequence of almost 800 nucleotides of simian virus 40 DNA that probably does not code for known viral proteins. The sequence spans the 5' end of the early mRNA at 0.67 map unit and overlaps a species of late RNA whose 5' end is at 0.65 map unit and whose 3' end is at 0.77 map unit. This RNA is retained on oligo(dT)-cellulose columns in high salt concentrations. Analysis of the sequence of late strand RNA suggests that this RNA is not covalently linked to the mRNA that encodes structural proteins. There is another species of late RNA of simian virus 40 whose 5' end is at 0.775 map unit. The nucleotide sequence of this region of simian virus 40 DNA contains several examples of repeated sequences, most of which are located in DNA that does not encode known peptides. These may be analogous to the reiterated sequences that have been described in animal cell DNA.

Base Sequence↗