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Inactivation of myosin heavy chain genes in the mouse: diverse and unexpected phenotypes.

Myosin heavy chain (MyHC) is a critical component of the cellular contractile apparatus. The mammalian genome contains two nonmuscle, two smooth muscle, and eight striated muscle isoforms of MyHC. Within each class of genes, there is extremely high sequence homology among different MyHC isoforms, raising the question of whether these isoforms are functionally redundant or whether they perform unique roles in cell function. Recently, strains of mice null for four different MyHC isoforms have been generated. Mice null for the nonmuscle II-B isoform experience significant prenatal lethality and surviving animals have several cardiac abnormalities [Tullio et al. (1997) Proc Natl Acad Sci USA 94:12407-12412]. Mice homozygous null for alpha cardiac MyHC are embryonic lethal, while heterozygous mice are viable but also have numerous cardiac defects [Jones et al. (1996) J Clin Invest 98:1906-1917]. Mice null for IIb or IId adult skeletal MyHC are viable but have skeletal muscle abnormalities compared to wild type mice, despite compensation of a neighboring MyHC gene [Acakpo-Satchivi et al. (1997) J Cell Biol 139:1219-1229]. Both IIb and IId null mice show significant decreases in body mass. Mean muscle mass is also significantly decreased in both null strains but the extent and the pattern of affected muscles differs between the two strains. Both strains show evidence of skeletal muscle pathology but again the pattern and extent differ between the two strains. Finally, both adult skeletal strains demonstrate distinct impairments in contractile function when compared to wild type. Together these observations support the hypothesis that the different isoforms of MyHC are functionally unique and cannot substitute for one another.

Animals↗

Genetic Architecture of Idiopathic Inflammatory Myopathies From Meta-Analyses.

OBJECTIVE: Idiopathic inflammatory myopathies (IIMs, myositis) are rare systemic autoimmune disorders that lead to muscle inflammation, weakness, and extramuscular manifestations, with a strong genetic component influencing disease development and progression. Previous genome-wide association studies identified loci associated with IIMs. In this study, we imputed data from two prior genome-wide myositis studies and analyzed the largest myositis data set to date to identify novel risk loci and susceptibility genes associated with IIMs and its clinical subtypes. METHODS: We performed association analyses on 14,903 individuals (3,206 patients and 11,697 controls) with genotypes and imputed data from the Trans-Omics for Precision Medicine reference panel. Fine-mapping and expression quantitative trait locus colocalization analyses in myositis-relevant tissues indicated potential causal variants. Functional annotation and network analyses using the random walk with restart (RWR) algorithm explored underlying genetic networks and drug repurposing opportunities. RESULTS: Our analyses identified novel risk loci and susceptibility genes, such as FCRLA, NFKB1, IRF4, DCAKD, and ATXN2 in overall IIMs; NEMP2 in polymyositis; ACBC11 in dermatomyositis; and PSD3 in myositis with anti-histidyl-transfer RNA synthetase autoantibodies (anti-Jo-1). We also characterized effects of HLA region variants and the role of C4. Colocalization analyses suggested putative causal variants in DCAKD in skin and muscle, HCP5 in lung, and IRF4 in Epstein-Barr virus (EBV)-transformed lymphocytes, lung, and whole blood. RWR further prioritized additional candidate genes, including APP, CD74, CIITA, NR1H4, and TXNIP, for future investigation. CONCLUSION: Our study uncovers novel genetic regions contributing to IIMs, advancing our understanding of myositis pathogenesis and offering new insights for future research.

Humans↗

Proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium Rhodopirellula baltica.

The marine bacterium Rhodopirellula baltica is a model organism for aerobic carbohydrate degradation in marine systems, where polysaccharides represent the dominant components of biomass. On the basis of the genome sequence and a 2-D map of soluble proteins, the central catabolic routes of R. baltica were reconstructed. Almost all enzymes of glycolysis and TCA cycle were identified. In addition, almost all enzymes of the oxidative branch of the pentose phosphate cycle were detected. This proteomic reconstruction was corroborated by determination of selected enzymatic activities. To study substrate-dependent regulation in R. baltica, cells were adapted to growth with eight different carbohydrates and profiled with 2-DE for changes in protein patterns. Relative abundances of regulated proteins were determined using the 2-D DIGE technology and protein identification was achieved by PMF. Most of the up-regulated proteins were either dehydrogenases/oxidoreductases or proteins of unknown function which are unique for R. baltica. For only some of the regulated proteins, the coding genes are located in a physiologically meaningful genomic context. e.g., a ribose-induced alcohol dehydrogenase is encoded within an operon-like structure together with genes coding for a ribose-specific ABC-transporter. However, most of the regulated genes are randomly distributed across the genome.

Bacteria↗

Genetics of ethylene biosynthesis and restriction fragment length polymorphisms (RFLPs) of ACC oxidase and synthase genes in melon ( Cucumis melo L.).

We investigated the genetics of ethylene biosynthesis and its linkage to the RFLPs of the ACC oxidase and synthase genes in melon ( Cucumis melo L.). The results suggested that the A(0) and B(0) fragments of RFLP-MEL1 of the ACC oxidase gene were two alleles from a single locus, as were the B and C fragments of RFLP-MEACS1 of the ACC synthase gene. The B(0) allele seemed to be partially dominant over the A(0) allele, whereas B and C alleles appeared to map to quantitative trait loci (QTLs), which most likely contributed to ethylene production. Both RFLPs were linked to ethylene production rates, but they were not linked to each other. The interaction effects of the ACC oxidase and synthase genes on ethylene production were revealed by segregation of RFLP-MEL1 and RFLP-MEACS1. The results of single-copy-reconstruction assays suggested that the ACC oxidase gene is a single copy, whereas the ACC synthase gene is a component of a multigene family in the melon genome. The abscission phenotype appeared to be controlled by an independent locus, with the abscission (full-slip) allele dominant over the non-abscission (not full-slip) allele. These results may facilitate efforts toward mapping the quantitative trait loci (QTLs) of ethylene production. The RFLPs may be used in marker-assisted selection in developing melons with a more-desirable low ethylene production rate for enhancing postharvest storage life.

Journal Article↗

On the origin and functions of RNA-mediated silencing: from protists to man.

Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways. We have examined the taxonomic distribution and the phylogenetic relationship of key components of the RNA interference (RNAi) machinery in members of five eukaryotic supergroups. On the basis of the parsimony principle, our analyses suggest that a relatively complex RNAi machinery was already present in the last common ancestor of eukaryotes and consisted, at a minimum, of one Argonaute-like polypeptide, one Piwi-like protein, one Dicer, and one RNA-dependent RNA polymerase. As proposed before, the ancestral (but non-essential) role of these components may have been in defense responses against genomic parasites such as transposable elements and viruses. From a mechanistic perspective, the RNAi machinery in the eukaryotic ancestor may have been capable of both small-RNA-guided transcript degradation as well as transcriptional repression, most likely through histone modifications. Both roles appear to be widespread among living eukaryotes and this diversification of function could account for the evolutionary conservation of duplicated Argonaute-Piwi proteins. In contrast, additional RNAi-mediated pathways such as RNA-directed DNA methylation, programmed genome rearrangements, meiotic silencing by unpaired DNA, and miRNA-mediated gene regulation may have evolved independently in specific lineages.

Animals↗

Proposal for genetic characterisation of wild-type mumps strains: preliminary standardisation of the nomenclature.

Though mumps virus (MuV) is a monotypic virus, genetic variation between strains has been described. Viruses have been placed into genotypes designated A-L based on the nucleotide sequence of the small hydrophobic (SH) gene, which is the most variable gene in the mumps genome. Molecular characterisation of MuV is an important component of mumps surveillance because it can help identify the transmission pathways of the virus as well as distinguish between wild-type and vaccine strains. Here, we propose a standardized nomenclature and an analysis protocol for the genetic characterisation of mumps strains to facilitate expansion of molecular epidemiological studies. In addition to assigning standard reference strains for the recognized genotypes of MuV, a convention is proposed for naming for strains and criteria to designate a new genotype.

Humans↗

Primary structure of a Plasmodium falciparum rhoptry antigen.

The high-molecular-weight rhoptry complex of Plasmodium falciparum consists of 3 non-covalently associated polypeptides of 150, 135 and 105 kDa. We present the complete nucleotide sequence of the 105-kDa (RhopH3) component of this complex derived from analysis of genomic and cDNA clones. The genomic structure is unusually complex for P. falciparum, consisting of 7 exons including 2 mini-exons of 19 and 21 amino acids. The sequence lacks tandem repeats and is conserved among several parasite isolates. B cell epitopes that induce antibody responses during natural infection were mapped to five different regions of the polypeptide.

Amino Acid Sequence↗

Mitochondrial glutathione depletion in alcoholic liver disease.

Alcoholic liver disease (ALD) is one the most serious consequences of chronic alcohol abuse. Liver cirrhosis, the culmination of the illness, is one of the leading causes of death in Western countries. Mitochondria are a target of ethanol intoxication mainly due to the toxic effects of acetaldehyde, a byproduct of ethanol metabolism. Morphological and functional changes in mitochondria are one of the key hallmarks of chronic ethanol exposure in both chronic alcoholics and experimental models of alcoholism. The functional changes observed in mitochondria from ethanol-treated animals are translated in an overall decrease in ATP levels resulting from a lower rate of ATP synthesis as a consequence of impaired processing at the translational level of some components of oxidative phosphorylation encoded by mitochondrial DNA genome. Mitochondrial glutathione (GSH) plays a critical role in the maintenance of cell functions and viability and in mitochondrial physiology by metabolism of oxygen free radicals generated in the respiratory chain. GSH in mitochondria originates from cytosol by a transport system which translocates GSH into the matrix. This transport system is impaired in chronic ethanol-fed rats, which translates in a selective and significant depletion of the mitochondrial GSH content resulting in the development of an increased susceptibility to oxidant stress. Using the intragastric infusion model of experimental ALD in rats, the profound and selective mitochondrial GSH depletion precedes the onset of alcoholic liver disease, mitochondrial lipid peroxidation, and progression of liver damage.(ABSTRACT TRUNCATED AT 250 WORDS)

Alcoholic Intoxication↗

Initiation of endospore formation in Clostridium acetobutylicum.

Endospore formation in bacilli and clostridia shows remarkable similarities in morphology as well as in physiological and molecular biological cellular events. Major differences are the formation of clostridial stage cells and granulose accumulation in clostridia. In both genera, a cascade of sigma factors is activated after septation (by help of sigma(H) and Spo0A approximately P) in the sequence sigma(F), sigma(E), sigma(G), and sigma(K). Of these, sigma(F) and sigma(G) are active inside the forespore and are regulated by anti-sigma factors and anti-anti-sigma factors, whereas sigma(E) and sigma(K) (mother cell-specific sigma factors) are synthesized as precursor proteins and activated by proteolysis. Each of these sigma factors allows transcription of a specific set of genes and operons, thus leading to the orchestral expression of stage-specific proteins required for successful sporulation. Both, the genetic organization of the respective operons and the expression pattern of the sigma factors are very similar in Bacillus subtilis and Clostridium acetobutylicum, the model organisms of the two genera. However, a major regulatory difference is found in initiation of endospore formation. Genome sequencing revealed that clostridia do not contain components of the so-called phosphorelay, with the exception of the essential transcription factor Spo0A. This might reflect recognition of different environmental signals, as for clostridia nutrient limitation is no prerequisite for sporulation. In contrast to Bacillus, the clostridial sigH gene is constitutively expressed at a low level, with no increase at the onset of spore formation. The spo0A gene in C. acetobutylicum is also constitutively expressed, but Spo0A synthesis only occurs during the early and mid-exponential growth phase, indicating a posttranscriptional or cotranslational regulation. Mutational studies revealed an important regulatory function of a dual palindrome region upstream of the spo0A gene of C. acetobutylicum, part of which overlaps with a Spo0A-binding site. In addition to controlling sporulation genes, phosphorylated clostridial Spo0A is involved in regulation of acetone and butanol synthesis.

Journal Article↗

Identification of methylated sequences in genomic DNA of adult Drosophila melanogaster.

The genome of Drosophila melanogaster contains methylated cytosines. Recent studies indicate that DNA methylation in the fruit fly depends on one DNA methyltransferase, dDNMT2. No obvious phenotype is associated with the downregulation of this DNA methyltransferase. Thus, identifying the target sequences methylated by dDNMT2 may constitute the first step towards understanding the biological functions of this enzyme. We used anti-5-methylcytosine antibodies as affinity column to identify the methylated sequences in the genome of adult flies. Our analysis demonstrates that components of retrotransposons and repetitive DNA sequences are putative substrates for dDNMT2. The methylation status of DNA encoding Gag, a protein involved in delivering the transposition template to its DNA target, was confirmed by sodium bisulfite sequencing.

Animals↗

Modeling operon dynamics: the tryptophan and lactose operons as paradigms.

Understanding the regulation of gene control networks and their ensuing dynamics will be a critical component in the understanding of the mountain of genomic data being currently collected. This paper reviews recent mathematical modeling work on the tryptophan and lactose operons which are, respectively, the classical paradigms for repressible and inducible operons.

Escherichia coli↗

The many faces of the helix-turn-helix domain: transcription regulation and beyond.

The helix-turn-helix (HTH) domain is a common denominator in basal and specific transcription factors from the three super-kingdoms of life. At its core, the domain comprises of an open tri-helical bundle, which typically binds DNA with the 3rd helix. Drawing on the wealth of data that has accumulated over two decades since the discovery of the domain, we present an overview of the natural history of the HTH domain from the viewpoint of structural analysis and comparative genomics. In structural terms, the HTH domains have developed several elaborations on the basic 3-helical core, such as the tetra-helical bundle, the winged-helix and the ribbon-helix-helix type configurations. In functional terms, the HTH domains are present in the most prevalent transcription factors of all prokaryotic genomes and some eukaryotic genomes. They have been recruited to a wide range of functions beyond transcription regulation, which include DNA repair and replication, RNA metabolism and protein-protein interactions in diverse signaling contexts. Beyond their basic role in mediating macromolecular interactions, the HTH domains have also been incorporated into the catalytic domains of diverse enzymes. We discuss the general domain architectural themes that have arisen amongst the HTH domains as a result of their recruitment to these diverse functions. We present a natural classification, higher-order relationships and phyletic pattern analysis of all the major families of HTH domains. This reconstruction suggests that there were at least 6-11 different HTH domains in the last universal common ancestor of all life forms, which covered much of the structural diversity and part of the functional versatility of the extant representatives of this domain. In prokaryotes the total number of HTH domains per genome shows a strong power-equation type scaling with the gene number per genome. However, the HTH domains in two-component signaling pathways show a linear scaling with gene number, in contrast to the non-linear scaling of HTH domains in single-component systems and sigma factors. These observations point to distinct evolutionary forces in the emergence of different signaling systems with HTH transcription factors. The archaea and bacteria share a number of ancient families of specific HTH transcription factors. However, they do not share any orthologous HTH proteins in the basal transcription apparatus. This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus.

Amino Acid Sequence↗

During the early phase of HIV-1 DNA synthesis, nucleocapsid protein directs hybridization of the TAR complementary sequences via the ends of their double-stranded stem.

Reverse transcription of HIV-1 genomic RNA requires two obligatory strand transfers. During the first strand transfer reaction, the minus strand strong-stop DNA (ss-cDNA) is transferred by hybridization of complementary sequences located at the 3' ends of the ss-cDNA and genomic template, respectively. In HIV-1, the major components of ss-cDNA transfer are the terminally redundant structured TAR elements and the nucleocapsid protein NCp7, which actively chaperones the hybridization of cTAR DNA to TAR. In the present study, we investigated the annealing kinetics of TAR with fluorescently labelled cTAR derivatives both in the absence and in the presence of NC(12-55), a peptide that contains the finger and C-terminal domains of NCp7. The annealing of TAR with cTAR involves two second-order kinetic components that are activated by at least two orders of magnitude by NC(12-55). The NC-promoted activation of cTAR-TAR annealing was correlated with its ability to destabilize the lower half of TAR stem, in order to generate the single-stranded complementary regions for nucleating the duplex structures. The two kinetics components have been assigned to two different pathways. The rapid one does not lead to extended duplex formation but is associated with a limited annealing of the terminal bases of cTAR to TAR. On the other hand, extended duplex formation follows a slower pathway that is limited kinetically by the nucleation of residues located mainly within the central double-stranded segment of both cTAR and TAR stems. An alternative mechanism involving an interaction through TAR and cTAR loops has been observed but is a minor pathway in the present conditions.

Amino Acid Sequence↗

Sense and sensibility: nutritional response and signal integration in yeast.

Yeast cells respond to the quantity and quality of carbon and nitrogen sources in the environment both by adjusting their transcriptional and metabolic profiles to make optimum use of the available nutrients and by selecting a developmental program--budding, pseudohyphal differentiation, quiescence or sporulation--that maximizes their potential for survival under the existing nutrient conditions. Recent studies fueled by genomic tools have refined our knowledge of the components and connections within individual pathways and the interconnections between pathways. More significantly, these studies begin to paint an as yet inchoate portrait of the yeast cells' means of processing its environmental information, in which specific transcription factors and chromatin modifying activities coordinate input from several signaling pathways to yield an appropriate and coherent response of genes involved in mass accumulation and metabolism.

Carbon↗

In search of drug treatment for genetic defects in the DNA damage response: the example of ataxia-telangiectasia.

Most genetic disorders are severe diseases that cannot be treated. In the majority of them, enzyme and gene therapy can be significantly curtailed by technical difficulties and the nature of the physiological defects and affected tissues. A rational search for drug treatment for such diseases must be based on understanding the corresponding molecular defects. For example, in a disease stemming from a defective signaling pathway, a drug that can activate redundant pathways could be useful. Screening for such a drug would then depend on the availability of a laboratory assay that faithfully reflects the molecular defect in the corresponding disease, and a technology for applying the assay in a high throughput setup. Deficiencies in various components of the DNA damage response lead to genomic instability syndromes characterized by tissue degeneration, sensitivity to DNA damaging agents, and cancer predisposition. A typical example is ataxia-telangiectasia (A-T), caused by deficiency of the nuclear protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. ATM phosphorylates a multitude of substrates, each of which in turn modulates a branch of the damage response network. A certain redundancy among ATM and related proteins gives hope that activation of ATM-redundant activities might form a basis for drug treatment of A-T. This article describes a high throughput strategy for drug screening for A-T that is based on the above principles. A similar strategy can potentially be applied to drug screening for other genetic disorders.

Animals↗

Bacteriophage MS2: molecular weight and spatial distribution of the protein and RNA components by small-angle neutron scattering and virus counting.

Small-angle neutron scattering (SANS) has been used to extend the structural characterization of the MS2 phage by examining its physical characteristics in solution. Specifically, the contrast variation technique was employed to determine the molecular weight of the individual components of the MS2 virion (protein shell and genomic RNA) and the spatial relationship of the genomic RNA to its protein shell. A consequence of this work was to evaluate a novel particle counting instrument, the integrated virus detection system (IVDS) that, in combination with SANS, has the potential to provide rapid quantitative physical characterization of unidentified viruses and phage.

Electrophoresis, Polyacrylamide Gel↗

Emerging MAP kinase pathways in plant stress signalling.

Mitogen-activated protein kinase (MAPK) pathways transfer information from sensors to cellular responses in all eukaryotes. A surprisingly large number of genes encoding MAPK pathway components have been uncovered by analysing model plant genomes, suggesting that MAPK cascades are abundant players of signal transduction. Recent investigations have confirmed major roles of defined MAPK pathways in development, cell proliferation and hormone physiology, as well as in biotic and abiotic stress signalling. Latest insights and findings are discussed in the context of novel MAPK pathways in plant stress signalling.

Extracellular Signal-Regulated MAP Kinases↗

Activation of refractory T cell responses against hepatitis C virus core protein by ablation of interfering hydrophobic domains.

Hepatitis C virus (HCV) is the major pathogen of chronic hepatitis and liver disease, but currently there are no prophylactic HCV vaccines available. The HCV core protein-encoding sequence is among the most conserved genes in the HCV genome, making it a prime candidate for a component of a vaccine. The core protein localizes to the endoplasmic reticulum (ER) through a C-terminal hydrophobic region that is cotranslationally inserted into the ER membrane. Here we show that removal of the C-terminal hydrophobic region confers nuclear localization and enhances proteasomal degradation of the core protein in mammalian cells. This efficient protein proteolysis induces enhanced core-specific CD8(+) T cell responses in BALB/c mice immunized with plasmids expressing C-terminal deletions of the HCV core protein. These results suggest that more potent HCV vaccines can be achieved by targeting the core protein for proteasomal degradation by deletion of its C-terminal hydrophobic domain.

Animals↗