Elena I. Shagimardanova

Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge

Anhydrobiosis represents an extreme example of tolerance adaptation to water loss, where an organism can survive in an ametabolic state until water returns. Here we report the first comparative analysis examining the genomic background of extreme desiccation tolerance, which is exclusively found in larvae of the only anhydrobiotic insect, Polypedilum vanderplanki. We compare the genomes of P. vanderplanki and a congeneric desiccation-sensitive midge P. nubifer. We determine that the genome of the anhydrobiotic species specifically contains clusters of multi-copy genes with products that act as molecular shields. In addition, the genome possesses several groups of genes with high similarity to known protective proteins. However, these genes are located in distinct paralogous clusters in the genome apart from the classical orthologues of the corresponding genes shared by both chironomids and other insects. The transcripts of these clustered paralogues contribute to a large majority of the mRNA pool in the desiccating larvae and most likely define successful anhydrobiosis. Comparison of expression patterns of orthologues between two chironomid species provides evidence for the existence of desiccation-specific gene expression systems in P. vanderplanki.

Draft Genome Sequence of Bacillus pumilus 7P, Isolated from the Soil of the Tatarstan Republic, Russia

ABSTRACT Here, we present a draft genome sequence of Bacillus pumilus strain 7P. This strain was isolated from soil as an extracellular RNase-producing microorganism. The RNase of B. pumilus 7P is considered to be a potential antiviral and therapeutic antitumor agent, and it might be appropriate for agriculture and academic synthesis of oligoribonucleotides.

Bacterial enzymes effectively digest Alzheimer's β-amyloid peptide

Aggregated β-amyloid peptides play key roles in the development of Alzheimers disease, and recent evidence suggests that microbial particles, among others, can facilitate their polymerization. Bacterial enzymes, however, have been proved to be beneficial in degrading pathological fibrillar structures in clinical settings, such as strepto-kinases in resolving blood-clots. The purpose of this study was to investigate the ability of bacterial substances to effectively hydrolyze β-amyloid peptides. Degrading products of several proteinases from Bacillus pumilus were evaluated using MALDI-TOF mass-spectrometry, and their toxicity was assessed in vitro using cell-culture assays and morphological studies. These enzymes have proved to be non-toxic and were demonstrated to cleave through the functional domains of β-amyloid peptide. By yielding inactive fragments, proteinases of Bacillus pumilus may be used as candidate anti-amyloid agents.

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki

Significance Anhydrobiosis is an ametabolic state found in several organisms that can survive extreme desiccation. It is of practical interest because its application to other systems might allow room temperature preservation of cells, tissues, or organs in the dry state. The insect Polypedilum vanderplanki is the most complex animal that can enter anhydrobiosis. Proteins responsible for desiccation tolerance in P. vanderplanki are relatively well studied, but little is known about mechanisms underlying their induction during desiccation. Here, we show that the heat shock transcription factor regulatory network was coopted during the evolution of P. vanderplanki to activate many known desiccation-protective genes, including genes encoding late embryogenesis abundant (LEA) proteins. Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration–rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the Drosophila melanogaster heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in P. vanderplanki, such as genes encoding late embryogenesis abundant (LEA) proteins, thioredoxins, or trehalose metabolism-related genes, but not in P. nubifer. Unlike P. nubifer, P. vanderplanki has double TCTAGAA sites upstream of the Hsf gene itself, which is probably responsible for the stronger activation of Hsf in P. vanderplanki during desiccation compared with P. nubifer. To confirm the role of Hsf in desiccation-induced gene activation, we used the Pv11 cell line, derived from P. vanderplanki embryo. After preincubation with trehalose, Pv11 cells can enter anhydrobiosis and survive desiccation. We showed that Hsf knockdown suppresses trehalose-induced activation of multiple predicted Hsf targets (including P. vanderplanki-specific LEA protein genes) and reduces the desiccation survival rate of Pv11 cells fivefold. Thus, cooption of the heat shock regulatory system has been an important evolutionary mechanism for adaptation to desiccation in P. vanderplanki.

Draft genome sequence of Brevibacterium epidermidis EZ-K02 isolated from nitrocellulose-contaminated wastewater environments

Brevibacterium spp. are aerobic, nonbranched, asporogenous, gram-positive, rod-shaped bacteria which may exhibit a rod-coccus cycle when cells get older and can be found in various environments. Several Brevibacterium species have industrial importance and are capable of biotransformation of various contaminants. Here we describe the draft genome sequence of Brevibacterium epidermidis EZ-K02 isolated from nitrocellulose-contaminated wastewater environments. The genome comprises 3,885,924 bp, with a G + C content of 64.2%. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PDHL00000000.

Draft Genome Sequence of Serratia grimesii Strain A2.

ABSTRACT We report the first draft genome assembly of Serratia grimesii strain A2, previously identified as Escherichia coli strain A2, which produces protease ECP32 with a high specificity toward actin. S. grimesii strain A2 has multidrug resistance associated with a number of efflux pump genes.

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera)

Interpretation of how partnerships between fungi, bacteria, archaea, and insects are maintained through the life of the hosts is a big challenge within the framework of symbiosis research. The main goal of this work was to characterize the gut microbiota in larvae of several Coleoptera species using sequencing of the bacterial and archaeal 16S rRNA genes and fungal internal transcribed spacer (ITS) region. Thus, larvae with various food preferences, including Amphimallon solstitiale, Oryctes nasicornis, Cucujus cinnaberinus, Schizotus pectinicornis, Rhagium mordax, and Rhagium inquisitor, were thoroughly investigated in this work. We revealed an association of these beetle species mainly with four bacterial phyla, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, as well as with three fungal phyla, Ascomycota, Zygomycota, and Basidiomycota, but microbial communities varied depending on the beetle host, individual organism, and surrounding environment. Moreover, archaea within the phyla Euryarchaeota and Crenarchaeota in the hindgut content of O. nasicornis and A. solstitiale were additionally detected. The identified microbial communities suggest their potential role in the exploitation of various resources, providing nutritional needs for the host organism. These microorganisms can also represent a valuable source of novel metabolic capacities for their application in different biotechnologies.

Cerebellar Atrophy and Changes in Cytokines Associated with the CACNA1A R583Q Mutation in a Russian Familial Hemiplegic Migraine Type 1 Family

Background: Immune mechanisms recently emerged as important contributors to migraine pathology with cytokines affecting neuronal excitation. Therefore, elucidating the profile of cytokines activated in various forms of migraine, including those with a known genetic cause, can help in diagnostic and therapeutic approaches. Methods: Here we (i) performed exome sequencing to identify the causal gene mutation and (ii) measured, using Bio-Plex technology, 22 cytokines in serum of patients with familial migraine (two with hemiplegic migraine and two with migraine with aura) from a Russian family that ethnically belongs to the Tatar population. MRI scanning was used to assess cerebellar atrophy associated with migraine in mutation carriers. Results: Whole-exome sequencing revealed the R583Q missense mutation in the CACNA1A gene in the two patients with hemiplegic migraine and cerebellar ataxia with atrophy, confirming a FHM1 disorder. Two further patients did not have the mutation and suffered from migraine with aura. Elevated serum levels of pro-inflammatory and pro-nociceptive IL-6 and IL-18 were found in all four patients (compared to a reference panel), whereas pro-apoptotic SCGF-β and TRAIL were higher only in the patients with the FHM1 mutation. Also, cytokines CXCL1, HGF, LIF, and MIF were found particularly high in the two mutation carriers, suggesting a possible role of vascular impairment and neuroinflammation in disease pathogenesis. Notably, some “algesic” cytokines, such as β-NGF and TNFβ, remained unchanged or even were down-regulated. Conclusion: We present a detailed genetic, neurological, and biochemical characterization of a small Russian FHM1 family and revealed evidence for higher levels of specific cytokines in migraine patients that support migraine-associated neuroinflammation in the pathology of migraine.

Heterologous expression of Bacillus intermedius gene of glutamyl endopeptidase in Bacillus subtilis strains defective in regulatory proteins

Expression of the gene of glutamyl endopeptidase from Bacillus intermedius (gseBi) cloned on the plasmid pV has been studied in Bacillus subtilis recombinant strains with mutations of the regulatory proteins involved in sporogenesis and spore germination. It has been established that inactivation of the regulatory protein Spo0A involved in sporulation initiation resulted in a decrease in the expression of the gseBi gene by 65% on average. A mutation in the gene of the sensor histidine kinase kinA had no effect on the biosynthesis of the enzyme. Inactivation of Ger proteins regulating bacterial spore germination resulted in a 1.5–5-fold decrease in glutamyl endopeptidase activity. It has been concluded that expression of the B. intermedius glutamyl endopeptidase gene from plasmid pV in recombinant cells of B. subtilis is under impaired control by the regulatory system of Spo0F/Spo0A phosphorelay, which participates in sporulation initiation. The regulatory Ger proteins responsible for spore germination also affect expression of the gene of this enzyme.

Bacillus pumilus strains with inactivated genes of extracellular serine proteinases

Two Bacillus pumilus strains with inactivated genes of extracellular serine proteinases (subtilisin-like proteinase and glutamyl endopeptidase) were obtained. Inactivation of the gseBp and aprBp genes resulted in an increase in cell size, changed colony shape, and more rapid cell lysis that started during the growth retardation phase. Protease-deficient stains partially changed the ability to decompose carbohydrates (sugars), reduced resistance to variations in temperature of cultivation, and did not respond to the fluctuations of phosphate concentration in the medium. Proteinases gene disruption resulted in alteration of hydrolases secretion level by these bacteria.