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PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins
No full textLow complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToLoCo - PLAtform of TOols for LOw COmplexity—a meta-server that integrates and collects the output of five different state-of-the-art tools for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies. In addition, the union or intersection of the results of the search on a query sequence can be obtained. By developing the PlaToLoCo meta-server, we provide the community with a fast and easily accessible tool for the analysis of LCRs with additional information included to aid the interpretation of the results. The PlaToLoCo platform is available at: http://platoloco.aei.polsl.pl/
Transcriptional Organization of the Stability Module of BroadHost-Range Plasmid RA3, from the IncU Group
Get PDFThe broad-host-range (BHR) conjugative plasmids have developed diverse
adaptive mechanisms defining the range of their promiscuity. The BHR conjugative
RA3 plasmid, the archetype of the IncU group, can transfer between, replicate
in, and be maintained in representatives of Alpha-, Beta-, and Gammaproteobacteria.
Its stability module encompasses ten open reading frames (ORFs) apparently organized
into five operons, all transcribed in the same direction from several strong
promoters that are tightly regulated either by autorepressors or by global plasmidencoded
regulators. In this paper, we demonstrate that owing to an efficient RNA
polymerase (RNAP) read-through, the transcription from the first promoter, orf02p,
may continue through the whole module. Moreover, an analysis of mRNA produced
from the wild-type (WT) stability module and its deletion variants deprived of particular
internal transcription initiation sites reveals that in fact each operon may be
transcribed from any upstream promoter, giving rise to multicistronic transcripts of
variable length and creating an additional level of gene expression control by transcript
dosage adjustment. The gene expression patterns differ among various hosts,
indicating that promoter recognition, regulation, and the RNAP read-through mechanisms
are modulated in a species-specific manner
Molecular identification of Trichocera maculipennis, an invasive fly species in the Maritime Antarctic
Get PDFTrichocera maculipennis, an invasive Diptera, was described for the first time in Antarctica in 2006 in a sewage system of one of the scientific stations on King George Island, South Shetland Islands, and started to increase its distribution within the island. To date, only taxonomical description of this species, based on morphological data has been available, as there were no molecular data recorded. In the present study, we present two methods of molecular identification of this species—based on partial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) genes. An appropriate and easy-to-use assay for proper and fast identification of invasive species is a key requirement for further management decisions, especially in such a fragile environment as found in terrestrial Antarctica
A Family Affected by a Life-Threatening Erythrocyte Defect Caused by Pyruvate Kinase Deficiency With Normal Iron Status: A Case Report
Get PDFBackground: Red cell pyruvate kinase deficiency (PKD) is a defect of glycolysis causing congenital non-spherocytic hemolytic anemia. PKD is transmitted as an autosomal recessive trait. The clinical features of PKD are highly variable, from mild to life-threatening anemia which can lead to death in the neonatal period. Most patients with PKD must receive regular transfusions in early childhood and as a consequence suffer from iron overloading.
Patient: Here, we report a Polish family with life-threatening hemolytic anemia of unknown etiology. Whole exome sequencing identified two heterozygous mutations, c.1529 G > A (p.R510Q) and c.1495 T > C (p.S499P) in the PKLR gene. Molecular modeling showed that the both PKLR mutations are responsible for major disturbance of the protein structure and functioning. Despite frequent transfusions the patients do not show any signs of iron overload and hepcidin, a major regulator of iron uptake, is undetectable in their serum. The patients were homozygous for the rs855791 variant of the TMPRSS6 gene which has earlier been shown to down-regulate iron absorption and accumulation.
Conclusion: The lack of iron overload despite a reduced level of hepcidin in two transfusion-dependent PKD patients suggests the existence of a hepcidin-independent mechanism of iron regulation preventing iron overloading
Spatial Nano-Morphology of the Prolamellar Body in Etiolated Arabidopsis thaliana Plants With Disturbed Pigment and Polyprenol Composition
Get PDFThe prolamellar body (PLB) is a periodic bicontinuous membrane structure based on tubular tetrahedral units. PLBs are present in plant etioplasts and, upon illumination, directly transform into the lamellar thylakoid networks within chloroplasts. Efficient tubular-lamellar rearrangement and later formation of the photosynthetically active thylakoid membranes are crucial steps in the development of plant autotrophy. PLB membranes are mainly composed of galactolipids, carotenoids, and protochlorophyllide (Pchlide), the chlorophyll precursor, bound in a complex with NADPH and Pchlide oxidoreductase. Although the PLB structure has been studied for over 50 years, the direct role of particular membrane components in the formation of the PLB paracrystalline network remains elusive. Moreover, despite the numerous literature data regarding the PLB geometry, their reliable comparative analysis is complicated due to variable experimental conditions. Therefore, we performed comprehensive ultrastructural and low-temperature fluorescence analysis of wild type Arabidopsis thaliana (Arabidopsis) seedlings grown in different conditions typical for studies on etiolated seedlings. We established that the addition of sucrose to the growing media significantly affected the size and compactness of the PLB. The etiolation period was also an important factor influencing the PLB structural parameters and the ratio of free to complex-bound Pchlide. Thus, a reliable PLB structural and spectral analysis requires particular attention to the applied experimental conditions. We investigated the influence of the pigment and polyprenol components of the etioplast membranes on the formation of the PLB spatial structure. The PLB 3D structure in several Arabidopsis mutants (ccr1-1, lut5-1, szl1-1npq1-2, aba1-6, pif1, cpt7) with disturbed levels of particular pigments and polyprenols using electron tomography technique was studied. We found that the PLB nano-morphology was mainly affected in the pif1 and aba1-6 mutants. An increased level of Pchlide (pif1) resulted in the substantial shift of the structural balance between outer and inner PLB water channels and overall PLB compactness compared to wild type plants. The decrease in the relative content of β-branch xanthophylls in aba1-6 plants was manifested by local disturbances in the paracrystalline structure of the PLB network. Therefore, proper levels of particular etioplast pigments are essential for the formation of stable and regular PLB structure
Key Intermediate Species Reveal the Copper(II)‐Exchange Pathway in Biorelevant ATCUN/NTS Complexes
Get PDFThe amino-terminal copper and nickel/N-terminal site (ATCUN/NTS) present in proteins and bioactive peptides exhibits high affinity towards CuII ions and have been implicated in human copper physiology. Little is known, however, about the rate and exact mechanism of formation of such complexes. We used the stopped-flow and microsecond freeze-hyperquenching (MHQ) techniques supported by steady-state spectroscopic and electrochemical data to demonstrate the formation of partially coordinated intermediate CuII complexes formed by glycyl-glycyl-histidine (GGH) peptide, the simplest ATCUN/NTS model. One of these novel intermediates, characterized by two-nitrogen coordination, t1/2 ≈100 ms at pH 6.0 and the ability to maintain the CuII /CuI redox pair is the best candidate for the long-sought reactive species in extracellular copper transport
Individual Nudix hydrolases affect diverse features of Pseudomonas aeruginosa
Get PDFNudix proteins catalyze the hydrolysis of pyrophosphate bonds in a variety of substrates
and are ubiquitous in all domains of life. The genome of an important opportunistic
human pathogen, Pseudomonas aeruginosa, encodes multiple Nudix proteins.
To determine the role of nine Nudix hydrolases of the P. aeruginosa PAO1161 strain
in its fitness, virulence or antibiotic resistance mutants devoid of individual enzymes
were constructed and analyzed for growth rate, motility, biofilm formation, pyocyanin
production, and susceptibility to oxidative stress and different antibiotics. The potential
effect on bacterial virulence was studied using the Caenorhabditis elegans–P. aeruginosa
infection model. Of the nine mutants tested, five had an altered phenotype in
comparison with the wild-type strain. The ΔPA3470, ΔPA3754, and ΔPA4400 mutants
showed increased pyocyanin production, were more resistant to the β-lactam antibiotic
piperacillin, and were more sensitive to killing by H2O2. In addition, ΔPA4400
and ΔPA5176 had impaired swarming motility and were less virulent for C. elegans.
The ΔPA4841 had an increased sensitivity to oxidative stress. These changes were
reversed by providing the respective nudix gene in trans indicating that the observed
phenotype alterations were indeed due to the lack of the particular Nudix protein
Similar but Not Identical—Binding Properties of LSU (Response to Low Sulfur) Proteins From Arabidopsis thaliana
Get PDFMembers of the plant-specific LSU (RESPONSE TO LOW SULFUR) family are strongly induced during sulfur starvation. The molecular functions of these proteins are unknown; however, they were identified as important stress-related hubs in several studies. In Arabidopsis thaliana, there are four members of the LSU family (LSU1–4). These proteins are small (approximately 100 amino acids), with coiled-coil structures. In this work, we
investigated interactions between different monomers of LSU1–4. Differences in homo and heterodimer formation were observed. Our structural models of LSU1–4 homo- and
heterodimers were in agreement with our experimental observations and may help understand their binding properties. LSU proteins are involved in multiple protein–protein interactions, with the literature suggesting they can integrate abiotic and biotic stress responses. Previously, LSU partners were identified using the yeast two hybrid approach, therefore we sought to determine proteins co-purifying with LSU family members using protein extracts isolated from plants ectopically expressing TAP-tagged LSU1–4 constructs. These experiments revealed 46 new candidates for LSU partners. We tested four of them (and two other proteins, CAT2 and NBR1) for interaction with LSU1–4 by other methods. Binding of all six proteins with LSU1–4 was confirmed by Bimolecular Fluorescence Complementation, while only three of them were interacting with LSUs in yeast-two-hybrid. Additionally, we conducted network analysis of LSU interactome and revealed novel clues for the possible cellular function of these proteins
Mapping Glacier Forelands Based on UAV BVLOS Operation in Antarctica
Get PDFThe aim of this article is to show geomorphological mapping of remote Antarctic locations usingimagestakenbyafixed-wingunmannedaerialvehicle(UAV)duringtheBeyondVisualLineof Sight (BVLOS) operations. We mapped landform assemblages developed in forelands of Ecology Glacier (EGF), Sphinx Glacier (SGF) and Baranowski Glacier (BGF) in Antarctic Specially Protected Area No. 128 (ASPA 128) on King George Island (South Shetland Islands) and inferred about glacial dynamics. The orthophoto and digital elevation model allowed for geomorphological mapping of glacial forelands, including (i) glacial depositional landforms, (ii) fluvial and fluvioglacial landforms, (iii) littoral and lacustrine landforms, (iv) bodies of water, and (v) other. The largest area is occupied by ground moraine and glacial lagoons on EGF and BGF. The most profound features of EGF are the largelatero-frontalmoraineridgesfromLittleIceAgeandthefirsthalfofthe20thcentury. Largeareas of ground moraine, frequently fluted and marked with large recessional moraine ridges, dominate on SGF. A significant percentage of bedrock outcrops and end moraine complexes characterize BGF. The landform assemblages are typical for discontinuous fast ice flow of tidewater glaciers over a deformable bed. It is inferred that ice flow velocity decreased as a result of recession from the sea coast, resulting in a significant decrease in the length of ice cliffs and decrease in calving rate. Image acquisition during the fixed-wing UAV BVLOS operation proved to be a very robust technique in harsh polar conditions of King George Island