scholarly journals Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes

2019 ◽  
Author(s):  
Georgy Smyshlyaev ◽  
Orsolya Barabas ◽  
Alex Bateman
Keyword(s):  
Comparative Analysis ◽  
Functional Annotation ◽  
Genetic Recombination ◽  
Structural Features ◽  
Specific Protein ◽  
Protein Domain ◽  
Tyrosine Recombinase ◽  
Phylogenetic Groups ◽  
Genetic Traits ◽  
Tyrosine Recombinases

Background: Tyrosine recombinases perform site-specific genetic recombination in bacteria and archaea. They safeguard genome integrity by resolving chromosome multimers, as well as mobilize transposons, phages and integrons, driving dissemination of genetic traits and antibiotic resistance. Despite their abundance and genetic impact, tyrosine recombinase diversity and evolution has not been thoroughly characterized, which greatly hampers their functional classification. Results: Here, we conducted a comprehensive search and comparative analysis of diverse tyrosine recombinases from bacterial, archaeal and phage genomes. We characterized their major phylogenetic groups and show that recombinases of integrons and insertion sequences are closely related to the chromosomal Xer proteins, while integrases of integrative and conjugative elements (ICEs) and phages are more distant. We find that proteins in distinct phylogenetic groups share specific structural features and have characteristic taxonomic distribution. We further trace tyrosine recombinase evolution and propose that phage and ICE integrases originated by acquisition of an N-terminal arm-binding domain. Based on this phylogeny, we classify numerous known ICEs and predict new ones. Conclusions: This work provides a new resource for comparative analysis and functional annotation of tyrosine recombinases. We reconstitute protein evolution and show that adaptation for a role in gene transfer involved acquisition of a specific protein domain, which allows precise regulation of excision and integration.

scholarly journals Analysis of the structure of door bottom drop sealing device

2021 ◽  
Vol 236 ◽  
pp. 02027
Author(s):  
Yuan Fei
Keyword(s):  
Comparative Analysis ◽  
Structural Features ◽  
Sound Insulation ◽  
The Common ◽  
Sealing Device

-Drop Seals Is A Kind Of Hardware That Can Solve The Tightness Of The Door Bottom. This article will briefly introduce the common structural features of this hardware and analyze its impact on the sound insulation of the door leaf according to the experiment. Based on the comparative analysis of 5 sets of data, the experiment proved the effectiveness of the drop seals for the door bottom seal.

scholarly journals Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Xue Fei ◽  
Tristan A Bell ◽  
Simon Jenni ◽  
Benjamin M Stinson ◽  
Tania A Baker ◽  
...  
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Functional Results ◽  
Structural Features ◽  
Specific Protein ◽  
Power Stroke ◽  
E Coli ◽  
Protein Substrates ◽  
Biophysical Studies ◽  
Sequential Models

ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.

scholarly journals Ubiquitin-dependent regulation of a conserved DMRT protein controls sexually dimorphic synaptic connectivity and behavior

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Emily A Bayer ◽  
Rebecca C Stecky ◽  
Lauren Neal ◽  
Phinikoula S Katsamba ◽  
Goran Ahlsen ◽  
...  
Keyword(s):  
Specific Protein ◽  
Protein Stabilization ◽  
Protein Domain ◽  
Synaptic Connectivity ◽  
Sexually Dimorphic ◽  
Posttranslational Regulation ◽  
Neuronal Function ◽  
Related Transcription Factor ◽  
Sex Specificity ◽  
And Behavior

Sex-specific synaptic connectivity is beginning to emerge as a remarkable, but little explored feature of animal brains. We describe here a novel mechanism that promotes sexually dimorphic neuronal function and synaptic connectivity in the nervous system of the nematode Caenorhabditis elegans. We demonstrate that a phylogenetically conserved, but previously uncharacterized Doublesex/Mab-3 related transcription factor (DMRT), dmd-4, is expressed in two classes of sex-shared phasmid neurons specifically in hermaphrodites but not in males. We find dmd-4 to promote hermaphrodite-specific synaptic connectivity and neuronal function of phasmid sensory neurons. Sex-specificity of DMD-4 function is conferred by a novel mode of posttranslational regulation that involves sex-specific protein stabilization through ubiquitin binding to a phylogenetically conserved but previously unstudied protein domain, the DMA domain. A human DMRT homolog of DMD-4 is controlled in a similar manner, indicating that our findings may have implications for the control of sexual differentiation in other animals as well.

scholarly journals Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Agronomy ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 159 ◽  
Author(s):  
Xiaojun Nie ◽  
Xian Zhao ◽  
Sue Wang ◽  
Ting Zhang ◽  
Chong Li ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Panicum Virgatum ◽  
Genome Structure ◽  
Structural Features ◽  
Panicum Miliaceum ◽  
Genomic Knowledge ◽  
Broomcorn Millet ◽  
Evolutionary Studies ◽  
Cp Genome

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

scholarly journals Detection of Intravascular Hemolysis in Newborn Infants Using Urinary Carbonic Anhydrase I Immunoreactivity

2020 ◽  
Vol 5 (5) ◽  
pp. 921-934
Author(s):  
Alzbeta Hulikova ◽  
Holger Kramer ◽  
Hammad Khan ◽  
Pawel Swietach
Keyword(s):  
Carbonic Anhydrase ◽  
Point Of Care ◽  
Newborn Infants ◽  
Cost Effective ◽  
Specific Protein ◽  
Intravascular Hemolysis ◽  
Genetic Traits ◽  
Healthcare Facilities ◽  
Abo Incompatibility ◽  
Carbonic Anhydrase I

Abstract Background Mild hemolysis occurs physiologically in neonates, but more severe forms can lead to life-threatening anemia. Newborns in developing regions are particularly at-risk due to the higher incidence of triggers (protozoan infections, sepsis, certain genetic traits). In advanced healthcare facilities, hemolysis is monitored indirectly using resource-intensive methods that probe downstream ramifications. These approaches could potentially delay critical decisions in early-life care, and are not suitable for point-of-care testing. Rapid and cost-effective testing could be based on detecting red blood cell (RBC)-specific proteins, such as carbonic anhydrase I (CAI), in accessible fluids (e.g., urine). Methods Urine was collected from 26 full-term male neonates and analyzed for CAI using immunoassays (ELISA, western blot) and proteomics (mass spectrometry). The cohort included a range of hemolytic states, including admissions with infection, ABO incompatibility, and receiving phototherapy. Data were paired with hemoglobin, serum bilirubin (SBR), and C-reactive protein (CRP) measurements. Results Urine from a control cohort (CRP < 20 mg/L, SBR < 125µmol/L) had no detectable CAI, in line with results from healthy adults. CAI excretion was elevated in neonates with raised SBR (>125 µmol/L), including those qualifying for phototherapy. Newborns with low SBR (<125 µmol/L) but elevated CRP (>20 mg/L) produced urine with strong CAI immunoreactivity. Proteomics showed that CAI was the most abundant RBC-specific protein in CAI-immunopositive samples, and did not associate with other RBC-derived peptides, indicating an intravascular hemolytic source followed by CAI-selective excretion. Conclusions CAI is a direct biomarker of intravascular hemolysis that can be measured routinely in urine using non-invasive methods under minimal-laboratory conditions.

scholarly journals Inositol Pyrophosphate Pathways and Mechanisms: What Can We Learn from Plants?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2789 ◽  
Author(s):  
Caitlin Cridland ◽  
Glenda Gillaspy
Keyword(s):  
Inositol Phosphate ◽  
Specific Protein ◽  
Protein Domain ◽  
Growth And Survival ◽  
Inositol Pyrophosphate ◽  
Protein Partners ◽  
Inositol Pyrophosphates ◽  
Energy Sensing ◽  
And Function ◽  
Complex Signaling

The ability of an organism to maintain homeostasis in changing conditions is crucial for growth and survival. Eukaryotes have developed complex signaling pathways to adapt to a readily changing environment, including the inositol phosphate (InsP) signaling pathway. In plants and humans the pyrophosphorylated inositol molecules, inositol pyrophosphates (PP-InsPs), have been implicated in phosphate and energy sensing. PP-InsPs are synthesized from the phosphorylation of InsP6, the most abundant InsP. The plant PP-InsP synthesis pathway is similar but distinct from that of the human, which may reflect differences in how molecules such as Ins(1,4,5)P3 and InsP6 function in plants vs. animals. In addition, PP-InsPs can potentially interact with several major signaling proteins in plants, suggesting PP-InsPs play unique signaling roles via binding to protein partners. In this review, we will compare the biosynthesis and role of PP-InsPs in animals and plants, focusing on three central themes: InsP6 synthesis pathways, synthesis and regulation of the PP-InsPs, and function of a specific protein domain called the Syg1, Pho1, Xpr1 (SPX ) domain in binding PP-InsPs and regulating inorganic phosphate (Pi) sensing. This review will provide novel insights into the biosynthetic pathway and bioactivity of these key signaling molecules in plant and human systems.

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