Search bioRxivSearch

SEARCH · Search bioRxiv

Results for “Biochemistry”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources

A novel rotifer-derived alkaloid paralyzes schistosome larvae and prevents infection

Schistosomes are parasitic flatworms that infect over 200 million people, causing the neglected tropical disease, schistosomiasis. A single drug, praziquantel, is used to treat schistosome infection. Limitations in mass drug administration programs and the emergence of schistosomiasis in non-tropical areas indicate the need for new strategies to prevent infection. It has been known for several decades that rotifers colonizing the schistosomes snail intermediate host produce a water-soluble factor that paralyzes cercariae, the life-cycle stage infecting humans. In spite of its potential for preventing infection, the nature of this factor has remained obscure. Here, we report the purification and chemical characterization of Schistosome Paralysis Factor (SPF), a novel tetracyclic alkaloid produced by the rotifer Rotaria rotatoria. We show that this compound paralyzes schistosome cercariae and prevents infection, and does so more effectively than analogous compounds. This molecule provides new directions for understanding cercariae motility and new strategies for preventing schistosome infection.

biochemistry

A well-controlled BioID design for endogenous bait proteins.

The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate overexpression of bait proteins. Control cell lines are typically non-engineered cells or engineered clones implying a considerable risk for artefacts because of clonal variation. Genome engineering can also transform BioID, a proximity labelling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bi-cistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A auto-cleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over classical ectopic expression of p53-BirA*, and we provide a first well-controlled view on the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC=\"FIGDIR/small/427807v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@404da1org.highwire.dtl.DTLVardef@1a8af36org.highwire.dtl.DTLVardef@18741a6org.highwire.dtl.DTLVardef@e73ab3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry

The structural basis for forkhead box family specificity revealed by the crystal structure of human FOXN1 in complex with DNA

SignificanceFOXN1 is a transcription factor that is essential for the development of the thymus and the production of T-lymphocytes. It is a member of a large family of transcription factors which recognize DNA sequences through the conserved Forkhead (FH) domain. FOXN1 recognizes a DNA sequence that is different from the common consensus binding sequence of FH domains, although key binding residues are identical. We present crystal structures of the FH domain of FOXN1, free and DNA-bound, which shed light on the different binding specificities; the structure also revelas the basis of the immunocompromised nude mutation, as well as a preferential binding to non-methylated CpG motifs.\n\nAbstractFOXN1 is a member of the forkhead box (FOX) family of transcription factors, and plays an important role in thymic epithelial cell differentiation and function. FOXN1 mutations in humans and mice give rise to the \"nude\" phenotype which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognize an alternate consensus sequence (GACGC), which is different from the more widely-recognized canonical sequence consensus RYAAAYA. Here, we present the structure of FOXN1 in complex with DNA at 1.6 [A] resolution, in which the DNA sequence is recognised by a mixture of direct and water-mediated contacts provided by residues in an a-helix inserted in the DNA major groove (the recognition helix). Comparisons with other FOX family structures reveal that the canonical and alternate DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identify a single alternate rotamer within the recognition helix itself as an important determinant of DNA specificity, and indicate sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally we demonstrate that FOXN1 has a significantly reduced affinity for DNA containing 5-methylcytosine, which may have implications for the role of FOXN1 in thymic senescence.

biochemistry

Mitotic CDK promotes replisome disassembly, fork breakage, and complex DNA rearrangements

DNA replication errors generate complex chromosomal rearrangements and thereby contribute to tumorigenesis and other human diseases. Although the events that trigger these errors are not well understood, one candidate is mitotic entry before the completion of DNA replication. To address the impact of mitosis on DNA replication, we employed Xenopus egg extracts. When mitotic CDK (Cyclin B1-CDK1) is used to drive these extracts into mitosis, the E3 ubiquitin ligase TRAIP promotes ubiquitylation of the replicative CMG (CDC45/MCM2-7/GINS) helicase at stalled forks and at forks that have completed DNA synthesis. In both cases, ubiquitylation is followed by CMG extraction from chromatin by the CDC48/p97 ATPase. At stalled forks, CMG removal results in fork breakage and complex end joining events involving deletions and template-switching. Our results identify TRAIP-dependent replisome disassembly as a novel trigger of replication fork collapse and propose it underlies complex DNA rearrangements in mitosis.\n\nHIGHLIGHTSO_LITRAIP-dependent MCM7 ubiquitylation removes all CMGs from chromatin in mitosis\nC_LIO_LICMG unloading from stalled forks causes replication fork breakage\nC_LIO_LIReplication fork breakage in mitosis causes complex rearrangements\nC_LIO_LINew model of replication fork collapse\nC_LI

biochemistry

Molecular basis of human asparagine synthetase inhibitor specificity

Expression of the enzyme human asparagine synthetase (ASNS) promotes metastatic progression in breast cancer, which affects L-asparagine levels and tumor cell invasiveness. Human ASNS has therefore emerged as a bona fide drug target for cancer therapy. We have reported a slow-onset, tight binding ASNS inhibitor with nanomolar affinity, but our compound exhibits poor cell permeability. On the other hand, we show here that this inhibitor exhibits remarkable selectivity for the human ASNS in HCT-116 cell lysates. By determining the first high-resolution (1.85 [A]) X-ray crystal structure for human ASNS, we have built a computational model of the enzyme complexed to our inhibitor, which provides the first insights into the intermolecular interactions mediating specificity. These findings should facilitate the development of a second generation of ASNS inhibitors, leading to the discovery of drugs to prevent metastasis.

biochemistry

The bacterial DNA binding protein MatP involved in linking the nucleoid terminal domain to the divisome at midcell interacts with lipid membranes

Division ring formation at midcell is controlled by various mechanisms in Escherichia coli, one of them being the linkage between the chromosomal Ter macrodomain and the Z-ring mediated by MatP, a DNA binding protein that organizes this macrodomain and contributes to the prevention of premature chromosome segregation. Here we show that, during cell division, just before splitting the daughter cells, MatP seems to localize close to the cytoplasmic membrane, suggesting that this protein might interact with lipids. To test this hypothesis, we investigated MatP interaction with lipids in vitro. We found that MatP, when encapsulated inside microdroplets generated by microfluidics and giant vesicles, accumulates at phospholipid bilayers and monolayers matching the lipid composition in the E. coli inner membrane. MatP binding to lipids was independently confirmed using lipid coated microbeads and bio-layer interferometry assays. Interaction of MatP with the lipid membranes also occurs in the presence of the DNA sequences specifically targeted by the protein but there is no evidence of ternary membrane/protein/DNA complexes. We propose that the interaction of MatP with lipids may modulate its spatiotemporal localization and its recognition of other ligands.\n\nIMPORTANCEThe division of an E. coli cell into two daughter cells with equal genomic information and similar size requires duplication and segregation of the chromosome and subsequent scission of the envelope by a protein ring, the Z-ring. MatP is a DNA binding protein that contributes both to the positioning of the Z-ring at midcell and the temporal control of nucleoid segregation. Our integrated in vivo and in vitro analysis provides evidence that MatP can interact with lipid membranes comprising the phospholipid mixture in the E. coli inner membrane, without concomitant recruitment of the short DNA sequences specifically targeted by MatP. This observation strongly suggests that the membrane may play a role in the regulation of the function and localization of MatP, which could be relevant for the coordination of the two fundamental processes in which this protein participates, nucleoid segregation and cell division.

biochemistry

Allosteric network in Ube2T drives specificity for RING E3 catalysed ubiquitin signals.

In eukaryotes, DNA damage repair is implemented by a host of proteins that are coordinated by defined molecular signals. One such signal that transpires during the Fanconi Anemia (FA) - interstrand crosslink (ICL) repair pathway is the site-specific monoubiquitination of FANCD2 and FANCI proteins by a large, multi-protein FA core complex. The mechanics for this exquisitely specific monoubiquitin signal has been elusive. Here we show FANCL, the RING E3 module of the FA core complex, allosterically activates its cognate E2 Ube2T for monoubiquitination by a mechanism distinct from the typical RING-based catalysis. FANCL triggers intricate re-wiring of Ube2Ts intra-residue network thus activating the E2 for precision targeting. This network is intrinsically regulated by conserved gates and loops which can be engineered to yield Ube2T variants that enhance FANCD2 ubiquitination by ~30-fold without compromising on target specificity. Finally, we also uncover allosteric networks in other ubiquitin E2s that can be leveraged by RING E3 ligases to drive specific ubiquitination.

biochemistry

Alternative splicing of bicistronic MOCS1 defines a novel mitochondrial protein maturation mechanism

Molybdenum cofactor biosynthesis is a conserved multistep pathway. The first step, the conversion of GTP to cyclic pyranopterin monophosphate (cPMP), requires bicsistronic MOCS1. Alternative splicing of MOCS1 in exons 1 and 9 produces four different N-terminal and three different C-terminal products (type I-III). Type I splicing results in bicistronic transcripts with two open reading frames, of which only the first, MOCS1A, is translated, whereas type II/III splicing produces two-domain MOCS1AB proteins. Here, we report and characterize the mitochondrial translocation of alternatively spliced MOCS1 proteins. While MOCS1A requires exon 1a for mitochondrial translocation, MOCS1AB variants target to mitochondria via an internal motif overriding the N-terminal targeting signal. Within mitochondria, MOCS1AB undergoes proteolytic cleavage resulting in mitochondrial matrix localization of the MOCS1B domain. In conclusion we found that MOCS1 produces two functional proteins, MOCS1A and MOCS1B, which follow different translocation routes before mitochondrial matrix import, where both proteins collectively catalyze cPMP biosynthesis. MOCS1 protein maturation provides a novel mechanism of alternative splicing ensuring the coordinated targeting of two functionally related mitochondrial proteins encoded by a single gene.

biochemistry

Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants

Flavonoids are important polyphenolic natural products, ubiquitous in land plants, that play diverse functions in plants survival in their ecological niches, including UV protection, pigmentation for attracting pollinators, symbiotic nitrogen fixation, and defense against herbivores. Chalcone synthase (CHS) catalyzes the first committed step in plant flavonoid biosynthesis and is highly conserved in all land plants. In several previously reported crystal structures of flowering plant CHSs, the catalytic cysteine is oxidized to sulfinic acid, indicating enhanced nucleophilicity in this residue associated with its increased susceptibility to oxidation. In this study, we report a set of new crystal structures of CHSs representing all five major lineages of land plants. We reveal that the structures of CHS from a lycophyte and a moss species preserve the catalytic cysteine in a reduced state, in contrast to the cysteine sulfinic acid seen in all euphyllophyte CHS structures. In vivo complementation, in vitro biochemical and mutagenesis analyses, as well as molecular dynamics simulations identify a set of residues that differ between basal-plant and euphyllophyte CHSs and modulate catalytic cysteine reactivity. We propose that the CHS active-site environment has evolved in euphyllophytes to further enhance the nucleophilicity of the catalytic cysteine since the divergence of euphyllophytes from other vascular plant lineages 400 million years ago. These changes in CHS could have contributed to the diversification of flavonoid biosynthesis in euphyllophytes, which in turn contributed to their dominance in terrestrial ecosystems.

biochemistry

Specificity for deubiquitination of monoubiquitinated FANCD2 is driven by the N-terminus of USP1

The DNA damage response depends on ubiquitin signalling to orchestrate DNA repair. The Fanconi Anemia pathway for interstrand crosslink repair, and the translesion synthesis pathway for DNA damage tolerance, both require cycles of monoubiquitination and deubiquitination. The ubiquitin specific protease USP1 regulates both these pathways by deubiquitinating monoubiquitinated PCNA, FANCD2 and FANCI. Loss of USP1 activity gives rise to chromosomal instability. While many USPs hydrolyse ubiquitin-ubiquitin linkages, USP1 targets ubiquitin-substrate conjugates at specific sites. The molecular basis of USP1s specificity for multiple substrates is poorly understood. Here we show that the molecular determinants for substrate deubiquitination by USP1 reside within the highly conserved and extended N-terminus. We find that the N-terminus of USP1 harbours a FANCD2-specific binding sequence required for deubiquitination of K561 on FANCD2. In contrast, the N-terminus is not required for PCNA or FANCI deubiquitination. Furthermore, we show that the N-terminus of USP1 is sufficient to engineer specificity in a more promiscuous USP.

biochemistry

Metabolomic analyses of plasma and liver of mice fed with immature Citrus tumida peel

Supplementing food with functional small molecules has been shown to prevent diseases and improve the quality of life, especially in elderly people. Citrus fruits and citrus fruit-products are popular food supplements across the world. In this study, we focused on a Japanese citrus fruit, Citrus tumida hort. ex Tanaka (C. tumida), and elucidated the effects of supplementation of the peels of immature C. tumida (PIC) on food intake, body and fat tissue weights, and metabolic profiles of plasma and liver in mice. Supplementation with 5% (w/w) PIC for 4 weeks significantly suppressed body weight gain and decreased adipose tissue weight, including that of the epididymal, perirenal, and subcutaneous fats. Metabolome analyses using capillary electrophoresis time-of-flight mass spectrometry showed that the level of 2-hydroxyvaleric acid was reduced in the blood plasma of mice fed with PIC. Supplementation with PIC significantly elevated the levels of dipeptides (Thr-Asp, Ser-Glu, and Ala-Ala), glucuronic acid (and/or galacturonic acid-2), and S-methylglutathione, and significantly reduced the levels of betaine aldehyde in the liver. In conclusion, PIC supplementation affects the metabolism of fatty acids, pectin, glutathione, and choline. Our study demonstrates the potential beneficial effects of PIC, especially in metabolic syndrome and obesity. PIC may be developed as a functional food and used in the treatment of these diseases. Nutritional and metabolome studies are effective in studying the effects of specific dietary supplements and will contribute to the development of functional foods.

biochemistry

Mechanism of IRSp53 inhibition by 14-3-3

Filopodia are precursors of dendritic spines and polarized cell migration. The I-BAR-domain protein IRSp53 is an essential regulator of filopodia dynamics that couples Rho-GTPase signaling to cytoskeleton and membrane remodeling, playing essential roles in neuronal development and cell motility. Here, we describe a mechanism whereby phosphorylation-dependent inhibition of IRSp53 by 14-3-3 counters membrane binding and activation by Cdc42 or downstream cytoskeletal effectors. Phosphoproteomics, quantitative binding studies and crystal structures show that 14-3-3 binds to two pairs of phosphorylation sites in IRSp53. Using bicistronic expression we obtained a heterodimer of IRSp53 in which only one subunit is phosphorylated, and show that each subunit of the IRSp53 dimer independently binds a 14-3-3 dimer. A FRET-sensor assay developed using natively phosphorylated and 14-3-3-binding competent IRSp53 purified from mammalian cells reveals opposite conformational changes in IRSp53 upon binding of activatory (Cdc42, Eps8) vs. inhibitory (14-3-3) inputs.

biochemistry

Crystal structures reveal that Lewis-x and fucose bind to secondary cholera toxin binding site - in contrast to fucosyl-GM1

Cholera is a life-threatening diarrhoeal disease caused by the human pathogen Vibrio cholerae. Infection occurs after ingestion of the bacteria, which colonize the human small intestine and secrete their major virulence factor - the cholera toxin (CT). Recent studies suggest that the GM1 receptor may not be the only target of the CT, and that fucosylated receptors such as Lewisx (Lex) and histo-blood group antigens may also be important for cellular uptake and toxicity. However, where and how Lex binds to the CT remains unclear. Here we report the high-resolution crystal structure (1.5 [A]) of the receptor-binding B-subunit of the CT bound to the Lex trisaccharide, and present matching SPR data for CT holotoxins. Lex, and also O_SCPCAPLC_SCPCAP-fucose alone (at 500-fold molar excess), bind to the secondary binding site of the toxin, distinct from the GM1 binding site. In contrast, fucosyl-GM1 mainly binds to the primary binding site due to high-affinity interactions of its GM1 core. The two binding sites are likely connected by allosteric cross-talk, potentially affecting toxin uptake. We also discuss why secretors are protected from severe cholera.\n\nAuthor summaryCholera is a severe diarrhoeal disease that is still a major killer in many parts of the world, especially in regions struck by natural disasters and wars. However, some individuals experience milder cholera symptoms. These so-called secretors, who have blood group antigens also in their bodily fluids like their saliva and the slimy mucus layer covering their stomach and intestines, appear to be somewhat protected. Here we present detailed atomic structures of cholera toxin and quantitative binding data that give clues of the protective mechanisms. Interactions of the protein toxin with sugar molecules are of crucial importance both for toxicity and protection. In addition, we identify a new tool for biochemical studies, and lay the groundwork for the design of cholera drugs and vaccines that may save countless human lives.

biochemistry

Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea

Iron is an essential element for many biological processes; however, due to its high reactivity iron can also be very toxic, producing reactive oxygen species through Fenton chemistry. Ferritins protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing the resulting iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. We recently characterised the Rhodospirillum rubrum EncFtn, showing that although enzymatically active, due to its open structure it requires the association with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether the structure and catalytic activity is conserved across the family. Here we structurally characterise two EncFtn members from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the same distinct annular decamer topology observed in R. rubrum EncFtn, with the ferroxidase centre (FOC) formed between one of the dimer interfaces. Solution and native mass spectrometr analyses show that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The catalytic role of the EncFtn proteins was confirmed by biochemical assays, and we show that Zn(II) ions inhibit the ferroxidase activity of the EncFtn proteins to varying degrees. Our results represent a further step in the characterisation of the recently discovered EncFtn ferritin-like sub-family, indicating a common structural organisation and catalytic activity, despite diverse host environments.

biochemistry

Hetero-oligomeric CPN60 resembles highly symmetric group I chaperonin structure revealed by Cryo-EM

The chloroplast chaperonin system is indispensable for the biogenesis of Rubisco, the key enzyme in photosynthesis. Using Chlamydomonas reinhardtii as the model system, we revealed that chloroplast chaperonin is consisted of CPN60, CPN60{beta}1, and CPN60{beta}2, and co-chaperonin is composed of three subunits CPN20, CPN11 and CPN23 in vivo. CPN20 homo-oligomers and all possible other chloroplast co-chaperonin hetero-oligomers are functional, but only CPN11/20/23-CPN60{beta}1{beta}2 pair can fully replace GroES/GroEL in E. coli at stringent growth condition. Endogenous CPN60 was purified and its stoichiometry was determined to be 6:2:6 for CPN60:CPN60{beta}1:CPN60{beta}2. The cryo-EM structures of endogenous CPN60{beta}1{beta}2/ADP and CPN60{beta}1{beta}2/co-chaperonin/ADP were solved at resolutions of 4.06 [A] and 3.82[A], respectively. In both hetero-oligomeric complexes the chaperonin subunits within each ring are highly symmetric. The chloroplast co-chaperonin CPN11/20/23 formed seven GroES-like domains through hetero-oligomerization which symmetrically interact with CPN60{beta}1{beta}2. Our structures also reveal an uneven distribution of roof-like structures in the dome-shaped CPN11/20/23 and potentially diversified surface properties in the folding cavity of CPN60{beta}1{beta}2 that might enable the chloroplast chaperonin system to assist in the folding of specific substrates.

biochemistry

Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein

Diversity-generating retroelements (DGRs) are widely distributed in bacteria, archaea, and microbial viruses, and bring about unparalleled levels of sequence variation in target proteins. While DGR variable proteins share low sequence identity, the structures of several such proteins have revealed the C-type lectin (CLec)-fold as a conserved scaffold for accommodating massive sequence variation. This conservation has led to the suggestion that the CLec-fold may be useful in molecular surface display applications. Thermostability is an attractive feature in such applications, and thus we studied the variable protein of a DGR encoded by the thermophile Thermus aquaticus. We report here the 2.8 [A] resolution crystal structure of the variable protein from the T. aquaticus DGR, called TaqVP, and confirm that it has a CLec-fold. Remarkably, its variable region is nearly identical in structure to those of several other CLec-fold DGR variable proteins despite low sequence identity among these. TaqVP was found to be thermostable, which appears to be a property shared by several CLec-fold DGR variable proteins. These results provide impetus for the pursuit of the DGR variable protein CLec-fold in molecular display applications.

biochemistry

Molecular mechanisms of gating in the calcium-activated chloride channel bestrophin

Bestrophin (BEST1-4 in humans) channels are ligand gated chloride (Cl-) channels that are activated by calcium (Ca2+). Mutations in BEST1 cause retinal degenerative diseases. Partly because these channels have no sequence or structural similarity to other ion channels, the molecular mechanisms underlying gating are unknown. Here, we present a series of cryo-electron microscopy (cryo-EM) structures of chicken BEST1, determined at 3.1 [A] resolution or better, that represent the principal gating states of the channel. Unlike other channels, opening of the pore is due to the repositioning of tethered pore-lining helices within a surrounding protein shell that dramatically widens a \"neck\" of the pore through a concertina of amino acid rearrangements within the protein core. The neck serves as both the activation and the inactivation gate. The binding of Ca2+ to a cytosolic domain instigates pore opening and the structures reveal that, unlike voltage-gated Na+ and K+ channels, similar molecular rearrangements are responsible for inactivation and deactivation. A single aperture within the 95 [A]-long opened pore separates the cytosol from the extracellular milieu and controls anion permeability. The studies define the basis for Ca2+-activated Cl- channel function and reveal a new molecular paradigm for gating in ligand-gated ion channels.

biochemistry

Study of the action of lactic acid bacteria on acrylamide in food products

The aim of this study is to extract Lactic acid bacteria (LAB) and test its effect on starchy food products. We extracted LAB as it is GRAS (Generally Recognised As Safe) and is abundantly present in probiotics like curd. After extraction of LAB colonies and were tested for its effect on foods rich in acrylamide content. Acrylamide formation is studied by the maillard reaction. Acrylamide is found in food products which have been subjected to very high temperatures. The application of LAB to remove many mutagens, by using the binding mechanism was assessed for acrylamide. When this acrylamide degrades it produces toxic gases like ammonia, hydrogen and carbon monoxide. Asparagine is an important precursor to acrylamide formation. So in foods containing free asparagine group with reducing sugars will form acrylamide. We used liquid chromatography to determine the presence of acrylamide in the food product. Acrylamide content in the body is responsible for various mutations at the genomic level thereby, leading to cancers like colon, breast. It also leads to neural damages and is directly linked to Alzhimers disease. This study concludes the beneficial effects of consuming probiotics and suggests a way to reduce the acrylamide formation in food products.

biochemistry