An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

Background: Mutagenesis plays an essential role in molecular biology and biochemistry. It has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. The ability to quickly and specifically mutate a residue(s) in protein is important for mechanistic and functional studies. Although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable. Results: We have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the QuikChange (TM) site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. This modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized DNA to be used as the template in subsequent amplification cycles. These two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis. Conclusion: Our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard QuikChange (TM). Furthermore the new protocol required significantly less parental DNA which facilitated the DpnI digestion after the PCR amplification and enhanced the overall efficiency and reliability. Using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. The results demonstrated that this new protocol imposed no additional reagent costs (beyond basic QuikChange T) but increased the overall success rates.Publisher PDFPeer reviewe

A model for 3-methyladenine recognition by 3-methyladenine DNA glycosylase I (TAG) from Staphylococcus aureus

The structure of 3-methyladenine DNA glycosylase I in complex with 3-methyladenine is reported

The association between quality of life and subjective wellbeing among older adults based on canonical correlation analysis

IntroductionThe study explored the relationship between subjective well-being and the quality of life among older adults. It highlights the importance of understanding how these factors are interconnected in the context of an aging population.MethodsDescriptive statistics were used to analyze the scores of general demographic characteristics, subjective wellbeing and quality of life. Simple correlation analysis and canonical correlation analysis were employed to analyze the relationship between subjective wellbeing and quality of life among older adults.ResultsData from 892 older adults were collected. Canonical correlation analysis revealed four pairs of canonical variables, with the first four pairs of canonical correlation coefficients all being statistically significant (0.695, 0.179, 0.147, 0.121) (p < 0.05), and the first pair of canonical variables explaining 93.03% of the information content. From the canonical loading coefficients, Vitality and mental health contributed the most to the quality of life (U1) canonical variable. The canonical variable V1, which corresponded to subjective wellbeing, was reflected by a combination of positive affect, negative affect, positive experience and negative experience. X1 (physical functioning), X2 (role-physical), X3 (bodily pain), X4 (general health), X5 (vitality), X6 (social functioning), X7 (role-emotional) and X8 (mental health) were positively correlated with Y1 (positive affect) and Y3 (positive experience), negatively correlated with Y2 (negative affect) and Y4 (negative experience). Cross-loadings revealed that physical functioning, bodily pain, general health, vitality, social functioning and mental health were the main factors reflecting the subjective wellbeing of older adults.DiscussionAs quality of life among older adults was highly correlated with subjective wellbeing, appropriate measures should be taken to account for individual characteristics of older adults, and various factors should be integrated to improve their subjective wellbeing

Uncovering the chemistry of C-C bond formation in C-nucleoside biosynthesis : crystal structure of a C -glycoside synthase/PRPP complex

Authors thank the Diamond Light Source for beam time allocation and beam line staff for assistance with data collection. Funding for these studies was provided by BBSRC (BB/T006161/1 & BB/T006188/1 to J. H. N. & N. G. J. R., respectively), and the National Institutes of Health (R01 GM129793 to V. d. C.-L.)The enzyme ForT catalyzes C–C bond formation between 5′-phosphoribosyl-1′-pyrophosphate (PRPP) and 4-amino-1H-pyrazole-3,5-dicarboxylate to make a key intermediate in the biosynthesis of formycin A 5′-phosphate by Streptomyces kaniharaensis. We report the 2.5 Å resolution structure of the ForT/PRPP complex and locate active site residues critical for PRPP recognition and catalysis.Publisher PDFPeer reviewe

Pironetin reacts covalently with cysteine-316 of α-tubulin to destabilize microtubule

This work was funded by grants to C.L. from the National Natural Science Foundation of China (81373283 and U1402222). J.H.N. is supported as an award holder of Chinese National Thousand Talents Program, Wellcome Trust Senior Investigator Award (WT100209MA) and Royal Society Wolfson Merit Award. X.Z. is supported by Sichuan Province Thousand Talents Scheme in China and the State Key Program of National Natural Science of China (21534008).Molecules which alter the normal dynamics of microtubule assembly and disassembly include many anticancer drugs in clinical use. So far all such therapeutics target β-tubulin and structural biology has explained the basis of their action and permitted design of new drugs. However by shifting the profile of β-tubulin isoforms, cancer cells become resistant to treatment. Compounds that bind to α-tubulin are less well characterized and unexploited. The natural product pironetin is known to bind to α-tubulin and is a potent inhibitor of microtubule polymerization. Previous reports had identified that pironetin reacts with lysine-352 residue however analogues designed on this model had much lower potency which was difficult to explain, hindering further development. We report crystallographic and mass spectrometric data that reveal that pironetin forms a covalent bond to cysteine-316 in α-tubulin via a Michael addition reaction. These data provide a basis for the rational design of α-tubulin targeting chemotherapeutics.Publisher PDFPeer reviewe

Structure and mechanism of the CMR complex for CRISPR-Mediated antiviral immunity

The prokaryotic clusters of regularly interspaced palindromic repeats (CRISPR) system utilizes genomically encoded CRISPR RNA (crRNA), derived from invading viruses and incorporated into ribonucleoprotein complexes with CRISPR-associated (CAS) proteins, to target and degrade viral DNA or RNA on subsequent infection. RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse "payload" of targeting crRNA. The crystal structure of Cmr7 and low-resolution structure of the complex are presented. S. solfataricus CMR cleaves RNA targets in an endo-nucleolytic reaction at UA dinucleotides. This activity is dependent on the 8 nt repeat-derived 5' sequence in the crRNA, but not on the presence of a proto-spacer-associated motif (PAM) in the target. Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets.Publisher PDFPeer reviewe

PMP–diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis

We thank Mr ThomasWilliams for mass spectrometry, acquired using LCMS equipment funded by the EPSRC (EP/L027240/1). JHN is funded by the ERC (TNT-NCB 339367), NGJR by the BBSRC (BB/P018017/1) and VdCL by NIH (R01GM129793).ForI is a PLP-dependent enzyme from the biosynthetic pathway of the C-nucleoside antibiotic formycin. Cycloserine is thought to inhibit PLP-dependent enzymes by irreversibly forming a PMP–isoxazole. We now report that ForI forms novel PMP–diketopiperazine derivatives following incubation with both d and l cycloserine. This unexpected result suggests chemical diversity in the chemistry of cycloserine inhibition.Publisher PDFPeer reviewe

Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance

The ardA gene, found in many prokaryotes including important pathogenic species, allows associated mobile genetic elements to evade the ubiquitous Type I DNA restriction systems and thereby assist the spread of resistance genes in bacterial populations. As such, ardA contributes to a major healthcare problem. We have solved the structure of the ArdA protein from the conjugative transposon Tn916 and find that it has a novel extremely elongated curved cylindrical structure with defined helical grooves. The high density of aspartate and glutamate residues on the surface follow a helical pattern and the whole protein mimics a 42-base pair stretch of B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of this dimeric structure comprises three alpha–beta domains, each with a different fold. These domains have the same fold as previously determined proteins possessing entirely different functions. This DNA mimicry explains how ArdA can bind and inhibit the Type I restriction enzymes and we demonstrate that 6 different ardA from pathogenic bacteria can function in Escherichia coli hosting a range of different Type I restriction systems

Crystallization of Ranasmurfin, a blue-coloured protein from Polypedates leucomystax

A novel blue protein from frog nests has been crystallized

The lipid linked oligosaccharide polymerase Wzy and its regulating co-polymerase, Wzz, from enterobacterial common antigen biosynthesis form a complex

The enterobacterial common antigen (ECA) is a carbohydrate polymer that is associated with the cell envelope in the Enterobacteriaceae. ECA contains a repeating trisaccharide which is polymerized by WzyE, a member of the Wzy membrane protein polymerase superfamily. WzyE activity is regulated by a membrane protein polysaccharide co-polymerase, WzzE. Förster resonance energy transfer experiments demonstrate that WzyE and WzzE from Pectobacterium atrosepticum form a complex in vivo, and immunoblotting and cryo-electron microscopy (cryo-EM) analysis confirm a defined stoichiometry of approximately eight WzzE to one WzyE. Low-resolution cryo-EM reconstructions of the complex, aided by an antibody recognizing the C-terminus of WzyE, reveals WzyE sits in the central membrane lumen formed by the octameric arrangement of the transmembrane helices of WzzE. The pairing of Wzy and Wzz is found in polymerization systems for other bacterial polymers, including lipopolysaccharide O-antigens and capsular polysaccharides. The data provide new structural insight into a conserved mechanism for regulating polysaccharide chain length in bacteria