Double agent indole-3-acetic acid: mechanistic analysis of indole-3-acetaldehyde dehydrogenase AldA that synthesizes IAA,an auxin that aids bacterial virulence

The large diversity of organisms inhabiting various environmental niches on our planet are engaged in a lively exchange of biomolecules, including nutrients, hormones, and vitamins. In a quest to survive, organisms that we define as pathogens employ innovative methods to extract valuable resources from their host leading to an infection. One such instance is where plant-associated bacterial pathogens synthesize and deploy hormones or their molecular mimics to manipulate the physiology of the host plant. This commentary describes one such specific example—the mechanism of the enzyme AldA, an aldehyde dehydrogenase (ALDH) from the bacterial plant pathogen Pseudomonas syringae which produces the plant auxin hormone indole-3-acetic acid (IAA) by oxidizing the substrate indole-3-acetaldehyde (IAAld) using the cofactor nicotinamide adenine dinucleotide (NAD⁺) (Bioscience Reports (2020) 40(12), https://doi.org/10.1042/BSR20202959). Using mutagenesis, enzyme kinetics, and structural analysis, Zhang et al. established that the progress of the reaction hinges on the formation of two distinct conformations of NAD(H) during the reaction course. Additionally, a key mutation in the AldA active site ‘aromatic box’ changes the enzyme’s preference for an aromatic substrate to an aliphatic one. Our commentary concludes that such molecular level investigations help to establish the nature of the dynamics of NAD(H) in ALDH-catalyzed reactions, and further show that the key active site residues control substrate specificity. We also contemplate that insights from the present study can be used to engineer novel ALDH enzymes for environmental, health, and industrial applications.     

Identification and organization of genes for diutan polysaccharide synthesis from <Emphasis Type="Italic">Sphingomonas</Emphasis> sp. ATCC 53159

A cluster of genes for diutan polysaccharide synthesis was isolated from a library of Sphingomonas sp. ATCC 53159 genomic DNA by complementation of glucosyl-isoprenylphosphate transferase-deficient mutants of Sphingomonas elodea ATCC 31461 (producing gellan) and Xanthomonas campestris (producing xanthan). The synthesis of polysaccharide in these strains shares a common first step, transfer of glucose-1-phosphate from UDP-glucose to the isoprenylphosphate lipid. The cluster of 24 genes was compared to genes for biosynthesis of gellan, and S-88 sphingan from Sphingomonas sp. ATCC 31554. Diutan, gellan and S-88 sphingan have a common four-sugar backbone but different side chains, one rhamnose for S-88 sphingan, a two-rhamnose side chain for diutan and no side chain for gellan. The genes for biosynthesis of diutan, gellan and S-88 sphingan were similar in general organization but differed in location of some genes, in particular, dpsG (putative polymerase), dpsR (putative lyase) and dpsS (putative repeat unit transporter). An unidentified reading frame urf31, present in the gene clusters for diutan and S-88 sphingan but not gellan, had similarity to glycosyl transferase group 2 proteins, and was detrimental when cloned in Sphingomonas elodea producing gellan that lacks a side chain, but not in Sphingomonas ATCC 31554 producing S-88 sphingan with a rhamnose side chain. Gene urf31 could possibly encode a side-chain rhamnosyl transferase. Another gene urf31.4 was unique to the diutan gene cluster. A plasmid containing 20 of the 24 genes resulted in a slight increase in the amount of diutan produced, but a significant increase in the rheological properties of diutan.     

First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina

This is the first structural evidence of recognition of mRNA cap structures by a ribosome inactivating protein. It is well known that a unique cap structure is formed at the 5′ end of mRNA for carrying out various processes including mRNA maturation, translation initiation, and RNA turnover. The binding studies and crystal structure determinations of type 1 ribosome inactivating protein (RIP‐1) from Momordica balsamina (MbRIP‐1) were carried out with mRNA cap structures including (i) N7‐methyl guanine (m7G), (ii) N7‐methyl guanosine diphosphate (m7GDP), and (iii) N7‐methyl guanosine triphosphate (m7GTP). These compounds showed affinities to MbRIP‐1 at nanomolar concentrations. The structure determinations of the complexes of MbRIP‐1 with m7G, m7GDP, and m7GTP at 2.65, 1.77, and 1.75 Å resolutions revealed that all the three compounds bound to MbRIP‐1 in the substrate binding site at the positions which are slightly shifted towards Glu85 as compared to those of rRNA substrates. In this position, Glu85 forms several hydrogen bonds with guanine moiety while N‐7 methyl group forms van der Waals contacts. However, the guanine rings are poorly stacked in these complexes. Thus, the mode of binding by MbRIP‐1 to mRNA cap structures is different which results in the inhibition of depurination. Since some viruses are known to exploit the capping property of the host, this action of MbRIP‐1 may have implications for the antiviral activity of this protein in vivo. The understanding of the mode of binding of MbRIP‐1 to cap structures may also assist in the design of anti‐viral agents. Proteins 2012. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.)

With the aim of developing additional genomic resources in safflower, a set of 41,011 ESTs of safflower were mined for the presence of SSRs. 18,773 SSR containing ESTs (SSR-ESTs) were identified and were analyzed to remove redundant sequences leading to identification of 8,810 non-redundant SSR-ESTs (categorized into 6104 singletons and 2,706 contigs) having 13,085 non-redundant SSRs. The average number of non-redundant SSRs per EST was 0.32 and they predominantly consisted of dinucleotide (57.7 %), and trinucleotide (37.7 %) repeat motifs. 500 primer pairs were designed for the non-redundant EST-SSRs of which, 151 were tested. 60 markers which gave robust amplicons, were validated in a set of 19 Carthamus lines. A subset of EST-SSR markers, having average polymorphism information content (PIC) ≥0.4 could precisely elucidate the pedigree relatedness among these lines. Further, these markers exhibited high cross-species transferability to five other wild species of Carthamus. The markers reported here would be a valuable addition to existing safflower marker resources aiding in hastening its improvement.     

Three phase liquid phase microextraction of phenylacetic acid and phenylpropionic acid from biological fluids

Three phase liquid phase microextraction (three phase LPME) technique coupled with HPLC-UV has been applied as a sensitive and efficient sample preparation method to determine phenylacetic acid (PAA) as a biomarker of depressive disorders and phenylpropionic acid (PPA) in biological fluids. The compounds were extracted from 3.0 ml aqueous solution with the adjustment of pH at a fixed value in the range of 2.0-3.5 (donor solution) into an organic phase (1-hexanol) layered on the surface of the donor solution and finally back-extracted into 4.0 microl of the acceptor microdrop (pH 11.1) located at the end of the microsyringe needle. After a prescribed back-extraction time, the acceptor microdrop was withdrawn into the microsyringe and then directly injected into the HPLC system. In order to achieve maximum extraction efficiency, different parameters affecting the extraction conditions were optimized. At the optimum conditions (donor solution: 2.3M Na(2)SO(4), pH 2.0-3.5; organic membrane: 95 microl of 1-hexanol; acceptor solution: 4.0 microl of 0.1M NH(3)/NH(4)(+) with pH 11.1; donor solution temperature: 45-50 degrees C; extraction time: 20 min and back-extraction time: 12 min), up to 110-fold enrichment factor was obtained. The calibration curve for these analytes was linear in the range of 1-5000 microg/l with r(2)>0.998. The intraday and interday RSD% were below 6.5% and the limits of detection (LODs) for both analytes were 0.2 microg/l (based on S/N=3). The proposed technique is a low cost, simple and sensitive method with highly clean-up effect. Finally, this technique was successfully utilized for the detection of target analytes in human urine, serum and plasma.     

Design,synthesis and biological evaluation of 2-(3,4-dimethoxyphenyl)-6 (1,2,3,6-tetrahydropyridin-4-yl)imidazo[1,2-a]pyridine analogues as antiproliferative agents

Two series of forty five novel 2-(3,4-dimethoxyphenyl)-6-(1,2,3,6-tetrahydropyridin-4-yl) imidazo[1,2-a]pyridine analogues (IPA 1–22, IPS 1–22 and IP-NH) have been designed, synthesized and structures confirmed by ¹H NMR, ¹³C NMR, mass spectrometry. Furthermore, single crystal was developed for IPS-13. All the final derived conjugates were evaluated for their in vitro antiproliferative activity against a panel of diverse cancer cell lines viz., A549 (lung cancer), HeLa (cervical cancer), B16F10 (melanoma) and found to show potent anticancer activity on the tested cell lines. Many of them showed the IC₅₀ values in the range 2.0–20.0 µM. The most active compounds (IPA 5,6,8,9,12,16,17,19 and IPS 7,8,9,22) from IPA and IPS series were screened to determine their cytotoxicity on HEK-293 (human embryonic kidney) normal cell line and were found to be nontoxic to normal human cells. The molecular interactions of the derivatised conjugates were also supported by molecular docking simulations. These derivatives may serve as lead structures for development of novel potential anticancer drug candidates.     

Technical issues in using robots to reproduce joint specific gait

Reproduction of the in vivo motions of joints has become possible with improvements in robot technology and in vivo measuring techniques. A motion analysis system has been used to measure the motions of the tibia and femur of the ovine stifle joint during normal gait. These in vivo motions are then reproduced with a parallel robot. To ensure that the motion of the joint is accurately reproduced and that the resulting data are reliable, the testing frame, the data acquisition system, and the effects of limitations of the testing platform need to be considered. Of the latter, the stiffness of the robot and the ability of the control system to process sequential points on the path of motion in a timely fashion for repeatable path accuracy are of particular importance. Use of the system developed will lead to a better understanding of the mechanical environment of joints and ligaments in vivo.     

The quality of reporting of RCTs used within a postoperative pain management meta-analysis, using the CONSORT statement

Background

Randomized controlled trials (RCTs) are routinely used in systematic reviews and meta-analyses that help inform healthcare and policy decision making. The proper reporting of RCTs is important because it acts as a proxy for health care providers and researchers to appraise the quality of the methodology, conduct and analysis of an RCT. The aims of this study are to analyse the overall quality of reporting in 23 RCTs that were used in a meta-analysis by assessing 3 key methodological items, and to determine factors associated with high quality of reporting. It is hypothesized that studies with larger sample sizes, that have funding reported, that are published in journals with a higher impact factor and that are in journals that have adopted or endorsed the CONSORT statement will be associated with better overall quality of reporting and reporting of key methodological items.

Methods

We systematically reviewed RCTs used within an anesthesiology related post-operative pain management meta-analysis. We included all of the 23 RCTs used, all of which were parallel design that addressed the use of femoral nerve block in improving outcomes after total knee arthroplasty. Data abstraction was done independently by two reviewers. The two main outcomes were: 1) 15 point overall quality of reporting score (OQRS) based on the Consolidated Standards for Reporting Trials (CONSORT) and 2) 3 point key methodological item score (KMIS) based on allocation concealment, blinding and intention-to-treat analysis.

Results

Twenty-three RCTs were included. The median OQRS was 9.0 (Interquartile Range?=?3). A multivariable regression analysis did not show any significant association between OQRS or KMIS and our four predictor variables hypothesized to improve reporting. The direction and magnitude of our results when compared to similar studies suggest that the sample size and impact factor are associated with improved key methodological item reporting.

Conclusions

The quality of reporting of RCTs used within an anesthesia related meta-analysis is poor to moderate. The information gained from this study should be used by journals to register the urgency for RCTs to be clear and transparent in reporting to help make literature accessible and comparable.     

Structural studies on molecular interactions between camel peptidoglycan recognition protein, CPGRP-S, and peptidoglycan moieties N-acetylglucosamine and N-acetylmuramic acid

Peptidoglycan (PGN) consists of repeating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), which are cross-linked by short peptides. It is well known that PGN forms a major cell wall component of bacteria making it an important ligand for the recognition by peptidoglycan recognition proteins (PGRPs) of the host. The binding studies showed that PGN, GlcNAc, and MurNAc bind to camel PGRP-S (CPGRP-S) with affinities corresponding to dissociation constants of 1.3 × 10(-9), 2.6 × 10(-7), and 1.8 × 10(-7) M, respectively. The crystal structure determinations of the complexes of CPGRP-S with GlcNAc and MurNAc showed that the structures consist of four crystallographically independent molecules, A, B, C, and D, in the asymmetric unit that exists as A-B and C-D units of two neighboring linear polymers. The structure determinations showed that compounds GlcNAc and MurNAc bound to CPGRP-S at the same subsite in molecule C. Both GlcNAc and MurNAc form several hydrogen bonds and extensive hydrophobic interactions with protein atoms, indicating the specific nature of their bindings. Flow cytometric studies showed that PGN enhanced the secretions of TNF-α and IL-6 from human peripheral blood mononuclear cells. The introduction of CPGRP-S to the PGN-challenged cultured peripheral blood mononuclear cells reduced the expressions of proinflammatory cytokines, TNF-α and IL-6. This showed that CPGRP-S inhibited PGN-induced production of proinflammatory cytokines and down-regulated macrophage-mediated inflammation, indicating its potential applications as an antibacterial agent.     

Structural modification and aggregation of mucin by chromium(III) complexes

Metal ions binding to proteins regulate the functions of proteins and may also lead to structural changes. In this communication we demonstrate the interaction and subsequent conformational changes induced in pig gastric mucin (PGM) upon binding to certain chromium(III) complexes like, [Cr(salen)(H(2)O)(2)](ClO(4)) (1), [Cr(en)(3)]Cl(3) (2) and [Cr(EDTA)(H(2)O)]Na (3) which vary in charge and ionic character. Complexes 1 and 3 have been shown to interact coordinately with PGM whereas complex 2 binds through electrostatic interaction and hydrogen bonding. Steady state fluorescence experiment reveals that at lower concentration of complex 2 there is partial quenching of the tyrosine emission, whereas at higher concentration of the complex the emission intensity is enhanced. On the other hand with complexes 1 and 3 a decrease in fluorescence intensity was observed. PGM viscosity was found to decrease in the presence of complex 1 and 3 due to the formation of flexible fibres through coordinate interaction. Complex 2 was found to facilitate metal induced intertangling of PGM fibres which tends to stabilize the interaction and leads to sol-gel transition with subsequent increase in viscosity. A significant change in CD spectrum of PGM was observed in the presence of complex 2, where random coil spectrum became typical of a alpha-helical structure with 80% alpha helix content. In the case of complexes 1 and 3 only minor changes in the amplitude of the spectrum were observed. Histochemical analysis supports the contention that complex 2 favors the oligomerisation of PGM and leads to the formation of aggregated mass of macromolecules.