Stereospecific conversion of 1-aminocyclopropanecarboxylic Acid to ethylene by plant tissues : conversion of stereoisomers of 1-amino-2-ethylcyclopropanecarboxylic Acid to 1-butene

Inasmuch as the molecule of 1-aminocyclopropanecarboxylic acid (ACC) possesses reflective symmetry but lacks rotational symmetry, the two chemically alike methylene groups can be distinguished by a stereospecific enzyme. To determine whether ACC conversion to ethylene by plant tissues proceeds in a stereospecific fashion, the four stereoisomers of 1-amino-2-ethylcyclopropanecarboxylic acid (AEC) were administered to postclimacteric apple (Malus sylvestris Mill., var. Golden Delicious), excised preclimacteric cantaloupe (Cucumis melo L., var. reticulatis Naud cv. PMR-45), and etiolated mung bean (Vigna radiata L., Wilczek, var. Berken) hypocotyls. In each case (1R,2S)-AEC was the preferred substrate yielding 1-butene. In contrast, all AEC isomers were converted equally well to butene by chemical oxidation using NaOCl. Both ACC and AEC appear to be substrates for the same enzyme since both reactions are inhibited in parallel by N₂ or Co²⁺, both reactions are induced in parallel by excision, and when both substrates are present simultaneously each will act as an inhibitor with respect to the other. The aforementioned observations indicate that ACC is stereospecifically converted to ethylene. For AEC to be the most active precursor of 1-butene, the ethyl substituent should be trans to the carboxyl group and the pro-(S) methylene group should be unsubstituted. This observation leads to the suggestion that the enzyme interacts with amino, carboxyl, and pro-(S) methylene groups, a configuration corresponding to a l-amino acid. This view is consistent with the observation that the l-forms of alanine and methionine inhibit the conversion of ACC to ethylene more than the corresponding d-amino acids in the mung bean hypocotyl system.     

Seneca Valley Virus 3Cpro Substrate Optimization Yields Efficient Substrates for Use in Peptide-Prodrug Therapy

The oncolytic picornavirus Seneca Valley Virus (SVV-001) demonstrates anti-tumor activity in models of small cell lung cancer (SCLC), but may ultimately need to be combined with cytotoxic therapies to improve responses observed in patients. Combining SVV-001 virotherapy with a peptide prodrug activated by the viral protease 3C^pro is a novel strategy that may increase the therapeutic potential of SVV-001. Using recombinant SVV-001 3C^pro, we measured cleavage kinetics of predicted SVV-001 3C^pro substrates. An efficient substrate, L/VP4 (k_cat/K_M = 1932 ± 183 M^-1s^-1), was further optimized by a P2’ N→P substitution yielding L/VP4.1 (k_cat/K_M = 17446 ± 2203 M^-1s^-1). We also determined essential substrate amino acids by sequential N-terminal deletion and substitution of amino acids found in other picornavirus genera. A peptide corresponding to the L/VP4.1 substrate was selectively cleaved by SVV-001 3C^pro in vitro and was stable in human plasma. These data define an optimized peptide substrate for SVV-001 3C^pro, with direct implications for anti-cancer therapeutic development.     

Stereospecificity of isotopic exchange of C-α-protons of glycine catalyzed by three PLP-dependent lyases: the unusual case of tyrosine phenol-lyase

A comparative study of the kinetics and stereospecificity of isotopic exchange of the pro-2R- and pro-2S protons of glycine in ²H₂O under the action of tyrosine phenol-lyase (TPL), tryptophan indole-lyase (TIL) and methionine γ-lyase (MGL) was undertaken. The kinetics of exchange was monitored using both ¹H- and ¹³C-NMR. In the three compared lyases the stereospecificities of the main reactions with natural substrates dictate orthogonal orientation of the pro-2R proton of glycine with respect to the cofactor pyridoxal 5′-phosphate (PLP) plane. Consequently, according to Dunathan’s postulate with all the three enzymes pro-2R proton should exchange faster than does the pro-2S one. In fact the found ratios of 2R:2S reactivities are 1:20 for TPL, 108:1 for TIL, and 1,440:1 for MGL. Thus, TPL displays an unprecedented inversion of stereospecificity. A probable mechanism of the observed phenomenon is suggested, which is based on the X-ray data for the quinonoid intermediate, formed in the reaction of TPL with l-alanine. The mechanism implies different conformational changes in the active site upon binding of glycine and alanine. These changes can lead to relative stabilization of either the neutral amino group, accepting the α-proton, or the respective ammonium group, which is formed after the proton abstraction.     

Foliar application of plant nutrients and kinetin modifies growth and essential oil profile in <Emphasis Type="Italic">Rosa damascena</Emphasis> under acidic conditions

Rosa damascena Mill. is cultivated for its high-value essential oil in different parts of the world. The flower yield and the composition of essential oil of R. damascena are strongly affected by a number of factors. Nevertheless, the interactive effects of foliar application of plant nutrients and kinetin and its time of application on yield and secondary metabolites profile of R. damascena under acidic conditions are still unclear. Thus, a field experiment comprising two different times of spray and five foliar spray treatments was conducted to test the hypothesis that flowering behavior and secondary metabolites profile can be modified through proper nutrient supply at right time. The foliar spray at flower bud appearance stage (S₂) significantly (P ≤ 0.05) increased flower yield by about 10.0 % compared with the foliar application at axillary bud development stage (S₁) during both years, regardless of plant nutrients. Among the foliar spray treatments, kinetin at 0.20 g L^?1 registered about 23–39 % higher flower yield compared with the water spray control; however, remained statistically at par (P ≤ 0.05) with Ca(NO₃)₂ at 4.06 g L^?1. Moreover, the percentage of major fragrance-bearing compounds of essential oil (β-citronellol + nerol, linalool, E-geraniol, and Z-citral) was marginally increased with Ca(NO₃)₂ compared with kinetin treatment. However, the percentages of major hydrocarbons, nonadecane and heneicosane, were noticeably increased when kinetin was applied at S₁. Foliar application of kinetin and Ca(NO₃)₂ might be done to improve flower yield and essential oil content in R. damascena flowers.     

Metabolism of Proline, Glutamate, and Ornithine in Proline Mutant Root Tips of Zea mays (L.)

In excised pro_1-1 mutant and corresponding normal type roots of Zea mays L. the uptake and interconversion of [¹⁴C]proline, [¹⁴C]glutamic acid, [¹⁴C]glutamine, and [¹⁴C]ornithine and their utilization for protein synthesis was measured with the intention of finding an explanation for the proline requirement of the mutant. Uptake of these four amino acids, with the exception of proline, was the same in mutant and normal roots, but utilization differed. Higher than normal utilization rates for proline and glutamic acid were noted in mutant roots leading to increased CO₂ production, free amino acid interconversion, and protein synthesis. Proline was synthesized from either glutamic acid (or glutamine) or ornithine in both mutant and normal roots; it did not accumulate but rather was used for protein synthesis. Ornithine was not a good precursor for proline in either system, but was preferentially converted to arginine and glutamine, particularly in mutant roots. The pro_1-1 mutant was thus not deficient in its ability to make proline. Based on these findings, and on the fact that ornithine, arginine, glutamic acid and aspartic acid are elevated as free amino acids in mutant roots, it is suggested that in the pro_1-1 mutant proline catabolism prevails over proline synthesis.     

Foot and mouth disease leader protease (Lbpro): Investigation of prime side specificity allows the synthesis of a potent inhibitor

Foot and mouth disease virus expresses its genetic information as a single polyprotein that is translated from the single-stranded RNA genome. Proteinases contained within the polyprotein then generate the mature viral proteins. The leader protease (Lb^pro) performs the initial cleavage by freeing itself from the growing polypeptide chain; subsequently, Lb^pro cleaves the two homologues of the host cell protein eukaryotic initiation factor 4G (eIF4G). We showed that Lb^pro possesses specific binding sites at the non prime side from S₁ down to S₇ [Santos et al. (2009) Biochemistry, 48, 7948–7958]. Here, we demonstrate that Lb^pro has high prime side specificity at least down to the S′₅ site. Lb^pro is thus not only one of the smallest papain-like cysteine peptidases but also one of the most specific. It can still however cleave between both K↓G and G↓R pairs. We further determined the two-step irreversible inhibition (E + I ↔ EI→ E − I) kinetic parameters of two known irreversible epoxide-based inhibitors of cysteine proteinases, E64 and CA074 on Lb^pro that show for the reversible step (E + I ↔ EI) K_i = 3.4 μM and 11.6 μM, and for the irreversible step (EI→E−I) k₄ = 0.16 and 0.06 min⁻¹, respectively. Knowledge of the Lb^pro specificity led us to extend E64 by addition of the dipeptide R–P. This compound, termed E64-R-P-NH₂, irreversibly inhibited Lb^pro with a K_i = 30 nM and k₄ = 0.01 min⁻¹ and can serve as the basis for design of specific inhibitors of FMDV replication.     

Metabolomic fingerprinting using nuclear magnetic resonance and multivariate data analysis as a tool for biodiversity informatics: A case study on the classification of Rosa x damascena

Metabolomics is the comprehensive and simultaneous identification and quantification of metabolites in living cells. The term metabolome is used to describe the observable chemical profile or fingerprint of the metabolites in a whole tissue. Although being a new approach to study natural compounds, metabolomics uses traditional analytical techniques, including extraction methods, which can be followed by nuclear magnetic resonance (NMR) spectroscopy and multivariate data analysis. Although metabolomics has been successfully applied to quality control issues, the examples of its use for chemosystematics are few. Thus, the analysis of four taxa of Rosa x damascena (R. damascena Mill., R. damascenasemperflorens, R. damascenatrigintipetala and R. duchesse of Portland) was carried out by NMR spectroscopy as a tool for their classification. A principal component analysis of the ¹H NMR spectra, based on the metabolites found in organic and aqueous fractions, showed a clear similarity of the samples. In particular, the major contributions from the aqueous fraction, preliminarily considered as a biomarker of R. x damascena group, are the flavonoids kaempferol and quercetin, glycosilated with glucose and rhamnose units. Our analysis demonstrated a close chemotaxonomic correlation among the four taxa, making this method a reliable tool for chemosystematics.     

Poly(C)-Binding Protein 1, a Novel Npro-Interacting Protein Involved in Classical Swine Fever Virus Growth

N^pro is a multifunctional autoprotease unique to pestiviruses. The interacting partners of the N^pro protein of classical swine fever virus (CSFV), a swine pestivirus, have been insufficiently defined. Using a yeast two-hybrid screen, we identified poly(C)-binding protein 1 (PCBP1) as a novel interacting partner of the CSFV N^pro protein and confirmed this by coimmunoprecipitation, glutathione S-transferase (GST) pulldown, and confocal assays. Knockdown of PCBP1 by small interfering RNA suppressed CSFV growth, while overexpression of PCBP1 promoted CSFV growth. Furthermore, we showed that type I interferon was downregulated by PCBP1, as well as N^pro. Our results suggest that cellular PCBP1 positively modulates CSFV growth.     

Inhibition of growth of proline-requiring Chinese hamster ovary cells (CHO-K1) resulting from antagonism by a system amino acids

CHO-K1 requires proline for growth. Two proline-independent revertants were isolated—K1-J and K1-6. CHO-K1 pro^? is much more sensitive than the pro⁺ cell lines to inhibition of growth by addition to the medium of amino acids and amino acid analogues that are transported through the A system. In contrast, pro⁺ cells are as sensitive as, or in some cases slightly more sensitive than, pro^? cells to glycine, basic amino acids, and to amino acids that are mainly transported by the L system. The A system analogue α(methylamino) isobutyric acid (MAIB) in low concentrations reacts competitively with proline to regulate the growth of pro^? cells, yielding a K_i for MAIB of 0.56 mM. CHO-K1 and K1-6 transport proline at the same initial rate and are equally sensitive to the inhibition of proline transport by alanine. Alanine and MAIB inhibit proline transport strongly and similarly in CHO-K1. Thus although these compounds inhibit the transport of proline by both cell types to the same extent, pro⁺ cells are immune to the effect of this starvation since they are able to synthesize their own proline. We also describe a secondary inhibition caused by high A system amino acid concentrations that affects both pro^? and pro⁺ cells.     

Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression

Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human pathogen that was first isolated in 2012. MERS-CoV replication depends in part on a virus-encoded papain-like protease (PL^pro) that cleaves the viral replicase polyproteins at three sites releasing non-structural protein 1 (nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV PL^pro was recently shown to be a deubiquitinating enzyme (DUB) and to possess deISGylating activity, as previously reported for other coronaviral PL^pro domains, including that of severe acute respiratory syndrome coronavirus. These activities have been suggested to suppress host antiviral responses during infection. To understand the molecular basis for ubiquitin (Ub) recognition and deconjugation by MERS-CoV PL^pro, we determined its crystal structure in complex with Ub. Guided by this structure, mutations were introduced into PL^pro to specifically disrupt Ub binding without affecting viral polyprotein cleavage, as determined using an in trans nsp3↓4 cleavage assay. Having developed a strategy to selectively disable PL^pro DUB activity, we were able to specifically examine the effects of this activity on the innate immune response. Whereas the wild-type PL^pro domain was found to suppress IFN-β promoter activation, PL^pro variants specifically lacking DUB activity were no longer able to do so. These findings directly implicate the DUB function of PL^pro, and not its proteolytic activity per se, in the inhibition of IFN-β promoter activity. The ability to decouple the DUB activity of PL^pro from its role in viral polyprotein processing now provides an approach to further dissect the role(s) of PL^pro as a viral DUB during MERS-CoV infection.     

The stereochemistry of hydroxylation of the carotenoid lutein in Calendula officinalis

Excised, opening inflorescences of Calendula officinalis incorporated (3RS, 5R)- and (3RS, 5S)-[2-¹⁴C,5-³H₁]mevalonates into the carotenoid fraction. The ¹⁴C:³H ratios of lutein isolated from these tissues showed the hydrogen atom at C-3 of the β-ring is derived from the 5-pro-S position of mevalonate, while that at C-3 of the ε-ring is derived from the 5-pro-R position of mevalonate. Oxidation of lutein to monoketolutein showed that both hydrogen atoms at the C-15,15′ central double bond are derived from the 5-pro-R position of mevalonate.     

Investigation of changes in protein stability and substrate affinity of 3CL-protease of SARS-CoV-2 caused by mutations

3CL^pro of SARS-CoV-2 is one of the enzymes required for the replication process of the virus responsible for the COVID-19 pandemic. In this study, changes in protein stability and substrate affinity caused by mutations were investigated to stir the development of potent inhibitors. Sequence data of samples were obtained from the NCBI Virus database. Mutation analyses were performed with RDP4 and MegaX. 3CL^pro tertiary models were created using Robetta. Molecular docking for peptidomimetic substrate and inhibitor ligand was done with Autodock v4.2 and Haddock v2.4. Protein stability analysis was performed using mCSM stability and DynaMut2. Twenty-four missense mutations in 3CL^pro were identified in this study. Changes in the 3CL^pro structure induced by the mutations Met49Thr, Leu167Ser, and Val202Ala resulted in significant levels of instability (-2.029,-2.612,-2.177 kcal.mol^-1, respectively). The lowest interaction energy for substrate was -58.7 kcal.mol^-1 and -62.6 kcal.mol^-1 in wild-type and mutant, respectively. The lowest docking energy for ligand was -6.19 and -9.52 kcal.mol^-1 for wild-type and mutant, respectively. This study reports for the first time that mutations cause increased substrate affinity of 3CL^pro from SARS-CoV-2. This research provides important data for the development of potent peptidomimetic inhibitors for the treatment of COVID-19. Keywords: 3CL-protease, mutation analysis, protein stability, SARS-CoV-2 genome, substrate affinity     

Maturation Mechanism of Severe Acute Respiratory Syndrome (SARS) Coronavirus 3C-like Proteinase

The 3C-like proteinase (3CL^pro) of the severe acute respiratory syndrome (SARS) coronavirus plays a vital role in virus maturation and is proposed to be a key target for drug design against SARS. Various in vitro studies revealed that only the dimer of the matured 3CL^pro is active. However, as the internally encoded 3CL^pro gets matured from the replicase polyprotein by autolytic cleavage at both the N-terminal and the C-terminal flanking sites, it is unclear whether the polyprotein also needs to dimerize first for its autocleavage reaction. We constructed a large protein containing the cyan fluorescent protein (C), the N-terminal flanking substrate peptide of SARS 3CL^pro (XX), SARS 3CL^pro (3CLP), and the yellow fluorescent protein (Y) to study the autoprocessing of 3CL^pro using fluorescence resonance energy transfer. In contrast to the matured 3CL^pro, the polyprotein, as well as the one-step digested product, 3CLP-Y-His, were shown to be monomeric in gel filtration and analytic ultracentrifuge analysis. However, dimers can still be induced and detected when incubating these large proteins with a substrate analog compound in both chemical cross-linking experiments and analytic ultracentrifuge analysis. We also measured enzyme activity under different enzyme concentrations and found a clear tendency of substrate-induced dimer formation. Based on these discoveries, we conclude that substrate-induced dimerization is essential for the activity of SARS-3CL^pro in the polyprotein, and a modified model for the 3CL^pro maturation process was proposed. As many viral proteases undergo a similar maturation process, this model might be generally applicable.     

Dieckol,a SARS-CoV 3CLpro inhibitor,isolated from the edible brown algae Ecklonia cava

SARS-CoV 3CL^pro plays an important role in viral replication. In this study, we performed a biological evaluation on nine phlorotannins isolated from the edible brown algae Ecklonia cava. The nine isolated phlorotannins (1–9), except phloroglucinol (1), possessed SARS-CoV 3CL^pro inhibitory activities in a dose-dependently and competitive manner. Of these phlorotannins (1–9), two eckol groups with a diphenyl ether linked dieckol (8) showed the most potent SARS-CoV 3CL^pro trans/cis-cleavage inhibitory effects (IC₅₀s = 2.7 and 68.1 μM, respectively). This is the first report of a (8) phlorotannin chemotype significantly blocking the cleavage of SARS-CoV 3CL^pro in a cell-based assay with no toxicity. Furthermore, dieckol (8) exhibited a high association rate in the SPR sensorgram and formed extremely strong hydrogen bonds to the catalytic dyad (Cys145 and His41) of the SARS-CoV 3CL^pro.     

Functional binding of hexanucleotides to 3C protease of hepatitis A virus

Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C^pro). Inhibition assays in vitro identified the hexanucleotide 5′-GGGGGT-3′ (G₅T) as a 3C^pro protease inhibitor. Using ¹H NMR spectroscopy, G₅T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of ¹H, ¹⁵N-HSQC experiments the binding site for G₅T was located to the C-terminal β-barrel of HAV 3C^pro. Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G₅T-binding site, nor does G₅T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid–protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance.     

Seeds of Arabidopsis plants expressing dominant-negative AtSKD1 under control of the GL2 promoter show a transparent testa phenotype and a mucilage defect

We have recently shown that overexpression of dominant-negative AtSKD1 versions under control of the trichome and non-root-hair-cell specific GL2 promoter (GL2_pro) blocks trafficking of soluble cargo to the vacuole, resulting in its fragmentation and ultimately cell death. GL2_pro is also active in the Arabidopsis seeds. When we inspected seeds of the dominant-negative AtSKD1 variants we found two phenotypes. The seeds display a transparent testa phenotype caused by a lack of proanthocyanidin (PA) and do not possess seed coat mucilage. Both phenotypes could be connected by cell death induced by the overexpression of dominant-negative AtSKD1.Key words: VPS4, ESCRT, plant, Arabidopsis, SKD1, ATPase, MVB, proanthocyanidin, transparent testa, mucilage, tannin, seed coat, AtSKD1AAA ATPases are important regulators of a plethora of cellular functions such as peroxisome biogenesis, vesicle-mediated transport, control of cell divisions and gene expression. This variety is based on a common mechanism, the energy dependent unfolding, remodeling and disassembly of proteins and protein complexes.¹Mammalian SKD1 and its yeast homolog VPS4 are AAA ATPases involved in the sorting of monoubiquitylated trans-membrane cargo to the lysosome/vacuole by dismantling the members of the endosomal sorting complex required for transport (ESCRT) complexes from the endosomal membrane.² The Arabidopsis SKD1 homolog, AtSKD1, has been characterized recently and has been shown to be an ortholog of SKD1/Vps4.^3,4 Mutations for all three ATPases are known that alone or in combination render them dominant-negative.^3–6 Overexpression of dominant-negative AtSKD1 is, however, lethal for Arabidopsis plants. Therefore, we have used the trichome and non-root-hair-cell-specific GL2_pro promoter to address the function of AtSKD1 in planta. Cells that express the dominant-negative versions show multiple nuclei, fragmented vacuoles and ultimately die. These phenotypes are most likely due to a block in vacuolar trafficking of soluble cargo that is instead secreted.⁴GL2_pro is also active in the coat of developing Arabidopsis seeds. We therefore inspected seeds of lines overexpressing dominant-negative and wild-type AtSKD1.     

Enterovirus 71 3C Protease Cleaves a Novel Target CstF-64 and Inhibits Cellular Polyadenylation

Identification of novel cellular proteins as substrates to viral proteases would provide a new insight into the mechanism of cell–virus interplay. Eight nuclear proteins as potential targets for enterovirus 71 (EV71) 3C protease (3C^pro) cleavages were identified by 2D electrophoresis and MALDI-TOF analysis. Of these proteins, CstF-64, which is a critical factor for 3′ pre-mRNA processing in a cell nucleus, was selected for further study. A time-course study to monitor the expression levels of CstF-64 in EV71-infected cells also revealed that the reduction of CstF-64 during virus infection was correlated with the production of viral 3C^pro. CstF-64 was cleaved in vitro by 3C^pro but neither by mutant 3C^pro (in which the catalytic site was inactivated) nor by another EV71 protease 2A^pro. Serial mutagenesis was performed in CstF-64, revealing that the 3C^pro cleavage sites are located at position 251 in the N-terminal P/G-rich domain and at multiple positions close to the C-terminus of CstF-64 (around position 500). An accumulation of unprocessed pre-mRNA and the depression of mature mRNA were observed in EV71-infected cells. An in vitro assay revealed the inhibition of the 3′-end pre-mRNA processing and polyadenylation in 3C^pro-treated nuclear extract, and this impairment was rescued by adding purified recombinant CstF-64 protein. In summing up the above results, we suggest that 3C^pro cleavage inactivates CstF-64 and impairs the host cell polyadenylation in vitro, as well as in virus-infected cells. This finding is, to our knowledge, the first to demonstrate that a picornavirus protein affects the polyadenylation of host mRNA.     

Steric course of the tyrosine ammonia-lyase reaction

The tyrosine ammonia-lyase reaction proceeds with loss of the pro-3S and retention of the pro-3R hydrogen from the tyrosine side chain and thus involves anti-periplanar elimination of the elements of ammonia.