Efficient protein depletion by genetically controlled deprotection of a dormant N‐degron

Methods that allow for the manipulation of genes or their products have been highly fruitful for biomedical research. Here, we describe a method that allows the control of protein abundance by a genetically encoded regulatory system. We developed a dormant N‐degron that can be attached to the N‐terminus of a protein of interest. Upon expression of a site‐specific protease, the dormant N‐degron becomes deprotected. The N‐degron then targets itself and the attached protein for rapid proteasomal degradation through the N‐end rule pathway. We use an optimized tobacco etch virus (TEV) protease variant combined with selective target binding to achieve complete and rapid deprotection of the N‐degron‐tagged proteins. This method, termed TEV protease induced protein inactivation (TIPI) of TIPI‐degron (TDeg) modified target proteins is fast, reversible, and applicable to a broad range of proteins. TIPI of yeast proteins essential for vegetative growth causes phenotypes that are close to deletion mutants. The features of the TIPI system make it a versatile tool to study protein function in eukaryotes and to create new modules for synthetic or systems biology.     

Expression and recovery of biologically active recombinant Apolipoprotein AIMilano from transgenic safflower (Carthamus tinctorius) seeds

Apolipoprotein AI Milano (ApoAI_Milano) was expressed as a fusion protein in transgenic safflower seeds. High levels of expression corresponding to 7 g of ApoAI_Milano per kilogram of seed have been identified in a line selected for commercialization. The ApoAI_Milano fusion protein was extracted from seed using an oilbody‐based process and matured in vitro prior to final purification. This yielded a Des‐1,2‐ApoAI_Milano product which was confirmed by biochemical characterization including immunoreactivity against ApoAI antibodies, isoelectric point, N‐terminal sequencing and electrospray mass spectrometry. Purified Des‐1,2‐ApoAI_Milano readily associated with dimyristoylphosphatidylcholine in clearance assays comparable to Human ApoAI. Its biological activity was assessed by cholesterol efflux assays using Des‐1,2‐ApoAI_Milano:1‐palmitoyl‐2‐oleoyl phosphatidylcholine complexes in vitro and in vivo. This study has established that high levels of biologically functional ApoAI_Milano can be produced using a plant‐based expression system.     

Integrative analysis of genome‐wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids

Polyploidization, as a significant evolution force, has been considered to facilitate plant diversity. The expression levels of lncRNAs and how they control the expression of protein‐coding genes in allopolyploids remain largely unknown. In this study, lncRNA expression profiles were compared between Brassica hexaploid and its parents using a high‐throughput sequencing approach. A total of 2,725, 1,672, and 2,810 lncRNAs were discovered in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. It was also discovered that 725 lncRNAs were differentially expressed between Brassica hexaploid and its parents, and 379 lncRNAs were nonadditively expressed in this hexaploid. LncRNAs have multiple expression patterns between Brassica hexaploid and its parents and show paternal parent‐biased expression. These lncRNAs were found to implement regulatory functions directly in the long‐chain form, and acted as precursors or targets of miRNAs. According to the prediction of the targets of differentially expressed lncRNAs, 109 lncRNAs were annotated, and their target genes were involved in the metabolic process, pigmentation, reproduction, exposure to stimulus, biological regulation, and so on. Compared with the paternal parent, differentially expressed lncRNAs between Brassica hexaploid and its maternal parent participated in more regulation pathways. Additionally, 61 lncRNAs were identified as putative targets of known miRNAs, and 15 other lncRNAs worked as precursors of miRNAs. Some conservative motifs of lncRNAs from different groups were detected, which indicated that these motifs could be responsible for their regulatory roles. Our findings may provide a reference for the further study of the function and action mechanisms of lncRNAs during plant evolution.     

Monitoring enzyme expression of a branched respiratory chain of <Emphasis Type="Italic">corynebacterium glutamicum</Emphasis> using an EGFP reporter gene

To investigate the expressional control of branched respiratory chain complexes of the amino-acid producing bacterium Corynebacterium glutamicum according to growth conditions, the expression indexes of the ndh, sdh, qcrCAB, ctaCF, ctaD, ctaE, and cydAB genes were estimated under aerobic and microaerobic, and carbon-rich and -poor conditions. The promoter region of each target gene was cloned upstream of the EGFP gene on expression vector pVK6, and the nine reporter constructs were transformed into C. glutamicum ssp. lactofermentum. The cytochrome content of cellular membranes obtained from each growth phase closely corresponded to the expression indexes based on EGFP fluorescence and cell density, indicating that this rapid and convenient method is suitable for analyzing the expression levels of respiratory chain complexes. Using this method, we demonstrated that a reciprocal change in the expression levels of cytochrome bd-type and aa ₃-type oxidases occurs when C. glutamicum cells are held in stationary phase for extended periods.     

Structure of the Mycobacterium tuberculosis type VII secretion system chaperone EspG5 in complex with PE25–PPE41 dimer

The growth or virulence of Mycobacterium tuberculosis bacilli depends on homologous type VII secretion systems, ESX‐1, ESX‐3 and ESX‐5, which export a number of protein effectors across membranes to the bacterial surface and environment. PE and PPE proteins represent two large families of highly polymorphic proteins that are secreted by these ESX systems. Recently, it was shown that these proteins require system‐specific cytoplasmic chaperones for secretion. Here, we report the crystal structure of M. tuberculosis ESX‐5‐secreted PE25–PPE41 heterodimer in complex with the cytoplasmic chaperone EspG₅. EspG₅ represents a novel fold that is unrelated to previously characterized secretion chaperones. Functional analysis of the EspG₅‐binding region uncovered a hydrophobic patch on PPE41 that promotes dimer aggregation, and the chaperone effectively abolishes this process. We show that PPE41 contains a characteristic chaperone‐binding sequence, the hh motif, which is highly conserved among ESX‐1‐, ESX‐3‐ and ESX‐5‐specific PPE proteins. Disrupting the interaction between EspG₅ and three different PPE target proteins by introducing different point mutations generally affected protein secretion. We further demonstrate that the EspG₅ chaperone plays an important role in the ESX secretion mechanism by keeping aggregation‐prone PE–PPE proteins in their soluble state.     

The miRNA machinery targets Mei‐P26 and regulates Myc protein levels in the Drosophila wing

MicroRNAs (miRNAs) have been implicated in cell‐cycle regulation and in some cases shown to have a role in tissue growth control. Depletion of miRNAs was found to have an effect on tissue growth rates in the wing primordium of Drosophila, a highly proliferative epithelium. Dicer‐1 (Dcr‐1) is a double‐stranded RNAseIII essential for miRNA biogenesis. Adult cells lacking dcr‐1, or with reduced dcr‐1 activity, were smaller than normal cells and gave rise to smaller wings. dcr‐1 mutant cells showed evidence of being susceptible to competition by faster growing cells in vivo and the miRNA machinery was shown to promote G₁–S transition. We present evidence that Dcr‐1 acts by regulating the TRIM‐NHL protein Mei‐P26, which in turn regulates dMyc protein levels. Mei‐P26 is a direct target of miRNAs, including the growth‐promoting bantam miRNA. Thus, regulation of tissue growth by the miRNA pathway involves a double repression mechanism to control dMyc protein levels in a highly proliferative and growing epithelium.     

Thermodynamics of an aminoglycoside modifying enzyme with low substrate promiscuity: The aminoglycoside N3 acetyltransferase‐VIa

Kinetic, thermodynamic, and structural properties of the aminoglycoside N3‐acetyltransferase‐VIa (AAC‐VIa) are determined. Among the aminoglycoside N3‐acetyltransferases, AAC‐VIa has one of the most limited substrate profiles. Kinetic studies showed that only five aminoglycosides are substrates for this enzyme with a range of fourfold difference in k_cat values. Larger differences in K_M (～40‐fold) resulted in ～30‐fold variation in k_cat/K_M. Binding of aminoglycosides to AAC‐VIa was enthalpically favored and entropically disfavored with a net result of favorable Gibbs energy (ΔG < 0). A net deprotonation of the enzyme, ligand, or both accompanied the formation of binary and ternary complexes. This is opposite of what was observed with several other aminoglycoside N3‐acetyltransferases, where ligand binding causes more protonation. The change in heat capacity (ΔCp) was different in H₂O and D₂O for the binary enzyme–sisomicin complex but remained the same in both solvents for the ternary enzyme–CoASH–sisomicin complex. Unlike, most other aminoglycoside‐modifying enzymes, the values of ΔCp were within the expected range of protein‐carbohydrate interactions. Solution behavior of AAC‐VIa was also different from the more promiscuous aminoglycoside N3‐acetyltransferases and showed a monomer‐dimer equilibrium as detected by analytical ultracentrifugation (AUC). Binding of ligands shifted the enzyme to monomeric state. Data also showed that polar interactions were the most dominant factor in dimer formation. Overall, thermodynamics of ligand‐protein interactions and differences in protein behavior in solution provide few clues on the limited substrate profile of this enzyme despite its >55% sequence similarity to the highly promiscuous aminoglycoside N3‐acetyltransferase. Proteins 2017; 85:1258–1265. © 2017 Wiley Periodicals, Inc.     

Cisgenic overexpression of cytosolic glutamine synthetase improves nitrogen utilization efficiency in barley and prevents grain protein decline under elevated CO2

Cytosolic glutamine synthetase (GS1) plays a central role in nitrogen (N) metabolism. The importance of GS1 in N remobilization during reproductive growth has been reported in cereal species but attempts to improve N utilization efficiency (NUE) by overexpressing GS1 have yielded inconsistent results. Here, we demonstrate that transformation of barley (Hordeum vulgare L.) plants using a cisgenic strategy to express an extra copy of native HvGS1‐1 lead to increased HvGS1.1 expression and GS1 enzyme activity. GS1 overexpressing lines exhibited higher grain yields and NUE than wild‐type plants when grown under three different N supplies and two levels of atmospheric CO₂. In contrast with the wild‐type, the grain protein concentration in the GS1 overexpressing lines did not decline when plants were exposed to elevated (800–900 μL/L) atmospheric CO₂. We conclude that an increase in GS1 activity obtained through cisgenic overexpression of HvGS1‐1 can improve grain yield and NUE in barley. The extra capacity for N assimilation obtained by GS1 overexpression may also provide a means to prevent declining grain protein levels under elevated atmospheric CO₂.     

Cloning and expression of the gene for an insect haemocyte anti‐aggregation protein (VPr3), from the venom of the endoparasitic wasp,Pimpla hypochondriaca

A venom protein from the endoparasitic wasp, Pimpla hypochondriaca, was recently biochemically isolated. This protein possessed haemocyte anti‐aggregation activity in vitro and shares the same N‐terminal amino acid sequence as that deduced from a gene termed vpr3. The vpr3 gene was identified by sequence analysis of randomly isolated cDNAs from a P. hypochondriaca venom gland library. Presently, the gene for the full‐length sequence of mature VPr3 protein was amplified from the P. hypochondriaca venom gland cDNA library by PCR. The amplicon was directionally cloned into a pET expression vector so that recombinant VPr3 (rVPr3) would have an N‐terminal polyhistidine (His) tag. High levels of target protein expression were obtained following addition of IPTG (1 mM) and growth of the bacteria at 37°C for 5 h, or at 24°C for 20 h. Following lysis of bacteria grown at 37°C, the target protein partitioned into the insoluble fraction. However, at 24°C, a small amount of soluble protein was consistently detected. The amount of soluble rVPr3 was subsequently increased when the transformed bacteria were grown in Overnight Express Instant TB medium at 24°C. Soluble rVPr3 was purified utilizing the MagneHis Protein Purification System. Recombinant VPr3 was determined to have adverse effects on the cytoskeleton of Lacanobia oleracea haemocytes and to inhibit the ability of these cells to form aggregates in vitro. © 2009 Wiley Periodicals, Inc.     

The Pseudomonas syringae type III effector HopG1 targets mitochondria,alters plant development and suppresses plant innate immunity

The bacterial plant pathogen Pseudomonas syringae uses a type III protein secretion system to inject type III effectors into plant cells. Primary targets of these effectors appear to be effector‐triggered immunity (ETI) and pathogen‐associated molecular pattern (PAMP)‐triggered immunity (PTI). The type III effector HopG1 is a suppressor of ETI that is broadly conserved in bacterial plant pathogens. Here we show that HopG1 from P. syringae pv. tomato DC3000 also suppresses PTI. Interestingly, HopG1 localizes to plant mitochondria, suggesting that its suppression of innate immunity may be linked to a perturbation of mitochondrial function. While HopG1 possesses no obvious mitochondrial signal peptide, its N‐terminal two‐thirds was sufficient for mitochondrial localization. A HopG1–GFP fusion lacking HopG1's N‐terminal 13 amino acids was not localized to the mitochondria reflecting the importance of the N‐terminus for targeting. Constitutive expression of HopG1 in Arabidopsis thaliana, Nicotiana tabacum (tobacco) and Lycopersicon esculentum (tomato) dramatically alters plant development resulting in dwarfism, increased branching and infertility. Constitutive expression of HopG1 in planta leads to reduced respiration rates and an increased basal level of reactive oxygen species. These findings suggest that HopG1's target is mitochondrial and that effector/target interaction promotes disease by disrupting mitochondrial functions.     

Elevated CO2 alters birch resistance to Lagomorpha herbivores

We studied the three‐way interaction of elevated CO₂, nitrogen (N), and temperature (T), and the two‐way interaction of elevated CO₂ and early‐season defoliation on the secondary chemistry and resistance of Eurasian silver birch (Betula pendula) and North American paper birch (B. papyrifera) against the Eurasian hare (Lepus timidus) and the North American eastern cottontail rabbit (Sylvilagus floridanus), respectively. Elevated CO₂ decreased the palatability of winter‐dormant silver and paper birch stems to both hares and rabbits, respectively. But the effect on hares was only apparent at intermediate levels of N fertilization. Elevated T had no effect on palatability. The effects of elevated CO₂, N, and T on levels of silver birch bark phenolics and terpenoids were dominated by two‐way interactions between N and CO₂, and N and T. Generally, however, N amendments elicited a parabolic response in carbon partitioning to most biosynthetic classes of silver birch phenolics (i.e. highest concentrations occurring at intermediate N). CO₂ elevation was most enhancing at highest levels of N. On the other hand, T increases, more often than not, elicited reductions in phenolics, but especially so at the highest N level. In the case of B. papyrifera, elevated CO₂ increased carbon partitioning to Folin‐Denis stem and branch phenolics and condensed tannins. Early‐season defoliation, on the other hand, had no effect on phenolics and tannins but lowered both N and energy levels of branches. Elevated CO₂ substantially ameliorated the negative effects of severe defoliation on tree growth. These results support the hypothesis that continuing anthropogenic alterations of the atmosphere may trigger significant changes in plant phenotypic resistance to mammalian herbivores owing to an increasing net carbon balance between the highly vagile supply and demand capacities of plant carbon sources and sinks.     

Assessing Targets for the Restoration of Herbaceous Vegetation in Ponderosa Pine Forests

A restoration project is considered a success when the initial target is met, but many targets are plausible. We evaluated the success of a restoration project in its 11th year since treatment in a southwestern ponderosa pine–bunchgrass community and the appropriateness of several targets. We measured the responses of (1) total standing crop; (2) standing crop of five functional groups (C₃ and C₄ graminoids, leguminous forbs, and nonleguminous perennial and annual forbs); (3) graminoid community composition; and (4) standing crop of five common graminoid species (Festuca arizonica, Muhlenbergia montana, Elymus elymoides, Carex geophila, and Poa fendleriana). Targets were quantified in remnant grass patches, which provided the standards for these targets, and were assessed in three other forest patch types (pre‐settlement tree patches, post‐settlement tree patches, and patches where all post‐settlement trees were removed). Patches where all post‐settlement trees were removed reached target levels for total standing crop, C₃ and C₄ graminoid standing crop, graminoid community composition, and M. montana, E. elymoides, and C. geophila standing crops. Standing crop of legumes and of F. arizonica did not increase over time in any patch type. Targets were not met in pre‐settlement patches or in patches where some post‐settlement trees were left standing, suggesting that it is unrealistic to expect equal responses across all patch types. If increasing herbaceous standing crop is a major goal, practitioners should create gaps within the pine forest canopy.