Intra- and interspecific variation in flower color is a hallmark of angiosperm diversity. The evolutionary forces underlying the variety of flower colors can be nearly as diverse as the colors themselves. In addition to pollinator preferences, non- pollinator agents of selection can have a major influence on the evolution of flower color polymorphisms, especially when the pigments in question are also expressed in vegetative tissues. In such cases, identifying the target(s) of selection starts with determining the biochemical and molecular basis for the flower color variation and examining any pleiotropic effects manifested in vegetative tissues. Herein, we describe a widespread purple-white flower color polymorphism in the mustard Parrya nudicaulis spanning Alaska. The frequency of white-flowered individuals increases with increasing growing-season temperature, consistent with the role of anthocyanin pigments in stress tolerance. White petals fail to produce the stress responsive flavonoid intermediates in the anthocyaninbiosyntheticpathway (ABP), suggesting an early pathway blockage. Petal cDNA sequences did not reveal blockages in any of the eight enzyme-coding genes in white-flowered individuals, nor any color differentiating SNPs. A qRT-PCR analysis of white petals identified a 24-fold reduction in chalcone synthase (CHS) at the threshold of the ABP, but no change in CHS expression in leaves and sepals. This arctic species has avoided the deleterious effects associated with the loss of flavonoid intermediates in vegetative tissues by decoupling CHS expression in petals and leaves, yet the correlation of flower color and climate suggests that the loss of flavonoids in the petals alone may affect the tolerance of white-flowered individuals to colder environments.
S. cerevisiae was engineered to produce the orange-brown polyketide pigment rubrofusarin, a common intermediate in a range of biosynthetic pathways found in different fila- mentous fungal species, by introduction of the three F. graminearum genes PKS12, aurZ and aurJ together with the PKS-activating PPTase gene npgA. A titer of 1.1 mg/L rubrofusarin was detected. The biosynthetic reconstruc- tion further provides the evidence that PKS12 is respon- sible for formation of the pigment YWA1, whereas AurZ catalyzes the formation of the pigment nor-rubrofusarin from YWA1. The results confirm the previously proposed biosyntheticpathway for the formation of rubrofusarin using a bottom-up approach and show that no other en- zymes are necessary. The study also demonstrates that it is possible to produce complex fungal polyketide products in S. cerevisiae, which opens up for the industrial produc- tion of a diversity of active and commercially interesting polyketides in the future.
To further improve the production of 1-propanol, we also aimed to enhance the threonine biosynthetic path- way via aspartate as shown Fig. 1d. To increase the car- bon flux from aspartate to threonine, we selected four genes (bifunctional thrA, encoding aspartokinase and homoserine dehydrogenase I; thrB, encoding homoser- ine kinase; thrC, encoding threonine synthase; and asd, encoding aspartate-semialdehyde dehydrogenase) derived from E. coli . In addition to cimA, leuC, leuD, and tdcB, these four genes (thrA, thrB, thrC, and asd) or alternatively just three genes (thrA, thrB and thrC), were introduced into the YPH499ΔGLY1 strain to generate YG5C4232 and YG5C4231, respectively. Following fer- mentation in SD media, both YG5C4231 and YG5C4232 produced ~ 100 mg/L of 1-propanol, with the presence or absence of the asd gene thus appearing to make little difference (Fig. 6). Compared to YPH499ΔGLY1 express- ing cimA, leuC, leuD, and tdcB (YG5C42; 68.3 mg/L in Fig. 5b), these strains therefore demonstrated an addi- tional increase in 1-propanol production. This indicates that enhancement of aspartate-mediated threonine bio- synthesis co-operates with the GLY1 deletion in regard to enhancement of 1-propanol production via the citra- malate, threonine, and 2 KB pathways.
family specific perturbations will allow us have a deep and comprehensive understanding of the contribution of specific genes to specific pathway flux. Besides, redundancy, feedback, feed-forward effect of one specific gene or gene family perturbation to the other pathway related enzyme and metabolite can also be studied based on the quantification result. Protein cleavage isotope dilution mass spectrometry (PCIDMS)8 is the method we use to absolutely quantify the enzyme component of the pathway in the P. trichocarpa stem differentiating xylem (SDX) tissue extraction. The idea of PCIDMS is determining the concentration of specific target protein by using the concentration of an enzymatically digested peptide, which is unique to the target protein. The concentration of the native peptide can be obtained by spiking a certain amount of isotopically labeled peptide as internal standard. With the peak ratio of the isotopically labeled and native peptide, and the amount of the isotope, we can calculate the native peptide amount, and that is assumed to be the amount of the protein. The peptides unique to the target protein are further screened to meet a series of criteria9 including: avoiding peptide with sites of known chemical modiﬁcations (e.g., Met, Asn, Gln, Cys) or highly probable post- translational modiﬁcations and favoring peptides with higher detected ion abundances. Eventually, if peptides selected are not stable or synthesizable, it would be necessary go back to unique peptide list for substitute. Method development includes SRM transition selection, maximizing ion sensitivity, specifically determining the quantity of the peptide, transition validation using ion relative abundance assessment, collision energy optimization, and digestion condition optimization to ensure complete proteolysis of protein to produce expected target peptide 9 .
The regions involved in the interaction between p53 and MDM2 is the MDM2-binding domain on p53 and have residues between 1 and 52. The other is the p53-binding domain having residues between 1 and 118. The MDM2 acts as ubiquitin ligase promoting ubiquitination of p53 followed by degradation of proteasome. Since MDM2 gene is regulated by p53 pathway, the proper level of p53 is maintained by auto regulatory feedback. MDM2 interacts with p53 through its 100 residue N-terminal domain with the N-terminal transactivation domain of p53. MDM2 binds to p53 transactivation domain (Fig 2) and inhibits its transcriptional activity by promoting its degradation and favours the export of p53 from the nucleus. Therefore in presence of MDM2, p53 protein is inactivated and does not stimulate expression of genes involved in apoptosis or cell cycle arrest. In some of the tumours, when MDM2 is overexpressed, p53 is constantly inhibited and tumour growth is favoured. The inactivation of MDM2 in these tumours should activate p53 pathway which activates apoptosis. 7
Concanavalin A (ConA) kills the procyclic (insect) form of Trypanosoma brucei by binding to its major surface glycoprotein, procyclin. We previously isolated a mutant cell line, ConA 1-1, that is less agglutinated and more resistant to ConA killing than are wild-type (WT) cells. Subsequently we found that the ConA resistance phenotype in this mutant is due to the fact that the procyclin either has no N-glycan or has an N-glycan with an altered structure. Here we demonstrate that the alteration in procyclin N-glycosylation correlates with two defects in the N-linked oligosaccharide biosyntheticpathway. First, ConA 1-1 has a defect in activity of polyprenol reductase, an enzyme involved in synthesis of dolichol. Metabolic incorporation of [ 3 H]mevalonate showed that ConA 1-1 synthesizes equal amounts of dolichol and polyprenol, whereas WT cells
Sepsis, which is the product of a poorly controlled inflammatory response, is a major health problem. Adequate therapies for sepsis are unavailable, and patient care is mainly supportive. Statins, widely used for the treatment of hypercholesterolemia, have been found to be antiinflammatory, but the mechanisms responsible for this alteration in the inflammatory response are not well understood. We investigated the effect of statins on CD14 expression, the major binding site for bacterial lipopolysaccharide (LPS) on the macrophage surface. CD14 is found in both a membrane-bound form on the cell surface (mCD14) and in a soluble vari- ant in circulation (sCD14). Treatment of RAW 264.7 macrophages with lovastatin resulted in elevated mCD14 levels and de- creased sCD14 levels after LPS stimulation. The increase in mCD14 was dependent on depletion of geranylgeranyl pyrophos- phate (GGPP) and subsequent inhibition of Rho GTPases, whereas the effect of lovastatin on sCD14 was independent of this pathway. The increase in mCD14 expression correlated with an enhanced response to LPS, at least at the level of tumor necro- sis factor (TNF)- α secretion. These results suggest that statin treatment can modulate macrophage functon, which may have an impact on inflammation and the outcome from sepsis.
Although the artemisinin biosyntheticpathway has been fully investigated and great progress has been made in cloning biosynthetic enzymes, the non enzymatic/ photo oxidative reaction step of this peculiar synthesis is not yet completely understood. It is suggested that the last step is probably a typical plant non enzymatic photo oxidative reaction that cannot be inserted into fast growing organisms .
Three agents were used in these studies to disrupt Rab geranylgeranylation: lovastatin, DGBP, and 3-PEHPC. That each of these agents disrupts Rab geranylgeranylation in different ways has allowed us to differentiate between the roles of prenylated proteins and the isoprenoid pathway in regulating autophagy. Treatment with lovastatin disrupts all protein prenylation as well as depletes cells of all isoprenoids downstream of mevalonate (Figure 1, Supplementary Figure 2). DGBP, by virtue of the fact that it targets the pathway more downstream, selectively disrupts protein geranylgeranylation and depletes cells of isoprenoids derived from GGPP. 3-PEHPC directly inhibits GGTase II and does not impact isoprenoid levels. We hypothesized that these agents could influence autophagy in a number of ways including: 1) induction as a consequence of isoprenoid depletion, 2) induction as a consequence of aggregated monoclonal protein, 3) inhibition as a consequence of disruption of geranylgeranylation of Rabs known to be involved in autophagic vesicles, or 4) inhibition or induction as a consequence of disruption of protein farnesylation or geranylgeranylation. Thus depending on the extent to which an agent affects each of these processes there could be varying degrees of both induction and inhibition of autophagy.
in alphaproteobacteria represents a major step forward in our understanding of the lipid A biosyntheticpathway in Gram- negative bacteria. Recently, a potent small-molecule inhibitor of E. coli LpxH has been discovered through high-throughput screening (23). The exceedingly low sequence identity of the unique UDP-DAGn pyrophosphatase LpxG compared with LpxH and LpxI forecasts distinct structural features within LpxG that could be exploited for developing highly specific antibiotics for treating Chlamydia infections without causing major alterations in resident microbial communities or leading to unintended an- tibiotic resistance among other coinfecting pathogens.
Background: Serratia plymuthica WS3236 was selected for whole genome sequencing based on preliminary genetic and chemical screening indicating the presence of multiple natural product pathways. This led to the identification of a putative sodorifen biosynthetic gene cluster (BGC). The natural product sodorifen is a volatile organic compound (VOC) with an unusual polymethylated hydrocarbon bicyclic structure (C 16 H 26 ) produced by selected strains of S. plymuthica. The BGC encoding sodorifen consists of four genes, two of which (sodA, sodB) are homologs of genes encoding enzymes of the non-mevalonate pathway and are thought to enhance the amounts of available farnesyl pyrophosphate (FPP), the precursor of sodorifen. Proceeding from FPP, only two enzymes are necessary to produce sodorifen: an S-adenosyl methionine dependent methyltransferase (SodC) with additional cyclisation activity and a terpene-cyclase (SodD). Previous analysis of S. plymuthica found sodorifen production titers are generally low and vary significantly among different producer strains. This precludes studies on the still elusive biological function of this structurally and biosynthetically fascinating bacterial terpene.
Moreover, the architecture of the N. oceanica sterol biosyntheticpathway also displays both animal and plant features. The underlying mechanisms remained elusive, but evolutionary pressure may have driven the pro- duction or elimination of certain sterol structures to adapt to a particular niche. Yeast strains carrying mu- tations early in the ergosterol pathway exhibit lower survival rates than those with mutations at later parts of the pathway . An SMT2-overexpressing Arabi- dopsis mutant exhibited an altered campesterol-to- sitosterol ratio and dramatic phenotypic alterations, whereas a CYP710A1-overexpressing mutant, with an equivalent campesterol-to-stigmasterol ratio, carried a nor- mal phenotype . These results suggest a crucial role of the order of enzymes in the sterol biosyntheticpathway. In addition, N. oceanica harbors an animal-signature DHCR24 instead of a plant-type DWF1. Besides the roles in sterol and BR synthesis, DWF1 has a Ca 2+ /calmodulin domain related to BR signaling . The domain is absent in animal DHCR24, implying that N. oceanica uses a differ- ent BR signaling cascade from that of higher plants. There- fore, although the backbone of the sterol biosyntheticpathway appears to be highly conserved in eukaryotic cells, variations in sterol profile and pathway architecture likely have contributed to the distinct morphology.
It is a scientific tool used as an algorithm for comparing various biological sequences especially primary sequences such as amino acids, nucleotides etc. BLAST searches for high scoring sequence alignment between the query sequences and the sequences stored in the database using an approach called smith-waterman algorithm. With the help of BLAST tool homologies for the enzyme which were present in the biosyntheticpathway of the alkaloid berberine, were found .
fumarylacetoacetate hydrolase. It is known that patients with this hereditary disease excrete excessive amounts of d-aminolevulinic acid (ALA) in urine and that certain patients have an accompanying clinical syndrome resembling that of acute intermittent porphyria (AIP). In order to elucidate the relation of succinylacetone to the heme biosyntheticpathway, we have examined the effects of this metabolite on the cellular heme content of cultured avian hepatocytes and on the activity of purified ALA dehydratase from normal human
We investigated whether the deletion of the isobutyrate, pantothenate, or isoleucine biosynthetic pathways (dele- tion of ALD6, ECM31 or ILV1, respectively) improved isobutanol production by S. cerevisiae. Although the dele- tions of ILV1 and ALD6 have been mentioned in the pat- ents (US8828694 and US20110201073), this is the first research paper that the effects of these gene deletions were examined closely. The deletion of each pathway in- creased isobutanol production, with the ILV1 knockout being the most effective. The ILV1 knockout prevented the competitive outflow of carbon from glucose into iso- leucine biosynthesis; consequently, isobutanol biosynthesis was enhanced in isoleucine-supplemented medium. Thus, the deletion of competitive pathways for reducing carbon
flux of upstream was increased due to consumption of me- tabolites by downstream pathway. In this study, the pulling effect was mainly owing to alleviation of inhibitory regula- tion, which resulted in decreased loss of carbon flux to the branched pathways and enhanced the tryptophan supply to violacein synthesis. TnaA, pheA, and trpR play roles in de- grading tryptophan, competing carbon flux from trypto- phan and inhibiting the transcription of trp operon when tryptophan accumulated, while when the downstream pathway for violacein synthesis was docked, less typtophan was accumulated, thus decreasing the effect of knockout of tnaA, pheA and trpR. This could explain why strain B1 with pED and pVio is already a suitable producer of crude violacein. Previous studies had used multivariate modules with different transcriptional or translational levels to ex- plore a balanced module as precursor supply [19,35]. Thus, the pulling effect on these cases was hard to be found obvi- ously as 1) this effect may not exited in these situations and/or 2) the yields of the precursor and target chemicals were not compared quantitatively to find this effect [19,35]. In the present study, we demonstrated that the down- stream violacein biosyntheticpathway could obviously draw the carbon flux of the upstream pathway to produce more precursors from glucose. This kind of interactive pull effect was possible to occur when the accumulated metab- olites was consumed effectively by a docked pathway and finally resulted in self-balancing of the long pathway, which dynamically drew more, but not excess, precursor for the downstream pathway to achieve high productivity of the target products.
The integrity of the cholesterol biosynthesis pathway is required for efficient African swine fever virus (ASFV) infection. Incor- poration of prenyl groups into Rho GTPases plays a key role in several stages of ASFV infection, since both geranylgeranyl and farnesyl pyrophosphates are required at different infection steps. We found that Rho GTPase inhibition impaired virus morpho- genesis and resulted in an abnormal viral factory size with the accumulation of envelope precursors and immature virions. Fur- thermore, abundant defective virions reached the plasma membrane, and filopodia formation in exocytosis was abrogated. Rac1 was activated at early ASFV infection stages, coincident with microtubule acetylation, a process that stabilizes microtubules for virus transport. Rac1 inhibition did not affect the viral entry step itself but impaired subsequent virus production. We found that specific Rac1 inhibition impaired viral induced microtubule acetylation and viral intracellular transport. These findings highlight that viral infection is the result of a carefully orchestrated modulation of Rho family GTPase activity within the host cell; this modulation results critical for virus morphogenesis and in turn, triggers cytoskeleton remodeling, such as microtubule stabilization for viral transport during early infection.