Young Moo Lee

A systemic small RNA signaling system in plants.

Systemic translocation of RNA exerts non-cell-autonomous control over plant development and defense. Long-distance delivery of mRNA has been proven, but transport of small interfering RNA and microRNA remains to be demonstrated. Analyses performed on phloem sap collected from a range of plants identified populations of small RNA species. The dynamic nature of this population was reflected in its response to growth conditions and viral infection. The authenticity of these phloem small RNA molecules was confirmed by bioinformatic analysis; potential targets for a set of phloem small RNA species were identified. Heterografting studies, using spontaneously silencing coat protein (CP) plant lines, also established that transgene-derived siRNA move in the long-distance phloem and initiate CP gene silencing in the scion. Biochemical analysis of pumpkin (Cucurbita maxima) phloem sap led to the characterization of C. maxima Phloem SMALL RNA BINDING PROTEIN1 (CmPSRP1), a unique component of the protein machinery probably involved in small RNA trafficking. Equivalently sized small RNA binding proteins were detected in phloem sap from cucumber (Cucumis sativus) and lupin (Lupinus albus). PSRP1 binds selectively to 25-nucleotide single-stranded RNA species. Microinjection studies provided direct evidence that PSRP1 could mediate the cell-to-cell trafficking of 25-nucleotide single-stranded, but not double-stranded, RNA molecules. The potential role played by PSRP1 in long-distance transmission of silencing signals is discussed with respect to the pathways and mechanisms used by plants to exert systemic control over developmental and physiological processes.

A strategy for the identification of proteins targeted by thioredoxin

Thioredoxins are 12-kDa proteins functional in the regulation of cellular processes throughout the animal, plant, and microbial kingdoms. Growing evidence with seeds suggests that an h-type of thioredoxin, reduced by NADPH via NADP-thioredoxin reductase, reduces disulfide bonds of target proteins and thereby acts as a wakeup call in germination. A better understanding of the role of thioredoxin in seeds as well as other systems could be achieved if more were known about the target proteins. To this end, we have devised a strategy for the comprehensive identification of proteins targeted by thioredoxin. Tissue extracts incubated with reduced thioredoxin are treated with a fluorescent probe (monobromobimane) to label sulfhydryl groups. The newly labeled proteins are isolated by conventional two-dimensional electrophoresis: (i) nonreducing/reducing or (ii) isoelectric focusing/reducing SDS/PAGE. The isolated proteins are identified by amino acid sequencing. Each electrophoresis system offers an advantage: the first method reveals the specificity of thioredoxin in the reduction of intramolecular vs. intermolecular disulfide bonds, whereas the second method improves the separation of the labeled proteins. By application of both methods to peanut seed extracts, we isolated at least 20 thioredoxin targets and identified 5—three allergens (Ara h2, Ara h3, and Ara h6) and two proteins not known to occur in peanut (desiccation-related and seed maturation protein). These findings open the door to the identification of proteins targeted by thioredoxin in a wide range of systems, thereby enhancing our understanding of its function and extending its technological and medical applications.

Keratin 8 and 18 mutations are risk factors for developing liver disease of multiple etiologies

Keratin 8 and 18 (K8/K18) mutations are found in patients with cryptogenic cirrhosis, but the role of keratin mutations in noncryptogenic cirrhosis and the incidence of keratin mutations in the general population are not known. We screened for K8/K18 mutations in genomic DNA isolated from 314 liver explants of patients who primarily had noncryptogenic cirrhosis, and from 349 blood bank volunteers. Seven unique K8/K18 mutations were found in 11 independent patients with biliary atresia, hepatitis B/C, alcohol, primary biliary cirrhosis, and fulminant hepatitis. Seven of the 11 patients had mutations previously described in patients with cryptogenic cirrhosis: K8 Tyr-53 → His, K8 Gly-61 → Cys, and K18 His-127 → Leu. The four remaining patients had mutations at one K8 and three other K18 new sites. Of the 349 blood bank control samples, only one contained the Tyr-53 → His and one the Gly-61 → Cys K8 mutations (P < 0.004 when comparing cirrhosis versus control groups). Two additional mutations were found in both the liver disease and blood bank groups and, hence, likely represent polymorphisms. Livers with keratin mutations had cytoplasmic filamentous deposits that were less frequent in livers without the mutations (P = 0.03). Therefore, K8/K18 are likely susceptibility genes for developing cryptogenic and noncryptogenic forms of liver disease.

Interactions of heme proteins with hydrogen peroxide: Protein crosslinking and covalent binding of benzo[a]pyrene and 17β-estradiol

This work reveals two biochemical effects of hydrogen peroxide treatment on hemoglobin, myoglobin, and cytochrome c. First, these heme proteins rapidly formed covalently crosslinked dimers and polymers detectable by detergent gel electrophoresis. Second, when treated in the presence of radioactive benzo[a]pyrene or 17 beta-estradiol, the heme proteins became covalently labeled. Nonheme proteins exhibited both cross-linking and radioactive labeling upon peroxide treatment in the presence but not the absence of heme protein or free hemin. Benzoyl peroxide or glucose and glucose oxidase effectively replaced direct addition of hydrogen peroxide. These results indicate that adventitious peroxidase activity expressed by oxygen carrying and electron transport proteins yields active oxygen species that can damage these heme proteins and nearby macromolecules, a possible biochemical mechanism for the lethal and other deleterious intracellular effects of peroxide.

Proteome Analysis of Human Hair Shaft From Protein Identification to Posttranslational Modification

The human hair proteome was investigated using two-dimensional LC-MS/MS. Among the 343 identified proteins, 70 were detected in high relative abundance, including keratin intermediate filament proteins, largely extractable with denaturants. Over 300 proteins were found to constitute the insoluble complex formed by transglutaminase cross-linking. The intracellular distribution of identified proteins is wide from cytoplasm to nucleus, mitochondria, ribosome, and plasma membrane. These results help rationalize ultrastructural features visible in the mature hair. Keratins and several substrates for transglutaminase were found to be posttranslationally modified by methylation and dimethylation. Evidence for ubiquitination of hair proteins was also obtained.

Attomole level protein sequencing by Edman degradation coupled with accelerator mass spectrometry

Edman degradation remains the primary method for determining the sequence of proteins. In this study, accelerator mass spectrometry was used to determine the N-terminal sequence of glutathione S-transferase at the attomole level with zeptomole precision using a tracer of 14C. The transgenic transferase was labeled by growing transformed Escherichia coli on [14C]glucose and purified by microaffinity chromatography. An internal standard of peptides on a solid phase synthesized to release approximately equal amounts of all known amino acids with each cycle were found to increase yield of gas phase sequencing reactions and subsequent semimicrobore HPLC as did a lactoglobulin carrier. This method is applicable to the sequencing of proteins from cell culture and illustrates a path to more general methods for determining N-terminal sequences with high sensitivity.

Structural and functional differences among purified recombinant mammalian aromatases: glycosylation, N-terminal sequence and kinetic analysis of human, bovine and the porcine placental and gonadal isozymes

Recombinant porcine gonadal and placental, and the human and bovine, isozymes of aromatase cytochrome P450 (P450arom) were over-expressed in insect cells, purified and quantified by difference spectroscopy. Human and bovine P450arom exhibited greater apparent molecular size than either porcine isozyme prompting an examination of N-linked glycosylation and amino-terminal peptide sequence. Comparisons of substrate affinities and turnover were also made. In contrast to human and bovine P450arom which are N-linked glycoproteins, neither isozyme of porcine P450arom is glycosylated, explaining in part their lower molecular size. Differences found in N-terminal peptide sequences were unlikely to influence apparent molecular size or enzyme function. Human and bovine P450arom had similar affinities and turnovers for androstenedione (approximately 200 nM, 3/min) and testosterone (approximately 350 nM, 2/min). The porcine isozymes had 10-fold higher affinities but correspondingly lower turnovers, particularly the gonadal P450arom. Overall, the catalytic efficiency (Vmax/Km) was similar for all but porcine gonadal P450arom which was much lower. These data emphasize the structural and functional variability of even the most conserved of proteins among diverse species wherein such differences have previously remained unexpected.

Rapsyn interacts with the muscle acetylcholine receptor via α-helical domains in the α, β, and ε subunit intracellular loops

At the developing vertebrate neuromuscular junction, the acetylcholine receptor becomes aggregated at high density in the postsynaptic muscle membrane. Receptor localization is regulated by the motoneuron-derived factor, agrin, and requires an intracellular, scaffolding protein called rapsyn. However, it remains unclear where rapsyn binds on the acetylcholine receptor and how their interaction is regulated. In this study, we identified rapsyns binding site on the acetylcholine receptor using chimeric constructs where the intracellular domain of CD4 was substituted for the major intracellular loop of each mouse acetylcholine receptor subunit. When expressed in heterologous cells, we found that rapsyn clustered and cytoskeletally anchored CD4-alpha, beta and epsilon subunit loops but not CD4-delta loop. Rapsyn-mediated clustering and anchoring was highest for beta loop, followed by epsilon and alpha, suggesting that rapsyn interacts with the loops with different affinities. Moreover, by making deletions within the beta subunit intracellular loop, we show that rapsyn interacts with the alpha-helical region, a secondary structural motif present in the carboxyl terminal portion of the subunit loops. When expressed in muscle cells, rapsyn co-immunoprecipitated together with a CD4-alpha helical region chimera, independent of agrin signaling. Together, these findings demonstrate that rapsyn interacts with the acetylcholine receptor via an alpha-helical structural motif conserved between the alpha, beta and epsilon subunits. Binding at this site likely mediates the critical rapsyn interaction involved in localizing the acetylcholine receptor at the neuromuscular junction.

Core of the partner switching signalling mechanism is conserved in the obligate intracellular pathogen Chlamydia trachomatis.

Chlamydia trachomatis is an obligate intracellular bacterial pathogen that can cause sexually transmitted and ocular diseases in humans. Its biphasic developmental cycle and ability to evade host‐cell defences suggest that the organism responds to external signals, but its genome encodes few recognized signalling pathways. One such pathway is predicted to function by a partner switching mechanism, in which key protein interactions are controlled by serine phosphorylation. From genome analysis this mechanism is both ancient and widespread among eubacteria, but it has been experimentally characterized in only a few. C. trachomatis has no system of genetic exchange, so here an in vitro approach was used to establish the activities and interactions of the inferred partner switching components: the RsbW switch protein/kinase and its RsbV antagonists. The C. trachomatis genome encodes two RsbV paralogs, RsbV1 and RsbV2. We found that each RsbV protein was specifically phosphorylated by RsbW, and tandem mass spectrometry located the phosphoryl group on a conserved serine residue. Mutant RsbV1 and RsbV2 proteins in which this conserved serine was changed to alanine could activate the yeast two‐hybrid system when paired with RsbW, whereas mutant proteins bearing a charged aspartate failed to activate. From this we infer that the phosphorylation state of RsbV1 and RsbV2 controls their interaction with RsbW in vivo. This experimental demonstration that the core of the partner switching mechanism is conserved in C. trachomatis indicates that its basic features are maintained over a large evolutionary span. Although the molecular target of the C. tra‐chomatis switch remains to be identified, based on the predicted properties of its input phosphatases we propose that the pathway controls an important aspect of the developmental cycle within the host, in response to signals external to the C. trachomatis cytoplasmic membrane.

Rapsyn carboxyl terminal domains mediate muscle specific kinase–induced phosphorylation of the muscle acetylcholine receptor

At the developing vertebrate neuromuscular junction, postsynaptic localization of the acetylcholine receptor (AChR) is regulated by agrin signaling via the muscle specific kinase (MuSK) and requires an intracellular scaffolding protein called rapsyn. In addition to its structural role, rapsyn is also necessary for agrin-induced tyrosine phosphorylation of the AChR, which regulates some aspects of receptor localization. Here, we have investigated the molecular mechanism by which rapsyn mediates AChR phosphorylation at the rodent neuromuscular junction. In a heterologous COS cell system, we show that MuSK and rapsyn induced phosphorylation of beta subunit tyrosine 390 (Y390) and delta subunit Y393, as in muscle cells. Mutation of beta Y390 or delta Y393 did not inhibit MuSK/rapsyn-induced phosphorylation of the other subunit in COS cells, and mutation of beta Y390 did not inhibit agrin-induced phosphorylation of the delta subunit in Sol8 muscle cells; thus, their phosphorylation occurs independently, downstream of MuSK activation. In COS cells, we further show that MuSK-induced phosphorylation of the beta subunit was mediated by rapsyn, as MuSK plus rapsyn increased beta Y390 phosphorylation more than rapsyn alone and MuSK alone had no effect. Intriguingly, MuSK also induced tyrosine phosphorylation of rapsyn itself. We then used deletion mutants to map the rapsyn domains responsible for activation of cytoplasmic tyrosine kinases that phosphorylate the AChR subunits. We found that rapsyn C-terminal domains (amino acids 212-412) are both necessary and sufficient for activation of tyrosine kinases and induction of cellular tyrosine phosphorylation. Moreover, deletion of the rapsyn RING domain (365-412) abolished MuSK-induced tyrosine phosphorylation of the AChR beta subunit. Together, these findings suggest that rapsyn facilitates AChR phosphorylation by activating or localizing tyrosine kinases via its C-terminal domains.