Length recognition at the N-terminal tail for the initiation of FtsH-mediated proteolysis

FtsH-mediated proteolysis against membrane proteins is processive, and presumably involves dislocation of the substrate into the cytosol where the enzymatic domains of FtsH reside. To study how such a mode of proteolysis is initiated, we manipulated N-terminal cytosolic tails of three membrane proteins. YccA, a natural substrate of FtsH was found to require the N-terminal tail of 20 amino acid residues or longer to be degraded by FtsH in vivo. Three unrelated sequences of this segment conferred the FtsH sensitivity to YccA. An artificially constructed TM9-PhoA protein, derived from SecY, as well as the SecE protein, were sensitized to FtsH by addition of extra amino acid sequences to their N-terminal cytosolic tails. Thus, FtsH recognizes a cytosolic region of sufficient length (~20 amino acids) to initiate the processive proteolysis against membrane proteins. Such a region is typically at the N-terminus and can be diverse in amino acid sequences.     

In vitro prothrombin synthesis from a purified precursor protein III. Preparation of an acid-soluble substrate for vitamin K-dependent carboxylase by limited proteolysis of bovine descarboxyprothrombin

Bovine descarboxyprothrombin and descarboxyfragment-1 can be used as substrates for rat and bovine vitamin K-dependent carboxylase. In both enzyme systems, however, these substrates have a high K_m (0.3–0.4 mM). A better substrate (K_m = 0.001–0.003 mM) was prepared from bovine descarboxyprothrombin by limited proteolysis with subtilisin Carlsberg. This substrate is called Fragment-Su and is composed of the amino acids 13–29 of descarboxyprothrombin.     

Amino Acid Metabolism of Lemna minor L. : IV. N-Labeling Kinetics of the Amide and Amino Groups of Glutamine and Asparagine

A serious limitation to the use of N(O,S)-heptafluorobutyryl isobutyl amino acid derivatives in the analysis of ¹⁵N-labeling kinetics of amino acids in plant tissues, is that the amides glutamine and asparagine undergo acid hydrolysis to glutamate and aspartate, respectively, during derivatization. This led us to consider an alternative procedure (G Fortier et al. [1986] J Chromatogr 361: 253-261) for derivatization of glutamine and asparagine with N-methyl-N-(tert-butyldimethylsilyl)-trifluoroacetamide in pyridine. Gas chromatography-mass spectrometry (electron ionization) yielded fragment ions (M-57) of mass 417 and 431 for the [¹⁴N]asparagine and [¹⁴N]glutamine derivatives, respectively, suitable for monitoring unlabeled, single-¹⁵N- and double-¹⁵N-labeled amide species from the ion clusters at mass to charge ratio (m/z) 415 to 423 for asparagine, and m/z 429 to 437 for glutamine. From separate analyses of the specific isotope abundance of the amino-N groups of asparagine and glutamine as their N-heptafluorobutyryl isobutyl derivatives, the specific amide-[¹⁵N] abundance of these amino acids was determined. We demonstrate that this approach to ¹⁵N analysis of the amides can yield unique insights as to the compartmentation of asparagine and glutamine in vivo. The ratios of unlabeled:single-¹⁵N:double-¹⁵N-labeled species are highly diagnostic of the relative sizes and turnover of metabolically active and inactive pools of the amides and their precursors. Kinetic evidence is presented to indicate that a significant proportion (approximately 10%) of the free asparagine pool may be metabolically inactive (vacuolar). If the amide group of asparagine is derived exclusively from glutamine-amide, then asparagine must be synthesized in a compartment of the cell in which both glutamine-amide and aspartate are more heavily labeled with ¹⁵N than the bulk pools of these amino acids. This compartment is presumably the chloroplast. The transaminase inhibitor aminooxyacetate is shown to markedly inhibit amino acid synthesis; several amino acid pools accumulated in the presence of aminooxyacetate and [¹⁵N]H₄⁺ are ¹⁴N-enriched and must be derived primarily from protein turnover.     

The identification of N-acetylglycine as a contaminant of glacial acetic acid.

This paper provides evidence by gas chromatography-mass spectrometry (GC-MS) that N-acetylglycine is present, in varying amounts, as a contaminant of all samples of analytical grade glacial acetic acid that have been examined in our laboratory. Supportive evidence for the GC-MS data was obtained by amino acid analyses of evaporated samples of acetic acid which were subjected to acid hydrolysis and then analyzed by ion-exchange chromatography.Although the identification of N-acetylglycine has been established with certainty, small quantities of other amino acid derivatives which have not yet been identified are also present in glacial acetic acid. These additional amino acids have been identified after acid hydrolysis. It should be pointed out that although amino acids are of chief interest here, they comprise approximately 1% or less of the total organic contamination.A very marked reduction of the concentration of N-acetylglycine and all other contaminants was accomplished by slow distillation of the glacial acetic acid through a column of packed Raschig rings.     

N-ε-fructosyllysine and N-ε-carboxymethyllysine,but not lysinoalanine,are available for absorption after simulated gastrointestinal digestion

Food processing leads to a variety of chemical modifications of amino acids in food proteins. Recent studies have shown that some modified amino acids resulting from glycation reactions can pass the intestinal barrier when they are bound in dipeptides. In this study, we investigated as to what extent modified amino acids are released from post-translationally modified casein during simulated gastrointestinal digestion. Casein was enriched with N-ε-fructoselysine, N-ε-carboxymethyllysine, and lysinoalanine, in different degrees of modification. The casein samples were subjected to a two-step proteolysis procedure, simulating gastrointestinal digestion. The digestibility of modified casein as measured by analytical size-exclusion chromatography (SEC) decreased with increasing degree of modification especially after enrichment of fructoselysine and lysinoalanine. Semi-preparative SEC of digested casein samples revealed that fructoselysine and carboxymethyllysine are released bound in peptides smaller than 1,000 Da, which is comparable to native amino acids. The glycation compounds should, therefore, be available for absorption. Lysinoalanine as a crosslinking amino acid, however, is mostly released into longer peptides of at least 30–40 amino acids which should strongly impair its absorption availability.     

Studies on Proteolysis in Stored Muscle

Changes in the nonprotein nitrogenous compounds produced from rabbit skeletal muscle (L. dorsi) by proteolysis were investigated.

The value of trichloroacetic acid soluble nitrogen, ninhydrin positive materials and phenol reagent positive materials increased during storage at low and high temperature. Changes in bound and free amino acid contents produced by proteolysis during storage were assayed by amino acid analyzer. Most of free amino acids except taurine increased remarkably. Amounts of asparatic acid, glutamic acid, glycine, β-alanine and histidine were increased after hydrolysis as compared with those before hydrolysis.

By using five kinds of Dowex 50 columns, changes in the distributive patterns of the nonprotein nitrogenous compounds were also studied.     

Pollen feeding proteomics: Salivary proteins of the passion flower butterfly,Heliconius melpomene

While most adult Lepidoptera use flower nectar as their primary food source, butterflies in the genus Heliconius have evolved the novel ability to acquire amino acids from consuming pollen. Heliconius butterflies collect pollen on their proboscis, moisten the pollen with saliva, and use a combination of mechanical disruption and chemical degradation to release free amino acids that are subsequently re-ingested in the saliva. Little is known about the molecular mechanisms of this complex pollen feeding adaptation. Here we report an initial shotgun proteomic analysis of saliva from Heliconius melpomene. Results from liquid-chromatography tandem mass-spectrometry confidently identified 31 salivary proteins, most of which contained predicted signal peptides, consistent with extracellular secretion. Further bioinformatic annotation of these salivary proteins indicated the presence of four distinct functional classes: proteolysis (10 proteins), carbohydrate hydrolysis (5), immunity (6), and “housekeeping” (4). Additionally, six proteins could not be functionally annotated beyond containing a predicted signal sequence. The presence of several salivary proteases is consistent with previous demonstrations that Heliconius saliva has proteolytic capacity. It is likely that these proteins play a key role in generating free amino acids during pollen digestion. The identification of proteins functioning in carbohydrate hydrolysis is consistent with Heliconius butterflies consuming nectar, like other lepidopterans, as well as pollen. Immune-related proteins in saliva are also expected, given that ingestion of pathogens is a likely route to infection. The few “housekeeping” proteins are likely not true salivary proteins and reflect a modest level of contamination that occurred during saliva collection. Among the unannotated proteins were two sets of paralogs, each seemingly the result of a relatively recent tandem duplication. These results offer a first glimpse into the molecular foundation of Heliconius pollen feeding and provide a substantial advance towards comprehensively understanding this striking evolutionary novelty.     

Characterization of the peptidases of Calliphora: Many features allow the utilization of small peptides as an amino acid reservoir

Electrophoretic separation of whole flies and of haemolymph indicates the presence of four peptidases, named dipeptidase A, B and C (Dip A, B and C) and leucine amino peptidase (LAP) after enzymes of similar substrate specificities and electrophoretic mobilities found in Drosophila (Laurie-Ahlberg, Biochem. Genet.20, 407–424, 1982; Walker et al., Insect Biochem.10, 535–541, 1980). Prominent in both tissues and haemolymph, dipeptidase A and B together hydrolyse a variety of dipeptides in vitro and probably most of the fly's small peptide component in vivo. Though Dip A and Dip B hydrolyse many of the same substrates, their activities differ in at least several respects. Dip A's K_ms are higher than Dip B's K_ms and hence in vivo the two enzymes together are likely to provide peptide hydrolysis through a wide range of substrate concentration. Dip A's unique hydrolyses are of peptides with biosynthesized amino acids in the N-terminal position and Dip B's unique hydrolyses are of peptides with essential amino acids in the N-terminal position. Dip B, but not Dip A, is inhibited by free amino acid. It is inhibited non-competitively and most strongly by essential amino acids. In cell-free haemolymph Dip B's activity is more stable than Dip A's. The accumulation and maintenance of small peptides in times of dietary sufficiency and the utilization of the small peptides as a source of amino acid in times of dietary scarcity (Collett, Insect Biochem.6, 179–185, 1976a; J. Insect Physiol.22, 1433–1440, 1976b) may be attributed to these features.     

The disappearance of dry matter,nitrogen and amino acids in the gastrointestinal tract from Calliandra leaves

The total tract disappearance of dry matter (DM), nitrogen and amino acids in different Calliandra leaves harvested from Kenya and Zimbabwe were measured using the mobile bag technique. In the mobile bag measurements, disappearance was measured in the rumen in sacco, by pepsin–HCl hydrolysis in vitro and in the intestine. The hydrolysis in the pepsin–HCl solution was designed to mimic digestion in the abomasum. The total tract disappearance of DM, nitrogen, and amino acids were generally low. The highest total apparent DM, nitrogen and total amino acid disappearance obtained were 425 (g/kg), 458 (g/kg total nitrogen), and 593 (g/kg amino acid), respectively. There were differences between the leaves in the disappearance of DM, nitrogen and amino acids, and in the proportion of nutrients lost in the rumen, after pepsin–HCl hydrolysis and in the intestine. More DM, nitrogen, and amino acids in the leaves from Kenya disappeared in the intestine in comparison to the disappearance in leaves from Zimbabwe. The reasons for the differences between the nutritive values of the leaves is unclear but appears to be strongly influenced by the stage of growth and conditions in which the plants were grown.     

Analysis of adipimidate-crosslinked lysine

The chromatographic conditions for separation of N,N′-bislysyl(?-N)adipamidine and N-lysyl(?-N)adipamidinic acid, which were the products of acid hydrolysis of proteins treated with adipimidate esters, from other amino acids on an amino acid analyzer were established including their ninhydrin color values. Kinetics of decomposition of these lysine derivatives under the conditions of total acid hydrolysis of protein are also reported.     

The involvement of amino acids in latex lipid synthesis in Euphorbia lathyris seedlings

The breakdown of triglycerides and proteins in the endosperm of Euphorbia lathyris was assayed in a 14 day germination period. Six days after germination, the average daily production was 2.7 μmol of amino acids. Arginine, glutamine, asparagine and glutamic acid accounted for 53% of the total amino acids. Excised cotyledons with 1 cm hypocotyls were used for amino acid uptake and their involvement in terpenoid synthesis was studied. Glutamine and aspartate were hardly involved in apolar lipid synthesis. Leucine, isoleucine, valine and threonine were mainly incorporated into the triterpenes in the laticifers. Alanine and serine were also involved in phytosterol synthesis in the adjacent tissue. In the 14 day germination period, ca3% of the daily yield of latex triterpenes may be synthesized from a variety of amino acids.     

A Model of Proteolysis and Amino Acid Biosynthesis for Lactobacillus delbrueckii subsp. bulgaricus in Whey

Lactobacillus delbrueckii subsp. bulgaricus 2038 (L. bulgaricus 2038) is a bacterium that is used as a starter for dairy products by Meiji Co., Ltd of Japan. Culturing L. bulgaricus 2038 with whey as the sole nitrogen source results in a shorter lag phase than other milk proteins under the same conditions (carbon source, minerals, and vitamins). Microarray results of gene expression revealed characteristics of amino acid anabolism with whey as the nitrogen source and established a model of proteolysis and amino acid biosynthesis for L. bulgaricus. Whey peptides and free amino acids are readily metabolized, enabling rapid entry into the logarithmic growth phase. The oligopeptide transport system is the primary pathway for obtaining amino acids. Amino acid biosynthesis maintains the balance between amino acids required for cell growth and the amount obtained from environment. The interconversion of amino acids is also important for L. bulgaricus 2038 growth.     

Amino Acid metabolism in pea leaves : utilization of nitrogen from amide and amino groups of [N]asparagine

The flow of nitrogen from the amino and amide groups of asparagine has been followed in young pea (Pisum sativum CV Little Marvel) leaves, supplied through the xylem with ¹⁵N-labeled asparagine. The results confirm that there are two main routes for asparagine metabolism: deamidation and transamination.

Nitrogen from the amide group is found predominantly in 2-hydroxy-succinamic acid (derived from transamination of asparagine) and in the amide group of glutamine. The amide nitrogen is also found in glutamate and dispersed through a range of amino acids. Transfer to glutamineamide results from assimilation of ammonia produced by deamidation of both asparagine and its transamination products: this assimilation is blocked by methionine sulfoximine. The release of amide nitrogen as ammonia is greatly reduced by aminooxyacetate, suggesting that, for much of the metabolized asparagine, transamination precedes deamidation.

The amino group of asparagine is widely distributed in amino acids, especially aspartate, glutamate, alanine, and homoserine. For homoserine, a comparison of N and C labeling, and use of a transaminase inhibitor, suggests that it is not produced from the main pool of aspartate, and transamination may play a role in the accumulation of homoserine in peas.

     

The Use of Ascorbate as an Oxidation Inhibitor in Prebiotic Amino Acid Synthesis: A Cautionary Note

It is generally thought that the terrestrial atmosphere at the time of the origin of life was CO₂-rich and that organic compounds such as amino acids would not have been efficiently formed abiotically under such conditions. It has been pointed out, however, that the previously reported low yields of amino acids may have been partially due to oxidation by nitrite/nitrate during acid hydrolysis. Specifically, the yield of amino acids was found to have increased significantly (by a factor of several hundred) after acid hydrolysis with ascorbic acid as an oxidation inhibitor. However, it has not been shown that CO₂ was the carbon source for the formation of the amino acids detected after acid hydrolysis with ascorbic acid. We therefore reinvestigated the prebiotic synthesis of amino acids in a CO₂-rich atmosphere using an isotope labeling experiment. Herein, we report that ascorbic acid does not behave as an appropriate oxidation inhibitor, because it contributes amino acid contaminants as a consequence of its reactions with the nitrogen containing species and formic acid produced during the spark discharge experiment. Thus, amino acids are not efficiently formed from a CO₂-rich atmosphere under the conditions studied.     

Estimating the number of protein molecules in a plant cell: protein and amino acid homeostasis during drought

During drought stress, cellular proteostasis on the one hand and amino acid homeostasis on the other hand are severely challenged, because the decrease in photosynthesis induces massive proteolysis, leading to drastic changes in both the proteome and the free amino acid pool. Thus, we selected progressive drought stress in Arabidopsis (Arabidopsis thaliana) as a model to investigate on a quantitative level the balance between protein and free amino acid homeostasis. We analyzed the mass composition of the leaf proteome based on proteomics datasets, and estimated how many protein molecules are present in a plant cell and its subcellular compartments. In addition, we calculated stress-induced changes in the distribution of individual amino acids between the free and protein-bound pools. Under control conditions, an average Arabidopsis mesophyll cell contains about 25 billion protein molecules, of which 80% are localized in chloroplasts. Severe water deficiency leads to degradation of more than 40% of the leaf protein mass, and thus causes a drastic shift in distribution toward the free amino acid pool. Stress-induced proteolysis of just half of the 340 million RubisCO hexadecamers present in the chloroplasts of a single mesophyll cell doubles the cellular content of free amino acids. A major fraction of the amino acids released from proteins is channeled into synthesis of proline, which is a compatible osmolyte. Complete oxidation of the remaining fraction as an alternative respiratory substrate can fully compensate for the lack of photosynthesis-derived carbohydrates for several hours.

A quantitative perspective on the protein and amino acid composition of a leaf cell illustrates the dimension and specific consequences of massive proteolysis induced by severe water deficit.     

Amino acid specificity of the transfer RNA species coded for by HeLa cell mitochondrial DNA

The amino acid specificity of the tRNA species coded for by HeLa cell mitochondrial DNA has been investigated by carrying out hybridizations between amino acid-tRNA complexes labeled in the amino acid and separated mitochondrial DNA strands.The results indicate that there are in HeLa cell mitochondria at least 17 distinct tRNA species hybridizable with mitochondrial DNA, which are specific for 16 amino acids. For 14 of the 16 amino acids, amino-acyl-tRNA synthetase activities distinct from the cytoplasmic ones have been detected in mitochondria. The remaining four amino acids (asparagine, glutamine, histidine and proline) have consistently failed to charge to any detectable extent mitochondrial tRNA species hybridizable with mitochondrial DNA.No obvious relationship appears to exist between the amino acids incorporated into tRNAs hybridizable to mitochondrial DNA and the previously observed pattern of chloramphenicol-sensitive amino acid incorporation by HeLa cell mitochondria.     

Amino Acids from Heterodera glycines

Amino acids emitted and extracted from surface-sterilized larvae and adults of Heterodera glycines were identified by paper chromatography and quantitatively analyzed by column chromatography. Five amino acids (alanine, aspartic acid, glutamic acid, glycine and serine) were emitted by H. glycines larvae and eight others (asparagine, glutamine, leucine/isoleucine, lysine, methionine sulfoxide, threonine, tyrosine, valine/methionine) were found in extracts from crushed larvae.In addition to the amino acids emitted or extracted from larvae, four others were emitted by adults (γ-aminobutyric acid, histidine, phenylalanine, and proline). Four different amino acids (arginine, cystathionine, hydroxyproline, and ornithine) were found only in the extract from crushed adults. Greater quantities of alanine, aspartic acid and glycine were emitted than could be detected in nematode extracts suggesting selective emission.Subsamples of nematode populations were taken from growing plants 19, 26, 33, and 40 days after inoculation and extracted to determine whether changes in specific amino acid content correlated with aging. Proline content shifted most, increasing from 4.1% to 21.5% of the total amino acid complement from the 19th to the 40th days.     

Evidence for the presence of N2-(1,3-dicarboxypropyl)-L-amino acids in crown-gall tumors induced by Agrobacterium tumefaciens strains 181 and EU6

Using crown-gall tumors induced by Agrobacterium tumefaciens strains 181 and EU6 several unusual compounds have been isolated in a single fraction. Physicochemical analysis of the compounds in this fraction showed that they are N²-(1,3-dicarboxypropyl)-L-amino acids derived from neutral and acidic amino acids. Asparagine and glutamine derivatives (asparaginopine and glutaminopine) are the main components. Synthesis of asparaginopine from asparagine, α-ketoglutarate and NADPH, and degradation of asparaginopine to asparagine have also been demonstrated using enzyme prepared from Pinto bean strain 181 tumor.     

Hydrogenation as an approach to study of reactions of oxidizing polyphenols with plant proteins

Coupling of oxidation products of o-diphenols with -NH₂ groups of plant proteins can damage nutritional availability of lysine residues. Relevant model coupling products (before or after reductive acetylation or permethylation) are unstable to acid hydrolysis. Hydrogenation over Rh/Al₂O₃, at room temperature and atmospheric pressure, gave cyclohexane derivatives stable to hydrolysis and retaining, with only partial hydrogenolysis, all groups originally attached to the aromatic nucleus. Plant bulk proteins were hydrogenated with substantial conversion of their aromatic amino acids; their S-containing amino acids were desulphurized. The technique is therefore promising for study of the fate of lysine residues in “enzymically browned” proteins.