scholarly journals Discovering the N-terminal Methylome by Repurposing of Proteomic Datasets

2021 ◽  
Author(s):  
Panyue Chen ◽  
Tiago Jose Paschoal Sobreira ◽  
Mark C. Hall ◽  
Tony Hazbun

AbstractProtein α-N-methylation is an underexplored post-translational modification involving the covalent addition of methyl groups to the free α-amino group at protein N-termini. To systematically explore the extent of α-N-terminal methylation in yeast and humans, we reanalyzed publicly accessible proteomic datasets to identify N-terminal peptides contributing to the α-N-terminome. This repurposing approach found evidence of α-N-methylation of established and novel protein substrates with canonical N-terminal motifs of established α-N-terminal methyltransferases, NTMT1/2 for humans, and Tae1 for yeast. NTMT1/2 has been implicated in cancer and aging processes. Moreover, α-N-methylation of non-canonical sequences was surprisingly prevalent, suggesting unappreciated and cryptic methylation events. Analysis of the amino acid frequencies of α-N-methylated peptides revealed a [S]1-[S/A/Q]2 pattern in yeast and [A/G/N]1-[A/S/V]2-[A]3 in humans, which differs from the canonical motif. We delineated the distribution of the two types of prevalent N-terminal modifications, acetylation and methylation, on amino acids at the 1st position. We tested three potentially methylated proteins and confirmed the α-N-terminal methylation of Hsp31. The other two proteins, Vma1 and Ssa3, were found to be predominantly acetylated indicating proteomic searching for α-N-terminal methylation can be difficult due to experimental approach or the methylated peptides are rare. This study demonstrates the feasibility of reprocessing proteomic data for global α-N-terminal methylome investigations. (Raw data deposited with PRIDE identifier: PXD022833)

1972 ◽  
Vol 50 (5) ◽  
pp. 538-542 ◽  
Author(s):  
J. C. Forest ◽  
F. Wightman

The different transaminase reactions for 22 protein amino acids were investigated in extracts of cotyledons and growing tissues of 8-day-old bushbean seedlings when either α-ketoglutarate, oxaloacetate, pyruvate, or glyoxylate was used as amino group acceptor. The results indicate that both cotyledons and growing tissues exhibited a similar pattern of transaminase activities with respect to the amino acids normally required for protein synthesis. It was found that with the exception of proline, hydroxyproline, and cystine which did not appear to be transaminated, and of serine and threonine which were transaminated only when pyruvate or glyoxylate was provided as the amino group acceptor, all the other 17 amino acids were transaminated to different extents when each of the four keto acids tested was supplied as the amino group acceptor. Glutamic acid, aspartic acid, and alanine were, by far, the best amino group donors and α-ketoglutarate was generally found to be the best amino acceptor. Consideration is given to the number and substrate specificity of the aminotransferases catalyzing the reactions demonstrated in this study.


1974 ◽  
Vol 141 (1) ◽  
pp. 113-118 ◽  
Author(s):  
T. C. Elleman

Studies of crude extracts of pea seeds (Pisum sativum, var. Green feast) revealed the presence of three enzymes that hydrolyse the amide bond of aminoacyl β-naphthylamides. They differ in their specificity towards the aminoacyl moiety; one is proline-specific, whereas the other two hydrolyse the β-naphthylamides of primary amino acids. Of the latter, one is highly specific for hydrophobic aminoacyl residues whereas the other has a broader, somewhat complementary specificity, showing preferential hydrolysis of non-hydrophobic aminoacyl residues. These latter two aminoacyl-β-naphthylamidases have been separated and partly characterized with regard to substrate specificity and antagonism by inhibitors. Both are true aminopeptidases, requiring the presence of a free amino group and hydrolysing the amide bonds of amino acid amides, dipeptides and oligopeptides consecutively from the N-terminal end.


2021 ◽  
Author(s):  
Jiarui Sun ◽  
Paul N. Evans ◽  
Emma J. Gagen ◽  
Ben J. Woodcroft ◽  
Brian P. Hedlund ◽  
...  

AbstractAsgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative organoheterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including deep subsurface, shallow lake, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four novel lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Hodarchaeia class nov. and Cand. Jordarchaeia class nov., derived from the gods Hod and Jord in Norse mythology. Metabolic inference suggests that both novel classes represent methylotrophic acetogens, encoding the transfer of methyl groups, such as methylated amines, to coenzyme M with acetate as the end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e. recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding on the other hand is restricted to Hodarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic lineage with an inferred complete Pyl machinery, likely providing this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of Bacteria and Eukaryotes, in both novel classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.


1948 ◽  
Vol 21 (4) ◽  
pp. 853-859
Author(s):  
R. F. A. Altman

Abstract As numerous investigators have shown, some of the nonrubber components of Hevea latex have a decided accelerating action on the process of vulcanization. A survey of the literature on this subject points to the validity of certain general facts. 1. Among the nonrubber components of latex which have been investigated, certain nitrogenous bases appear to be most important for accelerating the rate of vulcanization. 2. These nitrogen bases apparently occur partly naturally in fresh latex, and partly as the result of putrefaction, heating, and other decomposition processes. 3. The nitrogen bases naturally present in fresh latex at later stages have been identified by Altman to be trigonelline, stachhydrine, betonicine, choline, methylamine, trimethylamine, and ammonia. These bases are markedly active in vulcanization, as will be seen in the section on experimental results. 4. The nitrogenous substances formed by the decomposition processes have only partly been identified, on the one hand as tetra- and pentamethylene diamine and some amino acids, on the other hand as alkaloids, proline, diamino acids, etc. 5. It has been generally accepted that these nitrogenous substances are derived from the proteins of the latex. 6. Decomposition appears to be connected with the formation of a considerable amount of acids. 7. The production of volatile nitrogen bases as a rule accompanies the decomposition processes. These volatile products have not been identified. 8. The active nitrogen bases, either already formed or derived from complex nitrogenous substances, seem to be soluble in water but only slightly soluble in acetone.


1967 ◽  
Vol 45 (11) ◽  
pp. 2137-2153 ◽  
Author(s):  
A. Fuchs ◽  
R. Rohringer ◽  
D. J. Samborski

Wheat leaves infected with stem rust, especially those of susceptible plants, contained more phenylalanine and tyrosine than healthy leaves. The utilization of phenylalanine was increased in both the susceptible and resistant reaction, but the utilization of tyrosine was increased only in the susceptible reaction. No evidence of interconversion of these amino acids was obtained.In n-butanol extracts, which contained glycosides, many constituents were labelled after feeding of L-phenylalanine-U-14C. Most of the n-butanol extractives from resistant-reacting leaves contained more label than those from susceptible-reacting leaves or from healthy leaves. However, one of the n-butanol extractives from susceptible-reacting leaves was 5–10 times as active as that isolated from the other tissues.With L-phenylalanine-U-14C and ferulate-U-14C as precursors, more activity was recovered in insoluble than in soluble esters (of ferulate and p-coumarate). With L-tyrosine-U-14C as precursor, the reverse was observed. After infection, the proportion of label in insoluble esters increased more in resistant leaves than it did in susceptible leaves, regardless of the precursor used.A major portion of the activity from these precursors was recovered in the insoluble residue that contained protein and other polymers. In the experiment with L-phenylalanine-U-14C, this residue was fractionated into protein and non-hydrolyzable material. Susceptible-reacting leaves contained equal amounts of activity in these fractions, while resistant-reacting leaves incorporated 2.5 times as much activity into the non-hydrolyzable material as into protein.


2013 ◽  
Vol 55 ◽  
pp. 39-50 ◽  
Author(s):  
Hitoshi Nakatogawa

In autophagy, the autophagosome, a transient organelle specialized for the sequestration and lysosomal or vacuolar transport of cellular constituents, is formed via unique membrane dynamics. This process requires concerted actions of a distinctive set of proteins named Atg (autophagy-related). Atg proteins include two ubiquitin-like proteins, Atg12 and Atg8 [LC3 (light-chain 3) and GABARAP (γ-aminobutyric acid receptor-associated protein) in mammals]. Sequential reactions by the E1 enzyme Atg7 and the E2 enzyme Atg10 conjugate Atg12 to the lysine residue in Atg5, and the resulting Atg12–Atg5 conjugate forms a complex with Atg16. On the other hand, Atg8 is first processed at the C-terminus by Atg4, which is related to ubiquitin-processing/deconjugating enzymes. Atg8 is then activated by Atg7 (shared with Atg12) and, via the E2 enzyme Atg3, finally conjugated to the amino group of the lipid PE (phosphatidylethanolamine). The Atg12–Atg5–Atg16 complex acts as an E3 enzyme for the conjugation reaction of Atg8; it enhances the E2 activity of Atg3 and specifies the site of Atg8–PE production to be autophagy-related membranes. Atg8–PE is suggested to be involved in autophagosome formation at multiple steps, including membrane expansion and closure. Moreover, Atg4 cleaves Atg8–PE to liberate Atg8 from membranes for reuse, and this reaction can also regulate autophagosome formation. Thus these two ubiquitin-like systems are intimately involved in driving the biogenesis of the autophagosomal membrane.


1976 ◽  
Vol 154 (1) ◽  
pp. 43-48 ◽  
Author(s):  
J D Young ◽  
J C Ellory ◽  
E M Tucker

1. Uptake rates for 23 amino acids were measured for both normal (high-GSH) and GSH-deficient (low-GSH) erythrocytes from Finnish Landrace sheep. 2. Compared with high-GSH cells, low-GSH cells had a markedly diminished permeability to D-alanine, L-alanine, α-amino-n-butyrate, valine, cysteine, serine, threonine, asparagine, lysine and ornithine. Smaller differences were observed for glycine and proline, whereas uptake of the other amino acids was not significantly different in the two cell types.


1963 ◽  
Vol 53 (4) ◽  
pp. 681-713 ◽  
Author(s):  
R. G. Fennah

The feeding of the cacao thrips, Selenothrips rubrocinctus (Giard), on cashew, Anacardium occidentale, one of its host plants in Trinidad, West Indies, is considered in relation to the annual period of maximum population increase on this host and to the choice of feeding sites on individual leaves. On trees observed for three years, populations regularly increased during the dry season, from a low level in December and January to a peak in April or May, and then rapidly declined during the wet season. Even when thrips were most abundant, some trees were free from attack, and this could not be attributed to protective morphological features, to specific repellent substances in the leaf, or to chance. S. rubrocinctus was found to feed on leaves that were subjected to water-stress and to breed only on debilitated trees: the evidence suggested that the adequacy of its supply of nutrients depends on the induction of suitable metabolic conditions within the leaf by water-stress.Both nymphs and adults normally feed on the lower, stomata-bearing surface of the leaf, but in a very humid atmosphere only a weak preference is shown for this surface and if, under natural conditions, it is exposed to insolation by inversion of the leaf, the insects migrate to the other surface. Since the thrips were shown to be indifferent to bodily posture, the observation suggests that their behaviour is governed primarily by avoidance of exposure to undue heat or dryness and only secondarily by the attractiveness of the stomata-bearing surface.Leaves of cashew tend not to become infested while still immature, and become most heavily infested, if at all, soon after they have hardened. Breeding does not occur on senescent leaves. The positions of feeding thrips are almost random on leaves under abnormal water-stress, but otherwise conform to certain patterns that mainly develop in fixed sequence. On reversal of an undetached leaf and consequent transfer of thrips from one surface to the other, there is no appreciable change in their distribution pattern or the apparent acceptability of the substrate. Changes of pattern were readily induced by injury to the plant during a period of water-stress and less easily, or not at all, when water-stress was low. Injury of areas of the leaf by heat was followed by their colonisation by thrips, and partial severance of branches by increased attack on their leaves.Leaves detached from uninfested trees invariably became acceptable for feeding within four hours. During this period, leaf water-content declined and the ratios of soluble-carbohydrate content and α-amino acids to fresh-leaf weight fell slightly and rose considerably, respectively. In the field, the latter ratio was invariably higher for infested than for uninfested leaf tissue, even on portions of the same leaf. If the nutrient value of leaf tissue is determined by the rate at which α-amino acids are extractable through a stylet puncture, the observed change in acceptability for feeding following plucking may be accounted for by the increase in α-amino-acid concentration. Feeding that is restricted on any one tree to the margins of local leaf injuries during prolonged high water-stress and totally absent when stress is low can be correlated with an α-amino-acid content in the living marginal tissue that is high or low, respectively. The ability of thrips to establish themselves and breed on leaves of a particular tree in the dry season and their failure to do so on leaves of the same tree in the wet season conforms with the greater or less amino-acid concentration occurring in the leaf at these respective times.


1994 ◽  
Vol 196 (1) ◽  
pp. 297-305 ◽  
Author(s):  
H N Christensen ◽  
A A Greene ◽  
D K Kakuda ◽  
C L MacLeod

We point out an ability of certain amino acids to be recognized at a biological receptor site as though their amino group bore, instead of an alpha relationship to a carboxylate group, a beta, gamma or delta relationship to the same or a second carboxylate group. For aspartate, the unbalanced position of its amino group between a pair of carboxylates allows its occasional biorecognition as a beta-rather than as an alpha-amino acid, whereas for proline and its homologs, their cyclic arrangement may allow the imino group, without its being replicated, to be sensed analogously as falling at either of two distances from the single carboxylate group. The greater separation might allow proline to be seen as biologically analogous to gamma-aminobutyric acid. This more remote positioning of the imino group would allow the D-form of both amino acids to present its amino group in the orientation characteristic of the natural L-form. The dual modes of recognition should accordingly be signalled by what appears to be low stereospecificity, actually due to a distinction in the enantiorecognition of the two isomers. Competing recognition for transport between their respective D- and L-forms, although it does not prove that phenomenon, has been shown for proline and, significantly, even more strongly for its lower homolog, 2-azetidine carboxylate. Such indications have so far revealed themselves rather inconspicuously for the central nervous system binding of proline, reviewed here as a possible feature of a role suspected for proline in neurotransmission.


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