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1.
If the enzymes responsible for biosynthesis of a given amino acid are repressed and the cognate amino acid pool suddenly depleted, then derepression of these enzymes and replenishment of the pool would be problematic, if the enzymes were largely composed of the cognate amino acid. In the proverbial "Catch 22", cells would lack the necessary enzymes to make the amino acid, and they would lack the necessary amino acid to make the needed enzymes. Based on this scenario, we hypothesize that evolution would lead to the selection of amino acid biosynthetic enzymes that have a relatively low content of their cognate amino acid. We call this the "cognate bias hypothesis". Here we test several implications of this hypothesis directly using data from the proteome of Escherichia coli. Several lines of evidence show that low cognate bias is evident in 15 of the 20 amino acid biosynthetic pathways. Comparison with closely related Salmonella typhimurium shows similar results. Comparison with more distantly related Bacillus subtilis shows general similarities as well as significant differences in the detailed profiles of cognate bias. Thus, selection for low cognate bias plays a significant role in shaping the amino acid composition for a large class of cellular proteins. 相似文献
2.
Jun.-Prof. Dr. Christoph Kaleta Sascha Schäuble Ursula Rinas Stefan Schuster 《Biotechnology journal》2013,8(9):1105-1114
Escherichia coli is the most popular microorganism for the production of recombinant proteins and is gaining increasing importance for the production of low-molecular weight compounds such as amino acids. The metabolic cost associated with the production of amino acids and (recombinant) proteins from glucose, glycerol and acetate was determined using three different computational techniques to identify those amino acids that put the highest burden on the biosynthetic machinery of E. coli. Comparing the costs of individual amino acids, we find that methionine is the most expensive amino acid in terms of consumed mol of ATP per molecule produced, while leucine is the most expensive amino acid when taking into account the cellular abundances of amino acids. Moreover, we show that the biosynthesis of a large number of amino acids from glucose and particularly from glycerol provides a surplus of energy, which can be used to balance the high energetic cost of amino acid polymerization. 相似文献
3.
Yanxia Zhou Pan Shen Qiuyan Lan Chen Deng Yao Zhang Yanchang Li Wei Wei Yihao Wang Na Su Ping Xu 《Proteomics》2017,17(13-14)
Deinococcus radiodurans is a robust bacterium best known for its capacity to resist to radiation. In this study, the SDS‐PAGE coupled with high‐precision LC‐MS/MS was used to study the D. radiodurans proteome. A total of 1951 proteins were identified which covers 63.18% protein‐coding genes. Comparison of the identified proteins to the key enzymes in amino acid biosyntheses from KEGG database showed the methionine biosynthesis module is incomplete while other amino acid biosynthesis modules are complete, which indicated methionine auxotrophy in D. radiodurans. The subsequent amino acid‐auxotrophic screening has verified methionine instead of other amino acids is essential for the growth of D. radiodurans. With molecular evolutionary genetic analysis, we found the divergence in methionine biosynthesis during the evolution of the common ancestor of bacteria. We also found D. radiodurans lost the power of synthesizing methionine because of the missing metA and metX in two types of methionine biosyntheses. For the first time, this study used high‐coverage proteome analysis to identify D. radiodurans amino acid auxotrophy, which provides the important reference for the development of quantitative proteomics analysis using stable isotope labeling in metabolomics of D. radiodurans and in‐depth analysis of the molecular mechanism of radiation resistance. 相似文献
4.
Melhorn V Matsumi K Koiwai H Ikegami K Okamoto M Nambara E Bittner F Koshiba T 《Journal of plant research》2008,121(1):125-131
Abscisic acid (ABA) regulates stomatal closure in response to water loss. Here, we examined the competence of guard cells
to synthesize ABA, using two Arabidopsis ABA biosynthetic enzymes. 35S pro::AtNCED3-GFP and AAO3-GFP were introduced into guard cells of broad bean leaves. AtNCED3-GFP expression was detected at the chloroplasts, whereas green
fluorescent protein (GFP) and AAO3-GFP were in the cytosol. The stomatal aperture was decreased in AtNCED3-GFP- and AAO3-GFP-transformed guard cells. This indicated that ABA biosynthesis is stimulated by heterologous expression of AtNCED3 and Arabidopsis
aldehyde oxidase 3 (AAO3) proteins, which both seem to be regulatory enzymes for ABA biosynthesis in these cells. Furthermore,
stomatal closure by the expression of AtNCED3 and AAO3 suggested that the substrates of the enzymes are present and native
ABA-biosynthesis enzymes are active in guard cells.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
V. Melhorn and K. Matsumi contributed equally to this work. 相似文献
5.
For most proteins, multiple sequence alignments are a viable method to identify functionally and structurally important amino
acids, but for most organisms, there is a subset of proteins that are unique or found in a few closely related organisms.
For these proteins, it is not possible to produce sequence alignments that are useful in identifying functionally or structurally
important amino acids. We have investigated the relationship between amino acid conservation and five factors (the amino acid’s
identity, N-terminal neighbor, C-terminal neighbor, the local hydropathy of surrounding amino acids, and the local expected
net charge of the surrounding amino acids based on the primary sequence) in Escherichia coli proteins. For four of the factors examined (all but the amino acid’s identity), there is a significant relationship with
conservation for some of the standard 20 amino acids. Using the combination of all five factors, we show that it is possible
to calculate a score based on the primary sequences of a subset of E. coli proteins that has statistically significant predictive value with respect to predicting conserved amino acids in other E. coli proteins and Saccharomyces cerevisiae proteins. As these five variables show significant relationships with conservation, we have termed them conservation factors.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Raiford DW Heizer EM Miller RV Akashi H Raymer ML Krane DE 《Journal of molecular evolution》2008,67(6):621-630
Prokaryotic organisms preferentially utilize less energetically costly amino acids in highly expressed genes. Studies have
shown that the proteome of Saccharomyces cerevisiae also exhibits this behavior, but only in broad terms. This study examines the question of metabolic efficiency as a proteome-shaping
force at a finer scale, examining whether trends consistent with cost minimization as an evolutionary force are present independent
of protein function and amino acid physicochemical property, and consistently with respect to amino acid biosynthetic costs.
Inverse correlations between the average amino acid biosynthetic cost of the protein product and the levels of gene expression
in S. cerevisiae are consistent with natural selection to minimize costs. There are, however, patterns of amino acid usage that raise questions
about the strength (and possibly the universality) of this selective force in shaping S. cerevisiae’s proteome. 相似文献
10.
Koutaniemi S Warinowski T Kärkönen A Alatalo E Fossdal CG Saranpää P Laakso T Fagerstedt KV Simola LK Paulin L Rudd S Teeri TH 《Plant molecular biology》2007,65(3):311-328
Lignin biosynthesis is a major carbon sink in gymnosperms and woody angiosperms. Many of the enzymes involved are encoded
for by several genes, some of which are also related to the biosynthesis of other phenylpropanoids. In this study, we aimed
at the identification of those gene family members that are responsible for developmental lignification in Norway spruce (Picea abies (L.) Karst.). Gene expression across the whole lignin biosynthetic pathway was profiled using EST sequencing and quantitative
real-time RT-PCR. Stress-induced lignification during bending stress and Heterobasidion annosum infection was also studied. Altogether 7,189 ESTs were sequenced from a lignin forming tissue culture and developing xylem
of spruce, and clustered into 3,831 unigenes. Several paralogous genes were found for both monolignol biosynthetic and polymerisation-related
enzymes. Real-time RT-PCR results highlighted the set of monolignol biosynthetic genes that are likely to be responsible for
developmental lignification in Norway spruce. Potential genes for monolignol polymerisation were also identified. In compression
wood, mostly the same monolignol biosynthetic gene set was expressed, but peroxidase expression differed from the vertically
grown control. Pathogen infection in phloem resulted in a general up-regulation of the monolignol biosynthetic pathway, and
in an induction of a few new gene family members. Based on the up-regulation under both pathogen attack and in compression
wood, PaPAL2, PaPX2 and PaPX3 appeared to have a general stress-induced function.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
11.
Eveline J. Krab Johannes H. C. Cornelissen Simone I. Lang Richard S. P. van Logtestijn 《Plant and Soil》2008,304(1-2):199-208
Plants that can take up amino acids directly from the soil solution may have a competitive advantage in ecosystems where inorganic
nitrogen sources are scarce. We hypothesized that diverse mosses in cold, N-stressed ecosystems share this ability. We experimentally
tested 11 sub-arctic Swedish moss species of wide-ranging taxa and growth form for their ability to take up double labelled
(15N and 13C) glycine and aspartic acid in a laboratory setup as well as in a realistic field setting. All species were able to take
up amino acids injected into the soil solution to some extent, although field uptake was marginal to absent for the endohydric
Polytrichum commune. The 11 moss species on average took up 36 ± 5% of the injected glycine and 18 ± 2% of the aspartic acid in the lab experiment.
Field uptake of both glycine (24 ± 5%) and aspartic acid (10 ± 2%) was lower than in the lab. Overall differences in uptake
amongst species appeared to be positively associated with habitat wetness and/or turf density among different Sphagnum species and among non-Sphagnum species, respectively. Species from habitats of lower inorganic N availability, as indicated tentatively by lower tissue
N concentrations, showed relatively strong amino acid uptake, but this was only significant for the field uptake among non-Sphagnum mosses. Further experiments are needed to test for consistent differences in amino acid uptake capacity among species and
functional groups as determined by their functional traits, and to test how the affinity of cold-biome mosses for amino acids
compares to that for ammonium or nitrate. Still, our results support the view that widespread moss species in cold, N-stressed
ecosystems may derive a significant proportion of their nitrogen demand from free amino acids. This might give them a competitive
advantage over plants that depend strongly on inorganic N sources.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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13.
Swire J 《Journal of molecular evolution》2007,64(5):558-571
Most investigations of the forces shaping protein evolution have focussed on protein function. However, cells are typically
50%–75% protein by dry weight, with protein expression levels distributed over five orders of magnitude. Cells may, therefore,
be under considerable selection pressure to incorporate amino acids that are cheap to synthesize into proteins that are highly
expressed. Such selection pressure has been demonstrated to alter amino acid usage in a few organisms, but whether “cost selection”
is a general phenomenon remains unknown. One reason for this is that reliable protein expression level data is not available
for most organisms. Accordingly, I have developed a new method for detecting cost selection. This method depends solely on
interprotein gradients in amino acid usage. Applying it to an analysis of 43 whole genomes from all three domains of life,
I show that selection on the synthesis cost of amino acids is a pervasive force in shaping the composition of proteins. Moreover,
some amino acids have different price tags for different organisms—the cost of amino acids is changed for organisms living
in hydrothermal vents compared with those living at the sea surface or for organisms that have difficulty acquiring elements
such as nitrogen compared with those that do not—so I also investigated whether differences between organisms in amino acid
usage might reflect differences in synthesis or acquisition costs. The results suggest that organisms evolve to alter amino
acid usage in response to environmental conditions.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
[Reviewing Editor: Hector Musto] 相似文献
14.
Aminoacyl-tRNAs (aa-tRNAs) are the essential substrates for translation. Most aa-tRNAs are formed by direct aminoacylation of tRNA catalyzed by aminoacyl-tRNA synthetases. However, a smaller number of aa-tRNAs (Asn-tRNA, Gln-tRNA, Cys-tRNA and Sec-tRNA) are made by synthesizing the amino acid on the tRNA by first attaching a non-cognate amino acid to the tRNA, which is then converted to the cognate one catalyzed by tRNA-dependent modifying enzymes. Asn-tRNA or Gln-tRNA formation in most prokaryotes requires amidation of Asp-tRNA or Glu-tRNA by amidotransferases that couple an amidase or an asparaginase to liberate ammonia with a tRNA-dependent kinase. Both archaeal and eukaryotic Sec-tRNA biosynthesis and Cys-tRNA synthesis in methanogens require O-phosophoseryl-tRNA formation. For tRNA-dependent Cys biosynthesis, O-phosphoseryl-tRNA synthetase directly attaches the amino acid to the tRNA which is then converted to Cys by Sep-tRNA: Cys-tRNA synthase. In Sec-tRNA synthesis, O-phosphoseryl-tRNA kinase phosphorylates Ser-tRNA to form the intermediate which is then modified to Sec-tRNA by Sep-tRNA:Sec-tRNA synthase. Complex formation between enzymes in the same pathway may protect the fidelity of protein synthesis. How these tRNA-dependent amino acid biosynthetic routes are integrated into overall metabolism may explain why they are still retained in so many organisms. 相似文献
15.
Benjamin L. de Bivort Ethan O. Perlstein Sam Kunes Stuart L. Schreiber 《Journal of molecular evolution》2009,68(5):490-497
The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations
of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle
of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their
precursor’s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the
S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation
in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms
using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the
preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino
acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids
(e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed
proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been
modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating
endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Benjamin L. de Bivort and Ethan O. Perlstein have contributed equally to this work. 相似文献
16.
The development of seeds depends on the import of carbohydrates and amino acids supplied by the maternal tissue via the phloem.
Several amino acid transporters have been reported to be expressed during seed and silique development in Arabidopsis thaliana (L.) Heynh. Here we show that mutants lacking the high affinity amino acid permease 8 (At1g10010) display a severe seed phenotype.
The overall number of seeds and the number of normally developed seed is reduced by ∼50% in siliques of the Ataap8 T-DNA insertion mutant. This result could be reproduced in plants where expression of AtAAP8 is targeted with an RNAi approach. The seed phenotype is correlated with a specifically altered amino acid composition of
young siliques. Aspartic acid and glutamic acid are significantly reduced in young siliques of the mutants. In correlation
with the fact that AAP8 is a high affinity transporter for acidic amino acids, translocation of 14C-labelled aspartate fed via the root system to seeds of the mutants is reduced. AAP8 plays a crucial role for the uptake
of amino acids into the endosperm and supplying the developing embryo with amino acids during early embryogenesis. 相似文献
17.
Summary. Various α/β amino acid derivatives 5 were attached to compounds 3 to yield 2,3-dihydro-1H-pyrrol-3-ones amino acids derivatives 6. This rare heterocyclic amino acid skeleton including the pyrrolo[1,2-b][1,3]oxazol moiety was also successfully prepared
in the esteric form. The structure of the new compounds was characterized by spectroscopic methods. 相似文献
18.
The complexity of the regulatory mechanisms that govern amino acid biosynthesis, particularly in multibranched pathways, frequently results in sensitivity to growth inhibition by exogenous amino acids. Usually the inhibition caused by a given amino acid(s) is relieved by another amino acid(s), thus indicating the cause of inhibition to be a specific interference with endogenous formation of the latter amino acid(s). We recently summarized the evidence that Nicotiana silvestris (and probably most higher plants), in suspension culture, exhibits a separate phenomenon of amino acid mediated growth inhibition called general amino acid inhibition. Every amino acid provokes general amino acid inhibition except for
-glutamine. In fact,
-glutamine completely overcomes general amino acid inhibition. We have now demonstrated that specific amino acid inhibition can be recognized and characterized at the level of growth inhibition without interference caused by general amino acid inhibition by the simple provision of exogenous
-glutamine. Several examples of specific amino acid inhibition of growth were demonstrated in N. silvestris. In one case,
-threonine inhibits growth partially in the presence of
-glutamine. The residual amino acid inhibition was overcome by the additional presence of
-lysine and
-methionine, indicating that exogenous
-threonine specifically inhibits the biosynthesis of both
-lysine and
-methionine. As a second example, the
-valine-mediated inhibition of growth that persisted in the presence of
-glutamine was overcome by
-isoleucine, indicating that exogenous
-valine inhibits
-isoleucine biosynthesis. The use of amino acid analogs as experimental tools for biochemical-genetic studies in higher plants is also complicated by general amino acid inhibition. Conditions were demonstrated under which p-fluorophenylalanine and m-fluorotyrosine could be used as specific antimetabolites of
-phenylalanine and
-tyrosine biosynthesis without interference from general amino acid inhibition. We thus present a rigorous basis for recognition of specific relationships between metabolic branches that can guide detailed enzymological analyses. 相似文献
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19.
The Arabidopsis thaliana At2g01170 gene is annotated as a putative gamma amino butyric acid (GABA) permease based on its sequence similarity to a
yeast GABA transporting gene (UGA4). A cDNA of At2g01170 was expressed in yeast and analyzed for amino acid transport activity. Both direct measurement of amino
acid transport and yeast growth experiments demonstrated that the At2g01170 encoded-protein exhibits transport activity for
alanine, arginine, glutamate and lysine, but not for GABA or proline. Significantly, unlike other amino acid transporters
described in plants to date, At2g01170 displayed both export and import activity. Based on that observation, it was named
bidirectional amino acid transporter 1 (BAT1). Sequence comparisons show BAT1 is not a member of any previously defined amino acid transporter family. It does share,
however, several conserved protein domains found in a variety of prokaryotic and eukaryotic amino acid transporters, suggesting
membership in an ancient family of transporters. BAT1 is a single copy gene in the Arabidopsis genome, and its mRNA is ubiquitously expressed in all organs. A transposon—GUS gene-trap insert in the BAT1 gene displays GUS localization in the vascular tissues (Dundar in Ann Appl Biol, 2009) suggesting BAT1 may function in amino acid export from the phloem into sink tissues. 相似文献