scholarly journals Temperature and polarity based evolutionary model of the ribosomal complex in Thermus thermophilus and Escherichia coli

2019 ◽  
Author(s):  
Rashmi Tripathi
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Messenger Rna ◽  
Rna Binding ◽  
Rna World ◽  
Thermus Thermophilus ◽  
Evolutionary Model ◽  
Amino Acid Synthesis ◽  
Amino Acid Code

AbstractThe ribosome is considered a molecular fossil of the RNA world and is the oldest molecular machinery of living cells responsible for translating genetic information encoded by messenger RNA(mRNA) to proteins. Currently not much is known regarding how these proteins were assembled and the potential biogeochemical environment that could have shaped their evolution. In order to answer these questions, a comprehensive analysis of the amino acid frequencies of 30S and 50S ribosomal sub-units occurring in thermophile Thermus thermophilus and mesophile Escherichia coli was performed. The amino acid frequencies in proteins are believed to have been shaped by their pre-biotic abundances in the universe and by heavy bombardment of meteorites on planet earth (4.5-3.8 Ga). Absence of amino acid residues such as cysteine and tryptophan in T.thermophilus and E.coli proteins hints towards the evolution of small and large subunits prior to the origin of metabolic pathways of amino acid synthesis possibly under anoxic and sulphur free conditions. Moreover, an underrepresentation of readily oxidizable amino acids such as methionine, tyrosine and histidine, indicates that these proteins could have evolved in a more reducing environment as was prevalent on early earth. A comparison of amino acid biases with universal UNIPROT estimates, indicates arginine and lysine overrepresentation, linking a role of these amino acids in ribosomal RNA binding and stabilization corresponding to the RNA world hypothesis whereby RNA molecules drove the assembly of living systems. The continuing prevalence of these amino acid biases in modern proteins reflects the functional stability of ancient proteins constructed during billions of years of evolution and provides glimpses into the evolution of the ancient amino acid code. Step-wise accretion models involving increasing complexity of the amino acid code and the ribosomal sub-units are proposed for T.thermophilus and E.coli, providing potential insights regarding the origin of ribosomes in a temperature dependent and polar environment.

Enzymatic Synthesis of l - threo -β-Hydroxy-α-Amino Acids via Asymmetric Hydroxylation Using 2-Oxoglutarate-Dependent Hydroxylase from Sulfobacillus thermotolerans Y0017

2021 ◽  
Author(s):  
Ryotaro Hara ◽  
Yuta Nakajima ◽  
Hiroaki Yanagawa ◽  
Ryo Gawasawa ◽  
Izumi Hirasawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Enzymatic Synthesis ◽  
Scale Production ◽  
Dependent Manner ◽  
Amino Acid Synthesis ◽  
Preparative Scale ◽  
Whole Cell ◽  
Pharmaceutical Development

β-Hydroxy-α-amino acids are useful compounds for pharmaceutical development. Enzymatic synthesis of β-hydroxy-α-amino acids has attracted considerable interest as a selective, sustainable, and environmentally benign process. In this study, we identified a novel amino acid hydroxylase, AEP14369, from Sulfobacillus thermotolerans Y0017, which is included in a previously constructed CAS-like superfamily protein library, to widen the variety of amino acid hydroxylases. The detailed structures determined by nuclear magnetic resonance and X-ray crystallography analysis of the enzymatically produced compounds revealed that AEP14369 catalyzed threo -β-selective hydroxylation of l -His and l -Gln in a 2-oxoglutarate-dependent manner. Furthermore, the production of l - threo -β-hydroxy-His and l - threo -β-hydroxy-Gln was achieved using Escherichia coli expressing the gene encoding AEP14369 as a whole-cell biocatalyst. Under optimized reaction conditions, 137 mM (23.4 g L −1 ) l - threo -β-hydroxy-His and 150 mM l - threo -β-hydroxy-Gln (24.3 g L −1 ) were obtained, indicating that the enzyme is applicable for preparative-scale production. AEP14369, an l -His/ l -Gln threo -β-hydroxylase, increases the availability of 2-oxoglutarate-dependent hydroxylase and opens the way for the practical production of β-hydroxy-α-amino acids in the future. The amino acids produced in this study would also contribute to the structural diversification of pharmaceuticals that affect important bioactivities. Importance Owing to an increasing concern for sustainability, enzymatic approaches for producing industrially useful compounds have attracted considerable attention as a powerful complement to chemical synthesis for environment-friendly synthesis. In this study, we developed a bioproduction method for β-hydroxy-α-amino acid synthesis using a newly discovered enzyme. AEP14369 from the moderate thermophilic bacterium Sulfobacillus thermotolerans Y0017 catalyzed the hydroxylation of l -His and l -Gln in a regioselective and stereoselective fashion. Furthermore, we biotechnologically synthesized both l - threo -β-hydroxy-His and l - threo -β-hydroxy-Gln with a titer of over 20 g L −1 through whole-cell bioconversion using recombinant Escherichia coli cells. As β-hydroxy-α-amino acids are important compounds for pharmaceutical development, this achievement would facilitate future sustainable and economical industrial applications.

scholarly journals Petasis vs. Strecker Amino Acid Synthesis: Convergence, Divergence and Opportunities in Organic Synthesis

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1707
Author(s):  
Wayiza Masamba
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Organic Synthesis ◽  
Acid Synthesis ◽  
Physical Sciences ◽  
Amino Acid Synthesis

α-Amino acids find widespread applications in various areas of life and physical sciences. Their syntheses are carried out by a multitude of protocols, of which Petasis and Strecker reactions have emerged as the most straightforward and most widely used. Both reactions are three-component reactions using the same starting materials, except the nucleophilic species. The differences and similarities between these two important reactions are highlighted in this review.

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

Physiologische Bedeutung der „Stringent Control“ bei Escherichia coli unter extremen Hungerbedingungen / Stringent Control and Starvation Survival in Escherichia coli

1989 ◽  
Vol 44 (9-10) ◽  
pp. 838-844 ◽  
Author(s):  
H. Mach ◽  
M. Hecker ◽  
I. Hill ◽  
A. Schroeter ◽  
F. Mach
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Protein Turnover ◽  
Stringent Response ◽  
Phosphate Starvation ◽  
Pleiotropic Effects ◽  
Prolonged Starvation ◽  
Stringent Control ◽  
Starvation Survival

The viability of three isogenic relA+/relA strain pairs of Escherichia coli (CP78/CP79; NF 161/ NF162; CP 107/CP 143) was studied during prolonged starvation for amino acids, glucose or phosphate. After amino acid limitation we found a prolonged viability of all relA+ strains which synthesized ppGpp. We suggest that some ppGpp-mediated pleiotropic effects of the stringent response (e.g. glykogen accumulation, enhanced protein turnover) might be involved in this prolongation of survival. After glucose or phosphate starvation there was no difference in the relA+/relA strains either in the ppGpp content or in the survival.

scholarly journals Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

scholarly journals Characterization of the 6'-N-aminoglycoside acetyltransferase gene aac(6')-Im [corrected] associated with a sulI-type integron.

1997 ◽  
Vol 41 (2) ◽  
pp. 314-318 ◽  
Author(s):  
E Hannecart-Pokorni ◽  
F Depuydt ◽  
L de wit ◽  
E van Bossuyt ◽  
J Content ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Resistance Gene ◽  
Citrobacter Freundii ◽  
Gram Negative ◽  
Gene Environment ◽  
Insert Region ◽  
Klebsiella Spp

The amikacin resistance gene aac(6')-Im [corrected] from Citrobacter freundii Cf155 encoding an aminoglycoside 6'-N-acetyltransferase was characterized. The gene was identified as a coding sequence of 521 bp located down-stream from the 5' conserved segment of an integron. The sequence of this aac(6')-Im [corrected] gene corresponded to a protein of 173 amino acids which possessed 64.2% identity in a 165-amino-acid overlap with the aac(6')-Ia gene product (F.C. Tenover, D. Filpula, K.L. Phillips, and J. J. Plorde, J. Bacteriol. 170:471-473, 1988). By using PCR, the aac(6')-Im [corrected] gene could be detected in 8 of 86 gram-negative clinical isolates from two Belgian hospitals, including isolates of Citrobacter, Klebsiella spp., and Escherichia coli. PCR mapping of the aac(6')-Im [corrected] gene environment in these isolates indicated that the gene was located within a sulI-type integron; the insert region is 1,700 bases long and includes two genes cassettes, the second being ant (3")-Ib.

scholarly journals New aspects of amino acid metabolism in cancer

2019 ◽  
Vol 122 (2) ◽  
pp. 150-156 ◽  
Author(s):  
Lisa Vettore ◽  
Rebecca L. Westbrook ◽  
Daniel A. Tennant
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cancer Cells ◽  
Cancer Metabolism ◽  
Acid Synthesis ◽  
Response To Therapy ◽  
Direct Role ◽  
Amino Acid Synthesis ◽  
Metabolic Coupling ◽  
Abundant Supply

AbstractAn abundant supply of amino acids is important for cancers to sustain their proliferative drive. Alongside their direct role as substrates for protein synthesis, they can have roles in energy generation, driving the synthesis of nucleosides and maintenance of cellular redox homoeostasis. As cancer cells exist within a complex and often nutrient-poor microenvironment, they sometimes exist as part of a metabolic community, forming relationships that can be both symbiotic and parasitic. Indeed, this is particularly evident in cancers that are auxotrophic for particular amino acids. This review discusses the stromal/cancer cell relationship, by using examples to illustrate a number of different ways in which cancer cells can rely on and contribute to their microenvironment – both as a stable network and in response to therapy. In addition, it examines situations when amino acid synthesis is driven through metabolic coupling to other reactions, and synthesis is in excess of the cancer cell’s proliferative demand. Finally, it highlights the understudied area of non-proteinogenic amino acids in cancer metabolism and their potential role.

scholarly journals Amino Acid Toxicities of Escherichia coli That Are Prevented by Leucyl-tRNA Synthetase Amino Acid Editing

2007 ◽  
Vol 189 (23) ◽  
pp. 8765-8768 ◽  
Author(s):  
Vrajesh A. Karkhanis ◽  
Anjali P. Mascarenhas ◽  
Susan A. Martinis
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Trna Synthetase ◽  
Amino Acid Editing

ABSTRACT Leucyl-tRNA synthetase (LeuRS) has evolved an editing function to clear misactivated amino acids. An Escherichia coli-based assay was established to identify amino acids that compromise the fidelity of LeuRS and translation. Multiple nonstandard as well as standard amino acids were toxic to the cell when LeuRS editing was inactivated.

scholarly journals New Enzymatic Method of Chiral Amino Acid Synthesis by Dynamic Kinetic Resolution of Amino Acid Amides: Use of Stereoselective Amino Acid Amidases in the Presence of α-Amino-ε-Caprolactam Racemase

2007 ◽  
Vol 73 (16) ◽  
pp. 5370-5373 ◽  
Author(s):  
Shigenori Yamaguchi ◽  
Hidenobu Komeda ◽  
Yasuhisa Asano
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Kinetic Resolution ◽  
Acid Synthesis ◽  
Enzymatic Method ◽  
Ochrobactrum Anthropi ◽  
Dynamic Kinetic Resolution ◽  
Amino Acid Synthesis

ABSTRACT d- and l-amino acids were produced from l- and d-amino acid amides by d-aminopeptidase from Ochrobactrum anthropi C1-38 and l-amino acid amidase from Pseudomonas azotoformans IAM 1603, respectively, in the presence of α-amino-ε-caprolactam racemase from Achromobacter obae as the catalyst by dynamic kinetic resolution of amino acid amides.

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