PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 11591477

Preferential usage of some minor codons in bacteria.

H Ohno·H Sakai·T Washio·M Tomita
View original source ↗Export metadata ↓

Abstract

In many bacterial species, such as Deinococcus radiodurans, Haemophilus influenzae, and Methanobacterium thermoautotrophicum, some minor codons are preferentially used near the initiation codon. Among these codons, there are some minor codons that have strong preference for the initiation site in the high codon adaptation index (CAI) group (comprising of highly expressed genes) rather than in the low CAI genes group (comprising of low expressing genes). In the present study, codon usage in the initiation site and in the rest of the gene was systematically compared in the 27 complete bacterial genomes and Saccharomyces cerevisiae genome. Furthermore, we classified genes into two groups according to the CAI values and conducted the same analysis for each of the two groups. Our results suggest a role for some minor codons in the initiation site of the regulating translation system in many bacteria. We have summarized codons that are preferentially used in the initiation site and probably play a role in regulating genes expression in these organisms.

Explore related subjects

Amino AcidsBacteriaBase SequenceCodonCodon, InitiatorGenes, BacterialGenome, BacterialSpecies SpecificityJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

H Ohno, H Sakai, T Washio, M Tomita. 2001-10-03. Preferential usage of some minor codons in bacteria.. https://doi.org/10.1016/s0378-1119(01)00670-9

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Chimeric structural isomer fragments as cost-efficient internal standards for amino acid quantification by mass spectrometry.

Amino acid (AA) profiles from body fluids such as blood and urine are clinical indicators for diagnosing metabolic and hepatic diseases. Current quantitative methods, such as liquid chromatography-mass spectrometry (LC-MS) with isotopically labelled internal standards (ISs), are costly and technically demanding. This study proposes a cost-efficient alternative using structural isomers as ISs in a direct liquid infusion (DLI) tandem mass spectrometry (MS/MS) approach. The method leverages chimeric spectra and fragment intensity ratios to quantify AAs, demonstrating high linearity and precision even with a 3D ion trap mass analyser. This approach offers a viable strategy for AA quantification in preventive medicine, particularly for screening metabolic diseases such as phenylketonuria, diabetes, and liver dysfunction.

Amino Acids↗
PubMed2007

MODEL-molecular descriptor lab: a web-based server for computing structural and physicochemical features of compounds.

Molecular descriptors represent structural and physicochemical features of compounds. They have been extensively used for developing statistical models, such as quantitative structure activity relationship (QSAR) and artificial neural networks (NN), for computer prediction of the pharmacodynamic, pharmacokinetic, or toxicological properties of compounds from their structure. While computer programs have been developed for computing molecular descriptors, there is a lack of a freely accessible one. We have developed a web-based server, MODEL (Molecular Descriptor Lab), for computing a comprehensive set of 3,778 molecular descriptors, which is significantly more than the approximately 1,600 molecular descriptors computed by other software. Our computational algorithms have been extensively tested and the computed molecular descriptors have been used in a number of published works of statistical models for predicting variety of pharmacodynamic, pharmacokinetic, and toxicological properties of compounds. Several testing studies on the computed molecular descriptors are discussed. MODEL is accessible at http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi free of charge for academic use.

Amino Acids↗
PubMed2007

The penicillin G acylase production by B. megaterium is amino acid consumption dependent.

Aiming at to enhance the production of penicillin G acylase (PGA) by Bacillus megaterium, we have performed flasks experiments using different medium composition. Using 51 g/L of casein hydrolyzed with Alcalase and 2.7 g/L of phenylacetic acid (PhAc), the following carbon substrates were tested, individually and combined: glucose, glycerol, and lactose (present in cheese whey). Glycerol and glucose showed to be effective nutrients for the microorganism growth but delayed the PGA production. Cheese whey always increased enzyme production and cell mass. However, lactose (present in cheese whey) was not a significant carbon source for B. megaterium. PhAc, amino acids, and small peptides present in the hydrolyzed casein were the actual carbon sources for enzyme production. Replacement of hydrolyzed casein by free amino acids, 10.0 g/L, led to a significant increase in enzyme production (app. 150%), with a preferential consumption of alanine, aspartic acid, glycine, serine, arginine, threonine, lysine, and glutamic acid. A decrease of the enzyme production was observed when 20.0 g/L of amino acids were used. Using the single omission technique, it was shown that none of the 18 tested amino acids was essential for enzyme production. The use of a medium containing eight of the preferentially consumed amino acids lead to similar enzyme production level obtained when using 18 amino acids. PhAc, up to 2.7 g/L, did not inhibit enzyme production, even if added at the beginning of the cultivation.

Amino Acids↗