A genetic code Boolean structure. I. The meaning of Boolean deductions

This paper proposes a genetic code Boolean structure derived from hydrogen bond numbers and chemical types of bases, purines and pyrimidines. It shows that in such Boolean structure, deductions comprise physico-chemical meaning. In particular, codons with adenine as a second base coding to hydrophilic amino acids are not deductible from codons with uracil in the same position, which code to hydrophobic amino acids. Boolean deductions could help us describe the gene evolution process. For instance, most of the reported mutations that confer drug resistance to the HIV protease gene correspond to deductions. What is more, in the human beta-globin gene a similar situation appears where most of the single codon mutations correspond to Boolean deductions from the respective wild-type codon.     

Entropy of the genetic information and evolution

The entropy of the amino acid sequences coded by DNA is considered as a measure of diversity or variety of proteins, and is taken as a measure of evolution. The DNA or m-RNA sequence is corsidered as a stationary second-order Markov chain composed of four kinds of bases. Because of the biased nature of the genetic code table, increase of entropy of amino acid sequences is possible with biased nucleotide sequence. Thus the biased DNA base composition and the extreme rarity of the base doubletC _p G of higher organisms are explained. It is expected that the amino acid composition was highly biased at the days of the origin of the genetic code table, and the more frequent amino acids have tended to get rarer, and the rarer ones more frequent. This tendency is observed in the evolution of hemoglobin, cytochrome C, fibrinopeptide, immunoglobulin and lysozyme, and protein as a whole.     

Translation of immobilized genetic information by yeast cell-free protein synthesizing system

A cell-free protein-synthesizing system for the purpose of specific genetic information translation was constructed: ribosome, t-RNA, and enzymes extracted from yeast cells were combined with an immobilized mRNA. The soluble fraction mixed with energy sources and amino acids was incubated with the immobilized mRNA such as poly(U), yeast mRNA, and myeloma mRNA to incorporate [(3)H]phenylalanine into polypeptides of de novo synthesis. By supplying amino acids to these protein-synthesizing systems, amino acid incorporation was ascertained. Lower efficiency of the incorporation in the immobilized system than that of the homogeneous system was mainly attributed to the heterogeneous reaction where the mass-transfer process is diffusion limited. Results obtained show the possibility of a system for specific translation of a desired genetic code.     

Amino Acid Homochirality may be Linked to the Origin of Phosphate-Based Life

Phosphorylation has to have been one of the key events in prebiotic evolution on earth. In this article, the emergence of phosphoryl amino acid 5′-nucleosides having a P–N bond is described as a model of the origin of amino acid homochirality and Genetic Code. It is proposed that the intramolecular interaction between the nucleotide base and the amino acid side-chain influences the stability of particular amino acid 5′-nucleotides, and the interaction also selects for the chirality of amino acids. The differences between l- and d-conformation energies (ΔE _conf) are evaluated by DFT methods at the B3LYP/6-31G(d) level. Although, as expected, these ΔE _conf values are not large, they do give differences in energy that can distinguish the chirality of amino acids. Based on our calculations, the chiral selection of the earliest amino acids for l-enantiomers seems to be determined by a clear stereochemical/physicochemical relationship. As later amino acids developed from the earliest amino acids, we deduce that the chirality of these late amino acids was inherited from that of the early amino acids. This idea reaches far back into evolution, and we hope that it will guide further experiments in this area.     

The effects of dietary protein:energy ratio and amino acid pattern on nitrogen utilization and excretion of rainbow trout Oncorhynchus mykiss (Walbaum)

This study was undertaken to investigate: (1) the effects of both deficiencies and excesses in essential amino acids (EAAs) from an estimated optimum dietary EAA pattern on nitrogen (N) utilization and excretion of rainbow trout Oncorhynchus mykiss, (2) the effects of dietary digestible protein (P_D): digestible energy (E_D) ratio (P_D:E_D) on N utilization and excretion of O. mykiss and (3) the potential interaction of these two factors. A 3 × 3 factorial experiment was conducted, with the two factors EAA pattern and P_D:E_D ratio. The three levels of EAA pattern were: (1) optimum EAA pattern, (2) 60% deficiencies in the three amino acids arginine, histidine and lysine, and (3) 60% excesses in the three amino acids arginine, histidine and leucine. The three levels of P_D:E_D ratio were 18, 21 and 24 g MJ^?1. Amino acid deficiencies from an optimum amino acid pattern caused reductions in mean N retention of 29 to 37%, with the greatest reduction associated with the lowest P_D:E_D ratio, and similar substantial increases in total N and ammonia‐N excretion at all of the dietary P_D:E_D ratios investigated. Amino acid excesses, however, did not negatively affect N retention or excretion. Increasing P_D:E_D ratio was associated with decreasing N retention and increasing N excretion over the range of dietary protein and lipid levels tested. Results of this study showed that a diet with optimum dietary amino acid pattern and lowest P_D:E_D ratio produced the highest N retention (47% of ingested N) and the lowest total N and ammonia‐N excretion of O. mykiss.     

A methanogen hosted the origin of the genetic code

A comparison is made between orthologous proteins from a methanogen (Methanopyrus kandleri) and from a non-methanogen (Pyrococcus abyssi) in order to determine the amino acid substitution pattern. This analysis makes it possible to establish which amino acids are significantly and asymmetrically utilised by these two organisms. A methanophily index (MI) based on this asymmetry makes it possible for any protein to be associated with a numerical value which, when calculated for the same orthologous protein from methanogenic and non-methanogenic organisms, turns out to have the power to discriminate between these two groups of organisms, even if only for about 20% of the analysed proteins. The MI can also be associated to the genetic code under the assumption that the frequency of synonymous codons specifying the amino acids in the genetic code also reflects the frequency with which amino acids appeared in ancestral proteins. Finally a t-test shows that the MI value associated to the genetic code is not different from the mean value of the MI deriving from methanogen proteins, but it differs from the mean MI of non-methanogen proteins. This might indicate that the genetic code evolved in a methanogenic ‘organism’.     

Harmonic analysis of Boolean networks: determinative power and perturbations

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer this question, a notion that quantifies the determinative power of an input over the states of the nodes in the network is needed. We argue that the mutual information (MI) between a given subset of the inputs X={X₁,...,X_n} of some node i and its associated function f_i(X) quantifies the determinative power of this set of inputs over node i. We compare the determinative power of a set of inputs to the sensitivity to perturbations to these inputs, and find that, maybe surprisingly, an input that has large sensitivity to perturbations does not necessarily have large determinative power. However, for unate functions, which play an important role in genetic regulatory networks, we find a direct relation between MI and sensitivity to perturbations. As an application of our results, we analyze the large-scale regulatory network of Escherichia coli. We identify the most determinative nodes and show that a small subset of those reduces the overall uncertainty of the network state significantly. Furthermore, the network is found to be tolerant to perturbations of its inputs.     

Entity evidence for differentiation between Tia and Tib types of soybean Kunitz trypsin inhibitor: detection of a novel transitional variant type between Tia and Tib in wild soybean (Glycine soja Sieb. & Zucc.)

Soybean Kunit trypsin inhibitor (SKTI) has several polymorphic types. Of these SKTI, there are large differences of nine amino acid substitutions between Tia and Tib. So far no transitional type between them has been found. A novel transitional intermediate variant between Tia and Tib was detected in 11 lines from 720 Japanese wild soybeans (Glycine soja Sieb. & Zucc.). This variant showed identical electrophoretic mobility to Tib in the Davis system polyacrylamide gel electrophoresis (PAGE), but higher electric points than other SKTI proteins (Tia, Tib, Tic) in isoelectric focusing PAGE. The genetic analysis of SKTI in F₂ seeds from a cross between the novel variant type and Tib showed that this variant type is inherited as codominant alleles in a multiple allelic system at an SKTI locus. This variant also showed inhibitory activity to trypsin. We propose the genetic symbol Ti b ⁱ⁵ for this novel variant. The sequence analysis of Tib ⁱ⁵ revealed that six nucleotides were different between Tib ⁱ⁵ and Tia, and the nucleotides of these mutated positions were identical to Tib. This causes substitution of five amino acids at the residue position 62 (Tyr→Phe), 74 (Ser→Arg), 114 (Met→Val), 120 (Leu→Ile) and 137 (Pro→Thr). These substitutive amino acids are completely in accord with the amino acids of Tib, showing that Tib ⁱ⁵ is an intermediate between Tia and Tib types. Tib ⁱ⁵ type is widely distributed throughout seven separate areas from northeast to southwest Japan with a 1.5% frequency of total materials examined. This indicated that Tib ⁱ⁵ type did not originate from a recent mutation event, but had spread in wild soybean from ancient times.     

Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers

We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (N_A) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average H_O (0.240) was lower than the H_E and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs.     

Correlation between signal input and output in PctA and PctB amino acid chemoreceptor of Pseudomonas aeruginosa

The PctA and PctB chemoreceptors of Pseudomonas aeruginosa mediate chemotaxis toward amino acids. A general feature of signal transduction processes is that a signal input is converted into an output. We have generated chimeras combining the Tar signaling domain with either the PctA or PctB ligand binding domain (LBD). Escherichia coli harboring either PctA‐Tar or PctB‐Tar mediated chemotaxis toward amino acids. The responses of both chimeras were determined using fluorescence resonance energy transfer, and the derived EC₅₀ values are a measure of output. PctA‐Tar and PctB‐Tar responded to 19 and 11 L‐amino acids respectively. The EC₅₀ values of PctA‐Tar responses differed by more than three orders of magnitude, whereas PctB‐Tar responded preferentially to L‐Gln. The comparison of amino acid binding constants and the corresponding EC₅₀ values for both receptors revealed statistically significant correlations between inputs and outputs. PctA and PctB possess a double PDC (PhoQ‐DcuS‐CitA) LBD – a family of binding domain found in various other amino acid chemoreceptors. Similarly, various chemoreceptors share the preferential response to certain amino acids (e.g. L‐Cys, L‐Ser and L‐Thr) that we observed for PctA. Defining the specific inputs and outputs of these chemoreceptors is an important step toward better understanding of their physiological role.     

The establishment of essential and metabolically derived amino acid profiles in developing chick embryo organs

The accumulation of certain essential and metabolically derived amino acids in the free amino acid pools of three excitable tissues has been studied in the chick embryo. Valine together with leucine are at the onset present in the yolk at higher concentrations than any of the other essential amino acids. By 15 days all the amino acids studied have accumulated in the embryonic pools at a higher rate than valine, although certain amino acids, such as phenylalanine or methionine, always remain at lower relative concentrations than valine. This reflects their low supply in the yolk, rather than a more rapid rate of disappearance (utilization). During early embryogenesis (E₂–E₄), tissues preferentially concentrate glutamic acid, besides taurine and phosphoethanolamine (6). The next distinct stage of development (E₄–E₇) is marked in the brain by a gradual rise in glutamic acid, glutamine and aspartic acid; the same three amino, acids do not demonstrate a further increase in the pool of the heart, while in the whole eye the amino acid profile begins to resemble the blood. Leucine in all three tissues declines rapidly, to reach isoleucine levels by day 7 of development; tyrosine increases slowly in apparent reciprocity to an equally gradual phenylalanine decrease. Into the second week of embryo growth (E₇–E₁₅), GABA appears in the mesencephalon (E₇) and the eye (E₉–E₁₀). In the mesencephalon, the free amino acid pool composition exhibits a rather sudden increase of most metabolically derived amino acids. Glutamic acid and glutamine in the brain increase in parallel; the rate of GABA and aspartic acid accumulation is slower, and for GABA stabilizes on day 14, as does glutamine. In the eye, by day 15, GABA levels are more closely aligned with the aspartic acid content. Finally, throughout embryogenesis serine fluctuations in blood and tissues are in parallel with those of threonine, and different from glycine or alanine which also change in tandem.     

The regularities of the changes of amino acid physico-chemical properties within the genetic code

Summary All the codons of the genetic code can be arranged into the closed one-step mutation ring, containing three periods of the same sequence of mutations (2,3,3,3,1,3,3,3,1,3,3,3,1,3,3,3,2,3,3,3). The codons of Gly play a role of the connecting element between the end of the third, and the beginning of the first period of the genetic code. The reactivity of amino acids, expressed by the reaction rates of aminolysis reaction of N-hydroxysuccinimide esters of protected amino acids with p-anisidine, changes periodically with the respect to the mutation periods of the genetic code. Chou-Fasman P as well as P conformational parameters of amino acids, and also the compositional frequencies of amino acids in proteins, demonstrate the pseudosymmetry pattern with respect to the center of one-step mutation ring, which is situated between Thr ACY and ACR codons.     

Sequence-specific dynamic information in proteins

We examine the local and global properties of the average B-factor, 〈B〉, as a residue-specific indicator of protein dynamic characteristics. It has been shown that values of 〈B〉 for the 20 amino acids differ in a statistically significant manner, and that, while strongly determined by the static physical properties of amino acids, they also encode averaged information about the influence of global fold on single-residue dynamics. Therefore, complete sequences of amino acids also encode fold-related global dynamic information, in addition to the local information that arises from static physical properties. We show that the relative magnitudes of these two contributions can be determined using Fourier methods, which represent the global properties of the sequences. It has also been shown that the behavior of Fourier components of 〈B〉 differs, with very high statistical significance, between structural groups, and that this information is not available from a comparable analysis of static amino acid properties.     

Modelling Diurnal Courses of Photosynthesis and Transpiration of Leaves on the Basis of Stomatal and Non-Stomatal Responses,Including Photoinhibition

A mathematical model for photoinhibition of leaf photosynthesis was developed by formalising the assumptions that (1) the rate of photoinhibition is proportional to irradiance; and (2) the rate of recovery, derived from the formulae for a pseudo first-order process, is proportional to the extent of inhibition. The photoinhibition model to calculate initial photo yield is integrated into a photosynthesis-stomatal conductance (g _s) model that combines net photosynthetic rate (P _N), transpiration rate (E), and g _s, and also the leaf energy balance. The model was run to simulate the diurnal courses of P _N, E, g _s, photochemical efficiency, i.e., ratio of intercellular CO₂ concentration and CO₂ concentration over leaf surface (C _i/C _s), and leaf temperature (T ₁) under different irradiances, air temperature, and humidity separately with fixed time courses of others. When midday depression occurred under high temperature, g _s decreased the most and E the least. The duration of midday depression of g _s was the longest and that in E the shortest. E increased with increasing vapour pressure deficit (VPD) initially, but when VPD exceeded a certain value, it decreased with increasing VPD; this was caused by a rapid decrease in g _s. When air temperature exceeded a certain value, an increase in solar irradiance raised T ₁ and the degree of midday depression. High solar radiation caused large decrease in initial photon efficiency (). P _N, E, and g _s showed reasonable decreases under conditions causing photoinhibition compared with non-photoinhibition condition under high irradiance. The T ₁ under photoinhibition was higher than that under non-photoinhibition conditions, which was evident under high solar irradiance around noon. The decrease in C _i/C _s at midday implies that stomatal closure is a factor causing midday depression of photosynthesis.     

Resonant recognition model of neuropeptide Y family: hot spot amino acid distribution in the sequences

The resonant recognition model is used to predict structurally and functionally important amino acid residues (so-called hot spots) in the neuropeptide Y (NPY) family. Thirty-three polypeptides belong to this family. All of them consist of 36 amino acids. The model predicts that residues 10 and 28 in the polypeptides are hot spots. In the 33 polypeptides, most of the amino acids at residue 10 are acidic amino acids, glutamic acid and aspartic acid. Other minor amino acids, serine, glycine, and proline, have high probabilities of -turn occurrence. Amino acids at residue 28 are all branched hydrophobic amino acids, isoleucine, leucine, and valine. The profile for predicting hot spots indicates repeating patterns of residues 1–18 and residues 19–36. Absolute values at residue i and residue i + 18 are the same, but these residues have opposite signs. Therefore the model of the NPY family predicts hot spots concerning a combination of residue i and residue i + 18.     

Genetic position and amino acid replacements of several mutations in ribosomal protein S5 from Escherichia coli.

Summary The relative genetic position of the following four mutations of ribosomal protein S5 has been determined: spc-13, a mutation to spectinomycin resistance; str ⁱ _N421 and str ⁱ _d1023, mutations suppressing dependence on streptomycin and sup _0–1, a mutation suppressing partially the temperature-sensitive phenotype of an alanyl-tRNA synthetase mutation. The transduction experiments performed indicate that the spc-13 site is located in the S5 cistron proximal to the strA locus, that sup _0–1 maps proximal to the aroE gene and that the str ⁱ _N421 and str ⁱ _d1023 loci are located between these two mutational sites.Proteinchemical analysis of the amino acid replacement in protein S5 of strain N421 (carrying the str ⁱ _N421 allele) has shown that an arginine residue is replaced by leucine which results in the appearance of a trypsin intensitive bond between the tryptic peptides T2 and T16. The same alteration has been previously found by Itoh and Wittmann (1973) in the S5 protein of strain d1023.Determination of the alteration of ribosomal protein S5 of strain 0–1 (sup _0–1 allele) revealed that the C-terminal tryptic peptide is altered. It differs from that of the wild-type protein by the lack of five amino acids and the appearance of a C-terminal glycine residue instead of a lysine residue. This change can be explained by the deletion of eleven nucleotides in the S5 cistron of strain 0–1.The recent determination of the primary structure of ribosomal protein S5 (Wittmann-Liebold and Greuer, 1975) allows the ordering of the S5 alterations employed: The order is spc-13-str ⁱ _d1023 (str ⁱ _N421)-sup _0–1 with the spc-13 amino acid replacement being located at the NH₂-terminal portion of the S5 sequence and the alteration of strain 0–1 at the COOH-terminal end. The proteinchemical results are therefore in full agreement with the genetic data and unambiguously allow the conclusion that the S5 cistron is transcribed counterclock-wise on the Escherichia coli chromosome.     

Differential geometry and protein conformation. V. Medium-range conformational influence of the individual amino acids

A previous differential geometric analysis of the conformational properties of the various amino acids has been extended to study their influence on folding over a larger backbone interval. In addition, statistical effects associated with variation in the number of the individual amino acids in the database have been treated in greater detail, using a simulation method. It is found that the amino acids can be divided into three groups on the basis of their conformational influence over four-C^α units in the interval i ? 6 ? j ? i + 6. Group Ia is composed of seven amino acids (His, Leu, Ala, Met, Lys, Gln, Ile) that encourage the formation of A_R-helical structure. Group Ib (Glu, Phe, Trp, Val, Asp) is composed of amino acids with some helix-forming tendency but that also show positive extended-strand formation tendency. They therefore act as a bridge between group Ia and group II (Cys, Gly, Asn, Pro, Arg, Ser, Thr, Tyr) that contains amino acids that encourage the formation of extended structure and bends. The detailed four-C^α conformational properties of each of the amino acids are shown, and the ability of amino acids to exert conformational influence in both directions along the backbone is examined. It is shown that, in general, such influence extends farther in the N-terminal direction than in the C-terminal direction. A framework is briefly sketched for using the present data to investigate actual folding mechanisms.     

Mechanism of F1-ATPase studied by the genetic approach

E. coli F₁-ATPase has been studied mainly by the genetic approach. Mutations in either the or subunit modified the kinetics of multisite and uni-site hydrolysis of ATP. The mechanism of F₁-ATPase and the essential amino acid residues of subunits are discussed.Abbreviations used: P_i, inorganic phosphate; DCCD, dicyclohexylcarbodiimide.     

Growth and metabolism of the obligate photolithotroph Chlorobium thiosulfatophilum in the presence of added organic nutrients

Growth of Chlorobium vibrioforme f. thiosulfatophilum NCIB 8327 could be monitored by measurement of turbidity (E₆₀₀); absorbance at 745 and 665 nm; increase in methanol-extractable pigment (E₆₆₀); fixation of ¹⁴CO₂; and titration of thiosulphate and sulphide in the medium. Growth could be inhibited by formate, methionine, tryptophan, tyrosine, threonine, serine and glycine, but not by 14 other amino acids, shikimic acid, some alcohols, sugars or acetate. Inhibition could some-times be relieved by the presence of other amino acids. This was probably partly due to restoration of normal internal amino acid requirements by “feeding”, and partly because uptake of amino acids appeared to show some competition for two or more low specificity uptake systems. Numerous ¹⁴C-labelled amino acids, formate and glucose were shown to be photoassimilated by Chlorobium, and the labelling patterns obtained provided information on its pathways of intermediary biosynthesis. Growth inhibition by threonine could be related to the probable presence of a normal branched pathway for the synthesis of the aspartate family of amino acids, with an aspartokinase enzyme subject to strong inhibition by threonine and lysine, separately and in combination.