The evolutionary change of the genetic code as restricted by the anticodon and identity of transfer RNA

The discovery of non-universal genetic codes in several mitochondria and nuclear systems during the past ten years has necessitated a reconsideration of the concept that the genetic code is universal and frozen, as was once believed. Here, the flexibility of the relationship between codons and amino acids is discussed on the basis of the distribution of non-universal genetic codes in various organisms insofar as has been observed to date. Judging from the result of recent investigations into tRNA identity, it would appear that the non-participation of the anticodon in recognition by aminoacyl-tRNA synthetase has significantly influenced the variability of codons.     

Methane and hydrogen production in a termite-symbiont system

Methane and hydrogen emission rates and the ¹³C of CH₄ were observed for various termites in Australia, Thailand and Japan. Combined with the already reported emission rates of CH₄ in the literature, the phylogenetic trend was examined. Emission rates of the observed termites were categorized into five groups: group I with high CH₄ and low H₂ emission rates with a CH₄/H₂ ratio of typically 10/1; group II with high CH₄ and high H₂ emissions with a CH₄/H₂ ratio of 4/1–1/2; group III with low emission rates of CH₄ and H₂; group IV with high H₂ and insignificant CH₄ emissions; and group V with insignificant emissions for both CH₄ and H₂. In lower termites, there are both colonies infected and uninfected with methanogens even in the same species, and no specific trend in CH₄ and H₂ emissions was observed within a genus. Whether protozoa in the hindgut of termites are infected with methanogens or not and the differences in species compositions of protozoa are possibly responsible for the inter-colonial variations. The proportions of infected colonies were possibly small for the family Kalotermitidae (dry wood feeders), and relatively large for families of wet or damp wood feeders. The hydrogen emission rate possibly depends on the locality of methanogens: namely, whether they are intracellular symbionts of protozoa or whether they are attached to the hindgut wall. Emission rates of higher termites were classified into groups according to genera and the diet. Most species of soil or wood/soil interface feeders classified into group I, while the soil feeders Dicuspiditermes in Thailand and Amitermes in Australia were classified into groups with high H₂ emission rates. Typical wood-feeding termites and fungus-growing termites were classified into group III. The results indicate that higher termites tend to increase the CH₄ emission rate during dietary evolution from wood- to soil-feeding, and two types of the system with different efficiencies of interspecies transfer of H₂ have been formed. The ¹³C of CH₄ was discernible with a difference in the decomposition process in the termite–symbiont system among lower termites, fungus-growing termites and other higher termites.     

Macrocyclic zinc(II) complexes for selective recognition of nucleobases in single- and double-stranded polynucleotides

 As an extension of our earlier discoveries that Zn^II-cyclen complex (1) (cyclen=1,4,7,10-tetraazacyclododecane) and Zn^II-acridine-pendant cyclen complex Zn^II-N-(9-acridin)ylmethyl-cyclen (3) are the first compounds to selectively recognize thymidine and uridine nucleosides in aqueous solution at physiological pH, the interaction of these and a relevant complex, bis(Zn^II-cyclen) (7), has been investigated with a series of polynucleotides, single-stranded poly(U) and poly(G), and double-stranded poly(A)·poly(U), poly(dA)·poly(dT) and poly(dG)·poly(dC). These Zn^II-cyclen complexes interact with the imide-containing nucleobases in the single-stranded poly(U), unperturbed by the presence of the anionic phosphodiester backbone. The affinity constant of 1 for each N(3)-deprotonated uracil base in poly(U) is determined to be log K= 5.1 by a kinetic measurement, which is almost the same as log K=5.2 for the interaction of 1 with uridine. Thus, they disrupt the A-U (or A-T) hydrogen bonds to unzip the duplex of poly(A)·poly(U) or poly(dA)·poly(dT), as demonstrated by lowering of the melting temperatures (T _m) of poly(A)·poly(U) and poly(dA)·poly(dT) in 5 mM Tris-HCl buffer (pH 7.6, 10 mM NaCl) with increase in their concentrations. The order of the denaturing efficiency is well correlated with that of the 1 : 1 affinity constants for each complex with uracil or thymine;7>3>1. The comparison of circular dichroism (CD) spectra for poly(A)·poly(U), poly(A), and poly(U) in the presence of 3 has revealed a structural change from poly(A)·poly(U) to two single strands, poly(A) and poly(U), caused by 3 binding exclusively to uracils in poly(U). On the other hand, the acridine-pendant cyclen complex 3, which earlier was found to associate with guanine by the Zn^II coordinating with guanine N(7), in addition to the π-π stacking, interacts with guanine in the double helix of poly(dG)·poly(dC) from outside and stabilized the double-stranded structure, as indicated by higher T _m. Received: 31 December 1997 / Accepted: 23 February 1998     

Evidence for C---C coupling between two mutually cis carbon ligands, η-crotyl and aryl in organopalladium(II) complexes

Some (η³-crotyl) (2,5-dichlorophenyl)palladium(II) complexes containing phosphine and phosphite ligands Pd(η³-CH₂CH-CHMe)(Ar)(PR₃) (Ar = C₆H₃Cl₂-2,5) were isolated as crystalline solids or generated in solution. These existed as a mixture of two geometrical isomers arising from a different way of risposition of the crotyl-methyl group and the aryl ligand. The electronic nature of the PR₃ ligand controlled the relative rates of the interconversion between the two isomers and the reductive elimination of the complexes which released MeCH=CHCH₂Ar and CH₂=CHCH(Me)(Ar). Electron-withdrawing phosphite ligands were particularly effective in enhancing the reductive elimination rate, making the contribution of the isomerization path almost negligible and allowing the formation of two coupling products to be followed separately by spectroscopic means. The observations demonstrated the occurrence of C---C coupling between mutually cis carbon ligands in (η³-allyl)(hydrocarbyl)palladium(II) complexes. The η¹-crotyl complex, (Pd(η¹-CH₂CH=CHMe)(Ar) (dppen) (dppen = cis-Ph₂PCH=CHPPh₂) was isolated and shown to exist as a sole regio-isomer in solution. Reductive elimination of this η¹-crotyl complex gave MeCH=CHCH₂Ar exclusively.     

A defined mutation in the protein export gene within the spc ribosomal protein operon of Escherichia coli: isolation and characterization of a new temperature-sensitive secY mutant.

We describe the properties of a temperature-sensitive mutant, ts24, of Escherichia coli. The mutant has a conditional defect in export of periplasmic and outer membrane proteins. At 42 degrees C, precursor forms of these proteins accumulate within the cell where they are protected from digestion by externally added trypsin. The accumulated precursors are secreted and processed very slowly at 42 degrees C. The mutation is complemented by expression of the wild-type secY (or prlA) gene, which has been cloned into a plasmid vector from the promoter-distal part of the spc ribosomal protein operon. The mutant has a single base change in the middle of the secY gene, which would result in the replacement of a glycine residue by aspartic acid in the protein product. These results demonstrate that the gene secY (prlA) is essential for protein translocation across the E. coli cytoplasmic membrane.     

Social organization of colony movement in the tropical ponerine ant,Diacamma rugosum (Le Guillou)

This work is part of a study on the social organization ofDiacamma rugosum, a large ponerine ant, which lacks a distinctive reproductive queen. This ant forms a small colony and frequently changes its nest site when the environmental conditions become unfavourable. Experiments in the laboratory showed that slight physical disturbances easily caused colony movement. The process of movement consisted of 3 successive phases: a) an exploration period, b) an movement period and c) a final movement period. The movement was organized by leader ants and 5 to 25% of all workers became leaders. These workers showed both tandem running and carrying behaviour during movement, tandem running being employed to recruit workers, whereas carrying behaviour was strictly limited to carrying eggs, larvae, pupae and males. During movement most of the tandem leader ants are those engaged in outdoor works in daily life. Potential of workers to become tandem leaders was correlated with outside works undertaken in daily life.     

Distribution and Physiology of Aerobic Bacteria Containing Bacteriochlorophyll a on the East and West Coasts of Australia

Aerobic heterotrophic bacteria containing bacteriochlorophyll were isolated from specimens from a wide variety of marine environments on the west (Shark Bay, Lake Clifton, Lake Heyward, and Perth) and east (near Townsville and Brisbane) coasts of Australia. The bacteria were found in a high proportion (10 to 30%) of the total heterotrophic bacterial strains isolated from marine algae, seagrasses, stromatolites, the epiphytes on stromatolites, seawater, and sands; in some cases they constituted up to 49% of the total. This is much higher than the previous report of 6% from Japan. A high percentage, 13%, was also found in the seawater of Hamelin Pool, at Shark Bay, where the salinity was 66%. The number of these bacteria was generally low in seawater and sands, with a few exceptions. There were no aerobic bacteriochlorophyll-containing bacteria on sponges or corals. The isolated strains were orange or pink, and most had absorption maxima around 800 and 850 to 870 nm, the latter range being the absorption of bacteriochlorophyll a in vivo. The maximum bacteriochlorophyll content was 1 nmol/mg (dry weight) of bacterial cells. Most of the bacteria did not grow phototrophically under anaerobic conditions in a broth medium containing succinate. Cells and cell extracts grown under aerobic conditions had photochemical activities such as reversible photooxidations of the reaction center and cytochrome(s). Some strains showed denitrifying activity. The optimal salinity for bacterial growth varied between strains.     

Identity of hemolysins produced by Bacillus thuringiensis and Bacillus cereus

A hemolysin (Bt-hemolysin) produced by Bacillus thuringiensis var. kurstaki HD-1 producing crystalline toxin(s) was purified by successive treatments of ammonium sulfate (45-65%) and column chromatography using DEAE-cellulose, Sephadex G-75 and KB-002 (a hydroxyapatite column for fast protein liquid chromatography). A hemolysin (Bc-hemolysin) produced by B. cereus HG-6A was also purified by the same procedure. The purified Bt-hemolysin and Bc-hemolysin, both of which are thiol-activated hemolysins, were biologically, physicochemically and immunologically identical. These findings provide further evidence of the similarity of B. thuringiensis, which is being used as a biological insecticide, to B. cereus, a toxigenic organism of food poisoning.     

Screening and identification of a novel lipase from Burkholderia sp. YY62 which hydrolyzes t-butyl esters effectively

Fatty acid esters composed of sterically hindered alcohol are very poor substrates for known lipases. In order to obtain a novel lipase, t-butyl octanoate (TBO) was selected as a model substrate to screen for bacteria-producing lipase(s) which can preferentially hydrolyze bulky esters. Of 279 strains isolated from 350 soil samples based on the ability to grow with TBO as a sole carbon source, one strain (YY62) was chosen for its strong TBO-hydrolyzing activity. Strain YY62 is a Gram-negative motile rod and was identified as Burkholderia sp. from the taxonomic characters and phylogenetic analysis of 16S rDNA nucleotide sequences. Using the activity ratio between TBO and p-nitrophenyl acetate as a measure for preference to bulky esters, we confirmed that the lipase of strain YY62 was 100-fold superior to commercial lipases in terms of TBO-hydrolyzing activity.