On the nature of global classification.

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.

Regulation by molecular oxygen and organic substrates of hydrogenase synthesis in Alcaligenes eutrophus.

Chemoautotrophic growth of Alcaligenes eutrophus 17707 is inhibited by 20% oxygen in the gas phase. Lowering the oxygen concentration to 4% results in chloramphenicol-sensitive derepression of soluble and membrane-bound hydrogenase activity (and of soluble hydrogenase antigen), showing that oxygen inhibition is due at least in part to repression of hydrogenase synthesis. Mutations resulting in derepression of hydrogenase activity (and antigen) under 25% oxygen (Ose-) mobilized with a self-transmissable plasmid which is already known to carry genes necessary for hydrogenase expression. Plasmid-borne mutations resulting in loss of soluble hydrogenase activity have no effect on the Ose phenotype, but chromosomal mutations resulting in reduction or loss of both hydrogenase activities cannot be made Ose-. The Ose- mutation does not alter the thermostability of either hydrogenase, and soluble hydrogenase in the mutant reacts with complete identity with that of the wild type, indicating that the Ose- phenotype does not result from structural alterations in either enzyme. Ose- mutants are also relieved of normal hydrogenase repression by organic substrates, which aggravates hydrogenase-mediated inhibition of heterotrophic growth by hydrogen. Regulation of hydrogenase in Ose- strains of A. eutrophus 17707 is nearly identical to that of wild-type A. eutrophus strains H1 and H16.

Histidine dissimilation in Streptomyces coelicolor.

A growth technique that allows strains of Streptomyces coelicolor to grow dispersed in defined liquid medium has been devised and used to determine the pathway of histidine degradation by S. coelicolor. Enzymic, chromatographic and stoichiometric analyses indicated that histidine is dissimilated via N-formyl-L-glutamic acid. The enzymes for histidine utilization (hut) are induced when histidine or urocanate is included in the culture medium. Biochemical evidence suggested that urocanate, or a further metabolite, is the physiological inducer. Three hut mutants were isolated and characterized. Two of the mutants exhibit an uninducible phenotype, whereas the third mutant appears to be defective in the structural gene for formiminoglutamate iminohydrolase. Haploid recombinant analysis was employed to locate all three mutations in the left empty region of the chromosomal map.

Active transport of benzoate in Pseudomonas putida.

Benzoate uptake in Pseudomonas putida is mediated by an active transport system capable of accumulating benzoate against a 150-fold concentration gradient when subsequent metabolism is blocked by mutation. Initial benzoate transport rates are inhibited by CCCP, sodium azide, arsenate and DCCD. Uptake is stimulated by including a respirable carbon source during preincubation of the bacteria. The initial uptake rate and the ATP pool levels are not correlated and no periplasmic components were found to bind benzoate. These observations indicate that benzoate uptake is energized by the membrane potential, rather than by ATP hydrolysis.

Use of an internal standard in monitoring the bacterial degradation of crude oil.

Hexachloroethane is nonvolatile, insoluble in water, and apparently not toxic to or metabolized by bacteria. Its addition to cultures growing at the expense of crude oil thus provides an internal standard against which the rate of degradation of individual crude oil components can be conveniently and reproducibly measured.

Characterization of a benzoate permease mutant of Pseudomonas putida.

A spontaneous mutant of Pseudomonas putida (PRS 2017) has been isolated which is incapable of growth on benzoate, does not induce the enzymes of the catechol branch of the beta-ketoadipate pathway when grown in the presence of benzoate, cannot accumulate radioactively labeled benzoate, yet grows well with mandelate as sole source of carbon and energy. This strain apparently lacks a benzoate permease, which in the wild type shows a Km of about 0.1 mM for benzoate, is inducible, and is not under the control of the regulatory system which governs the induction of the enzymes of the catechol branch of the beta-ketoadapate pathway. The lesion in PRS2017 is apparently single site and maps near other genes governing benzoate dissimilation.

Supra-operonic clustering of genes specifying glucose dissimilation in Pseudomonas putida.

The linkage arrangements of genes governing glucolysis in Pseudomonas putida have been determined by transductional analysis. Five genes (gdh, kgtA, kgtB, edd and eda), comprising at least three operons, are contransducible with each other, but not with ggu (glucose and gluconate uptake) nor with genes of a known supra-operonic cluster of genes specifying enzymes of other dissimilatory pathways, nor with a biochemically uncharacterized his marker. It thus appears that P. putida may have more than one chromosomal region in which genes with dissimilatory function are clustered in a supro-operonic fashion.

Genetic control of enzyme induction in the -ketoadipate pathway of Pseudomonas putida: deletion mapping of cat mutations.

A number of spontaneous mutant strains of Pseudomonas putida, obtained by repeated selection for inability to grow with cis,cis-muconate, have been shown to carry deletions in catB, the structural gene for muconate lactonizing enzyme. These strains have been employed for deletion mapping of the genetic region containing catB and catC (the structural gene for muconolactone isomerase, the synthesis of which is coordinate with that of muconate lactonizing enzyme). All deletions that overlap mutant sites located on the left side of the genetic map, as well as the point mutations in that region, lead to a pleiotropic loss of both catB and catC activities. We propose that this region to the left of catB has a regulatory function. Although the details of regulation at the molecular level are unclear, our data indicate that catB and catC may well be controlled by a mechanism unlike any yet described by workers on enteric bacteria.

Comparison of the two isofunctional enol-lactone hydrolases from Acinetobacter calcoaceticus.

The rates of thermal denaturation and the molecular weights of the two isofunctional enol-lactone hydrolases (ELH I and ELH II) of Acinetobacter calcoaceticus were determined. The molecular weights of ELH I and ELH II were found by gel filtration to be approximately 24,000 and 21,000, respectively. In crude extract at 45 C the two enzymes showed a marked difference in rate of thermal denaturation. After chromatography on Sephadex G-100, however, the rates were nearly identical. The thermolability of ELH II in crude extract was shown to be due to its sensitivity to an unidentified component of the crude extract which modified its rate of thermal denaturation. In the light of the physical similarities of the two enzymes, it is concluded that the different regulatory patterns imposed upon the two enzymes do not provide sufficient evidence that they are the product of two different structural genes.