Ramesh Gupta

The phylogeny of purple bacteria: The alpha subdivision

The technique of oligonucleotide cataloging shows the purple photosynthetic eubacteria to comprise three major subdivisions, temporarily called alpha, beta, and gamma--previously designated groups I-III by Gibson et al. (1979). Each subdivision contains a number of non-photosynthetic genera in addition to the photosynthetic ones. The alpha subdivision, the subject of the present report, contains most but not all of the species that fall into the classically defined genera Rhodospirillum, Rhodopseudomonas and Rhodomicrobium. Intermingled with these are a variety of non-photosynthetic species from genera such as Agrobacterium, Rhizobium, Azospirillum, Nitrobacter, Erythrobacter, Phenylobacterium, Aquaspirillum, and Paracoccus. The phylogenetic substructure of the alpha subdivision is presented and the evolutionary significance of the admixture of biochemical phenotypes is discussed.

Were the original eubacteria thermophiles

Thermotoga maritima is one of the more unusual eubacteria: It is highly thermophilic, growing at temperatures higher than any other eubacterium; its cell wall appears to have a unique structure and its lipids a unique composition; and the organism is surrounded by a loose-fitting sheath of unknown function. Its phenotypic uniqueness is matched by its phylogenetic position; Thermotoga maritima represents the deepest known branching in the eubacterial line of descent, as measured by ribosomal RNA sequence comparisons. T. maritima also represents the most slowly evolving of eubacterial lineages. The fact that the two deepest branchings in the eubacterial line of descent (the other, the green non-sulfur bacteria and relatives, i.e. Chloroflexus, Thermomicrobium, etc.) are both basically thermophilic and slowly evolving, strongly suggests that all eubacteria have ultimately arisen from a thermophilic ancestor.

A phylogenetic analysis of the purple photosynthetic bacteria

Seven species of purple photosynthetic bacteria have been characerized by oligonucleotide cataloging of their 16S ribosomal RNAs. The relationships so revealed among them do not agree well with their classical taxonomic classification. However, they are in agreement with those derived from comparative analysis of cytochromec sequences. Since the two macromolecules, rRNA and cytochromec, are functionally unrelated, the agreement between the two methods virtually rules out lateral gene transfer as the cause of either result. The patterns seen reflect the true genealogies of the organisms. The purple photosynthetic bacteria constitute a major phylogenetic unit—apparently as extensive as the Gram-positive bacteria—but a unit that is not phylogenetically isolated. Intermixed genealogically with these photosynthetic species are many classically recognized nonphotosynthetic Gram-negative organisms. A number of the latter have specific relatives within the photosynthetic cluster.

Sequence of the 16S Ribosomal RNA from Halobacterium volcanii, an Archaebacterium.

The sequence of the 16S ribosomal RNA (rRNA) from the archaebacterium Halobacterium volcanii has been determined by DNA sequencing methods. The archaebacterial rRNA is similar to its eubacterial counterpart in secondary structure. Although it is closer in sequence to the eubacterial 16S rRNA than to the eukaryotic 16S-like rRNA, the H. volcanii sequence also shows certain points of specific similarity to its eukaryotic counterpart. Since the H. volcanii sequence is closer to both the eubacterial and the eukaryotic sequences than these two are to one another, it follows that the archaebacterial sequence resembles their common ancestral sequence more closely than does either of the other two versions.

Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications

SummaryThe sequence of the small-subunit rRNA from the thermoacidophilic archaebacteriumSulfolobus solfataricus has been determined and compared with its counterparts from halophilic and methanogenic archaebacteria, eukaryotes, and eubacteria. TheS. solfataricus sequence is specifically related to those of the other archaebacteria, to the exclusion of the eukaryotic and eubacterial sequences, when examined either by evolutionary distance matrix analyses or by the criterion of minimum change (maximum parsimony). The archaebacterial 16S rRNA sequences all conform to a common secondary structure, with theS. solfataricus structure containing a higher proportion of canonical base pairs and fewer helical irregularities than the rRNAs from the mesophilic archaebacteria.S. solfataricus is unusual in that its 16S rRNA-23S rRNA intergenic spacer lacks a tRNA gene.

The Phylogenetic Relationships of Three Sulfur Dependent Archaebacteria

Oligonucleotide catalogs have been determined for the 16S ribosomal RNAs of three sulfur dependent (i.e. thermoacidophilic) archaebacteria--Sulfolobus acidocaldarius, S. solfataricus, and Thermoproteus tenax. The three form a group specifically related to one another, but are only distantly related to the other archaebacteria--i.e. the group comprising the methanogens, extreme halophiles, and (peripherially) the genus Thermoplasma. The three catalogs exhibit two features unique among bacteria: (1) an unusually high number of long pyrimidine runs, and (2) a remarkably high number of (post-transcriptionally) modified nucleotides.

An efficient enantiocontrolled synthesis of (+)-4-demethoxydaunomycinone

Abstract A chromatography-free, seven-step synthesis of the title compound ( 3 ) is described. The tetracyclic carbon skeleton is elaborated by a Diels-Alder strategy in which the 6a,7- and 1O.1Oa-bonds are constructed the epoxy-tetrone ( 9 ) and the D-glucose-derived diene ( 10b ) serving as precursors. Interestingly, the cycloaddition reaction leads mainly to the “desired” cycloadduct ( 11b ), revealing a notable diastereofacial reactivity of the diene (10b). Hydrolysis of the cycloadduct ( 11b ) leads to the epoxy-pentone ( 12b ) which is reduced to the dihydroxy-trione ( 13b ). The reaction of the last-cited compound with ethynylmagnesium bromide affords a mixture of the ethynyl-diones ( 20b ) and ( 21b ), the latter compound arising from the precursor (13b) by a prior epimerisation at the 10a-position. The mixture of ethynyldiones ( 20b ) and ( 21b ) is converted into the anthracycline ( 14b ) by the action of lead ( IV ) acetate. By a hydrolysis-hydration sequence, the anthracycline ( 14b ) is transformed into (+)-4-demethoxydaunomycinone (3).

A phylogenetic analysis of anaerobic eubacteria capable of synthesizing acetate from carbon dioxide

Acetobacterium woodii, Acetogenium kivui, Clostridium aceticum, C. acidiurici, C. cylindrosporum, C. formicoaceticum, C. thermoaceticum, Eubacterium limosum, andPeptococcus glycinophilus were characterized by oligonucleotide cataloging of their 16S ribosomal RNA to determine whether the ability to synthesize acetate from CO2 is a phylogenetic trait. The ability to synthesize acetate from CO2 apparently is not a valid phylogenetic marker. TheEubacterium andPeptococcus species examined here are less related to other species in their genera than they are to different species ofClostridium. TheEubacterium species examined here show little relatedness to the genusPropionibacterium. The acetogenic eubacteria belong to the phylogenetic group defined basically by the Gram-positive sporeforming anaerobes.

Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract.

RNA splicing in archaea requires at least an endonuclease and a ligase, as is the case for the splicing of eukaryal nuclear tRNAs. Splicing endonucleases from archaea and eukarya are homologous, although they differ in subunit composition and substrate recognition properties. However, they all produce 2,3 cyclic phosphate and 5-hydroxyl termini. An in vitro-transcribed, partial intron-deleted Haloferax volcanii elongator tRNA(Met) has been used to study splicing by H. volcanii cell extracts. Substrates and products were analyzed by nearest neighbor analyses using nuclease P1 and RNase T2, and fingerprinting analyses using acid-urea gels in the first dimension and gradient thin layer chromatography in the second dimension. The results suggest that 2,3 cyclic phosphate at the 3 end of the 5 exon is converted into the splice junction phosphate forming a 3,5-phosphodiester linkage. This resembles the animal cell type systems where the junction phosphate preexists in the transcript, and differs from yeast type systems, where GTP is the source of junction phosphate.

Unusual modification patterns in the transfer ribonucleic acids of archaebacteria

The modification patterns of the transfer RNAs of ten archaebacteria (Halobacterium volcanii, Halococcus morrhuae, Methanobacterium bryantii, Methanobrevibacter smithii, Methanococcus vannielii, Methanococcus voltae, Methanomicrobium mobile, Methanosarcina barkeri, Thermoplasma acidophilum, andSulfolobus acidocaldarius) were analyzed by two-dimensional thin-layer chromatography of the32P-labeled nucleotides. All species lack ribothymidine and 7-methylguanosine, and dihydrouridine is absent from all butM. barkeri. Pseudouridine, 2′-O-methylcytidine, 1-methylguanosine, andN2,N2-dimethylguanosine are present in all of them; except forM. barkeri andT. acidophilum, all haveN2-methylguanosine. All, exceptH. volcanii andH. morrhuae, contain 1-methyladenosine, and these two organisms andS. acidocalderius only contain 5-methylcytidine. The transfer RNA modification patterns of the archaebacteria are distinct from those of typical eubacteria (Escherichia coli) and typical eukaryotes (Saccharomyces cerevisiae), although they are somewhat more similar to the latter than the former.