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S G Andersson

Publications and source records attributed to S G Andersson.

At least 37 records · Page 2Linked to original sources
PubMed1998

The genome sequence of Rickettsia prowazekii and the origin of mitochondria.

We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.

DNA Replication↗
PubMed1998

A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae.

We have cloned and sequenced the genes encoding cytochrome b (cob) and cytochrome c oxidase subunit I (cox1) from Rickettsia prowazekii, a member of the alpha-proteobacteria. The phylogenetic analysis supports the hypothesis that mitochondria are derived from the alpha-proteobacteria and more specifically from within the Rickettsiaceae. We have estimated that the common ancestor of mitochondria and Rickettsiaceae dates back to more than 1500 million years ago.

Amino Acids↗
PubMed1998

Bioenergetics of the obligate intracellular parasite Rickettsia prowazekii.

Mitochondria are thought to be derived from an ancestor of the alpha-proteobacteria and more specifically from the Rickettsiaceae. The bioenergetic repertoire of the obligate intracellular parasite Rickettsia prowazekii is consistent with its postulated role as the ancestor of the mitochondria. For example, the R. prowazekii genome contains genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system, but lacks genes to support glycolysis. In addition, the R. prowazekii genome contains multiple genes coding for adenine nucleotide translocators which enables this intracellular parasite to exploit the cytoplasmic ATP of its host cell as a source of energy. The aim of this review is to describe the different aspects of the bioenergetic system in R. prowazekii and to discuss the results of phylogenetic reconstructions based on a variety of bioenergetic molecules which shed light on the origin and evolution of the mitochondrial genomes.

Citric Acid↗
PubMed1998

Reductive evolution of resident genomes.

Small, asexual populations are expected to accumulate deleterious substitutions and deletions in an irreversible manner, which in the long-term will lead to mutational meltdown and genome decay. Here, we discuss the influence of such reductive processes on the evolution of genomes that replicate within the domain of a host genome.

Animals↗
PubMed1998

Evolutionary rates for tuf genes in endosymbionts of aphids.

The gene encoding elongation factor Tu (tuf) in aphid endosymbionts (genus Buchnera) evolves at rates of 1.3 x 10(-10) to 2.5 x 10(-10) nonsynonymous substitutions and 3.9 x 10(-9) to 8.0 x 10(-9) synonymous substitutions per position per year. These rates, which are at present among the most reliable substitution rates for protein-coding genes of bacteria, have been obtained by calibrating the nodes in the phylogenetic tree produced from the Buchnera EF-Tu sequences using divergence times for the corresponding ancestral aphid hosts. We also present data suggesting that the rates of nonsynonymous substitutions are significantly higher in the endosymbiont lineages than in the closely related free-living bacteria Escherichia coli and Salmonella typhimurium. Synonymous substitution rates for Buchnera approximate estimated mutation rates for E. coli and S. typhimurium, as expected if synonymous changes act as neutral mutations in Buchnera. We relate the observed differences in substitution frequencies to the absence of selective codon preferences in Buchnera and to the influence of Muller's ratchet on small asexual populations.

Amino Acid Sequence↗
PubMed1997

GRS: a graphic tool for genome retrieval and segment analysis.

GRS is a graphic tool for retrieval and visualization of genome segments from partially or completely sequenced genomes. To facilitate visual identification of conserved genomic motifs, genes are color-coded according to their presumed functional roles. Aligned genes can be rapidly screened for potential homology by automatic retrieval and alignment of the corresponding protein sequences. Furthermore, the map location of any genome segment can be visually compared to the position of the same segment in other genomes or to the position of other segments within the same genome. The gene string analysis option of GRS allows the identification of genes that are identically arranged in any pairwise set of genomes. Finally, the program allows the user to create new gene table format files to enable comparisons of gene order structures in recently determined sequence data to the patterns of genes in already existing microbial and organellar databases. With the help of GRS, the genomic contexts of genes for which no identifiable homologues exist can be analyzed to provide an additional source of information for sequence annotations. We illustrate the use of GRS by analyzing the structure and distribution of phylogenetically conserved motifs in closely as well as more distantly related microbial genomes.

Computer Graphics↗
PubMed1996

Codon usage and base composition in Rickettsia prowazekii.

Codon usage and base composition in sequences from the A + T-rich genome of Rickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21 R. prowazekii proteins with that of a homologous set of proteins from Escherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests that R. prowazekii has around 800 genes and that 60-70% of the genome may be coding.

Base Composition↗
PubMed1996

A chimeric disposition of the elongation factor genes in Rickettsia prowazekii.

An exceptional disposition of the elongation factor genes is observed in Rickettsia prowazekii, in which there is only one tuf gene, which is distant from the lone fus gene. In contrast, the closely related bacterium Agrobacterium tumefaciens has the normal bacterial arrangement of two tuf genes, of which one is tightly linked to the fus gene. Analysis of the flanking sequences of the single tuf gene in R. prowazekii shows that it is preceded by two of the four tRNA genes located in the 5' region of the Escherichia coli tufB gene and that it is followed by rpsJ as well as associated ribosomal protein genes, which in E. coli are located downstream of the tufA gene. The fus gene is located within the str operon and is followed by one tRNA gene as well as by the genes secE and nusG, which are located in the 3' region of tufB in E. coli. This atypical disposition of genes suggests that intrachromosomal recombination between duplicated tuf genes has contributed to the evolution of the unique genomic architecture of R. prowazekii.

Agrobacterium tumefaciens↗
PubMed1996

The Rickettsia prowazekii genome: a random sequence analysis.

We describe here the first general survey of the genomic content and the coding capacity of the 1.1 Mb genome of Rickettsia prowazekii based on an analysis of a total of 200 kb of unique sequence data collected in a random manner. Based on nucleotide distribution profiles, we estimate that the R. prowazekii genome may have a coding density of 60%-70% and that it may contain a total of circa 800 genes. Here, we have tentatively identified and classified 173 of these genes. Our analysis suggests that the R. prowazekii genome is a highly derived, reduced genome that has lost many genes involved in amino acid biosynthetic pathways and regulatory functions. Furthermore, the R. prowazekii genome seems to lack glycolytic genes, but it does contain genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system. We have also encountered a family of homologous genes coding for ATP/ADP translocases, as observed in several mitochondrial genomes. We relate these findings to previous phylogenetic studies that suggest that Rickettsia and mitochondria share a common ancestor.

Base Sequence↗
PubMed1995

Unusual organization of the rRNA genes in Rickettsia prowazekii.

We describe here the organization of the rRNA genes in Rickettsia prowazekii. In this organism, the 23S and the 5S rRNA genes are tightly linked to each other, whereas the 16S rRNA gene is separated from this cluster. The 23S-5S unit is preceded by the methionyl-tRNAfMet formyltransferase gene.

Acyltransferases↗
PubMed1990

Codon preferences in free-living microorganisms.

A popular interpretation of the major codon preference is that it reflects the operation of a regulatory device that controls the expression of individual proteins. In this popular model, rapidly translated codons are thought to promote the accumulation of the highly expressed proteins and slowly translated codons are thought to retard the expression of poorly expressed proteins. However, this widely accepted model is not supported by kinetic theory or by experimental results. A less fashionable model in which the major codon preference has nothing to do with the expression level of the individual proteins is forwarded. In this model, the major codon preference is viewed as a global strategy to support the efficient function of the translation system and thereby to maximize the growth rates of cells under favorable conditions.

Animals↗
PubMed1988

Effects of erythromycin base and erythromycin esters on protein synthesis in vivo in Escherichia coli.

The inhibitory effects on protein synthesis in vivo of erythromycin base and several erythromycin esters have been determined. An experimental method was used, especially suited for studies on short-lived antibiotics causing low levels of inhibition. Most of the tested derivatives were 2-3% as active as erythromycin base while a split product of erythromycin, anhydroerythromycin, was 4% as effective.

Bacterial Proteins↗
PubMed1986

Functional interactions between mutated forms of ribosomal proteins S4, S5 and S12.

Here we show that ram mutations, either in ribosomal protein S4 or S5, decrease the proofreading flows for both cognate and noncognate ternary complexes bound by streptomycin-dependent (SmD) ribosomes. This effect is accompanied by a slight increase in the overall error frequency. More important, however, is the decreased proofreading of the cognate species which is almost reduced to wild-type levels. The data suggest that it may be the reduction of the proofreading of the cognate substrate that is important for suppressing streptomycin dependence. Furthermore, we show that rpsE mutants, selected from streptomycin-dependent strains, behave kinetically very similarly to the previously described rpsD mutants.

Codon↗
PubMed1984

Does codon composition influence ribosome function?

Escherichia coli ribosomes pre-initiated with N-acetyl-Val-tRNAVal elongate strictly alternating poly(U-G) at a rate between eight and 12 peptide bonds per second per ribosome in vitro. Comparisons with poly(U)-primed poly(Phe) synthesis show that these systems function with the same rates which are close to those of protein synthesis in vivo. This indicates that, at least in vitro, codon composition has no marked influence on the speed of elongation when the concentration of ternary complex is saturating. Furthermore, the missense frequencies for the two polymers are within the same range: the missense substitution of Trp for Cys is 10(-4) and that of Met for Val is 10(-3) in the poly(U-G)-primed system. These data argue against models that explain the codon preference of certain gene families by postulating effects of high or low GC content of codons on the performance characteristics of ribosomes.

Codon↗
PubMed1984

ppGpp inhibition of elongation factors Tu, G and Ts during polypeptide synthesis.

The inhibition of elongation factors G, Tu and Ts by ppGpp was studied in vitro in a translation system with missense frequency and elongation rate similar to those in vivo. ppGpp inhibits EF-G with KI = 6 X 10(-5) M. When ppGpp is in twofold excess over GTP and EF-G is the rate-limiting component, the elongation rate is reduced twofold by ppGpp. EF-Tu is inhibited with KI = 7 X 10(-7) M in the absence of EF-Ts. When EF-Ts is added, the binding of ppGpp to EF-Tu becomes successively weaker. 1/KI depends linearly on 1/[Ts] and the intercept at the abscissa gives KI = 4 X 10(-5) M. This reflects the binding of ppGpp to the binary TuTs complex. The slope reveals that the binding of EF-Ts to the TuMS binary complex is strong (10(-6) M). ppGpp may thus inhibit the cycling of EF-Tu indirectly by the removal of the free EF-Ts by its adsorption to TuMS, as well as directly by simple binding to Tu. EF-Tu inhibition by ppGpp can be fully reversed by high levels of aminoacyl-tRNA only in the presence of EF-Ts and at low ribosomal activity. Our in vitro observations have been extrapolated to in vivo conditions with conclusions as follows: Under strong amino acid starvation ppGpp in twofold excess over GTP cannot reduce significantly the elongation rate of ribosomes and thereby restore the errors to their normal levels as in the stringent response. Under weak starvation, in contrast, a significant rate reduction can be achieved by the trapping of EF-Ts in complex with TuppGpp.

Bacterial Proteins↗