The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.

https://science.sciencemag.org/content/sci/270/5235/397.full.pdf

The minimal gene complement of Mycoplasma genitalium

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Ribosomal DNA: molecular evolution and phylogenetic inference.

We describe a rapid, sensitive process for comprehensively identifying proteins in macromolecular complexes that uses multidimensional liquid chromatography (LC) and tandem mass spectrometry (MS/MS) to separate and fragment peptides. The SEQUEST algorithm, relying upon translated genomic sequences, infers amino acid sequences from the fragment ions. The method was applied to the Saccharomyces cerevisiae ribosome leading to the identification of a novel protein component of the yeast and human 40S subunit. By offering the ability to identify >100 proteins in a single run, this process enables components in even the largest macromolecular complexes to be analyzed comprehensively.

Direct analysis of protein complexes using mass spectrometry

Network reconstructions are a common denominator in systems biology. Bottom–up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

/pdf/a-protocol-for-generating-a-high-quality-genome-scale-uku9cd6dnf.pdf

A protocol for generating a high-quality genome-scale metabolic reconstruction.

[This corrects the article on p. 116 in vol. 40.].

https://mmbr.asm.org/content/mmbr/40/1/116.full.pdf

Recalibrated linkage map of Escherichia coli K-12.

Ribosomal proteins of bacterial cells: strain- and species-specificity.

We have examined the number of rRNA genes in Mycoplasma capricolum (KID) by hybridization of BglII-, EcoRI- and XbaI-digests of DNA to [3′-32P] 16S, 23S and 5S rRNAs according to the Southern procedure (1975). All the restriction gels gave two radioactive bands with three kinds of rRNA. Furthermore, band positions were indistinguishable from one another when 16S, 23S and 5S rRNAs were used as probes, indicating that each band contains sequences corresponding to the 3′-termini of 16S, 23S and 5S rRNAs. It is thus concluded that Mycoplasma capricolum chromosome carries at least two sets of genes for 16S, 23S and 5S rRNAs.

The number of ribosomal RNA genes in Mycoplasma capricolum.

A tentative nomenclature (YP number) for yeast (Saccharomyces cerevisiae) cytoplasmic ribosomal proteins, which is used in our laboratory (Otaka and Kobata 1978; Higo and Otaka 1979), has been correlated with those of Warner and Gorenstein (1978) and several others. Our nomenclature is based on the two-dimensional gel electrophoretic pattern of proteins as analyzed by a modified method of Mets and Bogorad (1974), while others have used various modifications of Kaltschmidt and Wittmann's two-dimensional gel electrophoresis (1970). The method of correlation involved the examination in our twodimensional electrophoresis system of each protein spot excised from gel patterns prepared by Kaltschmidt and Wittmann's method or vice versa.

Syozo Osawa

Papers

Ribosomal proteins of bacterial cells: strain- and species-specificity.

The number of ribosomal RNA genes in Mycoplasma capricolum.

Yeast ribosomal proteins: V. Correlation of several nomenclatures and proposal of a standard nomenclature

Biosynthesis of 50 s ribosomal subunit in Escherichia coli.

Ribosomes from erythromycin-resistant mutants of Escherichia coli Q13.