Sequence similarity between a translated nucleotide sequence and a known biological protein can provide strong evidence for the presence of a homologous coding region, even between distantly related genes. The computer program BLASTX performed conceptual translation of a nucleotide query sequence followed by a protein database search in one programmatic step. We characterized the sensitivity of BLASTX recognition to the presence of substitution, insertion and deletion errors in the query sequence and to sequence divergence. Reading frames were reliably identified in the presence of 1% query errors, a rate that is typical for primary sequence data. BLASTX is appropriate for use in moderate and large scale sequencing projects at the earliest opportunity, when the data are most prone to containing errors.

Identification of protein coding regions by database similarity search.

Ribosomal proteins. VII. Two-dimensional polyacrylamide gel electrophoresis for fingerprinting of ribosomal proteins.

These companion volumes have been edited by two of the leading personalities in British obstetrics and gynaecology. Both have made notable contributions to their subjects, and each is an outstanding teacher who has always subscribed to the dictum that teaching needs research and research needs teaching. With such a philosophy inspiring their professional work, it would follow, therefore, that any publication of theirs would be devoid of pedantry. The reader will not be disappointed and will find an original, lucid, and constructive presentation. Their aim has been to present, so far as possible, a description of obstetrics and gynaecology as practised in Britain. It may be pertinently asked in what way British practice differs from that in other countries. The editors have forestalled this question. They believe that in obstetrics the chief modern contribution from Britain has been \" the results of the study of the relation of social and economic conditions to the health of the pregnant woman and the condition of her child.\" In gynaecology it is conservatism that has been the characteristic British contribution. Sir Eardley Holland has been responsible for the general editorship of the volume on obstetrics and has been assisted by 38 contributors selected from almost all the university and teaching centres. Professor Bruce Mayes, of Sydney University, is the sole overseas contributor. Included in this obstetric oligarchy are physicians, paediatricians, anatomists, a psychiatrist, a venereologist, a medical statistician, and a barrister. The co-authors have been allocated subjects in which they are acknowledged experts; thus each chapter is authoritative and at the same time original. Mr. Aleck Bourne has enlisted the help of 21 authors for the volume on gynaecology, and among these is an anatomist, a psychiatrist, a venereologist, and a barrister. He has always emphasized the importance of the basic sciences in relation to clinical medicine ; the reader will appreciate this from the contents and their presentation. It is doubtful whether a general work of this calibre should contain even brief accounts and exiguous illustrations of operations. The excellent chapter on the cervix uteri is impaired by the descriptions (and diagrams) of the operations for amputation of the cervix and trachelorrhaphy. Those who need pictorial assistance for their surgical technique would refer to a tome on operative surgery. Both volumes are illustrated with diagrams and plates of artistic distinction, and the publishers are to be congratulated on their production. The editors have succeeded in their aim. Their task has been sisyphean, but they have produced a magnunm opus which for many years will be indispensable to those who practise obstetrics and gynaecology. W. C. W. NIXON.

https://www.bmj.com/content/bmj/1/4957/29.2.full.pdf

Identification of enterobacteriaceae

Publisher Summary This chapter highlights endosymbiont hypothesis. All contemporary genomes (including those of plastids and mitochondria) ultimately derive from a single genome—the genome of a single, presumably cellular, entity which was the ancestor of all surviving forms of live. The construction and interpretation of phylogenetic trees based on small subunit (SSU, or 16S-like) and large subunit (LSU, or 23S-like) rRNA sequences have proven especially informative in instances where morphological diversity tends to confound traditional methods of phylogenetic analysis. In addition to ribosomal RNA (rRNA) sequence, there are a number of traits that characterize the archaebacteria as a distinct group of organisms, separate from all other prokaryotes. These include (1) cell walls that, when present, lack peptidoglycan and muramic acid; (2) the presence of lipids containing phytanyl side groups in ether linkage; and (3) the presence of RNA polymerases that are distinct from those of eubacteria in subunit composition, response to RNA synthesis inhibitors or stimulators, immunological reactivity, and gene sequence. Two major divisions of archaebacteria include (1) sulfur-dependent, extreme thermophiles; and (2) methane-producers (methanogens) and their relatives, including the extreme halophiles.

The endosymbiont hypothesis revisited.

Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.

/pdf/archaea-and-the-prokaryote-to-eukaryote-transition-3a977y9vbp.pdf

Archaea and the prokaryote-to-eukaryote transition.

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

Biosynthesis of 50 s ribosomal subunit in Escherichia coli.

Two proteins, YL41 and YL43, were isolated from 80S ribosomes of Saccharomyces cerevisiae by filtration through a Sephacryl S-200 column and by chromatography on a column of carboxymethylcellulose. Their amino acid compositions are presented. Twenty-four proteins including these two proteins were subjected to sequence analyses by automated Edman degradation. Amino-terminal amino acid sequences were determined for 17 proteins,YS3, YS9, YS23, YS24, YS29, YL6, YL8, YLll, YLI5,YL17, YL23, YL28, YL33, YL37, YL39, YL41, and YL43.YL41, which has a 72.7% lysine and arginine content, was found to be particular to eukaryotic ribosomes. The amino-termini of another seven proteins, YS2, YS5, YS8, YS12,YS13, YS20, and YS27, were suggested to be blocked. Comparison of the amino-terminal sequences with all other ribosomal protein sequences so far available indicates that YS9 shows sequence homology to rat liver ribosomal protein S8 (Wittmann-Liebold et al. 1979).

Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence characterization of twenty-four proteins from cytoplasmic ribosomes.

The cytoplasmic ribosomal proteins from a fission yeast Schizosaccharomyces pombe were analysed by two-dimensional polyacrylamide gel electrophoresis. Seventy-three protein species were identified in the 80S ribosome, and named SP-S1 to SP-S33 and SP-L1 to SP-L40 in the small and large subunits, respectively. Many of these proteins could be correlated to those of Saccharomyces cerevisiae on the basis of their electrophoretic mobilities. Eleven proteins were isolated from the 80S ribosome, and their amino acid compositions were determined. Of these, SP-S6, SP-L1, SP-L12, SP-L15, SP-L17, SP-L27, SP-L36 and SP-L40c and d were sequenced from their amino-termini. SP-S28 and SP-L2 appear to have their amino-termini blocked. These results were compared with the data available for the S. cerevisiae and rat liver ribosomal proteins. The S. cerevisiae counterparts of the eight proteins mentioned above were found to be YS4, YL1, YL10, YL14, YL35, YL40 and YL44c and d, respectively. The rat liver counter-parts of SP-S6, SP-L1, SP-L27 and SP-L40c and d were the rat S6, L4, L37 and P2, respectively. Comparison of the partial sequences of these ribosomal proteins suggests that these two yeasts are relatively far apart, phylogenetically.

Yeast ribosomal proteins: VII. Cytoplasmic ribosomal proteins from Schizosaccharomyces pombe

DNA fragments cloned from the halophilic archaebacterium Halobacterium halobium including the gene for ribosomal 'A' protein (HhaL20) were sequenced. Sequence and transcript analyzes indicated that the 'A' protein message (ORFC) was co-transcribed with two neighbouring open reading frames (ORFA and B) as a single unit. Comparison of the amino acid sequences deduced from ORFA and B with those from other organisms demonstrated that ORFA encoded the protein homologous to the ribosomal protein L8 of Halobacterium cutirubrum (HcuL8) and L1 of Escherichia coli (EL1), while ORFB encoded the protein homologous with the human ribosomal protein P0. The sequences which were able to facilitate mRNA.16S-rRNA hybridization were found about 10-20 nucleotides upstream of the initiation codon ATG of each of the three ORFs. The 5'- and 3'-ends of the operon were mapped with nuclease S1. A putative promoter (A+T-rich) and termination signal (T-rich) were found to be present within the 5'- and 3'-flanking sequence.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1988.tb14281.x

Takuzi Itoh

Papers

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

Biosynthesis of 50 s ribosomal subunit in Escherichia coli.

Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence characterization of twenty-four proteins from cytoplasmic ribosomes.

Yeast ribosomal proteins: VII. Cytoplasmic ribosomal proteins from Schizosaccharomyces pombe

Complete nucleotide sequence of the ribosomal ‘A’ protein operon from the archaebacterium, Halobacterium halobium