The C-terminal extension domain of Saccharomyces cerevisiae MrpL32, a homolog of ribosomal protein L32, functions in trans to support mitochondrial translation.

Mitochondrial ribosomal protein L32 (MrpL32) of Saccharomyces cerevisiae is homologous to the bacterial L32 ribosomal protein. MrpL32 carries an N-terminal mitochondrion-targeting sequence (MTS) and is about 60 amino acid residues longer at the C-terminus. Adding to its function as a leader sequence, the MTS of MrpL32 has been reported to regulate ribosome biogenesis through its processing by m-AAA protease.

Compound heterozygotes for filaggrin gene mutations do not always show severe atopic dermatitis.

Background: Mutations in FLG, which encodes profilaggrin, cause ichthyosis vulgaris (IV) and are an important predisposing factor for atopic dermatitis (AD). IV shows autosomal hemidominant (semidominant) inheritance, and patients with bi-allelic FLG mutations tend to have severe IV phenotypes. However, the effect of bi-allelic FLG mutations on AD incidence and severity remains a subject of controversy.

Hepatitis C virus NS5A protein interacts with lysine methyltransferase SET and MYND domain-containing 3 and induces activator protein 1 activation.

Hepatitis C virus (HCV) non-structural protein 5A (NS5A) is a multifunctional protein that is involved in the HCV life cycle and pathogenesis. In this study, a host protein(s) interacting with NS5A by tandem affinity purification were searched for with the aim of elucidating the role of NS5A. An NS5A-interacting protein, SET and MYND domain-containing 3 (SMYD3), a lysine methyltransferase reportedly involved in the development of cancer, was identified.

Characterization of inner membrane protein YciB in Escherichia coli: YciB interacts with cell elongation and division proteins.

The function of inner membrane protein YciB in Escherichia coli has not been identified. In this study, the membrane topology of the protein that contains five transmembrane domains was clarified. YciB was found to interact with various proteins involved in cell elongation and cell division using a bacterial two-hybrid system.

Escherichia coli inner membrane protein YciB interacts with ZipA that is important for cell division.

Escherichia coli propagates by undergoing cycles of lateral elongation, septum formation, and cell fission at the mid-cell. A large number of genes involved in these processes have been identified, but it is likely that others remain. A deletion mutant of yciB (ΔyciB) is shorter in the cell length compared to wild type and, in contrast, over-expression of yciB causes elongation of the cell.

Inner Membrane Protein YhcB Interacts with RodZ Involved in Cell Shape Maintenance in Escherichia coli.

Depletion of YhcB, an inner membrane protein of Escherichia coli, inhibited the growth of rodZ deletion mutant showing that the loss of both YhcB and RodZ is synthetically lethal. Furthermore, YhcB was demonstrated to interact with RodZ as well as several other proteins involved in cell shape maintenance and an inner membrane protein YciS of unknown function, using bacterial two-hybrid system. These observations seem to indicate that YhcB is involved in the biogenesis of cell envelope and the maintenance of cell shape together with RodZ.

Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations.

Elongation factor 4 (EF4) is one of the most conserved proteins present in bacteria as well as in mitochondria and chloroplasts of eukaryotes. Although EF4 has the unique ability to catalyze the back-translocation reaction on posttranslocation state ribosomes, the physiological role of EF4 remains unclear. Here we demonstrate that EF4 is stored at the membrane of Escherichia coli cells and released into the cytoplasm upon conditions of high ionic strength or low temperature.

Characterization of rodZ mutants: RodZ is not absolutely required for the cell shape and motility.

RodZ (YfgA) is a membrane protein well conserved among bacterial species and important in the determination of cell shape and motility, although the molecular mechanism involved is not well established. We have characterized a DeltarodZ mutant and show that defective peptidoglycan synthesis might be the primary effect of the deletion. A motile pseudorevertant of DeltarodZ isolated possessed a near rod-shaped cell morphology, indicating that RodZ is not absolutely required for the elongation of the lateral cell wall and the synthesis of functional flagella.

A genome-wide approach to identify the genes involved in biofilm formation in E. coli.

Biofilm forming cells are distinctive from the well-investigated planktonic cells and exhibit a different type of gene expression. Several new Escherichia coli genes related to biofilm formation have recently been identified through genomic approaches such as DNA microarray analysis. However, many others involved in this process might have escaped detection due to poor expression, regulatory mechanism, or genetic backgrounds.

Identification and comparative analysis of the large subunit mitochondrial ribosomal proteins of Neurospora crassa.

The mitochondrial ribosome (mitoribosome) has highly evolved from its putative prokaryotic ancestor and varies considerably from one organism to another. To gain further insights into its structural and evolutionary characteristics, we have purified and identified individual mitochondrial ribosomal proteins of Neurospora crassa by mass spectrometry and compared them with those of the budding yeast Saccharomyces cerevisiae. Most of the mitochondrial ribosomal proteins of the two fungi are well conserved with each other, although the degree of conservation varies to a large extent.

Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation.

To understand the nature and function of bacterial biofilm and the process of its formation, we have performed systematic screening of a complete set of Escherichia coli genes/open reading frames (ORFs) to identify those that affect biofilm development upon over-expression. In contrast to the biofilm of strain AG1 used as a control, some of the genes/ORFs when over-expressed led to the formation of an abnormal biofilm such as thin, mat-like, filamentous or one easily detaching from various surfaces. Disruptants of selected genes were constructed in order to clarify their roles in the different stages of biofilm formation.

Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components.

Mitochondrial ribosomal proteins (mrps) of the budding yeast, Saccharomyces cerevisiae, have been extensively characterized genetically and biochemically. However, the list of the genes encoding individual mrps is still not complete and quite a few of the mrps are only predicted from their similarity to bacterial ribosomal proteins. We have constructed a yeast strain in which one of the small subunit proteins, termed Mrp4, was tagged with S-peptide and used for affinity purification of mitochondrial ribosome.

Mammalian mitochondrial ribosomal proteins. N-terminal amino acid sequencing, characterization, and identification of corresponding gene sequences.

The integrity of healthy mitochondria is supposed to depend largely on proper mitochondrial protein biosynthesis. Mitochondrial ribosomal proteins (MRPs) are directly involved in this process. To identify mammalian mitochondrial ribosomal proteins and their corresponding genes, we purified mature rat MRPs and determined 12 different N-terminal amino acid sequences.

Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae.

We have purified 13 large subunit proteins of the mitochondrial ribosome of the yeast Saccharomyces cerevisiae and determined their partial amino acid sequences. To elucidate the structure and function of these proteins, we searched for their genes by comparing our sequence data with those deduced from the genomic nucleotide sequence data of S. cerevisiae and analyzed them.

A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map.

The 465,813 base pair sequence corresponding to the 40.1-50.0 min region on the genetic map of Escherichia coli K-12 (W3110) was determined.

A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map.

The 569,750 base pair sequence corresponding to the 28.0-40.1 min region on the genetic map of Escherichia coli K-12 (W3110) was determined.

Gene MRP-L4, encoding mitochondrial ribosomal protein YmL4, is indispensable for proper non-respiratory cell functions in yeast.

In order to characterize individual protein components of the mitochondrial (mt) ribosome for regulatory, functional and evolutionary studies, the yeast nuclear gene MRP-L4 (accession No. Z30582), coding for the mt ribosomal protein (MRP) YmL4, has been cloned using oligodeoxyribonucleotides (oligos) deduced from a partial amino acid (aa) sequence [Graack et al., FEBS Lett.

The yeast nuclear gene MRP-L13 codes for a protein of the large subunit of the mitochondrial ribosome.

The nuclear gene MRP-L13 of Saccharomyces cerevisiae, which codes for the mitochondrial ribosomal protein YmL13, has been cloned and characterized. It is a single-copy gene residing on chromosome XI. Its nucleotide sequence was found to be identical to that of the previously reported ORF YK105.

Cloning and nucleotide sequencing of the genes, rpIU and rpmA, for ribosomal proteins L21 and L27 of Escherichia coli.

The rpIU and rpmA genes that encode ribosomal proteins (r-proteins) L21 and L27 of Escherichia coli K-12 have been isolated from the ordered clone bank of this bacterium. They were found to be located at coordinates 3,351.7-3,352.

Efficient large-scale sequencing of the Escherichia coli genome: implementation of a transposon- and PCR-based strategy for the analysis of ordered lambda phage clones.

We have developed a strategy for efficient sequence analysis of the genome of E. coli K-12 using insertions of a Tn5-derived mini-transposon into overlapping ordered lambda phage clones to provide universal primer-binding sites, and PCR amplification of DNA segments adjacent to the insertions. Transposon-containing clones were selected by blue plaque formation on a dnaBamber lacZamber E.

YmL9, a nucleus-encoded mitochondrial ribosomal protein of yeast, is homologous to L3 ribosomal proteins from all natural kingdoms and photosynthetic organelles.

The nuclear gene for mitochondrial ribosomal protein YmL9 (MRP-L9) of yeast has been cloned and sequenced. The deduced amino acid sequence characterizes YmL9 as a basic (net charge + 30) protein of 27.5 kDa with a putative signal peptide for mitochondrial import of 19 amino acid residues.

Cloning and analysis of the nuclear gene for YmL33, a protein of the large subunit of the mitochondrial ribosome in Saccharomyces cerevisiae.

The N-terminal amino acid sequence of a large subunit protein, termed YmL33, of the mitochondrial ribosome of the yeast Saccharomyces cerevisiae was determined. The data were obtained to synthesize two kinds of oligonucleotide primers, which were used in the polymerase chain reaction to amplify and clone the nuclear gene for this protein. By nucleotide sequencing, the cloned gene, MRP-L33, was found to encode a basic protein of 11 kDa with 98 amino acid residues.