Growth phase coupled modulation of <i>Escherichia coli </i>ribosomes

Wada, Akira

doi:10.1046/j.1365-2443.1998.00187.x

Cited by 117 publications

(141 citation statements)

References 27 publications

(32 reference statements)

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“…) Despite its relatively low evolutionary rate, the rpsV gene of E. coli, like other ORFans, is short and A+T rich. The RpsV protein is associated with the small subunit of ribosomes during the early stages of the stationary phase (Wada 1998), and based on a genome-wide survey using E. coli microarrays, rpsV expression increases substantially in nongrowing cells (Selinger et al 2000). Surprisingly, among the 25 genes showing the greatest increase in expression in stationary phase (Selinger et al 2000), we found that, in addition to rpsV, 10 were ORFans (mostly n 2 ) and five were HOPs.…”

Section: The Function Of Orfansmentioning

confidence: 80%

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Daubin¹,

Ochman²

2004

Genome Res.

244

259

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Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to γ-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions

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Section: The Function Of Orfansmentioning

confidence: 80%

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Daubin¹,

Ochman²

2004

Genome Res.

244

259

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“…Using the RFHR method, Wada and his colleagues newly identified three r-proteins (L31, L35 and L36) and four ribosome-associated proteins (RMF, YfiA, YhbH and SRA) (Izutsu et al, 2001;Maki et al, 2000;Wada, 1986a, b;Wada et al, 1990). They also found growth-dependent changes of the E. coli ribosome profile: YfiA, YhbH and SRA (or S22) occur in low copy numbers per ribosome during the exponential phase of growth and increase in the stationary phase (Izutsu et al, 2001;Maki et al, 2000;Wada, 1998); RMF (ribosome modulation factor) is only detected in the stationary-phase ribosomes (Wada et al, 1990). RMF associates 70S ribosomes to convert them to a dimeric form, 100S ribosomes, which is a storage form of ribosome with no translation activity (Wada et al, 1990).…”

Section: Proteomics Study Of the Ecoli Ribosomes Using Rfhr 2-d Gel mentioning

confidence: 99%

Proteomic study of the Bacillus subtilis ribosome: Finding of zinc-dependent replacement for ribosomal protein L31 paralogues

Nanamiya

Kawamura

Kosono

2006

J. Gen. Appl. Microbiol.

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The ribosome is a universal molecular machinery of translation comprising three kinds of ribosomal RNA (rRNA) and many ribosomal proteins (r-proteins). The functional domains of the ribosome, which are involved in the decoding of genetic information in messenger RNA and formation of peptide bonds, consist entirely of rRNAs (reviewed in Ramakrishnan, 2002). As rRNAs are subjected to strong selective pressure and are highly conserved, they have been used as a reference molecule in phylogeny. In contrast, r-proteins show more diversity in their sequences and composition, compared to rRNAs.Recent development of genomics and proteomics has enabled an examination of r-protein genes in prokaryotic, eukaryotic and organelle genomes. A recent comprehensive study of ribosomal genes in completed genomes revealed 57 r-protein families in the bacterial domain, 68 in the archaeal domain and 78 in the eukaryotic domain (Lecompte et al., 2002 Recent advanced studies of genomics and proteomics have revealed the variation and diversity of ribosomal proteins (r-proteins) in different organisms and organelles. Radical free and highly reducing (RFHR) two-dimensional (2-D) electrophoresis is known to be powerful for separating ribosomal proteins that are usually small and basic, and not separated well by standard 2-D electrophoresis. Using the RFHR method, we investigated the protein profile of the Bacillus subtilis ribosomes by a proteomic approach. We found that two L31 paralogue proteins (RpmE and YtiA) showed different temporal expression patterns in the ribosomes. The RpmE protein, which is an L31 variant with a Zn-binding motif, binds one zinc ion at the motif, which is required for stabilization of the protein in the cell. On the other hand, the expression of the ytiA gene, which encodes another L31 variant (YtiA) without the Zn-binding motif, is negatively controlled by the zinc-specific transcriptional repressor Zur and is likely induced by zinc starvation. This article reviews the recent findings that replacement of two types of L31 proteins in the ribosome is controlled by the intracellular zinc concentration.

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“…Synthetic RMF binds to 70S ribosomes, which are then converted into 100S dimers (Wada et al 1995). Since the 100S dimers are virtually inactive in translation that is directed by synthetic homopolymers or phage RNA in vitro (Wada et al 1995), we have proposed that the dimeric form of ribosomes represents an inactive stored form of ribosomes that is unused in the stationary phase (Wada et al 1993;Wada 1998). After the transfer of a stationary-phase culture into fresh medium, the ribosome dimers are converted into 70S monomers within a few minutes (Wada et al 1990).…”

Section: Modulation Of the Translation Machinerymentioning

confidence: 99%