Importance of the 5 S rRNA-binding Ribosomal Proteins for Cell Viability and Translation in Escherichia coli

Korepanov, Alexey P.; Gongadze, G.M.; Garber, Maria; Court, Donald L.; Bubunenko, Mikhail

doi:10.1016/j.jmb.2006.11.097

Cited by 41 publications

(34 citation statements)

References 40 publications

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“…Recombineering is a novel technique of manipulating the DNA sequences in bacterial cells using the Red recombination functions of phage (4). It has been shown to be very efficient in generating gene knockouts in E. coli (2,16,45). Recombineering was carried out according to the methods described by Thomason et al (39) with some modifications.…”

Section: Methodsmentioning

confidence: 99%

Transcription Antitermination by Translation Initiation Factor IF1

et al. 2007

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Bacterial translation initiation factor IF1 is an S1 domain protein that belongs to the oligomer binding (OB) fold proteins. Cold shock domain (CSD)-containing proteins such as CspA (the major cold shock protein of Escherichia coli) and its homologues also belong to the OB fold protein family. The striking structural similarity between IF1 and CspA homologues suggests a functional overlap between these proteins. Certain members of the CspA family of cold shock proteins act as nucleic acid chaperones: they melt secondary structures in nucleic acids and act as transcription antiterminators. This activity may help the cell to acclimatize to low temperatures, since cold-induced stabilization of secondary structures in nascent RNA can impede transcription elongation. Here we show that the E. coli translation initiation factor, IF1, also has RNA chaperone activity and acts as a transcription antiterminator in vivo and in vitro. We further show that the RNA chaperone activity of IF1, although critical for transcription antitermination, is not essential for its role in supporting cell growth, which presumably functions in translation. The results thus indicate that IF1 may participate in transcription regulation and that cross talk and/or functional overlap may exist between the Csp family proteins, known to be involved in transcription regulation at cold shock, and S1 domain proteins, known to function in translation.Shifting exponentially growing Escherichia coli cells from 37°C to 15°C elicits a cold shock response, during which the synthesis of most cellular proteins is strongly decreased while the synthesis of several cold shock proteins is strongly increased. The most highly produced cold shock protein is the CspA protein. E. coli has nine CspA homologues, only some of which are cold shock inducible. CspA and its homologues destabilize secondary structures in both RNA and DNA and are therefore referred to as nucleic acid chaperones (13). In our previous studies, we showed that CspA and its homologues CspC and CspE act as transcription antiterminators (1). Stabilization of secondary structures in RNA upon a temperature downshift affects transcription elongation by RNA polymerase. Therefore, the RNA chaperoning activity of CspA and its cold-inducible homologues might facilitate transcription at low temperatures. Indeed, the nucleic acid melting activity of CspA family proteins is essential both for transcription antitermination and for cold acclimation of cells (27).X-ray and nuclear magnetic resonance structures of E. coli CspA and Bacillus subtilis CspB reveal a barrel of five antiparallel ␤-strands with a surface-exposed patch of several aromatic amino acids (8,23,31,32,34). These amino acids are involved in nucleic acid binding activity (11,35), and some are essential for nucleic acid chaperoning activity (27,29).The common fold of CspA homologues has been named the cold shock domain (CSD). The structure of the CSD is very similar to the S1 domain structure. On the basis of this similarity, the CSD and S1 domain...

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Section: Methodsmentioning

confidence: 99%

Transcription Antitermination by Translation Initiation Factor IF1

et al. 2007

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“…It has been shown that during the folding of 23S rRNA, these proteins initiate the formation of two main and independent assembly centers (161a). Proteins L5, L18, and L25 mediate the principal interactions between the 5S and 23S rRNA and are necessary for the correct formation of the central protuberance (112).…”

Section: Assembly Of Ribosomal Subunits (I) Assembly Of the 30smentioning

confidence: 99%

Ribosome Biogenesis and the Translation Process inEscherichia coli

Kaczanowska

Rydén-Aulin

2007

Microbiol Mol Biol Rev

354

379

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SUMMARY Translation, the decoding of mRNA into protein, is the third and final element of the central dogma. The ribosome, a nucleoprotein particle, is responsible and essential for this process. The bacterial ribosome consists of three rRNA molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. When finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. The focus of this review is ribosome biogenesis in Escherichia coli and its cross-talk with the ongoing protein synthesis. We discuss how the ribosomal components are produced and how their synthesis is regulated according to growth rate and the nutritional contents of the medium. We also present the many accessory factors important for the correct assembly process, the list of which has grown substantially during the last few years, even though the precise mechanisms and roles of most of the proteins are not understood.

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“…Bacterial 5S RNA interacts directly with three ribosomal proteins (r-proteins)-L18, L25, and L5 (Chen-Schmeisser and Garret 1977), two of which, L5 and L18, are essential for viability (Korepanov et al 2007). Although the rplY gene encoding L25 is not absolutely required for survival, Escherichia coli cells deficient in L25 reveal a slow growth phenotype even in rich media under normal growth conditions, indicating importance of L25 for ribosome functioning (Korepanov et al 2007). As shown recently (Korepanov et al 2012), L5 plays a crucial role in the CP formation during assembly of the 50S subunit, but precise roles for L18 and L25 still remain to be elucidated.…”

Section: Introductionmentioning

confidence: 99%

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

Aseev

Bylinkina

Boni

2015

RNA

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Ribosomal protein (r-protein) L25 is one of the three r-proteins (L25, L5, L18) that interact with 5S rRNA in eubacteria. Specific binding of L25 with a certain domain of 5S r-RNA, a so-called loop E, has been studied in detail, but information about regulation of L25 synthesis has remained totally lacking. In contrast to the rplE (L5) and rplR (L18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein S8, the rplY (L25) gene forms an independent transcription unit. The main goal of this work was to study the regulation of the rplY expression in vivo. We show that the rplY promoter is down-regulated by ppGpp and its cofactor DksA in response to amino acid starvation. At the level of translation, the rplY expression is subjected to the negative feedback control. The 5 ′ -untranslated region of the rplY mRNA comprises specific sequence/structure features, including an atypical SD-like sequence, which are highly conserved in a subset of gammaproteobacterial families. Despite the lack of a canonical SD element, the rplY'-'lacZ single-copy reporter showed unusually high translation efficiency. Expression of the rplY gene in trans decreased the translation yield, indicating the mechanism of autogenous repression. Site-directed mutagenesis of the rplY 5 ′ UTR revealed an important role of the conserved elements in the translation control. Thus, the rplY expression regulation represents one more example of regulatory pathways that control ribosome biogenesis in Escherichia coli and related bacteria.

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Importance of the 5 S rRNA-binding Ribosomal Proteins for Cell Viability and Translation in Escherichia coli

Cited by 41 publications

References 40 publications

Transcription Antitermination by Translation Initiation Factor IF1

Transcription Antitermination by Translation Initiation Factor IF1

Ribosome Biogenesis and the Translation Process inEscherichia coli

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

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