Mechanisms of EF-Tu, a pioneer GTPase

Krab, Ivo M.; Parmeggiani, Andrea

doi:10.1016/s0079-6603(02)71050-7

Cited by 54 publications

(51 citation statements)

References 134 publications

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“…In terms of increased RNA accumulation, the greatest changes were noted after phosphate deprivation ( Ϫ P; e.g., atpB , ϩ 294%; tufA , ϩ 455%). The mRNA of the tufA gene, which is involved in translation elongation (Krab and Parmeggiani, 2002), showed the most variation in abundance, ranging from a 4.5-fold phosphate-related increase to an 87% decline when cells were grown at 12 Њ C (L). Other conditions that elicited major responses were sulfate deprivation ( Ϫ S) and 24-h exposure to 254-nm UV light (UV).…”

Section: Chloroplast Transcript Accumulation Changes With Culture Conmentioning

confidence: 99%

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

2002

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The Chlamydomonas reinhardtii plastid and mitochondrial transcriptomes were surveyed for changes in RNA profiles resulting from growth in 12 culture conditions representing 8 abiotic stimuli. Organellar RNA abundance exhibited marked changes during nutrient stress and exposure to UV light, as revealed by both RNA gel blot and DNA microarray analyses. Of particular note were large increases in tufA and clpP transcript abundance during nutrient limitation. Phosphate and sulfur limitation resulted in the most global, yet opposite, effects on organellar RNA abundance, changes that were dissected further using run-on transcription assays. Removal of sulfate from the culture medium, which is known to reduce photosynthesis, resulted in 2-fold to 10-fold decreases in transcription rates, which were reflected in lower RNA abundance. The decrease in transcriptional activity was completely reversible and recovered to twice the control level after sulfate replenishment. Conversely, phosphate limitation resulted in a twofold to threefold increase in RNA abundance that was found to be a post-transcriptional effect, because it could be accounted for by increased RNA stability. This finding is consistent with the known metabolic slowdown under phosphate stress. Additionally, inhibitor studies suggested that unlike those in higher plants, Chlamydomonas chloroplasts lack a nucleusencoded plastid RNA polymerase. The apparently single type of polymerase could contribute to the rapid and genomewide transcriptional responses observed within the chloroplast.

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Section: Chloroplast Transcript Accumulation Changes With Culture Conmentioning

confidence: 99%

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

2002

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“…RNA polymerase subunits (Bd2950 and rnpO, data not shown), some isoforms of EF-Tu (Bd2994) (37), and translation elongation factor P (EF-P) (Bd2491) were strongly enhanced in GP, consistent with an increased rate of protein production during growth. EF-Tu modifications regulate its activity: methylation occurs in response to nutrient deprivation (74), reducing GTP hydrolysis and thus slowing translation and increasing accuracy (70).…”

Section: Discussionmentioning

confidence: 88%

Proteome-Based Comparative Analyses of Growth Stages Reveal New Cell Cycle-Dependent Functions in the Predatory Bacterium Bdellovibrio bacteriovorus

Dori-Bachash

Dassa

Pietrokovski

et al. 2008

Appl Environ Microbiol

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Bdellovibrio and like organisms are obligate predators of bacteria that are ubiquitously found in the environment. Most exhibit a peculiar dimorphic life cycle during which free-swimming attack-phase (AP) cells search for and invade bacterial prey cells. The invader develops in the prey as a filamentous polynucleoidcontaining cell that finally splits into progeny cells. Therapeutic and biocontrol applications of Bdellovibrio in human and animal health and plant health, respectively, have been proposed, but more knowledge of this peculiar cell cycle is needed to develop such applications. A proteomic approach was applied to study cell cycle-dependent expression of the Bdellovibrio bacteriovorus proteome in synchronous cultures of a facultative host-independent (HI) strain able to grow in the absence of prey. Results from two-dimensional gel electrophoresis, mass spectrometry, and temporal expression of selected genes in predicted operons were analyzed. In total, about 21% of the in silico predicted proteome was covered. One hundred ninety-six proteins were identified, including 63 hitherto unknown proteins and 140 life stage-dependent spots. Of those, 47 were differentially expressed, including chemotaxis, attachment, growth-and replication-related, cell wall, and regulatory proteins. Novel cell cycle-dependent adhesion, gliding, mechanosensing, signaling, and hydrolytic functions were assigned. The HI model was further studied by comparing HI and wild-type AP cells, revealing that proteins involved in DNA replication and signaling were deregulated in the former. A complementary analysis of the secreted proteome identified 59 polypeptides, including cell contact proteins and hydrolytic enzymes specific to predatory bacteria.

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“…Although there is no indication that the ribosome directly inserts a catalytic residue, there are also no convincing candidates in EFTu itself, as judged by crystal structures and mutational studies (168,169). It is also known that kirromycin and the closely related aurodox somewhat stimulate the GTPase activity of EF-Tu even in the absence of the ribosome (170).…”

Section: Interactions With Ef-tu and The 50s Subunitmentioning

confidence: 99%

Structural Insights Into Translational Fidelity

Ogle

Ramakrishnan

2005

Annu. Rev. Biochem.

555

538

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■ Abstract The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75Å away. The ribosome recognizes the geometry of codonanticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting. CONTENTS

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Mechanisms of EF-Tu, a pioneer GTPase

Cited by 54 publications

References 134 publications

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

Proteome-Based Comparative Analyses of Growth Stages Reveal New Cell Cycle-Dependent Functions in the Predatory Bacterium Bdellovibrio bacteriovorus

Structural Insights Into Translational Fidelity

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