1,721,017 research outputs found
The ribosome as novel target for small regulatory RNAs
No full textSmall non-protein-coding RNA (ncRNA) molecules have been recognized recently as major contributors to regulatory networks in controlling gene expression in a highly efficient manner. While the list of validated ncRNAs that regulate crucial cellular processes grows steadily, not a single ncRNA has been identified that directly interacts and regulates the ribosome during protein biosynthesis (with the notable exceptions of 7SL RNA and tmRNA). All of the recently discovered regulatory ncRNAs that act on translation (e.g. microRNAs, siRNAs or antisense RNAs) target the mRNA rather than the ribosome. This is unexpected, given the central position the ribosome plays during gene expression. Furthermore it is strongly assumed that the primordial translation system in the ‘RNA world’ most likely received direct regulatory input from ncRNA-like cofactors. The fundamental question that we would like to ask is: Does the ‘RNA world still communicate’ with the ribosome?
To address this question, we have analyzed the small ncRNA interactomes of ribosomes of prokaryotic (H. volcanii, S. aureus) and unicellular eukaryotic model organisms. Deep-sequencing and subsequent bioinformatic analyses revealed thousands of putative ribosome-associated ncRNAs. For a subset of these ncRNA candidates we have gathered experimental evidence that they are expressed in a stress-dependent manner and indeed directly target the ribosome. In the archaeon H. volcanii a tRNA-derived fragment was identified to target the small ribosomal subunit upon alkaline stress in vitro and in vivo. As a consequence of ribosome binding, this tRNA-fragment reduces protein synthesis by interfering with the peptidyl transferase activity.
Our data reveal the ribosome as a novel target for small regulatory ncRNAs in all domains of life. Ribosome-bound ncRNAs are capable of fine tuning translation and might represent a so far largely unexplored class of regulatory sRNAs
Ribosome-associated ncRNAs (rancRNAs) An emerging class of translation regulators
No full textSmall non-protein-coding RNA (ncRNA) molecules represent major contributors to regulatory networks in controlling gene expression in a highly efficient manner. Most of the recently discovered regulatory ncRNAs acting on translation target the mRNA rather than the ribosome (e.g.: miRNAs, siRNAs, antisense RNAs).
To address the question, whether ncRNA regulators exist that are capable of modulating the rate of protein production by directly interacting with the ribosome, we have analyzed the small ncRNA interactomes of ribosomes. Deep-sequencing analyses revealed thousands of putative rancRNAs in various model organisms (1,2). For a subset of these ncRNA candidates we have gathered experimental evidence that they associate with ribosomes in a stress-dependent manner and fine-tune the rate of protein biosynthesis (3,4). Many of the investigated rancRNAs appear to be processing products of larger functional RNAs, such as tRNAs (2,3), mRNAs (3), or snoRNAs (2). Post-transcriptional cleavage of RNA to generate smaller fragments is a widespread mechanism that enlarges the structural and functional complexity of cellular RNomes.
Our data disclose the ribosome as target for small regulatory RNAs. rancRNAs are found in all domains of life and represent a prevalent but so far largely unexplored class of regulatory molecules (5). Ongoing work in our lab revealed first insight into rancRNA processing and mechanism of this emerging class of translation regulators
The role of tRNA-derived fragments in stress response
No full textSmall non-protein-coding RNAs (ncRNAs) represent major contributors to regulatory networks in controlling gene expression in a highly efficient manner. In recently performed screens for ribosome-associated ncRNAs (rancRNAs) in various model organisms, tRNA-derived fragments and tRNA halve molecules were among the most abundant RNA-Seq reads. Post-transcriptional cleavage and/or alterations of tRNA molecules to generate smaller fragments appear to be widespread mechanisms enlarging the structural and functional complexities of cellular RNomes.
For a subset of tRNA-derived fragments we have gathered experimental evidence demonstrating ribosome association in a stress-dependent manner. Subsequent functional analyses revealed tRNA-fragments and tRNA-halves as regulators of protein biosynthesis during specific environmental stress situations in the archaeon Haloferax volcanii, the human pathogen Trypanosoma brucei, and in Chinese hamster ovary cells, respectively. In Haloferax volcanii we identified a tRNA fragment originating from Val-tRNA to bind the small ribosomal subunit and to interfere with efficient translation initiation. Certain tRNA-derived fragments are truly rancRNAs and seem to be involved in the first wave of cellular stress response by fine-tuning the rate of protein biosynthesis. Ongoing work in our lab focuses on uncovering the biology of tRNA-derived fragments and other post-transcriptional tRNA alterations during stress response
The multifaceted roles of ribosome-associated ncRNAs (rancRNAs)
No full textncRNA molecules represent major contributors to regulatory networks in controlling gene expression. Most of the recently discovered ncRNAs that act on translation target the mRNA rather than the ribosome (e.g.: miRNAs, siRNAs, antisense RNAs).
We performed targeted screens for ribosome-associated ncRNAs (rancRNAs) in various model organisms spanning all three domains of life. For a subset of rancRNA candidates we have gathered experimental evidence demonstrating ribosome association in a stress-dependent manner. The rancRNAs appear to be involved in the first wave of cellular stress response by fine-tuning the rate of protein biosynthesis (1-3). From a mechanistic point of view rancRNAs were found to affect translation quite differently. While some inhibit protein biosynthesis by dimming the initiation or elongation phases by competing with tRNA or mRNA for ribosome binding, respectively, others even stimulate translation. Many of the investigated rancRNAs are processing products of larger functional RNAs, such as mRNAs (1), tRNAs (2), or snoRNAs (4). Cleavage of RNA to generate smaller regulatory fragments is a widespread mechanism that enlarges the structural and functional complexity of cellular RNomes.
Our data disclose the ribosome as target for small regulatory RNAs. rancRNAs represent a prevalent but so far largely unexplored class of regulatory molecules (5). Ongoing work in our lab revealed first aspects of rancRNA processing, structure and functioning of this emerging class of translation regulators
The ribosome as novel target for stress-induced small regulatory RNAs
No full textSmall non-protein-coding RNA (ncRNA) molecules represent major contributors to regulatory networks in controlling gene expression in a highly efficient manner. All of the recently discovered regulatory ncRNAs that act on translation (e.g. microRNAs, siRNAs or antisense RNAs) target the mRNA rather than the ribosome.
To address the question, whether small ncRNA regulators exist that are capable of modulating the rate of protein production by directly interacting with the ribosome, we have analyzed the small ncRNA interactomes of ribosomes Deep-sequencing and subsequent bioinformatic analyses revealed thousands of putative ribosome-associated ncRNAs in various model organisms (1,2). For a subset of these ncRNA candidates we have gathered experimental evidence that they associate with ribosomes in a stress-dependent manner and are capable of regulating gene expression by fine-tuning the rate of protein biosynthesis (3,4). Many of the investigated ribosome-bound small ncRNA appear to be processing products from larger functional RNAs, such as tRNAs (2,3) or mRNAs (3). Post-transcriptional cleavage of RNA molecules to generate smaller fragments is a widespread mechanism that enlarges the structural and functional complexity of cellular RNomes.
Our data reveal the ribosome as a target for small regulatory ncRNAs and demonstrate the existence of a yet unknown mechanism of translation regulation. Ribosome-associated ncRNAs (rancRNAs) are found in all domains of life and represent a prevalent but so far largely unexplored class of regulatory molecules (5). Future work on the small ncRNA interactomes of ribosomes in a variety of model systems will allow deeper insight into the conservation and functional repertoire of this emerging class of regulatory ncRNA molecules
The origin of translational control: Are there small ncRNAs interacting with the archaeal ribosome?
No full textRibosome Shut-Down by 16S rRNA Fragmentation in Stationary-Phase Escherichia coli
No full textStationary-phase bacterial cells are characterized by vastly reduced metabolic activities yielding a dormant-like phenotype. Several hibernation programs ensure the establishment and maintenance of this resting growth state. Some of the stationary phase-specific modulations affect the ribosome and its translational activity directly. In stationary-phase Escherichia coli, we observed the appearance of a 16S rRNA fragmentation event at the tip of helix 6 within the small ribosomal subunit (30S).
Stationary-phase 30S subunits showed markedly reduced activities in protein biosynthesis. On the other hand, the functional performance of stationary-phase large ribosomal subunits (50S) was indistinguishable from particles isolated from exponentially growing cells. Introduction of the 16S rRNA cut in vitro at helix 6 of exponential phase 30S subunits renders them less efficient in protein biosynthesis. This indicates that the helix 6 fragmentation is necessary and sufficient to attenuate translational activities of 30S ribosomal subunits. These results suggest that stationary phasespecific cleavage of 16S rRNA within the 30S subunit is an efficient means to reduce global translation activities under non-proliferating growth conditions.
To understand better the process of before-mentioned 16S rRNA fragmentation and its physiological importance we are currently in the process of identifying factors involved. In addition, by mutating sequence of the helix 6 we want to identify important structural properties of the helix and the role of the before-mentioned 16S rRNA fragmentation in the cellular physiology
Atomic Mutagenesis of the Ribosome: Towards a Molecular Understanding of Translation
Get PDFThe multifaceted repertoire of non-protein-coding RNAs (ncRNAs) in organisms of all three domains of life emphasizes their fundamental role in biology. Research in my lab focuses on revealing the regulatory and catalytic function of small and large ncRNAs in different model organisms.
In particular we are interested in understanding ncRNA/protein complexes such as the vault complex or the ribosome. The ribosome, the central enzyme of protein biosynthesis, is a multifunctional ribonucleoprotein particle composed of two unequal subunits that translates the genome\u27s message
into all proteins needed for life. The crucial role the translation machinery plays in gene expression is also mirrored by the fact that the ribosome represents the main target for antibiotics. Decades of genetic, biochemical and recent crystallographic studies revealed the ribosome as an
RNA-enzyme with roots in the \u27RNA world\u27. Despite these experimental insights, the catalytic and regulatory mechanisms of the ribosomal RNA are still not fully understood at the molecular level. To unravel the detailed contributions of rRNA nucleotides for protein synthesis we have developed
and applied an \u27atomic mutagenesis\u27 approach. This tool allows the role of specific 23S rRNA functional groups and even individual atoms to be studied during various stages of the ribosomal elongation cycle with thus far unequalled precision. This experimental approach bridges the disciplines
of biochemistry and organic chemistry and has recently revealed specific functional 23S rRNA groups involved in peptide bond synthesis, peptidyl-tRNA hydrolysis, GTPase activation, and tRNA translocation
- …
