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*  Regulating Ribosome Function Via The Ribosome Exit Tunnel :: UMBC Electronic Theses and Dissertations
The large subunit of the ribosome contains the site at which peptide bonds are formed in the process of translation. Another striking feature of the large subunit is the exit tunnel. This feature begins at the site of peptide bond formation traversing 100 angstroms before opening to the cytosolic environment on the opposite side of the large subunit. It has been known for some time that the ribosome exit tunnel is the site of action for MLS antibiotics, one such example being erythromycin. More recently the exit tunnel has been shown to be involved in sensing and regulating the egress of newly synthesized peptides. As the exact mechanisms by which either macrolides such as erythromycin or nascent peptides inhibit ribosome function is not known, understanding how both of these regulatory activities are accomplished remains an important challenge in understanding ribosome structure and function. Through mutational analysis and the use of translational reporters, I have obtained results which show ...
http://contentdm.ad.umbc.edu/cdm/singleitem/collection/ETD/id/24401/rec/13
*  Structural Biochemistry/Biophysical Studies of Bacterial Ribosome Assembly - Wikibooks, open books for an open world
The structure of bacterial ribosomes is composed of over 50 proteins and three large domain RNA molecules. Modifications in the rRNA require dozens of gene products but the role of these modifications in ribosome function are not fully understood or seem nonessential. It is believed that these modifications are a part of stabilizing RNA structure or RNA-protein interactions, mediate translation, or as checkpoints in ribosome assembly. The development of certain biophysical methods have helped better the understanding of how bacterial ribosome was constructed along with how its structure leads to function. Ribosome assembles improperly can lead to various diseases in human body because ribosomes assembly plays an important role in cells as RNA protein recognition. Therefore, understanding the ribosome assembly is a need to see how they connect together. Studies how ribosomes are regulated helps to figure out how and why errors occur in assembly biogenesis. ...
https://en.wikibooks.org/wiki/Structural_Biochemistry/Biophysical_Studies_of_Bacterial_Ribosome_Assembly
*  "The Role of SmpB in Licensing tmRNA Entry into Stalled Ribosomes" by Mickey R. Miller
Ribosomes translate the genetic information contained in mRNAs into protein by linking together amino acids with the help of aminoacyl-tRNAs. In bacteria, protein synthesis stalls when the ribosome reaches the 3'-end of truncated mRNA transcripts lacking a stop codon. Trans-translation is a conserved bacterial quality control process that rescues stalled ribosomes. Transfer-messenger RNA (tmRNA) and its protein partner SmpB mimic a tRNA by entering the A site of the ribosome and accepting the growing peptide chain. The ribosome releases the truncated mRNA and resumes translation on the tmRNA template. The open reading frame found on tmRNA encodes a peptide tag that marks the defective nascent peptide for proteolysis. A stop codon at the end of the open reading frame allows the ribosome to be recycled and engage in future rounds of translation.The entry of tmRNA into stalled ribosomes presents a challenge to our understanding of ribosome function because ...
https://scholarsarchive.byu.edu/etd/4162/
*  A sub-population of rat liver membrane-bound ribosomes that are detached in vitro by carcinogens and centrifugation |...
The chemical-carcinogen-induced detachment of ribosomes from rat liver endoplasmic reticulum was studied in vitro. Incubation of postmitochondrial supernatant with 0.2 mM-diethylnitrosamine or N-2-acetylaminofluorene removed approx. 16% of membrane-bound ribosomes, measured as differences in RNA/protein values of membrane separated from unbound ribosomes by flotation. These ribosomes are also detached by exposure to high centrifugal forces (160000g) and are among those removed by NADPH-catalysed lipid peroxidation. Extensive lipid peroxidation prohibits any measurement. The ribosomes (polyribosomes) removed are not those detached from the membrane by exposure to high KC1 concentrations (loosely bound) or high KC1 concentrations in the presence of puromycin (tightly bound). It is concluded then that centrifugally labile and carcinogen-sensitive represent a previously unreported sub-population of ...
http://www.biochemj.org/content/176/1/9
*  Endurance training lowers ribosome density despite increasing ribosome biogenesis markers in rodent skeletal muscle. |...
Interestingly, total RNA (i.e., ribosome density) was 2.3-fold greater in O-WD/SED versus O-WD/EX rats (p = 0.003) despite levels of upstream binding factor protein, RNA polymerase I protein and pre-45S rRNA being greater in O-WD/EX rats. Ribophagy (USP10 and G3BP1) and TRAMP-exosome rRNA degradation pathway (EXOSC10 and SKIV2L2) proteins were assayed to determine if these pathways were involved with lower ribosome density in O-WD/EX rats. While USP10 was higher in O-CON versus O-WD/SED and O-WD/EX rats (p < 0.001 and p < 0.001, respectively), G3BP1, EXOSC10 and SKIV2L2 did not differ between groups. Nop56 and Ncl mRNAs, ribosome assembly markers, were highest in O-WD/EX rats. However, Fbl mRNA and 28S rRNA, downstream ribosome processing markers, were lowest in O-WD/EX rats. Collectively these data suggest that, in WD-fed rats, endurance training increases select skeletal muscle ribosome biogenesis markers. However, endurance training may reduce muscle ribosome density by interfering with rRNA ...
https://www.physiciansweekly.com/endurance-training-lowers-ribosome-density-despite-increasing-ribosome-biogenesis-markers-in-rodent-skeletal-muscle-2/
*  Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets. | Haldane's Sieve
Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets. Patrick O'Connor , Dmitry Andreev , Pavel Baranov doi: http://dx.doi.org/10.1101/018762 Ribosome profiling is a promising technology for exploring gene expression. However, ribosome profiling data are characterized by a substantial number of outliers due to technical and biological factors. Here…
https://haldanessieve.org/2015/05/01/surveying-the-relative-impact-of-mrna-features-on-local-ribosome-profiling-read-density-in-28-datasets/
*  INVOLVEMENT OF RIBOSOMAL PROTEINS IN RIBOSOME BIOGENESIS, CELL CYCLE PROGRESSION, AND BUDDING PATTERNS IN SACCHAROMYCES...
Ribosome biogenesis and cell cycle are coordinated processes (Du and Stillman, 2001 Bernstein and Baserga, 2004; Fatica and Tollervey, 2002; Li et al., 2009; Strezoska et al., 2002). Mutations in genes encoding factors that are involved in ribosome biogenesis cause defects in ribosomal RNA processing as well as cell cycle arrest. Recent studies with mammalian cell lines have shown that ribosome biogenesis is also linked to tumorgenesis, that is mutation or depletion of ribosomal factors, leads to cancer cell proliferation (Montanaro et al., 2008). The yeast Saccharomyces cerevisiae is a useful model organism for understanding the connections between ribosome biogenesis and cell cycle control. Only a handful of studies have been done and these have mainly focused on different transacting factors involved in ribosome biogenesis; few studies have focused on the roles of r-proteins themselves in linking cell cycle progression and rRNA processing. I wanted to investigate what roles these r-proteins ...
http://contentdm.ad.umbc.edu/cdm/singleitem/collection/ETD/id/24644/rec/11096
*  Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. « RNomics
Related Articles Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A. 2014 May 20;111(20):7284-9 Authors: Kaushal PS, Sharma MR, Booth TM, Haque EM, Tung CS, Sanbonmatsu KY, Spremulli LL, Agrawal RK Abstract The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form…
https://rnomics.wordpress.com/2014/07/18/cryo-em-structure-of-the-small-subunit-of-the-mammalian-mitochondrial-ribosome/
*  Ribosome - Biology-Online Dictionary
Supplement A ribosome is a molecule consisting of two subunits that fit together and work as one to build proteins according to the genetic sequence held within the messenger RNA (mRNA). Using the mRNA as a template, the ribosome traverses each codon, pairing it with the appropriate amino acid. This is done through interacting with transfer RNA (tRNA) containing a complementary anticodon on one end and the appropriate amino acid on the other. Some ribosomes occur freely in the cytosol whereas others are attached to the nuclear membrane or to the endoplasmic reticulum (ER) giving the latter a rough appearance, hence, the name rough ER or rER. Ribosomes of prokaryotes (e.g. bacteria) are smaller than most of the ribosomes of eukaryotes (e.g. plants and animals). However, the plastids and mitochondria in eukaryotes have smaller ribosomes similar to those in prokaryotes - a possible indication of the evolutionary origin of these organelles. In ...
https://www.biology-online.org/dictionary/Ribosome
*  Zinc in the structure of Crystal Structure Of The E. Coli Ribosome Bound to Erythromycin. This File Contains The 50S Subunit of...
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Zinc atom in PDB 3ofq: Crystal Structure Of The E. Coli Ribosome Bound to Erythromycin. This File Contains The 50S Subunit of the Second 70S Ribosome.
http://zinc.atomistry.com/pdb3ofq.html
*  Zinc in the structure of Crystal Structure Of The E. Coli Ribosome Bound to Chloramphenicol. This File Contains The 50S Subunit...
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Zinc atom in PDB 3ofd: Crystal Structure Of The E. Coli Ribosome Bound to Chloramphenicol. This File Contains The 50S Subunit of the Second 70S Ribosome.
http://zinc.atomistry.com/pdb3ofd.html
*  Final touches and quality control on the assembly of the eukaryotic ribosome | The EMBO Journal
The eukaryotic ribosome consists of four ribosomal RNA molecules (rRNA) and ~80 ribosomal proteins (r‐proteins). These components are organized into the 40S small and 60S large subunits that associate forming the 80S ribosome. Ribosome assembly starts in the nucleus and is completed in the cytoplasm, with immature particles exported from the nucleus to the cytoplasm during this process. Assembly of the eukaryotic ribosome involves more than 200 biogenesis factors that support folding, processing and modifications of the rRNA, enable nuclear export of the assembling ribosomal particles or functionally test the active sites of the subunits (Karbstein, 2013; Woolford & Baserga, 2013; Greber, 2016). The general mechanisms by which these factors perform their functions remain poorly understood.. Pioneering work from the Hurt and Beckman's laboratories (Bradatsch et al, 2012) provided the first moderate resolution (11.9 Å) cryo‐EM reconstruction of a pre‐60S particle revealing how multiple ...
http://emboj.embopress.org/content/early/2017/03/13/embj.201796722
*  The polypeptide tunnel exit of the mitochondrial ribosome is tailored to meet the specific requirements of the organelle. -...
The ribosomal polypeptide tunnel exit is the site where a variety of factors interact with newly synthesized proteins to guide them through the early steps of their biogenesis. In mitochondrial ribosomes, this site has been considerably modified in the course of evolution. In contrast to all other translation systems, mitochondrial ribosomes are responsible for the synthesis of only a few hydrophobic membrane proteins that are essential subunits of the mitochondrial respiratory chain. Membrane insertion of these proteins occurs co-translationally and is connected to a sophisticated assembly process that not only includes the assembly of the different subunits but also the acquisition of redox co-factors. Here, we describe how mitochondrial translation is organized in the context of respiratory chain assembly and speculate how alteration of the ribosomal tunnel exit might allow the establishment of a subset of specialized ribosomes that individually organize ...
https://www.semanticscholar.org/paper/The-polypeptide-tunnel-exit-of-the-mitochondrial-r-Gruschke-Ott/d39390d5c1927be0f4bb4ad26fed9c0405459bb6
*  Ribosome | Research | Craig Lab | Biochemistry | UW-Madison
The Hsp70 Ssb, which is associated with ribosomes regardless of their translational state, is the major ribosome-associated chaperone. It can be crosslinked to short nascent chains that extend only a few amino acids beyond the ribosome exit site. Like all Hsp70s, Ssb has a J-type protein as a co-chaperone. Zuo1, Ssb's J-partner binds directly to the ribosome. Surprisingly, Zuo1 forms a stable complex with an Hsp70-related protein Ssz1, tethering it to the ribosome. Ssz1 does not appear to act as a classical Hsp70 however, as deletion of the putative peptide-binding domain has no obvious effect on its in vivo function. Intriguingly, when not bound to ribosomes, Ssz1 or Zuo1 activates a signal transduction pathway. ...
https://biochem.wisc.edu/labs/craig/research/ribosome
*  Ten remarks on peptide bond formation on the ribosome | Biochemical Society Transactions
Peptide-bond formation is the enzymatic activity of the ribosome. The catalytic site is made up of ribosomal RNA, indicating that the ribosome is a ribozyme. This review summarizes the recent progress in understanding the mechanism of peptide bond formation. The results of biochemical and kinetic experiments, mutagenesis studies and ribosome crystallography suggest that the approx. 107-fold rate enhancement of peptide bond formation by the ribosome is mainly due to substrate positioning within the active site, rather than to chemical catalysis.. ...
http://www.biochemsoctrans.org/content/33/3/493
*  Mimicking Living Cells: Synthesizing Ribosomes - Redorbit
Synthetic biology technology could lead to new antibiotics, modified protein-generators. Synthetic biology researchers at Northwestern University, working with partners at Harvard Medical School, have for the first time synthesized ribosomes -- cell structures responsible for generating all proteins and enzymes in our bodies -- from scratch in a test tube.. Others have previously tried to synthesize ribosomes from their constituent parts, but the efforts have yielded poorly functional ribosomes under conditions that do not replicate the environment of a living cell. In addition, attempts to combine ribosome synthesis and assembly in a single process have failed for decades.. Michael C. Jewett, a synthetic biologist at Northwestern, George M. Church, a geneticist at Harvard Medical School, and colleagues recently took another approach: they mimicked the natural synthesis of a ribosome, allowing natural enzymes of a cell to help facilitate the man-made ...
http://www.redorbit.com/news/science/1112888159/mimicking-living-cells-synthesizing-ribosomes/
*  HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions
Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coil HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock, These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.. ...
http://uu.diva-portal.org/smash/record.jsf?pid=diva2:877200
*  What are the two types of ribosomes? | Reference.com
The two types of ribosomes are free ribosomes and bound ribosomes. The classification of the ribosome depends on where it is located within a cell. Both types serve different...
https://www.reference.com/science/two-types-ribosomes-dcc9db24362fad0b
*  The functional half-life of an mRNA depends on the ribosome spacing in an early coding region - Search
Bacterial mRNAs are translated by closely spaced ribosomes and degraded from the 5'-end, with half-lives of around 2 min at 37 °C in most cases. Ribosome-free or "naked" mRNA is known to be readily degraded, but the initial event that inactivates the mRNA functionally has not been fully described. Here, we characterize a determinant of the functional stability of an mRNA, which is located in the early coding region. Using literature values for the mRNA half-lives of variant lacZ mRNAs in Escherichia coli, we modeled how the ribosome spacing is affected by the translation rate of the individual codons. When comparing the ribosome spacing at various segments of the mRNA to its functional half-life, we found a clear correlation between the functional mRNA half-life and the ribosome spacing in the mRNA region approximately between codon 20 and codon 45. From this finding, we predicted that inserts of slowly translated codons before codon 20 or after codon 45 should shorten or prolong, ...
http://research.ku.dk/search/?pure=en/publications/the-functional-halflife-of-an-mrna-depends-on-the-ribosome-spacing-in-an-early-coding-region
*  NASA Astrobiology Institute
Ribosome peptide exit tunnel plays a crucial role in the functioning of ribosomes across all domains of life.1 2 3 Before the transition of nascent peptides to mature functional proteins, they must travel through the functionally conserved peptide exit tunnel. 4 Additionally, the latent chaperone activity of the exit tunnel 5 6 suggests its role in ribosomal evolution, in the transition from short non-structured peptides to extant globular proteins. The wall of the tunnel is constructed mostly from RNA. As high as 80% of the tunnel is RNA in some species. 4 Our objective is to gain an understanding of the molecular basis of the latent chaperone activity and the preferential construction of the ribosome exit tunnel from the RNA component of the ribosome. Toward this end we have designed ketolide-peptide compounds (peptolides) to probe the mechanisms employed by the ribosome to, (i) facilitate in-tunnel folding of nascent peptides and (ii) distinguish between some peptide sequences while ...
https://nai.nasa.gov/annual-reports/2010/gatech/
*  Stringent Response: Antibiotics affecting ribosome's protein composition
Exhibit A: kasugamycin, an antibiotic that inhibits translation initiation in bacteria by interfering with binding of the the initiator tRNA. Amazingly enough, treatment with kasugamycin results in dramatic change in the ribosomal composition which is in turn changing ribosome's functional properties. Several proteins dissociate from the small ribosomal subunit (S1, S2, S6, S12, S18 and S21) which turns the 70S ribosome into a 61S kasugamycin particle. Ribosomal protein S1 is of particular interest here, because it is very important for the mRNA:ribosome interactions and is responsible for A/U rich sequences acting as translational activators ...
http://stringentresponse.blogspot.com/2011/05/antibiotics-affecting-ribosomes-protein.html
*  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling | Science
Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible. ...
http://science.sciencemag.org/content/324/5924/218
*  Abiogenesis & Evolution: Ribosome and RNA world
11.03.2005 - New X-rays of cell's ribosome could lead to better antibiotics: "Ribosomes are found in all organisms, ranging from bacteria to humans, and probably arose nearly 2 billion years ago. They have changed so little through evolution that a bacterial ribosome can often translate human genes into protein. Some people suspect that ribosomes, which at their core consist of ribonucleic acid (RNA), a sister of the DNA that comprises our genes, arose when RNA, not DNA, carried our genetic dowry ...
http://abiogenesisevo.blogspot.com/1990/01/ribosome-and-rna-world.html
*  Stringent Response: All ribosomes are equal, but some ribosomes are more equal than others
Alternative approach is to have many different ribosomes for different mRNAs. This is seemingly what we have in yeast (see above). Specific localization of different ribosomes and use of different mRNA-specific factors would then ensure proper coupling of appropriate ribosome with the right mRNA. Different localization of different paralogues of r-proteins in Saccharomyces cerevisiae is shown experimentally, and these proteins have different requirements for assembly into the 80S ...
http://stringentresponse.blogspot.com/2011/01/all-ribosomes-are-equal-but-some.html
*  Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome | Science
Transfer RNA (tRNA) molecules play a crucial role in protein biosynthesis in all organisms. Their interactions with ribosomes mediate the translation of genetic messages into polypeptides. Three tRNAs bound to the Escherichia coli 70S ribosome were visualized directly with cryoelectron microscopy and three-dimensional reconstruction. The detailed arrangement of A- and P-site tRNAs inferred from this study allows localization of the sites for anticodon interaction and peptide bond formation on the ribosome. ...
http://science.sciencemag.org/content/271/5251/1000