scholarly journals Co-Translational Protein Folding and Sorting in Chloroplasts

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 214 ◽  
Author(s):  
Fabian Ries ◽  
Claudia Herkt ◽  
Felix Willmund
Keyword(s):  
Protein Folding ◽  
Protein Synthesis ◽  
Carbon Fixation ◽  
Current Knowledge ◽  
Protein Coding ◽  
Light Reaction ◽  
Fast Kinetics ◽  
Final Maturation ◽  
Nascent Chain ◽  
Early Processing

Cells depend on the continuous renewal of their proteome composition during the cell cycle and in order to replace aberrant proteins or to react to changing environmental conditions. In higher eukaryotes, protein synthesis is achieved by up to five million ribosomes per cell. With the fast kinetics of translation, the large number of newly made proteins generates a substantial burden for protein homeostasis and requires a highly orchestrated cascade of factors promoting folding, sorting and final maturation. Several of the involved factors directly bind to translating ribosomes for the early processing of emerging nascent polypeptides and the translocation of ribosome nascent chain complexes to target membranes. In plant cells, protein synthesis also occurs in chloroplasts serving the expression of a relatively small set of 60–100 protein-coding genes. However, most of these proteins, together with nucleus-derived subunits, form central complexes majorly involved in the essential processes of photosynthetic light reaction, carbon fixation, metabolism and gene expression. Biogenesis of these heterogenic complexes adds an additional level of complexity for protein biogenesis. In this review, we summarize the current knowledge about co-translationally binding factors in chloroplasts and discuss their role in protein folding and ribosome translocation to thylakoid membranes.

Spatial localization of unknown proteins in the endoplasmic reticulum predicts functions

2007 ◽  
Vol 30 (4) ◽  
pp. 84
Author(s):  
Michael D. Jain ◽  
Hisao Nagaya ◽  
Annalyn Gilchrist ◽  
Miroslaw Cygler ◽  
John J.M. Bergeron
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Folding ◽  
Protein Synthesis ◽  
Protein Function ◽  
Protein Translocation ◽  
Spatial Localization ◽  
Predict Protein Function ◽  
Insight Into ◽  
Soluble Fractions ◽  
Er Membrane

Protein synthesis, folding and degradation functions are spatially segregated in the endoplasmic reticulum (ER) with respect to the membrane and the ribosome (rough and smooth ER). Interrogation of a proteomics resource characterizing rough and smooth ER membranes subfractionated into cytosolic, membrane, and soluble fractions gives a spatial map of known proteins involved in ER function. The spatial localization of 224 identified unknown proteins in the ER is predicted to give insight into their function. Here we provide evidence that the proteomics resource accurately predicts the function of new proteins involved in protein synthesis (nudilin), protein translocation across the ER membrane (nicalin), co-translational protein folding (stexin), and distal protein folding in the lumen of the ER (erlin-1, TMX2). Proteomics provides the spatial localization of proteins and can be used to accurately predict protein function.

scholarly journals Conserved long-range base pairings are associated with pre-mRNA processing of human genes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Svetlana Kalmykova ◽  
Marina Kalinina ◽  
Stepan Denisov ◽  
Alexey Mironov ◽  
Dmitry Skvortsov ◽  
...  
Keyword(s):  
Long Range ◽  
Rna Folding ◽  
Current Knowledge ◽  
Rna Structures ◽  
Base Pairs ◽  
Protein Coding ◽  
Proximity Ligation ◽  
Transcriptional Suppression ◽  
Human Genes ◽  
Cleavage And Polyadenylation

AbstractThe ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3’-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.

scholarly journals Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

2007 ◽  
Vol 51 (12) ◽  
pp. 4462-4465 ◽  
Author(s):  
Susan J. Schroeder ◽  
Gregor Blaha ◽  
Peter B. Moore
Keyword(s):  
Protein Synthesis ◽  
Small Molecule ◽  
Ribosomal Subunit ◽  
Small Molecule Inhibitor ◽  
Single Site ◽  
Haloarcula Marismortui ◽  
Molecule Inhibitor ◽  
Nascent Chain ◽  
Exit Tunnel ◽  
Inhibitor Of Protein Synthesis

ABSTRACT Negamycin, a small-molecule inhibitor of protein synthesis, binds the Haloarcula marismortui 50S ribosomal subunit at a single site formed by highly conserved RNA nucleotides near the cytosolic end of the nascent chain exit tunnel. The mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.

Morphological and Histochemical Studies of the Chromatoid Body and Related Elements in the Spermatogenesis of the Rat

1961 ◽  
Vol s3-102 (60) ◽  
pp. 495-506
Author(s):  
BHUPINDER N. SUD
Keyword(s):  
Protein Synthesis ◽  
Chemical Composition ◽  
Sertoli Cell ◽  
Protein Component ◽  
Residual Body ◽  
Chromatoid Body ◽  
Progressive Decrease ◽  
Caudal Region ◽  
Final Maturation ◽  
Late Stages

In the spermatogenesis of the rat the chromatoid body is present during the growth of the primary and secondary spermatocytes, disappears at telophase of both the meiotic divisions, and is absent during interkinesis. It is reconstructed during the early stages of spermateleosis but after the elongation and condensation of the nucleus it gradually becomes smaller and disappears. Simultaneously, in the caudal region von Ebner's stainable granules appear and gradually fuse together to form a single voluminous body, Regaud's sphère chromatophile, which is discarded with the residual body and is phagocytosed by the Sertoli cell. The histochemical studies reveal that the chromatoid body, von Ebner's stainable granules, and the sphère chromatophile are similar in composition. They consist mainly of RNA and proteins, and this suggests that they may be centres of protein synthesis. The RNA content of von Ebner's stainable granules and the sphère chromatophile appears to be higher than that of the chromatoid body. This probably means that there is a progressive decrease in the protein component of the chromatoid material. Also there is a distinct change in the chemical composition of the protein component of the chroma tin during the late stages of spermateleosis. It is tentatively suggested that the function of the chromatoid material may be to provide basic proteins for the final maturation of the chromatin of the late spermatid. It appears that the chromatoid elements originate from the ground cytoplasm and disappear by merging into the latter. An enigmatic granular satellite has been found associated with the chromatoid body. It differs from the latter in its chemical composition.

scholarly journals RNA Modifications in Cancer: Functions, Mechanisms, and Therapeutic Implications

2020 ◽  
Vol 4 (1) ◽  
pp. 221-240 ◽  
Author(s):  
Huilin Huang ◽  
Hengyou Weng ◽  
Xiaolan Deng ◽  
Jianjun Chen
Keyword(s):  
Gene Expression ◽  
Current Knowledge ◽  
Global Gene Expression ◽  
Rna Modifications ◽  
Aberrant Expression ◽  
Protein Coding ◽  
Therapeutic Implications ◽  
Underlying Mechanisms ◽  
Aberrant Rna ◽  
Gene Expression Dysregulation

Over 170 chemical modifications have been identified in protein-coding and noncoding RNAs and shown to exhibit broad impacts on gene expression. Dysregulation of RNA modifications caused by aberrant expression of or mutations in RNA modifiers aberrantly reprograms the epitranscriptome and skews global gene expression, which in turn leads to tumorigenesis and drug resistance. Here we review current knowledge of the functions and underlying mechanisms of aberrant RNA modifications in human cancers, particularly several common RNA modifications, including N6-methyladenosine (m6A), A-to-I editing, pseudouridine (ψ), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), N1-methyladenosine (m1A), and N4-acetylcytidine (ac4C), providing insights into therapeutic implications of targeting RNA modifications and the associated machineries for cancer therapy.

scholarly journals Small Family with Key Contacts: Par14 and Par17 Parvulin Proteins, Relatives of Pin1, Now Emerge in Biomedical Research

2008 ◽  
Vol 2 ◽  
pp. PMC.S496 ◽  
Author(s):  
Jonathan W Mueller ◽  
Peter Bayer
Keyword(s):  
Cell Cycle ◽  
Protein Folding ◽  
Biomedical Research ◽  
Drug Targets ◽  
Cell Cycle Regulation ◽  
Current Knowledge ◽  
Primate Species ◽  
Protein Species ◽  
Cycle Regulation ◽  
Human Specific

The parvulin-type peptidyl-prolyl cis/trans isomerase Pin1 is subject of intense biochemical and clinical research as it seems to be involved in the pathogenesis of certain cancers and protein folding illnesses like Alzheimer's and Parkinson's disease. In addition to Pin1, the human genome only contains a single other parvulin locus encoding two protein species–-Par14 and Par17. Much less is known about these enzymes although their sequences are highly conserved in all metazoans. Parvulin has been proposed to function as Pin1 complementing enzyme in cell cycle regulation and in chromatin remodelling. Pharmaceutical modulation of Par14 might therefore have benefits for certain types of cancer. Moreover, the Par17 protein that has been shown to be confined to anthropoid primate species only might provide a deeper understanding for human-specific brain development. This review aims at stimulating further research on Par14 and Par17 that are overlooked drug targets in the shadow of an overwhelming plethora of Pin1 literature by summarising all current knowledge on these parvulin proteins.

scholarly journals Chaperoning ribosome assembly

2010 ◽  
Vol 189 (1) ◽  
pp. 11-12 ◽  
Author(s):  
Katrin Karbstein
Keyword(s):  
Protein Folding ◽  
Ribosome Assembly ◽  
Cell Biol ◽  
Nascent Chain ◽  
Cellular Compartments

Chaperones help proteins fold in all cellular compartments, and many associate directly with ribosomes, capturing nascent chains to assist their folding and prevent aggregation. In this issue, new data from Koplin et al. (2010. J. Cell Biol. doi: 10.1083/jcb.200910074) and Albanèse et al. (2010. J. Cell Biol. doi: 10.1083/jcb.201001054) suggest that in addition to promoting protein folding, the chaperones ribosome-associated complex (RAC), nascent chain–associated complex (NAC), and Jjj1 also help in the assembly of ribosomes.

Protein Synthesis by Lake Plankton Measured Using in situ Carbon Dioxide and Sulfate Assimilation

1987 ◽  
Vol 44 (12) ◽  
pp. 2102-2117 ◽  
Author(s):  
Russell L. Cuhel ◽  
David R. S. Lean
Keyword(s):  
Carbon Dioxide ◽  
Protein Synthesis ◽  
Carbon Fixation ◽  
Total Carbon ◽  
Light Limitation ◽  
Sulfate Assimilation ◽  
Sulfate Uptake ◽  
Chl A ◽  
Total Sulfate

Sequential 4- to 6-h in situ measurements of carbon dioxide and sulfate uptake showed midday deepening of the depth of Pmax and photoinhibition of upper water column samples. Analysis of subcellular fractions accentuated total uptake measurements, with net protein synthesis providing a direct measure of growth. The percentage of carbon assimilated into protein was smallest at the depth of maximum photosynthesis and increased with light limitation. Summed incubations agreed well with all-day deployments for total carbon fixation and protein synthesis. Assimilation numbers were consistently low (<2.5 g C∙g Chl a−1∙h-1 with integrated (0–20 m) areal production of 616–1467 mg C∙m−2 and 7.5–32.4 mg S∙m−2 during the light day. Nonreductive sulfate assimilation (predominantly ester-SO4−) accounted for up to 40% of the total sulfate uptake when diatoms predominated. Protein synthesis measured with 35S (200–1000 mg protein∙m−2 during the light day) increased 57–89% overnight. Hourly rates were similar during light and scotophase incubations. Night metabolism substantially altered the biochemical composition (e.g. protein, lipid, and carbohydrate) of the plankton with respect to newly incorporated carbon. Combined plant-specific H14CO3− and general microbial 3SSO42− techniques suggested algal dominance in the mixed layer.

Mitochondrial DNA Medicine

2007 ◽  
Vol 27 (1-3) ◽  
pp. 5-9 ◽  
Author(s):  
Salvatore DiMauro
Keyword(s):  
Mitochondrial Dna ◽  
Protein Synthesis ◽  
Mitochondrial Protein ◽  
Point Mutations ◽  
Specific Protein ◽  
Mitochondrial Protein Synthesis ◽  
Mitochondrial Genetics ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mitochondrial Medicine

The small, maternally inherited mitochondrial DNA (mtDNA) has turned out to be a hotbed of pathogenic mutations: 15 years into the era of ‘mitochondrial medicine’, over 150 pathogenic point mutations and countless rearrangements have been associated with a variety of multisystemic or tissue-specific human diseases. MtDNA-related disorders can be divided into two major groups: those due to mutations in genes affecting mitochondrial protein synthesis in toto and those due to mutations in specific protein-coding genes. Here we review the mitochondrial genetics and the clinical features of the mtDNA-related diseases.

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