The use of ribosome-nascent chain complex-seq to reveal the translated mRNA profile and the role of ASN1 in resistance to Verticillium wilt in cotton

Genomics ◽  
2021 ◽  
Author(s):  
Chaowei Cai ◽  
Ping Wang ◽  
Chenyu Zhao ◽  
Wei Lei ◽  
Zongyan Chu ◽  
...  
Keyword(s):  
Verticillium Wilt ◽  
Chain Complex ◽  
Nascent Chain ◽  
Mrna Profile

scholarly journals Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon

2015 ◽  
Vol 211 (1) ◽  
pp. 91-104 ◽  
Author(s):  
Patrick Kuhn ◽  
Albena Draycheva ◽  
Andreas Vogt ◽  
Narcis-Adrian Petriman ◽  
Lukas Sturm ◽  
...  
Keyword(s):  
Protein Targeting ◽  
Signal Recognition Particle ◽  
Resonance Energy Transfer ◽  
Chain Complex ◽  
Resonance Energy ◽  
Endoplasmic Reticulum Membrane ◽  
Signal Recognition ◽  
Ribosomal Tunnel ◽  
Nascent Chain

Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex.

scholarly journals Emerging role of long noncoding RNA-encoded micropeptides in cancer

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Mujie Ye ◽  
Jingjing Zhang ◽  
Meng Wei ◽  
Baihui Liu ◽  
Kuiran Dong
Keyword(s):  
Noncoding Rna ◽  
Cancer Metabolism ◽  
Chain Complex ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Clinical Value ◽  
Anti Cancer ◽  
Nascent Chain ◽  
Reading Frames

Abstract Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.

scholarly journals Oxidized RNA Bodies compartmentalize translation quality control in Saccharomyces cerevisiae

2020 ◽  
Author(s):  
James S. Dhaliwal ◽  
Cristina Panozzo ◽  
Lionel Benard ◽  
William Zerges
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Quality Control ◽  
Chain Complex ◽  
Processing Bodies ◽  
Rna Granules ◽  
Translation Quality ◽  
Control Factors ◽  
Cytoplasmic Rna ◽  
Nascent Chain

ABSTRACTCytoplasmic RNA granules compartmentalize phases of the translation cycle. We previously reported on the localization of oxidized RNA in human cells to cytoplasmic foci called oxidized RNA bodies (ORBs). Oxidized mRNAs are substrates of translation quality control, wherein defective mRNAs and nascent polypeptides are released from stalled ribosomes and targeted for degradation. Therefore, we asked whether ORBs compartmentalize translation quality control. Here, we identify ORBs in Saccharomyces cerevisiae and characterize them using fluorescence microscopy and proteomics. ORBs are RNA granules that are distinct from processing bodies and stress granules. Several lines of evidence support a role of ORBs in the compartmentalization of central steps in the translation quality control pathways No-Go mRNA decay and ribosome quality control. Active translation is required by both translation quality control and ORBs. ORBs contain two substrates of translation quality control: oxidized RNA and a stalled mRNA-ribosome-nascent chain complex. Translation quality control factors localize to ORBs. Translation quality control mutants have altered ORB number per cell, size, or both. Therefore, ORBs are an intracellular hub of translational quality control.

Roles of SLP-76, phosphoinositide 3-kinase, and gelsolin in the platelet shape changes initiated by the collagen receptor GPVI/FcRγ-chain complex

Blood ◽  
2000 ◽  
Vol 96 (12) ◽  
pp. 3786-3792 ◽  
Author(s):  
Hervé Falet ◽  
Kurt L. Barkalow ◽  
Vadim I. Pivniouk ◽  
Michael J. Barnes ◽  
Raif S. Geha ◽  
...  
Keyword(s):  
Platelet Activation ◽  
Shape Change ◽  
Chain Complex ◽  
Actin Assembly ◽  
Coated Surface ◽  
Phosphoinositide 3 Kinase ◽  
Collagen Receptor ◽  
Shape Changes ◽  
Platelet Shape

Abstract How platelet shape change initiated by a collagen-related peptide (CRP) specific for the GPVI/FcRγ-chain complex (GPVI/FcRγ-chain) is coupled to SLP-76, phosphoinositide (PI) 3-kinase, and gelsolin is reported. As shown by video microscopy, platelets rapidly round and grow dynamic filopodial projections that rotate around the periphery of the cell after they contact a CRP-coated surface. Lamellae subsequently spread between the projections. All the actin-driven shape changes require SLP-76 expression. SLP-76 is essential for the Ca++mobilization induced by CRP, whereas PI 3-kinase only modulates it. The extension of lamellae requires net actin assembly and an exposure of actin filament barbed ends downstream of PI 3-kinase. Gelsolin expression is also required for the extension of lamellae, but not for the formation of filopodia. Altogether, the data describe the role of SLP-76 in the platelet activation initiated by GPVI/FcRγ-chain and the roles of PI 3-kinase and gelsolin in lamellae spreading.

scholarly journals Early encounters of a nascent membrane protein

2005 ◽  
Vol 170 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Edith N.G. Houben ◽  
Raz Zarivach ◽  
Bauke Oudega ◽  
Joen Luirink
Keyword(s):  
Membrane Protein ◽  
Ribosomal Proteins ◽  
Transmembrane Domain ◽  
Signal Recognition Particle ◽  
Chain Complex ◽  
Signal Recognition ◽  
Inner Membrane ◽  
Ribosomal Tunnel ◽  
Nascent Chain ◽  
Inner Membrane Protein

An unbiased photo–cross-linking approach was used to probe the “molecular path” of a growing nascent Escherichia coli inner membrane protein (IMP) from the peptidyl transferase center to the surface of the ribosome. The nascent chain was initially in proximity to the ribosomal proteins L4 and L22 and subsequently contacted L23, which is indicative of progression through the ribosome via the main ribosomal tunnel. The signal recognition particle (SRP) started to interact with the nascent IMP and to target the ribosome–nascent chain complex to the Sec–YidC complex in the inner membrane when maximally half of the transmembrane domain (TM) was exposed from the ribosomal exit. The combined data suggest a flexible tunnel that may accommodate partially folded nascent proteins and parts of the SRP and SecY. Intraribosomal contacts of the nascent chain were not influenced by the presence of a functional TM in the ribosome.

Proteomic and functional analysis of proline dehydrogenase 1 link proline catabolism to mitochondrial electron transport in Arabidopsis thaliana

2016 ◽  
Vol 473 (17) ◽  
pp. 2623-2634 ◽  
Author(s):  
Cécile Cabassa-Hourton ◽  
Peter Schertl ◽  
Marianne Bordenave-Jacquemin ◽  
Kaouthar Saadallah ◽  
Anne Guivarc'h ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Arabidopsis Thaliana ◽  
Respiratory Chain ◽  
Chain Complex ◽  
Respiratory Chain Complex ◽  
Proline Dehydrogenase ◽  
Mitochondrial Membranes ◽  
Proline Catabolism ◽  
Biochemical Analyses

Molecular and biochemical analyses indicate a key role of proline dehydrogenase 1 in proline oxidation. ProDH1 binds to mitochondrial membranes, is part of small respiratory chain complex and delivers its electrons to the respiratory chain.

Studies on a single immunoglobulin-binding domain of protein L from Peptostreptococcus magnus: the role of tyrosine-53 in the reaction with human IgG

2001 ◽  
Vol 353 (2) ◽  
pp. 395-401 ◽  
Author(s):  
Jennifer A. BECKINGHAM ◽  
Nicholas G. HOUSDEN ◽  
Nicola M. MUIR ◽  
Stephen P. BOTTOMLEY ◽  
Michael G. GORE
Keyword(s):  
Chain Complex ◽  
Binding Domain ◽  
Protein L ◽  
Human Igg ◽  
Tyrosine Residues ◽  
Kd Values ◽  
Trp Mutant ◽  
The Stability ◽  
Immunoglobulin Binding

Chemical modification experiments with tetranitromethane (TNM) have been used to investigate the role of tyrosine residues in the formation of the complex between PpL (the single Ig-binding domain of protein L, isolated from P. magnus strain 3316) and the kappa light chain (κ-chain). Reaction of PpL with TNM causes the modification of 1.9 equiv. of tyrosine (Tyr51 and Tyr53) and results in an approx. 140-fold decrease in affinity for human IgG. Similar experiments with mutated PpL proteins suggest that nitration predominantly inactivates the protein by modification of Tyr53. Reduction of the nitrotyrosine groups to aminotyrosine by incubation with sodium hydrosulphite does not restore high affinity for IgG. Modification of κ-chain by TNM resulted in the nitration of 3.1±0.09 tyrosine residues. When the PpLŐκ-chain complex was incubated with TNM, 4.1±0.04 tyrosine residues were nitrated, indicating that one tyrosine residue previously modified by the reagent was protected from TNM when the proteins are in complex with each other. The Kd for the equilibrium between PpL, human IgG and their complex has been shown by ELISA to be 112±20nM. A similar value (153±33nM) was obtained for the complex formed between IgG and the Tyr64 → Trp mutant (Y64W). However, the Kd values for the equilibria involving the PpL mutants Y53F and Y53F,Y64W were found to be 3.2±0.2 and 4.6±1µM respectively. These suggest that the phenol group of Tyr53 in PpL is important to the stability of the PpLŐκ-chain complex.

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