scholarly journals Structural basis of transcription-translation coupling and collision in bacteria

2020 ◽  
Author(s):  
Michael William Webster ◽  
Maria Takacs ◽  
Chengjin Zhu ◽  
Vita Vidmar ◽  
Ayesha Eduljee ◽  
...  
Keyword(s):  
Molecular Assembly ◽  
Supramolecular Complex ◽  
Structural Basis ◽  
Messenger Rnas ◽  
Exit Channel ◽  
Electron Cryomicroscopy ◽  
Interaction Interface ◽  
Translation Coupling ◽  
Shed Light ◽  
Variable Interaction

AbstractProkaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The pioneering ribosome potentially contacts RNA polymerase (RNAP), forming a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here we present a series of structures representing uncoupled, coupled and collided expressome states determined by electron cryomicroscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, stabilizing an otherwise variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance-channel to the RNAP exit-channel. In this collided complex, NusG-linkage is no longer possible.These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.One Sentence SummaryStructures of the molecular assembly executing gene expression shed light on transcription translation coupling.

scholarly journals Structural basis of transcription-translation coupling and collision in bacteria

Science ◽  
2020 ◽  
Vol 369 (6509) ◽  
pp. 1355-1359 ◽  
Author(s):  
Michael William Webster ◽  
Maria Takacs ◽  
Chengjin Zhu ◽  
Vita Vidmar ◽  
Ayesha Eduljee ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transcription Factor ◽  
Supramolecular Complex ◽  
Structural Basis ◽  
Messenger Rnas ◽  
Exit Channel ◽  
Cryo Electron Microscopy ◽  
Interaction Interface ◽  
Translation Coupling ◽  
Variable Interaction

Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo–electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.

scholarly journals Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Matthew J. Belousoff ◽  
Zohar Eyal ◽  
Mazdak Radjainia ◽  
Tofayel Ahmed ◽  
Rebecca S. Bamert ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Structural Information ◽  
Structural Basis ◽  
Common Mechanism ◽  
Resistance Mutations ◽  
Antimicrobial Drugs ◽  
Linezolid Resistance ◽  
Drug Modification ◽  
Antibiotic Resistance Mutations ◽  
Shed Light

ABSTRACT An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus. This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821–832, 2015, https://doi.org/10.1038/nrd4675 ). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821–832, 2015, https://doi.org/10.1038/nrd4675 ). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.

scholarly journals Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase

2020 ◽  
Vol 117 (33) ◽  
pp. 19914-19925 ◽  
Author(s):  
Anahita Daruwalla ◽  
Jianye Zhang ◽  
Ho Jun Lee ◽  
Nimesh Khadka ◽  
Erik R. Farquhar ◽  
...  
Keyword(s):  
Active Site ◽  
Molecular Basis ◽  
Structural Basis ◽  
Reaction Intermediates ◽  
Catalytic Activities ◽  
Selective Stabilization ◽  
Carotenoid Cleavage Dioxygenases ◽  
Active Site Cavity ◽  
Binding Cleft ◽  
Shed Light

Apocarotenoids are important signaling molecules generated from carotenoids through the action of carotenoid cleavage dioxygenases (CCDs). These enzymes have a remarkable ability to cleave carotenoids at specific alkene bonds while leaving chemically similar sites within the polyene intact. Although several bacterial and eukaryotic CCDs have been characterized, the long-standing goal of experimentally visualizing a CCD–carotenoid complex at high resolution to explain this exquisite regioselectivity remains unfulfilled. CCD genes are also present in some archaeal genomes, but the encoded enzymes remain uninvestigated. Here, we address this knowledge gap through analysis of a metazoan-like archaeal CCD fromCandidatusNitrosotalea devanaterra (NdCCD).NdCCD was active toward β-apocarotenoids but did not cleave bicyclic carotenoids. It exhibited an unusual regiospecificity, cleaving apocarotenoids solely at the C14′–C13′ alkene bond to produce β-apo-14′-carotenals. The structure ofNdCCD revealed a tapered active site cavity markedly different from the broad active site observed for the retinal-formingSynechocystisapocarotenoid oxygenase (SynACO) but similar to the vertebrate retinoid isomerase RPE65. The structure ofNdCCD in complex with its apocarotenoid product demonstrated that the site of cleavage is defined by interactions along the substrate binding cleft as well as selective stabilization of reaction intermediates at the scissile alkene. These data on the molecular basis of CCD catalysis shed light on the origins of the varied catalytic activities found in metazoan CCDs, opening the possibility of modifying their activity through rational chemical or genetic approaches.

scholarly journals Structural basis for transcriptional start site control of HIV-1 RNA fate

Science ◽  
2020 ◽  
Vol 368 (6489) ◽  
pp. 413-417 ◽  
Author(s):  
Joshua D. Brown ◽  
Siarhei Kharytonchyk ◽  
Issac Chaudry ◽  
Aishwarya S. Iyer ◽  
Hannah Carter ◽  
...  
Keyword(s):  
Transcriptional Start Site ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Structural Basis ◽  
Energetic Cost ◽  
Messenger Rnas ◽  
Start Site ◽  
Eukaryotic Translation ◽  
Central Helix ◽  
Hiv 1

Heterogeneous transcriptional start site usage by HIV-1 produces 5′-capped RNAs beginning with one, two, or three 5′-guanosines (Cap1G, Cap2G, or Cap3G, respectively) that are either selected for packaging as genomes (Cap1G) or retained in cells as translatable messenger RNAs (mRNAs) (Cap2G and Cap3G). To understand how 5′-guanosine number influences fate, we probed the structures of capped HIV-1 leader RNAs by deuterium-edited nuclear magnetic resonance. The Cap1G transcript adopts a dimeric multihairpin structure that sequesters the cap, inhibits interactions with eukaryotic translation initiation factor 4E, and resists decapping. The Cap2G and Cap3G transcripts adopt an alternate structure with an elongated central helix, exposed splice donor residues, and an accessible cap. Extensive remodeling, achieved at the energetic cost of a G-C base pair, explains how a single 5′-guanosine modifies the function of a ~9-kilobase HIV-1 transcript.

The floral development and anatomy of Carica papaya (Caricaceae)

1999 ◽  
Vol 77 (4) ◽  
pp. 582-598 ◽  
Author(s):  
LP Ronse Decraene ◽  
E F Smets
Keyword(s):  
Calcium Oxalate ◽  
Carica Papaya ◽  
Floral Development ◽  
Floral Anatomy ◽  
Structural Basis ◽  
Unisexual Flowers ◽  
Stigmatic Exudate ◽  
Large Ovary ◽  
Further Development ◽  
Shed Light

Floral development and anatomy of Carica papaya L. have been investigated to shed light on (i) the morphology of the flower, (ii) the structural basis for the pollination mechanism, and (iii) the relationships of the Caricaceae. Carica is mostly dioecious with a strong dimorphism between staminate and pistillate flowers. The development of staminate flowers resembles that of pistillate flowers up to the initiation of the stamens. Further development leads to highly diverging morphologies. In staminate flowers a combination of contorted growth and the development of a common stamen-petal tube produces a long floral tube. The gynoecium grows into a central spearlike pistillode. The pistillate flowers have no traces of stamens and initiate five antesepalous carpel primordia. Common basal growth leads to the development of a large ovary with staglike stigmatic lobes and intruding placentae covered with numerous ascending ovules. Floral anatomy of staminate and pistillate flowers is described. The nature of the colleters is discussed. The morphological basis for reward production in C. papaya is clarified, and conflicting views on pollination are discussed. Nectaries of staminate flowers are located on the central rudimentary pistil and not at the base of the stamens, as previously reported. The anthers contain packages of calcium oxalate crystals. Pistillate flowers produce no nectar but have a stigmatic exudate. We compared the floral development and anatomy of Carica with that of Adenia (Passifloraceae) and Moringa (Moringaceae) in the view of a relationship with other glucosinolate-producing families. Although a derivation of the unisexual flowers from bisexual ancestors is probable, Storey's hypothetical derivation of pistillate flowers is not supported by the floral ontogeny and vasculature.Key words: Adenia, Caricaceae, Moringa anatomy, calcium oxalate packages, dioecy, floral structure, nectaries, ontogeny, pollination, systematic relationships.

scholarly journals Structural basis of Q-dependent antitermination

2019 ◽  
Author(s):  
Zhou Yin ◽  
Jason Kaelber ◽  
Richard H. Ebright
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Rna Polymerase ◽  
Structural Basis ◽  
Exit Channel ◽  
Late Genes ◽  
Q Protein ◽  
Rna Hairpins

AbstractLambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and an adjacent sigma-dependent pause element (SDPE) to yield a “Q-loading complex,” and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient “Q-loaded complex.” Here, we report high-resolution structures of four states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus--a “nozzle”--that narrows and extends the RNAP RNA-exit channel, extruding single-stranded RNA and preventing formation of pause and terminator hairpins.One Sentence SummaryQ forms a “nozzle” that narrows the RNA polymerase RNA-exit channel and extrudes ssRNA, preventing formation of RNA hairpins.

scholarly journals Pseudouridine-free Ribosome Exhibits Distinct Inter-subunit Movements

2021 ◽  
Author(s):  
Yu Zhao ◽  
Jay Rai ◽  
Hong-Guo Yu ◽  
Hong Li
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cancer Predisposition ◽  
Rna Modification ◽  
Structural Basis ◽  
Free Ribosome ◽  
Electron Cryomicroscopy ◽  
Pseudouridine Synthase ◽  
Phosphate Backbone ◽  
Close Contacts

Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition. The structural basis for how pseudouridine impacts ribosome function remains uncharacterized. Here we report electron cryomicroscopy structures of a fully modified and a pseudouridine-free ribosome from Saccharomyces cerevisiae. In the modified ribosome, the rearranged N1 atom of pseudouridine is observed to stabilize key functional motifs by establishing predominately water-mediated close contacts with the phosphate backbone. The pseudouridine-free ribosome, however, is devoid of such interactions and displays conformations reflective of abnormal inter-subunit movements. The erroneous motions of the pseudouridine-free ribosome may explain its observed deficiencies in translation.

scholarly journals Structural basis of ALC1/CHD1L autoinhibition and the mechanism of activation by the nucleosome

2021 ◽  
Author(s):  
zhucheng chen ◽  
li wang ◽  
kangjing chen
Keyword(s):  
Crystal Structure ◽  
Liver Cancer ◽  
Chromatin Remodeling ◽  
Structural Basis ◽  
Chromatin Remodeler ◽  
Macro Domain ◽  
Regulation Mechanisms ◽  
Shed Light ◽  
The Way

Chromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is regulated remain unclear. Here we report the crystal structure of human ALC1 and the cryoEM structure bound to the nucleosome. The structure shows the macro domain of ALC1 binds to lobe 2 of the ATPase motor, sequestering two elements for nucleosome recognition, explaining the autoinhibition mechanism of the enzyme. The H4 tail competes with the macro domain for lobe 2-binding, explaining the requirement for this nucleosomal epitope for ALC1 activation. A dual-arginine-anchor motif of ALC1 recognizes the acidic pocket of the nucleosome, which is critical for chromatin remodeling in vitro. Together, our findings illustrate the structures of ALC1 and shed light on its regulation mechanisms, paving the way for the discovery of drugs targeting ALC1 for the treatment of cancer.

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