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Article ; Online: Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.

Stevens, Alexander / Cui, Yanxiang / Shivakoti, Sakar / Zhou, Z Hong

2023 Volume 14, Issue 7, Page(s) 544–548

MeSH term(s)	Reoviridae ; Cryoelectron Microscopy
Language	English
Publishing date	2023-03-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2543451-2
ISSN	1674-8018 ; 1674-8018
ISSN (online)	1674-8018
ISSN	1674-8018
DOI	10.1093/procel/pwad002
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Article ; Online: Multiple conformations of trimeric spikes visualized on a non-enveloped virus.

Zhang, Yinong / Cui, Yanxiang / Sun, Jingchen / Zhou, Z Hong

Nature communications

2022 Volume 13, Issue 1, Page(s) 550

Abstract: Many viruses utilize trimeric spikes to gain entry into host cells. However, without in situ structures of these trimeric spikes, a full understanding of this dynamic and essential process of viral infections is not possible. Here we present four in situ ...

Abstract	Many viruses utilize trimeric spikes to gain entry into host cells. However, without in situ structures of these trimeric spikes, a full understanding of this dynamic and essential process of viral infections is not possible. Here we present four in situ and one isolated cryoEM structures of the trimeric spike of the cytoplasmic polyhedrosis virus, a member of the non-enveloped Reoviridae family and a virus historically used as a model in the discoveries of RNA transcription and capping. These structures adopt two drastically different conformations, closed spike and opened spike, which respectively represent the penetration-inactive and penetration-active states. Each spike monomer has four domains: N-terminal, body, claw, and C-terminal. From closed to opened state, the RGD motif-containing C-terminal domain is freed to bind integrins, and the claw domain rotates to expose and project its membrane insertion loops into the cellular membrane. Comparison between turret vertices before and after detachment of the trimeric spike shows that the trimeric spike anchors its N-terminal domain in the iris of the pentameric RNA-capping turret. Sensing of cytosolic S-adenosylmethionine (SAM) and adenosine triphosphate (ATP) by the turret triggers a cascade of events: opening of the iris, detachment of the spike, and initiation of endogenous transcription.
MeSH term(s)	Binding Sites ; Cryoelectron Microscopy ; Liposomes ; Molecular Conformation ; Reoviridae/genetics ; Reoviridae/metabolism ; Reoviridae/ultrastructure ; Viral Fusion Proteins/chemistry ; Viral Fusion Proteins/genetics ; Virion
Chemical Substances	Liposomes ; Viral Fusion Proteins
Language	English
Publishing date	2022-01-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28114-0
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Article ; Online: MicroRNA-4732 is downregulated in non-small cell lung cancer and inhibits tumor cell proliferation, migration, and invasion.

Tang, Xiaochun / Liu, Shuzhen / Cui, Yanxiang / Zhao, Yuling

Respiratory medicine and research

2021 Volume 80, Page(s) 100865

Abstract: Background: Non-small cell lung cancer (NSCLC) is the leading cause of cancer death with increasing morbidity and mortality. MicroRNA-4732-5p (miR-4732-5p) has been reported to be dysregulated in various cancers and identified as a tumor suppressor. ... ...

Abstract	Background: Non-small cell lung cancer (NSCLC) is the leading cause of cancer death with increasing morbidity and mortality. MicroRNA-4732-5p (miR-4732-5p) has been reported to be dysregulated in various cancers and identified as a tumor suppressor. This study aims to explore the expression and role of miR-4732-5p in NSCLC. Methods: Reverse transcription-quantitative polymerase chain reaction (qRT-PCR) assay was employed to detect the expression of miR-4732-5p in NSCLC. With the help of Kaplan-Meier survival and Cox regression, the prognostic significance of miR-4732-5p was investigated. Meanwhile, the effects of miR-4732-5p on cell proliferation, migration, and invasion were also studied. Results: The expression of miR-4732-5p decreased in NSCLC tissues and cells. The downregulation of miR-4732-5p was closely associated with lymph node metastasis, TNM stage, and poor prognosis. Multivariate Cox regression analysis results showed that miR-4732-5p was an independent prognosis factor for NSCLC. In addition, the overexpression of miR-4732-5p inhibited the proliferation, migration, and invasion of NSCLC cells through modulating TSPAN13. Conclusions: These data showed that miR-4732-5p might be involved in the development of NSCLC, which can act as an independent prognostic biomarker and therapeutic target.
MeSH term(s)	Carcinoma, Non-Small-Cell Lung/genetics ; Cell Movement/genetics ; Cell Proliferation/genetics ; Down-Regulation ; Humans ; Lung Neoplasms/genetics ; MicroRNAs/genetics ; Tetraspanins
Chemical Substances	MIRN4739 microRNA, human ; MicroRNAs ; TSPAN13 protein, human ; Tetraspanins
Language	English
Publishing date	2021-10-21
Publishing country	France
Document type	Journal Article
ISSN	2590-0412
ISSN (online)	2590-0412
DOI	10.1016/j.resmer.2021.100865
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Article ; Online: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.

Kim, Jinseok / Li, Chia-Lung / Chen, Xuemin / Cui, Yanxiang / Golebiowski, Filip M / Wang, Huaibin / Hanaoka, Fumio / Sugasawa, Kaoru / Yang, Wei

Nature

2023 Volume 617, Issue 7959, Page(s) 170–175

Abstract: Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky ... ...

Abstract	Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts
MeSH term(s)	Humans ; DNA/chemistry ; DNA/metabolism ; DNA Damage ; DNA Helicases/metabolism ; DNA Repair ; DNA-Binding Proteins/metabolism ; Transcription Factor TFIIH/metabolism ; Xeroderma Pigmentosum Group A Protein/metabolism ; Substrate Specificity ; DNA-Directed RNA Polymerases/metabolism
Chemical Substances	DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-) ; DNA-Binding Proteins ; Transcription Factor TFIIH (148710-81-0) ; Xeroderma Pigmentosum Group A Protein ; XPA protein, human ; XPC protein, human (156533-34-5) ; ERCC2 protein, human (EC 5.99.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2023-04-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-05959-z
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Article ; Online: Atomic Structure of the Trichomonas vaginalis Double-Stranded RNA Virus 2.

Stevens, Alexander / Muratore, Katherine / Cui, Yanxiang / Johnson, Patricia J / Zhou, Z Hong

mBio

2021 Volume 12, Issue 2

Abstract: Trichomonas ... ...

Abstract	Trichomonas vaginalis
MeSH term(s)	Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Cryoelectron Microscopy ; Genome, Viral ; Protein Conformation, alpha-Helical ; RNA Viruses/classification ; RNA Viruses/genetics ; RNA Viruses/isolation & purification ; RNA Viruses/ultrastructure ; RNA, Double-Stranded/chemistry ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Totiviridae/classification ; Totiviridae/genetics ; Totiviridae/isolation & purification ; Totiviridae/ultrastructure ; Trichomonas vaginalis/virology
Chemical Substances	Capsid Proteins ; RNA, Double-Stranded ; RNA, Viral
Language	English
Publishing date	2021-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02924-20
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Article ; Online: Bluetongue virus capsid protein VP5 perforates membranes at low endosomal pH during viral entry.

Xia, Xian / Wu, Weining / Cui, Yanxiang / Roy, Polly / Zhou, Z Hong

Nature microbiology

2021 Volume 6, Issue 11, Page(s) 1424–1432

Abstract: Bluetongue virus (BTV) is a non-enveloped virus and causes substantial morbidity and mortality in ruminants such as sheep. Fashioning a receptor-binding protein (VP2) and a membrane penetration protein (VP5) on the surface, BTV releases its genome- ... ...

Abstract	Bluetongue virus (BTV) is a non-enveloped virus and causes substantial morbidity and mortality in ruminants such as sheep. Fashioning a receptor-binding protein (VP2) and a membrane penetration protein (VP5) on the surface, BTV releases its genome-containing core (VP3 and VP7) into the host cell cytosol after perforation of the endosomal membrane. Unlike enveloped ones, the entry mechanisms of non-enveloped viruses into host cells remain poorly understood. Here we applied single-particle cryo-electron microscopy, cryo-electron tomography and structure-guided functional assays to characterize intermediate states of BTV cell entry in endosomes. Four structures of BTV at the resolution range of 3.4-3.9 Å show the different stages of structural rearrangement of capsid proteins on exposure to low pH, including conformational changes of VP5, stepwise detachment of VP2 and a small shift of VP7. In detail, sensing of the low-pH condition by the VP5 anchor domain triggers three major VP5 actions: projecting the hidden dagger domain, converting a surface loop to a protonated β-hairpin that anchors VP5 to the core and stepwise refolding of the unfurling domains into a six-helix stalk. Cryo-electron tomography structures of BTV interacting with liposomes show a length decrease of the VP5 stalk from 19.5 to 15.5 nm after its insertion into the membrane. Our structures, functional assays and structure-guided mutagenesis experiments combined indicate that this stalk, along with dagger domain and the WHXL motif, creates a single pore through the endosomal membrane that enables the viral core to enter the cytosol. Our study unveils the detailed mechanisms of BTV membrane penetration and showcases general methods to study cell entry of other non-enveloped viruses.
MeSH term(s)	Animals ; Bluetongue/virology ; Bluetongue virus/chemistry ; Bluetongue virus/genetics ; Bluetongue virus/metabolism ; Bluetongue virus/ultrastructure ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Cryoelectron Microscopy ; Endosomes/chemistry ; Endosomes/virology ; Hydrogen-Ion Concentration ; Models, Molecular ; Sheep ; Sheep Diseases/virology ; Virus Internalization
Chemical Substances	Capsid Proteins ; VP5 protein, Bluetongue virus
Language	English
Publishing date	2021-10-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-021-00988-8
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Article ; Online: Increased neutrophil-lymphocyte ratio independently predicts poor survival in non-metastatic triple-negative breast cancer patients.

Qiu, Xiangting / Song, Yucui / Cui, Yanxiang / Liu, Yan

IUBMB life

2018 Volume 70, Issue 6, Page(s) 529–535

Abstract: Inflammation plays an important role in tumor initiation, progression, and metastasis. The neutrophil-lymphocyte ratio (NLR) is widely used to evaluate global inflammation in various tumor types. However, the prognostic role of NLR in non-metastatic ... ...

Abstract	Inflammation plays an important role in tumor initiation, progression, and metastasis. The neutrophil-lymphocyte ratio (NLR) is widely used to evaluate global inflammation in various tumor types. However, the prognostic role of NLR in non-metastatic triple-negative breast cancer (TNBC) patients was poorly known. The aim of this study was to explore the association between pre-treatment NLR and survival in TNBC patients. Data were collected for patients with stages I-III TNBC from 2006 to 2013 at Linyi Central Hospital to analyze pre-treatment NLR and survival. Overall survival (OS) and disease-free survival (DFS) were estimated by the Kaplan-Meier method, and Cox analysis was performed to determine clinicopathological parameters for their prognostic relevance. A total of 406 patients were eligible. Patients with NLR lower than 2.85 exhibited significantly higher OS (P < 0.001) and DFS (P < 0.001) than patients with higher NLR. Higher pre-treatment NLR was independently correlated with poor OS and DFS, with hazard ratios of 2.69 (95% confidence interval [CI]: 1.94-3.72, P = 0.001) and 2.13 (95% CI: 1.68-2.65, P = 0.008), respectively, in the Cox proportional multivariate hazard model. In conclusion, our results indicate that pre-treatment NLR may be correlated with OS and DFS in early-stage TNBC patients, and that it may have considerable clinical applications. © 2018 IUBMB Life, 70(6):529-535, 2018.
MeSH term(s)	Biomarkers, Tumor/analysis ; Carcinoma, Ductal, Breast/mortality ; Carcinoma, Ductal, Breast/pathology ; Carcinoma, Ductal, Breast/therapy ; Carcinoma, Lobular/mortality ; Carcinoma, Lobular/pathology ; Carcinoma, Lobular/therapy ; Combined Modality Therapy ; Female ; Follow-Up Studies ; Humans ; Lymphocytes/pathology ; Middle Aged ; Neutrophils/pathology ; Prognosis ; Retrospective Studies ; Survival Rate ; Triple Negative Breast Neoplasms/mortality ; Triple Negative Breast Neoplasms/pathology ; Triple Negative Breast Neoplasms/therapy
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2018-04-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1492141-8
ISSN	1521-6551 ; 1521-6543
ISSN (online)	1521-6551
ISSN	1521-6543
DOI	10.1002/iub.1745
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Article: Exploration and verification of the feasibility of sulfide-driven partial denitrification coupled with anammox for wastewater treatment

Deng, Yang-Fan / Wu, Di / Huang, Hao / Cui, Yan-Xiang / van Loosdrecht, Mark C.M / Chen, Guang-Hao

Water research. 2021 Apr. 01, v. 193

2021

Abstract: Anaerobic ammonia oxidation (anammox) is a well-developed biotechnology for treating high-strength ammonium wastewaters. Recently, partial denitrification has been considered as an alternative to supply anammox with the required nitrite. In this study, a ...

Abstract	Anaerobic ammonia oxidation (anammox) is a well-developed biotechnology for treating high-strength ammonium wastewaters. Recently, partial denitrification has been considered as an alternative to supply anammox with the required nitrite. In this study, a process of sulfide-driven partial denitrification and anammox (SPDA) was developed and operated continuously in an upflow anaerobic sludge blanket (UASB) reactor for 392 days. This reactor was fed with synthetic wastewater containing 100 mgN/L nitrate, 80 mgN/L ammonium and 20–80 mgS/L sulfide. After 160 days of operation, the reactor reached stable performance, and the nitrogen removal efficiency and rate were maintained at 80% and 0.29 kgN/(m³•d), respectively. The estimated nitrogen removal via anammox and sulfide-driven denitrification were 87.2% and 12.8%. Additional batch experiments were conducted to investigate the effects of sulfide on anammox and the mechanisms of nitrogen removal in the SPDA system. The following results were obtained: (1) sulfide had an inhibitory effect on the specific anammox activity with IC₅₀ of 9.7 mgS-H₂S/L. (2) The rapid oxidation of sulfide by sulfur-oxidizing bacteria (SOB) could relieve the toxic effects of sulfide on the anammox in the SPDA system. (3) Sulfide bio-oxidation was a two-step reaction with biologically produced elemental sulfur (BPS⁰) as the intermediate, and the second step using BPS⁰ as the electron donor, can efficiently produce nitrite via partial denitrification (NO₃⁻ → NO₂⁻) as a supply for anammox. Finally, a high-throughput sequencing analysis identified Thiobacillus and Sulfurimonas as the dominant genera of SOB in the SPDA system, and Candidatus Kuenenia as the dominant anammox bacteria. Overall, this research gives the foundation for the practical application of sulfide-driven partial denitrification and anammox process in the future.
Keywords	Thiobacillus ; ammonium ; anaerobic ammonium oxidation ; anaerobic digestion ; bacteria ; denitrification ; nitrates ; nitrites ; nitrogen ; sulfides ; sulfur ; upflow anaerobic sludge blanket reactor ; wastewater treatment
Language	English
Dates of publication	2021-0401
Publishing place	Elsevier Ltd
Document type	Article
Note	golden set
ZDB-ID	202613-2
ISSN	1879-2448 ; 0043-1354
ISSN (online)	1879-2448
ISSN	0043-1354
DOI	10.1016/j.watres.2021.116905
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Article ; Online: How mouse RAG recombinase avoids DNA transposition.

Chen, Xuemin / Cui, Yanxiang / Wang, Huaibin / Zhou, Z Hong / Gellert, Martin / Yang, Wei

Nature structural & molecular biology

2020 Volume 27, Issue 2, Page(s) 127–133

Abstract: The RAG1-RAG2 recombinase (RAG) cleaves DNA to initiate V(D)J recombination, but RAG also belongs to the RNH-type transposase family. To learn how RAG-catalyzed transposition is inhibited in developing lymphocytes, we determined the structure of a DNA- ... ...

Abstract	The RAG1-RAG2 recombinase (RAG) cleaves DNA to initiate V(D)J recombination, but RAG also belongs to the RNH-type transposase family. To learn how RAG-catalyzed transposition is inhibited in developing lymphocytes, we determined the structure of a DNA-strand transfer complex of mouse RAG at 3.1-Å resolution. The target DNA is a T form (T for transpositional target), which contains two >80° kinks towards the minor groove, only 3 bp apart. RAG2, a late evolutionary addition in V(D)J recombination, appears to enforce the sharp kinks and additional inter-segment twisting in target DNA and thus attenuates unwanted transposition. In contrast to strand transfer complexes of genuine transposases, where severe kinks occur at the integration sites of target DNA and thus prevent the reverse reaction, the sharp kink with RAG is 1 bp away from the integration site. As a result, RAG efficiently catalyzes the disintegration reaction that restores the RSS (donor) and target DNA.
MeSH term(s)	Animals ; Cryoelectron Microscopy ; DNA/chemistry ; DNA/metabolism ; DNA Cleavage ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; HEK293 Cells ; Homeodomain Proteins/chemistry ; Homeodomain Proteins/metabolism ; Humans ; Mice ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation
Chemical Substances	DNA-Binding Proteins ; Homeodomain Proteins ; Rag2 protein, mouse ; RAG-1 protein (128559-51-3) ; DNA (9007-49-2)
Language	English
Publishing date	2020-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-019-0366-z
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Zs.A 4101: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Atomic Structures of Anthrax Prechannel Bound with Full-Length Lethal and Edema Factors.

Zhou, Kang / Liu, Shiheng / Hardenbrook, Nathan J / Cui, Yanxiang / Krantz, Bryan A / Zhou, Z Hong

Structure (London, England : 1993)

2020 Volume 28, Issue 8, Page(s) 879–887.e3

Abstract: Pathogenesis of anthrax disease involves two cytotoxic enzymes-edema factor (EF) and lethal factor (LF)-which are individually recruited by the protective antigen heptamer ( ... ...

Abstract	Pathogenesis of anthrax disease involves two cytotoxic enzymes-edema factor (EF) and lethal factor (LF)-which are individually recruited by the protective antigen heptamer (PA
MeSH term(s)	Antigens, Bacterial/chemistry ; Antigens, Bacterial/metabolism ; Bacterial Toxins/chemistry ; Bacterial Toxins/metabolism ; Cryoelectron Microscopy ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Multimerization
Chemical Substances	Antigens, Bacterial ; Bacterial Toxins ; anthrax toxin
Language	English
Publishing date	2020-06-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2020.05.009
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