1
|
Zhang Q, Lam WH, Zhai Y. Assembly and activation of replicative helicases at origin DNA for replication initiation. Curr Opin Struct Biol 2024; 88:102876. [PMID: 38986167 DOI: 10.1016/j.sbi.2024.102876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
Abstract
To initiate DNA replication, it is essential to properly assemble a pair of replicative helicases at each replication origin. While the general principle of this process applies universally from prokaryotes to eukaryotes, the specific mechanisms governing origin selection, helicase loading, and subsequent helicase activation vary significantly across different species. Recent advancements in cryo-electron microscopy (cryo-EM) have revolutionized our ability to visualize large protein or protein-DNA complexes involved in the initiation of DNA replication. Complemented by real-time single-molecule analysis, the available high-resolution cryo-EM structures have greatly enhanced our understanding of the dynamic regulation of this process at origin DNA. This review primarily focuses on the latest structural discoveries that shed light on the key molecular machineries responsible for driving replication initiation, with a particular emphasis on the assembly of pre-replication complex (pre-RC) in eukaryotes.
Collapse
Affiliation(s)
- Qiongdan Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Wai Hei Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong.
| |
Collapse
|
2
|
Ruan ML, Ni WX, Chu JCH, Lam TL, Law KC, Zhang Y, Yang G, He Y, Zhang C, Fung YME, Liu T, Huang T, Lok CN, Chan SLF, Che CM. Iridium(III) carbene complexes as potent girdin inhibitors against metastatic cancers. Proc Natl Acad Sci U S A 2024; 121:e2316615121. [PMID: 38861602 PMCID: PMC11194514 DOI: 10.1073/pnas.2316615121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/27/2024] [Indexed: 06/13/2024] Open
Abstract
Many cancer-driving protein targets remain undruggable due to a lack of binding molecular scaffolds. In this regard, octahedral metal complexes with unique and versatile three-dimensional structures have rarely been explored as inhibitors of undruggable protein targets. Here, we describe antitumor iridium(III) pyridinium-N-heterocyclic carbene complex 1a, which profoundly reduces the viability of lung and breast cancer cells as well as cancer patient-derived organoids at low micromolar concentrations. Compound 1a effectively inhibits the growth of non-small-cell lung cancer and triple-negative breast cancer xenograft tumors, impedes the metastatic spread of breast cancer cells, and can be modified into an antibody-drug conjugate payload to achieve precise tumor delivery in mice. Identified by thermal proteome profiling, an important molecular target of 1a in cellulo is Girdin, a multifunctional adaptor protein that is overexpressed in cancer cells and unequivocally serves as a signaling hub for multiple pivotal oncogenic pathways. However, specific small-molecule inhibitors of Girdin have not yet been developed. Notably, 1a exhibits high binding affinity to Girdin with a Kd of 1.3 μM and targets the Girdin-linked EGFR/AKT/mTOR/STAT3 cancer-driving pathway, inhibiting cancer cell proliferation and metastatic activity. Our study reveals a potent Girdin-targeting anticancer compound and demonstrates that octahedral metal complexes constitute an untapped library of small-molecule inhibitors that can fit into the ligand-binding pockets of key oncoproteins.
Collapse
Affiliation(s)
- Mei-Ling Ruan
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan430079, China
| | - Wen-Xiu Ni
- Department of Medicinal Chemistry, Shantou University Medical College, Shantou515041, Guangdong, China
- Chemistry and Chemical Engineering of Guangdong Laboratory, Shantou515041, Guangdong, China
| | - Jacky C. H. Chu
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tsz-Lung Lam
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Kwok-Chung Law
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yiwei Zhang
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Guanya Yang
- AI And Life Sciences Institute (Hong Kong) Limited, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Ying He
- AI And Life Sciences Institute (Hong Kong) Limited, Hong Kong Science Park, Shatin, Hong Kong, China
| | - Chunlei Zhang
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yi Man Eva Fung
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tao Liu
- Department of Medicinal Chemistry, Shantou University Medical College, Shantou515041, Guangdong, China
- Chemistry and Chemical Engineering of Guangdong Laboratory, Shantou515041, Guangdong, China
| | - Tao Huang
- Department of Medicinal Chemistry, Shantou University Medical College, Shantou515041, Guangdong, China
- Chemistry and Chemical Engineering of Guangdong Laboratory, Shantou515041, Guangdong, China
| | - Chun-Nam Lok
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Sharon Lai-Fung Chan
- Department of Applied Biology and Chemical Biology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Chi-Ming Che
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| |
Collapse
|
3
|
Li N, Gao N. A commentary of "Initial DNA melting in human DNA replication initiation": Top 10 Scientific Advances of 2023, China. FUNDAMENTAL RESEARCH 2024; 4:701-703. [PMID: 38933211 PMCID: PMC11197563 DOI: 10.1016/j.fmre.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 06/28/2024] Open
Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
4
|
Liu D, Sonalkar J, Prasanth SG. ORChestra coordinates the replication and repair music. Bioessays 2023; 45:e2200229. [PMID: 36811379 PMCID: PMC10023367 DOI: 10.1002/bies.202200229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
Error-free genome duplication and accurate cell division are critical for cell survival. In all three domains of life, bacteria, archaea, and eukaryotes, initiator proteins bind replication origins in an ATP-dependent manner, play critical roles in replisome assembly, and coordinate cell-cycle regulation. We discuss how the eukaryotic initiator, Origin recognition complex (ORC), coordinates different events during the cell cycle. We propose that ORC is the maestro driving the orchestra to coordinately perform the musical pieces of replication, chromatin organization, and repair.
Collapse
Affiliation(s)
- Dazhen Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
| | - Jay Sonalkar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
| | - Supriya G. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
- Cancer center at Illinois, UIUC
| |
Collapse
|
5
|
Abstract
Rift Valley fever virus (RVFV) belongs to the order Bunyavirales and is the type species of genus Phlebovirus, which accounts for over 50% of family Phenuiviridae species. RVFV is mosquito-borne and causes severe diseases in both humans and livestock, and consists of three segments (S, M, L) in the genome. The L segment encodes an RNA-dependent RNA polymerase (RdRp, L protein) that is responsible for facilitating the replication and transcription of the virus. It is essential for the virus and has multiple drug targets. Here, we established an expression system and purification procedures for full-length L protein, which is composed of an endonuclease domain, RdRp domain, and cap-binding domain. A cryo-EM L protein structure was reported at 3.6 Å resolution. In this first L protein structure of genus Phlebovirus, the priming loop of RVFV L protein is distinctly different from those of other L proteins and undergoes large movements related to its replication role. Structural and biochemical analyses indicate that a single template can induce initiation of RNA synthesis, which is notably enhanced by 5' viral RNA. These findings help advance our understanding of the mechanism of RNA synthesis and provide an important basis for developing antiviral inhibitors. Importance The zoonosis RVF virus (RVFV) is one of the most serious arbovirus threats to both human and animal health. RNA-dependent RNA polymerase (RdRp) is a multifunctional enzyme catalyzing genome replication as well as viral transcription, so the RdRp is essential for studying the virus and has multiple drug targets. In our study, we report the structure of RVFV L protein at 3.6 Å resolution by cryo-EM. This is the first L protein structure of genus Phlebovirus. Strikingly, a single template can initiate RNA replication. The structure and assays provide a comprehensive and in-depth understanding of the catalytic and substrate recognition mechanism of RdRp.
Collapse
|
6
|
Investigation of the Interaction of Human Origin Recognition Complex Subunit 1 with G-Quadruplex DNAs of Human c-myc Promoter and Telomere Regions. Int J Mol Sci 2021; 22:ijms22073481. [PMID: 33801762 PMCID: PMC8036949 DOI: 10.3390/ijms22073481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Origin recognition complex (ORC) binds to replication origins in eukaryotic DNAs and plays an important role in replication. Although yeast ORC is known to sequence-specifically bind to a replication origin, how human ORC recognizes a replication origin remains unknown. Previous genome-wide studies revealed that guanine (G)-rich sequences, potentially forming G-quadruplex (G4) structures, are present in most replication origins in human cells. We previously suggested that the region comprising residues 413–511 of human ORC subunit 1, hORC1413–511, binds preferentially to G-rich DNAs, which form a G4 structure in the absence of hORC1413–511. Here, we investigated the interaction of hORC1413-511 with various G-rich DNAs derived from human c-myc promoter and telomere regions. Fluorescence anisotropy revealed that hORC1413–511 binds preferentially to DNAs that have G4 structures over ones having double-stranded structures. Importantly, circular dichroism (CD) and nuclear magnetic resonance (NMR) showed that those G-rich DNAs retain the G4 structures even after binding with hORC1413–511. NMR chemical shift perturbation analyses revealed that the external G-tetrad planes of the G4 structures are the primary binding sites for hORC1413–511. The present study suggests that human ORC1 may recognize replication origins through the G4 structure.
Collapse
|