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Singh D, Tripathi P, Sharma R, Grover S, Batra JK. Role of a substrate binding pocket in the amino terminal domain of Mycobacterium tuberculosis caseinolytic protease B (ClpB) in its function. J Biomol Struct Dyn 2024; 42:6189-6199. [PMID: 37418201 DOI: 10.1080/07391102.2023.2232032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis when infects the host encounters several stresses within the host, resulting in aggregation of its proteins. To resolve this problem Mtb uses chaperones to either repair the damage or degrade the aggregated proteins. Mtb caseinolytic protein B (ClpB) helps in the prevention of aggregation and also resolubilization of aggregated proteins in bacteria, which is important for the survival of Mtb in the host. To function optimally, ClpB associates with its co-partners DnaK, DnaJ, and GrpE. The role of N-terminal domain (NTD) of Mtb ClpB in its function is not well understood. In this context, we investigated the interaction of three substrate mimicking peptides with the NTD of Mtb ClpB in silico. A substrate binding pocket, within the NTD of ClpB comprising of residues L136, R137, E138, K142, R144, R148, V149, Y158, and Y162 forming an ɑ-helix was thus identified. The residues L136 and R137 of the ɑ-helix were found to be important for the interaction of DnaK to ClpB. Further, nine single alanine recombinant variants of the identified residues were generated. As compared to the wild-type Mtb ClpB all the Mtb ClpB variants generated in this study were found to have reduced ATPase and protein refolding activity indicating the importance of the substrate binding pocket in ClpB function. The study demonstrates that the NTD of Mtb ClpB is important for its substrate interaction activity, and the substrate binding pocket identified in this study plays a crucial role in this interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Digvijay Singh
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | | - Rahul Sharma
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Sonam Grover
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Janendra K Batra
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- ICMR-National Institute of Pathology, Safdarjung Hospital Complex, New Delhi, India
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2
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Reed TT, Kendal AH, Wozniak KJ, Simmons LA. DNA replication initiation timing is important for maintaining genome integrity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599555. [PMID: 38948856 PMCID: PMC11212987 DOI: 10.1101/2024.06.18.599555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
DNA replication is regulated by factors that promote or inhibit initiation. In Bacillus subtilis, YabA is a negative regulator of DNA replication initiation while the newly identified kinase CcrZ is a positive regulator. The consequences of under-initiation or over-initiation of DNA replication to genome stability remain unclear. In this work, we measure origin to terminus ratios as a proxy for replication initiation activity. We show that ΔccrZ and several ccrZ alleles under-initiate DNA replication while ablation of yabA or overproduction of CcrZ leads to over-initiation. We find that cells under-initiating DNA replication have few incidents of replication fork stress as determined by low formation of RecA-GFP foci compared with wild type. In contrast, cells over-initiating DNA replication show levels of RecA-GFP foci formation analogous to cells directly challenged with DNA damaging agents. We show that cells under-initiating and over-initiating DNA replication were both sensitive to mitomycin C and that changes in replication initiation frequency cause increased sensitivity to genotoxic stress. With these results, we propose that cells under-initiating DNA replication are sensitive to DNA damage due to a shortage of DNA for repair through homologous recombination. For cells over-initiating DNA replication, we propose that an increase in the number of replication forks leads to replication fork stress which is further exacerbated by chromosomal DNA damage. Together, our study shows that DNA replication initiation frequency must be tightly controlled as changes in initiation influence replication fork fate and the capacity of cells to efficiently repair damage to their genetic material.
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Affiliation(s)
- Tristan T. Reed
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Abigail H. Kendal
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Katherine J Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Present address: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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Fang T, Mohseni A, Lonardi S, Ben Mamoun C. Properties and predicted functions of large genes and proteins of apicomplexan parasites. NAR Genom Bioinform 2024; 6:lqae032. [PMID: 38584870 PMCID: PMC10993292 DOI: 10.1093/nargab/lqae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024] Open
Abstract
Evolutionary constraints greatly favor compact genomes that efficiently encode proteins. However, several eukaryotic organisms, including apicomplexan parasites such as Toxoplasma gondii, Plasmodium falciparum and Babesia duncani, the causative agents of toxoplasmosis, malaria and babesiosis, respectively, encode very large proteins, exceeding 20 times their average protein size. Although these large proteins represent <1% of the total protein pool and are generally expressed at low levels, their persistence throughout evolution raises important questions about their functions and possible evolutionary pressures to maintain them. In this study, we examined the trends in gene and protein size, function and expression patterns within seven apicomplexan pathogens. Our analysis revealed that certain large proteins in apicomplexan parasites harbor domains potentially important for functions such as antigenic variation, erythrocyte invasion and immune evasion. However, these domains are not limited to or strictly conserved within large proteins. While some of these proteins are predicted to engage in conventional metabolic pathways within these parasites, others fulfill specialized functions for pathogen-host interactions, nutrient acquisition and overall survival.
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Affiliation(s)
- Tiffany Fang
- Department of Internal Medicine, Section of Infectious Diseases, Department of Microbial Pathogenesis and Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
| | - Amir Mohseni
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521 USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521 USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Department of Microbial Pathogenesis and Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
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Warnock JL, Ball JA, Najmi SM, Henes M, Vazquez A, Koshnevis S, Wieden HJ, Conn GL, Ghalei H. Differential roles of putative arginine fingers of AAA + ATPases Rvb1 and Rvb2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593962. [PMID: 38798342 PMCID: PMC11118528 DOI: 10.1101/2024.05.13.593962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The evolutionarily conserved AAA+ ATPases Rvb1 and Rvb2 proteins form a heteromeric complex (Rvb1/2) required for assembly or remodeling of macromolecular complexes in essential cellular processes ranging from chromatin remodeling to ribosome biogenesis. Rvb1 and Rvb2 have a high degree of sequence and structural similarity, and both contain the classical features of ATPases of their clade, including an N-terminal AAA+ subdomain with the Walker A motif, an insertion domain that typically interacts with various binding partners, and a C-terminal AAA+ subdomain containing a Walker B motif, the Sensor I and II motifs, and an arginine finger. In this study, we find that despite the high degree of structural similarity, Rvb1 and Rvb2 have distinct active sites that impact their activities and regulation within the Rvb1/2 complex. Using a combination of biochemical and genetic approaches, we show that replacing the homologous arginine fingers of Rvb1 and Rvb2 with different amino acids not only has distinct effects on the catalytic activity of the complex, but also impacts cell growth, and the Rvb1/2 interactions with binding partners. Using molecular dynamics simulations, we find that changes near the active site of Rvb1 and Rvb2 cause long-range effects on the protein dynamics in the insertion domain, suggesting a molecular basis for how enzymatic activity within the catalytic site of ATP hydrolysis can be relayed to other domains of the Rvb1/2 complex to modulate its function. Further, we show the impact that the arginine finger variants have on snoRNP biogenesis and validate the findings from molecular dynamics simulations using a targeted genetic screen. Together, our results reveal new aspects of the regulation of the Rvb1/2 complex by identifying a relay of long-range molecular communication from the ATPase active site of the complex to the binding site of cofactors. Most importantly, our findings suggest that despite high similarity and cooperation within the same protein complex, the two proteins have evolved with unique properties critical for the regulation and function of the Rvb1/2 complex.
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Affiliation(s)
- Jennifer L. Warnock
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Jacob A. Ball
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Saman M. Najmi
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Mina Henes
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell & Developmental Biology (BCDB), Emory University, Atlanta, Georgia, USA
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amanda Vazquez
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Sohail Koshnevis
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Hans-Joachim Wieden
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Graeme L. Conn
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Homa Ghalei
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
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Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA. eLife 2024; 13:RP94800. [PMID: 38739430 PMCID: PMC11090510 DOI: 10.7554/elife.94800] [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] [Indexed: 05/14/2024] Open
Abstract
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with three distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
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Affiliation(s)
- Ryan T Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
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6
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Comba-González NB, Chaves-Moreno D, Santamaría-Vanegas J, Montoya-Castaño D. A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments. Heliyon 2024; 10:e27820. [PMID: 38560215 PMCID: PMC10981035 DOI: 10.1016/j.heliyon.2024.e27820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.
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Affiliation(s)
| | - Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Dolly Montoya-Castaño
- Bioprocesses and Bioprospecting Group, Biotechnology Institute, Universidad Nacional de Colombia, Colombia
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7
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Singh MK, Shin Y, Ju S, Han S, Choe W, Yoon KS, Kim SS, Kang I. Heat Shock Response and Heat Shock Proteins: Current Understanding and Future Opportunities in Human Diseases. Int J Mol Sci 2024; 25:4209. [PMID: 38673794 PMCID: PMC11050489 DOI: 10.3390/ijms25084209] [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: 03/15/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The heat shock response is an evolutionarily conserved mechanism that protects cells or organisms from the harmful effects of various stressors such as heat, chemicals toxins, UV radiation, and oxidizing agents. The heat shock response triggers the expression of a specific set of genes and proteins known as heat shock genes/proteins or molecular chaperones, including HSP100, HSP90, HSP70, HSP60, and small HSPs. Heat shock proteins (HSPs) play a crucial role in thermotolerance and aiding in protecting cells from harmful insults of stressors. HSPs are involved in essential cellular functions such as protein folding, eliminating misfolded proteins, apoptosis, and modulating cell signaling. The stress response to various environmental insults has been extensively studied in organisms from prokaryotes to higher organisms. The responses of organisms to various environmental stressors rely on the intensity and threshold of the stress stimuli, which vary among organisms and cellular contexts. Studies on heat shock proteins have primarily focused on HSP70, HSP90, HSP60, small HSPs, and ubiquitin, along with their applications in human biology. The current review highlighted a comprehensive mechanism of heat shock response and explores the function of heat shock proteins in stress management, as well as their potential as therapeutic agents and diagnostic markers for various diseases.
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Affiliation(s)
- Manish Kumar Singh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yoonhwa Shin
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Songhyun Ju
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sunhee Han
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Wonchae Choe
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kyung-Sik Yoon
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Soo Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Insug Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.J.); (S.H.); (W.C.); (K.-S.Y.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
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Przanowska RK, Chen Y, Uchida TO, Shibata E, Hao X, Rueda IS, Jensen K, Przanowski P, Trimboli A, Shibata Y, Leone G, Dutta A. Endo-reduplication in mouse liver after conditional mutation of ORC2 and combined mutation of ORC1 and ORC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588006. [PMID: 38617300 PMCID: PMC11014565 DOI: 10.1101/2024.04.04.588006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The six subunit Origin Recognition Complex (ORC) is essential for loading MCM2-7 at origins of DNA replication to promote initiation of DNA replication in organisms ranging from S. cerevisiae to humans. In rare instances, as in cancer cell-lines in culture with mutations in ORC1 , ORC2 or ORC5 , or in endo-reduplicating mouse hepatocytes in vivo without ORC1 , DNA replication has been observed in the virtual absence of individual ORC subunits. Although ORC1 is dispensable in the mouse liver for endo-reduplication, because of the homology of ORC1 with CDC6, it could be argued that CDC6 was substituting for ORC1 to restore functional ORC. Here, we have created mice with a conditional deletion of ORC2 , to demonstrate that mouse embryo fibroblasts require ORC2 for proliferation, but that the mouse hepatocytes can carry out DNA synthesis in vitro and endo-reduplicate in vivo , despite the deletion of ORC2 . Combining the conditional mutation of ORC1 and ORC2 revealed that the mouse liver can still carry out endo-reduplication despite the deletion of the two genes, both during normal development and after partial hepatectomy. Since endo-reduplication, like normal S phase replication, requires the presence of MCM2-7 on the chromatin, these results suggest that in primary hepatocytes there is a mechanism to load sufficient MCM2-7 to carry out effective DNA replication despite the virtual absence of two subunits of ORC.
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Nautiyal A, Thakur M. Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution. ACS OMEGA 2024; 9:12515-12538. [PMID: 38524412 PMCID: PMC10956419 DOI: 10.1021/acsomega.3c09866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.
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Affiliation(s)
- Astha Nautiyal
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manoj Thakur
- Sri
Venkateswara College, Benito Juarez Road, University of Delhi, New Delhi 110021, India
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Marcus K, Huang Y, Subramanian S, Gee CL, Gorday K, Ghaffari-Kashani S, Luo XR, Zheng L, O'Donnell M, Subramaniam S, Kuriyan J. Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM. Nat Struct Mol Biol 2024; 31:424-435. [PMID: 38177685 PMCID: PMC10950542 DOI: 10.1038/s41594-023-01177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Clamp loaders are AAA+ ATPases that facilitate high-speed DNA replication. In eukaryotic and bacteriophage clamp loaders, ATP hydrolysis requires interactions between aspartate residues in one protomer, present in conserved 'DEAD-box' motifs, and arginine residues in adjacent protomers. We show that functional defects resulting from a DEAD-box mutation in the T4 bacteriophage clamp loader can be compensated by widely distributed single mutations in the ATPase domain. Using cryo-EM, we discovered an unsuspected inactive conformation of the clamp loader, in which DNA binding is blocked and the catalytic sites are disassembled. Mutations that restore function map to regions of conformational change upon activation, suggesting that these mutations may increase DNA affinity by altering the energetic balance between inactive and active states. Our results show that there are extensive opportunities for evolution to improve catalytic efficiency when an inactive intermediate is involved.
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Affiliation(s)
- Kendra Marcus
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yongjian Huang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Subu Subramanian
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christine L Gee
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Kent Gorday
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Sam Ghaffari-Kashani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Xiao Ran Luo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lisa Zheng
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael O'Donnell
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - John Kuriyan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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11
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Geng Y, Liu C, Xu N, Shi X, Suen MC, Zhou B, Yan B, Wu C, Li H, Song Y, Chen X, Wang Z, Cai Q, Zhu G. The N-terminal region of Cdc6 specifically recognizes human DNA G-quadruplex. Int J Biol Macromol 2024; 260:129487. [PMID: 38237821 DOI: 10.1016/j.ijbiomac.2024.129487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/28/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
Guanine (G)-rich nucleic acid sequences can form diverse G-quadruplex structures located in functionally significant genome regions, exerting regulatory control over essential biological processes, including DNA replication in vivo. During the initiation of DNA replication, Cdc6 is recruited by the origin recognition complex (ORC) to target specific chromosomal DNA sequences. This study reveals that human Cdc6 interacts with G-quadruplex structure through a distinct region within the N-terminal intrinsically disordered region (IDR), encompassing residues 7-20. The binding region assumes a hook-type conformation, as elucidated by the NMR solution structure in complex with htel21T18. Significantly, mutagenesis and in vivo investigations confirm the highly specific nature of Cdc6's recognition of G-quadruplex. This research enhances our understanding of the fundamental mechanism governing the interaction between G-quadruplex and the N-terminal IDR region of Cdc6, shedding light on the intricate regulation of DNA replication processes.
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Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China; Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Changdong Liu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Naining Xu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xiao Shi
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Monica Ching Suen
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bo Zhou
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bing Yan
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Caiming Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hui Li
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuanjian Song
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xueqin Chen
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhanxiang Wang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China.
| | - Guang Zhu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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12
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Guan S, Li Z, Han Y, Tian A, Zhou S, Chen H, Peng G, Song Y. Crystal structure of the ATPase domain of porcine circovirus type 2 Rep protein. J Gen Virol 2024; 105. [PMID: 38506716 DOI: 10.1099/jgv.0.001972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
PCV2 belongs to the genus Circovirus in the family Circoviridae, whose genome is replicated by rolling circle replication (RCR). PCV2 Rep is a multifunctional enzyme that performs essential functions at multiple stages of viral replication. Rep is responsible for nicking and ligating single-stranded DNA and unwinding double-stranded DNA (dsDNA). However, the structure and function of the Rep are still poorly understood, which significantly impedes viral replication research. This study successfully resolved the structure of the PCV2 Rep ATPase domain (PRAD) using X-ray crystallography. Homologous structure search revealed that Rep belonged to the superfamily 3 (SF3) helicase, and multiple conserved residues were identified during sequence alignment with SF3 family members. Simultaneously, a hexameric PRAD model was generated for analysing characteristic structures and sites. Mutation of the conserved site and measurement of its activity showed that the hallmark motifs of the SF3 family influenced helicase activity by affecting ATPase activity and β-hairpin just caused the loss of helicase activity. The structural and functional analyses of the PRAD provide valuable insights for future research on PCV2 replication and antiviral strategies.
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Affiliation(s)
- Shuaiyin Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhen Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yang Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ang Tian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Saisai Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
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13
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Ajiboye J, Uldry AC, Heller M, Naguleswaran A, Fan E, Van Voorhis WC, Hemphill A, Müller J. Molecular Targets of the 5-Amido-Carboxamide Bumped Kinase Inhibitor BKI-1748 in Cryptosporidium parvum and HCT-8 Host Cells. Int J Mol Sci 2024; 25:2707. [PMID: 38473953 PMCID: PMC10931551 DOI: 10.3390/ijms25052707] [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: 02/02/2024] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Cryptosporidium parvum is an apicomplexan parasite causing persistent diarrhea in humans and animals. Issuing from target-based drug development, calcium-dependent protein kinase 1 inhibitors, collectively named bumped kinase inhibitors (BKIs), with excellent efficacies in vitro and in vivo have been generated. Some BKIs including BKI-1748 share a core structure with similarities to the first-generation antiprotozoal drug quinine, which is known to exert notorious side effects. Unlike quinine, BKI-1748 rapidly interfered with C. parvum proliferation in the human colon tumor (HCT) cell line HCT-8 cells and caused dramatic effects on the parasite ultrastructure. To identify putative BKI targets in C. parvum and in host cells, we performed differential affinity chromatography with cell-free extracts from non-infected and infected HCT-8 cells using BKI-1748 and quinine epoxy-activated sepharose columns followed by mass spectrometry. C. parvum proteins of interest were identified in eluates from columns coupled to BKI-1748, or in eluates from both BKI-1748 and quinine columns. However, no C. parvum proteins could be identified binding exclusively to BKI-1748. In contrast, 25 BKI-1748-specific binding proteins originating from HCT-8 cells were detected. Moreover, 29 C. parvum and 224 host cell proteins were identified in both BKI-1748 as well as in quinine eluates. In both C. parvum and host cells, the largest subset of binding proteins was involved in RNA binding and modification, with a focus on ribosomal proteins and proteins involved in RNA splicing. These findings extend previous results, showing that BKI-1748 interacts with putative targets involved in common, essential pathways such as translation and RNA processing.
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Affiliation(s)
- Jubilee Ajiboye
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland;
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland; (A.-C.U.); (M.H.)
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland; (A.-C.U.); (M.H.)
| | - Arunasalam Naguleswaran
- Institute of Molecular Pathology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland;
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA 98109, USA;
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-Emerging Infectious Diseases (CERID), Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98109, USA;
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland;
| | - Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland;
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14
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Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.31.551357. [PMID: 37790407 PMCID: PMC10542128 DOI: 10.1101/2023.07.31.551357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote CoCoNuTs (coiled-coil nuclease tandems) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with 3 distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
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Affiliation(s)
- Ryan T. Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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15
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Iljina M, Mazal H, Dayananda A, Zhang Z, Stan G, Riven I, Haran G. Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine. Biophys J 2024; 123:374-388. [PMID: 38196191 PMCID: PMC10870172 DOI: 10.1016/j.bpj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
AAA+ proteins (ATPases associated with various cellular activities) comprise a family of powerful ring-shaped ATP-dependent translocases that carry out numerous vital substrate-remodeling functions. ClpB is a AAA+ protein disaggregation machine that forms a two-tiered hexameric ring, with flexible pore loops protruding into its center and binding to substrate proteins. It remains unknown whether these pore loops contribute only passively to substrate-protein threading or have a more active role. Recently, we have applied single-molecule FRET spectroscopy to directly measure the dynamics of substrate-binding pore loops in ClpB. We have reported that the three pore loops of ClpB (PL1-3) undergo large-scale fluctuations on the microsecond timescale that are likely to be mechanistically important for disaggregation. Here, using single-molecule FRET, we study the allosteric coupling between the pore loops and the two nucleotide-binding domains of ClpB (NBD1-2). By mutating the conserved Walker B motifs within the NBDs to abolish ATP hydrolysis, we demonstrate how the nucleotide state of each NBD tunes pore-loop dynamics. This effect is surprisingly long-ranged; in particular, PL2 and PL3 respond differentially to a Walker B mutation in either NBD1 or NBD2, as well as to mutations in both. We characterize the conformational dynamics of pore loops and the allosteric paths connecting NBDs to pore loops by molecular dynamics simulations and find that both principal motions and allosteric paths can be altered by changing the ATPase state of ClpB. Remarkably, PL3, which is highly conserved in AAA+ machines, is found to favor an upward conformation when only NBD1 undergoes ATP hydrolysis but a downward conformation when NBD2 is active. These results explicitly demonstrate a significant long-range allosteric effect of ATP hydrolysis sites on pore-loop dynamics. Pore loops are therefore established as active participants that undergo ATP-dependent conformational changes to translocate substrate proteins through the central pores of AAA+ machines.
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Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Ashan Dayananda
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - Zhaocheng Zhang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio.
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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16
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Liu W, Bruggeman JW, Lei Q, van Pelt AMM, Koster J, Hamer G. Germline specific genes increase DNA double-strand break repair and radioresistance in lung adenocarcinoma cells. Cell Death Dis 2024; 15:38. [PMID: 38216586 PMCID: PMC10786935 DOI: 10.1038/s41419-024-06433-y] [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: 04/24/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
In principle, germline cells possess the capability to transmit a nearly unaltered set of genetic material to infinite future generations, whereas somatic cells are limited by strict growth constraints necessary to assure an organism's physical structure and eventual mortality. As the potential to replicate indefinitely is a key feature of cancer, we hypothesized that the activation of a "germline program" in somatic cells can contribute to oncogenesis. Our group recently described over one thousand germline specific genes that can be ectopically expressed in cancer, yet how germline specific processes contribute to the malignant properties of cancer is poorly understood. We here show that the expression of germ cell/cancer (GC) genes correlates with malignancy in lung adenocarcinoma (LUAD). We found that LUAD cells expressing more GC genes can repair DNA double strand breaks more rapidly, show higher rates of proliferation and are more resistant to ionizing radiation, compared to LUAD cells that express fewer GC genes. In particular, we identified the HORMA domain protein regulator TRIP13 to be predominantly responsible for this malignant phenotype, and that TRIP13 inhibition or expression levels affect the response to ionizing radiation and subsequent DNA repair. Our results demonstrate that GC genes are viable targets in oncology, as they induce increased radiation resistance and increased propagation in cancer cells. Because their expression is normally restricted to germline cells, we anticipate that GC gene directed therapeutic options will effectively target cancer, with limited side effects besides (temporary) infertility.
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Affiliation(s)
- Wenqing Liu
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jan Willem Bruggeman
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Qijing Lei
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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17
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Dougan DA, Truscott KN, Kirstein J. Editorial: Guardians of protein homeostasis (proteostasis) in health, disease and aging. Front Mol Biosci 2023; 10:1350666. [PMID: 38170003 PMCID: PMC10759985 DOI: 10.3389/fmolb.2023.1350666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- David A. Dougan
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Kaye N. Truscott
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Janine Kirstein
- Faculty of Biosciences, Institute of Biochemistry and Biophysics, Friedrich-Schiller-Universität Jena, Jena, Germany
- Leibniz-Institute on Aging/Fritz-Lipmann Institute, Jena, Germany
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18
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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19
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Luthuli SD, Shonhai A. The multi-faceted roles of R2TP complex span across regulation of gene expression, translation, and protein functional assembly. Biophys Rev 2023; 15:1951-1965. [PMID: 38192347 PMCID: PMC10771493 DOI: 10.1007/s12551-023-01127-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/27/2023] [Indexed: 01/10/2024] Open
Abstract
Macromolecular complexes play essential roles in various cellular processes. The assembly of macromolecular assemblies within the cell must overcome barriers imposed by a crowded cellular environment which is characterized by an estimated concentration of biological macromolecules amounting to 100-450 g/L that take up approximately 5-40% of the cytoplasmic volume. The formation of the macromolecular assemblies is facilitated by molecular chaperones in cooperation with their co-chaperones. The R2TP protein complex has emerged as a co-chaperone of Hsp90 that plays an important role in macromolecular assembly. The R2TP complex is composed of a heterodimer of RPAP3:P1H1DI that is in turn complexed to members of the ATPase associated with diverse cellular activities (AAA +), RUVBL1 and RUVBL2 (R1 and R2) families. What makes the R2TP co-chaperone complex particularly important is that it is involved in a wide variety of cellular processes including gene expression, translation, co-translational complex assembly, and posttranslational protein complex formation. The functional versatility of the R2TP co-chaperone complex makes it central to cellular development; hence, it is implicated in various human diseases. In addition, their roles in the development of infectious disease agents has become of interest. In the current review, we discuss the roles of these proteins as co-chaperones regulating Hsp90 and its partnership with Hsp70. Furthermore, we highlight the structure-function features of the individual proteins within the R2TP complex and describe their roles in various cellular processes.
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Affiliation(s)
- Sifiso Duncan Luthuli
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Addmore Shonhai
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
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20
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Chang S, Xiao W, Xie Y, Xu Z, Li B, Wang G, Hu K, Zhang Y, Zhou J, Song D, Zhu H, Wu X, Lu Y, Shi J, Zhu W. TI17, a novel compound, exerts anti-MM activity by impairing Trip13 function of DSBs repair and enhancing DNA damage. Cancer Med 2023; 12:21321-21334. [PMID: 37942576 PMCID: PMC10726904 DOI: 10.1002/cam4.6706] [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: 05/29/2023] [Revised: 10/08/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Thyroid hormone receptor interacting protein 13 (Trip13) is an AAA-ATPase that regulates the assembly or disassembly protein complexes and mediates Double-strand breaks (DSBs) repair. Overexpression of Trip13 has been detected in many cancers and is associated with myeloma progression, disease relapse and poor prognosis inmultiple myeloma (MM). METHODS We have identified a small molecular, TI17, through a parallel compound-centric approach, which specifically targets Trip13. To identify whether TI17 targeted Trip13, pull-down and nuclear magnetic resonance spectroscopy (NMR) assays were performed. Cell counting kit-8, clone formation, apoptosis and cell cycle assays were applied to investigate the effects of TI17. We also utilized a mouse model to investigate the effects of TI17 in vivo. RESULTS TI17 effectively inhibited the proliferation of MM cells, and induced the cycle arrest and apoptosis of MM cells. Furthermore, treatment with TI17 abrogates tumor growth and has no apparent side effects in mouse xenograft models. TI17 specifically impaired Trip13 function of DSBs repair and enhanced DNA damage responses in MM. Combining with melphalan or HDAC inhibitor panobinostat triggers synergistic anti-MM effect. CONCLUSIONS Our study suggests that TI17 could be acted as a specific inhibitor of Trip13 and supports a preclinical proof of concept for therapeutic targeting of Trip13 in MM.
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Affiliation(s)
- Shuaikang Chang
- Department of Hematology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Wenqin Xiao
- Department of Gastroenterology, Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yongsheng Xie
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Zhijian Xu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Bo Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Guanli Wang
- Department of Hematology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Ke Hu
- Department of Hematology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Yong Zhang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Jinfeng Zhou
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Dongliang Song
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Huabin Zhu
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Xiaosong Wu
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Yumeng Lu
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Jumei Shi
- Department of Hematology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Weiliang Zhu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
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21
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Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023; 51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency-free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
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Affiliation(s)
- Gianlucca G Nicastro
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
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22
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Hamali B, Amine AAA, Al-Sady B. Regulation of the heterochromatin spreading reaction by trans-acting factors. Open Biol 2023; 13:230271. [PMID: 37935357 PMCID: PMC10645111 DOI: 10.1098/rsob.230271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
Heterochromatin is a gene-repressive protein-nucleic acid ultrastructure that is initially nucleated by DNA sequences. However, following nucleation, heterochromatin can then propagate along the chromatin template in a sequence-independent manner in a reaction termed spreading. At the heart of this process are enzymes that deposit chemical information on chromatin, which attracts the factors that execute chromatin compaction and transcriptional or co/post-transcriptional gene silencing. Given that these enzymes deposit guiding chemical information on chromatin they are commonly termed 'writers'. While the processes of nucleation and central actions of writers have been extensively studied and reviewed, less is understood about how the spreading process is regulated. We discuss how the chromatin substrate is prepared for heterochromatic spreading, and how trans-acting factors beyond writer enzymes regulate it. We examine mechanisms by which trans-acting factors in Suv39, PRC2, SETDB1 and SIR writer systems regulate spreading of the respective heterochromatic marks across chromatin. While these systems are in some cases evolutionarily and mechanistically quite distant, common mechanisms emerge which these trans-acting factors exploit to tune the spreading reaction.
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Affiliation(s)
- Bulut Hamali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Ahmed A A Amine
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
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23
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Chernova LS, Vishnyakov IE, Börner J, Bogachev MI, Thormann KM, Kayumov AR. The Functionality of IbpA from Acholeplasma laidlawii Is Governed by Dynamic Rearrangement of Its Globular-Fibrillar Quaternary Structure. Int J Mol Sci 2023; 24:15445. [PMID: 37895124 PMCID: PMC10607609 DOI: 10.3390/ijms242015445] [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: 08/18/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Small heat shock proteins (sHSPs) represent a first line of stress defense in many bacteria. The primary function of these molecular chaperones involves preventing irreversible protein denaturation and aggregation. In Escherichia coli, fibrillar EcIbpA binds unfolded proteins and keeps them in a folding-competent state. Further, its structural homologue EcIbpB induces the transition of EcIbpA to globules, thereby facilitating the substrate transfer to the HSP70-HSP100 system for refolding. The phytopathogenic Acholeplasma laidlawii possesses only a single sHSP, AlIbpA. Here, we demonstrate non-trivial features of the function and regulation of the chaperone-like activity of AlIbpA according to its interaction with other components of the mycoplasma multi-chaperone network. Our results show that the efficiency of the A. laidlawii multi-chaperone system is driven with the ability of AlIbpA to form both globular and fibrillar structures, thus combining functions of both IbpA and IbpB when transferring the substrate proteins to the HSP70-HSP100 system. In contrast to EcIbpA and EcIbpB, AlIbpA appears as an sHSP, in which the competition between the N- and C-terminal domains regulates the shift of the protein quaternary structure between a fibrillar and globular form, thus representing a molecular mechanism of its functional regulation. While the C-terminus of AlIbpA is responsible for fibrils formation and substrate capture, the N-terminus seems to have a similar function to EcIbpB through facilitating further substrate protein disaggregation using HSP70. Moreover, our results indicate that prior to the final disaggregation process, AlIbpA can directly transfer the substrate to HSP100, thereby representing an alternative mechanism in the HSP interaction network.
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Affiliation(s)
- Liliya S. Chernova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia;
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia;
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Innokentii E. Vishnyakov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia;
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Mikhail I. Bogachev
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University, Professora Popova 5, 197376 St. Petersburg, Russia;
| | - Kai M. Thormann
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Airat R. Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia;
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24
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Delerue T, Chareyre S, Anantharaman V, Gilmore MC, Popham DL, Cava F, Aravind L, Ramamurthi KS. Bacterial cell surface nanoenvironment requires a specialized chaperone to activate a peptidoglycan biosynthetic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561273. [PMID: 37986874 PMCID: PMC10659427 DOI: 10.1101/2023.10.06.561273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Bacillus subtilis spores are produced inside the cytosol of a mother cell. Spore surface assembly requires the SpoVK protein in the mother cell, but its function is unknown. Here, we report that SpoVK is a dedicated chaperone from a distinct higher-order clade of AAA+ ATPases that activates the peptidoglycan glycosyltransferase MurG during sporulation, even though MurG does not normally require activation by a chaperone during vegetative growth. MurG redeploys to the spore surface during sporulation, where we show that the local pH is reduced and propose that this change in cytosolic nanoenvironment necessitates a specific chaperone for proper MurG function. Further, we show that SpoVK participates in a developmental checkpoint in which improper spore surface assembly inactivates SpoVK, which leads to sporulation arrest. The AAA+ ATPase clade containing SpoVK includes other dedicated chaperones involved in secretion, cell-envelope biosynthesis, and carbohydrate metabolism, suggesting that such fine-tuning might be a widespread feature of different subcellular nanoenvironments.
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Affiliation(s)
- Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael C. Gilmore
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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25
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Rish AD, Shen Z, Chen Z, Zhang N, Zheng Q, Fu TM. Molecular mechanisms of Holliday junction branch migration catalyzed by an asymmetric RuvB hexamer. Nat Commun 2023; 14:3549. [PMID: 37322069 PMCID: PMC10272136 DOI: 10.1038/s41467-023-39250-6] [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: 09/22/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
The Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here we report two cryo-EM structures of RuvB, providing a comprehensive understanding of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, encircling dsDNA. Four protomers of RuvB contact the DNA backbone with a translocation step size of 2 nucleotides. The variation of nucleotide-binding states in RuvB supports a sequential model for ATP hydrolysis and nucleotide recycling, which occur at separate, singular positions. RuvB's asymmetric assembly also explains the 6:4 stoichiometry between the RuvB/RuvA complex, which coordinates HJ migration in bacteria. Taken together, we provide a mechanistic understanding of HJ branch migration facilitated by RuvB, which may be universally shared by prokaryotic and eukaryotic organisms.
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Affiliation(s)
- Anthony D Rish
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Cancer Metabolism, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Cancer Metabolism, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Zhenhang Chen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Cancer Metabolism, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nan Zhang
- Center for Cancer Metabolism, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Qingfei Zheng
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- Center for Cancer Metabolism, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Tian-Min Fu
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Cancer Metabolism, The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA.
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26
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Zaninello M, Bean C. Highly Specialized Mechanisms for Mitochondrial Transport in Neurons: From Intracellular Mobility to Intercellular Transfer of Mitochondria. Biomolecules 2023; 13:938. [PMID: 37371518 DOI: 10.3390/biom13060938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The highly specialized structure and function of neurons depend on a sophisticated organization of the cytoskeleton, which supports a similarly sophisticated system to traffic organelles and cargo vesicles. Mitochondria sustain crucial functions by providing energy and buffering calcium where it is needed. Accordingly, the distribution of mitochondria is not even in neurons and is regulated by a dynamic balance between active transport and stable docking events. This system is finely tuned to respond to changes in environmental conditions and neuronal activity. In this review, we summarize the mechanisms by which mitochondria are selectively transported in different compartments, taking into account the structure of the cytoskeleton, the molecular motors and the metabolism of neurons. Remarkably, the motor proteins driving the mitochondrial transport in axons have been shown to also mediate their transfer between cells. This so-named intercellular transport of mitochondria is opening new exciting perspectives in the treatment of multiple diseases.
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Affiliation(s)
- Marta Zaninello
- Institute for Genetics, University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Camilla Bean
- Department of Medicine, University of Udine, 33100 Udine, Italy
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27
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Blaine HC, Simmons LA, Stallings CL. Diverse Mechanisms of Helicase Loading during DNA Replication Initiation in Bacteria. J Bacteriol 2023; 205:e0048722. [PMID: 36877032 PMCID: PMC10128896 DOI: 10.1128/jb.00487-22] [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] [Indexed: 03/07/2023] Open
Abstract
Initiation of DNA replication is required for cell viability and passage of genetic information to the next generation. Studies in Escherichia coli and Bacillus subtilis have established ATPases associated with diverse cellular activities (AAA+) as essential proteins required for loading of the replicative helicase at replication origins. AAA+ ATPases DnaC in E. coli and DnaI in B. subtilis have long been considered the paradigm for helicase loading during replication in bacteria. Recently, it has become increasingly clear that most bacteria lack DnaC/DnaI homologs. Instead, most bacteria express a protein homologous to the newly described DciA (dnaC/dnaI antecedent) protein. DciA is not an ATPase, and yet it serves as a helicase operator, providing a function analogous to that of DnaC and DnaI across diverse bacterial species. The recent discovery of DciA and of other alternative mechanisms of helicase loading in bacteria has changed our understanding of DNA replication initiation. In this review, we highlight recent discoveries, detailing what is currently known about the replicative helicase loading process across bacterial species, and we discuss the critical questions that remain to be investigated.
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Affiliation(s)
- Helen C. Blaine
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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28
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Moon S, Ham S, Jeong J, Ku H, Kim H, Lee C. Temperature Matters: Bacterial Response to Temperature Change. J Microbiol 2023; 61:343-357. [PMID: 37010795 DOI: 10.1007/s12275-023-00031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 04/04/2023]
Abstract
Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.
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Affiliation(s)
- Seongjoon Moon
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Juwon Jeong
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Heechan Ku
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
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29
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Xu W, Sun C, Gao W, Scharf DH, Zhu C, Bu Q, Zhao Q, Li Y. Degradation mechanism of AtrA mediated by ClpXP and its application in daptomycin production in Streptomyces roseosporus. Protein Sci 2023; 32:e4617. [PMID: 36882943 PMCID: PMC10031807 DOI: 10.1002/pro.4617] [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: 11/01/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
The efficiency of drug biosynthesis depends on different transcriptional regulatory pathways in Streptomyces, and the protein degradation system adds another layer of complexity to the regulatory processes. AtrA, a transcriptional regulator in the A-factor regulatory cascade, stimulates the production of daptomycin by binding to the dptE promoter in Streptomyces roseosporus. Using pull-down assays, bacterial two-hybrid system and knockout verification, we demonstrated that AtrA is a substrate for ClpP protease. Furthermore, we showed that ClpX is necessary for AtrA recognition and subsequent degradation. Bioinformatics analysis, truncating mutation, and overexpression proved that the AAA motifs of AtrA were essential for initial recognition in the degradation process. Finally, overexpression of mutated atrA (AAA-QQQ) in S. roseosporus increased the yield of daptomycin by 225% in shake flask and by 164% in the 15 L bioreactor. Thus, improving the stability of key regulators is an effective method to promote the ability of antibiotic synthesis.
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Affiliation(s)
- Wei‐Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Chen‐Fan Sun
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Wen‐Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Daniel H. Scharf
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Chen‐Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Qing‐Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
| | - Qing‐Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
| | - Yong‐Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical BiotechnologyZhejiang University School of MedicineHangzhouChina
- Institute of Pharmaceutical BiotechnologyZhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic EngineeringHangzhouChina
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30
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Weitao T, Grandinetti G, Guo P. Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces. EXPLORATION (BEIJING, CHINA) 2023; 3:20210056. [PMID: 37324034 PMCID: PMC10191066 DOI: 10.1002/exp.20210056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/28/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the parallel architectures of biomotors in both prokaryotic and eukaryotic systems suggest a similar revolving mechanism in the use of ATP to drive translocation of the lengthy double-stranded (ds)DNA genomes. This mechanism is exemplified by the dsDNA packaging motor of bacteriophage phi29 that operates through revolving but not rotating dsDNA to "Push through a one-way valve". This unique and novel revolving mechanism discovered in phi29 DNA packaging motor was recently reported in other systems including the dsDNA packaging motor of herpesvirus, the dsDNA ejecting motor of bacteriophage T7, the plasmid conjugation machine TraB in Streptomyces, the dsDNA translocase FtsK of gram-negative bacteria, and the genome-packaging motor in mimivirus. These motors exhibit an asymmetrical hexameric structure for transporting the genome via an inch-worm sequential action. This review intends to delineate the revolving mechanism from a perspective of conformational changes and electrostatic interactions. In phi29, the positively charged residues Arg-Lys-Arg in the N-terminus of the connector bind the negatively charged interlocking domain of pRNA. ATP binding to an ATPase subunit induces the closed conformation of the ATPase. The ATPase associates with an adjacent subunit to form a dimer facilitated by the positively charged arginine finger. The ATP-binding induces a positive charging on its DNA binding surface via an allostery mechanism and thus the higher affinity for the negatively charged dsDNA. ATP hydrolysis induces an expanded conformation of the ATPase with a lower affinity for dsDNA due to the change of the surface charge, but the (ADP+Pi)-bound subunit in the dimer undergoes a conformational change that repels dsDNA. The positively charged lysine rings of the connector attract dsDNA stepwise and periodically to keep its revolving motion along the channel wall, thus maintaining the one-way translocation of dsDNA without reversal and sliding out. The finding of the presence of the asymmetrical hexameric architectures of many ATPases that use the revolving mechanism may provide insights into the understanding of translocation of the gigantic genomes including chromosomes in complicated systems without coiling and tangling to speed up dsDNA translocation and save energy.
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Affiliation(s)
- Tao Weitao
- UT Southwestern Medical CenterCenter for the Genetics of Host DefenseDallasTXUSA
- College of Science and MathematicsSouthwest Baptist UniversityBolivarMOUSA
| | - Giovanna Grandinetti
- Center for Electron Microscopy and AnalysisThe Ohio State UniversityColumbusOHUSA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and NanomedicineDivision of Pharmaceutics and Pharmacology, College of PharmacyDorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of MedicineThe Ohio State UniversityColumbusOHUSA
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31
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He S, Gillies JP, Zang JL, Córdoba-Beldad CM, Yamamoto I, Fujiwara Y, Grantham J, DeSantis ME, Shibuya H. Distinct dynein complexes defined by DYNLRB1 and DYNLRB2 regulate mitotic and male meiotic spindle bipolarity. Nat Commun 2023; 14:1715. [PMID: 36973253 PMCID: PMC10042829 DOI: 10.1038/s41467-023-37370-7] [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] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Spindle formation in male meiosis relies on the canonical centrosome system, which is distinct from acentrosomal oocyte meiosis, but its specific regulatory mechanisms remain unknown. Herein, we report that DYNLRB2 (Dynein light chain roadblock-type-2) is a male meiosis-upregulated dynein light chain that is indispensable for spindle formation in meiosis I. In Dynlrb2 KO mouse testes, meiosis progression is arrested in metaphase I due to the formation of multipolar spindles with fragmented pericentriolar material (PCM). DYNLRB2 inhibits PCM fragmentation through two distinct pathways; suppressing premature centriole disengagement and targeting NuMA (nuclear mitotic apparatus) to spindle poles. The ubiquitously expressed mitotic counterpart, DYNLRB1, has similar roles in mitotic cells and maintains spindle bipolarity by targeting NuMA and suppressing centriole overduplication. Our work demonstrates that two distinct dynein complexes containing DYNLRB1 or DYNLRB2 are separately used in mitotic and meiotic spindle formations, respectively, and that both have NuMA as a common target.
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Affiliation(s)
- Shuwen He
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Juliana L Zang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carmen M Córdoba-Beldad
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - Io Yamamoto
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - Yasuhiro Fujiwara
- Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Tokyo, 113-0032, Japan
| | - Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden.
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32
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Jeje O, Ewunkem AJ, Jeffers-Francis LK, Graves JL. Serving Two Masters: Effect of Escherichia coli Dual Resistance on Antibiotic Susceptibility. Antibiotics (Basel) 2023; 12:antibiotics12030603. [PMID: 36978471 PMCID: PMC10044975 DOI: 10.3390/antibiotics12030603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The prevalence of multidrug-resistant bacteria and their increased pathogenicity has led to a growing interest in metallic antimicrobial materials and bacteriophages as potential alternatives to conventional antibiotics. This study examines how resistance to excess iron (III) influences the evolution of bacteriophage resistance in the bacterium Escherichia coli. We utilized experimental evolution in E. coli to test the effect of the evolution of phage T7 resistance on populations resistant to excess iron (III) and populations without excess iron resistance. Phage resistance evolved rapidly in both groups. Dual-resistant (iron (III)/phage) populations were compared to their controls (excess iron (III)-resistant, phage-resistant, no resistance to either) for their performance against each stressor, excess iron (III) and phage; and correlated resistances to excess iron (II), gallium (III), silver (I) and conventional antibiotics. Excess iron (III)/phage-resistant populations demonstrated superior 24 h growth compared to all other populations when exposed to increasing concentrations of iron (II, III), gallium (III), ampicillin, and tetracycline. No differences in 24 h growth were shown between excess iron (III)/phage-resistant and excess iron (III)-resistant populations in chloramphenicol, sulfonamide, and silver (I). The genomic analysis identified selective sweeps in the iron (III) resistant (rpoB, rpoC, yegB, yeaG), phage-resistant (clpX →/→ lon, uvaB, yeaG, fliR, gatT, ypjF, waaC, rpoC, pgi, and yjbH) and iron (III)/phage resistant populations (rcsA, hldE, rpoB, and waaC). E. coli selected for resistance to both excess iron (III) and T7 phage showed some evidence of a synergistic effect on various components of fitness. Dual selection resulted in correlated resistances to ionic metals {iron (II), gallium (III), and silver (I)} and several conventional antibiotics. There is a likelihood that this sort of combination antimicrobial treatment may result in bacterial variants with multiple resistances.
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Affiliation(s)
- Olusola Jeje
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Akamu J Ewunkem
- Department of Biological Sciences, Winston Salem State University, 601 S Martin Luther King Jr Drive, Winston Salem, NC 27110, USA
| | - Liesl K Jeffers-Francis
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Joseph L Graves
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
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Park JW, Lee EJ, Moon E, Kim HL, Kim IB, Hodzic D, Kim N, Kweon HS, Kim JW. Orthodenticle homeobox 2 is transported to lysosomes by nuclear budding vesicles. Nat Commun 2023; 14:1111. [PMID: 36849521 PMCID: PMC9971051 DOI: 10.1038/s41467-023-36697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Transcription factors (TFs) are transported from the cytoplasm to the nucleus and disappear from the nucleus after they regulate gene expression. Here, we discover an unconventional nuclear export of the TF, orthodenticle homeobox 2 (OTX2), in nuclear budding vesicles, which transport OTX2 to the lysosome. We further find that torsin1a (Tor1a) is responsible for scission of the inner nuclear vesicle, which captures OTX2 using the LINC complex. Consistent with this, in cells expressing an ATPase-inactive Tor1aΔE mutant and the LINC (linker of nucleoskeleton and cytoskeleton) breaker KASH2, OTX2 accumulated and formed aggregates in the nucleus. Consequently, in the mice expressing Tor1aΔE and KASH2, OTX2 could not be secreted from the choroid plexus for transfer to the visual cortex, leading to failed development of parvalbumin neurons and reduced visual acuity. Together, our results suggest that unconventional nuclear egress and secretion of OTX2 are necessary not only to induce functional changes in recipient cells but also to prevent aggregation in donor cells.
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Affiliation(s)
- Jun Woo Park
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Eun Jung Lee
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Eunyoung Moon
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Hong-Lim Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - In-Beom Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Didier Hodzic
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Namsuk Kim
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.,Neurovascular Unit, Korea Brain Research Institute, Daegu, 41062, South Korea
| | - Hee-Seok Kweon
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Jin Woo Kim
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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Qu Y, Mueller-Cajar O, Yamori W. Improving plant heat tolerance through modification of Rubisco activase in C3 plants to secure crop yield and food security in a future warming world. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:591-599. [PMID: 35981868 DOI: 10.1093/jxb/erac340] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
The world's population may reach 10 billion by 2050, but 10% still suffer from food shortages. At the same time, global warming threatens food security by decreasing crop yields, so it is necessary to develop crops with enhanced resistance to high temperatures in order to secure the food supply. In this review, the role of Rubisco activase as an important factor in plant heat tolerance is summarized, based on the conclusions of recent findings. Rubisco activase is a molecular chaperone determining the activation of Rubisco, whose heat sensitivity causes reductions of photosynthesis at high temperatures. Thus, the thermostability of Rubisco activase is considered to be critical for improving plant heat tolerance. It has been shown that the introduction of thermostable Rubisco activase through gene editing into Arabidopsis thaliana and from heat-adapted wild Oryza species or C4Zea mays into Oryza sativa improves Rubisco activation, photosynthesis, and plant growth at high temperatures. We propose that developing a universal thermostable Rubisco activase could be a promising direction for further studies.
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Affiliation(s)
- Yuchen Qu
- Graduate School of Agricultural and Life Sciences, Institute for Sustainable Agri-ecosystem Services, The University of Tokyo, Tokyo, Japan
| | | | - Wataru Yamori
- Graduate School of Agricultural and Life Sciences, Institute for Sustainable Agri-ecosystem Services, The University of Tokyo, Tokyo, Japan
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Guo H, Yi J, Wang F, Lei T, Du H. Potential application of heat shock proteins as therapeutic targets in Parkinson's disease. Neurochem Int 2023; 162:105453. [PMID: 36402293 DOI: 10.1016/j.neuint.2022.105453] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/08/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Parkinson's disease (PD) is a common chronic neurodegenerative disease, and the heat shock proteins (HSPs) are proved to be of great value for PD. In addition, HSPs can maintain protein homeostasis, degrade and inhibit protein aggregation by properly folding and activating intracellular proteins in PD. This study mainly summarizes the important roles of HSPs in PD and explores their feasibility as targets. We introduced the structural and functional characteristics of HSPs and the physiological functions of HSPs in PD. HSPs can protect neurons from damage by degrading aggregates with three mechanisms, including the aggregation and removing α-Synuclein (α-Syn) aggregates, promotion the autophagy of abnormal proteins, and inhibition the apoptosis of degenerated neurons. This study underscores the importance of HSPs as targets in PD and helps to expand new mechanisms in PD treatment strategies.
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Affiliation(s)
- Haodong Guo
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jingsong Yi
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Fan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tong Lei
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hongwu Du
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China.
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Dougan DA, Truscott KN. Affinity isolation and biochemical characterization of N-degron ligands using the N-recognin, ClpS. Methods Enzymol 2023. [PMID: 37532398 DOI: 10.1016/bs.mie.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The N-degron pathways are a set of proteolytic systems that relate the half-life of a protein to its N-terminal (Nt) residue. In Escherichia coli the principal N-degron pathway is known as the Leu/N-degron pathway. Proteins degraded by this pathway contain an Nt degradation signal (N-degron) composed of an Nt primary destabilizing (Nd1) residue (Leu, Phe, Trp or Tyr). All Leu/N-degron substrates are recognized by the adaptor protein, ClpS and delivered to the ClpAP protease for degradation. Although many components of the pathway are well defined, the physiological role of this pathway remains poorly understood. To address this gap in knowledge we developed a biospecific affinity chromatography technique to isolate physiological substrates of the Leu/N-degron pathway. In this chapter we describe the use of peptide arrays to determine the binding specificity of ClpS. We demonstrate how the information obtained from the peptide array, when coupled with ClpS affinity chromatography, can be used to specifically elute physiological Leu/N-degron ligands from a bacterial lysate. These techniques are illustrated using E. coli ClpS (EcClpS), but both are broadly suitable for application to related N-recognins and systems, not only for the determination of N-recognin specificity, but also for the identification of natural Leu/N-degron ligands from various bacterial and plant species that contain ClpS homologs.
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Törner R, Kupreichyk T, Hoyer W, Boisbouvier J. The role of heat shock proteins in preventing amyloid toxicity. Front Mol Biosci 2022; 9:1045616. [PMID: 36589244 PMCID: PMC9798239 DOI: 10.3389/fmolb.2022.1045616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The oligomerization of monomeric proteins into large, elongated, β-sheet-rich fibril structures (amyloid), which results in toxicity to impacted cells, is highly correlated to increased age. The concomitant decrease of the quality control system, composed of chaperones, ubiquitin-proteasome system and autophagy-lysosomal pathway, has been shown to play an important role in disease development. In the last years an increasing number of studies has been published which focus on chaperones, modulators of protein conformational states, and their effects on preventing amyloid toxicity. Here, we give a comprehensive overview of the current understanding of chaperones and amyloidogenic proteins and summarize the advances made in elucidating the impact of these two classes of proteins on each other, whilst also highlighting challenges and remaining open questions. The focus of this review is on structural and mechanistic studies and its aim is to bring novices of this field "up to speed" by providing insight into all the relevant processes and presenting seminal structural and functional investigations.
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Affiliation(s)
- Ricarda Törner
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
| | - Tatsiana Kupreichyk
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jerome Boisbouvier
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
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Xu W, Gao W, Bu Q, Li Y. Degradation Mechanism of AAA+ Proteases and Regulation of Streptomyces Metabolism. Biomolecules 2022; 12:biom12121848. [PMID: 36551276 PMCID: PMC9775585 DOI: 10.3390/biom12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Hundreds of proteins work together in microorganisms to coordinate and control normal activity in cells. Their degradation is not only the last step in the cell's lifespan but also the starting point for its recycling. In recent years, protein degradation has been extensively studied in both eukaryotic and prokaryotic organisms. Understanding the degradation process is essential for revealing the complex regulatory network in microorganisms, as well as further artificial reconstructions and applications. This review will discuss several studies on protein quality-control family members Lon, FtsH, ClpP, the proteasome in Streptomyces, and a few classical model organisms, mainly focusing on their structure, recognition mechanisms, and metabolic influences.
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Affiliation(s)
- Weifeng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wenli Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qingting Bu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
- Correspondence:
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Cymbopogom Citratus Essential Oils: A Promising Source of Antifungals Against Panax Notoginseng-Associated Pathogenic Fungi. Curr Microbiol 2022; 80:17. [PMID: 36460935 DOI: 10.1007/s00284-022-03119-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Due to the great threat of chemical pesticides to the ecosystem environment, it is a long-term goal to find environmentally friendly green pesticides. Essential oils (EOs) are considered weapons in plant chemical defense and are important sources of green pesticides. Therefore, the antifungal effects and action mechanisms of Cymbopogom citratus (C. citratus) EOs against seven kinds of Panax notoginseng (P. notoginseng) pathogenic fungi were investigated. Oxford Cup results showed that C. citratus EOs had an excellent detraction effects against seven fungi of P. notoginseng. Gas chromatography-mass spectrometry (GC-MS) was used to construct the chemical profiles of C. citratus EOs, disclosed that the main categories are terpenes and oxygenated terpenes. In addition, compared with the hymexazol, the minimum inhibitory concentration (MIC) showed that EOs and their main components had strong antifungal activities. Besides, EOs had a synergistic effect with hymexazol (a chemical pesticide). The antifungal mechanism of C. citratus EOs was studied by using Fusarium oxysporum (F. oxysporum) as the dominant pathogen. C. citratus EOs may affect the metabolism of fungi and induce mycotoxins to destroy the cell wall to achieve antifungal effects. Finally, EOs were found to significantly retard P. notoginseng infection by F. oxysporum. According to our research, C. citratus EOs are potential green antifungal agent that can be used in the cultivation of P. notoginseng.
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Two Distinct Modes of DNA Binding by an MCM Helicase Enable DNA Translocation. Int J Mol Sci 2022; 23:ijms232314678. [PMID: 36499022 PMCID: PMC9735655 DOI: 10.3390/ijms232314678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022] Open
Abstract
A six-subunit ATPase ring forms the central hub of the replication forks in all domains of life. This ring performs a helicase function to separate the two complementary DNA strands to be replicated and drives the replication machinery along the DNA. Disruption of this helicase/ATPase ring is associated with genetic instability and diseases such as cancer. The helicase/ATPase rings of eukaryotes and archaea consist of six minichromosome maintenance (MCM) proteins. Prior structural studies have shown that MCM rings bind one encircled strand of DNA in a spiral staircase, suggesting that the ring pulls this strand of DNA through its central pore in a hand-over-hand mechanism where the subunit at the bottom of the staircase dissociates from DNA and re-binds DNA one step above the staircase. With high-resolution cryo-EM, we show that the MCM ring of the archaeal organism Saccharolobus solfataricus binds an encircled DNA strand in two different modes with different numbers of subunits engaged to DNA, illustrating a plausible mechanism for the alternating steps of DNA dissociation and re-association that occur during DNA translocation.
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41
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Yeager C, Carter G, Gohara DW, Yennawar NH, Enemark E, Arnold J, Cameron CE. Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP. Nucleic Acids Res 2022; 50:11775-11798. [PMID: 36399514 PMCID: PMC9723501 DOI: 10.1093/nar/gkac1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
The enteroviral 2C protein is a therapeutic target, but the absence of a mechanistic framework for this enzyme limits our understanding of inhibitor mechanisms. Here, we use poliovirus 2C and a derivative thereof to elucidate the first biochemical mechanism for this enzyme and confirm the applicability of this mechanism to other members of the enterovirus genus. Our biochemical data are consistent with a dimer forming in solution, binding to RNA, which stimulates ATPase activity by increasing the rate of hydrolysis without impacting affinity for ATP substantially. Both RNA and DNA bind to the same or overlapping site on 2C, driven by the phosphodiester backbone, but only RNA stimulates ATP hydrolysis. We propose that RNA binds to 2C driven by the backbone, with reorientation of the ribose hydroxyls occurring in a second step to form the catalytically competent state. 2C also uses a two-step mechanism for binding to ATP. Initial binding is driven by the α and β phosphates of ATP. In the second step, the adenine base and other substituents of ATP are used to organize the active site for catalysis. These studies provide the first biochemical description of determinants driving specificity and catalytic efficiency of a picornaviral 2C ATPase.
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Affiliation(s)
- Calvin Yeager
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Griffin Carter
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David W Gohara
- Department of Biochemistry and Molecular Biology, St. Louis University, St. Louis, MO 63104, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Eric J Enemark
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jamie J Arnold
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig E Cameron
- To whom correspondence should be addressed. Tel: +1 919 966 9699; Fax: +1 919 962 8103;
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Kang H, Fan T, Wu J, Zhu Y, Shen WH. Histone modification and chromatin remodeling in plant response to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:986940. [PMID: 36262654 PMCID: PMC9574397 DOI: 10.3389/fpls.2022.986940] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Tianyi Fan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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Bollhagen A, Bechtel W. Discovering autoinhibition as a design principle for the control of biological mechanisms. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2022; 95:145-157. [PMID: 36029564 DOI: 10.1016/j.shpsa.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they exhibited a second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them.
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Affiliation(s)
- Andrew Bollhagen
- UC San Diego Philosophy Department, Ridge Walk Academic Complex - Arts & Humanities Bldg. Room 0435, La Jolla, CA 92093-0119, USA.
| | - William Bechtel
- UC San Diego Philosophy Department, Ridge Walk Academic Complex - Arts & Humanities Bldg. Room 0455, La Jolla, CA 92093-0119, USA.
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Gustchina A, Li M, Andrianova AG, Kudzhaev AM, Lountos GT, Sekula B, Cherry S, Tropea JE, Smirnov IV, Wlodawer A, Rotanova TV. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. Int J Mol Sci 2022; 23:11425. [PMID: 36232729 PMCID: PMC9569914 DOI: 10.3390/ijms231911425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to three subfamilies (A, B, and C). All Lons are single-chain, multidomain proteins containing an ATPase and protease domains, with different additional elements present in each subfamily. LonA and LonC proteases are soluble cytoplasmic enzymes, whereas LonBs are membrane-bound. Based on an analysis of the available sequences of Lon proteases, we identified a number of enzymes currently assigned to the LonB subfamily that, although presumably membrane-bound, include structural features more similar to their counterparts in the LonA subfamily. This observation was confirmed by the crystal structure of the proteolytic domain of the enzyme previously assigned as Bacillus subtilis LonB, combined with the modeled structure of its ATPase domain. Several structural features present in both domains differ from their counterparts in either LonA or LonB subfamilies. We thus postulate that this enzyme is the founding member of a newly identified LonBA subfamily, so far found only in the gene sequences of firmicutes.
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Affiliation(s)
- Alla Gustchina
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna G Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Arsen M Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - George T Lountos
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bartosz Sekula
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Lodz, Poland
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Joseph E Tropea
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Kozlova MI, Shalaeva DN, Dibrova DV, Mulkidjanian AY. Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases. Biomolecules 2022; 12:biom12101345. [PMID: 36291554 PMCID: PMC9599529 DOI: 10.3390/biom12101345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/20/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
The P-loop fold nucleoside triphosphate (NTP) hydrolases (also known as Walker NTPases) function as ATPases, GTPases, and ATP synthases, are often of medical importance, and represent one of the largest and evolutionarily oldest families of enzymes. There is still no consensus on their catalytic mechanism. To clarify this, we performed the first comparative structural analysis of more than 3100 structures of P-loop NTPases that contain bound substrate Mg-NTPs or their analogues. We proceeded on the assumption that structural features common to these P-loop NTPases may be essential for catalysis. Our results are presented in two articles. Here, in the first, we consider the structural elements that stimulate hydrolysis. Upon interaction of P-loop NTPases with their cognate activating partners (RNA/DNA/protein domains), specific stimulatory moieties, usually Arg or Lys residues, are inserted into the catalytic site and initiate the cleavage of gamma phosphate. By analyzing a plethora of structures, we found that the only shared feature was the mechanistic interaction of stimulators with the oxygen atoms of gamma-phosphate group, capable of causing its rotation. One of the oxygen atoms of gamma phosphate coordinates the cofactor Mg ion. The rotation must pull this oxygen atom away from the Mg ion. This rearrangement should affect the properties of the other Mg ligands and may initiate hydrolysis according to the mechanism elaborated in the second article.
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Affiliation(s)
- Maria I. Kozlova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria N. Shalaeva
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria V. Dibrova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Center of Cellular Nanoanalytics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Correspondence: ; Tel.: +49-541-969-2698
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Kudzhaev AM, Andrianova AG, Gustchina AE, Smirnov IV, Rotanova TV. ATP-Dependent Lon Proteases in the Cellular Protein Quality Control System. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Bhandari V, Van Ommen DAJ, Wong KS, Houry WA. Analysis of the Evolution of the MoxR ATPases. J Phys Chem A 2022; 126:4734-4746. [PMID: 35852937 DOI: 10.1021/acs.jpca.2c02554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MoxR proteins comprise a family of ATPases Associated with diverse cellular Activities (AAA+). These proteins are widespread and found across the diversity of prokaryotic species. Despite their ubiquity, members of the group remain poorly characterized. Only a few examples of MoxR proteins have been associated with cellular roles, where they have been shown to perform chaperone-like functions. A characteristic feature of MoxR proteins is their association with proteins containing the von Willebrand factor type A (VWA) domain. In an effort to understand the spread and diversity of the MoxR family, an evolutionary approach was undertaken. Phylogenetic techniques were used to define nine major subfamilies within the MoxR family. A combination of phylogenetic and genomic approaches was utilized to explore the extent of the partnership between the MoxR and VWA domain containing proteins (VWA proteins). These analyses led to the clarification of genetic linkages between MoxR and VWA proteins. A significant partnership is described here, as seven of nine MoxR subfamilies were found to be linked to VWA proteins. Available genomic data were also used to assess the intraprotein diversification of MoxR and VWA protein sequences. Data clearly indicated that, in MoxR proteins, the ATPase domain is maintained with high conservation while the remaining protein sequence evolves at a faster rate; a similar pattern was observed for the VWA domain in VWA proteins. Overall, our data present insights into the modular evolution of MoxR ATPases.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - David A J Van Ommen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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48
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Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea. mSystems 2022; 7:e0134821. [PMID: 35604119 PMCID: PMC9239133 DOI: 10.1128/msystems.01348-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PspA protein domain is found in all domains of life, highlighting its central role in Psp networks. To date, all insights into the core functions of Psp responses derive mainly from protein network blueprints representing only three bacterial phyla.
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49
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Fan Y, Murgia M, Linder MI, Mizoguchi Y, Wang C, Łyszkiewicz M, Ziȩtara N, Liu Y, Frenz S, Sciuccati G, Partida-Gaytan A, Alizadeh Z, Rezaei N, Rehling P, Dennerlein S, Mann M, Klein C. HAX1-dependent control of mitochondrial proteostasis governs neutrophil granulocyte differentiation. J Clin Invest 2022; 132:153153. [PMID: 35499078 PMCID: PMC9057593 DOI: 10.1172/jci153153] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 03/10/2022] [Indexed: 01/18/2023] Open
Abstract
The relevance of molecular mechanisms governing mitochondrial proteostasis to the differentiation and function of hematopoietic and immune cells is largely elusive. Through dissection of the network of proteins related to HCLS1-associated protein X-1, we defined a potentially novel functional CLPB/HAX1/(PRKD2)/HSP27 axis with critical importance for the differentiation of neutrophil granulocytes and, thus, elucidated molecular and metabolic mechanisms underlying congenital neutropenia in patients with HAX1 deficiency as well as bi- and monoallelic mutations in CLPB. As shown by stable isotope labeling by amino acids in cell culture (SILAC) proteomics, CLPB and HAX1 control the balance of mitochondrial protein synthesis and persistence crucial for proper mitochondrial function. Impaired mitochondrial protein dynamics are associated with decreased abundance of the serine-threonine kinase PRKD2 and HSP27 phosphorylated on serines 78 and 82. Cellular defects in HAX1–/– cells can be functionally reconstituted by HSP27. Thus, mitochondrial proteostasis emerges as a critical molecular and metabolic mechanism governing the differentiation and function of neutrophil granulocytes.
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Affiliation(s)
- Yanxin Fan
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Marta Murgia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Monika I. Linder
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Yoko Mizoguchi
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Cong Wang
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Marcin Łyszkiewicz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Natalia Ziȩtara
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Yanshan Liu
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Stephanie Frenz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Gabriela Sciuccati
- Hematology and Oncology Department, Hospital de Pediatria “Prof. Dr. J.P. Garrahan,” Buenos Aires, Argentina
| | - Armando Partida-Gaytan
- Unidad de Investigación en Inmunodeficiencias Primarias, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | - Nima Rezaei
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells,” University of Goettingen, Goettingen, Germany
- Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
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Zmasek CM, Lefkowitz EJ, Niewiadomska A, Scheuermann RH. Genomic evolution of the Coronaviridae family. Virology 2022; 570:123-133. [PMID: 35398776 PMCID: PMC8965632 DOI: 10.1016/j.virol.2022.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 01/03/2023]
Abstract
The current outbreak of coronavirus disease-2019 (COVID-19) caused by SARS-CoV-2 poses unparalleled challenges to global public health. SARS-CoV-2 is a Betacoronavirus, one of four genera belonging to the Coronaviridae subfamily Orthocoronavirinae. Coronaviridae, in turn, are members of the order Nidovirales, a group of enveloped, positive-stranded RNA viruses. Here we present a systematic phylogenetic and evolutionary study based on protein domain architecture, encompassing the entire proteomes of all Orthocoronavirinae, as well as other Nidovirales. This analysis has revealed that the genomic evolution of Nidovirales is associated with extensive gains and losses of protein domains. In Orthocoronavirinae, the sections of the genomes that show the largest divergence in protein domains are found in the proteins encoded in the amino-terminal end of the polyprotein (PP1ab), the spike protein (S), and many of the accessory proteins. The diversity among the accessory proteins is particularly striking, as each subgenus possesses a set of accessory proteins that is almost entirely specific to that subgenus. The only notable exception to this is ORF3b, which is present and orthologous over all Alphacoronaviruses. In contrast, the membrane protein (M), envelope small membrane protein (E), nucleoprotein (N), as well as proteins encoded in the central and carboxy-terminal end of PP1ab (such as the 3C-like protease, RNA-dependent RNA polymerase, and Helicase) show stable domain architectures across all Orthocoronavirinae. This comprehensive analysis of the Coronaviridae domain architecture has important implication for efforts to develop broadly cross-protective coronavirus vaccines.
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Affiliation(s)
- Christian M Zmasek
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, UAB School of Medicine, Birmingham, AL, 35294, USA
| | - Anna Niewiadomska
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA; Department of Pathology, University of California, San Diego, CA, 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA; Global Virus Network, Baltimore MD, 21201, USA.
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