1
|
Pozdnyakov IR, Selyuk AO, Kalashnikova VA, Karpov SA. HMG-B transcription factors of unicellular opisthokonts and their relatedness to the Sox-Tcf/Lef-Mata proteins of Metazoa and fungi. Gene 2024; 921:148520. [PMID: 38702020 DOI: 10.1016/j.gene.2024.148520] [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: 10/19/2023] [Revised: 04/05/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
A phylogenetic analysis of transcription factors of the Sox-Tcf/Lef-Mata (STM) family of the HMG-B superfamily was carried out in order to clarify the evolutionary roots of the Wnt signaling pathway in unicellular organisms. The data set for analysis included protein sequences of metazoans, fungi, unicellular opisthokonts, apusomonads and amoebozoans. The topology of the phylogenetic tree suggests that STM-related proteins arose in the common ancestor of Opisthokonta and Amoebozoa, two of amoebozoan STM proteins are sister-related to opisthokont ones and the three known lineages of STM transcription factors (STM family in narrow sence) are found in Opisthokonta only. Of these, the holozoan Sox protein branch is the result of either the first or second branching, that originated in the common ancestor of Opisthokonta. The lineage containing Tcf/Lef proteins (holozoan) and the lineage containing Mata proteins (holomycotan) are sister. They derived either at the time of the Holozoa and Holomycota divergence or originate from two paralogs of the common ancestor of Opisthokonta, which arose after the separation of the Sox lineage. Interaction with Armadillo-like proteins may be an original feature of the STM protein family and existed in the unicellular ancestors of multicellular animals; a connection is possible between the presence of Mata-related proteins in Aphelidium protococcorum and specific genome feature of this species.
Collapse
Affiliation(s)
- Igor R Pozdnyakov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia.
| | - Alexey O Selyuk
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia; Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg University, St. Petersburg 199034, Russia
| | - Vera A Kalashnikova
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg University, St. Petersburg 199034, Russia
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
| |
Collapse
|
2
|
Liu X, Li Y, Castro L, Yu Z, Cheng Y, Daugherty MD, Gross JD. Structure of the E3 ligase CRL2-ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600508. [PMID: 38979164 PMCID: PMC11230176 DOI: 10.1101/2024.06.24.600508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
ZYG11B is a substrate specificity factor for Cullin-RING ubiquitin ligase (CRL2) involved in many biological processes, including Gly/N-degron pathways. Yet how the binding of ZYG11B with CRL2 is coupled to substrate recognition and ubiquitination is unknown. We present the Cryo-EM structures of the CRL2-ZYG11B holoenzyme alone and in complex with a Gly/N-peptide from the inflammasome-forming pathogen sensor NLRP1. The structures indicate ZYG11B folds into a Leucine-Rich Repeat followed by two armadillo repeat domains that promote assembly with CRL2 and recognition of NLRP1 Gly/N-degron. ZYG11B promotes activation of the NLRP1 inflammasome through recognition and subsequent ubiquitination of the NLRP1 Gly/N-degron revealed by viral protease cleavage. Our structural and functional data indicate that blocking ZYG11B recognition of the NLRP1 Gly/N-degron inhibits NLRP1 inflammasome activation by a viral protease. Overall, we show how the CRL2-ZYG11B E3 ligase complex recognizes Gly/N-degron substrates, including those that are involved in viral protease-mediated activation of the NLRP1 inflammasome.
Collapse
|
3
|
Xiao G, Laksanavilat N, Cesari S, Lambou K, Baudin M, Jalilian A, Telebanco-Yanoria MJ, Chalvon V, Meusnier I, Fournier E, Tharreau D, Zhou B, Wu J, Kroj T. The unconventional resistance protein PTR recognizes the Magnaporthe oryzae effector AVR-Pita in an allele-specific manner. NATURE PLANTS 2024; 10:994-1004. [PMID: 38834685 DOI: 10.1038/s41477-024-01694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/08/2024] [Indexed: 06/06/2024]
Abstract
Blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating rice diseases. Disease resistance genes such as Pi-ta or Pi-ta2 are critical in protecting rice production from blast. Published work reports that Pi-ta codes for a nucleotide-binding and leucine-rich repeat domain protein (NLR) that recognizes the fungal protease-like effector AVR-Pita by direct binding. However, this model was challenged by the recent discovery that Pi-ta2 resistance, which also relies on AVR-Pita detection, is conferred by the unconventional resistance gene Ptr, which codes for a membrane protein with a cytoplasmic armadillo repeat domain. Here, using NLR Pi-ta and Ptr RNAi knockdown and CRISPR/Cas9 knockout mutant rice lines, we found that AVR-Pita recognition relies solely on Ptr and that the NLR Pi-ta has no role in it, indicating that it is not the Pi-ta resistance gene. Different alleles of Ptr confer different recognition specificities. The A allele of Ptr (PtrA) detects all natural sequence variants of the effector and confers Pi-ta2 resistance, while the B allele of Ptr (PtrB) recognizes a restricted set of AVR-Pita alleles and, thereby, confers Pi-ta resistance. Analysis of the natural diversity in AVR-Pita and of mutant and transgenic strains identified one specific polymorphism in the effector sequence that controls escape from PtrB-mediated resistance. Taken together, our work establishes that the M. oryzae effector AVR-Pita is detected in an allele-specific manner by the unconventional rice resistance protein Ptr and that the NLR Pi-ta has no function in Pi-ta resistance and the recognition of AVR-Pita.
Collapse
Affiliation(s)
- Gui Xiao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- International Rice Research Institute, Metro Manila, Philippines
| | - Nutthalak Laksanavilat
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Karine Lambou
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Maël Baudin
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Ahmad Jalilian
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Veronique Chalvon
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Isabelle Meusnier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, PHIM, Montpellier, France
| | - Bo Zhou
- International Rice Research Institute, Metro Manila, Philippines.
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China.
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
| |
Collapse
|
4
|
Chereddy SCRR, Makino T. Conserved Genes in Highly Regenerative Metazoans Are Associated with Planarian Regeneration. Genome Biol Evol 2024; 16:evae082. [PMID: 38652806 PMCID: PMC11077316 DOI: 10.1093/gbe/evae082] [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: 01/10/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
Metazoan species depict a wide spectrum of regeneration ability which calls into question the evolutionary origins of the underlying processes. Since species with high regeneration ability are widely distributed throughout metazoans, there is a possibility that the metazoan ancestor had an underlying common molecular mechanism. Early metazoans like sponges possess high regenerative ability, but, due to the large differences they have with Cnidaria and Bilateria regarding symmetry and neuronal systems, it can be inferred that this regenerative ability is different. We hypothesized that the last common ancestor of Cnidaria and Bilateria possessed remarkable regenerative ability which was lost during evolution. We separated Cnidaria and Bilateria into three classes possessing whole-body regenerating, high regenerative ability, and low regenerative ability. Using a multiway BLAST and gene phylogeny approach, we identified genes conserved in whole-body regenerating species and lost in low regenerative ability species and labeled them Cnidaria and Bilaterian regeneration genes. Through transcription factor analysis, we identified that Cnidaria and Bilaterian regeneration genes were associated with an overabundance of homeodomain regulatory elements. RNA interference of Cnidaria and Bilaterian regeneration genes resulted in loss of regeneration phenotype for HRJDa, HRJDb, DUF21, DISP3, and ARMR genes. We observed that DUF21 knockdown was highly lethal in the early stages of regeneration indicating a potential role in wound response. Also, HRJDa, HRJDb, DISP3, and ARMR knockdown showed loss of regeneration phenotype after second amputation. The results strongly correlate with their respective RNA-seq profiles. We propose that Cnidaria and Bilaterian regeneration genes play a major role in regeneration across highly regenerative Cnidaria and Bilateria.
Collapse
Affiliation(s)
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| |
Collapse
|
5
|
Zhao S, Liu Q, Su L, Meng L, Tan C, Wei C, Zhang H, Luo T, Zhang Q, Tan YQ, Tu C, Chen H, Gao X. Identification of novel homozygous asthenoteratospermia-causing ARMC2 mutations associated with multiple morphological abnormalities of the sperm flagella. J Assist Reprod Genet 2024; 41:1297-1306. [PMID: 38492154 PMCID: PMC11143164 DOI: 10.1007/s10815-024-03087-9] [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: 11/16/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
PURPOSE To identify the genetic causes of multiple morphological abnormalities in sperm flagella (MMAF) and male infertility in patients from two unrelated Han Chinese families. METHODS Whole-exome sequencing was conducted using blood samples from the two individuals with MMAF and male infertility. Hematoxylin and eosin staining and scanning electron microscopy were performed to evaluate sperm morphology. Ultrastructural and immunostaining analyses of the spermatozoa were performed. The HEK293T cells were used to confirm the pathogenicity of the variants. RESULTS We identified two novel homozygous missense ARMC2 variants: c.314C > T: p.P105L and c.2227A > G: p.N743D. Both variants are absent or rare in the human population genome data and are predicted to be deleterious. In vitro experiments indicated that both ARMC2 variants caused a slightly increased protein expression. ARMC2-mutant spermatozoa showed multiple morphological abnormalities (bent, short, coiled, absent, and irregular) in the flagella. In addition, the spermatozoa of the patients revealed a frequent absence of the central pair complex and disrupted axonemal ultrastructure. CONCLUSION We identified two novel ARMC2 variants that caused male infertility and MMAF in Han Chinese patients. These findings expand the mutational spectrum of ARMC2 and provide insights into the complex causes and pathogenesis of MMAF.
Collapse
Affiliation(s)
- Siyi Zhao
- Department of Urology, The First Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Qiong Liu
- Reproductive Medical Center, Jiangxi Maternal and Child Health Hospital, Affiliated Maternal and Child Health Hospital of Nanchang University, Nanchang, China
- Nanchang Medical College, Nanchang, China
| | - Lilan Su
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Lanlan Meng
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya and Clinical Research Center For Reproduction and Genetics in Hunan Province, Changsha, China
| | - Chen Tan
- Reproductive and Genetic Hospital of CITIC-Xiangya and Clinical Research Center For Reproduction and Genetics in Hunan Province, Changsha, China
| | - Chunjia Wei
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Huan Zhang
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya and Clinical Research Center For Reproduction and Genetics in Hunan Province, Changsha, China
| | - Tao Luo
- Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Qianjun Zhang
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya and Clinical Research Center For Reproduction and Genetics in Hunan Province, Changsha, China
| | - Yue-Qiu Tan
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya and Clinical Research Center For Reproduction and Genetics in Hunan Province, Changsha, China
| | - Chaofeng Tu
- National Engineering and Research Center of Human Stem Cells and Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China.
- Reproductive and Genetic Hospital of CITIC-Xiangya and Clinical Research Center For Reproduction and Genetics in Hunan Province, Changsha, China.
| | - Houyang Chen
- Reproductive Medical Center, Jiangxi Maternal and Child Health Hospital, Affiliated Maternal and Child Health Hospital of Nanchang University, Nanchang, China.
| | - Xingcheng Gao
- Department of Urology, The First Clinical College of Guangzhou Medical University, Guangzhou, China.
| |
Collapse
|
6
|
Mizuike A, Hanada K. DGARM/C10orf76/ARMH3 for Ceramide Transfer Zone at the Endoplasmic Reticulum-Distal Golgi Contacts. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241239443. [PMID: 38515862 PMCID: PMC10956147 DOI: 10.1177/25152564241239443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Phosphatidylinositol 4-monophosphate (PtdIns(4)P) is one of the key membrane components which mark the membrane contact sites. In the mammalian Golgi complex, PtdIns(4)P is produced at various subregions via specific mechanisms for each site. Particularly, PtdIns(4)P pools generated at the distal Golgi regions are pivotal for the determination of membrane contacts between the endoplasmic reticulum (ER) and Golgi, at which inter-organelle lipid transport takes place. In this short review, we will focus on C10orf76 (or ARMH3), which we propose to rename as DGARM after a distal Golgi armadillo repeat protein, for its function in generating a PtdIns(4)P pool crucial for ER-to-distal Golgi ceramide transport. We further discuss from the viewpoint of the evolutionary conservation of DGARM.
Collapse
Affiliation(s)
- Aya Mizuike
- Department of Quality Assurance, Radiation Safety and Information System, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Hanada
- Department of Quality Assurance, Radiation Safety and Information System, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
7
|
Wang T, Song Y, Yang L, Liu W, He Z, Shi Y, Song B, Yu Z. Photobiomodulation Facilitates Rat Cutaneous Wound Healing by Promoting Epidermal Stem Cells and Hair Follicle Stem Cells Proliferation. Tissue Eng Regen Med 2024; 21:65-79. [PMID: 37882982 PMCID: PMC10764690 DOI: 10.1007/s13770-023-00601-5] [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: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Cutaneous wound healing represents a common fundamental phenomenon requiring the participation of cells of distinct types and a major concern for the public. Evidence has confirmed that photobiomodulation (PBM) using near-infrared (NIR) can promote wound healing, but the cells involved and the precise molecular mechanisms remain elusive. METHODS Full-thickness skin defects with a diameter of 1.0 cm were made on the back of rats and randomly divided into the control group, 10 J, 15 J, and 30 J groups. The wound healing rate at days 4, 8, and 12 postoperatively was measured. HE and Masson staining was conducted to reveal the histological characteristics. Immunofluorescence staining was performed to label the epidermal stem cells (ESCs) and hair follicle stem cells (HFSCs). Western blot was performed to detect the expressions of proteins associated with ESCs and HFSCs. Cutaneous wound tissues were collected for RNA sequencing. Gene ontology and the Kyoto Encyclopedia of Genes and Genomes analysis was performed, and the hub genes were identified using CytoHubba and validated by qRT-PCR. RESULTS PBM can promote reepithelialization, extracellular matrix deposition, and wound healing, increase the number of KRT14+/PCNA+ ESCs and KRT15+/PCNA+ HFSCs, and upregulate the protein expression of P63, Krt14, and PCNA. Three hundred and sixty-six differentially expressed genes (DEGs) and 7 hub genes including Sox9, Krt5, Epcam, Cdh1, Cdh3, Dsp, and Pkp3 were identified. These DEGs are enriched in skin development, cell junction, and cadherin binding involved in cell-cell adhesion etc., while these hub genes are related to skin derived stem cells and cell adhesion. CONCLUSION PBM accelerates wound healing by enhancing reepithelialization through promoting ESCs and HFSCs proliferation and elevating the expression of genes associated with stem cells and cell adhesion. This may provide a valuable alternative strategy to promote wound healing and reepithelialization by modulating the proliferation of skin derived stem cells and regulating genes related to cell adhesion.
Collapse
Affiliation(s)
- Tong Wang
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Yajuan Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Liu Yang
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Wei Liu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Zhen'an He
- Shaanxi Institute of Medical Device Quality Inspection, Xi'an, 712046, China
| | - Yi Shi
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Baoqiang Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| | - Zhou Yu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| |
Collapse
|
8
|
Komori T, Kuwahara T. An Update on the Interplay between LRRK2, Rab GTPases and Parkinson's Disease. Biomolecules 2023; 13:1645. [PMID: 38002327 PMCID: PMC10669493 DOI: 10.3390/biom13111645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Over the last decades, research on the pathobiology of neurodegenerative diseases has greatly evolved, revealing potential targets and mechanisms linked to their pathogenesis. Parkinson's disease (PD) is no exception, and recent studies point to the involvement of endolysosomal defects in PD. The endolysosomal system, which tightly controls a flow of endocytosed vesicles targeted either for degradation or recycling, is regulated by a number of Rab GTPases. Their associations with leucine-rich repeat kinase 2 (LRRK2), a major causative and risk protein of PD, has also been one of the hot topics in the field. Understanding their interactions and functions is critical for unraveling their contribution to PD pathogenesis. In this review, we summarize recent studies on LRRK2 and Rab GTPases and attempt to provide more insight into the interaction of LRRK2 with each Rab and its relationship to PD.
Collapse
Affiliation(s)
| | - Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| |
Collapse
|
9
|
Alagundagi DB, Ghate SD, Shetty P, Gollapalli P, Shetty P, Patil P. Integrated molecular-network analysis reveals infertility-associated key genes and transcription factors in the non-obstructive azoospermia. Eur J Obstet Gynecol Reprod Biol 2023; 288:183-190. [PMID: 37549510 DOI: 10.1016/j.ejogrb.2023.07.023] [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: 11/11/2022] [Revised: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Male infertility is a multifactorial reproductive health problem with complex causes. Non-obstructive azoospermia (NOA) is characterized by failure of spermatogenesis, leading to the absence of spermatozoa in ejaculates. The molecular mechanism underlying the NOA is still not well understood. OBJECTIVES This study aims to identify the key genes involved in male infertility that could be a potential biomarker in the diagnosis and prognosis of azoospermia. STUDY DESIGN The microarray expression profiles dataset GSE45885 and GSE45887 were downloaded from the NCBI's Gene Expression Omnibus (GEO) database and analyzed for male infertility-associated differentially expressed genes (DEGs) using the GEO2R tool. The common DEGs between the two datasets were combined and their protein-protein interaction (PPI) network was constructed using Cytoscape to reveal the hub genes by topology and module analysis. In addition, transcription factors (TFs) and protein kinases regulating the hub genes were identified using the X2K tool. Then, the expression of the hub genes was validated by analyzing the GSE190752 microarray dataset. Further, the PPI network was screened for biological roles and enriched pathways using DAVID software. RESULTS About 256 DEGs associated with NOA were identified and constructed the PPI network to find the infertility-associated proteins. The biological processes linked with these proteins were spermatogenesis, cell differentiation, flagellated sperm motility, and spermatid development. The topology and module analysis of the infertility-associated protein network identified the hub genes TEX38, FAM71F, PRR30, FAM166A, LYZL6, TPPP2, ARMC12, SPACA4, and FAM205A, which were found to be upregulated in the non-obstructive azoospermia. In addition, a total of 23 transcription factors and 3 protein kinases that are regulating these key hub genes were identified. Further these hub genes expression was validated using the microarray data and found that their expression was increased in the testicular biopsies obtained from NOA subjects, compared to healthy individuals. CONCLUSION The identified key genes and its associated transcription factors are known to regulate the infertility-related processes in the non-obstructive azoospermia. Also, the clinical sample-based microarray data validation for the expression of these key hub genes indicates their potentiality to develop them as diagnostic or prognostic biomarkers for NOA.
Collapse
Affiliation(s)
- Dhananjay B Alagundagi
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Sudeep D Ghate
- Center for Bioinformatics and Biostatistics, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Prasannakumar Shetty
- Department of Obstetrics and Gynecology, Justice K S Hegde Charitable Hospital, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Praveenkumar Shetty
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India; Department of Biochemistry, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Prakash Patil
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| |
Collapse
|
10
|
Chen E, Hou Q, Liu K, Gu Z, Dai B, Wang A, Feng Q, Zhao Y, Zhou C, Zhu J, Shangguan Y, Wang Y, Lv D, Fan D, Huang T, Wang Z, Huang X, Han B. Armadillo repeat only protein GS10 negatively regulates brassinosteroid signaling to control rice grain size. PLANT PHYSIOLOGY 2023; 192:967-981. [PMID: 36822628 PMCID: PMC10231457 DOI: 10.1093/plphys/kiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 06/01/2023]
Abstract
Grain yield and grain quality are major determinants in modern breeding controlled by many quantitative traits loci (QTLs) in rice (Oryza sativa). However, the mechanisms underlying grain shape and quality are poorly understood. Here, we characterize a QTL for grain size and grain quality via map-based cloning from wild rice (W1943), GS10 (Grain Size on Chromosome 10), which encodes a protein with 6 tandem armadillo repeats. The null mutant gs10 shows slender and narrow grains with altered cell size, which has a pleiotropic effect on other agronomical traits. Functional analysis reveals that GS10 interacts with TUD1 (Taihu Dwarf1) and is epistatic to OsGSK2 (glycogen synthase kinase 2) through regulating grain shape and lamina joint inclination, indicating it is negatively involved in brassinosteroid (BR) signaling. Pyramiding gs10 and the grain size gene GW5 into cultivar GLA4 substantially improved grain shape and appearance quality. Natural variation analysis revealed that gs10 from the wild rice Oryza rufipogon W1943 is a rare allele across the rice population. Collectively, these findings advance our understanding of the underlying mechanism of grain shape and provide the beneficial allele of gs10 for future rice breeding and genetic improvement.
Collapse
Affiliation(s)
- Erwang Chen
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230027, China
| | - Qingqing Hou
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu 611130, China
| | - Kun Liu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Zhoulin Gu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bingxin Dai
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Ahong Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Congcong Zhou
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jingjie Zhu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yingying Shangguan
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yongchun Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danfeng Lv
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danlin Fan
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Tao Huang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Zixuan Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| |
Collapse
|
11
|
Gupta J, Rangarajan ES, Troyanovsky RB, Indra I, Troyanovsky SM, Izard T. Plakophilin-3 Binds the Membrane and Filamentous Actin without Bundling F-Actin. Int J Mol Sci 2023; 24:9458. [PMID: 37298410 PMCID: PMC10253835 DOI: 10.3390/ijms24119458] [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: 04/28/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Plakophilin-3 is a ubiquitously expressed protein found widely in epithelial cells and is a critical component of desmosomes. The plakophilin-3 carboxy-terminal domain harbors nine armadillo repeat motifs with largely unknown functions. Here, we report the 5 Å cryogenic electron microscopy (cryoEM) structure of the armadillo repeat motif domain of plakophilin-3, one of the smaller cryoEM structures reported to date. We find that this domain is a monomer or homodimer in solution. In addition, using an in vitro actin co-sedimentation assay, we show that the armadillo repeat domain of plakophilin-3 directly interacts with F-actin. This feature, through direct interactions with actin filaments, could be responsible for the observed association of extra-desmosomal plakophilin-3 with the actin cytoskeleton directly attached to the adherens junctions in A431 epithelial cells. Further, we demonstrate, through lipid binding analyses, that plakophilin-3 can effectively be recruited to the plasma membrane through phosphatidylinositol-4,5-bisphosphate-mediated interactions. Collectively, we report on novel properties of plakophilin-3, which may be conserved throughout the plakophilin protein family and may be behind the roles of these proteins in cell-cell adhesion.
Collapse
Affiliation(s)
- Jyoti Gupta
- Cell Adhesion Laboratory, UF Scripps, Jupiter, FL 33458, USA
| | | | - Regina B. Troyanovsky
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL 606112, USA
| | - Indrajyoti Indra
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL 606112, USA
| | - Sergey M. Troyanovsky
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL 606112, USA
| | - Tina Izard
- Cell Adhesion Laboratory, UF Scripps, Jupiter, FL 33458, USA
- The Skaggs Graduate School, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
12
|
Kim H, Park J, Kim H, Ko N, Park J, Jang E, Yoon S, Diaz J, Lee C, Jun Y. Structures of Vac8-containing protein complexes reveal the underlying mechanism by which Vac8 regulates multiple cellular processes. Proc Natl Acad Sci U S A 2023; 120:e2211501120. [PMID: 37094131 PMCID: PMC10161063 DOI: 10.1073/pnas.2211501120] [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: 07/06/2022] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Vac8, a yeast vacuolar protein with armadillo repeats, mediates various cellular processes by changing its binding partners; however, the mechanism by which Vac8 differentially regulates these processes remains poorly understood. Vac8 interacts with Nvj1 to form the nuclear-vacuole junction (NVJ) and with Atg13 to mediate cytoplasm-to-vacuole targeting (Cvt), a selective autophagy-like pathway that delivers cytoplasmic aminopeptidase I directly to the vacuole. In addition, Vac8 associates with Myo2, a yeast class V myosin, through its interaction with Vac17 for vacuolar inheritance from the mother cell to the emerging daughter cell during cell divisions. Here, we determined the X-ray crystal structure of the Vac8-Vac17 complex and found that its interaction interfaces are bipartite, unlike those of the Vac8-Nvj1 and Vac8-Atg13 complexes. When the key amino acids present in the interface between Vac8 and Vac17 were mutated, vacuole inheritance was severely impaired in vivo. Furthermore, binding of Vac17 to Vac8 prevented dimerization of Vac8, which is required for its interactions with Nvj1 and Atg13, by clamping the H1 helix to the ARM1 domain of Vac8 and thereby preventing exposure of the binding interface for Vac8 dimerization. Consistently, the binding affinity of Vac17-bound Vac8 for Nvj1 or Atg13 was markedly lower than that of free Vac8. Likewise, free Vac17 had no affinity for the Vac8-Nvj1 and Vac8-Atg13 complexes. These results provide insights into how vacuole inheritance and other Vac8-mediated processes, such as NVJ formation and Cvt, occur independently of one another.
Collapse
Affiliation(s)
- Hyejin Kim
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Jihyeon Park
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Hyunwoo Kim
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Naho Ko
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Jumi Park
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Eunhong Jang
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - So Young Yoon
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Joyce Anne R. Diaz
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Changwook Lee
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
| | - Youngsoo Jun
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| |
Collapse
|
13
|
Lin C, Feng S, DeOliveira CC, Crane BR. Cryptochrome-Timeless structure reveals circadian clock timing mechanisms. Nature 2023; 617:194-199. [PMID: 37100907 PMCID: PMC11034853 DOI: 10.1038/s41586-023-06009-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/23/2023] [Indexed: 04/28/2023]
Abstract
Circadian rhythms influence many behaviours and diseases1,2. They arise from oscillations in gene expression caused by repressor proteins that directly inhibit transcription of their own genes. The fly circadian clock offers a valuable model for studying these processes, wherein Timeless (Tim) plays a critical role in mediating nuclear entry of the transcriptional repressor Period (Per) and the photoreceptor Cryptochrome (Cry) entrains the clock by triggering Tim degradation in light2,3. Here, through cryogenic electron microscopy of the Cry-Tim complex, we show how a light-sensing cryptochrome recognizes its target. Cry engages a continuous core of amino-terminal Tim armadillo repeats, resembling how photolyases recognize damaged DNA, and binds a C-terminal Tim helix, reminiscent of the interactions between light-insensitive cryptochromes and their partners in mammals. The structure highlights how the Cry flavin cofactor undergoes conformational changes that couple to large-scale rearrangements at the molecular interface, and how a phosphorylated segment in Tim may impact clock period by regulating the binding of Importin-α and the nuclear import of Tim-Per4,5. Moreover, the structure reveals that the N terminus of Tim inserts into the restructured Cry pocket to replace the autoinhibitory C-terminal tail released by light, thereby providing a possible explanation for how the long-short Tim polymorphism adapts flies to different climates6,7.
Collapse
Affiliation(s)
- Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Shi Feng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
14
|
Cui J, Ren G, Bai Y, Gao Y, Yang P, Chang J. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum ( Sorghum bicolor L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1141617. [PMID: 37008506 PMCID: PMC10063820 DOI: 10.3389/fpls.2023.1141617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Plant U-box (PUB) E3 ubiquitin ligases play essential roles in many biological processes and stress responses, but little is known about their functions in sorghum (Sorghum bicolor L.). In the present study, 59 SbPUB genes were identified in the sorghum genome. Based on the phylogenetic analysis, the 59 SbPUB genes were clustered into five groups, which were also supported by the conserved motifs and structures of these genes. SbPUB genes were found to be unevenly distributed on the 10 chromosomes of sorghum. Most PUB genes (16) were found on chromosome 4, but there were no PUB genes on chromosome 5. Analysis of cis-acting elements showed that SbPUB genes were involved in many important biological processes, particularly in response to salt stress. From proteomic and transcriptomic data, we found that several SbPUB genes had diverse expressions under different salt treatments. To verify the expression of SbPUBs, qRT-PCR analyses also were conducted under salt stress, and the result was consistent with the expression analysis. Furthermore, 12 SbPUB genes were found to contain MYB-related elements, which are important regulators of flavonoid biosynthesis. These results, which were consistent with our previous multi-omics analysis of sorghum salt stress, laid a solid foundation for further mechanistic study of salt tolerance in sorghum. Our study showed that PUB genes play a crucial role in regulating salt stress, and might serve as promising targets for the breeding of salt-tolerant sorghum in the future.
Collapse
Affiliation(s)
- Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Genzeng Ren
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Yuzhe Bai
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Yukun Gao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Puyuan Yang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Jinhua Chang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| |
Collapse
|
15
|
Wang Y, Teng Z, Li H, Wang W, Xu F, Sun K, Chu J, Qian Y, Loake GJ, Chu C, Tang J. An activated form of NB-ARC protein RLS1 functions with cysteine-rich receptor-like protein RMC to trigger cell death in rice. PLANT COMMUNICATIONS 2023; 4:100459. [PMID: 36203361 PMCID: PMC10030324 DOI: 10.1016/j.xplc.2022.100459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/14/2022] [Accepted: 10/04/2022] [Indexed: 05/04/2023]
Abstract
A key event that follows pathogen recognition by a resistance (R) protein containing an NB-ARC (nucleotide-binding adaptor shared by Apaf-1, R proteins, and Ced-4) domain is hypersensitive response (HR)-type cell death accompanied by accumulation of reactive oxygen species and nitric oxide. However, the integral mechanisms that underlie this process remain relatively opaque. Here, we show that a gain-of-function mutation in the NB-ARC protein RLS1 (Rapid Leaf Senescence 1) triggers high-light-dependent HR-like cell death in rice. The RLS1-mediated defense response is largely independent of salicylic acid accumulation, NPR1 (Nonexpressor of Pathogenesis-Related Gene 1) activity, and RAR1 (Required for Mla12 Resistance 1) function. A screen for suppressors of RLS1 activation identified RMC (Root Meander Curling) as essential for the RLS1-activated defense response. RMC encodes a cysteine-rich receptor-like secreted protein (CRRSP) and functions as an RLS1-binding partner. Intriguingly, their co-expression resulted in a change in the pattern of subcellular localization and was sufficient to trigger cell death accompanied by a decrease in the activity of the antioxidant enzyme APX1. Collectively, our findings reveal an NB-ARC-CRRSP signaling module that modulates oxidative state, the cell death process, and associated immunity responses in rice.
Collapse
Affiliation(s)
- Yiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenfeng Teng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fan Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kai Sun
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- Institute of Genetics and Developmental Biology and National Center for Plant Gene Research (Beijing), Chinese Academy of Sciences, Beijing 100101, China
| | - Yangwen Qian
- Biogle Genome Editing Center, Changzhou 213125, China
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
16
|
Silva Dos Santos F, Neves RAF, Bernay B, Krepsky N, Teixeira VL, Artigaud S. The first use of LC-MS/MS proteomic approach in the brown mussel Perna perna after bacterial challenge: Searching for key proteins on immune response. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108622. [PMID: 36803779 DOI: 10.1016/j.fsi.2023.108622] [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: 12/16/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The brown mussel Perna perna is a valuable fishing resource, primarily in tropical and subtropical coastal regions. Because of their filter-feeding habits, mussels are directly exposed to bacteria in the water column. Escherichia coli (EC) and Salmonella enterica (SE) inhabit human guts and reach the marine environment through anthropogenic sources, such as sewage. Vibrio parahaemolyticus (VP) is indigenous to coastal ecosystems but can be harmful to shellfish. In this study, we aimed to assess the protein profile of the hepatopancreas of P. perna mussel challenged by introduced - E. coli and S. enterica - and indigenous marine bacteria - V. parahaemolyticus. Bacterial-challenge groups were compared with non-injected (NC) and injected control (IC) - that consisted in mussels not challenged and mussels injected with sterile PBS-NaCl, respectively. Through LC-MS/MS proteomic analysis, 3805 proteins were found in the hepatopancreas of P. perna. From the total, 597 were significantly different among conditions. Mussels injected with VP presented 343 proteins downregulated compared with all the other conditions, suggesting that VP suppresses their immune response. Particularly, 31 altered proteins - upregulated or downregulated - for one or more challenge groups (EC, SE, and VP) compared with controls (NC and IC) are discussed in detail in the paper. For the three tested bacteria, significantly different proteins were found to perform critical roles in immune response at all levels, namely: recognition and signal transduction; transcription; RNA processing; translation and protein processing; secretion; and humoral effectors. This is the first shotgun proteomic study in P. perna mussel, therefore providing an overview of the protein profile of the mussel hepatopancreas, focused on the immune response against bacteria. Hence, it is possible to understand the immune-bacteria relationship at molecular levels better. This knowledge can support the development of strategies and tools to be applied to coastal marine resource management and contribute to the sustainability of coastal systems.
Collapse
Affiliation(s)
- Fernanda Silva Dos Santos
- Graduate Program in Sciences and Biotechnology, Institute of Biology, Fluminense Federal University (UFF), R. Mario Santos Braga, S/n. Centro, Niterói, RJ, CEP 24.020-141, Brazil; Research Group of Experimental and Aquatic Ecology, Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458-307, Urca, Rio de Janeiro, RJ, CEP: 22.290-240, Brazil.
| | - Raquel A F Neves
- Graduate Program in Neotropical Biodiversity (PPGBIO), Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458, Urca, Rio de Janeiro, RJ, CEP: 22.290-255, Brazil; Research Group of Experimental and Aquatic Ecology, Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458-307, Urca, Rio de Janeiro, RJ, CEP: 22.290-240, Brazil.
| | - Benoît Bernay
- Plateforme Proteogen, SFR ICORE 4206, Université de Caen Basse-Normandie, Esplanade de la paix, 14032, Caen cedex, France.
| | - Natascha Krepsky
- Graduate Program in Neotropical Biodiversity (PPGBIO), Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458, Urca, Rio de Janeiro, RJ, CEP: 22.290-255, Brazil.
| | - Valéria Laneuville Teixeira
- Graduate Program in Sciences and Biotechnology, Institute of Biology, Fluminense Federal University (UFF), R. Mario Santos Braga, S/n. Centro, Niterói, RJ, CEP 24.020-141, Brazil; Graduate Program in Neotropical Biodiversity (PPGBIO), Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458, Urca, Rio de Janeiro, RJ, CEP: 22.290-255, Brazil.
| | - Sébastien Artigaud
- Université de Brest, CNRS, IRD, Ifremer, UMR 6539 LEMAR, F-29280, Plouzané, France.
| |
Collapse
|
17
|
Zhang S, Lv C, Niu Y, Li C, Li X, Shang Y, Zhang Y, Zhang Y, Zhang Y, Zeng Y. RBM3 suppresses stemness remodeling of prostate cancer in bone microenvironment by modulating N6-methyladenosine on CTNNB1 mRNA. Cell Death Dis 2023; 14:91. [PMID: 36750551 PMCID: PMC9905585 DOI: 10.1038/s41419-023-05627-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/09/2023]
Abstract
Bone metastasis is the most happened metastatic event in prostate cancer (PCa) and needs a large effort in treatment. When PCa metastasizes to the bone, the new microenvironment can induce the epigenome reprogramming and stemness remodeling of cancer cells, thereby increasing the adaptability of cancer cells to the bone microenvironment, and this even leads to the occurrence of secondary tumor metastasis. Our group has previously found that RNA binding motif 3 (RBM3) affects the stem cell-like properties of PCa by interfering with alternative splicing of CD44. However, whether RBM3, as a stress-response protein, can resist microenvironmental remodeling of PCa particularly in bone metastasis remains unknown. By co-culturing PCa cells with osteoblasts to mimic PCa bone metastases, we found that RBM3 upregulates the N6-methyladenosine (m6A) methylation on the mRNA of catenin beta 1 (CTNNB1) in a manner dependent on methyltransferase 3 (METTL3), an N6-adenosine-methyltransferase complex catalytic subunit. Consequently, this modification results in a decreased stability of CTNNB1 mRNA and a followed inactivation of Wnt signaling, which ultimately inhibits the stemness remodeling of PCa cells by osteoblasts. Thus, the present study may extend our understanding of the inhibitory role of RBM3 on particularly bone metastasis of PCa.
Collapse
Affiliation(s)
- Shouyi Zhang
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Chengcheng Lv
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yichen Niu
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110001, China
| | - Changqi Li
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Xiuming Li
- Department of Urology, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, 067000, China
| | - Yu Shang
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, 116000, China
| | - Yunchao Zhang
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yue Zhang
- Department of Pathology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yong Zhang
- Department of Pathology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yu Zeng
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China.
| |
Collapse
|
18
|
Hou J, Chen H, Zhang K, Liu W, Cao C, Ruan Y, Deng Y, Liu Y, Yuan X, Sun C, Fu Y. The GZnC1 variant from common wild rice influences grain Zn content. PLANT MOLECULAR BIOLOGY 2023; 111:263-273. [PMID: 36414883 DOI: 10.1007/s11103-022-01325-1] [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: 08/18/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Zinc (Zn) deficiency, caused by inadequate Zn intake in the human diet, has serious health implications. Rice (Oryza sativa) is the staple food in regions with a high incidence of Zn deficiency, so raising Zn levels in rice grain could help alleviate Zn deficiency. The wild relatives of cultivated rice vary widely in grain Zn content and thus are suitable resources for improving this trait. However, few loci underlying grain Zn content have been identified in wild rice relatives. Here, we identified a major quantitative trait locus for grain Zn content, Grain Zn Content 1 (qGZnC1), from Yuanjiang common wild rice (Oryza rufipogon Griff.) using map-based cloning. Down-regulating GZnC1 expression reduced the grain Zn content, whereas the presence of GZnC1 had the opposite effect, indicating that GZnC1 is involved in grain Zn content in rice. Notably, GZnC1 is identical to a previously reported gene, EMBRYO SAC ABORTION 1 (ESA1), involved in seed setting rate. The mutation in GZnC1/ESA1 at position 1819 (T1819C) causes delayed termination of protein translation. In addition, GZnC1 is specifically expressed in developing panicles. Several genes related to Zn-transporter genes were up-regulated in the presence of GZnC1. Our results suggest that GZnC1 activates Zn transporters to promote Zn distribution in panicles. Our work thus sheds light on the genetic mechanism of Zn accumulation in rice grain and provides a new genetic resource for improving Zn content in rice.
Collapse
Affiliation(s)
- Jingjing Hou
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hao Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences; Fujian Engineering Research Center for Characteristic Upland Crops Breeding; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, 350013, China
| | - Kun Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Wenjing Liu
- Institute of Agricultural Quality Standards and Testing Technology Research, Fujian Academy of Agricultural Sciences; Fujian Key Laboratory of Agro-Products Quality and Safety, Fuzhou, 350003, China
| | - Caihong Cao
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yini Ruan
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yanyan Deng
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yaxin Liu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuzhao Yuan
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Chuanqing Sun
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongcai Fu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
19
|
Pinho-Correia LM, Prokop A. Maintaining essential microtubule bundles in meter-long axons: a role for local tubulin biogenesis? Brain Res Bull 2023; 193:131-145. [PMID: 36535305 DOI: 10.1016/j.brainresbull.2022.12.005] [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: 10/16/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Axons are the narrow, up-to-meter long cellular processes of neurons that form the biological cables wiring our nervous system. Most axons must survive for an organism's lifetime, i.e. up to a century in humans. Axonal maintenance depends on loose bundles of microtubules that run without interruption all along axons. The continued turn-over and the extension of microtubule bundles during developmental, regenerative or plastic growth requires the availability of α/β-tubulin heterodimers up to a meter away from the cell body. The underlying regulation in axons is poorly understood and hardly features in past and contemporary research. Here we discuss potential mechanisms, particularly focussing on the possibility of local tubulin biogenesis in axons. Current knowledge might suggest that local translation of tubulin takes place in axons, but far less is known about the post-translational machinery of tubulin biogenesis involving three chaperone complexes: prefoldin, CCT and TBC. We discuss functional understanding of these chaperones from a range of model organisms including yeast, plants, flies and mice, and explain what is known from human diseases. Microtubules across species depend on these chaperones, and they are clearly required in the nervous system. However, most chaperones display a high degree of functional pleiotropy, partly through independent functions of individual subunits outside their complexes, thus posing a challenge to experimental studies. Notably, we found hardly any studies that investigate their presence and function particularly in axons, thus highlighting an important gap in our understanding of axon biology and pathology.
Collapse
Affiliation(s)
- Liliana Maria Pinho-Correia
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK
| | - Andreas Prokop
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK.
| |
Collapse
|
20
|
Lan M, Liu X, Kang E, Fu Y, Zhu L. ARK2 stabilizes the plus-end of microtubules and promotes microtubule bundling in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:100-116. [PMID: 36169006 DOI: 10.1111/jipb.13373] [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: 07/16/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Microtubule dynamics and organization are important for plant cell morphogenesis and development. The microtubule-based motor protein kinesins are mainly responsible for the transport of some organelles and vesicles, although several have also been shown to regulate microtubule organization. The ARMADILLO REPEAT KINESIN (ARK) family is a plant-specific motor protein subfamily that consists of three members (ARK1, ARK2, and ARK3) in Arabidopsis thaliana. ARK2 has been shown to participate in root epidermal cell morphogenesis. However, whether and how ARK2 associates with microtubules needs further elucidation. Here, we demonstrated that ARK2 co-localizes with microtubules and facilitates microtubule bundling in vitro and in vivo. Pharmacological assays and microtubule dynamics analyses indicated that ARK2 stabilizes cortical microtubules. Live-cell imaging revealed that ARK2 moves along cortical microtubules in a processive mode and localizes both at the plus-end and the sidewall of microtubules. ARK2 therefore tracks and stabilizes the growing plus-ends of microtubules, which facilitates the formation of parallel microtubule bundles.
Collapse
Affiliation(s)
- Miao Lan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xianan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Erfang Kang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
21
|
Bracher A, Verghese J. Nucleotide Exchange Factors for Hsp70 Molecular Chaperones: GrpE, Hsp110/Grp170, HspBP1/Sil1, and BAG Domain Proteins. Subcell Biochem 2023; 101:1-39. [PMID: 36520302 DOI: 10.1007/978-3-031-14740-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Molecular chaperones of the Hsp70 family are key components of the cellular protein-folding machinery. Substrate folding is accomplished by iterative cycles of ATP binding, hydrolysis, and release. The ATPase activity of Hsp70 is regulated by two main classes of cochaperones: J-domain proteins stimulate ATPase hydrolysis by Hsp70, while nucleotide exchange factors (NEFs) facilitate the conversion from the ADP-bound to the ATP-bound state, thus closing the chaperone folding cycle. NEF function can additionally be antagonized by ADP dissociation inhibitors. Beginning with the discovery of the prototypical bacterial NEF, GrpE, a large diversity of nucleotide exchange factors for Hsp70 have been identified, connecting it to a multitude of cellular processes in the eukaryotic cell. Here we review recent advances toward structure and function of nucleotide exchange factors from the Hsp110/Grp170, HspBP1/Sil1, and BAG domain protein families and discuss how these cochaperones connect protein folding with cellular quality control and degradation pathways.
Collapse
Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
| | - Jacob Verghese
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- Trophic Communications GmbH, Munich, Germany
| |
Collapse
|
22
|
Colombo G, Astori E, Landoni L, Garavaglia ML, Altomare A, Lionetti MC, Gagliano N, Giustarini D, Rossi R, Milzani A, Dalle‐Donne I. Effects of the uremic toxin indoxyl sulphate on human microvascular endothelial cells. J Appl Toxicol 2022; 42:1948-1961. [PMID: 35854198 PMCID: PMC9796800 DOI: 10.1002/jat.4366] [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: 06/08/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 01/07/2023]
Abstract
Indoxyl sulphate (IS) is a uremic toxin accumulating in the plasma of chronic kidney disease (CKD) patients. IS accumulation induces side effects in the kidneys, bones and cardiovascular system. Most studies assessed IS effects on cell lines by testing higher concentrations than those measured in CKD patients. Differently, we exposed a human microvascular endothelial cell line (HMEC-1) to the IS concentrations measured in the plasma of healthy subjects (physiological) or CKD patients (pathological). Pathological concentrations reduced cell proliferation rate but did not increase long-term oxidative stress level. Indeed, total protein thiols decreased only after 24 h of exposure in parallel with an increased Nrf-2 protein expression. IS induced actin cytoskeleton rearrangement with formation of stress fibres. Proteomic analysis supported this hypothesis as many deregulated proteins are related to actin filaments organization or involved in the endothelial to mesenchymal transition. Interestingly, two proteins directly linked to cardiovascular diseases (CVD) in in vitro and in vivo studies underwent deregulation: COP9 signalosome complex subunit 9 and thrombomodulin. Future experiments will be needed to investigate the role of these proteins and the signalling pathways in which they are involved to clarify the possible link between CKD and CVD.
Collapse
Affiliation(s)
- Graziano Colombo
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| | - Emanuela Astori
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| | - Lucia Landoni
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| | - Maria L. Garavaglia
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| | - Alessandra Altomare
- Department of Pharmaceutical SciencesUniversità degli Studi di MilanoMilanItaly
| | - Maria C. Lionetti
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| | - Nicoletta Gagliano
- Department of Biomedical Sciences for HealthUniversità degli Studi di MilanoMilanItaly
| | - Daniela Giustarini
- Department of Life Sciences, Laboratory of Pharmacology and ToxicologyUniversity of SienaSienaItaly
| | - Ranieri Rossi
- Department of Life Sciences, Laboratory of Pharmacology and ToxicologyUniversity of SienaSienaItaly
| | - Aldo Milzani
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| | - Isabella Dalle‐Donne
- Department of Biosciences (Department of Excellence 2018–2022)Università degli Studi di MilanoMilanItaly
| |
Collapse
|
23
|
Dean WF, Mattheyses AL. Defining domain-specific orientational order in the desmosomal cadherins. Biophys J 2022; 121:4325-4341. [PMID: 36225113 PMCID: PMC9703042 DOI: 10.1016/j.bpj.2022.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/12/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023] Open
Abstract
Desmosomes are large, macromolecular protein assemblies that mechanically couple the intermediate filament cytoskeleton to sites of cadherin-mediated cell adhesion, thereby providing structural integrity to tissues that routinely experience large forces. Proper desmosomal adhesion is necessary for the normal development and maintenance of vertebrate tissues, such as epithelia and cardiac muscle, while dysfunction can lead to severe disease of the heart and skin. Therefore, it is important to understand the relationship between desmosomal adhesion and the architecture of the molecules that form the adhesive interface, the desmosomal cadherins (DCs). However, desmosomes are embedded in two plasma membranes and are linked to the cytoskeletal networks of two cells, imposing extreme difficulty on traditional structural studies of DC architecture, which have yielded conflicting results. Consequently, the relationship between DC architecture and adhesive function remains unclear. To overcome these challenges, we utilized excitation-resolved fluorescence polarization microscopy to quantify the orientational order of the extracellular and intracellular domains of three DC isoforms: desmoglein 2, desmocollin 2, and desmoglein 3. We found that DC ectodomains were significantly more ordered than their cytoplasmic counterparts, indicating a drastic difference in DC architecture between opposing sides of the plasma membrane. This difference was conserved among all DCs tested, suggesting that it may be an important feature of desmosomal architecture. Moreover, our findings suggest that the organization of DC ectodomains is predominantly the result of extracellular adhesive interactions. We employed azimuthal orientation mapping to show that DC ectodomains are arranged with rotational symmetry about the membrane normal. Finally, we performed a series of mathematical simulations to test the feasibility of a recently proposed antiparallel arrangement of DC ectodomains, finding that it is supported by our experimental data. Importantly, the strategies employed here have the potential to elucidate molecular mechanisms for diseases that result from defective desmosome architecture.
Collapse
Affiliation(s)
- William F Dean
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Alexa L Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.
| |
Collapse
|
24
|
Yi S, Chen F, Qin Z, Yi S, Huang L, Huang L, Feng Y, Wei H, Yang Q, Zhang Q, Luo J. Novel Synonymous and Frameshift Variants in the TRIP12 Gene Identified in 2 Chinese Patients With Intellectual Disability. NEUROLOGY GENETICS 2022; 8:e200025. [PMID: 36275919 PMCID: PMC9585485 DOI: 10.1212/nxg.0000000000200025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/20/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives Clark-Baraitser syndrome is characterized by intellectual disability with or without autism spectrum disorders, speech delay, motor delay, behavioral abnormalities, and facial dysmorphism. It is caused by a heterozygous pathogenic variant in the thyroid hormone receptor interactor 12 (TRIP12) gene. However, loss of function and haploinsufficiency are the pathogenic mechanisms behind the TRIP12-related disorder. Methods We conducted an exome sequencing analysis for 2 unrelated patients with moderate intellectual disability, speech delay, and motor delay. Results We identified 2 de novo TRIP12 mutations in these 2 patients. One patient had a frameshift duplication, whereas the other had a synonymous variant. Both patients presented with common features of the syndrome, but clinical heterogeneity has been also observed between them. For the synonymous variant, reverse transcription PCR in RNA extracted from leukocytes demonstrated the presence of a truncated messenger RNA (mRNA) transcript that skipped exon 12. This transcript escapes degradation at the mRNA level. To assess the effect of the synonymous substitute on TRIP12 proteolytic activity, the expression of 9 known responsive genes at the mRNA level was measured, of which 3 genes were upregulated at least 2-fold in the patient. Discussion We reported 2 patients with Clark-Baraitser syndrome caused by novel synonymous and frameshift variants in the TRIP12 gene, and our study expands the mutation spectrum of the TRIP12 gene. This study will help to improve our understanding of variable phenotypic presentations in TRIP12-related disorders.
Collapse
|
25
|
Lessey LR, Robinson SC, Chaudhary R, Daniel JM. Adherens junction proteins on the move—From the membrane to the nucleus in intestinal diseases. Front Cell Dev Biol 2022; 10:998373. [PMID: 36274850 PMCID: PMC9581404 DOI: 10.3389/fcell.2022.998373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The function and structure of the mammalian epithelial cell layer is maintained by distinct intercellular adhesion complexes including adherens junctions (AJs), tight junctions, and desmosomes. The AJ is most integral for stabilizing cell-cell adhesion and conserving the structural integrity of epithelial tissues. AJs are comprised of the transmembrane protein E-cadherin and cytoplasmic catenin cofactors (α, β, γ, and p120-catenin). One organ where malfunction of AJ is a major contributor to disease states is the mammalian intestine. In the intestine, cell-cell adhesion complexes work synergistically to maintain structural integrity and homeostasis of the epithelium and prevent its malfunction. Consequently, when AJ integrity is compromised in the intestinal epithelium, the ensuing homeostatic disruption leads to diseases such as inflammatory bowel disease and colorectal carcinoma. In addition to their function at the plasma membrane, protein components of AJs also have nuclear functions and are thus implicated in regulating gene expression and intracellular signaling. Within the nucleus, AJ proteins have been shown to interact with transcription factors such as TCF/LEF and Kaiso (ZBTB33), which converge on the canonical Wnt signaling pathway. The multifaceted nature of AJ proteins highlights their complexity in modulating homeostasis and emphasizes the importance of their subcellular localization and expression in the mammalian intestine. In this review, we summarize the nuclear roles of AJ proteins in intestinal tissues; their interactions with transcription factors and how this leads to crosstalk with canonical Wnt signaling; and how nuclear AJ proteins are implicated in intestinal homeostasis and disease.
Collapse
|
26
|
Mu J, Yuan P, Luo J, Chen Y, Tian Y, Ding L, Zhao B, Wang X, Wang B, Liu L. Upregulated SPAG6 promotes acute myeloid leukemia progression through MYO1D that regulates the EGFR family expression. Blood Adv 2022; 6:5379-5394. [PMID: 35667090 PMCID: PMC9631693 DOI: 10.1182/bloodadvances.2021006920] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/02/2022] [Indexed: 11/20/2022] Open
Abstract
Chromosomal aberrations and gene mutations have been considered to be the major reasons for high recurrence rates and poor survival among acute myeloid leukemia (AML) patients. However, the underlying molecular mechanism of AML gene mutation remains largely unclear. Here, we show that SPAG6 (sperm-associated antigen 6), one of the most markedly increased SPAG genes in AML, significantly contributed to the proliferation and migration of leukemic cells. SPAG6 was highly expressed in AML, and its upregulation was negatively correlated with the prognosis of the disease. In vitro, SPAG6 promoted the proliferation and migration of leukemia cells and promoted cell cycle progression from the G1 phase to the S phase. In vivo, low expression of SPAG6 reduced the proliferation and infiltration of leukemia cells and prolonged the survival of xenograft tumor mice. Furthermore, immunoprecipitation and mass spectrometry analysis showed that SPAG6 interacts with MYO1D (myosin 1D). Specifically, overexpression of SPAG6 promoted the translocation of MYO1D into the cell membrane, thus upgrading the expression level of the EGFR family and thereby promoting the progression of AML. Overall, our study found that SPAG6 combined with MYO1D and translocated MYO1D from the cytosol to the cytomembrane, which induced the PI3K (phosphoinositide 3-kinase)/AKT (protein kinase B) signaling and ERK (extracellular signal-regulated kinase) signaling pathway to regulate the growth and prognosis of AML. SPAG6 may become a new target gene for the treatment of AML.
Collapse
Affiliation(s)
- Jiao Mu
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Yuan
- Department of Interventional Radiology and Pain Treatment, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Jie Luo
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yafan Chen
- Department of Human Movement Science, Xi’an Physical Education University, Xi’an, China
| | - Yiyuan Tian
- Department of Physiology, Medical College of Yan’an University, Yan’an, China; and
| | - Li Ding
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Beibei Zhao
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaocheng Wang
- Center of Clinical Aerospace Medicine, School of Aerospace Medicine, Key Laboratory of Aerospace Medicine of Ministry of Education
- Department of Aviation Medicine, The First Affiliated Hospital, and
| | - Bao Wang
- Tangdu Hospital, Department of Neurosurgery, Air Force Medical University, Xi’an, China
| | - Lin Liu
- Department of Hematology, and
- Laboratory Research Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
27
|
Rodriguez-Valbuena H, Gonzalez-Muñoz A, Cadavid LF. Multiple Alr genes exhibit allorecognition-associated variation in the colonial cnidarian Hydractinia. Immunogenetics 2022; 74:559-581. [PMID: 35761101 DOI: 10.1007/s00251-022-01268-3] [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: 03/26/2022] [Accepted: 06/19/2022] [Indexed: 11/25/2022]
Abstract
The genetics of allorecognition has been studied extensively in inbred lines of Hydractinia symbiolongicarpus, in which genetic control is attributed mainly to the highly polymorphic loci allorecognition 1 (Alr1) and allorecognition 2 (Alr2), located within the Allorecognition Complex (ARC). While allelic variation at Alr1 and Alr2 can predict the phenotypes in inbred lines, these two loci do not entirely predict the allorecognition phenotypes in wild-type colonies and their progeny, suggesting the presence of additional uncharacterized genes that are involved in the regulation of allorecognition in this species. Comparative genomics analyses were used to identify coding sequence differences from assembled chromosomal intervals of the ARC and from genomic scaffold sequences between two incompatible H. symbiolongicarpus siblings from a backcross population. New immunoglobulin superfamily (Igsf) genes are reported for the ARC, where five of these genes are closely related to the Alr1 and Alr2 genes, suggesting the presence of multiple Alr-like genes within this complex. Complementary DNA sequence evidence revealed that the allelic polymorphism of eight Igsf genes is associated with allorecognition phenotypes in a backcross population of H. symbiolongicarpus, yet that association was not found between parental colonies and their offspring. Alternative splicing was found as a mechanism that contributes to the variability of these genes by changing putative activating receptors to inhibitory receptors or generating secreted isoforms of allorecognition proteins. Our findings demonstrate that allorecognition in H. symbiolongicarpus is a multigenic phenomenon controlled by genetic variation in at least eight genes in the ARC complex.
Collapse
Affiliation(s)
- Henry Rodriguez-Valbuena
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia.
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Andrea Gonzalez-Muñoz
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Luis F Cadavid
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| |
Collapse
|
28
|
Lao L, Bourdeau I, Gagliardi L, He X, Shi W, Hao B, Tan M, Hu Y, Peng J, Coulombe B, Torpy DJ, Scott HS, Lacroix A, Luo H, Wu J. ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia. Nucleic Acids Res 2022; 50:6343-6367. [PMID: 35687106 PMCID: PMC9226510 DOI: 10.1093/nar/gkac483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 12/13/2022] Open
Abstract
ARMC5 is implicated in several pathological conditions, but its function remains unknown. We have previously identified CUL3 and RPB1 (the largest subunit of RNA polymerase II (Pol II) as potential ARMC5-interacting proteins. Here, we show that ARMC5, CUL3 and RBX1 form an active E3 ligase complex specific for RPB1. ARMC5, CUL3, and RBX1 formed an active E3 specific for RPB1. Armc5 deletion caused a significant reduction in RPB1 ubiquitination and an increase in an accumulation of RPB1, and hence an enlarged Pol II pool in normal tissues and organs. The compromised RPB1 degradation did not cause generalized Pol II stalling nor depressed transcription in the adrenal glands but did result in dysregulation of a subset of genes, with most upregulated. We found RPB1 to be highly expressed in the adrenal nodules from patients with primary bilateral macronodular adrenal hyperplasia (PBMAH) harboring germline ARMC5 mutations. Mutant ARMC5 had altered binding with RPB1. In summary, we discovered that wildtype ARMC5 was part of a novel RPB1-specific E3. ARMC5 mutations resulted in an enlarged Pol II pool, which dysregulated a subset of effector genes. Such an enlarged Pol II pool and gene dysregulation was correlated to adrenal hyperplasia in humans and KO mice.
Collapse
Affiliation(s)
- Linjiang Lao
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Isabelle Bourdeau
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Endocrinology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Lucia Gagliardi
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA5000, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA5006, Australia.,Endocrine and Diabetes Unit, Queen Elizabeth Hospital, Adelaide, SA5011, Australia
| | - Xiao He
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Wei Shi
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Bingbing Hao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yan Hu
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Junzheng Peng
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - David J Torpy
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA5000, Australia
| | - Hamish S Scott
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA5006, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, SA5001, Australia.,UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA5001, Australia
| | - Andre Lacroix
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Endocrinology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Hongyu Luo
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Jiangping Wu
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Nephrology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| |
Collapse
|
29
|
Structural and Functional Insights into GID/CTLH E3 Ligase Complexes. Int J Mol Sci 2022; 23:ijms23115863. [PMID: 35682545 PMCID: PMC9180843 DOI: 10.3390/ijms23115863] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Multi-subunit E3 ligases facilitate ubiquitin transfer by coordinating various substrate receptor subunits with a single catalytic center. Small molecules inducing targeted protein degradation have exploited such complexes, proving successful as therapeutics against previously undruggable targets. The C-terminal to LisH (CTLH) complex, also called the glucose-induced degradation deficient (GID) complex, is a multi-subunit E3 ligase complex highly conserved from Saccharomyces cerevisiae to humans, with roles in fundamental pathways controlling homeostasis and development in several species. However, we are only beginning to understand its mechanistic basis. Here, we review the literature of the CTLH complex from all organisms and place previous findings on individual subunits into context with recent breakthroughs on its structure and function.
Collapse
|
30
|
Patient with multiple morphological abnormalities of sperm flagella caused by a novel ARMC2 mutation has a favorable pregnancy outcome from intracytoplasmic sperm injection. J Assist Reprod Genet 2022; 39:1673-1681. [PMID: 35543806 DOI: 10.1007/s10815-022-02516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE To investigate the potential genetic cause in a primary infertility patient with multiple morphological abnormalities of sperm flagella (MMAF). METHODS The patient's sperm was observed by light and electron microscopy. Whole-exome sequencing (WES) was carried out to identify candidate genes. Then, the mutation found by WES was verified by Sanger sequencing. The proteins interacting with ARMC2 were revealed by co-immunoprecipitation (co-IP) and mass spectrometry. Intracytoplasmic sperm injection (ICSI) was carried out to achieve successful pregnancy. RESULTS Typical MMAF phenotype (absent, short, coiled, bent irregular flagella) was shown in the patient's sperm. A novel homozygous mutation in ARMC2 (c.1264C > T) was identified. The proteins interacting with ARMC2 we found were CEP78, PGAM5, RHOA, FXR1, and SKIV2L2. The ICSI therapy was successful, and boy-girl twins were given birth. CONCLUSION We found a novel mutation in ARMC2 which led to MMAF and male infertility. This is the first report of ICSI outcome of patient harboring ARMC2 mutation. The interacting proteins indicated that ARMC2 might be involved in multiple processes of spermatogenesis.
Collapse
|
31
|
Targeting β-catenin in acute myeloid leukaemia: past, present, and future perspectives. Biosci Rep 2022; 42:231097. [PMID: 35352805 PMCID: PMC9069440 DOI: 10.1042/bsr20211841] [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: 02/27/2022] [Revised: 03/14/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Acute myeloid leukaemia (AML) is an aggressive disease of the bone marrow with a poor prognosis. Evidence suggests long established chemotherapeutic regimens used to treat AML are reaching the limits of their efficacy, necessitating the urgent development of novel targeted therapies. Canonical Wnt signalling is an evolutionary conserved cascade heavily implicated in normal developmental and disease processes in humans. For over 15 years its been known that the central mediator of this pathway, β-catenin, is dysregulated in AML promoting the emergence, maintenance, and drug resistance of leukaemia stem cells. Yet, despite this knowledge, and subsequent studies demonstrating the therapeutic potential of targeting Wnt activity in haematological cancers, β-catenin inhibitors have not yet reached the clinic. The aim of this review is to summarise the current understanding regarding the role and mechanistic dysregulation of β-catenin in AML, and assess the therapeutic merit of pharmacologically targeting this molecule, drawing on lessons from other disease contexts.
Collapse
|
32
|
The Valuable Role of ARMC1 in Invasive Breast Cancer as a Novel Biomarker. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1740295. [PMID: 35378785 PMCID: PMC8976651 DOI: 10.1155/2022/1740295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Background Invasive breast carcinoma (BRCA) is a common type of breast cancer with a high clinical incidence. Thus, it is significant to find effective biomarkers for BRCA diagnosis and treatment. Although some members of armadillo (ARM) repeat family of proteins are confirmed to be biomarkers in cancers, the role of armadillo repeat-containing 1 (ARMC1) in BRCA remains unknown. Methods We firstly analyzed the ARMC1 expression in normal breast tissues and BRCA samples and its association with overall survival by the public database. Next, the χ2 test was used to evaluate the prognostic significance of ARMC1 expression in TCGA-BRCA patient samples. The ARMC1 mutations in BRCA were explored in the cBioportal database. Besides, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to explore the biological functions of ARMC1 in BRCA. Finally, immunohistochemistry and immunofluorescence staining were performed to validate the ARMC1 expression in BRCA. Results ARMC1 expression in tumor samples was significantly higher than that in normal tissues, and higher expression of ARMC1 was related to lower survival. Moreover, the tumor stage and histology of BRCA patients were associated with ARMC1 expression. ARMC1 genetic mutations occurred in 32% of BRCA patients, and the amplification and high expression of ARMC1 accounted for most of them. Furthermore, functional enrichment analysis suggested that ARMC1 might be involved in the cell cycle in BRCA. Ultimately, increased ARMC1 expression was found in clinical breast carcinoma tissues by our confirmatory experiments. Conclusions ARMC1 may play a significant role in BRCA and act as a biomarker, which provides valuable clues for the treatment and diagnosis of BRCA.
Collapse
|
33
|
Functional and Conformational Plasticity of an Animal Group 1 LEA Protein. Biomolecules 2022; 12:biom12030425. [PMID: 35327618 PMCID: PMC8946055 DOI: 10.3390/biom12030425] [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] [Received: 01/15/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 12/24/2022] Open
Abstract
Group 1 (Dur-19, PF00477, LEA_5) Late Embryogenesis Abundant (LEA) proteins are present in organisms from all three domains of life, Archaea, Bacteria, and Eukarya. Surprisingly, Artemia is the only genus known to include animals that express group 1 LEA proteins in their desiccation-tolerant life-history stages. Bioinformatics analysis of circular dichroism data indicates that the group 1 LEA protein AfLEA1 is surprisingly ordered in the hydrated state and undergoes during desiccation one of the most pronounced disorder-to-order transitions described for LEA proteins from A. franciscana. The secondary structure in the hydrated state is dominated by random coils (42%) and β-sheets (35%) but converts to predominately α-helices (85%) when desiccated. Interestingly, AfLEA1 interacts with other proteins and nucleic acids, and RNA promotes liquid–liquid phase separation (LLPS) of the protein from the solvent during dehydration in vitro. Furthermore, AfLEA1 protects the enzyme lactate dehydrogenase (LDH) during desiccation but does not aid in restoring LDH activity after desiccation-induced inactivation. Ectopically expressed in D. melanogaster Kc167 cells, AfLEA1 localizes predominantly to the cytosol and increases the cytosolic viscosity during desiccation compared to untransfected control cells. Furthermore, the protein formed small biomolecular condensates in the cytoplasm of about 38% of Kc167 cells. These findings provide additional evidence for the hypothesis that the formation of biomolecular condensates to promote water stress tolerance during anhydrobiosis may be a shared feature across several groups of LEA proteins that display LLPS behaviors.
Collapse
|
34
|
Aweya JJ, Zhuang K, Liu Y, Fan J, Yao D, Wang F, Chen X, Li S, Ma H, Zhang Y. The ARM repeat domain of hemocyanin interacts with MKK4 to modulate antimicrobial peptides expression. iScience 2022; 25:103958. [PMID: 35265821 PMCID: PMC8898971 DOI: 10.1016/j.isci.2022.103958] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 11/02/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) intracellular signaling pathway mediates numerous biological processes, including antimicrobial immune response by inducing antimicrobial peptides (AMPs) production. Although MAPK signaling cascade proteins have been identified in penaeid shrimp, their modulation via the MKK4-p38-c-Jun cascade and effect on AMPs production is unknown. Here, we show that hemocyanin (PvHMC), antimicrobial peptides (anti-lipopolysaccharide factor, crustin, and penaeidins), and MKK4-p38-c-Jun cascade proteins are simultaneously induced by pathogens (Vibrio parahaemolyticus, Staphylococcus aureus, and white spot syndrome virus) in Penaeus vannamei. Intriguingly, knockdown of PvHMC with or without pathogen challenge attenuated the expression of MKK4-p38-c-Jun cascade proteins and their phosphorylation level, which consequently decreased AMPs expression. Further analysis revealed that PvHMC interacts via its armadillo (ARM) repeat domain with PvMKK4 to modulate the p38 MAPK signaling pathway. Thus, the ARM repeat domain enables penaeid shrimp hemocyanin to modulate AMPs expression during antimicrobial response by activating the p38 MAPK signaling pathway. Pathogens induce hemocyanin, MKK4-p38-c-Jun proteins, and antimicrobial peptide genes Hemocyanin modulates MKK4-p38-c-Jun cascade proteins to regulate AMPs gene expression Hemocyanin interacts with MKK4 to modulate p38 MAPK signaling in penaeid shrimp Deletion of the ARM repeat domain attenuates the interaction of hemocyanin with MKK4
Collapse
|
35
|
Araiso Y, Imai K, Endo T. Role of the TOM Complex in Protein Import into Mitochondria: Structural Views. Annu Rev Biochem 2022; 91:679-703. [PMID: 35287471 DOI: 10.1146/annurev-biochem-032620-104527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are central to energy production, metabolism and signaling, and apoptosis. To make new mitochondria from preexisting mitochondria, the cell needs to import mitochondrial proteins from the cytosol into the mitochondria with the aid of translocators in the mitochondrial membranes. The translocase of the outer membrane (TOM) complex, an outer membrane translocator, functions as an entry gate for most mitochondrial proteins. Although high-resolution structures of the receptor subunits of the TOM complex were deposited in the early 2000s, those of entire TOM complexes became available only in 2019. The structural details of these TOM complexes, consisting of the dimer of the β-barrel import channel Tom40 and four α-helical membrane proteins, revealed the presence of several distinct paths and exits for the translocation of over 1,000 different mitochondrial precursor proteins. High-resolution structures of TOM complexes now open up a new era of studies on the structures, functions, and dynamics of the mitochondrial import system. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Yuhei Araiso
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan; .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| |
Collapse
|
36
|
Xu S, Zheng J, Xiao H, Wu R. Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells. Anal Chem 2022; 94:3343-3351. [PMID: 35132862 DOI: 10.1021/acs.analchem.1c05438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycoproteins with diverse glycans are essential to human cells, and subtle differences in glycan structures may result in entirely different functions. One typical example is proteins modified with O-linked β-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc) (the Tn antigen), in which the two glycans have very similar structures and identical chemical compositions, making them extraordinarily challenging to be distinguished. Here, we developed an effective method benefiting from selective enrichment and the enzymatic specificity to simultaneously identify and distinguish glycoproteins with O-GlcNAc and O-GalNAc. Metabolic labeling was combined with bioorthogonal chemistry for enriching glycoproteins modified with O-GlcNAc and O-GalNAc. Then, the enzymatic reaction with galactose oxidase was utilized to specifically oxidize O-GalNAc, but not O-GlcNAc, generating the different tags between glycopeptides with O-GlcNAc and O-GalNAc that can be easily distinguishable by mass spectrometry (MS). Among O-GlcNAcylated proteins commonly identified in three types of human cells, those related to transcription and RNA binding are highly enriched. Cell-specific features are also revealed. Among glycoproteins exclusively in Jurkat cells, those involved in human T-lymphotropic virus type 1 (HTLV-1) infection are overrepresented, which is consistent with the cell line source and suggests that protein O-GlcNAcylation participated in the response to the virus infection. Furthermore, glycoproteins with the Tn antigen have different subcellular distributions in different cells, which may be attributed to the distinct mechanisms for the formation of protein O-GalNAcylation.
Collapse
Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jiangnan Zheng
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
37
|
Yap YT, Li W, Zhou Q, Haj-Diab S, Chowdhury DD, Vaishnav A, Harding P, Williams DC, Edwards BF, Strauss JF, Zhang Z. The Ancient and Evolved Mouse Sperm-Associated Antigen 6 Genes Have Different Biologic Functions In Vivo. Cells 2022; 11:336. [PMID: 35159146 PMCID: PMC8834003 DOI: 10.3390/cells11030336] [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: 11/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
Sperm-associated antigen 6 (SPAG6) is the mammalian orthologue of Chlamydomonas PF16, an axonemal central pair protein involved in flagellar motility. In mice, two Spag6 genes have been identified. The ancestral gene, on mouse chromosome 2, is named Spag6. A related gene originally called Spag6, localized on mouse chromosome 16, evolved from the ancient Spag6 gene. It has been renamed Spag6-like (Spag6l). Spag6 encodes a 1.6 kb transcript consisting of 11 exons, while Spag6l encodes a 2.4 kb transcript which contains an additional non-coding exon in the 3'-end as well as the 11 exons found in Spag6. The two Spag6 genes share high similarities in their nucleotide and amino acid sequences. Unlike Spag6l mRNA, which is widely expressed, Spag6 mRNA expression is limited to a smaller number of tissues, including the testis and brain. In transfected mammalian cells, SPAG6/GFP is localized on microtubules, a similar localization as SPAG6L. A global Spag6l knockout mouse model was generated previously. In addition to a role in modulating the ciliary beat, SPAG6L has many unexpected functions, including roles in the regulation of ciliogenesis/spermatogenesis, hearing, and the immunological synapse, among others. To investigate the role of the ancient Spag6 gene, we phenotyped global Spag6 knockout mice. All homozygous mutant mice were grossly normal, and fertility was not affected in both males and females. The homozygous males had normal sperm parameters, including sperm number, motility, and morphology. Examination of testis histology revealed normal spermatogenesis. Testicular protein expression levels of selected SPAG6L binding partners, including SPAG16L, were not changed in the Spag6 knockout mice, even though the SPAG16L level was significantly reduced in the Spag6l knockout mice. Structural analysis of the two SPAG6 proteins shows that both adopt very similar folds, with differences in a few amino acids, many of which are solvent-exposed. These differences endow the two proteins with different functional characteristics, even though both have eight armadillo repeats that mediate protein-protein interaction. Our studies suggest that SPAG6 and SPAG6L have different functions in vivo, with the evolved SPAG6L protein being more important. Since the two proteins have some overlapping binding partners, SPAG6 could have functions that are yet to be identified.
Collapse
Affiliation(s)
- Yi Tian Yap
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
| | - Wei Li
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
| | - Qi Zhou
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
- Department of Occupational and Environmental Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430060, China
| | - Sarah Haj-Diab
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology & Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.D.C.); (A.V.); (B.F.E.)
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology & Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.D.C.); (A.V.); (B.F.E.)
| | - Pamela Harding
- Hypertension & Vascular Research Division, Henry Ford Health System, Detroit, MI 48201, USA;
| | - David C. Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Brian F. Edwards
- Department of Biochemistry, Microbiology & Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.D.C.); (A.V.); (B.F.E.)
| | - Jerome F. Strauss
- Center for Research on Reproduction and Women’s Health, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Zhibing Zhang
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (Y.T.Y.); (W.L.); (Q.Z.); (S.H.-D.)
- The C.S. Mott Center for Human Growth and Development, Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI 48201, USA
| |
Collapse
|
38
|
Huang Y, Jiang Z, Gao X, Luo P, Jiang X. ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases. Front Mol Biosci 2021; 8:791597. [PMID: 34912852 PMCID: PMC8666550 DOI: 10.3389/fmolb.2021.791597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Armadillo repeat-containing proteins (ARMCs) are widely distributed in eukaryotes and have important influences on cell adhesion, signal transduction, mitochondrial function regulation, tumorigenesis, and other processes. These proteins share a similar domain consisting of tandem repeats approximately 42 amino acids in length, and this domain constitutes a substantial platform for the binding between ARMCs and other proteins. An ARMC subfamily, including ARMC1∼10, ARMC12, and ARMCX1∼6, has received increasing attention. These proteins may have many terminal regions and play a critical role in various diseases. On the one hand, based on their similar central domain of tandem repeats, this ARMC subfamily may function similarly to other ARMCs. On the other hand, the unique domains on their terminals may cause these proteins to have different functions. Here, we focus on the ARMC subfamily (ARMC1∼10, ARMC12, and ARMCX1∼6), which is relatively conserved in vertebrates and highly conserved in mammals, particularly primates. We review the structures, biological functions, evolutions, interactions, and related diseases of the ARMC subfamily, which involve more than 30 diseases and 40 bypasses, including interactions and relationships between more than 100 proteins and signaling molecules. We look forward to obtaining a clearer understanding of the ARMC subfamily to facilitate further in-depth research and treatment of related diseases.
Collapse
Affiliation(s)
- Yutao Huang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zijian Jiang
- Department of Hepato-biliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiangyu Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
39
|
Ding L, Luo J, Zhang JP, Wang J, Li ZQ, Huang J, Chai L, Mu J, Zhao B, Zhong YR, Zhang LY, Liu L. Aberrant expression of SPAG6 may affect the disease phenotype and serve as a tumor biomarker in BCR/ABL1-negative myeloproliferative neoplasms. Oncol Lett 2021; 23:10. [PMID: 34820009 PMCID: PMC8607346 DOI: 10.3892/ol.2021.13128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022] Open
Abstract
Sperm-associated antigen 6 (SPAG6) is a newly identified cancer-testis antigen that has been revealed to contribute to the occurrence and development of various types of human cancer, such as ovarian, bladder, breast and lung cancer. However, to the best of our knowledge, the expression levels of SPAG6 in breakpoint cluster region (BCR)/ABL1-negative myeloproliferative neoplasms (MPNs) have not been investigated previously. Using reverse transcription-quantitative PCR and different tissue staining techniques, the present study revealed that SPAG6 was expressed by MPN cells, both at the mRNA and protein levels, and that nucleated erythroid precursors and megakaryocytes expressed the highest levels of SPAG6. In addition, SPAG6, which is known as a microtubule-associated protein, was found to exhibit nucleic, cytoplasmic or both cytoplasmic and nucleic subcellular localization patterns within the same patient or cell type; however, it did not always co-localize with β-tubulin. Furthermore, SPAG6 expression was revealed to be associated with fewer splenomegaly [P=0.015 for polycythemia vera (PV) and essential thrombocythemia (ET); and P=0.012 for primary myelofibrosis (PMF)] and myelofibrosis events (P=0.014 for PV and ET; and P=0.004 for PMF). In patients with PMF, upregulated expression levels of SPAG6 were also found to be associated with lower white blood cell counts (P=0.042) and lactate dehydrogenase levels (P=0.012), and higher hemoglobin levels (P=0.031) and platelet counts (P=0.025). In addition, the receiver operating characteristic curve analysis indicated that SPAG6 may be a potential biomarker for distinguishing MPN cases from healthy individuals. In conclusion, to the best of our knowledge, the present study is the first to report that aberrant SPAG6 expression may affect the disease phenotype and serve as a tumor biomarker in BCR/ABL1-negative MPNs.
Collapse
Affiliation(s)
- Li Ding
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China.,Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jie Luo
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Jing Ping Zhang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Ji Wang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhao Quan Li
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Juan Huang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Li Chai
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jiao Mu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Beibei Zhao
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Yi Rui Zhong
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Lin Yi Zhang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Lin Liu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| |
Collapse
|
40
|
Khan I, Dil S, Zhang H, Zhang B, Khan T, Zeb A, Zhou J, Nawaz S, Zubair M, Khan K, Ma H, Shi Q. A novel stop-gain mutation in ARMC2 is associated with multiple morphological abnormalities of the sperm flagella. Reprod Biomed Online 2021; 43:913-919. [PMID: 34493464 DOI: 10.1016/j.rbmo.2021.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/23/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
RESEARCH QUESTION Male infertility is a global issue worldwide and multiple morphological abnormalities of the sperm flagella (MMAF) is one of the most severe forms of the qualitative sperm defects with a heterogeneous genetic cause that has not been completely understood. Can whole-exome sequencing (WES) reveal novel genetic causes contributing to MMAF in a consanguineous Pakistani family, comprising three infertile brothers? DESIGN WES and bioinformatic analysis were conducted to screen potential pathogenic variants. The identified variant was validated by Sanger sequencing in all available family members Transmission electron microscopy analyses was carried out to examine the flagella ultrastructure of spermatozoa from patient. RESULTS WES and Sanger sequencing identified a novel homozygous stop-gain mutation (ENST00000392644.4, c.182C>G, p.S61X) in ARMC2, which is expected to lead to loss of protein functions. Transmission electron microscopy analyses revealed that the flagellar ultrastructure of the patient's spermatozoa was disorganized along with a complete absence of central pair complex (CPC), suggesting that ARMC2 is involved in the assembly, stability of the axonemal complex, or both, particularly the CPC. CONCLUSION We report that a familial stop-gain mutation in ARMC2 is associated with male infertility in humans caused by MMAF accompanied with loss of CPCs and axonemal disorganization. We provide genetic evidence that ARMC2 is essential for human spermatogenesis and its mutation may be pathogenic for MMAF. These findings will improve the knowledge about the genetic basis of MMAF and provide information for genetic counselling of this disease.
Collapse
Affiliation(s)
- Ihsan Khan
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Sobia Dil
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Huan Zhang
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Beibei Zhang
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Teka Khan
- Bond life sciences Center, University of Missouri 65211, Columbia Missouri, USA
| | - Aurang Zeb
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Jianteng Zhou
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Shoaib Nawaz
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Zubair
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Khalid Khan
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China
| | - Hui Ma
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China.
| | - Qinghua Shi
- First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center of Genetics and Development, University of Science and Technology of China, Hefei 230027, China.
| |
Collapse
|
41
|
Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane. Int J Mol Sci 2021; 22:ijms22179455. [PMID: 34502365 PMCID: PMC8431560 DOI: 10.3390/ijms22179455] [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: 08/01/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 11/28/2022] Open
Abstract
Plant U-box armadillo repeat (PUB-ARM) ubiquitin (Ub) ligases have important functions in plant defense through the ubiquitination of target proteins. Defense against pathogens involves vesicle trafficking and the formation of extracellular vesicles. The PUB-ARM protein SENESCENCE ASSOCIATED UBIQUITIN E3 LIGASE1 (SAUL1) can form patches at the plasma membrane related to tethering multi-vesicular bodies (MVBs) to the plasma membrane. We uncovered the structure of a full-length plant ubiquitin ligase and the structural requirements of SAUL1, which are crucial for its function in patch formation. We resolved the structure of SAUL1 monomers by small-angle X-ray scattering (SAXS). The SAUL1 model showed that SAUL1 consists of two domains: a domain containing the N-terminal U-box and armadillo (ARM) repeats and the C-terminal ARM repeat domain, which includes a positively charged groove. We showed that all C-terminal ARM repeats are essential for patch formation and that this function requires arginine residue at position 736. By applying SAXS to polydisperse SAUL1 systems, the oligomerization of SAUL1 is detectable, with SAUL1 tetramers being the most prominent oligomers at higher concentrations. The oligomerization domain consists of the N-terminal U-box and some N-terminal ARM repeats. Deleting the U-box resulted in the promotion of the SAUL1 tethering function. Our findings indicate that structural changes in SAUL1 may be fundamental to its function in forming patches at the plasma membrane.
Collapse
|
42
|
Hu JH, Chang JW, Xu T, Wang J, Wang X, Lin R, Duanmu D, Liu L. Structural basis of bilin binding by the chlorophyll biosynthesis regulator GUN4. Protein Sci 2021; 30:2083-2091. [PMID: 34382282 DOI: 10.1002/pro.4164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/05/2022]
Abstract
The chlorophyll biosynthesis regulator GENOMES UNCOUPLED 4 (GUN4) is conserved in nearly all oxygenic photosynthetic organisms. Recently, GUN4 has been found to be able to bind the linear tetrapyrroles (bilins) and stimulate the magnesium chelatase activity in the unicellular green alga Chlamydomonas reinhardtii. Here, we characterize GUN4 proteins from Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 for their ability to bind bilins, and present the crystal structures of Synechocystis GUN4 in biliverdin-bound, phycocyanobilin-bound, and phytochromobilin-bound forms at the resolutions of 1.05, 1.10, and 1.70 Å, respectively. These linear molecules adopt a cyclic-helical conformation, and bind more tightly than planar porphyrins to the tetrapyrrole-binding pocket of GUN4. Based on structural comparison, we propose a working model of GUN4 in regulation of tetrapyrrole biosynthetic pathway, and address the role of the bilin-bound GUN4 in retrograde signaling.
Collapse
Affiliation(s)
- Jiu-Hui Hu
- School of Life Sciences, Anhui University, Hefei, China
| | | | - Tao Xu
- School of Life Sciences, Anhui University, Hefei, China
| | - Jia Wang
- School of Life Sciences, Anhui University, Hefei, China.,Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao Wang
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
| |
Collapse
|
43
|
Edogbanya J, Tejada-Martinez D, Jones NJ, Jaiswal A, Bell S, Cordeiro R, van Dam S, Rigden DJ, de Magalhães JP. Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. Cell Mol Life Sci 2021; 78:4365-4376. [PMID: 33625522 PMCID: PMC8164572 DOI: 10.1007/s00018-021-03789-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/28/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
The C1ORF112 gene initially drew attention when it was found to be strongly co-expressed with several genes previously associated with cancer and implicated in DNA repair and cell cycle regulation, such as RAD51 and the BRCA genes. The molecular functions of C1ORF112 remain poorly understood, yet several studies have uncovered clues as to its potential functions. Here, we review the current knowledge on C1ORF112 biology, its evolutionary history, possible functions, and its potential relevance to cancer. C1ORF112 is conserved throughout eukaryotes, from plants to humans, and is very highly conserved in primates. Protein models suggest that C1ORF112 is an alpha-helical protein. Interestingly, homozygous knockout mice are not viable, suggesting an essential role for C1ORF112 in mammalian development. Gene expression data show that, among human tissues, C1ORF112 is highly expressed in the testes and overexpressed in various cancers when compared to healthy tissues. C1ORF112 has also been shown to have altered levels of expression in some tumours with mutant TP53. Recent screens associate C1ORF112 with DNA replication and reveal possible links to DNA damage repair pathways, including the Fanconi anaemia pathway and homologous recombination. These insights provide important avenues for future research in our efforts to understand the functions and potential disease relevance of C1ORF112.
Collapse
Affiliation(s)
- Jacob Edogbanya
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Daniela Tejada-Martinez
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- Programa de Doctorado en Ciencias mención Ecología Y Evolución, Facultad de Ciencias, Instituto de Ciencias Ambientales Y Evolutivas, Universidad Austral de Chile, Valdivia, 5090000, Chile
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Nigel J Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Amit Jaiswal
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sarah Bell
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rui Cordeiro
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Sipko van Dam
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Ancora Health, Herestraat 106, 9711 LM, Groningen, The Netherlands
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK.
| |
Collapse
|
44
|
Gallardi D, Xue X, Mercier E, Mills T, Lefebvre F, Rise ML, Murray HM. RNA-seq analysis of the mantle transcriptome from Mytilus edulis during a seasonal spawning event in deep and shallow water culture sites on the northeast coast of Newfoundland, Canada. Mar Genomics 2021; 60:100865. [PMID: 33933383 DOI: 10.1016/j.margen.2021.100865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/23/2021] [Accepted: 03/15/2021] [Indexed: 11/29/2022]
Abstract
The blue mussel (Mytilus edulis) has global commercial and ecological importance both in wild and cultured conditions. However there is a qualitative and quantitative lack of knowledge of the molecular mechanisms associated with its reproductive physiology, especially with reference to environmental interactions. Here we initiated a transcriptomic analysis (RNA-sequencing (RNA-seq)) of the mantle from both sexes sampled during a seasonal spawning event and from two culture depths (shallow-5 m; deep- 15 m). Mantle libraries were produced from 3 males and 3 females sampled from each of two shallow sites and two deep sites for a total of 12 replicate male and 12 replicate female libraries (24 total libraries). Overall a total of 2.3 billion raw 100 base reads with an average of 96.5 million reads/library were obtained and assembled into 296,118 transcripts with an average length of 568 bp. Overall, 315 transcripts from male libraries and 25 from female libraries were found to be upregulated in deep water as compared to shallow (edgeR adjusted p value ≤ 0.05). Conversely, 126 transcripts from male libraries and 135 from female libraries were found to be significantly downregulated at the same depth. Thirteen transcripts were selected for qPCR validation based on importance in reproduction, antimicrobial defense and metabolism. Of these, 9 RNA-seq identified transcripts were shown by qPCR to be differentially expressed between groups: 2 were upregulated in deep compared with shallow water (dhx38, mt-co1), 2 were upregulated for female compared with male mantle (pias2, mapkap1) and 6 genes (fndc3a, acbd3, klhl10, ccnb3, armc4, mt-co1) showed to be upregulated in males compared to females. The majority of qPCR studied transcripts were identified as involved in gamete development based on the UniProt database. This study further characterizes the importance of the mantle transcriptome during reproductive activities of M. edulis.
Collapse
Affiliation(s)
- Daria Gallardi
- Fisheries and Oceans Canada, 80 East White Hills Road, PO Box 5667, St. John's, NL A1C 5X1, Canada.
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Eloi Mercier
- Canadian Centre for Computational Genomics - Montreal Node, McGill University and Genome Quebec Innovation Center, 740 Dr. Penfield Avenue, Montréal, Québec H3A 0G1, Canada
| | - Terry Mills
- Norlantic Processors Limited, P.O. Box 381, Botwood, NL A0H 1E0, Canada
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics - Montreal Node, McGill University and Genome Quebec Innovation Center, 740 Dr. Penfield Avenue, Montréal, Québec H3A 0G1, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Harry M Murray
- Fisheries and Oceans Canada, 80 East White Hills Road, PO Box 5667, St. John's, NL A1C 5X1, Canada
| |
Collapse
|
45
|
Figley MD, Gu W, Nanson JD, Shi Y, Sasaki Y, Cunnea K, Malde AK, Jia X, Luo Z, Saikot FK, Mosaiab T, Masic V, Holt S, Hartley-Tassell L, McGuinness HY, Manik MK, Bosanac T, Landsberg MJ, Kerry PS, Mobli M, Hughes RO, Milbrandt J, Kobe B, DiAntonio A, Ve T. SARM1 is a metabolic sensor activated by an increased NMN/NAD + ratio to trigger axon degeneration. Neuron 2021; 109:1118-1136.e11. [PMID: 33657413 PMCID: PMC8174188 DOI: 10.1016/j.neuron.2021.02.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/15/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022]
Abstract
Axon degeneration is a central pathological feature of many neurodegenerative diseases. Sterile alpha and Toll/interleukin-1 receptor motif-containing 1 (SARM1) is a nicotinamide adenine dinucleotide (NAD+)-cleaving enzyme whose activation triggers axon destruction. Loss of the biosynthetic enzyme NMNAT2, which converts nicotinamide mononucleotide (NMN) to NAD+, activates SARM1 via an unknown mechanism. Using structural, biochemical, biophysical, and cellular assays, we demonstrate that SARM1 is activated by an increase in the ratio of NMN to NAD+ and show that both metabolites compete for binding to the auto-inhibitory N-terminal armadillo repeat (ARM) domain of SARM1. We report structures of the SARM1 ARM domain bound to NMN and of the homo-octameric SARM1 complex in the absence of ligands. We show that NMN influences the structure of SARM1 and demonstrate via mutagenesis that NMN binding is required for injury-induced SARM1 activation and axon destruction. Hence, SARM1 is a metabolic sensor responding to an increased NMN/NAD+ ratio by cleaving residual NAD+, thereby inducing feedforward metabolic catastrophe and axonal demise.
Collapse
Affiliation(s)
- Matthew D Figley
- Department of Developmental Biology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Yo Sasaki
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA
| | - Katie Cunnea
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK; Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Forhad K Saikot
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Helen Y McGuinness
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mohammad K Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Todd Bosanac
- Disarm Therapeutics, a wholly owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Philip S Kerry
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK; Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Mehdi Mobli
- Centre for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert O Hughes
- Disarm Therapeutics, a wholly owned subsidiary of Eli Lilly & Co., Cambridge, MA, USA
| | - Jeffrey Milbrandt
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.
| |
Collapse
|
46
|
Cheng C, Pei X, Li SW, Yang J, Li C, Tang J, Hu K, Huang G, Min WP, Sang Y. CRISPR/Cas9 library screening uncovered methylated PKP2 as a critical driver of lung cancer radioresistance by stabilizing β-catenin. Oncogene 2021; 40:2842-2857. [PMID: 33742119 DOI: 10.1038/s41388-021-01692-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Radiation resistance is a major cause of lung cancer treatment failure. Armadillo (ARM) superfamily proteins participate in various fundamental cellular processes; however, whether ARM proteins regulate radiation resistance is not fully understood. Here, we used an unbiased CRISPR/Cas9 library screen and identified plakophilin 2 (PKP2), a member of the ARM superfamily of proteins, as a critical driver of radiation resistance in lung cancer. The PKP2 level was significantly higher after radiotherapy than before radiotherapy, and high PKP2 expression after radiotherapy predicted poor overall survival (OS) and postprogression survival (PPS). Mechanistically, mass spectrometry analysis identified that PKP2 was methylated at the arginine site and interacted with protein arginine methyltransferase 1 (PRMT1). Methylation of PKP2 by PRMT1 stabilized β-catenin by recruiting USP7, further inducing LIG4, a key DNA ligase in nonhomologous end-joining (NHEJ) repair. Concomitantly, PKP2-induced radioresistance depended on facilitating LIG4-mediated NHEJ repair in lung cancer. More strikingly, after exposure to irradiation, treatment with the PRMT1 inhibitor C-7280948 abolished PKP2-induced radioresistance, and C-7280948 is a potential radiosensitizer in lung cancer. In summary, our results demonstrate that targeting the PRMT1/PKP2/β-catenin/LIG4 pathway is an effective approach to overcome radiation resistance in lung cancer.
Collapse
Affiliation(s)
- Chun Cheng
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaofeng Pei
- Department of Thoracic Oncology, The Cancer Center of the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Si-Wei Li
- Department of Oncology, Tongji Huangzhou Hospital of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Yang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chenxi Li
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianjun Tang
- Department of Respiratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guofu Huang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei-Ping Min
- Department of Surgery, Pathology and Oncology, University of Western Ontario, London, ON, Canada
| | - Yi Sang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| |
Collapse
|
47
|
Marondedze C, Elia G, Thomas L, Wong A, Gehring C. Citrullination of Proteins as a Specific Response Mechanism in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:638392. [PMID: 33897727 PMCID: PMC8060559 DOI: 10.3389/fpls.2021.638392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/17/2021] [Indexed: 05/19/2023]
Abstract
Arginine deimination, also referred to as citrullination of proteins by L-arginine deiminases, is a post-translational modification affecting histone modifications, epigenetic transcriptional regulation, and proteolysis in animals but has not been reported in higher plants. Here we report, firstly, that Arabidopsis thaliana proteome contains proteins with a specific citrullination signature and that many of the citrullinated proteins have nucleotide-binding regulatory functions. Secondly, we show that changes in the citrullinome occur in response to cold stress, and thirdly, we identify an A. thaliana protein with peptidyl arginine deiminase activity that was shown to be calcium-dependent for many peptide substrates. Taken together, these findings establish this post-translational modification as a hitherto neglected component of cellular reprogramming during stress responses.
Collapse
Affiliation(s)
- Claudius Marondedze
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Rijk Zwaan, De Lier, Netherlands
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
- Claudius Marondedze,
| | - Giuliano Elia
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Ludivine Thomas
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center of Wenzhou-Kean University, Wenzhou, China
| | - Chris Gehring
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
- *Correspondence: Chris Gehring,
| |
Collapse
|
48
|
Bhardwaj E, Lal M, Anand S, Das S. Independent recurrent evolution of MICRORNA genes converging onto similar non-canonical organisation across green plant lineages is driven by local and segmental duplication events in species, family and lineages. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110661. [PMID: 33218629 DOI: 10.1016/j.plantsci.2020.110661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The relationship between evolutionary history, organisation and transcriptional regulation of genes are intrinsically linked. These have been well studied in canonically organised protein-coding genes but not of MIRNAs. In the present study, we investigated the non-canonical arrangement of MIRNAs across taxonomic boundaries from algae to angiosperms employing a combination of genome organization, phylogeny and synteny. We retrieved the complete dataset of MIRNA from twenty-five species to identify and classify based on organisational patterns. The median size of cluster was between 2-5 kb and between 1-20 % of all MIRNAs are organized in head-to-head (with bidirectional promoter), head-to-tail (tandem), and overlapping manner. Although majority of the clusters are composed of MIRNA homologs, 25% of all clusters comprises of non-homologous genes with a potential of generating functional and regulatory complexity. A comparison of phylogeny and organizational patterns revealed that multiple independent events, some of which are species-specific, and some ancient, in different lineages, are responsible for non-canonical organization. Detailed investigation of MIR395 family across the plants revealed a complex origin of non-canonical arrangement through ancient and recent, segmental and local duplications; analysis of MIR399 family revealed major expansion occurred prior to monocot-dicot split, with few lineage-specific events. Evolution of "convergent" organization pattern of non-canonical arrangement originating from independent loci through recurrent event highlights our poor understanding of evolutionary process of MIRNA genes. The present investigation thus paves way for comparative functional genomics to understand the role of non-canonical organization on transcriptional regulation and regulatory diversity in MIRNA gene families.
Collapse
Affiliation(s)
- Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - S Anand
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India.
| |
Collapse
|
49
|
Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut ( Arachis hypogaea L.). Genes (Basel) 2020; 11:genes11121402. [PMID: 33255801 PMCID: PMC7761091 DOI: 10.3390/genes11121402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/24/2023] Open
Abstract
Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and a synthetic wild allotetraploid (Arachis ipaensis × Arachis duranensis)4x. In the AB-QTL population, a major QTL for pod and seed size was detected in a ~5 Mb interval in the proximal region of chromosome A07. In the CSSL population, the line 12CS_091, which carries the QTL region and that produces smaller pods and seeds than Fleur11, was identified. In this study, we used a two-step strategy to fine-map the seed size QTL region on chromosome A07. We developed new SSR and SNP markers, as well as near-isogenic lines (NILs) in the target QTL region. We first located the QTL in ~1 Mb region between two SSR markers, thanks to the genotyping of a large F2 population of 2172 individuals and a single marker analysis approach. We then used nine new SNP markers evenly distributed in the refined QTL region to genotype 490 F3 plants derived from 88 F2, and we selected 10 NILs. The phenotyping of the NILs and marker/trait association allowed us to narrowing down the QTL region to a 168.37 kb chromosome segment, between the SNPs Aradu_A07_1148327 and Aradu_A07_1316694. This region contains 22 predicted genes. Among these genes, Aradu.DN3DB and Aradu.RLZ61, which encode a transcriptional regulator STERILE APETALA-like (SAP) and an F-box SNEEZY (SNE), respectively, were of particular interest. The function of these genes in regulating the variation of fruit and seed size is discussed. This study will contribute to a better knowledge of genes that have been targeted during peanut domestication.
Collapse
|
50
|
Zhang JH, Yuan H, Wang X, Dai HE, Zhang M, Liu L. Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis. Proteins 2020; 89:462-467. [PMID: 33210347 DOI: 10.1002/prot.26023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/01/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022]
Abstract
Cobaltochelatase in aerobic cobalamin biosynthesis is a complex composed of three subunits. The large subunit CobN is a 140-kDa protein and is homologous to the ChlH subunit of magnesium chelatase. Previously we have reported the 2.5-Å structure of a cyanobacterial ChlH. Here we present the 1.8-Å structure of CobN from Mycobacterium tuberculosis. The overall structure of CobN and ChlH is similar, but significant difference occurs in the head domain. Structural comparison of domains between the two proteins unravels candidate regions for substrate binding and helps to locate a triad of residues that may be essential for metal ion binding.
Collapse
Affiliation(s)
- Jia-Hui Zhang
- School of Life Sciences, Anhui University, Hefei, China
| | - Hui Yuan
- School of Life Sciences, Anhui University, Hefei, China
| | - Xiao Wang
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
| | - Huai-En Dai
- School of Life Sciences, Anhui University, Hefei, China
| | - Min Zhang
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, China.,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
| |
Collapse
|