1
|
Blazie SM, Fortunati D, Zhao Y, Jin Y. C. elegans LIN-66 mediates EIF-3/eIF3-dependent protein translation via a cold-shock domain. Life Sci Alliance 2024; 7:e202402673. [PMID: 38886018 PMCID: PMC11184513 DOI: 10.26508/lsa.202402673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Protein translation initiation is a conserved process involving many proteins acting in concert. The 13 subunit eukaryotic initiation factor 3 (eIF3) complex is essential for assembly of the pre-initiation complex that scans mRNA and positions ribosome at the initiation codon. We previously reported that a gain-of-function (gf) mutation affecting the G subunit of the Caenorhabditis elegans eIF3 complex, eif-3.g(gf), selectively modulates protein translation in the ventral cord cholinergic motor neurons. Here, through unbiased genetic suppressor screening, we identified that the gene lin-66 mediates eif-3.g(gf)-dependent protein translation in motor neurons. LIN-66 is composed largely of low-complexity amino acid sequences with unknown functional domains. We combined bioinformatics analysis with in vivo functional dissection and identified a cold-shock domain in LIN-66 critical for its function. In cholinergic motor neurons, LIN-66 shows a close association with EIF-3.G in the cytoplasm. The low-complexity amino acid sequences of LIN-66 modulate its subcellular pattern. As cold-shock domains function broadly in RNA regulation, we propose that LIN-66 mediates stimulus-dependent protein translation by facilitating the interaction of mRNAs with EIF-3.G.
Collapse
Affiliation(s)
- Stephen M Blazie
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Fortunati
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yan Zhao
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
2
|
Modic M, Kuret K, Steinhauser S, Faraway R, van Genderen E, Ruiz de Los Mozos I, Novljan J, Vičič Ž, Lee FCY, Ten Berge D, Luscombe NM, Ule J. Poised PABP-RNA hubs implement signal-dependent mRNA decay in development. Nat Struct Mol Biol 2024:10.1038/s41594-024-01363-x. [PMID: 39054355 DOI: 10.1038/s41594-024-01363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Signaling pathways drive cell fate transitions largely by changing gene expression. However, the mechanisms for rapid and selective transcriptome rewiring in response to signaling cues remain elusive. Here we use deep learning to deconvolve both the sequence determinants and the trans-acting regulators that trigger extracellular signal-regulated kinase (ERK)-mitogen-activated protein kinase kinase (MEK)-induced decay of the naive pluripotency mRNAs. Timing of decay is coupled to embryo implantation through ERK-MEK phosphorylation of LIN28A, which repositions pLIN28A to the highly A+U-rich 3' untranslated region (3'UTR) termini of naive pluripotency mRNAs. Interestingly, these A+U-rich 3'UTR termini serve as poly(A)-binding protein (PABP)-binding hubs, poised for signal-induced convergence with LIN28A. The multivalency of AUU motifs determines the efficacy of pLIN28A-PABP convergence, which enhances PABP 3'UTR binding, decreases the protection of poly(A) tails and activates mRNA decay to enable progression toward primed pluripotency. Thus, the signal-induced convergence of LIN28A with PABP-RNA hubs drives the rapid selection of naive mRNAs for decay, enabling the transcriptome remodeling that ensures swift developmental progression.
Collapse
Affiliation(s)
- Miha Modic
- The Francis Crick Institute, London, UK.
- UK Dementia Research Institute at King's College London, London, UK.
- National Institute of Chemistry, Ljubljana, Slovenia.
| | - Klara Kuret
- The Francis Crick Institute, London, UK
- National Institute of Chemistry, Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | | | - Rupert Faraway
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Emiel van Genderen
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Jona Novljan
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Žiga Vičič
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Flora C Y Lee
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Jernej Ule
- The Francis Crick Institute, London, UK.
- UK Dementia Research Institute at King's College London, London, UK.
- National Institute of Chemistry, Ljubljana, Slovenia.
| |
Collapse
|
3
|
Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
Collapse
Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| |
Collapse
|
4
|
Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA. eLife 2024; 13:RP94800. [PMID: 38739430 PMCID: PMC11090510 DOI: 10.7554/elife.94800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with three distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
Collapse
Affiliation(s)
- Ryan T Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| |
Collapse
|
5
|
Wang S, Sun H, Chen G, Wu C, Sun B, Lin J, Lin D, Zeng D, Lin B, Huang G, Lu X, Lin H, Liang Y. RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities. Crit Rev Oncol Hematol 2024; 195:104271. [PMID: 38272151 DOI: 10.1016/j.critrevonc.2024.104271] [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: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.
Collapse
Affiliation(s)
- Shimeng Wang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Hexing Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Guanyuan Chen
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Chengyu Wu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Bingmei Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Jiajia Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Danping Lin
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - Baohang Lin
- Department of Thyroid, Breast and Vascular Surgery, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Xiaofeng Lu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Haoyu Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| | - Yuanke Liang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| |
Collapse
|
6
|
Brandt S, Bernhardt A, Häberer S, Wolters K, Gehringer F, Reichardt C, Krause A, Geffers R, Kahlfuß S, Jeron A, Bruder D, Lindquist JA, Isermann B, Mertens PR. Comparative Analysis of Acute Kidney Injury Models and Related Fibrogenic Responses: Convergence on Methylation Patterns Regulated by Cold Shock Protein. Cells 2024; 13:367. [PMID: 38474331 DOI: 10.3390/cells13050367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/02/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Fibrosis is characterized by excessive extracellular matrix formation in solid organs, disrupting tissue architecture and function. The Y-box binding protein-1 (YB-1) regulates fibrosis-related genes (e.g., Col1a1, Mmp2, and Tgfβ1) and contributes significantly to disease progression. This study aims to identify fibrogenic signatures and the underlying signaling pathways modulated by YB-1. METHODS Transcriptomic changes associated with matrix gene patterns in human chronic kidney diseases and murine acute injury models were analyzed with a focus on known YB-1 targets. Ybx1-knockout mouse strains (Ybx1ΔRosaERT+TX and Ybx1ΔLysM) were subjected to various kidney injury models. Fibrosis patterns were characterized by histopathological staining, transcriptome analysis, qRT-PCR, methylation analysis, zymography, and Western blotting. RESULTS Integrative transcriptomic analyses revealed that YB-1 is involved in several fibrogenic signatures related to the matrisome, the WNT, YAP/TAZ, and TGFß pathways, and regulates Klotho expression. Changes in the methylation status of the Klotho promoter by specific methyltransferases (DNMT) are linked to YB-1 expression, extending to other fibrogenic genes. Notably, kidney-resident cells play a significant role in YB-1-modulated fibrogenic signaling, whereas infiltrating myeloid immune cells have a minimal impact. CONCLUSIONS YB-1 emerges as a master regulator of fibrogenesis, guiding DNMT1 to fibrosis-related genes. This highlights YB-1 as a potential target for epigenetic therapies interfering in this process.
Collapse
Affiliation(s)
- Sabine Brandt
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Anja Bernhardt
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Saskia Häberer
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Katharina Wolters
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Fabian Gehringer
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Charlotte Reichardt
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Anna Krause
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sascha Kahlfuß
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Andreas Jeron
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Research Group Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dunja Bruder
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Research Group Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Jonathan A Lindquist
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig University, 04103 Leipzig, Germany
| | - Peter R Mertens
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| |
Collapse
|
7
|
Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.31.551357. [PMID: 37790407 PMCID: PMC10542128 DOI: 10.1101/2023.07.31.551357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote CoCoNuTs (coiled-coil nuclease tandems) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with 3 distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.
Collapse
Affiliation(s)
- Ryan T. Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
8
|
Cardoza E, Singh H. From Stress Tolerance to Virulence: Recognizing the Roles of Csps in Pathogenicity and Food Contamination. Pathogens 2024; 13:69. [PMID: 38251376 PMCID: PMC10819108 DOI: 10.3390/pathogens13010069] [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: 10/30/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Be it for lab studies or real-life situations, bacteria are constantly exposed to a myriad of physical or chemical stresses that selectively allow the tolerant to survive and thrive. In response to environmental fluctuations, the expression of cold shock domain family proteins (Csps) significantly increases to counteract and help cells deal with the harmful effects of stresses. Csps are, therefore, considered stress adaptation proteins. The primary functions of Csps include chaperoning nucleic acids and regulating global gene expression. In this review, we focus on the phenotypic effects of Csps in pathogenic bacteria and explore their involvement in bacterial pathogenesis. Current studies of csp deletions among pathogenic strains indicate their involvement in motility, host invasion and stress tolerance, proliferation, cell adhesion, and biofilm formation. Through their RNA chaperone activity, Csps regulate virulence-associated genes and thereby contribute to bacterial pathogenicity. Additionally, we outline their involvement in food contamination and discuss how foodborne pathogens utilize the stress tolerance roles of Csps against preservation and sanitation strategies. Furthermore, we highlight how Csps positively and negatively impact pathogens and the host. Overall, Csps are involved in regulatory networks that influence the expression of genes central to stress tolerance and virulence.
Collapse
Affiliation(s)
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University, Vile Parle West, Mumbai 400056, India
| |
Collapse
|
9
|
Maklad A, Sedeeq M, Chan KM, Gueven N, Azimi I. Exploring Lin28 proteins: Unravelling structure and functions with emphasis on nervous system malignancies. Life Sci 2023; 335:122275. [PMID: 37984514 DOI: 10.1016/j.lfs.2023.122275] [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: 07/11/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Cancer and stem cells share many characteristics related to self-renewal and differentiation. Both cell types express the same critical proteins that govern cellular stemness, which provide cancer cells with the growth and survival benefits of stem cells. LIN28 is an example of one such protein. LIN28 includes two main isoforms, LIN28A and LIN28B, with diverse physiological functions from tissue development to control of pluripotency. In addition to their physiological roles, LIN28A and LIN28B affect the progression of several cancers by regulating multiple cancer hallmarks. Altered expression levels of LIN28A and LIN28B have been proposed as diagnostic and/or prognostic markers for various malignancies. This review discusses the structure and modes of action of the different LIN28 proteins and examines their roles in regulating cancer hallmarks with a focus on malignancies of the nervous system. This review also highlights some gaps in the field that require further exploration to assess the potential of targeting LIN28 proteins for controlling cancer.
Collapse
Affiliation(s)
- Ahmed Maklad
- School of Pharmacy and Pharmacology, College of Health and Medicine, University of Tasmania, Hobart 7005, Tasmania, Australia
| | - Mohammed Sedeeq
- School of Pharmacy and Pharmacology, College of Health and Medicine, University of Tasmania, Hobart 7005, Tasmania, Australia
| | - Kai Man Chan
- School of Pharmacy and Pharmacology, College of Health and Medicine, University of Tasmania, Hobart 7005, Tasmania, Australia
| | - Nuri Gueven
- School of Pharmacy and Pharmacology, College of Health and Medicine, University of Tasmania, Hobart 7005, Tasmania, Australia
| | - Iman Azimi
- School of Pharmacy and Pharmacology, College of Health and Medicine, University of Tasmania, Hobart 7005, Tasmania, Australia; Monash Biomedicine Discovery Institute, Department of Pharmacology, Monash University, Clayton 3168, Victoria, Australia.
| |
Collapse
|
10
|
Chen F, Wang S, Zeng C, Tang S, Gu H, Wang Z, Li J, Feng P, Zhang Y, Wang P, Wu Y, Shen H. Silencing circSERPINE2 restrains mesenchymal stem cell senescence via the YBX3/PCNA/p21 axis. Cell Mol Life Sci 2023; 80:325. [PMID: 37831180 PMCID: PMC10575817 DOI: 10.1007/s00018-023-04975-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Increasing evidence indicates that circular RNAs (circRNAs) accumulate in aging tissues and nonproliferating cells due to their high stability. However, whether upregulation of circRNA expression mediates stem cell senescence and whether circRNAs can be targeted to alleviate aging-related disorders remain unclear. Here, RNA sequencing analysis of differentially expressed circRNAs in long-term-cultured mesenchymal stem cells (MSCs) revealed that circSERPINE2 expression was significantly increased in late passages. CircSERPINE2 small interfering RNA delayed MSC senescence and rejuvenated MSCs, while circSERPINE2 overexpression had the opposite effect. RNA pulldown followed by mass spectrometry revealed an interaction between circSERPINE2 and YBX3. CircSERPINE2 increased the affinity of YBX3 for ZO-1 through the CCAUC motif, resulting in the sequestration of YBX3 in the cytoplasm, inhibiting the association of YBX3 with the PCNA promoter and eventually affecting p21 ubiquitin-mediated degradation. In addition, our results demonstrated that senescence-related downregulation of EIF4A3 gave rise to circSERPINE2. In vivo, intra-articular injection of si-circSerpine2 restrained native joint-resident MSC senescence and cartilage degeneration in mice with aging-related osteoarthritis. Taken together, our findings provide strong evidence for a regulatory role for the circSERPINE2/YBX3/PCNA/p21 axis in MSC senescence and the therapeutic potential of si-circSERPINE2 in alleviating aging-associated syndromes, such as osteoarthritis.
Collapse
Affiliation(s)
- Fenglei Chen
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Shan Wang
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Chenying Zeng
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Su'an Tang
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Huimin Gu
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Ziming Wang
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Jinteng Li
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Pei Feng
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Yunhui Zhang
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Peng Wang
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China.
| | - Yanfeng Wu
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China.
| | - Huiyong Shen
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China.
| |
Collapse
|
11
|
Baltazar-Cruz J, Rojas-Rios R, Larios-Serrato V, Mendoza-Sanchez I, Curiel-Quesada E, Pérez-Valdespino A. A Class 4-like Chromosomal Integron Found in Aeromonas sp. Genomospecies paramedia Isolated from Human Feces. Microorganisms 2023; 11:2548. [PMID: 37894206 PMCID: PMC10609294 DOI: 10.3390/microorganisms11102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Integrons are genetic elements that store, express and exchange gene cassettes. These elements are characterized by containing a gene that codes for an integrase (intI), a cassette integration site (attI) and a variable region holding the cassettes. Using bioinformatics and molecular biology methods, a functional integron found in Aeromonas sp. 3925, a strain isolated from diarrheal stools, is described. To confirm the integron class, a phylogenetic analysis with amino acid sequences was conducted. The integrase was associated to class 4 integrases; however, it is clearly different from them. Thus, we classified the associated element as a class 4-like integron. We found that the integrase activity is not under the control of the SOS or catabolic repression, since the expression was not increased in the presence of mitomycin or arabinose. The class-4-like integron is located on the chromosome and contains two well-defined gene cassettes: aadA1 that confers resistance to streptomycin and lpt coding for a lipoprotein. It also includes eight Open Reading frames (ORFs) with unknown functions. The strain was characterized through a Multilocus Phylogenetic Analyses (MLPA) of the gyrB, gyrA, rpoD, recA, dnaJ and dnaX genes. The phylogenetic results grouped it into a different clade from the species already reported, making it impossible to assign a species. We resorted to undertaking complete genome sequencing and a phylogenomic analysis. Aeromonas sp. 3925 is related to A. media and A. rivipollensis clusters, but it is clearly different from these species. In silico DNA-DNA hybridization (isDDH) and Average Nucleotide Identity (ANI) analyses suggested that this isolate belongs to the genomospecies paramedia. This paper describes the first class 4-like integron in Aeromonas and contributes to the establishment of genomospecies paramedia.
Collapse
Affiliation(s)
- Jesús Baltazar-Cruz
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Rogelio Rojas-Rios
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Violeta Larios-Serrato
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Itza Mendoza-Sanchez
- Department of Environmental & Occupational Health, Texas A&M University School of Public Health, College Station, TX 77843, USA;
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| |
Collapse
|
12
|
Cheng K, Zhang C, Lu Y, Li J, Tang H, Ma L, Zhu H. The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3504. [PMID: 37836244 PMCID: PMC10575402 DOI: 10.3390/plants12193504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
Collapse
Affiliation(s)
- Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hui Tang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| |
Collapse
|
13
|
Krishnappa G, Mandal M, Ganesan S, Babu S, Padavattan S, Haradara Bahubali VK, Padmanabhan B. Structural and biochemical insights into the bacteriophage PlyGRCS endolysin targeting methicillin-resistant Staphylococcus aureus (MRSA) and serendipitous discovery of its interaction with a cold shock protein C (CspC). Protein Sci 2023; 32:e4737. [PMID: 37497650 PMCID: PMC10443338 DOI: 10.1002/pro.4737] [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: 04/06/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes life-threatening human infections. Bacteriophage-encoded endolysins degrade the cell walls of Gram-positive bacteria by selectively hydrolyzing the peptidoglycan layer and thus are promising candidates to combat bacterial infections. PlyGRCS, the S. aureus-specific bacteriophage endolysin, contains a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Here, we show the crystal structure of full-length PlyGRCS refined to 2.1 Å resolution. In addition, a serendipitous finding revealed that PlyGRCS binds to cold-shock protein C (CspC) by interacting with its CHAP and SH3_5 domains. CspC is an RNA chaperone that plays regulatory roles by conferring bacterial adaptability to various stress conditions. PlyGRCS has substantial lytic activity against S. aureus and showed only minimal change in its lytic activity in the presence of CspC. Whereas the PlyGRCS-CspC complex greatly reduced CspC-nucleic acid binding, the aforesaid complex may downregulate the CspC function during bacterial infection. Overall, the crystal structure and biochemical results of PlyGRCS provide a molecular basis for the bacteriolytic activity of PlyGRCS against S. aureus.
Collapse
Affiliation(s)
- Gopinatha Krishnappa
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Mitali Mandal
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Saranya Ganesan
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Sudhagar Babu
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | - Sivaraman Padavattan
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| | | | - Balasundaram Padmanabhan
- Department of BiophysicsNational Institute of Mental Health and Neuro Sciences (NIMHANS)BengaluruIndia
| |
Collapse
|
14
|
Ramón A, Esteves A, Villadóniga C, Chalar C, Castro-Sowinski S. A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies. Braz J Microbiol 2023; 54:2259-2287. [PMID: 37477802 PMCID: PMC10484896 DOI: 10.1007/s42770-023-01057-4] [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: 03/20/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000 m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.
Collapse
Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Adriana Esteves
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Carolina Villadóniga
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Cora Chalar
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
| |
Collapse
|
15
|
Li Q, Kang C. Targeting RNA-binding proteins with small molecules: Perspectives, pitfalls and bifunctional molecules. FEBS Lett 2023; 597:2031-2047. [PMID: 37519019 DOI: 10.1002/1873-3468.14710] [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: 03/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
RNA-binding proteins (RBPs) play vital roles in organisms through binding with RNAs to regulate their functions. Small molecules affecting the function of RBPs have been developed, providing new avenues for drug discovery. Herein, we describe the perspectives on developing small molecule regulators of RBPs. The following types of small molecule modulators are of great interest in drug discovery: small molecules binding to RBPs to affect interactions with RNA molecules, bifunctional molecules binding to RNA or RBP to influence their interactions, and other types of molecules that affect the stability of RNA or RBPs. Moreover, we emphasize that the bifunctional molecules may play important roles in small molecule development to overcome the challenges encountered in the process of drug discovery.
Collapse
Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
| |
Collapse
|
16
|
Leys K, Stroe MS, Annaert P, Van Cruchten S, Carpentier S, Allegaert K, Smits A. Pharmacokinetics during therapeutic hypothermia in neonates: from pathophysiology to translational knowledge and physiologically-based pharmacokinetic (PBPK) modeling. Expert Opin Drug Metab Toxicol 2023; 19:461-477. [PMID: 37470686 DOI: 10.1080/17425255.2023.2237412] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/13/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023]
Abstract
INTRODUCTION Perinatal asphyxia (PA) still causes significant morbidity and mortality. Therapeutic hypothermia (TH) is the only effective therapy for neonates with moderate to severe hypoxic-ischemic encephalopathy after PA. These neonates need additional pharmacotherapy, and both PA and TH may impact physiology and, consequently, pharmacokinetics (PK) and pharmacodynamics (PD). AREAS COVERED This review provides an overview of the available knowledge in PubMed (until November 2022) on the pathophysiology of neonates with PA/TH. In vivo pig models for this setting enable distinguishing the effect of PA versus TH on PK and translating this effect to human neonates. Available asphyxia pig models and methodological considerations are described. A summary of human neonatal PK of supportive pharmacotherapy to improve neurodevelopmental outcomes is provided. EXPERT OPINION To support drug development for this population, knowledge from clinical observations (PK data, real-world data on physiology), preclinical (in vitro and in vivo (minipig)) data, and molecular and cellular biology insights can be integrated into a predictive physiologically-based PK (PBPK) framework, as illustrated by the I-PREDICT project (Innovative physiology-based pharmacokinetic model to predict drug exposure in neonates undergoing cooling therapy). Current knowledge, challenges, and expert opinion on the future directions of this research topic are provided.
Collapse
Affiliation(s)
- Karen Leys
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences KU Leuven, Leuven, Belgium
| | - Marina-Stefania Stroe
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Annaert
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences KU Leuven, Leuven, Belgium
- BioNotus GCV, Niel, Belgium
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Karel Allegaert
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Department of Hospital Pharmacy, Erasmus MC, GA, Rotterdam, The Netherlands
- Child and Youth Institute, KU Leuven, Leuven, Belgium
| | - Anne Smits
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Child and Youth Institute, KU Leuven, Leuven, Belgium
- Neonatal Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| |
Collapse
|
17
|
Toulany M, Lasham A. Close Links between Cold Shock Proteins and Cancer. Cancers (Basel) 2023; 15:cancers15092421. [PMID: 37173888 PMCID: PMC10177314 DOI: 10.3390/cancers15092421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Nine of the ten papers published in this Special Issue explore various aspects of the multifunctional protein Y-box binding protein-1 (YB-1) and its role in cancer [...].
Collapse
Affiliation(s)
- Mahmoud Toulany
- Division of Radiobiology & Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Roentgenweg 11, 72076 Tuebingen, Germany
| | - Annette Lasham
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland 1010, New Zealand
- Te Aka Mātauranga Matepukupuku, Faculty of Medical and Health Sciences, The University of Auckland, Auckland 1142, New Zealand
| |
Collapse
|
18
|
Protein-RNA interactions: from mass spectrometry to drug discovery. Essays Biochem 2023; 67:175-186. [PMID: 36866608 PMCID: PMC10070478 DOI: 10.1042/ebc20220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and RNAs form complexes and mutually affect their functions. In the present mini-review, we will first provide an overview of different mass spectrometry (MS)-based methods to study the RNA-binding proteome (RBPome), most of which are based on photochemical cross-linking. As we will show, some of these methods are also able to provide higher-resolution information about binding sites, which are important for the structural characterisation of protein-RNA interactions. In addition, classical structural biology techniques such as nuclear magnetic resonance (NMR) spectroscopy and biophysical methods such as electron paramagnetic resonance (EPR) spectroscopy and fluorescence-based methods contribute to a detailed understanding of the interactions between these two classes of biomolecules. We will discuss the relevance of such interactions in the context of the formation of membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes and their emerging importance as targets for drug discovery.
Collapse
|
19
|
The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells. J Genet Eng Biotechnol 2022; 20:173. [PMID: 36580173 PMCID: PMC9800685 DOI: 10.1186/s43141-022-00455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells. CONCLUSIONS This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.
Collapse
|
20
|
Biological Role of the 3β-Corner Structural Motif in Proteins. Processes (Basel) 2022. [DOI: 10.3390/pr10112159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
In this study, we analyze the occurrence of the unique structural motif, the 3β-corner, belonging to the Structural Classification of Proteins (SCOP) folds, in proteins of various origins. We further assess the structural and functional role of this motif as well as the clustering of the biological functions of proteins in which it occurs. It has been shown previously that the 3β-corner occurs with different probabilities in all beta proteins, alpha and beta proteins (α + β and α/β), and alpha classes occur most often in the composition of β-proteins. The 3β-corner is often found as a building block in protein structures, such as β-barrels, -sandwiches, and -sheets/-layers.
Collapse
|
21
|
Xia W, Zong J, Zheng K, Wang Y, Zhang D, Guo S, Sun G. DgCspC gene overexpression improves cotton yield and tolerance to drought and salt stress comparison with wild-type plants. FRONTIERS IN PLANT SCIENCE 2022; 13:985900. [PMID: 36147229 PMCID: PMC9485673 DOI: 10.3389/fpls.2022.985900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Drought and high salinity are key limiting factors for cotton quality and yield. Therefore, research is increasingly focused on mining effective genes to improve the stress resistance of cotton. Few studies have demonstrated that bacterial Cold shock proteins (Csps) overexpression can enhance plants stress tolerance. Here, we first identified and cloned a gene DgCspC encoding 88 amino acids (aa) with an open reading frame (ORF) of 264 base pairs (bp) from a Deinococcus gobiensis I-0 with high resistance to strong radiation, drought, and high temperature. In this study, heterologous expression of DgCspC promoted cotton growth, as exhibited by larger leaf size and higher plant height than the wild-type plants. Moreover, transgenic cotton lines showed higher tolerance to drought and salts stresses than wild-type plants, as revealed by susceptibility phenotype and physiological indexes. Furthermore, the enhanced stresses tolerance was attributed to high capacity of cellular osmotic regulation and ROS scavenging resulted from DgCspC expression modulating relative genes upregulated to cause proline and betaine accumulation. Meanwhile, photosynthetic efficiency and yield were significantly higher in the transgenic cotton than in the wild-type control under field conditions. This study provides a newly effective gene resource to cultivate new cotton varieties with high stresses resistance and yield.
Collapse
Affiliation(s)
- Wenwen Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
| | - Jiahang Zong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Kai Zheng
- College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongling Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
22
|
Tumor Temperature: Friend or Foe of Virus-Based Cancer Immunotherapy. Biomedicines 2022; 10:biomedicines10082024. [PMID: 36009571 PMCID: PMC9405776 DOI: 10.3390/biomedicines10082024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
The temperature of a solid tumor is often dissimilar to baseline body temperature and, compared to healthy tissues, may be elevated, reduced, or a mix of both. The temperature of a tumor is dependent on metabolic activity and vascularization and can change due to tumor progression, treatment, or cancer type. Despite the need to function optimally within temperature-variable tumors, oncolytic viruses (OVs) are primarily tested at 37 °C in vitro. Furthermore, animal species utilized to test oncolytic viruses, such as mice, dogs, cats, and non-human primates, poorly recapitulate the temperature profile of humans. In this review, we discuss the importance of temperature as a variable for OV immunotherapy of solid tumors. Accumulating evidence supports that the temperature sensitivity of OVs lies on a spectrum, with some OVs likely hindered but others enhanced by elevated temperatures. We suggest that in vitro temperature sensitivity screening be performed for all OVs destined for the clinic to identify potential hinderances or benefits with regard to elevated temperature. Furthermore, we provide recommendations for the clinical use of temperature and OVs.
Collapse
|
23
|
Chaudhary A, Chaurasia PK, Kushwaha S, Chauhan P, Chawade A, Mani A. Correlating multi-functional role of cold shock domain proteins with intrinsically disordered regions. Int J Biol Macromol 2022; 220:743-753. [PMID: 35987358 DOI: 10.1016/j.ijbiomac.2022.08.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/26/2022] [Accepted: 08/14/2022] [Indexed: 11/05/2022]
Abstract
Cold shock proteins (CSPs) are an ancient and conserved family of proteins. They are renowned for their role in response to low-temperature stress in bacteria and nucleic acid binding activities. In prokaryotes, cold and non-cold inducible CSPs are involved in various cellular and metabolic processes such as growth and development, osmotic oxidation, starvation, stress tolerance, and host cell invasion. In prokaryotes, cold shock condition reduces cell transcription and translation efficiency. Eukaryotic cold shock domain (CSD) proteins are evolved form of prokaryotic CSPs where CSD is flanked by N- and C-terminal domains. Eukaryotic CSPs are multi-functional proteins. CSPs also act as nucleic acid chaperons by preventing the formation of secondary structures in mRNA at low temperatures. In human, CSD proteins play a crucial role in the progression of breast cancer, colon cancer, lung cancer, and Alzheimer's disease. A well-defined three-dimensional structure of intrinsically disordered regions of CSPs family members is still undetermined. In this article, intrinsic disorder regions of CSPs have been explored systematically to understand the pleiotropic role of the cold shock family of proteins.
Collapse
Affiliation(s)
- Amit Chaudhary
- Department of Metallurgical Engineering & Materials Science, Indian Institute of Technology Bombay
| | - Pankaj Kumar Chaurasia
- PG Department of Chemistry, L.S. College, Babasaheb Bhimrao Ambedkar Bihar University, Muzaffarpur, Bihar 842001, India
| | - Sandeep Kushwaha
- National Institute of Animal Biotechnology, Hyderabad 500032, India.
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden.
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India.
| |
Collapse
|
24
|
Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
Collapse
Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
| |
Collapse
|
25
|
Kumar P, Soory A, Mustfa SA, Sarmah DT, Devvanshi H, Chatterjee S, Bossis G, Ratnaparkhi GS, Srikanth CV. Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signalling during Salmonella infection. J Cell Sci 2022; 135:276158. [PMID: 35904007 DOI: 10.1242/jcs.260096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Post-translational modifications (PTMs), such as SUMOylation, are known to modulate fundamental processes of a cell. Infectious agents such as Salmonella Typhimurium (STm) that causes gastroenteritis, utilizes PTM mechanism SUMOylation to highjack host cell. STm suppresses host SUMO-pathway genes Ubc9 and PIAS1 to perturb SUMOylation for an efficient infection. In the present study, the regulation of SUMO-pathway genes during STm infection was investigated. A direct binding of c-Fos, a component of AP-1 (Activator Protein-1), to promoters of both UBC9 and PIAS1 was observed. Experimental perturbation of c-Fos led to changes in expression of both Ubc9 and PIAS1. STm infection of fibroblasts with SUMOylation deficient c-Fos (c-FOS-KOSUMO-def-FOS) resulted in uncontrolled activation of target genes, resulting in massive immune activation. Infection of c-FOS-KOSUMO-def-FOS cells favored STm replication, indicating misdirected immune mechanisms. Finally, chromatin Immuno-precipitation assays confirmed a context dependent differential binding and release of AP-1 to/from target genes due to its Phosphorylation and SUMOylation respectively. Overall, our data point towards existence of a bidirectional cross-talk between c-Fos and the SUMO pathway and highlighting its importance in AP-1 function relevant to STm infection and beyond.
Collapse
Affiliation(s)
- Pharvendra Kumar
- Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India.,Kalinga Institute of Industrial Technology, Bhubaneshwar, India
| | | | | | - Dipanka Tanu Sarmah
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Himadri Devvanshi
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Samrat Chatterjee
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS, Montpellier, France
| | | | - C V Srikanth
- Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| |
Collapse
|
26
|
Louet C, Blot C, Shelest E, Guerillot P, Zannini F, Pétrowski J, Frey P, Duplessis S. Annotation survey and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit. Fungal Genet Biol 2022; 161:103698. [PMID: 35483517 DOI: 10.1016/j.fgb.2022.103698] [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: 10/19/2021] [Revised: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster -two of the most represented TF families in fungi- indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.
Collapse
Affiliation(s)
| | - Carla Blot
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Ekaterina Shelest
- School of biological Sciences, University of Portsmouth, King Henry 1 Street, PO1 D2Y, Portsmouth, United Kingdom
| | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | |
Collapse
|
27
|
Raguraman R, Shanmugarama S, Mehta M, Elle Peterson J, Zhao YD, Munshi A, Ramesh R. Drug delivery approaches for HuR-targeted therapy for lung cancer. Adv Drug Deliv Rev 2022; 180:114068. [PMID: 34822926 PMCID: PMC8724414 DOI: 10.1016/j.addr.2021.114068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/18/2021] [Indexed: 01/03/2023]
Abstract
Lung cancer (LC) is often diagnosed at an advanced stage and conventional treatments for disease management have limitations associated with them. Novel therapeutic targets are thus avidly sought for the effective management of LC. RNA binding proteins (RBPs) have been convincingly established as key players in tumorigenesis, and their dysregulation is linked to multiple cancers, including LC. In this context, we review the role of Human antigen R (HuR), an RBP that is overexpressed in LC, and further associated with various aspects of LC tumor growth and response to therapy. Herein, we describe the role of HuR in LC progression and outline the evidences supporting various pharmacologic and biologic approaches for inhibiting HuR expression and function. These approaches, including use of small molecule inhibitors, siRNAs and shRNAs, have demonstrated favorable results in reducing tumor cell growth, invasion and migration, angiogenesis and metastasis. Hence, HuR has significant potential as a key therapeutic target in LC. Use of siRNA-based approaches, however, have certain limitations that prevent their maximal exploitation as cancer therapies. To address this, in the conclusion of this review, we provide a list of nanomedicine-based HuR targeting approaches currently being employed for siRNA and shRNA delivery, and provide a rationale for the immense potential therapeutic benefits offered by nanocarrier-based HuR targeting and its promise for treating patients with LC.
Collapse
Affiliation(s)
- Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Santny Shanmugarama
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Meghna Mehta
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jo Elle Peterson
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yan D Zhao
- Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Anupama Munshi
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| |
Collapse
|
28
|
Evdokimova V. Y-box Binding Protein 1: Looking Back to the Future. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S5-S145. [PMID: 35501983 DOI: 10.1134/s0006297922140024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding protein 1 is a member of the cold shock domain (CSD) protein family and one of the most studied proteins associated with a large number of human diseases. This review aims to critically reassess the growing number of pathological functions ascribed to YB-1 in the past decades. The focus is given on the important role of YB-1 and related CSD proteins in the physiology of normal cells. The functional significance of these proteins is highlighted by their high evolutionary conservation from bacteria to men, where they are ubiquitously expressed and involved in coordinating all steps of mRNA biogenesis, including transcription, translation, storage, and degradation. Their activities are especially important under conditions requiring rapid change in the gene expression programs, such as early embryonic development, differentiation, stress, and adaptation to new environments. Therefore, to define a precise role of YB-1 in tumorigenic transformation and in other pathological conditions, it is important to understand its basic properties and functions in normal cells, and how they are interrupted in complex diseases including cancer.
Collapse
|
29
|
Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [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: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
Collapse
Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
| |
Collapse
|
30
|
Choi J, Salvail H, Groisman EA. RNA chaperone activates Salmonella virulence program during infection. Nucleic Acids Res 2021; 49:11614-11628. [PMID: 34751407 PMCID: PMC8599858 DOI: 10.1093/nar/gkab992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 11/17/2022] Open
Abstract
Organisms often harbor seemingly redundant proteins. In the bacterium Salmonella enterica serovar Typhimurium (S. Typhimurium), the RNA chaperones CspC and CspE appear to play redundant virulence roles because a mutant lacking both chaperones is attenuated, whereas mutants lacking only one exhibit wild-type virulence. We now report that CspC—but not CspE—is necessary to activate the master virulence regulator PhoP when S. Typhimurium experiences mildly acidic pH, such as inside macrophages. This CspC-dependent PhoP activation is specific to mildly acidic pH because a cspC mutant behaves like wild-type S. Typhimurium under other PhoP-activating conditions. Moreover, it is mediated by ugtL, a virulence gene required for PhoP activation inside macrophages. Purified CspC promotes ugtL translation by disrupting a secondary structure in the ugtL mRNA that occludes ugtL’s ribosome binding site. Our findings demonstrate that proteins that are seemingly redundant actually confer distinct and critical functions to the lifestyle of an organism.
Collapse
Affiliation(s)
- Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Hubert Salvail
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
| |
Collapse
|
31
|
Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
Collapse
Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| |
Collapse
|
32
|
Is It Possible to Create Antimicrobial Peptides Based on the Amyloidogenic Sequence of Ribosomal S1 Protein of P. aeruginosa? Int J Mol Sci 2021; 22:ijms22189776. [PMID: 34575940 PMCID: PMC8469417 DOI: 10.3390/ijms22189776] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
The development and testing of new antimicrobial peptides (AMPs) represent an important milestone toward the development of new antimicrobial drugs that can inhibit the growth of pathogens and multidrug-resistant microorganisms such as Pseudomonas aeruginosa, Gram-negative bacteria. Most AMPs achieve these goals through mechanisms that disrupt the normal permeability of the cell membrane, which ultimately leads to the death of the pathogenic cell. Here, we developed a unique combination of a membrane penetrating peptide and peptides prone to amyloidogenesis to create hybrid peptide: "cell penetrating peptide + linker + amyloidogenic peptide". We evaluated the antimicrobial effects of two peptides that were developed from sequences with different propensities for amyloid formation. Among the two hybrid peptides, one was found with antibacterial activity comparable to antibiotic gentamicin sulfate. Our peptides showed no toxicity to eukaryotic cells. In addition, we evaluated the effect on the antimicrobial properties of amino acid substitutions in the non-amyloidogenic region of peptides. We compared the results with data on the predicted secondary structure, hydrophobicity, and antimicrobial properties of the original and modified peptides. In conclusion, our study demonstrates the promise of hybrid peptides based on amyloidogenic regions of the ribosomal S1 protein for the development of new antimicrobial drugs against P. aeruginosa.
Collapse
|
33
|
Shah A, Lindquist JA, Rosendahl L, Schmitz I, Mertens PR. Novel Insights into YB-1 Signaling and Cell Death Decisions. Cancers (Basel) 2021; 13:3306. [PMID: 34282755 PMCID: PMC8269159 DOI: 10.3390/cancers13133306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
YB-1 belongs to the evolutionarily conserved cold-shock domain protein family of RNA binding proteins. YB-1 is a well-known transcriptional and translational regulator, involved in cell cycle progression, DNA damage repair, RNA splicing, and stress responses. Cell stress occurs in many forms, e.g., radiation, hyperthermia, lipopolysaccharide (LPS) produced by bacteria, and interferons released in response to viral infection. Binding of the latter factors to their receptors induces kinase activation, which results in the phosphorylation of YB-1. These pathways also activate the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), a well-known transcription factor. NF-κB is upregulated following cellular stress and orchestrates inflammatory responses, cell proliferation, and differentiation. Inflammation and cancer are known to share common mechanisms, such as the recruitment of infiltrating macrophages and development of an inflammatory microenvironment. Several recent papers elaborate the role of YB-1 in activating NF-κB and signaling cell survival. Depleting YB-1 may tip the balance from survival to enhanced apoptosis. Therefore, strategies that target YB-1 might be a viable therapeutic option to treat inflammatory diseases and improve tumor therapy.
Collapse
Affiliation(s)
- Aneri Shah
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany; (A.S.); (L.R.); (P.R.M.)
| | - Jonathan A. Lindquist
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany; (A.S.); (L.R.); (P.R.M.)
| | - Lars Rosendahl
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany; (A.S.); (L.R.); (P.R.M.)
| | - Ingo Schmitz
- Department of Molecular Immunology, ZKF2, Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Peter R. Mertens
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany; (A.S.); (L.R.); (P.R.M.)
| |
Collapse
|
34
|
Listeria monocytogenes Cold Shock Proteins: Small Proteins with A Huge Impact. Microorganisms 2021; 9:microorganisms9051061. [PMID: 34068949 PMCID: PMC8155936 DOI: 10.3390/microorganisms9051061] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/26/2023] Open
Abstract
Listeria monocytogenes has evolved an extensive array of mechanisms for coping with stress and adapting to changing environmental conditions, ensuring its virulence phenotype expression. For this reason, L. monocytogenes has been identified as a significant food safety and public health concern. Among these adaptation systems are cold shock proteins (Csps), which facilitate rapid response to stress exposure. L. monocytogenes has three highly conserved csp genes, namely, cspA, cspB, and cspD. Using a series of csp deletion mutants, it has been shown that L. monocytogenes Csps are important for biofilm formation, motility, cold, osmotic, desiccation, and oxidative stress tolerance. Moreover, they are involved in overall virulence by impacting the expression of virulence-associated phenotypes, such as hemolysis and cell invasion. It is postulated that during stress exposure, Csps function to counteract harmful effects of stress, thereby preserving cell functions, such as DNA replication, transcription and translation, ensuring survival and growth of the cell. Interestingly, it seems that Csps might suppress tolerance to some stresses as their removal resulted in increased tolerance to stresses, such as desiccation for some strains. Differences in csp roles among strains from different genetic backgrounds are apparent for desiccation tolerance and biofilm production. Additionally, hierarchical trends for the different Csps and functional redundancies were observed on their influences on stress tolerance and virulence. Overall current data suggest that Csps have a wider role in bacteria physiology than previously assumed.
Collapse
|
35
|
Zaheri B, Morse D. Assessing nucleic acid binding activity of four dinoflagellate cold shock domain proteins from Symbiodinium kawagutii and Lingulodinium polyedra. BMC Mol Cell Biol 2021; 22:27. [PMID: 33964870 PMCID: PMC8106185 DOI: 10.1186/s12860-021-00368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Background Dinoflagellates have a generally large number of genes but only a small percentage of these are annotated as transcription factors. Cold shock domain (CSD) containing proteins (CSPs) account for roughly 60% of these. CSDs are not prevalent in other eukaryotic lineages, perhaps suggesting a lineage-specific expansion of this type of transcription factors in dinoflagellates, but there is little experimental data to support a role for dinoflagellate CSPs as transcription factors. Here we evaluate the hypothesis that dinoflagellate CSPs can act as transcription factors by binding double-stranded DNA in a sequence dependent manner. Results We find that both electrophoretic mobility shift assay (EMSA) competition experiments and selection and amplification binding (SAAB) assays indicate binding is not sequence specific for four different CSPs from two dinoflagellate species. Competition experiments indicate all four CSPs bind to RNA better than double-stranded DNA. Conclusion Dinoflagellate CSPs do not share the nucleic acid binding properties expected for them to function as bone fide transcription factors. We conclude the transcription factor complement of dinoflagellates is even smaller than previously thought suggesting that dinoflagellates have a reduced dependance on transcriptional control compared to other eukaryotes. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00368-4.
Collapse
Affiliation(s)
- Bahareh Zaheri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke Est, Université de Montréal, Montréal, H1X 2B2, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke Est, Université de Montréal, Montréal, H1X 2B2, Canada.
| |
Collapse
|