1
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Saß A, Schneider R. Novel molecular insights into the machinery driving secondary cell wall synthesis and patterning. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102614. [PMID: 39142254 DOI: 10.1016/j.pbi.2024.102614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/16/2024]
Abstract
The essential role of water-conducting xylem tissue in plant growth and crop yield is well-established. However, the molecular mechanisms underlying xylem formation and its unique functionality, which is acquired post-mortem, remain poorly understood. Recent advancements in genetic tools and model systems have significantly enhanced the ability to microscopically study xylem development, particularly its distinctive cell wall patterning. Early molecular mechanisms enabling pattern formation have been elucidated and validated through computational models. Despite these advancements, numerous questions remain unresolved but are approachable with current methodologies. This mini-review takes in the latest research findings in xylem cell wall synthesis and patterning and highlights prospective directions for future investigations.
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Affiliation(s)
- Annika Saß
- Institute of Biochemistry and Biology, Plant Physiology Department, University of Potsdam, 14476 Potsdam-Golm, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - René Schneider
- Institute of Biochemistry and Biology, Plant Physiology Department, University of Potsdam, 14476 Potsdam-Golm, Germany.
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2
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Salazar OR, Chen K, Melino VJ, Reddy MP, Hřibová E, Čížková J, Beránková D, Arciniegas Vega JP, Cáceres Leal LM, Aranda M, Jaremko L, Jaremko M, Fedoroff NV, Tester M, Schmöckel SM. SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii. Nat Commun 2024; 15:4279. [PMID: 38769297 PMCID: PMC11106269 DOI: 10.1038/s41467-024-48595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.
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Affiliation(s)
- Octavio R Salazar
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Vanessa J Melino
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muppala P Reddy
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Juan Pablo Arciniegas Vega
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lina María Cáceres Leal
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Nina V Fedoroff
- Department of Biology, Penn State University, University Park, PA, 16801, US
| | - Mark Tester
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Sandra M Schmöckel
- Department Physiology of Yield Stability, Institute of Crop Science, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
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3
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JCA. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. Nucleic Acids Res 2024; 52:4702-4722. [PMID: 38572746 PMCID: PMC11077067 DOI: 10.1093/nar/gkae229] [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: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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4
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Crawshaw S, Murphy AM, Rowling PJE, Nietlispach D, Itzhaki LS, Carr JP. Investigating the Interactions of the Cucumber Mosaic Virus 2b Protein with the Viral 1a Replicase Component and the Cellular RNA Silencing Factor Argonaute 1. Viruses 2024; 16:676. [PMID: 38793558 PMCID: PMC11125589 DOI: 10.3390/v16050676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
The cucumber mosaic virus (CMV) 2b protein is a suppressor of plant defenses and a pathogenicity determinant. Amongst the 2b protein's host targets is the RNA silencing factor Argonaute 1 (AGO1), which it binds to and inhibits. In Arabidopsis thaliana, if 2b-induced inhibition of AGO1 is too efficient, it induces reinforcement of antiviral silencing by AGO2 and triggers increased resistance against aphids, CMV's insect vectors. These effects would be deleterious to CMV replication and transmission, respectively, but are moderated by the CMV 1a protein, which sequesters sufficient 2b protein molecules into P-bodies to prevent excessive inhibition of AGO1. Mutant 2b protein variants were generated, and red and green fluorescent protein fusions were used to investigate subcellular colocalization with AGO1 and the 1a protein. The effects of mutations on complex formation with the 1a protein and AGO1 were investigated using bimolecular fluorescence complementation and co-immunoprecipitation assays. Although we found that residues 56-60 influenced the 2b protein's interactions with the 1a protein and AGO1, it appears unlikely that any single residue or sequence domain is solely responsible. In silico predictions of intrinsic disorder within the 2b protein secondary structure were supported by circular dichroism (CD) but not by nuclear magnetic resonance (NMR) spectroscopy. Intrinsic disorder provides a plausible model to explain the 2b protein's ability to interact with AGO1, the 1a protein, and other factors. However, the reasons for the conflicting conclusions provided by CD and NMR must first be resolved.
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Affiliation(s)
- Sam Crawshaw
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (S.C.); (A.M.M.)
| | - Alex M. Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (S.C.); (A.M.M.)
| | - Pamela J. E. Rowling
- Department of Pharmacology, University of Cambridge, Tennis Court Rd., Cambridge CB2 1PD, UK; (P.J.E.R.); (L.S.I.)
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Rd., Cambridge CB2 1GA, UK;
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Rd., Cambridge CB2 1PD, UK; (P.J.E.R.); (L.S.I.)
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (S.C.); (A.M.M.)
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5
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Evans KV, Ransom E, Nayakoti S, Wilding B, Mohd Salleh F, Gržina I, Erber L, Tse C, Hill C, Polanski K, Holland A, Bukhat S, Herbert RJ, de Graaf BHJ, Denby K, Buchanan-Wollaston V, Rogers HJ. Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors. Sci Rep 2024; 14:7756. [PMID: 38565965 PMCID: PMC10987515 DOI: 10.1038/s41598-024-58161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
SAG21/LEA5 is an unusual late embryogenesis abundant protein in Arabidopsis thaliana, that is primarily mitochondrially located and may be important in regulating translation in both chloroplasts and mitochondria. SAG21 expression is regulated by a plethora of abiotic and biotic stresses and plant growth regulators indicating a complex regulatory network. To identify key transcription factors regulating SAG21 expression, yeast-1-hybrid screens were used to identify transcription factors that bind the 1685 bp upstream of the SAG21 translational start site. Thirty-three transcription factors from nine different families bound to the SAG21 promoter, including members of the ERF, WRKY and NAC families. Key binding sites for both NAC and WRKY transcription factors were tested through site directed mutagenesis indicating the presence of cryptic binding sites for both these transcription factor families. Co-expression in protoplasts confirmed the activation of SAG21 by WRKY63/ABO3, and SAG21 upregulation elicited by oligogalacturonide elicitors was partially dependent on WRKY63, indicating its role in SAG21 pathogen responses. SAG21 upregulation by ethylene was abolished in the erf1 mutant, while wound-induced SAG21 expression was abolished in anac71 mutants, indicating SAG21 expression can be regulated by several distinct transcription factors depending on the stress condition.
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Affiliation(s)
- Kelly V Evans
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Elspeth Ransom
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Swapna Nayakoti
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Ben Wilding
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Faezah Mohd Salleh
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
- Investigative and Forensic Sciences Research Group, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Irena Gržina
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Lieselotte Erber
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Carmen Tse
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Claire Hill
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Alistair Holland
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Sherien Bukhat
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Robert J Herbert
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
| | - Barend H J de Graaf
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Katherine Denby
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Heslington, York, YO10 5DD, UK
| | | | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK.
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6
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Kolimi N, Ballard J, Peulen T, Goutam R, Duffy FX, Ramírez-Sarmiento CA, Babul J, Medina E, Sanabria H. DNA controls the dimerization of the human FoxP1 forkhead domain. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101854. [PMID: 38585429 PMCID: PMC10997372 DOI: 10.1016/j.xcrp.2024.101854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences and gating access to genes. Even when the binding of TFs and their cofactors to DNA is reversible, indicating a reversible control of gene expression, there is little knowledge about the molecular effect DNA has on TFs. Using single-molecule multiparameter fluorescence spectroscopy, molecular dynamics simulations, and biochemical assays, we find that the monomeric form of the forkhead (FKH) domain of the human FoxP1 behaves as a disordered protein and increases its folded population when it dimerizes. Notably, DNA binding promotes a disordered FKH dimer bound to DNA, negatively controlling the stability of the dimeric FoxP1:DNA complex. The DNA-mediated reversible regulation on FKH dimers suggests that FoxP1-dependent gene suppression is unstable, and it must require the presence of other dimerization domains or cofactors to revert the negative impact exerted by the DNA.
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Affiliation(s)
- Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Jake Ballard
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Thomas Peulen
- Rudolf-Virchow-Zentrum – Center for Integrative and Translational Bioimaging, Haus D15, Josef-Schneider-Straße 2, 97080 Würzburg Germany
| | - Rajen Goutam
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Francis X. Duffy
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Exequiel Medina
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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7
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Gonzalez JP, Frandsen KEH, Kesten C. The role of intrinsic disorder in binding of plant microtubule-associated proteins to the cytoskeleton. Cytoskeleton (Hoboken) 2023; 80:404-436. [PMID: 37578201 DOI: 10.1002/cm.21773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/15/2023]
Abstract
Microtubules (MTs) represent one of the main components of the eukaryotic cytoskeleton and support numerous critical cellular functions. MTs are in principle tube-like structures that can grow and shrink in a highly dynamic manner; a process largely controlled by microtubule-associated proteins (MAPs). Plant MAPs are a phylogenetically diverse group of proteins that nonetheless share many common biophysical characteristics and often contain large stretches of intrinsic protein disorder. These intrinsically disordered regions are determinants of many MAP-MT interactions, in which structural flexibility enables low-affinity protein-protein interactions that enable a fine-tuned regulation of MT cytoskeleton dynamics. Notably, intrinsic disorder is one of the major obstacles in functional and structural studies of MAPs and represents the principal present-day challenge to decipher how MAPs interact with MTs. Here, we review plant MAPs from an intrinsic protein disorder perspective, by providing a complete and up-to-date summary of all currently known members, and address the current and future challenges in functional and structural characterization of MAPs.
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Affiliation(s)
- Jordy Perez Gonzalez
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kristian E H Frandsen
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Christopher Kesten
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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8
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Wang JW, Squire HJ, Goh NS, Ni HM, Lien E, Wong C, González-Grandío E, Landry MP. Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants. Commun Biol 2023; 6:840. [PMID: 37573467 PMCID: PMC10423278 DOI: 10.1038/s42003-023-05191-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
Using a fluorescence complementation assay, Delivered Complementation in Planta (DCIP), we demonstrate cell-penetrating peptide-mediated cytosolic delivery of peptides and recombinant proteins in Nicotiana benthamiana. We show that DCIP enables quantitative measurement of protein delivery efficiency and enables functional screening of cell-penetrating peptides for in-planta protein delivery. Finally, we demonstrate that DCIP detects cell-penetrating peptide-mediated delivery of recombinantly expressed proteins such as mCherry and Lifeact into intact leaves. We also demonstrate delivery of a recombinant plant transcription factor, WUSCHEL (AtWUS), into N. benthamiana. RT-qPCR analysis of AtWUS delivery in Arabidopsis seedlings also suggests delivered WUS can recapitulate transcriptional changes induced by overexpression of AtWUS. Taken together, our findings demonstrate that DCIP offers a new and powerful tool for interrogating cytosolic delivery of proteins in plants and highlights future avenues for engineering plant physiology.
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Affiliation(s)
- Jeffrey W Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Henry J Squire
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Heyuan Michael Ni
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Edward Lien
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Cerise Wong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Eduardo González-Grandío
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, Berkeley, CA, 94720, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94063, USA.
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9
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Flynn AJ, Miller K, Codjoe JM, King MR, Haswell ES. Mechanosensitive ion channels MSL8, MSL9, and MSL10 have environmentally sensitive intrinsically disordered regions with distinct biophysical characteristics in vitro. PLANT DIRECT 2023; 7:e515. [PMID: 37547488 PMCID: PMC10400277 DOI: 10.1002/pld3.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are highly dynamic sequences that rapidly sample a collection of conformations over time. In the past several decades, IDRs have emerged as a major component of many proteomes, comprising ~30% of all eukaryotic protein sequences. Proteins with IDRs function in a wide range of biological pathways and are notably enriched in signaling cascades that respond to environmental stresses. Here, we identify and characterize intrinsic disorder in the soluble cytoplasmic N-terminal domains of MSL8, MSL9, and MSL10, three members of the MscS-like (MSL) family of mechanosensitive ion channels. In plants, MSL channels are proposed to mediate cell and organelle osmotic homeostasis. Bioinformatic tools unanimously predicted that the cytosolic N-termini of MSL channels are intrinsically disordered. We examined the N-terminus of MSL10 (MSL10N) as an exemplar of these IDRs and circular dichroism spectroscopy confirms its disorder. MSL10N adopted a predominately helical structure when exposed to the helix-inducing compound trifluoroethanol (TFE). Furthermore, in the presence of molecular crowding agents, MSL10N underwent structural changes and exhibited alterations to its homotypic interaction favorability. Lastly, interrogations of collective behavior via in vitro imaging of condensates indicated that MSL8N, MSL9N, and MSL10N have sharply differing propensities for self-assembly into condensates, both inherently and in response to salt, temperature, and molecular crowding. Taken together, these data establish the N-termini of MSL channels as intrinsically disordered regions with distinct biophysical properties and the potential to respond uniquely to changes in their physiochemical environment.
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Affiliation(s)
- Aidan J. Flynn
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- Department of Biochemistry and BiophysicsWashington University in St. LouisSt. LouisMissouriUSA
| | - Kari Miller
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Jennette M. Codjoe
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Matthew R. King
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
| | - Elizabeth S. Haswell
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
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10
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Vainonen JP, Gossens R, Krasensky-Wrzaczek J, De Masi R, Danciu I, Puukko T, Battchikova N, Jonak C, Wirthmueller L, Wrzaczek M, Shapiguzov A, Kangasjärvi J. Poly(ADP-ribose)-binding protein RCD1 is a plant PARylation reader regulated by Photoregulatory Protein Kinases. Commun Biol 2023; 6:429. [PMID: 37076532 PMCID: PMC10115779 DOI: 10.1038/s42003-023-04794-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a reversible post-translational protein modification that has profound regulatory functions in metabolism, development and immunity, and is conserved throughout the eukaryotic lineage. Contrary to metazoa, many components and mechanistic details of PARylation have remained unidentified in plants. Here we present the transcriptional co-regulator RADICAL-INDUCED CELL DEATH1 (RCD1) as a plant PAR-reader. RCD1 is a multidomain protein with intrinsically disordered regions (IDRs) separating its domains. We have reported earlier that RCD1 regulates plant development and stress-tolerance by interacting with numerous transcription factors (TFs) through its C-terminal RST domain. This study suggests that the N-terminal WWE and PARP-like domains, as well as the connecting IDR play an important regulatory role for RCD1 function. We show that RCD1 binds PAR in vitro via its WWE domain and that PAR-binding determines RCD1 localization to nuclear bodies (NBs) in vivo. Additionally, we found that RCD1 function and stability is controlled by Photoregulatory Protein Kinases (PPKs). PPKs localize with RCD1 in NBs and phosphorylate RCD1 at multiple sites affecting its stability. This work proposes a mechanism for negative transcriptional regulation in plants, in which RCD1 localizes to NBs, binds TFs with its RST domain and is degraded after phosphorylation by PPKs.
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Affiliation(s)
- Julia P Vainonen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland
| | - Richard Gossens
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland
| | - Julia Krasensky-Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská1160/31, 370 05, České Budějovice, Czech Republic
| | - Raffaella De Masi
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195, Berlin, Germany
| | - Iulia Danciu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Tuomas Puukko
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland
| | - Natalia Battchikova
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Claudia Jonak
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Lennart Wirthmueller
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195, Berlin, Germany
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská1160/31, 370 05, České Budějovice, Czech Republic
| | - Alexey Shapiguzov
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Toivonlinnantie 518, FI-21500, Piikkiö, Finland
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, FI-00014, Helsinki, Finland.
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Late Embryogenesis Abundant Proteins Contribute to the Resistance of Toxoplasma gondii Oocysts against Environmental Stresses. mBio 2023; 14:e0286822. [PMID: 36809045 PMCID: PMC10128015 DOI: 10.1128/mbio.02868-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Toxoplasma gondii oocysts, which are shed in large quantities in the feces from infected felines, are very stable in the environment, resistant to most inactivation procedures, and highly infectious. The oocyst wall provides an important physical barrier for sporozoites contained inside oocysts, protecting them from many chemical and physical stressors, including most inactivation procedures. Furthermore, sporozoites can withstand large temperature changes, even freeze-thawing, as well as desiccation, high salinity, and other environmental insults; however, the genetic basis for this environmental resistance is unknown. Here, we show that a cluster of four genes encoding Late Embryogenesis Abundant (LEA)-related proteins are required to provide Toxoplasma sporozoites resistance to environmental stresses. Toxoplasma LEA-like genes (TgLEAs) exhibit the characteristic features of intrinsically disordered proteins, explaining some of their properties. Our in vitro biochemical experiments using recombinant TgLEA proteins show that they have cryoprotective effects on the oocyst-resident lactate dehydrogenase enzyme and that induced expression in E. coli of two of them leads to better survival after cold stress. Oocysts from a strain in which the four LEA genes were knocked out en bloc were significantly more susceptible to high salinity, freezing, and desiccation compared to wild-type oocysts. We discuss the evolutionary acquisition of LEA-like genes in Toxoplasma and other oocyst-producing apicomplexan parasites of the Sarcocystidae family and discuss how this has likely contributed to the ability of sporozoites within oocysts to survive outside the host for extended periods. Collectively, our data provide a first molecular detailed view on a mechanism that contributes to the remarkable resilience of oocysts against environmental stresses. IMPORTANCE Toxoplasma gondii oocysts are highly infectious and may survive in the environment for years. Their resistance against disinfectants and irradiation has been attributed to the oocyst and sporocyst walls by acting as physical and permeability barriers. However, the genetic basis for their resistance against stressors like changes in temperature, salinity, or humidity, is unknown. We show that a cluster of four genes encoding Toxoplasma Late Embryogenesis Abundant (TgLEA)-related proteins are important for this resistance to environmental stresses. TgLEAs have features of intrinsically disordered proteins, explaining some of their properties. Recombinant TgLEA proteins show cryoprotective effects on the parasite's lactate dehydrogenase, an abundant enzyme in oocysts, and expression in E. coli of two TgLEAs has a beneficial effect on growth after cold stress. Moreover, oocysts from a strain lacking all four TgLEA genes were more susceptible to high salinity, freezing, and desiccation compared to wild-type oocysts, highlighting the importance of the four TgLEAs for oocyst resilience.
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Wöhnke E, Cackett G, Werner F, Blome S, Mettenleiter TC, Karger A. Proteome Analysis of Swine Macrophages after Infection with Two Genotype II African Swine Fever Isolates of Different Pathogenicity. Viruses 2022; 14:v14102140. [PMID: 36298696 PMCID: PMC9607119 DOI: 10.3390/v14102140] [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: 09/07/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Since the introduction of a highly pathogenic genotype II isolate of the African swine fever virus (ASFV) into Georgia in 2007, African swine fever (ASF) has gone panzootic. Outbreaks have been reported in Europe, Asia and, more recently, Latin America. Thus, ASFV has become a major threat to the pig industry worldwide, as broadly applicable vaccines are not available. While the majority of ASFV strains show high virulence in domestic pigs and wild boar, variations within the ASFV genome have resulted in the emergence of attenuated strains with low or moderate virulence. However, the molecular basis of the differences in virulence has not yet been discovered. To reveal virulence-associated protein expression patterns, we analysed the proteomes of the natural target cells of ASFV, primary porcine macrophages, after infection with two genotype II ASFV strains displaying high (Armenia 2008) and moderate (Estonia 2014) virulence using quantitative mass spectrometry. Very similar expression patterns were observed for the viral genes, and any differences were limited to the deletions within the Estonia 2014 genome. In addition to the canonical ASFV proteins, twelve novel protein products from recently described transcripts were confirmed in both isolates. Pathway analyses showed that both isolates evoked a similar host proteome response, despite their difference in virulence. However, subtle differences in the manipulation of the proteins involved in the proinflammatory response mediated by the MAPK14/p38 signalling cascade were observed.
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Affiliation(s)
- Elisabeth Wöhnke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
| | - Gwenny Cackett
- Institute for Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Finn Werner
- Institute for Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
- Correspondence: ; Tel.: +49-38351-7-1247
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Vicioso-Mantis M, Aguirre S, Martínez-Balbás MA. JmjC Family of Histone Demethylases Form Nuclear Condensates. Int J Mol Sci 2022; 23:ijms23147664. [PMID: 35887017 PMCID: PMC9319511 DOI: 10.3390/ijms23147664] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 12/16/2022] Open
Abstract
The Jumonji-C (JmjC) family of lysine demethylases (KDMs) (JMJC-KDMs) plays an essential role in controlling gene expression and chromatin structure. In most cases, their function has been attributed to the demethylase activity. However, accumulating evidence demonstrates that these proteins play roles distinct from histone demethylation. This raises the possibility that they might share domains that contribute to their functional outcome. Here, we show that the JMJC-KDMs contain low-complexity domains and intrinsically disordered regions (IDR), which in some cases reached 70% of the protein. Our data revealed that plant homeodomain finger protein (PHF2), KDM2A, and KDM4B cluster by phase separation. Moreover, our molecular analysis implies that PHF2 IDR contributes to transcription regulation. These data suggest that clustering via phase separation is a common feature that JMJC-KDMs utilize to facilitate their functional responses. Our study uncovers a novel potential function for the JMJC-KDM family that sheds light on the mechanisms to achieve the competent concentration of molecules in time and space within the cell nucleus.
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Vicioso-Mantis M, Fueyo R, Navarro C, Cruz-Molina S, van Ijcken WFJ, Rebollo E, Rada-Iglesias Á, Martínez-Balbás MA. JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation. Nat Commun 2022; 13:3263. [PMID: 35672304 PMCID: PMC9174158 DOI: 10.1038/s41467-022-30614-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Enhancers are key regulatory elements that govern gene expression programs in response to developmental signals. However, how multiple enhancers arrange in the 3D-space to control the activation of a specific promoter remains unclear. To address this question, we exploited our previously characterized TGFβ-response model, the neural stem cells, focusing on a ~374 kb locus where enhancers abound. Our 4C-seq experiments reveal that the TGFβ pathway drives the assembly of an enhancer-cluster and precise gene activation. We discover that the TGFβ pathway coactivator JMJD3 is essential to maintain these structures. Using live-cell imaging techniques, we demonstrate that an intrinsically disordered region contained in JMJD3 is involved in the formation of phase-separated biomolecular condensates, which are found in the enhancer-cluster. Overall, in this work we uncover novel functions for the coactivator JMJD3, and we shed light on the relationships between the 3D-conformation of the chromatin and the TGFβ-driven response during mammalian neurogenesis. Here the authors demonstrate that TGFβ drives multi-enhancer contacts and ultimately gene activation during neuronal commitment, and that this requires the intrinsically disordered region (IDR) of the histone demethylase JMJD3 likely through its role in promoting phase-separated biomolecular condensates.
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Hanselmann RG, Welter C. Origin of Cancer: Cell work is the Key to Understanding Cancer Initiation and Progression. Front Cell Dev Biol 2022; 10:787995. [PMID: 35300431 PMCID: PMC8921603 DOI: 10.3389/fcell.2022.787995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
The cell is the smallest unit of life. It is a structure that maintains order through self-organization, characterized by a high level of dynamism, which in turn is characterized by work. For this work to take place, a continuous high flow of energy is necessary. However, a focused view of the physical relationship between energy and work is inadequate for describing complex biological/medical mechanisms or systems. In this review, we try to make a connection between the fundamental laws of physics and the mechanisms and functions of biology, which are characterized by self-organization. Many different physical work processes (work) in human cells are called cell work and can be grouped into five forms: synthetic, mechanical, electrical, concentration, and heat generation cell work. In addition to the flow of energy, these cell functions are based on fundamental processes of self-organization that we summarize with the term Entirety of molecular interaction (EoMI). This illustrates that cell work is caused by numerous molecular reactions, flow equilibrium, and mechanisms. Their number and interactions are so complex that they elude our perception in their entirety. To be able to describe cell functions in a biological/medical context, the parameters influencing cell work should be summarized in overarching influencing variables. These are “biological” energy, information, matter, and cell mechanics (EMIM). This makes it possible to describe and characterize the cell work involved in cell systems (e.g., respiratory chain, signal transmission, cell structure, or inheritance processes) and to demonstrate changes. If cell work and the different influencing parameters (EMIM influencing variables) are taken as the central property of the cell, specific gene mutations cannot be regarded as the sole cause for the initiation and progression of cancer. This reductionistic monocausal view does not do justice to the dynamic and highly complex system of a cell. Therefore, we postulate that each of the EMIM influencing variables described above is capable of changing the cell work and thus the order of a cell in such a way that it can develop into a cancer cell.
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The Emergence of New Catalytic Abilities in an Endoxylanase from Family GH10 by Removing an Intrinsically Disordered Region. Int J Mol Sci 2022; 23:ijms23042315. [PMID: 35216436 PMCID: PMC8874783 DOI: 10.3390/ijms23042315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Endoxylanases belonging to family 10 of the glycoside hydrolases (GH10) are versatile in the use of different substrates. Thus, an understanding of the molecular mechanisms underlying substrate specificities could be very useful in the engineering of GH10 endoxylanases for biotechnological purposes. Herein, we analyzed XynA, an endoxylanase that contains a (β/α)8-barrel domain and an intrinsically disordered region (IDR) of 29 amino acids at its amino end. Enzyme activity assays revealed that the elimination of the IDR resulted in a mutant enzyme (XynAΔ29) in which two new activities emerged: the ability to release xylose from xylan, and the ability to hydrolyze p-nitrophenyl-β-d-xylopyranoside (pNPXyl), a substrate that wild-type enzyme cannot hydrolyze. Circular dichroism and tryptophan fluorescence quenching by acrylamide showed changes in secondary structure and increased flexibility of XynAΔ29. Molecular dynamics simulations revealed that the emergence of the pNPXyl-hydrolyzing activity correlated with a dynamic behavior not previously observed in GH10 endoxylanases: a hinge-bending motion of two symmetric regions within the (β/α)8-barrel domain, whose hinge point is the active cleft. The hinge-bending motion is more intense in XynAΔ29 than in XynA and promotes the formation of a wider active site that allows the accommodation and hydrolysis of pNPXyl. Our results open new avenues for the study of the relationship between IDRs, dynamics and activity of endoxylanases, and other enzymes containing (β/α)8-barrel domain.
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Abstract
The 14-3-3 family proteins are vital scaffold proteins that ubiquitously expressed in various tissues. They interact with numerous protein targets and mediate many cellular signaling pathways. The 14-3-3 binding motifs are often embedded in intrinsically disordered regions which are closely associated with liquid-liquid phase separation (LLPS). In the past ten years, LLPS has been observed for a variety of proteins and biological processes, indicating that LLPS plays a fundamental role in the formation of membraneless organelles and cellular condensates. While extensive investigations have been performed on 14-3-3 proteins, its involvement in LLPS is overlooked. To date, 14-3-3 proteins have not been reported to undergo LLPS alone or regulate LLPS of their binding partners. To reveal the potential involvement of 14-3-3 proteins in LLPS, in this review, we summarized the LLPS propensity of 14-3-3 binding partners and found that about one half of them may undergo LLPS spontaneously. We further analyzed the phase separation behavior of representative 14-3-3 binders and discussed how 14-3-3 proteins may be involved. By modulating the conformation and valence of interactions and recruiting other molecules, we speculate that 14-3-3 proteins can efficiently regulate the functions of their targets in the context of LLPS. Considering the critical roles of 14-3-3 proteins, there is an urgent need for investigating the involvement of 14-3-3 proteins in the phase separation process of their targets and the underling mechanisms.
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Molisso D, Coppola M, Buonanno M, Di Lelio I, Monti SM, Melchiorre C, Amoresano A, Corrado G, Delano-Frier JP, Becchimanzi A, Pennacchio F, Rao R. Tomato Prosystemin Is Much More than a Simple Systemin Precursor. BIOLOGY 2022; 11:biology11010124. [PMID: 35053122 PMCID: PMC8772835 DOI: 10.3390/biology11010124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 02/04/2023]
Abstract
Simple Summary Prosystemin is a 200 amino acid precursor that releases, upon wounding and biotic attacks, an 18 amino acid peptide called Systemin. This peptide was traditionally considered as the principal actor of the resistance of tomato plants induced by triggering multiple defense pathways in response to a wide range of biotic/abiotic stress agents. Recent findings from our group discovered the disordered structure of Prosystemin that promotes the binding of different molecular partners and the possible activation of multiple stress-related pathways. All of our recent findings suggest that Prosystemin could be more than a simple precursor of Systemin peptide. Indeed, we hypothesized that it contains other sequences able to activate multiple stress-related responses. To verify this hypothesis, we produced a truncated Prosystemin protein deprived of the Systemin peptide and the relative deleted gene. Experiments with transgenic tomato plants overexpressing the truncated Prosystemin and with plants exogenously treated with the recombinant truncated protein demonstrated that both transgenic and treated plants modulated the expression of defense-related genes and were protected against a noctuid moth and a fungal pathogen. Taken together, our results demonstrated that Prosystemin is not a mere scaffold of Systemin, but itself contains other biologically active regions. Abstract Systemin (Sys) is an octadecapeptide, which upon wounding, is released from the carboxy terminus of its precursor, Prosystemin (ProSys), to promote plant defenses. Recent findings on the disordered structure of ProSys prompted us to investigate a putative biological role of the whole precursor deprived of the Sys peptide. We produced transgenic tomato plants expressing a truncated ProSys gene in which the exon coding for Sys was removed and compared their defense response with that induced by the exogenous application of the recombinant truncated ProSys (ProSys(1-178), the Prosystemin sequence devoid of Sys region). By combining protein structure analyses, transcriptomic analysis, gene expression profiling and bioassays with different pests, we demonstrate that truncated ProSys promotes defense barriers in tomato plants through a hormone-independent defense pathway, likely associated with the production of oligogalacturonides (OGs). Both transgenic and plants treated with the recombinant protein showed the modulation of the expression of genes linked with defense responses and resulted in protection against the lepidopteran pest Spodoptera littoralis and the fungus Botrytis cinerea. Our results suggest that the overall function of the wild-type ProSys is more complex than previously shown, as it might activate at least two tomato defense pathways: the well-known Sys-dependent pathway connected with the induction of jasmonic acid biosynthesis and the successive activation of a set of defense-related genes, and the ProSys(1-178)-dependent pathway associated with OGs production leading to the OGs mediate plant immunity.
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Affiliation(s)
- Donata Molisso
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
- Materias s.r.l., Corso N. Protopisani 50, 80146 Naples, Italy
| | - Mariangela Coppola
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
| | - Martina Buonanno
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Ilaria Di Lelio
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Naples, Italy;
- Correspondence: (S.M.M.); (R.R.)
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cinthia 4, 80126 Naples, Italy; (C.M.); (A.A.)
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cinthia 4, 80126 Naples, Italy; (C.M.); (A.A.)
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
| | - John Paul Delano-Frier
- Center for Research and Advanced Studies (CINVESTAV) Irapuato, Department of Biochemistry and Biotechnology, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato 36500, Mexico;
| | - Andrea Becchimanzi
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
| | - Francesco Pennacchio
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Via Università 100, 80055 Naples, Italy
| | - Rosa Rao
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples, Italy; (D.M.); (M.C.); (I.D.L.); (G.C.); (A.B.); (F.P.)
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Via Università 100, 80055 Naples, Italy
- Correspondence: (S.M.M.); (R.R.)
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De Coninck T, Van Damme EJM. Review: The multiple roles of plant lectins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111096. [PMID: 34763880 DOI: 10.1016/j.plantsci.2021.111096] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
For decades, the biological roles of plant lectins remained obscure and subject to speculation. With the advent of technological and scientific progress, researchers have compiled a vast amount of information regarding the structure, biological activities and functionality of hundreds of plant lectins. Data mining of genomes and transcriptome sequencing and high-throughput analyses have resulted in new insights. This review aims to provide an overview of what is presently known about plant lectins, highlighting their versatility and the importance of plant lectins for a multitude of biological processes, such as plant development, immunity, stress signaling and regulation of gene expression. Though lectins primarily act as readers of the glycocode, the multiple roles of plant lectins suggest that their functionality goes beyond carbohydrate-recognition.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Dept. of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Els J M Van Damme
- Laboratory of Glycobiology & Biochemistry, Dept. of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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Ginsawaeng O, Heise C, Sangwan R, Karcher D, Hernández-Sánchez IE, Sampathkumar A, Zuther E. Subcellular Localization of Seed-Expressed LEA_4 Proteins Reveals Liquid-Liquid Phase Separation for LEA9 and for LEA48 Homo- and LEA42-LEA48 Heterodimers. Biomolecules 2021; 11:biom11121770. [PMID: 34944414 PMCID: PMC8698616 DOI: 10.3390/biom11121770] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/05/2021] [Accepted: 11/20/2021] [Indexed: 12/27/2022] Open
Abstract
LEA proteins are involved in plant stress tolerance. In Arabidopsis, the LEA_4 Pfam group is the biggest group with the majority of its members being expressed in dry seeds. To assess subcellular localization in vivo, we investigated 11 seed-expressed LEA_4 proteins in embryos dissected from dry seeds expressing LEA_4 fusion proteins under its native promoters with the Venus fluorescent protein (proLEA_4::LEA_4:Venus). LEA_4 proteins were shown to be localized in the endoplasmic reticulum, nucleus, mitochondria, and plastids. LEA9, in addition to the nucleus, was also found in cytoplasmic condensates in dry seeds dependent on cellular hydration level. Most investigated LEA_4 proteins were detected in 4-d-old seedlings. In addition, we assessed bioinformatic tools for predicting subcellular localization and promoter motifs of 11 seed-expressed LEA_4 proteins. Ratiometric bimolecular fluorescence complementation assays showed that LEA7, LEA29, and LEA48 form homodimers while heterodimers were formed between LEA7-LEA29 and LEA42-LEA48 in tobacco leaves. Interestingly, LEA48 homodimers and LEA42-LEA48 heterodimers formed droplets structures with liquid-like behavior. These structures, along with LEA9 cytoplasmic condensates, may have been formed through liquid-liquid phase separation. These findings suggest possible important roles of LLPS for LEA protein functions.
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21
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García-Carnero LC, Salinas-Marín R, Lozoya-Pérez NE, Wrobel K, Wrobel K, Martínez-Duncker I, Niño-Vega GA, Mora-Montes HM. The Heat Shock Protein 60 and Pap1 Participate in the Sporothrixschenckii-Host Interaction. J Fungi (Basel) 2021; 7:jof7110960. [PMID: 34829247 PMCID: PMC8620177 DOI: 10.3390/jof7110960] [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: 10/20/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Sporothrixschenckii is one of the etiological agents of sporotrichosis, a worldwide-distributed subcutaneous mycosis. Its cell wall contains a glycoconjugate composed of rhamnose, mannose, glucuronic acid, and proteins, named peptidorhamnomannan, which harbors important Sporothrix-specific immunogenic epitopes. Although the peptidorhamnomannan carbohydrate moiety has been extensively studied, thus far, little is known about the protein core. Here, using LC-MS/MS, we analyzed the S.schenckii peptidorhamnomannan peptide fraction and generated mass signals of 325 proteins, most of them likely to be moonlighting proteins. Among the identified proteins, chaperonin GroEL/Hsp60 and the uncharacterized protein Pap1 were selected for further analysis. Both proteins were heterologously expressed in bacteria, and they showed adhesive properties to the extracellular matrix proteins laminin, elastin, fibrinogen, and fibronectin, although Pap1 also was bound to type-I and type-II collagen. The inoculation of concentrations higher than 40 μg of these proteins, separately, increased immune effectors in the hemolymph of Galleriamellonella larvae and protected animals from an S.schenckii lethal challenge. These observations were confirmed when yeast-like cells, pre-incubated with anti-rHsp60 or anti-rPap1 antibodies were used to inoculate larvae. The animals inoculated with pretreated cells showed increased survival rates when compared to the control groups. In conclusion, we report that Hsp60 and Pap1 are part of the cell wall peptidorhamnomannan, can bind extracellular matrix components, and contribute to the S.schenckii virulence. To our knowledge, this is the first report about moonlighting protein in the S.schenckii cell wall with an important role during the pathogen-host interaction.
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Affiliation(s)
- Laura C. García-Carnero
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
| | - Roberta Salinas-Marín
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mor., Mexico; (R.S.-M.); (I.M.-D.)
| | - Nancy E. Lozoya-Pérez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
| | - Katarzyna Wrobel
- Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (K.W.); (K.W.)
| | - Kazimierz Wrobel
- Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (K.W.); (K.W.)
| | - Iván Martínez-Duncker
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mor., Mexico; (R.S.-M.); (I.M.-D.)
| | - Gustavo A. Niño-Vega
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
| | - Héctor M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P., Guanajuato 36050, Gto., Mexico; (L.C.G.-C.); (N.E.L.-P.); (G.A.N.-V.)
- Correspondence: ; Tel.: +52-473-7320006 (ext. 8193)
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22
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Villagomez FR, Diaz-Valencia JD, Ovalle-García E, Antillón A, Ortega-Blake I, Romero-Ramírez H, Cerna-Cortes JF, Rosales-Reyes R, Santos-Argumedo L, Patiño-López G. TBC1D10C is a cytoskeletal functional linker that modulates cell spreading and phagocytosis in macrophages. Sci Rep 2021; 11:20946. [PMID: 34686741 PMCID: PMC8536695 DOI: 10.1038/s41598-021-00450-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/11/2021] [Indexed: 12/14/2022] Open
Abstract
Cell spreading and phagocytosis are notably regulated by small GTPases and GAP proteins. TBC1D10C is a dual inhibitory protein with GAP activity. In immune cells, TBC1D10C is one of the elements regulating lymphocyte activation. However, its specific role in macrophages remains unknown. Here, we show that TBC1D10C engages in functions dependent on the cytoskeleton and plasma membrane reorganization. Using ex vivo and in vitro assays, we found that elimination and overexpression of TBC1D10C modified the cytoskeletal architecture of macrophages by decreasing and increasing the spreading ability of these cells, respectively. In addition, TBC1D10C overexpression contributed to higher phagocytic activity against Burkholderia cenocepacia and to increased cell membrane tension. Furthermore, by performing in vitro and in silico analyses, we identified 27 TBC1D10C-interacting proteins, some of which were functionally classified as protein complexes involved in cytoskeletal dynamics. Interestingly, we identified one unreported TBC1D10C-intrinsically disordered region (IDR) with biological potential at the cytoskeleton level. Our results demonstrate that TBC1D10C shapes macrophage activity by inducing reorganization of the cytoskeleton-plasma membrane in cell spreading and phagocytosis. We anticipate our results will be the basis for further studies focused on TBC1D10C. For example, the specific molecular mechanism in Burkholderia cenocepacia phagocytosis and functional analysis of TBC1D10C-IDR are needed to further understand its role in health and disease.
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Affiliation(s)
- Fabian R Villagomez
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico.,Laboratorio de Microbiología Molecular, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Juan D Diaz-Valencia
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico
| | - Erasmo Ovalle-García
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Antillón
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Iván Ortega-Blake
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Héctor Romero-Ramírez
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad De México, Mexico
| | - Jorge F Cerna-Cortes
- Laboratorio de Microbiología Molecular, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Roberto Rosales-Reyes
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental de la Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Leopoldo Santos-Argumedo
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad De México, Mexico
| | - Genaro Patiño-López
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico.
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23
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Candelise N, Scaricamazza S, Salvatori I, Ferri A, Valle C, Manganelli V, Garofalo T, Sorice M, Misasi R. Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications. Int J Mol Sci 2021; 22:ijms22116016. [PMID: 34199513 PMCID: PMC8199687 DOI: 10.3390/ijms22116016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.
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Affiliation(s)
- Niccolò Candelise
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-338-891-2668
| | - Silvia Scaricamazza
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
| | - Illari Salvatori
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Alberto Ferri
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Cristiana Valle
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Valeria Manganelli
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Tina Garofalo
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Maurizio Sorice
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Roberta Misasi
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
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24
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Ainslie A, Huiting W, Barazzuol L, Bergink S. Genome instability and loss of protein homeostasis: converging paths to neurodegeneration? Open Biol 2021; 11:200296. [PMID: 33878947 PMCID: PMC8059563 DOI: 10.1098/rsob.200296] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genome instability and loss of protein homeostasis are hallmark events of age-related diseases that include neurodegeneration. Several neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease and amyotrophic lateral sclerosis are characterized by protein aggregation, while an impaired DNA damage response (DDR) as in many genetic DNA repair disorders leads to pronounced neuropathological features. It remains unclear to what degree these cellular events interconnect with each other in the development of neurological diseases. This review highlights how the loss of protein homeostasis and genome instability influence one other. We will discuss studies that illustrate this connection. DNA damage contributes to many neurodegenerative diseases, as shown by an increased level of DNA damage in patients, possibly due to the effects of protein aggregates on chromatin, the sequestration of DNA repair proteins and novel putative DNA repair functions. Conversely, genome stability is also important for protein homeostasis. For example, gene copy number variations and the loss of key DDR components can lead to marked proteotoxic stress. An improved understanding of how protein homeostasis and genome stability are mechanistically connected is needed and promises to lead to the development of novel therapeutic interventions.
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Affiliation(s)
- Anna Ainslie
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Wouter Huiting
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Lara Barazzuol
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Steven Bergink
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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25
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Fatafta H, Samantray S, Sayyed-Ahmad A, Coskuner-Weber O, Strodel B. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:135-185. [PMID: 34656328 DOI: 10.1016/bs.pmbts.2021.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; AICES Graduate School, RWTH Aachen University, Aachen, Germany
| | | | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, Istanbul, Turkey
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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26
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Salladini E, Jørgensen MLM, Theisen FF, Skriver K. Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications. Int J Mol Sci 2020; 21:E9755. [PMID: 33371315 PMCID: PMC7767404 DOI: 10.3390/ijms21249755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.
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Affiliation(s)
| | | | | | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; (E.S.); (M.L.M.J.); (F.F.T.)
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27
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Grahl MVC, Lopes FC, Martinelli AHS, Carlini CR, Fruttero LL. Structure-Function Insights of Jaburetox and Soyuretox: Novel Intrinsically Disordered Polypeptides Derived from Plant Ureases. Molecules 2020; 25:molecules25225338. [PMID: 33207637 PMCID: PMC7696265 DOI: 10.3390/molecules25225338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) do not have a stable 3D structure but still have important biological activities. Jaburetox is a recombinant peptide derived from the jack bean (Canavalia ensiformis) urease and presents entomotoxic and antimicrobial actions. The structure of Jaburetox was elucidated using nuclear magnetic resonance which reveals it is an IDP with small amounts of secondary structure. Different approaches have demonstrated that Jaburetox acquires certain folding upon interaction with lipid membranes, a characteristic commonly found in other IDPs and usually important for their biological functions. Soyuretox, a recombinant peptide derived from the soybean (Glycine max) ubiquitous urease and homologous to Jaburetox, was also characterized for its biological activities and structural properties. Soyuretox is also an IDP, presenting more secondary structure in comparison with Jaburetox and similar entomotoxic and fungitoxic effects. Moreover, Soyuretox was found to be nontoxic to zebra fish, while Jaburetox was innocuous to mice and rats. This profile of toxicity affecting detrimental species without damaging mammals or the environment qualified them to be used in biotechnological applications. Both peptides were employed to develop transgenic crops and these plants were active against insects and nematodes, unveiling their immense potentiality for field applications.
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Affiliation(s)
- Matheus V. Coste Grahl
- Graduate Program in Medicine and Health Sciences, Brain Institute of Rio Grande do Sul (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, Brazil;
| | - Fernanda Cortez Lopes
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Building 43431, Porto Alegre CEP 91501-970, RS, Brazil;
| | - Anne H. Souza Martinelli
- Department of Biophysics & Deparment of Molecular Biology and Biotechnology-Biosciences Institute (IB), Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil;
| | - Celia R. Carlini
- Graduate Program in Medicine and Health Sciences, Brain Institute of Rio Grande do Sul (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, Brazil;
- Brain Institute and School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
- Correspondence: (C.R.C.); (L.L.F.); Tel.: +55-51-3320-3485 (C.R.C.); +54-351-535-3850 (L.L.F.)
| | - Leonardo L. Fruttero
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba CP 5000, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba CP 5000, Argentina
- Correspondence: (C.R.C.); (L.L.F.); Tel.: +55-51-3320-3485 (C.R.C.); +54-351-535-3850 (L.L.F.)
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28
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The Role of CDKs and CDKIs in Murine Development. Int J Mol Sci 2020; 21:ijms21155343. [PMID: 32731332 PMCID: PMC7432401 DOI: 10.3390/ijms21155343] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) and their inhibitors (CDKIs) play pivotal roles in the regulation of the cell cycle. As a result of these functions, it may be extrapolated that they are essential for appropriate embryonic development. The twenty known mouse CDKs and eight CDKIs have been studied to varying degrees in the developing mouse, but only a handful of CDKs and a single CDKI have been shown to be absolutely required for murine embryonic development. What has become apparent, as more studies have shone light on these family members, is that in addition to their primary functional role in regulating the cell cycle, many of these genes are also controlling specific cell fates by directing differentiation in various tissues. Here we review the extensive mouse models that have been generated to study the functions of CDKs and CDKIs, and discuss their varying roles in murine embryonic development, with a particular focus on the brain, pancreas and fertility.
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