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Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. eLife 2024; 12:RP92093. [PMID: 38717010 PMCID: PMC11078544 DOI: 10.7554/elife.92093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here, I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors, and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode Caenorhabditis elegans. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
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2
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Lalit F, Jose AM. Selecting genes for analysis using historically contingent progress. bioRxiv 2024:2024.05.01.592119. [PMID: 38746289 PMCID: PMC11092662 DOI: 10.1101/2024.05.01.592119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Progress in biology has generated numerous lists of genes that share some property. But, advancing from the initial implication of a set of genes in a process to understanding their roles in the process is slow and unsystematic. Here we use RNA silencing in C. elegans to illustrate a general approach for comparing lists of data accumulated by a field to prioritize genes for detailed study given limited resources. The partially subjective relationships between genes forged by both functional relatedness of the genes and biased progress in the field was captured as historical mutual information (HMI) and used as a quantitative measure for clustering genes. These clusters suggest regulatory links connecting RNA silencing with other processes like the cell cycle and identify understudied regulated genes that could be used to sense perturbation or mediate feedback inhibition.
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Chey MS, Raman P, Ettefa F, Jose AM. Evidence for multiple forms of heritable RNA silencing. bioRxiv 2024:2024.04.28.591487. [PMID: 38746304 PMCID: PMC11092508 DOI: 10.1101/2024.04.28.591487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Heritable gene silencing has been proposed to rely on DNA methylation, histone modifications, and/or non-coding RNAs in different organisms. Here we demonstrate that multiple RNA-mediated mechanisms with distinct and easily detectable molecular signatures can underlie heritable silencing of the same open-reading frame in the nematode C. elegans . Using two-gene operons, we reveal three cases of gene-selective silencing that provide support for the transmission of heritable epigenetic changes through different mechanisms of RNA silencing independent of changes in chromatin that would affect all genes of an operon equally. Different heritable epigenetic states of a gene were associated with distinct populations of stabilized mRNA fragments with untemplated poly-UG (pUG) tails, which are known intermediates of RNA silencing. These 'pUG signatures' provide a way to distinguish the multiple mechanisms that can drive heritable RNA silencing of a single gene.
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Knudsen-Palmer DR, Raman P, Ettefa F, Ravin LD, Jose AM. Target-specific requirements for RNA interference can arise through restricted RNA amplification despite the lack of specialized pathways. bioRxiv 2024:2023.02.07.527351. [PMID: 36798330 PMCID: PMC9934570 DOI: 10.1101/2023.02.07.527351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Since double-stranded RNA (dsRNA) is effective for silencing a wide variety of genes, all genes are typically considered equivalent targets for such RNA interference (RNAi). Yet, loss of some regulators of RNAi in the nematode C. elegans can selectively impair the silencing of some genes. Here we show that such selective requirements can be explained by an intersecting network of regulators acting on genes with differences in their RNA metabolism. In this network, the Maelstrom domain-containing protein RDE-10, the intrinsically disordered protein MUT-16, and the Argonaute protein NRDE-3 work together so that any two are required for silencing one somatic gene, but each is singly required for silencing another somatic gene, where only the requirement for NRDE-3 can be overcome by enhanced dsRNA processing. Quantitative models and their exploratory simulations led us to find that (1) changing cis-regulatory elements of the target gene can reduce the dependence on NRDE-3, (2) animals can recover from silencing in non-dividing cells and (3) cleavage and tailing of mRNAs with UG dinucleotides, which makes them templates for amplifying small RNAs, is enriched within 'pUG zones' matching the dsRNA. Similar crosstalk between pathways and restricted amplification could result in apparently selective silencing by endogenous RNAs.
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Affiliation(s)
- Daphne R. Knudsen-Palmer
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA. Biological Sciences Graduate Program, University of Maryland, College Park, USA
| | - Pravrutha Raman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA. Biological Sciences Graduate Program, University of Maryland, College Park, USA
- Current address: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Farida Ettefa
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA. Biological Sciences Graduate Program, University of Maryland, College Park, USA
- Current address: Institute for Systems Genetics, New York University School of Medicine, New York, NY, USA
| | - Laura De Ravin
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA. Biological Sciences Graduate Program, University of Maryland, College Park, USA
| | - Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA. Biological Sciences Graduate Program, University of Maryland, College Park, USA
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Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. bioRxiv 2023:2023.06.07.544138. [PMID: 37333369 PMCID: PMC10274868 DOI: 10.1101/2023.06.07.544138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Such stable changes can (1) alter steady-state levels while preserving the architecture, (2) induce different architectures that persist for many generations, or (3) collapse the entire architecture. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that the evolution of mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of regulatory architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode C. elegans, which range from permanent silencing to recovery from silencing within a few generations and subsequent resistance to silencing. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
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Chey M, Jose AM. Heritable epigenetic changes at single genes: challenges and opportunities in Caenorhabditis elegans. Trends Genet 2022; 38:116-119. [PMID: 34493403 PMCID: PMC9436772 DOI: 10.1016/j.tig.2021.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023]
Abstract
Organisms rely on stereotyped patterns of gene expression for similar form and function in every generation. The analysis of epigenetic changes in the expression of different genes across generations can provide the rationale for measured actions in one generation that consider impact on future generations.
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Affiliation(s)
- Mary Chey
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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Devanapally S, Raman P, Chey M, Allgood S, Ettefa F, Diop M, Lin Y, Cho YE, Jose AM. Mating can initiate stable RNA silencing that overcomes epigenetic recovery. Nat Commun 2021; 12:4239. [PMID: 34244495 PMCID: PMC8270896 DOI: 10.1038/s41467-021-24053-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/29/2021] [Indexed: 01/09/2023] Open
Abstract
Stable epigenetic changes appear uncommon, suggesting that changes typically dissipate or are repaired. Changes that stably alter gene expression across generations presumably require particular conditions that are currently unknown. Here we report that a minimal combination of cis-regulatory sequences can support permanent RNA silencing of a single-copy transgene and its derivatives in C. elegans simply upon mating. Mating disrupts competing RNA-based mechanisms to initiate silencing that can last for >300 generations. This stable silencing requires components of the small RNA pathway and can silence homologous sequences in trans. While animals do not recover from mating-induced silencing, they often recover from and become resistant to trans silencing. Recovery is also observed in most cases when double-stranded RNA is used to silence the same coding sequence in different regulatory contexts that drive germline expression. Therefore, we propose that regulatory features can evolve to oppose permanent and potentially maladaptive responses to transient change.
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Affiliation(s)
| | | | - Mary Chey
- University of Maryland, College Park, MD, USA
| | | | | | | | - Yixin Lin
- University of Maryland, College Park, MD, USA
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Galford KF, Jose AM. The FDA-approved drugs ticlopidine, sertaconazole, and dexlansoprazole can cause morphological changes in C. elegans. Chemosphere 2020; 261:127756. [PMID: 32731027 PMCID: PMC7606649 DOI: 10.1016/j.chemosphere.2020.127756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Urgent need for treatments limit studies of therapeutic drugs before approval by regulatory agencies. Analyses of drugs after approval can therefore improve our understanding of their mechanism of action and enable better therapies. We screened a library of 1443 Food and Drug Administration (FDA)-approved drugs using a simple assay in the nematode C. elegans and found three compounds that caused morphological changes. While the anticoagulant ticlopidine and the antifungal sertaconazole caused both accumulations that resulted in distinct distortions of pharyngeal anatomy and lethality upon acute exposure, the proton-pump inhibitor dexlansoprazole caused molting defects and required exposure during larval development. Such easily detectable defects in a powerful genetic model system advocate the continued exploration of current medicines using a variety of model organisms to better understand drugs already prescribed to millions of patients.
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Affiliation(s)
- Kyle F Galford
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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Jose AM. Heritable Epigenetic Changes Alter Transgenerational Waveforms Maintained by Cycling Stores of Information. Bioessays 2020; 42:e1900254. [PMID: 32319122 PMCID: PMC7359639 DOI: 10.1002/bies.201900254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/27/2020] [Indexed: 11/07/2022]
Abstract
Our view of heredity can potentially be distorted by the ease of introducing heritable changes in the replicating gene sequences but not in the cycling assembly of regulators around gene sequences. Here, key experiments that have informed the understanding of heredity are reinterpreted to highlight this distortion and the possible variety of heritable changes are considered. Unlike heritable genetic changes, which are always associated with mutations in gene sequence, heritable epigenetic changes can be associated with physical or chemical changes in molecules or only changes in the system. The transmission of cycling stores along the continuous lineage of cells that connects successive generations creates waves of activity and localization of the molecules that together form the cell code for development in each generation. As a result, heritable epigenetic changes can include any that can alter a wave such as changes in form, midline, frequency, amplitude, or phase. Testing this integrated view of all heritable information will require the concerted application of multiple experimental approaches across generations.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
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Abstract
Life relies on phenomena that range from changes in molecules that occur within nanoseconds to changes in populations that occur over millions of years. Researchers have developed a vast range of experimental techniques to analyze living systems, but a given technique usually only works over a limited range of length or time scales. Therefore, gaining a full understanding of a living system usually requires the integration of information obtained at multiple different scales by two or more techniques. This approach has undoubtedly led to a much better understanding of living systems but, equally, the staggering complexity of these systems, the sophistication and limitations of the techniques available in modern biology, and the need to use two or more techniques, can lead to persistent illusions of knowledge. Here, in an effort to make better use of the experimental techniques we have at our disposal, I propose a broad classification of techniques into six complementary approaches: perturbation, visualization, substitution, characterization, reconstitution, and simulation. Such a taxonomy might also help increase the reproducibility of inferences and improve peer review.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
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Abstract
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here, I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.) and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This entity-sensor-property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.
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Affiliation(s)
- Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, Room 2136, Bioscience Research Building (Building #413), College Park, MD 20742, USA
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Ravikumar S, Devanapally S, Jose AM. Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference. Nucleic Acids Res 2019; 47:10059-10071. [PMID: 31501873 PMCID: PMC6821342 DOI: 10.1093/nar/gkz748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode Caenorhabditis elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we demonstrate that EGO-1 can compensate for the lack of RRF-1 when dsRNA from neurons is used to silence genes in intestinal cells. However, the lineal origins of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. Variability is masked in wild-type animals, which show extensive silencing by neuronal dsRNA. As a result, cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against inferring uniformity of mechanism based on uniformity of outcome. We speculate that functional mosaicism could contribute to escape from targeted therapies and could allow developmental systems to drift over evolutionary time.
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Affiliation(s)
- Snusha Ravikumar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sindhuja Devanapally
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Abstract
Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct stores: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome sequence, the arrangement of molecules, including DNA, RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome sequence are transmitted together from one generation to the next, analysis of both is necessary to understand evolution and origins of inherited diseases. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation. See also the video abstract here: https://youtu.be/IdWEL-T6TPU.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
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Raman P, Zaghab SM, Traver EC, Jose AM. The double-stranded RNA binding protein RDE-4 can act cell autonomously during feeding RNAi in C. elegans. Nucleic Acids Res 2017; 45:8463-8473. [PMID: 28541563 PMCID: PMC5737277 DOI: 10.1093/nar/gkx484] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
Long double-stranded RNA (dsRNA) can silence genes of matching sequence upon ingestion in many invertebrates and is therefore being developed as a pesticide. Such feeding RNA interference (RNAi) is best understood in the worm Caenorhabditis elegans, where the dsRNA-binding protein RDE-4 initiates silencing by recruiting an endonuclease to process long dsRNA into short dsRNA. These short dsRNAs are thought to move between cells because muscle-specific rescue of rde-4 using repetitive transgenes enables silencing in other tissues. Here, we extend this observation using additional promoters, report an inhibitory effect of repetitive transgenes, and discover conditions for cell-autonomous silencing in animals with tissue-specific rescue of rde-4. While expression of rde-4(+) in intestine, hypodermis, or neurons using a repetitive transgene can enable silencing also in unrescued tissues, silencing can be inhibited wihin tissues that express a repetitive transgene. Single-copy transgenes that express rde-4(+) in body-wall muscles or hypodermis, however, enable silencing selectively in the rescued tissue but not in other tissues. These results suggest that silencing by the movement of short dsRNA between cells is not an obligatory feature of feeding RNAi in C. elegans. We speculate that similar control of dsRNA movement could modulate tissue-specific silencing by feeding RNAi in other invertebrates.
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Affiliation(s)
- Pravrutha Raman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Soriayah M Zaghab
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Edward C Traver
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Choi YS, Edwards LO, DiBello A, Jose AM. Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs. Nucleic Acids Res 2017; 45:e87. [PMID: 28180294 PMCID: PMC5449620 DOI: 10.1093/nar/gkx091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/02/2017] [Indexed: 12/21/2022] Open
Abstract
Changes in small non-coding RNAs such as micro RNAs (miRNAs) can serve as indicators of disease and can be measured using next-generation sequencing of RNA (RNA-seq). Here, we highlight the need for approaches that complement RNA-seq, discover that northern blotting of small RNAs is biased against short sequences and develop a protocol that removes this bias. We found that multiple small RNA-seq datasets from the worm Caenorhabditis elegans had shorter forms of miRNAs that appear to be degradation products that arose during the preparatory steps required for RNA-seq. When using northern blotting during these studies, we discovered that miRNA-length probes can have ∼1000-fold bias against detecting even synthetic sequences that are 8 nt shorter. By using shorter probes and by performing hybridization and washes at low temperatures, we greatly reduced this bias to enable nearly equivalent detection of 24 to 14 nt RNAs. Our protocol can discriminate RNAs that differ by a single nucleotide and can detect specific miRNAs present in total RNA from C. elegans and pRNAs in total RNA from bacteria. This improved northern blotting is particularly useful to analyze products of RNA processing or turnover, and functional RNAs that are shorter than typical miRNAs.
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Affiliation(s)
- Yun S Choi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
| | - Lanelle O Edwards
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
| | - Aubrey DiBello
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
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Le HH, Looney M, Strauss B, Bloodgood M, Jose AM. Tissue homogeneity requires inhibition of unequal gene silencing during development. J Cell Biol 2016; 214:319-31. [PMID: 27458132 PMCID: PMC4970325 DOI: 10.1083/jcb.201601050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/29/2016] [Indexed: 11/22/2022] Open
Abstract
Multicellular organisms can generate and maintain homogenous populations of cells that make up individual tissues. However, cellular processes that can disrupt homogeneity and how organisms overcome such disruption are unknown. We found that ∼100-fold differences in expression from a repetitive DNA transgene can occur between intestinal cells in Caenorhabditis elegans These differences are caused by gene silencing in some cells and are actively suppressed by parental and zygotic factors such as the conserved exonuclease ERI-1. If unsuppressed, silencing can spread between some cells in embryos but can be repeat specific and independent of other homologous loci within each cell. Silencing can persist through DNA replication and nuclear divisions, disrupting uniform gene expression in developed animals. Analysis at single-cell resolution suggests that differences between cells arise during early cell divisions upon unequal segregation of an initiator of silencing. Our results suggest that organisms with high repetitive DNA content, which include humans, could use similar developmental mechanisms to achieve and maintain tissue homogeneity.
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Affiliation(s)
- Hai H Le
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Monika Looney
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Benjamin Strauss
- Center for Advanced Study of Language, University of Maryland, College Park, MD 20742
| | - Michael Bloodgood
- Center for Advanced Study of Language, University of Maryland, College Park, MD 20742
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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Blumenfeld AL, Jose AM. Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs. RNA 2016; 22:184-192. [PMID: 26647462 PMCID: PMC4712669 DOI: 10.1261/rna.054551.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
Small RNAs regulate gene expression and most genes in the worm Caenorhabditis elegans are subject to their regulation. Here, we analyze small RNA data sets and use reproducible features of RNAs present in multiple data sets to discover a new class of small RNAs and to reveal insights into two known classes of small RNAs--22G RNAs and 26G RNAs. We found that reproducibly detected 22-nt RNAs, although are predominantly RNAs with a G at the 5' end, also include RNAs with A, C, or U at the 5' end. These RNAs are synthesized downstream from characteristic sequence motifs on mRNA and have U-tailed derivatives. Analysis of 26G RNAs revealed that they are processed from a blunt end of double-stranded RNAs and that production of one 26G RNA generates a hotspot immediately downstream for production of another. To our surprise, analysis of RNAs shorter than 18 nt revealed a new class of RNAs, which we call NU RNAs (pronounced "new RNAs") because they have a NU bias at the 5' end, where N is any nucleotide. NU RNAs are antisense to genes and originate downstream from U bases on mRNA. Although many genes have complementary NU RNAs, their genome-wide distribution is distinct from that of previously known classes of small RNAs. Our results suggest that current approaches underestimate reproducibly detected RNAs that are shorter than 18 nt, and theoretical considerations suggest that such shorter RNAs could be used for sequence-specific gene regulation in organisms like C. elegans that have small genomes.
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Affiliation(s)
- Andrew L Blumenfeld
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
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Abstract
Recent studies suggest that RNA can move from one cell to another and regulate genes through specific base-pairing. Mechanisms that modify or select RNA for secretion from a cell are unclear. Secreted RNA can be stable enough to be detected in the extracellular environment and can enter the cytosol of distant cells to regulate genes. Mechanisms that import RNA into the cytosol of an animal cell can enable uptake of RNA from many sources including other organisms. This role of RNA is akin to that of steroid hormones, which cross cell membranes to regulate genes. The potential diagnostic use of RNA in human extracellular fluids has ignited interest in understanding mechanisms that enable the movement of RNA between animal cells. Genetic model systems will be essential to gain more confidence in proposed mechanisms of RNA transport and to connect an extracellular RNA with a specific biological function. Studies in the worm C. elegans and in other animals have begun to reveal parts of this novel mechanism of cell-to-cell communication. Here, I summarize the current state of this nascent field, highlight the many unknowns, and suggest future directions.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
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Jose AM, Garcia GA, Hunter CP. Two classes of silencing RNAs move between Caenorhabditis elegans tissues. Nat Struct Mol Biol 2011; 18:1184-8. [PMID: 21984186 PMCID: PMC3210371 DOI: 10.1038/nsmb.2134] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/09/2011] [Indexed: 12/27/2022]
Abstract
Organism-wide RNA interference (RNAi) is due to the transport of mobile silencing RNA throughout the organism but the identities of these mobile RNA species in animals are unknown. Here we present genetic evidence that both the initial double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNA in Caenorhabditis elegans. This dsRNA intermediate requires the long dsRNA-binding protein RDE-4, the endonuclease DCR-1, which cleaves long dsRNA into double-stranded short-interfering RNA (ds-siRNA), and the putative nucleotidyltransferase MUT-2 (RDE-3). However, single-stranded siRNA and downstream secondary siRNA produced upon amplification by the RNA-dependent RNA Polymerase RRF-1 do not generate mobile silencing RNA. Restricting inter-tissue transport to long dsRNA and directly processed siRNA intermediates rather than amplified siRNA may serve to modulate the extent of systemic silencing in proportion to available dsRNA.
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Affiliation(s)
- Antony M Jose
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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20
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Abstract
When eukaryotic cells encounter double-stranded RNA, genes of matching sequence are silenced through RNA interference. Surprisingly, in some animals and plants, the same gene is specifically silenced even in cells that did not encounter the double-stranded RNA, due to the transport of a gene-specific silencing signal between cells. This silencing signal likely has an RNA component that gives it sequence-specificity, however its precise identity remains unknown. Studies in the worm Caenorhabditis elegans and in plants have revealed parts of a complex protein machinery that transports this silencing signal. Some of these proteins are conserved in vertebrates, including mammals, raising the possibility that higher animals can communicate gene-specific silencing information between cells. Such communication provides antiviral immunity in plants and perhaps in C. elegans. Identifying the transported silencing signal and deciphering the evolutionarily selected role of the transport machinery are some of the key challenges for the future.
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Affiliation(s)
- Antony M Jose
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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21
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Jose AM, Bany IA, Chase DL, Koelle MR. A specific subset of transient receptor potential vanilloid-type channel subunits in Caenorhabditis elegans endocrine cells function as mixed heteromers to promote neurotransmitter release. Genetics 2006; 175:93-105. [PMID: 17057248 PMCID: PMC1774992 DOI: 10.1534/genetics.106.065516] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Transient receptor potential (TRP) channel subunits form homotetramers that function in sensory transduction. Heteromeric channels also form, but their physiological subunit compositions and functions are largely unknown. We found a dominant-negative mutant of the C. elegans TRPV (vanilloid-type) subunit OCR-2 that apparently incorporates into and inactivates OCR-2 homomers as well as heteromers with the TRPV subunits OCR-1 and -4, resulting in a premature egg-laying defect. This defect is reproduced by knocking out all three OCR genes, but not by any single knockout. Thus a mixture of redundant heteromeric channels prevents premature egg laying. These channels, as well as the G-protein G alpha(o), function in neuroendocrine cells to promote release of neurotransmitters that block egg laying until eggs filling the uterus deform the neuroendocrine cells. The TRPV channel OSM-9, previously suggested to be an obligate heteromeric partner of OCR-2 in sensory neurons, is expressed in the neuroendocrine cells but has no detectable role in egg laying. Our results identify a specific set of heteromeric TRPV channels that redundantly regulate neuroendocrine function and show that a subunit combination that functions in sensory neurons is also present in neuroendocrine cells but has no detectable function in these cells.
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Affiliation(s)
- Antony M Jose
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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22
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Jose AM, Koelle MR. Domains, amino acid residues, and new isoforms of Caenorhabditis elegans diacylglycerol kinase 1 (DGK-1) important for terminating diacylglycerol signaling in vivo. J Biol Chem 2004; 280:2730-6. [PMID: 15563467 PMCID: PMC2048986 DOI: 10.1074/jbc.m409460200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Diacylglycerol kinases (DGKs) inhibit diacylglycerol (DAG) signaling by phosphorylating DAG. DGK-1, the Caenorhabditis elegans ortholog of human neuronal DGK, inhibits neurotransmission to control behavior. DGK-1, like DGK, has three cysteine-rich domains (CRDs), a pleckstrin homology domain, and a kinase domain. To identify DGK domains and amino acid residues critical for terminating DAG signaling in vivo, we analyzed 20 dgk-1 mutants defective in DGK-1-controlled behaviors. We found by sequencing that the mutations included nine amino acid substitutions and seven premature stop codons that impair the physiological functions of DGK-1. All nine amino acid substitutions are in the second CRD, the third CRD, or the kinase domain. Thus, these domains are important for the termination of DAG signaling by DGK-1 in vivo. Seven of the substituted amino acid residues are present in all human DGKs and likely define key residues required for the function of all DGKs. An ATP-binding site mutation expected to inactivate the kinase domain retained very little physiological function, but we found two stop codon mutants predicted to truncate DGK-1 before its kinase domain that retained significantly more function. We detected novel splice forms of dgk-1 that can reconcile this apparent conflict, as they skip exons containing the stop codons to produce DGK-1 isoforms that contain the kinase domain. Two of these isoforms lack an intact pleckstrin homology domain and yet appear to have significant function. Additional novel isoform(s) account for all of the DGK-1 function necessary for one behavior, dopamine response.
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Affiliation(s)
- Antony M. Jose
- Departments of Molecular, Cellular, and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Michael R. Koelle
- Departments of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
- ¶ To whom correspondence should be addressed: Dept. of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar St., SHM CE-30, New Haven, CT 06520. Tel.: 203-737-5808; Fax: 203-785-6404; E-mail:
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23
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Jose AM. Ribozyme therapy: RNA enzymes to the rescue. Yale J Biol Med 2002; 75:215-9. [PMID: 12784972 PMCID: PMC2588793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Antony M Jose
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
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Jose AM, Soukup GA, Breaker RR. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 2001; 29:1631-7. [PMID: 11266567 PMCID: PMC31269 DOI: 10.1093/nar/29.7.1631] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2000] [Revised: 01/27/2001] [Accepted: 01/27/2001] [Indexed: 11/14/2022] Open
Abstract
An allosteric ribozyme that requires two different effectors to induce catalysis was created using modular rational design. This ribozyme construct comprises five conjoined RNA modules that operate in concert as an obligate FMN- and theophylline-dependent molecular switch. When both effectors are present, this 'binary' RNA switch self-cleaves with a rate enhancement of approximately 300-fold over the rate observed in the absence of effectors. Kinetic and structural studies implicate a switching mechanism wherein FMN binding induces formation of the active ribozyme conformation. However, the binding site for FMN is rendered inactive unless theophylline first binds to its corresponding site and reorganizes the RNA structure. This example of cooperative binding between allosteric effectors reveals a level of structural and functional complexity for RNA that is similar to that observed with allosteric proteins.
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Affiliation(s)
- A M Jose
- Department of Molecular, Cellular and Developmental Biology, KBT 452, Yale University, PO Box 208103, New Haven, CT 06520-8103, USA
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25
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Jose AM. Anatomy and Leonardo da Vinci. Yale J Biol Med 2001; 74:185-95. [PMID: 11501715 PMCID: PMC2588719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- A M Jose
- Yale School of Medicine, New Haven, Connecticut 06520-8024, USA.
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26
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Beggs CJ, Geile W, Holmes MG, Jabben M, Jose AM, Schäfer E. High irradiance response promotion of a subsequent light induction response in Sinapis alba L. Planta 1981; 151:135-140. [PMID: 24301720 DOI: 10.1007/bf00387814] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/1980] [Accepted: 10/01/1980] [Indexed: 06/02/2023]
Abstract
Relative quantum responsivity curves for inhibition of hypocotyl elongation in Sinapis alba L. seedlings previously grown in white light confirm that a marked "end of day" inhibition response can be induced by a monochromatic light treatment (30 min) at the end of the light period. In dark grown seedlings, however, no growth inhibition can be induced by a 30 min monochromatic light treatment. A prerequisite for an induction response appears to be a pretreatment with continuous light. Far red light is most effective with blue and red light showing a lesser effectiveness. The light pretreatment also shows a marked fluence rate dependency with respect to its ability to allow an induction response to manifest itself. The pretreatment required shows all the characteristics of a classical "HIR" response. The appearance of the effect in plants treated with the herbicide SAN 9789 seems to exclude chlorophyll as being the photoreceptor.
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Affiliation(s)
- C J Beggs
- Biologisches Institut II der Universität, Schänzlestraße 1, D-7800, Freiburg, Federal Republic of Germany
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27
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Jose AM, Schäfer E. Red/far-red modulation in vitro of enzyme activity in a membrane fraction from Phaseolus aureus. Planta 1979; 146:75-81. [PMID: 24317949 DOI: 10.1007/bf00381258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/1978] [Accepted: 03/16/1979] [Indexed: 06/02/2023]
Abstract
In a membrane fraction isolated from hypocotyls of Phaseolus aureus Roxb. the activity of a number of enzymes was regulated by red and far-red irradiation in vitro, provided that the tissue received a brief red light treatment before extraction. Other enzymes showed no photoregulation. There were two types of photocontrol, neither of which could be detected in the solute fraction, nor in extracts from completely etiolated material. One (Type I) was a red/far-red reversible regulation of the rate of enzyme activity, depending on the light given (in vivo or in vitro) before the assay was begun. The second (Type II) was a promotion of enzyme activity by red or far-red light given during the assay. The action spectra for type II responses do not coincide with either the phytochrome absorption or difference spectra. However, the effectiveness of red and far-red was correlated with the Pfr/P ratio present at the beginning of the assay, such that far-red was more efficient at high Pfr/P and red at low Pfr/P ratios. All enzymes that were regulated involved ATP. In samples that showed enzyme regulation, small changes in fluorescence yield of tryptophan and the covalent probe "Fluram" (Roche) accompanied the photoconversion of phytochrome, but no fluorescence changes could be measured after briefly incubating the membrane fraction with ATP. The results indicate that light may affect the interaction of ATP with the membrane fraction.
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Affiliation(s)
- A M Jose
- Biologisches Institut II der Universität, Schänzlestraße 1, D-7800, Freiburg/Br., Federal Republic of Germany
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28
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Abstract
Red light absorption by photosynthetic pigments screens stem tissue of Phaseolus vulgaris L. seedlings to such an extent that the most effective wavelength for the phytochrome induction control of stem growth is approximately 628 nm. Screening is greater in the first internode than in the hypocotyl. The consequences are that, compared with etiolated seedlings, much higher irradiances are required for phytochrome control in green plants, and the efficiency of 660 nm light is markedly reduced. Even very high exposures at 660 nm may not achieve appreciable photoconversion of P r to P fr.
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Affiliation(s)
- A M Jose
- Department of Botany, Plant Science Laboratories, University of Reading, Whiteknights, RG6 2AS, Reading, U.K
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29
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Jose AM, Vince-Prue D. Action spectra for the inhibition of growth in radish hypocotyls. Planta 1977; 136:131-134. [PMID: 24420317 DOI: 10.1007/bf00396188] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/1977] [Accepted: 05/04/1977] [Indexed: 06/03/2023]
Abstract
In etiolated seedlings of Raphanus sativus L. the inhibition of hypocotyl elongation by continuous light showed a major bimodal peak of action in the red and far-red, and two minor peaks in the blue regions of the spectrum. It is argued that, under conditions of prolonged irradiation, phytochrome is the pigment controlling the inhibition of hypocotyl elongation by red and far-red light, but that its mode of action in far-red is different from that in red. A distinct pigment is postulated for blue light.
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Affiliation(s)
- A M Jose
- Department of Botany, University of Reading, Whiteknights, RG6 2AS, Reading, UK
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30
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Jose AM. Phytochrome modulation of ATPase activity in a membrane fraction from Phaseolus. Planta 1977; 137:203-206. [PMID: 24420654 DOI: 10.1007/bf00388151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/1977] [Accepted: 08/30/1977] [Indexed: 06/03/2023]
Abstract
Membrane-bound phytochrome and ATPase (ATP phosphohydrolase EC 3.6.1.3.) activity extracted from hypocotyl hooks of etiolated Phaseolus aureus Roxb. were both separated from solute proteins by gel filtration on Sepharose C1-2B. The amount of phytochrome detected in the membrane fraction was very small and was not significantly increased by red irradiation (in vivo or in vitro). Membrane-bound ATPase activity was modulated in vitro by the phytochrome in the membrane fraction, being lower after red light than after far-red light. This effect was potentiated by a preliminary light reaction which occurred only in vivo and, in continuous red light, required 60 to 90 s at 25°C. Thus a two minute, in vivo, red irradiation reduced membrane-bound ATPase activity to about half that of the etiolated state. Subsequently bound-ATPase activity was determined by the form of phytochrome (Pr or Pfr) irrespective of whether established in vivo or in vitro. These results indicate that binding or release (of enzyme, cofactors or inhibitors) is not involved in phytochrome modulation of enzyme activity in the membrane fraction.
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Affiliation(s)
- A M Jose
- Department of Botany, University of Reading, Whiteknights, RG6 2AS, Reading, UK
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31
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Abstract
In etiolated hypocotyls of Raphanus sativus L. the growth responses to continuous red, far-red and blue light have been distinguished on the bases of photoreceptive sites and regions of physiological response. Blue light appeared to retard a fairly mature stage of elongation, acting immediately and directly on the cells irradiated. Far-red light caused a marked inhibition of all stages of elongation after a lag period, and the stimulus could be transmitted from the hook region. The effect of red light was complex and consisted of one promotive and two inhibitory responses.
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Affiliation(s)
- A M Jose
- Department of Botany, University of Reading, Whiteknights, RG6 2AS, Reading, UK
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Jose AM, Vince-Prue D, Hilton JR. Chlorophyll interference with phytochrome measurement. Planta 1977; 135:119-123. [PMID: 24420012 DOI: 10.1007/bf00387159] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/1976] [Accepted: 02/03/1977] [Indexed: 06/03/2023]
Abstract
Measurements of phytochrome by Δ (ΔA725-815 nm) were completely suppressed at chlorophyll concentrations of the order of 20-40 μg g(-1) f.wt. in vivo and 37 μg cm(-3) in vitro, and the readings were reduced by 50% at only 12 μg cm(-3) in vitro. At these concentrations of chlorophyll in aqueous methanol, the loss of phytochrome signal in vitro appeared to be due to failure of phytochrome photoconversion rather than to interference with ΔA measuremebt by chlorophyll fluorescence in the 125/815 nm measuring beam.
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Affiliation(s)
- A M Jose
- Department of Botany Plant Science Laboratories, University of Reading, Whiteknights, RG6 2AS, Reading, UK
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Abstract
Pelletable phytochrome from hypocotyl hooks of Cucurbita pepo L. seedlings has been separated into two fractions by gel filtration on Sepharose CL-2B. One fraction with a K av of 0.7 was detected only after red irradiation (in vivo or in vitro). This separated from a ribonucleoprotein fraction during gel filtration. The weak interaction with ribonucleo-protein which required magnesium (optimal at 10 mM) was overcome by high salt concentrations and prevented by ribonuclease treatment. The second phytochrome fraction was strongly associated with a high molecular weight material with a K av of less than 0.1. Low levels of this complex were detected in extracts from dark grown tissue but were increased by red irradiation of excised hooks or crude extracts. The binding of phytochrome to the high molecular weight material did not require magnesium, was unaffected by ribonuclease treatment, and was much more resistant to high salt concentrations than was the phytochrome-ribonucleoprotein association. These results suggest that the association of phytochrome with this membrane-containing fraction is not electrostatic.The separation by agarose-gel filtration offers a useful technique for the preparation of membraneassociated phytochrome for physiological studies.
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Affiliation(s)
- A M Jose
- Department of Botany, University of Reading, Whiteknights, RG6 2AS, Reading, UK
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Jose AM, Vince-Frue D. Light-induced changes in the photoresponses of plant stems the loss of a high irradiance response to far-red light. Planta 1977; 135:95-100. [PMID: 24420009 DOI: 10.1007/bf00387156] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/1976] [Accepted: 01/03/1977] [Indexed: 06/03/2023]
Abstract
De-etiolation results in phytochrome destruction, greening, and the loss of the far-red high irradiance responses (HIR). Evidence is presented against the hypothesis that the loss of the far-red HIR is a direct consequence of phytochrome destruction. Loss of the far-red HIR for the inhibition of elongation in hypocotyls of Raphanus sativus involves two different, but linked, actions of phytochrome. An induction reaction requires the far-red absorbing form of phytochrome for about 20 min after which accumulation of its product depends only on time. A second reaction requires continuous light or frequent short irradiations and involves cycling of the phytochrome system. This acts on the product of the induction reaction. It is proposed that in green plants an important mode of operation of phytochrome in the light depends on pigment cycling, and that during de-etiolation this system is established under phytochrome control.
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Affiliation(s)
- A M Jose
- Department of Botany, Plant Science Laboratories, University of Reading, Whiteknights, RG6 2AS, Reading, UK
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