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Article: Evidence That Ion-Based Signaling Initiating at the Cell Surface Can Potentially Influence Chromatin Dynamics and Chromatin-Bound Proteins in the Nucleus.

Matzke, Antonius J M / Lin, Wen-Dar / Matzke, Marjori

2019 Volume 10, Page(s) 1267

Abstract: We have developed tools and performed pilot experiments to test the hypothesis that an intracellular ion-based signaling pathway, provoked by an extracellular stimulus acting at the cell surface, can influence interphase chromosome dynamics and chromatin- ...

Abstract	We have developed tools and performed pilot experiments to test the hypothesis that an intracellular ion-based signaling pathway, provoked by an extracellular stimulus acting at the cell surface, can influence interphase chromosome dynamics and chromatin-bound proteins in the nucleus. The experimental system employs chromosome-specific fluorescent tags and the genome-encoded fluorescent pH sensor SEpHluorinA227D, which has been targeted to various intracellular membranes and soluble compartments in root cells of
Language	English
Publishing date	2019-10-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2019.01267
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Article ; Online: Expression and testing in plants of ArcLight, a genetically-encoded voltage indicator used in neuroscience research.

Matzke, Antonius J M / Matzke, Marjori

BMC plant biology

2015 Volume 15, Page(s) 245

Abstract: Background: It is increasingly appreciated that electrical controls acting at the cellular and supra-cellular levels influence development and initiate rapid responses to environmental cues. An emerging method for non-invasive optical imaging of ... ...

Abstract	Background: It is increasingly appreciated that electrical controls acting at the cellular and supra-cellular levels influence development and initiate rapid responses to environmental cues. An emerging method for non-invasive optical imaging of electrical activity at cell membranes uses genetically-encoded voltage indicators (GEVIs). Developed by neuroscientists to chart neuronal circuits in animals, GEVIs comprise a fluorescent protein that is fused to a voltage-sensing domain. One well-known GEVI, ArcLight, undergoes strong shifts in fluorescence intensity in response to voltage changes in mammalian cells. ArcLight consists of super-ecliptic (SE) pHluorin (pH-sensitive fluorescent protein) with an A227D substitution, which confers voltage sensitivity in neurons, fused to the voltage-sensing domain of the voltage-sensing phosphatase of C iona i ntestinalis (Ci-VSD). In an ongoing effort to adapt tools of optical electrophysiology for plants, we describe here the expression and testing of ArcLight and various derivatives in different membranes of root cells in Arabidopsis thaliana. Results: Transgenic constructs were designed to express ArcLight and various derivatives targeted to the plasma membrane and nuclear membranes of Arabidopsis root cells. In transgenic seedlings, changes in fluorescence intensity of these reporter proteins following extracellular ATP (eATP) application were monitored using a fluorescence microscope equipped with a high speed camera. Coordinate reductions in fluorescence intensity of ArcLight and Ci-VSD-containing derivatives were observed at both the plasma membrane and nuclear membranes following eATP treatments. However, similar responses were observed for derivatives lacking the Ci-VSD. The dispensability of the Ci-VSD suggests that in plants, where H(+) ions contribute substantially to electrical activities, the voltage-sensing ability of ArcLight is subordinate to the pH sensitivity of its SEpHluorin base. The transient reduction of ArcLight fluorescence triggered by eATP most likely reflects changes in pH and not membrane voltage. Conclusions: The pH sensitivity of ArcLight precludes its use as a direct sensor of membrane voltage in plants. Nevertheless, ArcLight and derivatives situated in the plasma membrane and nuclear membranes may offer robust, fluorescence intensity-based pH indicators for monitoring concurrent changes in pH at these discrete membrane systems. Such tools will assist analyses of pH as a signal and/or messenger at the cell surface and the nuclear periphery in living plants.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Animals ; Arabidopsis/genetics ; Arabidopsis/radiation effects ; Cell Membrane/metabolism ; Cell Membrane/radiation effects ; Drosophila melanogaster/radiation effects ; Light ; Luminescent Proteins/metabolism ; Neurosciences ; Plant Cells/metabolism ; Plant Cells/radiation effects ; Plant Roots/cytology ; Plant Roots/radiation effects ; Plants, Genetically Modified ; Recombinant Fusion Proteins/metabolism ; Research
Chemical Substances	Arclight fusion protein ; Luminescent Proteins ; Recombinant Fusion Proteins ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2015-10-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-015-0633-z
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Article ; Online: A Collection of Pre-mRNA Splicing Mutants in

Kanno, Tatsuo / Venhuizen, Peter / Wu, Ming-Tsung / Chiou, Phebe / Chang, Chia-Liang / Kalyna, Maria / Matzke, Antonius J M / Matzke, Marjori

G3 (Bethesda, Md.)

2020 Volume 10, Issue 6, Page(s) 1983–1996

Abstract: To investigate factors influencing pre-mRNA splicing in plants, we conducted a forward genetic screen using an alternatively- ... ...

Abstract	To investigate factors influencing pre-mRNA splicing in plants, we conducted a forward genetic screen using an alternatively-spliced
MeSH term(s)	Alternative Splicing ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Gene Expression Regulation, Plant ; Mutation ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Splicing
Chemical Substances	Arabidopsis Proteins ; RNA Precursors
Language	English
Publishing date	2020-06-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.119.400998
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Article: Membrane "potential-omics": toward voltage imaging at the cell population level in roots of living plants.

Matzke, Antonius J M / Matzke, Marjori

Frontiers in plant science

2013 Volume 4, Page(s) 311

Abstract: Genetically encoded voltage-sensitive fluorescent proteins (VSFPs) are being used in neurobiology as non-invasive tools to study synchronous electrical activities in specific groups of nerve cells. Here we discuss our efforts to adapt this "light-based ... ...

Abstract	Genetically encoded voltage-sensitive fluorescent proteins (VSFPs) are being used in neurobiology as non-invasive tools to study synchronous electrical activities in specific groups of nerve cells. Here we discuss our efforts to adapt this "light-based electrophysiology" for use in plant systems. We describe the production of transgenic plants engineered to express different versions of VSFPs that are targeted to the plasma membrane and internal membranes of root cells. The aim is to optically record concurrent changes in plasma membrane potential in populations of cells and at multiple membrane systems within single cells in response to various stimuli in living plants. Such coordinated electrical changes may globally orchestrate cell behavior to elicit successful reactions of the root as a whole to varying and unpredictable environments. Findings from membrane "potential-omics" can eventually be fused with data sets from other "omics" approaches to forge the integrated and comprehensive understanding that underpins the concept of systems biology.
Language	English
Publishing date	2013-08-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2013.00311
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Article ; Online: A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in

Kanno, Tatsuo / Lin, Wen-Dar / Chang, Chia-Liang / Matzke, Marjori / Matzke, Antonius J M

G3 (Bethesda, Md.)

2018 Volume 8, Issue 4, Page(s) 1367–1377

Abstract: Splicing of pre-mRNA involves two ... ...

Abstract	Splicing of pre-mRNA involves two consecutive
MeSH term(s)	Alternative Splicing/genetics ; Arabidopsis/genetics ; Arabidopsis Proteins/metabolism ; Fluorescence ; Gene Expression Regulation, Plant ; Genes, Reporter ; Genetic Complementation Test ; Genetic Testing ; Green Fluorescent Proteins/metabolism ; Introns/genetics ; Models, Biological ; Mutation/genetics ; Phenotype ; Plants, Genetically Modified ; RNA Splicing Factors/metabolism ; Sequence Analysis, RNA ; Spliceosomes/metabolism
Chemical Substances	Arabidopsis Proteins ; PRP18a protein, Arabidopsis ; RNA Splicing Factors ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2018-03-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.118.200022
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Article ; Online: RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants.

Matzke, Marjori A / Kanno, Tatsuo / Matzke, Antonius J M

Annual review of plant biology

2015 Volume 66, Page(s) 243–267

Abstract: RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA ...

Abstract	RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)-related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. We present current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and Pol V pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.
MeSH term(s)	Biological Evolution ; DNA Methylation ; DNA, Plant/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Gene Expression Regulation, Plant ; Gene Silencing ; Magnoliopsida/genetics ; Magnoliopsida/metabolism ; Plant Proteins/metabolism ; RNA, Plant/metabolism ; RNA, Small Interfering/metabolism
Chemical Substances	DNA, Plant ; Plant Proteins ; RNA, Plant ; RNA, Small Interfering ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1545-2123
ISSN (online)	1545-2123
DOI	10.1146/annurev-arplant-043014-114633
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Article ; Online: A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in

Kanno, Tatsuo / Lin, Wen-Dar / Fu, Jason L / Matzke, Antonius J M / Matzke, Marjori

RNA (New York, N.Y.)

2017 Volume 23, Issue 7, Page(s) 1068–1079

Abstract: To identify regulators of pre-mRNA splicing in plants, we developed a forward genetic screen based on an alternatively ... ...

Abstract	To identify regulators of pre-mRNA splicing in plants, we developed a forward genetic screen based on an alternatively spliced
MeSH term(s)	Alternative Splicing ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Gene Expression Regulation, Plant ; Genes, Reporter ; Mutation ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; RNA, Plant/genetics
Chemical Substances	Arabidopsis Proteins ; Nuclear Proteins ; RNA, Plant
Language	English
Publishing date	2017-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.060517.116
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Article: Expression and testing in plants of ArcLight, a geneticallyâencoded voltage indicator used in neuroscience research

Matzke, Antonius J.M / Marjori Matzke

BMC plant biology. 2015 Dec., v. 15, no. 1

2015

Abstract: BACKGROUND: It is increasingly appreciated that electrical controls acting at the cellular and supra-cellular levels influence development and initiate rapid responses to environmental cues. An emerging method for non-invasive optical imaging of ... ...

Abstract	BACKGROUND: It is increasingly appreciated that electrical controls acting at the cellular and supra-cellular levels influence development and initiate rapid responses to environmental cues. An emerging method for non-invasive optical imaging of electrical activity at cell membranes uses genetically-encoded voltage indicators (GEVIs). Developed by neuroscientists to chart neuronal circuits in animals, GEVIs comprise a fluorescent protein that is fused to a voltage-sensing domain. One well-known GEVI, ArcLight, undergoes strong shifts in fluorescence intensity in response to voltage changes in mammalian cells. ArcLight consists of super-ecliptic (SE) pHluorin (pH-sensitive fluorescent protein) with an A227D substitution, which confers voltage sensitivity in neurons, fused to the voltage-sensing domain of the voltage-sensing phosphatase of C iona i ntestinalis (Ci-VSD). In an ongoing effort to adapt tools of optical electrophysiology for plants, we describe here the expression and testing of ArcLight and various derivatives in different membranes of root cells in Arabidopsis thaliana. RESULTS: Transgenic constructs were designed to express ArcLight and various derivatives targeted to the plasma membrane and nuclear membranes of Arabidopsis root cells. In transgenic seedlings, changes in fluorescence intensity of these reporter proteins following extracellular ATP (eATP) application were monitored using a fluorescence microscope equipped with a high speed camera. Coordinate reductions in fluorescence intensity of ArcLight and Ci-VSD-containing derivatives were observed at both the plasma membrane and nuclear membranes following eATP treatments. However, similar responses were observed for derivatives lacking the Ci-VSD. The dispensability of the Ci-VSD suggests that in plants, where Hâº ions contribute substantially to electrical activities, the voltage-sensing ability of ArcLight is subordinate to the pH sensitivity of its SEpHluorin base. The transient reduction of ArcLight fluorescence triggered by eATP most likely reflects changes in pH and not membrane voltage. CONCLUSIONS: The pH sensitivity of ArcLight precludes its use as a direct sensor of membrane voltage in plants. Nevertheless, ArcLight and derivatives situated in the plasma membrane and nuclear membranes may offer robust, fluorescence intensity-based pH indicators for monitoring concurrent changes in pH at these discrete membrane systems. Such tools will assist analyses of pH as a signal and/or messenger at the cell surface and the nuclear periphery in living plants.
Keywords	adenosine triphosphate ; Arabidopsis thaliana ; cameras ; electrophysiology ; fluorescence ; fluorescence microscopes ; fluorescent proteins ; genetically modified organisms ; image analysis ; ions ; monitoring ; neurons ; neurophysiology ; pH ; plasma membrane ; protons ; roots ; seedlings
Language	English
Dates of publication	2015-12
Size	p. 245.
Publishing place	BioMed Central
Document type	Article
ISSN	1471-2229
DOI	10.1186/s12870-015-0633-z
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Article ; Online: Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera).

Huang, Ya-Yi / Matzke, Antonius J M / Matzke, Marjori

PloS one

2013 Volume 8, Issue 8, Page(s) e74736

Abstract: Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major ... ...

Abstract	Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.
MeSH term(s)	Anticodon/genetics ; Base Sequence ; Cocos/genetics ; Codon/genetics ; Gene Dosage/genetics ; Genome, Chloroplast/genetics ; Genome, Plant/genetics ; Inverted Repeat Sequences/genetics ; Molecular Sequence Data ; Phylogeny ; Pseudogenes/genetics ; RNA Editing/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA
Chemical Substances	Anticodon ; Codon
Language	English
Publishing date	2013-08-30
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0074736
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Article ; Online: PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in

Kanno, Tatsuo / Venhuizen, Peter / Wen, Tuan-Nan / Lin, Wen-Dar / Chiou, Phebe / Kalyna, Maria / Matzke, Antonius J M / Matzke, Marjori

Genetics

2018 Volume 210, Issue 4, Page(s) 1267–1285

Abstract: Splicing of precursor messenger RNAs (pre-mRNAs) is an essential step in the expression of most eukaryotic genes. Both constitutive splicing and alternative splicing, which produces multiple messenger RNA (mRNA) isoforms from a single primary transcript, ...

Abstract	Splicing of precursor messenger RNAs (pre-mRNAs) is an essential step in the expression of most eukaryotic genes. Both constitutive splicing and alternative splicing, which produces multiple messenger RNA (mRNA) isoforms from a single primary transcript, are modulated by reversible protein phosphorylation. Although the plant splicing machinery is known to be a target for phosphorylation, the protein kinases involved remain to be fully defined. We report here the identification of pre-mRNA processing 4 (PRP4) KINASE A (PRP4KA) in a forward genetic screen based on an alternatively spliced
MeSH term(s)	Alternative Splicing/genetics ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Gene Expression Regulation, Plant ; Phenotype ; Plant Development/genetics ; Plants, Genetically Modified/genetics ; Protein-Serine-Threonine Kinases/genetics ; RNA Splicing Factors ; Sequence Analysis, RNA ; Spliceosomes/genetics
Chemical Substances	Arabidopsis Proteins ; RNA Splicing Factors ; proline-rich protein, Arabidopsis ; Sac3 protein kinase (EC 2.7.1.-) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2018-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.118.301515
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