1
|
Tsuji A, Yamashita H, Hisatomi O, Abe M. Dimerization processes for light-regulated transcription factor Photozipper visualized by high-speed atomic force microscopy. Sci Rep 2022; 12:12903. [PMID: 35941201 PMCID: PMC9359980 DOI: 10.1038/s41598-022-17228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/09/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Dimerization is critical for transcription factors (TFs) to bind DNA and regulate a wide variety of cellular functions; however, the molecular mechanisms remain to be completely elucidated. Here, we used high-speed atomic force microscopy (HS-AFM) to observe the dimerization process for a photoresponsive TF Photozipper (PZ), which consists of light–oxygen–voltage-sensing (LOV) and basic-region-leucine-zipper (bZIP) domains. HS-AFM visualized not only the oligomeric states of PZ molecules forming monomers and dimers under controlled dark–light conditions but also the domain structures within each molecule. Successive AFM movies captured the dimerization process for an individual PZ molecule and the monomer–dimer reversible transition during dark–light cycling. Detailed AFM images of domain structures in PZ molecules demonstrated that the bZIP domain entangled under dark conditions was loosened owing to light illumination and fluctuated around the LOV domain. These observations revealed the role of the bZIP domain in the dimerization processes of a TF.
Collapse
Affiliation(s)
- Akihiro Tsuji
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University, Osaka, Japan.
| | - Osamu Hisatomi
- Graduate School of Science, Osaka University, Osaka, Japan
| | - Masayuki Abe
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| |
Collapse
|
2
|
Lu D, Zhang Y, Zhang A, Lu C. Non-Photochemical Quenching: From Light Perception to Photoprotective Gene Expression. Int J Mol Sci 2022; 23:687. [PMID: 35054872 DOI: 10.3390/ijms23020687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Light is essential for photosynthesis but light levels that exceed an organism's assimilation capacity can cause serious damage or even cell death. Plants and microalgae have developed photoprotective mechanisms collectively referred to as non-photochemical quenching to minimize such potential damage. One such mechanism is energy-dependent quenching (qE), which dissipates excess light energy as heat. Over the last 30 years, much has been learned about the molecular mechanism of qE in green algae and plants. However, the steps between light perception and qE represented a gap in our knowledge until the recent identification of light-signaling pathways that function in these processes in the green alga Chlamydomonas reinhardtii. In this review, we summarize the high light and UV-mediated signaling pathways for qE in Chlamydomonas. We discuss key questions remaining about the pathway from light perception to photoprotective gene expression in Chlamydomonas. We detail possible differences between green algae and plants in light-signaling mechanisms for qE and emphasize the importance of research on light-signaling mechanisms for qE in plants.
Collapse
|
3
|
Font-Muñoz JS, Sourisseau M, Cohen-Sánchez A, Tuval I, Basterretxea G. Pelagic diatoms communicate through synchronized beacon natural fluorescence signaling. Sci Adv 2021; 7:eabj5230. [PMID: 34910521 PMCID: PMC8673755 DOI: 10.1126/sciadv.abj5230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Communication between conspecific individuals is an essential part of life both in terrestrial and marine realms. Until recently, social behavior in marine phytoplankton was assumed to rely mainly on the secretion of a variety of infochemicals that allowed population-scale collective responses. Here, we demonstrate that pelagic diatoms also use Sun-stimulated fluorescence signals for synchronizing their behavior. These unicellular microorganisms, playing a key biogeochemical role in the ocean, use photoreceptor proteins and red–far-red fluorescent radiation to communicate. A characteristic beaconing signal is generated by rhythmic organelle displacement within the cell cytoplasm, triggering coordinated population behavior. These light-based communication networks could critically determine major facets of diatom ecology and fitness and regulate the dynamics of larger-scale ocean processes.
Collapse
Affiliation(s)
- Joan S. Font-Muñoz
- IFREMER, French Institute for Sea Research, DYNECO PELAGOS, 29280 Plouzané, France
- Université de Brest-UBO/CNRS/IFREMER/IRD, 29238 Brest, France
| | - Marc Sourisseau
- IFREMER, French Institute for Sea Research, DYNECO PELAGOS, 29280 Plouzané, France
| | - Amanda Cohen-Sánchez
- Mediterranean Institute for Advanced Studies, IMEDEA (UIB-CSIC), Miquel Marques 21, 07190 Esporles, Balearic Islands, Spain
| | - Idan Tuval
- Mediterranean Institute for Advanced Studies, IMEDEA (UIB-CSIC), Miquel Marques 21, 07190 Esporles, Balearic Islands, Spain
- Department of Physics, University of the Balearic Islands, Ctra. Valldemossa Km. 7.5, 07122 Palma, Balearic Islands, Spain
| | - Gotzon Basterretxea
- Mediterranean Institute for Advanced Studies, IMEDEA (UIB-CSIC), Miquel Marques 21, 07190 Esporles, Balearic Islands, Spain
| |
Collapse
|
4
|
Timsit Y, Lescot M, Valiadi M, Not F. Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:11311. [PMID: 34768741 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
Collapse
|
5
|
Sharma S, Sanyal SK, Sushmita K, Chauhan M, Sharma A, Anirudhan G, Veetil SK, Kateriya S. Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops. Curr Genomics 2021; 22:181-213. [PMID: 34975290 PMCID: PMC8640849 DOI: 10.2174/1389202922666210412104817] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022] Open
Abstract
Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.
Collapse
Affiliation(s)
- Sunita Sharma
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sibaji K Sanyal
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kumari Sushmita
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Gireesh Anirudhan
- Integrated Science Education and Research Centre (ISERC), Institute of Science (Siksha Bhavana), Visva Bharati (A Central University), Santiniketan (PO), West Bengal, 731235, India
| | - Sindhu K Veetil
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
6
|
Nakasone Y, Terazima M. A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules. Front Genet 2021; 12:691010. [PMID: 34276791 PMCID: PMC8278059 DOI: 10.3389/fgene.2021.691010] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.
Collapse
Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
7
|
Yang X, Wang X, Yao J, Li W, Duan D. MiR8181 is involved in the cell growth regulation of Saccharina japonica. J Plant Physiol 2021; 260:153394. [PMID: 33676110 DOI: 10.1016/j.jplph.2021.153394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Aureochrome, a blue-light receptor specifically found in photosynthetic stramenopiles, plays an important role in algal growth and development. It holds a reversed effector-sensor topology for the reception of blue light, acting as a candidate of optogenetic tool in transcriptional regulation. However, the inner regulatory mechanism of aureochrome is still unclear. In this study, we explored the potential regulatory relationship between microRNAs (miRNAs) and mRNAs by small RNA, transcriptome and degradome sequencing in Saccharina japonica. Through screening miRNA-mRNA interaction networks at the whole-genome level, we found that 18 miRNAs perfectly paired with aureochrome. Among these screened miRNAs, miR8181 was negatively correlated with aureochrome5 with high credibility, exhibiting tissue-specific expression in sporophyte of S. japonica. Degradome analysis further revealed the exact cleavage site of miR8181 on aureochrome5, confirming their targeting relationship. For the 54 target genes of miR8181, nine genes that exhibited similar expression to that of aureochrome5 competed for the same binding site, thus establishing a competing endogenous RNA network. Functional enrichment of the target genes revealed that miR8181 was involved in the regulation of cell differentiation and development in S. japonica. Moreover, overexpression of miR8181 resulted in significant decreases in the cell growth rates of Phaeodactylum tricornutum, suggesting negative roles of miR8181 in regulating cell growth. Our study revealed that miR8181, the targeting miRNA of aureochrome5, played negative roles in cell growth and development.
Collapse
Affiliation(s)
- Xiaoqi Yang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuliang Wang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jianting Yao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wei Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| |
Collapse
|
8
|
Iwata T, Masuda S. Photoreaction Mechanisms of Flavoprotein Photoreceptors and Their Applications. Adv Exp Med Biol 2021; 1293:189-206. [PMID: 33398814 DOI: 10.1007/978-981-15-8763-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Three classes of flavoprotein photoreceptors, cryptochromes (CRYs), light-oxygen-voltage (LOV)-domain proteins, and blue light using FAD (BLUF)-domain proteins, have been identified that control various physiological processes in multiple organisms. Accordingly, signaling activities of photoreceptors have been intensively studied and the related mechanisms have been exploited in numerous optogenetic tools. Herein, we summarize the current understanding of photoactivation mechanisms of the flavoprotein photoreceptors and review their applications.
Collapse
|
9
|
Abstract
Light oxygen voltage-sensing (LOV) domains are widely found in photoreceptor proteins of plants, algae, fungi, and bacteria. Structural studies of LOV domains suggest that Phe and Gln residues located in the proximity of the chromophore undergo conformational changes upon illumination; however, the molecular mechanism associated with activation of the effector domain remains to be elucidated. Photozipper (PZ) protein is an N-terminally truncated aureochrome-1 comprising a LOV domain and a basic leucine zipper domain. Blue light (BL) induces PZ dimerization and subsequently increases its affinity for target DNA. In this study, we prepared PZ mutants with substitutions of F298 and Q317 and performed quantitative analyses in dark and light states. Substitutions of Q317 significantly reduced the light-induced changes in PZ affinity for the target DNA, especially in the case of the high affinities observed in the dark state. Upon illumination, all PZ mutants showed increased affinity for the target sequence, which demonstrated a clear correlation with the dimer fraction of each PZ mutant. These results suggest the existence of a conformational equilibrium and that its shift by a synergistic interaction between the chromophore and protein moiety probably enables BL-regulated switching of aureochrome-1.
Collapse
Affiliation(s)
- Itsuki Kobayashi
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroto Nakajima
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
10
|
Hepp S, Trauth J, Hasenjäger S, Bezold F, Essen LO, Taxis C. An Optogenetic Tool for Induced Protein Stabilization Based on the Phaeodactylum tricornutum Aureochrome 1a Light-Oxygen-Voltage Domain. J Mol Biol 2020; 432:1880-1900. [PMID: 32105734 DOI: 10.1016/j.jmb.2020.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/10/2020] [Accepted: 02/14/2020] [Indexed: 01/02/2023]
Abstract
Control of cellular events by optogenetic tools is a powerful approach to manipulate cellular functions in a minimally invasive manner. A common problem posed by the application of optogenetic tools is to tune the activity range to be physiologically relevant. Here, we characterized a photoreceptor of the light-oxygen-voltage (LOV) domain family of Phaeodactylum tricornutum aureochrome 1a (AuLOV) as a tool for increasing protein stability under blue light conditions in budding yeast. Structural studies of AuLOVwt, the variants AuLOVM254, and AuLOVW349 revealed alternative dimer association modes for the dark state, which differ from previously reported AuLOV dark-state structures. Rational design of AuLOV-dimer interface mutations resulted in an optimized optogenetic tool that we fused to the photoactivatable adenylyl cyclase from Beggiatoa sp. This synergistic light-regulation approach using two photoreceptors resulted in an optimized, photoactivatable adenylyl cyclase with a cyclic adenosine monophosphate production activity that matches the physiological range of Saccharomyces cerevisiae. Overall, we enlarged the optogenetic toolbox for yeast and demonstrated the importance of fine-tuning the optogenetic tool activity for successful application in cells.
Collapse
Affiliation(s)
- Sebastian Hepp
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany; Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Sophia Hasenjäger
- Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany.
| | - Christof Taxis
- Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
| |
Collapse
|
11
|
Niklas KJ, Wayne R, Benítez M, Newman SA. Polarity, planes of cell division, and the evolution of plant multicellularity. Protoplasma 2019; 256:585-599. [PMID: 30368592 DOI: 10.1007/s00709-018-1325-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/22/2018] [Indexed: 05/21/2023]
Abstract
Organisms as diverse as bacteria, fungi, plants, and animals manifest a property called "polarity." The literature shows that polarity emerges as a consequence of different mechanisms in different lineages. However, across all unicellular and multicellular organisms, polarity is evident when cells, organs, or organisms manifest one or more of the following: orientation, axiation, and asymmetry. Here, we review the relationships among these three features in the context of cell division and the evolution of multicellular polarity primarily in plants (defined here to include the algae). Data from unicellular and unbranched filamentous organisms (e.g., Chlamydomonas and Ulothrix) show that cell orientation and axiation are marked by cytoplasmic asymmetries. Branched filamentous organisms (e.g., Cladophora and moss protonema) require an orthogonal reorientation of axiation, or a localized cell asymmetry (e.g., "tip" growth in pollen tubes and fungal hyphae). The evolution of complex multicellular meristematic polarity required a third reorientation of axiation. These transitions show that polarity and the orientation of the future plane(s) of cell division are dyadic dynamical patterning modules that were critical for multicellular eukaryotic organisms.
Collapse
Affiliation(s)
- Karl J Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Randy Wayne
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Mariana Benítez
- Instituto de Ecología Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- C3, Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| |
Collapse
|
12
|
Takahashi M, Mikami K. A Simple Procedure to Observe Phototropic Responses in the Red Seaweed Pyropia yezoensis. Methods Mol Biol 2019; 1924:121-30. [PMID: 30694470 DOI: 10.1007/978-1-4939-9015-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The marine red seaweed Pyropia yezoensis exhibits phototropic responses in gametophyte and conchosporangia phases, but not in sporophytes. These responses are easily monitored with a simple culturing box that has one side open to allow for unilateral light irradiation within an incubator. Confirmation of phototropic responses is achieved by changing the direction of unilateral light irradiation via rotation of the culture dishes clockwise 90°.
Collapse
|
13
|
Abstract
Photozipper (PZ) is a light-activatable basic leucine zipper (bZIP) protein composed of a bZIP domain and a light-oxygen-voltage-sensing domain of aureochrome-1. Blue light induces dimerization and subsequently increases the affinity of PZ for the target DNA sequence. We prepared site-directed PZ mutants in which Asn131 (N131) in the basic region was substituted with Ala and Gln. N131 mutants showed spectroscopic and dimerization properties almost identical to those of wild-type PZ and an increase in helical content in the presence of the target sequence. Quantitative analyses by an electrophoretic mobility shift assay and quartz crystal microbalance (QCM) measurements demonstrated that the half-maximal effective concentrations of N131 mutants to bind to the target sequence were significantly higher than those of PZ. QCM data also revealed that N131 substitutions accelerated the dissociation without affecting the association, suggesting that a base-specific interaction of N131 occurred after the association between PZ and DNA. Activation of PZ by illumination decreased both the standard errors and the unstable period of QCM data. Optical control of transcription factors will provide new knowledge of the recognition of the target sequence.
Collapse
Affiliation(s)
- Samu Tateyama
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| | - Itsuki Kobayashi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| |
Collapse
|
14
|
Tsukuno H, Ozeki K, Kobayashi I, Hisatomi O, Mino H. Flavin-Radical Formation in the Light-Oxygen-Voltage-Sensing Domain of the Photozipper Blue-light Sensor Protein. J Phys Chem B 2018; 122:8819-8823. [PMID: 30157376 DOI: 10.1021/acs.jpcb.8b05808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formation of the neutral flavin radical in the light-oxygen-voltage-sensing (LOV-sensing) domain of photozipper, based on VfAUREO1, was investigated by electron paramagnetic resonance spectroscopy. The flavin radical was observed in the presence of dithiothreitol by illumination of a LOV-domain mutant (C254S), in which a photoactive cysteine residue in close proximity to flavin was replaced with a serine. The radical did not form under low initial protein-concentration conditions (less than 20 μM). The flavin radicals accumulated with logistic time-dependent kinetics when the protein concentrations were higher than 30 μM. These results indicate that the radical is produced by concerted reactions involving protein interactions and that the radical is formed from the LOV dimer but not the LOV monomer. In contrast, logistic time dependencies were not observed for the sample adapted to the dark following radical formation by illumination, indicating that initialization of the proton pathway is essential for this fast sensing reaction.
Collapse
Affiliation(s)
- Hiroyuki Tsukuno
- Division of Material Science, Graduate School of Science , Nagoya University , Chikusa-ku, Furo-cho, Nagoya 464-8602 , Japan
| | - Kohei Ozeki
- Division of Material Science, Graduate School of Science , Nagoya University , Chikusa-ku, Furo-cho, Nagoya 464-8602 , Japan
| | - Itsuki Kobayashi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Osaka 560-0043 , Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Osaka 560-0043 , Japan
| | - Hiroyuki Mino
- Division of Material Science, Graduate School of Science , Nagoya University , Chikusa-ku, Furo-cho, Nagoya 464-8602 , Japan
| |
Collapse
|
15
|
Giovagnetti V, Ruban AV. The evolution of the photoprotective antenna proteins in oxygenic photosynthetic eukaryotes. Biochem Soc Trans 2018; 46:1263-77. [DOI: 10.1042/bst20170304] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/24/2022]
Abstract
Photosynthetic organisms require rapid and reversible down-regulation of light harvesting to avoid photodamage. Response to unpredictable light fluctuations is achieved by inducing energy-dependent quenching, qE, which is the major component of the process known as non-photochemical quenching (NPQ) of chlorophyll fluorescence. qE is controlled by the operation of the xanthophyll cycle and accumulation of specific types of proteins, upon thylakoid lumen acidification. The protein cofactors so far identified to modulate qE in photosynthetic eukaryotes are the photosystem II subunit S (PsbS) and light-harvesting complex stress-related (LHCSR/LHCX) proteins. A transition from LHCSR- to PsbS-dependent qE took place during the evolution of the Viridiplantae (also known as ‘green lineage’ organisms), such as green algae, mosses and vascular plants. Multiple studies showed that LHCSR and PsbS proteins have distinct functions in the mechanism of qE. LHCX(-like) proteins are closely related to LHCSR proteins and found in ‘red lineage’ organisms that contain secondary red plastids, such as diatoms. Although LHCX proteins appear to control qE in diatoms, their role in the mechanism remains poorly understood. Here, we present the current knowledge on the functions and evolution of these crucial proteins, which evolved in photosynthetic eukaryotes to optimise light harvesting.
Collapse
|
16
|
Nakasone Y, Ohshima M, Okajima K, Tokutomi S, Terazima M. Photoreaction Dynamics of LOV1 and LOV2 of Phototropin from Chlamydomonas reinhardtii. J Phys Chem B 2018; 122:1801-1815. [DOI: 10.1021/acs.jpcb.7b10266] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masumi Ohshima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Koji Okajima
- Graduate
School of Science and Technology, Keio University, Kanagawa 223-8522, Japan
| | - Satoru Tokutomi
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
17
|
Nakatani Y, Hisatomi O. Quantitative analyses of the equilibria among DNA complexes of a blue-light-regulated bZIP module, Photozipper. Biophys Physicobiol 2018; 15:8-17. [PMID: 29450110 PMCID: PMC5812316 DOI: 10.2142/biophysico.15.0_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/21/2017] [Indexed: 01/28/2023] Open
Abstract
Aureochrome1 is a blue-light-receptor protein identified in a stramenopile alga, Vaucheria frigida. Photozipper (PZ) is an N-terminally truncated, monomeric, V. frigida aureochrome1 fragment containing a basic leucine zipper (bZIP) domain and a light–oxygen–voltage (LOV)-sensing domain. PZ dimerizes upon photoexcitation and consequently increases its affinity for the target sequence. In the present study, to understand the equilibria among DNA complexes of PZ, DNA binding by PZ and mutational variants was quantitatively investigated by electrophoretic-mobility-shift assay and fluorescence-correlation spectroscopy in the dark and light states. DNA binding by PZ was sequence-specific and light-dependent. The half-maximal effective concentration of PZ for binding to the target DNA sequence was ~40 nM in the light, which was >10-fold less than the value in the dark. By contrast, the dimeric PZ-S2C variant (with intermolecular disulfide bonds) had higher affinity for the target sequence, with dissociation constants of ~4 nM, irrespective of the light conditions. Substitutions of Glu159 and Lys164 in the leucine zipper region decreased the affinity of PZ for the target sequence, especially in the light, suggesting that these residues form inter-helical salt bridges between leucine zipper regions, stabilizing the dimer–DNA complex. Our quantitative analyses of the equilibria in PZ–DNA-complex formation suggest that the blue-light-induced dimerization of LOV domains and coiled-coil formation by leucine zipper regions are the primary determinants of the affinity of PZ for the target sequence.
Collapse
Affiliation(s)
- Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
18
|
Ozeki K, Tsukuno H, Nagashima H, Hisatomi O, Mino H. Dimeric Structure of the Blue Light Sensor Protein Photozipper in the Active State. Biochemistry 2017; 57:494-497. [DOI: 10.1021/acs.biochem.7b01045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kohei Ozeki
- Division
of Material Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cho, Nagoya 464-8602, Japan
| | - Hiroyuki Tsukuno
- Division
of Material Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cho, Nagoya 464-8602, Japan
| | - Hiroki Nagashima
- Division
of Material Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cho, Nagoya 464-8602, Japan
| | - Osamu Hisatomi
- Department
of Earth and Space Science, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Hiroyuki Mino
- Division
of Material Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cho, Nagoya 464-8602, Japan
| |
Collapse
|
19
|
Duanmu D, Rockwell NC, Lagarias JC. Algal light sensing and photoacclimation in aquatic environments. Plant Cell Environ 2017; 40:2558-2570. [PMID: 28245058 PMCID: PMC5705019 DOI: 10.1111/pce.12943] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 10/30/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 05/05/2023]
Abstract
Anoxygenic photosynthetic prokaryotes arose in ancient oceans ~3.5 billion years ago. The evolution of oxygenic photosynthesis by cyanobacteria followed soon after, enabling eukaryogenesis and the evolution of complex life. The Archaeplastida lineage dates back ~1.5 billion years to the domestication of a cyanobacterium. Eukaryotic algae have subsequently radiated throughout oceanic/freshwater/terrestrial environments, adopting distinctive morphological and developmental strategies for adaptation to diverse light environments. Descendants of the ancestral photosynthetic alga remain challenged by a typical diurnally fluctuating light supply ranging from ~0 to ~2000 μE m-2 s-1 . Such extreme changes in light intensity and variations in light quality have driven the evolution of novel photoreceptors, light-harvesting complexes and photoprotective mechanisms in photosynthetic eukaryotes. This minireview focuses on algal light sensors, highlighting the unexpected roles for linear tetrapyrroles (bilins) in the maintenance of functional chloroplasts in chlorophytes, sister species to streptophyte algae and land plants.
Collapse
Affiliation(s)
- Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Corresponding authors: Deqiang Duanmu, State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Tel:+86-27-87282101; Fax:+86-27-87282469; ; J. Clark Lagarias, Department of Molecular and Cellular Biology, University of California, Davis CA 95616. Tel: 530-752-1865; Fax: 530-752-3085;
| | - Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis CA 95616
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis CA 95616
- Corresponding authors: Deqiang Duanmu, State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Tel:+86-27-87282101; Fax:+86-27-87282469; ; J. Clark Lagarias, Department of Molecular and Cellular Biology, University of California, Davis CA 95616. Tel: 530-752-1865; Fax: 530-752-3085;
| |
Collapse
|
20
|
Essen LO, Franz S, Banerjee A. Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. J Plant Physiol 2017; 217:27-37. [PMID: 28756992 DOI: 10.1016/j.jplph.2017.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Blue-light reception plays a pivotal role for algae to adapt to changing environmental conditions. In this review we summarize the current structural and mechanistic knowledge about flavin-dependent algal photoreceptors. We especially focus on the cryptochrome and aureochrome type photoreceptors in the context of their evolutionary divergence. Despite similar photochemical characteristics to orthologous photoreceptors from higher plants and animals the algal blue-light photoreceptors have developed a set of unique structural and mechanistic features that are summarized below.
Collapse
Affiliation(s)
- Lars-Oliver Essen
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology, Philipps-University, 35043 Marburg, Germany.
| | - Sophie Franz
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| | - Ankan Banerjee
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| |
Collapse
|
21
|
Allorent G, Petroutsos D. Photoreceptor-dependent regulation of photoprotection. Curr Opin Plant Biol 2017; 37:102-108. [PMID: 28472717 DOI: 10.1016/j.pbi.2017.03.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/26/2017] [Accepted: 03/28/2017] [Indexed: 05/05/2023]
Abstract
In photosynthetic organisms, proteins in the light-harvesting complex (LHC) harvest light energy to fuel photosynthesis, whereas photoreceptor proteins are activated by the different wavelengths of the light spectrum to regulate cellular functions. Under conditions of excess light, blue-light photoreceptors activate chloroplast avoidance movements in sessile plants, and blue- and green-light photoreceptors cause motile algae to swim away from intense light. Simultaneously, LHCs switch from light-harvesting mode to energy-dissipation mode, which was thought to be independent of photoreceptor-signaling up until recently. Recent advances, however, indicate that energy dissipation in green algae is controlled by photoreceptors activated by blue and UV-B light, and new molecular links have been established between photoreception and photoprotection.
Collapse
Affiliation(s)
- Guillaume Allorent
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France
| | - Dimitris Petroutsos
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France.
| |
Collapse
|
22
|
Jaubert M, Bouly JP, Ribera d'Alcalà M, Falciatore A. Light sensing and responses in marine microalgae. Curr Opin Plant Biol 2017; 37:70-77. [PMID: 28456112 DOI: 10.1016/j.pbi.2017.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
Marine eukaryotic phytoplankton are major contributors to global primary production. To adapt and thrive in the oceans, phytoplankton relies on a variety of light-regulated responses and light-acclimation capacities probably driven by sophisticated photoregulatory mechanisms. A plethora of photoreceptor-like sequences from marine microalgae have been identified in omics approaches. Initial studies have revealed that some algal photoreceptors are similar to those known in plants. In addition, new variants with different spectral tuning and algal-specific light sensors have also been found, changing current views and perspectives on how photoreceptor structure and function have diversified in phototrophs experiencing different environmental conditions.
Collapse
Affiliation(s)
- Marianne Jaubert
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France
| | - Maurizio Ribera d'Alcalà
- Stazione Zoologica Anton Dohrn, Laboratory of Ecology and Evolution of Plankton, Villa Comunale, 80121 Naples, Italy.
| | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France.
| |
Collapse
|
23
|
Abstract
Brown algae exhibit three patterns of sexual reproduction: isogamy, anisogamy, and oogamy. Unicellular swarmers including gametes and zoospores bear two heterogenous flagella, an anterior flagellum with mastigonemes (fine tripartite hairs) and a posterior one. In seawater, these flagellates usually receive physico-chemical signals for finding partners and good habitats. It is well known that brown algal swarmers change their swimming direction depending on blue light (phototaxis), and male gametes do so, based on the sex pheromones from female gametes (chemotaxis). In recent years, the comparative analysis of chemotaxis in isogamy, anisogamy, and oogamy has been conducted. In this paper, we focused on the phototaxis and chemotaxis of brown algal gametes comparing the current knowledge with our recent studies.
Collapse
Affiliation(s)
- Nana Kinoshita
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, Hokkaido, 051-0013, Japan
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, Hokkaido, 051-0013, Japan.
| |
Collapse
|
24
|
Lie AAY, Liu Z, Terrado R, Tatters AO, Heidelberg KB, Caron DA. Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp. BMC Genomics 2017; 18:163. [PMID: 28196482 PMCID: PMC5310065 DOI: 10.1186/s12864-017-3549-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/02/2017] [Indexed: 12/21/2022] Open
Abstract
Background Ochromonas is a genus of mixotrophic chrysophytes that is found ubiquitously in many aquatic environments. Species in this genus can be important consumers of bacteria but vary in their ability to perform photosynthesis. We studied the effect of light and bacteria on growth and gene expression of a predominantly phagotrophic Ochromonas species. Axenic cultures of Ochromonas sp. were fed with heat-killed bacteria (HKB) and grown in constant light or darkness. RNA was extracted from cultures in the light or in the dark with HKB present (Light + HKB; Dark + HKB), and in the light after HKB were depleted (Light + depleted HKB). Results There were no significant differences in the growth or bacterial ingestion rates between algae grown in light or dark conditions. The availability of light led to a differential expression of only 8% of genes in the transcriptome. A number of genes associated with photosynthesis, phagotrophy, and tetrapyrrole synthesis was upregulated in the Light + HKB treatment compared to Dark + HKB. Conversely, the comparison between the Light + HKB and Light + depleted HKB treatments revealed that the presence of HKB led to differential expression of 59% of genes, including the majority of genes involved in major carbon and nitrogen metabolic pathways. Genes coding for unidirectional enzymes for the utilization of glucose were upregulated in the presence of HKB, implying increased glycolytic activities during phagotrophy. Algae without HKB upregulated their expression of genes coding for ammonium transporters, implying uptake of inorganic nitrogen from the culture medium when prey were unavailable. Conclusions Transcriptomic results agreed with previous observations that light had minimal effect on the population growth of Ochromonas sp. However, light led to the upregulation of a number of phototrophy- and phagotrophy-related genes, while the availability of bacterial prey led to prominent changes in major carbon and nitrogen metabolic pathways. Our study demonstrated the potential of transcriptomic approaches to improve our understanding of the trophic physiologies of complex mixotrophs, and revealed responses in Ochromonas sp. not apparent from traditional culture studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3549-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alle A Y Lie
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA.
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Ramon Terrado
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Avery O Tatters
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| |
Collapse
|
25
|
Akiyama Y, Nakasone Y, Nakatani Y, Hisatomi O, Terazima M. Time-Resolved Detection of Light-Induced Dimerization of Monomeric Aureochrome-1 and Change in Affinity for DNA. J Phys Chem B 2016; 120:7360-70. [PMID: 27404115 DOI: 10.1021/acs.jpcb.6b05760] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aureochrome (Aureo) is a recently discovered blue light sensor protein initially from Vaucheria frigida, in which it controls blue light-dependent branch formation and/or development of a sex organ by a light-dependent change in the affinity for DNA. Although photochemical reactions of Aureo-LOV (LOV is a C-terminal light-oxygen-voltage domain) and the N-terminal truncated construct containing a bZIP (N-terminal basic leucine zipper domain) and a LOV domain have previously been reported, the reaction kinetics of the change in affinity for DNA have never been elucidated. The reactions of Aureo where the cysteines are replaced by serines (AureoCS) as well as the kinetics of the change in affinity for a target DNA are investigated in the time-domain. The dimerization rate constant is obtained as 2.8 × 10(4) M(-1) s(-1), which suggests that the photoinduced dimerization occurs in the LOV domain and the bZIP domain dimerizes using the interaction with DNA. Surprisingly, binding with the target DNA is completed very quickly, 7.7 × 10(4) M(-1) s(-1), which is faster than the protein dimerization rate. It is proposed that the nonspecific electrostatic interaction, which is observed as a weak binding with DNA, may play a role in the efficient searching for the target sequence within the DNA.
Collapse
Affiliation(s)
- Yuki Akiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University , Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University , Osaka 560-0043, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| |
Collapse
|
26
|
Affiliation(s)
- Sam-Geun Kong
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.
- Research Center for Live-Protein Dynamics, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Koji Okajima
- Department of Physics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
- RIKEN Harima Institute, Spring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
| |
Collapse
|
27
|
|