1
|
Liu HW, Urzica EI, Gallaher SD, Schmollinger S, Blaby-Haas CE, Iwai M, Merchant SS. Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium. PHOTOSYNTHESIS RESEARCH 2024; 161:213-232. [PMID: 39017982 DOI: 10.1007/s11120-024-01103-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/15/2024] [Indexed: 07/18/2024]
Abstract
Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
Collapse
Affiliation(s)
- Helen W Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA
| | - Eugen I Urzica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Competence Network IBD, Hopfenstrasse 60, 24103, Kiel, Germany
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Crysten E Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
2
|
Duenas MA, Craig RJ, Gallaher SD, Moseley JL, Merchant SS. Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.605010. [PMID: 39091764 PMCID: PMC11291117 DOI: 10.1101/2024.07.24.605010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Advances in sequencing technology have unveiled examples of nucleus-encoded polycistronic genes, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for polycistronic expression in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed 1) a preference for weak Kozak-like sequences for ORF 1 and 2) an underrepresentation of potential initiation codons before ORF 2, which are suitable conditions for leaky scanning to allow ORF 2 translation. We used mutational analysis in Auxenochlorella protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky ribosome scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames found across eukaryotic genomes and for transgene expression in synthetic biology applications.
Collapse
Affiliation(s)
- Marco A. Duenas
- Department of Plant and Microbial Biology, University of California Berkeley, University of California, Berkeley, CA 94720, USA
| | - Rory J. Craig
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Sean D. Gallaher
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey L. Moseley
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California Berkeley, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, CA, USA
| |
Collapse
|
3
|
Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
Collapse
Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| |
Collapse
|
4
|
Scholtysek L, Poetsch A, Hofmann E, Hemschemeier A. The activation of Chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its N-terminal aspartate kinase-chorismate mutase-tyrA (ACT) domain. PLANT DIRECT 2024; 8:e609. [PMID: 38911017 PMCID: PMC11190351 DOI: 10.1002/pld3.609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024]
Abstract
The coordination of assimilation pathways for all the elements that make up cellular components is a vital task for every organism. Integrating the assimilation and use of carbon (C) and nitrogen (N) is of particular importance because of the high cellular abundance of these elements. Starch is one of the most important storage polymers of photosynthetic organisms, and a complex regulatory network ensures that biosynthesis and degradation of starch are coordinated with photosynthetic activity and growth. Here, we analyzed three starch metabolism enzymes of Chlamydomonas reinhardtii that we captured by a cyclic guanosine monophosphate (cGMP) affinity chromatography approach, namely, soluble starch synthase STA3, starch-branching enzyme SBE1, and α-amylase AMA2. While none of the recombinant enzymes was directly affected by the presence of cGMP or other nucleotides, suggesting an indirect binding to cGMP, AMA2 activity was stimulated in the presence of L-glutamine (Gln). This activating effect required the enzyme's N-terminal aspartate kinase-chorismate mutase-tyrA domain. Gln is the first N assimilation product and not only a central compound for the biosynthesis of N-containing molecules but also a recognized signaling molecule for the N status. Our observation suggests that AMA2 might be a means to coordinate N and C metabolism at the enzymatic level, increasing the liberation of C skeletons from starch when high Gln levels signal an abundance of assimilated N.
Collapse
Affiliation(s)
- Lisa Scholtysek
- Faculty of Biology and Biotechnology, PhotobiotechnologyRuhr University BochumBochumGermany
| | - Ansgar Poetsch
- Faculty of Biology and Biotechnology, Department for Plant BiochemistryRuhr University BochumBochumGermany
- School of Basic Medical SciencesNanchang UniversityNanchangChina
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, Protein CrystallographyRuhr University BochumBochumGermany
| | - Anja Hemschemeier
- Faculty of Biology and Biotechnology, PhotobiotechnologyRuhr University BochumBochumGermany
| |
Collapse
|
5
|
Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS. Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577492. [PMID: 38328118 PMCID: PMC10849638 DOI: 10.1101/2024.01.26.577492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum , a vitamin B 12 -producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide - a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B 12 and supported the growth of a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
Collapse
|
6
|
Sun X, LaVoie M, Lefebvre PA, Gallaher SD, Glaesener AG, Strenkert D, Mehta R, Merchant SS, Silflow CD. Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586359. [PMID: 38586028 PMCID: PMC10996464 DOI: 10.1101/2024.03.22.586359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation of HYDA1 transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of the HYDA1 promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termed cehc1-1 , leads to constitutive expression of HYDA1 and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway. CRR1 was required for the constitutive expression of the HYDA1 reporter gene in cehc1-1 mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized in cehc1-1 cells, supporting the conclusion that CEHC1 acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in the CRR1 pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
Collapse
|
7
|
Nayana K, Babu VS, Vidya D, Sudhakar MP, Arunkumar K. Growth and productivity of Haematococcus pluvialis and Coelastrella saipanensis by photosystem modulation for understanding the heterotrophic nutritional strategy for bioremediation application. ENVIRONMENTAL RESEARCH 2024; 245:118077. [PMID: 38159661 DOI: 10.1016/j.envres.2023.118077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
In this study, Haematococcus pluvialis and Coelastrella saipanensis were evaluated for heterotrophic nutrition potential in dairy waste medium by blocking the PSII using DCMU. The study was done by four sets of experiments. In the first set, in the different concentrations DCMU-treatments, 20μL showed pronounced effect in H. pluvialis and C. saipanensis as 89 % and 83% decrease in cells (>30 and > 250 cells/mL) compared to control (536 ± 12.35 × 104 and 1167 ± 15.35 × 104 cells/mL, respectively). Damage to the PS II by DCMU interrupted the growth, which in turn produced a significant drop in the number of cells. In the second round of experiment, growth of algae in various dairy waste concentrations suggest that dairy wastewater (DWW) provides enough nutrients to produce 35.71 % and 64.74 % more cells in H. pluvialis and C. saipanensis, respectively compared to the control. In the third set, high DCMU concentration was added to microalgae cultures in DWW to assess the heterotrophic nutrition potential. Growth in cell number 34.4 ± 19 and 617.46 ± 60.44 cells/mL was recorded in H. pluvialis and C. saipanensis when grown control medium whereas addition of DCMU reduced the cell number to 1.53 ± 0.75 and 55.13 ± 0.75 cells/mL on 15th day, respectively. This shows cells in cultures treated with DCMU reveal that algae can sustain their metabolic activity by utilizing the nutrients of dairy waste inhibiting photosystem. Fourth round of experiments found that microalgae could resume their growth and productivity by adapting to heterotrophic nutritional behaviour when DCMU given in mild dose at different time interval. This study conclude as C. saipanensis grows more readily by absorbing dairy waste nutrients than H. pluvialis. Therefore, C. saipanensis is an excellent choice for wastewater treatment through sustainable environmentally benign process after scale-up investigation. These results provide useful information to advance to molecular study for measuring microalgae's capability for bioremediation application.
Collapse
Affiliation(s)
- K Nayana
- Microalgae Group, Phycoscience Lab, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Periye, 671 320, Kasaragod, Kerala, India.
| | - Vaishnav S Babu
- Microalgae Group, Phycoscience Lab, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Periye, 671 320, Kasaragod, Kerala, India.
| | - D Vidya
- Microalgae Group, Phycoscience Lab, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Periye, 671 320, Kasaragod, Kerala, India.
| | - M P Sudhakar
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences, Govt. of India, Pallikaranai, Chennai, 600100, Tamil Nadu, India; Marine Biopolymers & Advanced Bioactive Materials Research Lab, Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (Saveetha University), Chennai, 600 077, Tamil Nadu, India.
| | - Kulanthaiyesu Arunkumar
- Microalgae Group, Phycoscience Lab, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Periye, 671 320, Kasaragod, Kerala, India.
| |
Collapse
|
8
|
Santhanagopalan I, Netzl A, Mathur T, Smith A, Griffiths H, Holzer A. Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing. STAR Protoc 2024; 5:102764. [PMID: 38236771 PMCID: PMC10828896 DOI: 10.1016/j.xpro.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 02/03/2024] Open
Abstract
The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.
Collapse
Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
| | - Antonia Netzl
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Tanya Mathur
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alison Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Center for Bioinformatics and Department of Computer Science, Saarland University, 66123 Saarbrücken, Germany.
| |
Collapse
|
9
|
Balogun EJ, Ness RW. The Effects of De Novo Mutation on Gene Expression and the Consequences for Fitness in Chlamydomonas reinhardtii. Mol Biol Evol 2024; 41:msae035. [PMID: 38366781 PMCID: PMC10910851 DOI: 10.1093/molbev/msae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored. Here, we investigate the effects of >2,600 de novo mutations on gene expression across the transcriptome of 28 mutation accumulation lines derived from 2 independent wild-type genotypes of the green algae Chlamydomonas reinhardtii. We observed that the amount of genetic variance in gene expression created by mutation (Vm) was similar to the variance that mutation generates in typical polygenic phenotypic traits and approximately 15-fold the variance seen in the limited species where Vm in gene expression has been estimated. Despite the clear effect of mutation on expression, we did not observe a simple additive effect of mutation on expression change, with no linear correlation between the total expression change and mutation count of individual MA lines. We therefore inferred the distribution of expression effects of new mutations to connect the number of mutations to the number of differentially expressed genes (DEGs). Our inferred DEE is highly L-shaped with 95% of mutations causing 0-1 DEG while the remaining 5% are spread over a long tail of large effect mutations that cause multiple genes to change expression. The distribution is consistent with many cis-acting mutation targets that affect the expression of only 1 gene and a large target of trans-acting targets that have the potential to affect tens or hundreds of genes. Further evidence for cis-acting mutations can be seen in the overabundance of mutations in or near differentially expressed genes. Supporting evidence for trans-acting mutations comes from a 15:1 ratio of DEGs to mutations and the clusters of DEGs in the co-expression network, indicative of shared regulatory architecture. Lastly, we show that there is a negative correlation with the extent of expression divergence from the ancestor and fitness, providing direct evidence of the deleterious effects of perturbing gene expression.
Collapse
Affiliation(s)
- Eniolaye J Balogun
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga L5L-1C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto M5S-3B2, Canada
| | - Rob W Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga L5L-1C6, Canada
| |
Collapse
|
10
|
Liu D, Lopez-Paz C, Li Y, Zhuang X, Umen J. Subscaling of a cytosolic RNA binding protein governs cell size homeostasis in the multiple fission alga Chlamydomonas. PLoS Genet 2024; 20:e1010503. [PMID: 38498520 PMCID: PMC10977881 DOI: 10.1371/journal.pgen.1010503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/28/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Coordination of growth and division in eukaryotic cells is essential for populations of proliferating cells to maintain size homeostasis, but the underlying mechanisms that govern cell size have only been investigated in a few taxa. The green alga Chlamydomonas reinhardtii (Chlamydomonas) proliferates using a multiple fission cell cycle that involves a long G1 phase followed by a rapid series of successive S and M phases (S/M) that produces 2n daughter cells. Two control points show cell-size dependence: the Commitment control point in mid-G1 phase requires the attainment of a minimum size to enable at least one mitotic division during S/M, and the S/M control point where mother cell size governs cell division number (n), ensuring that daughter distributions are uniform. tny1 mutants pass Commitment at a smaller size than wild type and undergo extra divisions during S/M phase to produce small daughters, indicating that TNY1 functions to inhibit size-dependent cell cycle progression. TNY1 encodes a cytosolic hnRNP A-related RNA binding protein and is produced once per cell cycle during S/M phase where it is apportioned to daughter cells, and then remains at constant absolute abundance as cells grow, a property known as subscaling. Altering the dosage of TNY1 in heterozygous diploids or through mis-expression increased Commitment cell size and daughter cell size, indicating that TNY1 is a limiting factor for both size control points. Epistasis placed TNY1 function upstream of the retinoblastoma tumor suppressor complex (RBC) and one of its regulators, Cyclin-Dependent Kinase G1 (CDKG1). Moreover, CDKG1 protein and mRNA were found to over-accumulate in tny1 cells suggesting that CDKG1 may be a direct target of repression by TNY1. Our data expand the potential roles of subscaling proteins outside the nucleus and imply a control mechanism that ties TNY1 accumulation to pre-division mother cell size.
Collapse
Affiliation(s)
- Dianyi Liu
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- University of Missouri—St. Louis, Cell and Molecular Biology Program, St. Louis. Missouri, United States of America
| | - Cristina Lopez-Paz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Yubing Li
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Xiaohong Zhuang
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| |
Collapse
|
11
|
Zhang N, Venn B, Bailey CE, Xia M, Mattoon EM, Mühlhaus T, Zhang R. Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:979-1003. [PMID: 37877811 DOI: 10.1093/jxb/erad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 10/21/2023] [Indexed: 10/26/2023]
Abstract
High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.
Collapse
Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Benedikt Venn
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Timo Mühlhaus
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| |
Collapse
|
12
|
Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS. Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction. THE ISME JOURNAL 2024; 18:wrae140. [PMID: 39046282 PMCID: PMC11316394 DOI: 10.1093/ismejo/wrae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/29/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024]
Abstract
Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum, a vitamin B12-producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15NH4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide-a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B12 and supported the growth of a B12-dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
Collapse
Affiliation(s)
- Sunnyjoy Dupuis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, United States
| | - Usha F Lingappa
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Eve S Sindermann
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, United States
| | - Jordan L Chastain
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, United States
- College of Chemistry, University of California, Berkeley, CA 94720, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Rhona Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| |
Collapse
|
13
|
Kafri M, Patena W, Martin L, Wang L, Gomer G, Ergun SL, Sirkejyan AK, Goh A, Wilson AT, Gavrilenko SE, Breker M, Roichman A, McWhite CD, Rabinowitz JD, Cross FR, Wühr M, Jonikas MC. Systematic identification and characterization of genes in the regulation and biogenesis of photosynthetic machinery. Cell 2023; 186:5638-5655.e25. [PMID: 38065083 PMCID: PMC10760936 DOI: 10.1016/j.cell.2023.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 08/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Photosynthesis is central to food production and the Earth's biogeochemistry, yet the molecular basis for its regulation remains poorly understood. Here, using high-throughput genetics in the model eukaryotic alga Chlamydomonas reinhardtii, we identify with high confidence (false discovery rate [FDR] < 0.11) 70 poorly characterized genes required for photosynthesis. We then enable the functional characterization of these genes by providing a resource of proteomes of mutant strains, each lacking one of these genes. The data allow assignment of 34 genes to the biogenesis or regulation of one or more specific photosynthetic complexes. Further analysis uncovers biogenesis/regulatory roles for at least seven proteins, including five photosystem I mRNA maturation factors, the chloroplast translation factor MTF1, and the master regulator PMR1, which regulates chloroplast genes via nuclear-expressed factors. Our work provides a rich resource identifying regulatory and functional genes and placing them into pathways, thereby opening the door to a system-level understanding of photosynthesis.
Collapse
Affiliation(s)
- Moshe Kafri
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gillian Gomer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sabrina L Ergun
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Arthur K Sirkejyan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia E Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Asael Roichman
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Frederick R Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
14
|
Chaux F, Jarrige D, Rodrigues-Azevedo M, Bujaldon S, Caspari OD, Ozawa SI, Drapier D, Vallon O, Choquet Y, de Vitry C. Chloroplast ATP synthase biogenesis requires peripheral stalk subunits AtpF and ATPG and stabilization of atpE mRNA by OPR protein MDE1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1582-1599. [PMID: 37824282 DOI: 10.1111/tpj.16448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/14/2023]
Abstract
Chloroplast ATP synthase contains subunits of plastid and nuclear genetic origin. To investigate the coordinated biogenesis of this complex, we isolated novel ATP synthase mutants in the green alga Chlamydomonas reinhardtii by screening for high light sensitivity. We report here the characterization of mutants affecting the two peripheral stalk subunits b and b', encoded respectively by the atpF and ATPG genes, and of three independent mutants which identify the nuclear factor MDE1, required to stabilize the chloroplast-encoded atpE mRNA. Whole-genome sequencing revealed a transposon insertion in the 3'UTR of ATPG while mass spectrometry shows a small accumulation of functional ATP synthase in this knock-down ATPG mutant. In contrast, knock-out ATPG mutants, obtained by CRISPR-Cas9 gene editing, fully prevent ATP synthase function and accumulation, as also observed in an atpF frame-shift mutant. Crossing ATP synthase mutants with the ftsh1-1 mutant of the major thylakoid protease identifies AtpH as an FTSH substrate, and shows that FTSH significantly contributes to the concerted accumulation of ATP synthase subunits. In mde1 mutants, the absence of atpE transcript fully prevents ATP synthase biogenesis and photosynthesis. Using chimeric atpE genes to rescue atpE transcript accumulation, we demonstrate that MDE1, a novel octotricopeptide repeat (OPR) protein, genetically targets the atpE 5'UTR. In the perspective of the primary endosymbiosis (~1.5 Gy), the recruitment of MDE1 to its atpE target exemplifies a nucleus/chloroplast interplay that evolved rather recently, in the ancestor of the CS clade of Chlorophyceae, ~300 My ago.
Collapse
Affiliation(s)
- Frédéric Chaux
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Domitille Jarrige
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Marcio Rodrigues-Azevedo
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Sandrine Bujaldon
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Oliver D Caspari
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Shin-Ichiro Ozawa
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Dominique Drapier
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Olivier Vallon
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Yves Choquet
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Catherine de Vitry
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| |
Collapse
|
15
|
McQuillan JL, Cutolo EA, Evans C, Pandhal J. Proteomic characterization of a lutein-hyperaccumulating Chlamydomonas reinhardtii mutant reveals photoprotection-related factors as targets for increasing cellular carotenoid content. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:166. [PMID: 37925447 PMCID: PMC10625216 DOI: 10.1186/s13068-023-02421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Microalgae are emerging hosts for the sustainable production of lutein, a high-value carotenoid; however, to be commercially competitive with existing systems, their capacity for lutein sequestration must be augmented. Previous attempts to boost microalgal lutein production have focussed on upregulating carotenoid biosynthetic enzymes, in part due to a lack of metabolic engineering targets for expanding lutein storage. RESULTS Here, we isolated a lutein hyper-producing mutant of the model green microalga Chlamydomonas reinhardtii and characterized the metabolic mechanisms driving its enhanced lutein accumulation using label-free quantitative proteomics. Norflurazon- and high light-resistant C. reinhardtii mutants were screened to yield four mutant lines that produced significantly more lutein per cell compared to the CC-125 parental strain. Mutant 5 (Mut-5) exhibited a 5.4-fold increase in lutein content per cell, which to our knowledge is the highest fold increase of lutein in C. reinhardtii resulting from mutagenesis or metabolic engineering so far. Comparative proteomics of Mut-5 against its parental strain CC-125 revealed an increased abundance of light-harvesting complex-like proteins involved in photoprotection, among differences in pigment biosynthesis, central carbon metabolism, and translation. Further characterization of Mut-5 under varying light conditions revealed constitutive overexpression of the photoprotective proteins light-harvesting complex stress-related 1 (LHCSR1) and LHCSR3 and PSII subunit S regardless of light intensity, and increased accrual of total chlorophyll and carotenoids as light intensity increased. Although the photosynthetic efficiency of Mut-5 was comparatively lower than CC-125, the amplitude of non-photochemical quenching responses of Mut-5 was 4.5-fold higher than in CC-125 at low irradiance. CONCLUSIONS We used C. reinhardtii as a model green alga and identified light-harvesting complex-like proteins (among others) as potential metabolic engineering targets to enhance lutein accumulation in microalgae. These have the added value of imparting resistance to high light, although partially compromising photosynthetic efficiency. Further genetic characterization and engineering of Mut-5 could lead to the discovery of unknown players in photoprotective mechanisms and the development of a potent microalgal lutein production system.
Collapse
Affiliation(s)
- Josie L McQuillan
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.
| | - Edoardo Andrea Cutolo
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Caroline Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.
| |
Collapse
|
16
|
Karin J, Bornfeld Y, Nitzan M. scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching. Nat Biotechnol 2023; 41:1645-1654. [PMID: 36849830 PMCID: PMC10635821 DOI: 10.1038/s41587-023-01663-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 01/06/2023] [Indexed: 03/01/2023]
Abstract
Single-cell RNA sequencing has been instrumental in uncovering cellular spatiotemporal context. This task is challenging as cells simultaneously encode multiple, potentially cross-interfering, biological signals. Here we propose scPrisma, a spectral computational method that uses topological priors to decouple, enhance and filter different classes of biological processes in single-cell data, such as periodic and linear signals. We apply scPrisma to the analysis of the cell cycle in HeLa cells, circadian rhythm and spatial zonation in liver lobules, diurnal cycle in Chlamydomonas and circadian rhythm in the suprachiasmatic nucleus in the brain. scPrisma can be used to distinguish mixed cellular populations by specific characteristics such as cell type and uncover regulatory networks and cell-cell interactions specific to predefined biological signals, such as the circadian rhythm. We show scPrisma's flexibility in incorporating prior knowledge, inference of topologically informative genes and generalization to additional diverse templates and systems. scPrisma can be used as a stand-alone workflow for signal analysis and as a prior step for downstream single-cell analysis.
Collapse
Affiliation(s)
- Jonathan Karin
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonathan Bornfeld
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
17
|
de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
Collapse
Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| |
Collapse
|
18
|
Caccamo A, Vega de Luna F, Wahni K, Volkov AN, Przybyla-Toscano J, Amelii A, Kriznik A, Rouhier N, Messens J, Remacle C. Ascorbate Peroxidase 2 (APX2) of Chlamydomonas Binds Copper and Modulates the Copper Insertion into Plastocyanin. Antioxidants (Basel) 2023; 12:1946. [PMID: 38001799 PMCID: PMC10669542 DOI: 10.3390/antiox12111946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Recent phylogenetic studies have unveiled a novel class of ascorbate peroxidases called "ascorbate peroxidase-related" (APX-R). These enzymes, found in green photosynthetic eukaryotes, lack the amino acids necessary for ascorbate binding. This study focuses on the sole APX-R from Chlamydomonas reinhardtii referred to as ascorbate peroxidase 2 (APX2). We used immunoblotting to locate APX2 within the chloroplasts and in silico analysis to identify key structural motifs, such as the twin-arginine transport (TAT) motif for lumen translocation and the metal-binding MxxM motif. We also successfully expressed recombinant APX2 in Escherichia coli. Our in vitro results showed that the peroxidase activity of APX2 was detected with guaiacol but not with ascorbate as an electron donor. Furthermore, APX2 can bind both copper and heme, as evidenced by spectroscopic, and fluorescence experiments. These findings suggest a potential interaction between APX2 and plastocyanin, the primary copper-containing enzyme within the thylakoid lumen of the chloroplasts. Predictions from structural models and evidence from 1H-NMR experiments suggest a potential interaction between APX2 and plastocyanin, emphasizing the influence of APX2 on the copper-binding abilities of plastocyanin. In summary, our results propose a significant role for APX2 as a regulator in copper transfer to plastocyanin. This study sheds light on the unique properties of APX-R enzymes and their potential contributions to the complex processes of photosynthesis in green algae.
Collapse
Affiliation(s)
- Anna Caccamo
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Brussels Center for Redox Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Félix Vega de Luna
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Brussels Center for Redox Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Jonathan Przybyla-Toscano
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| | - Antonello Amelii
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| | - Alexandre Kriznik
- CNRS, IMoPA and IBSLor, Université de Lorraine, F-54000 Nancy, France;
| | | | - Joris Messens
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (K.W.); (A.N.V.)
- Brussels Center for Redox Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium; (A.C.); (F.V.d.L.); (J.P.-T.); (A.A.)
| |
Collapse
|
19
|
Dupuis S, Merchant SS. Chlamydomonas reinhardtii: a model for photosynthesis and so much more. Nat Methods 2023; 20:1441-1442. [PMID: 37803226 DOI: 10.1038/s41592-023-02023-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Affiliation(s)
- Sunnyjoy Dupuis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
20
|
He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
Collapse
Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| |
Collapse
|
21
|
Carrera-Pacheco SE, Hankamer B, Oey M. Environmental and nuclear influences on microalgal chloroplast gene expression. TRENDS IN PLANT SCIENCE 2023; 28:955-967. [PMID: 37080835 DOI: 10.1016/j.tplants.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/09/2023] [Accepted: 03/18/2023] [Indexed: 05/03/2023]
Abstract
Microalgal chloroplasts, such as those of the model organism Chlamydomonas reinhardtii, are emerging as a new platform to produce recombinant proteins, including industrial enzymes, diagnostics, as well as animal and human therapeutics. Improving transgene expression and final recombinant protein yields, at laboratory and industrial scales, require optimization of both environmental and cellular factors. Most studies on C. reinhardtii have focused on optimization of cellular factors. Here, we review the regulatory influences of environmental factors, including light (cycle time, intensity, and quality), carbon source (CO2 and organic), and temperature. In particular, we summarize their influence via the redox state, cis-elements, and trans-factors on biomass and recombinant protein production to support the advancement of emerging large-scale light-driven biotechnology applications.
Collapse
Affiliation(s)
- Saskya E Carrera-Pacheco
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170527, Ecuador
| | - Ben Hankamer
- The University of Queensland, Institute for Molecular Bioscience, 306 Carmody Road, St Lucia, Australia.
| | - Melanie Oey
- The University of Queensland, Institute for Molecular Bioscience, 306 Carmody Road, St Lucia, Australia.
| |
Collapse
|
22
|
Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. JOURNAL OF PHYCOLOGY 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
Collapse
Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| |
Collapse
|
23
|
Pang X, Nawrocki WJ, Cardol P, Zheng M, Jiang J, Fang Y, Yang W, Croce R, Tian L. Weak acids produced during anaerobic respiration suppress both photosynthesis and aerobic respiration. Nat Commun 2023; 14:4207. [PMID: 37452043 PMCID: PMC10349137 DOI: 10.1038/s41467-023-39898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
While photosynthesis transforms sunlight energy into sugar, aerobic and anaerobic respiration (fermentation) catabolizes sugars to fuel cellular activities. These processes take place within one cell across several compartments, however it remains largely unexplored how they interact with one another. Here we report that the weak acids produced during fermentation down-regulate both photosynthesis and aerobic respiration. This effect is mechanistically explained with an "ion trapping" model, in which the lipid bilayer selectively traps protons that effectively acidify subcellular compartments with smaller buffer capacities - such as the thylakoid lumen. Physiologically, we propose that under certain conditions, e.g., dim light at dawn, tuning down the photosynthetic light reaction could mitigate the pressure on its electron transport chains, while suppression of respiration could accelerate the net oxygen evolution, thus speeding up the recovery from hypoxia. Since we show that this effect is conserved across photosynthetic phyla, these results indicate that fermentation metabolites exert widespread feedback control over photosynthesis and aerobic respiration. This likely allows algae to better cope with changing environmental conditions.
Collapse
Affiliation(s)
- Xiaojie Pang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wojciech J Nawrocki
- Department of Physics and Astronomy and LaserLab Amsterdam Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR7141, Centre National de la Recherche Scientifique, Sorbonne Université, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005, Paris, France
| | - Pierre Cardol
- Génétique et Physiologie des Microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, B22, 4000, Liège, Belgium
| | - Mengyuan Zheng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jingjing Jiang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
| | - Yuan Fang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Roberta Croce
- Department of Physics and Astronomy and LaserLab Amsterdam Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
24
|
Puzanskiy RK, Romanyuk DA, Kirpichnikova AA, Shishova MF. Effects of Trophic Acclimation on Growth and Expression Profiles of Genes Encoding Enzymes of Primary Metabolism and Plastid Transporters of Chlamydomonas reinhardtii. Life (Basel) 2023; 13:1398. [PMID: 37374180 DOI: 10.3390/life13061398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/28/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
In this paper, the effect of prolonged trophic acclimation on the subsequent growth of Chlamydomonas reinhardtii batch cultures was studied. The mixotrophic (light + acetate) acclimation stimulated subsequent growth at both mixotrophy and autotrophy conditions and altered the expression profile of genes encoding enzymes of primary metabolism and plastid transporters. Besides the trophic effect, the influence of Chlamydomonas culture growth stage on gene expression was determined. Under mixotrophic conditions, this effect was most pronounced in the first half of the exponential growth with partial retention of the previous acclimation period traits. The autotrophy acclimation effect was more complex and its significance was enhanced at the end of the growth and in the stationary phase.
Collapse
Affiliation(s)
- Roman K Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197022, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Daria A Romanyuk
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg 196608, Russia
| | | | - Maria F Shishova
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
25
|
Arend M, Yuan Y, Ruiz-Sola MÁ, Omranian N, Nikoloski Z, Petroutsos D. Widening the landscape of transcriptional regulation of green algal photoprotection. Nat Commun 2023; 14:2687. [PMID: 37164999 PMCID: PMC10172295 DOI: 10.1038/s41467-023-38183-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/17/2023] [Indexed: 05/12/2023] Open
Abstract
Availability of light and CO2, substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO2 Concentrating Mechanism (CCM) under low CO2, to raise intracellular CO2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomic data compendium of Chlamydomonas reinhardtii's responses to different light and carbon supply, we reconstruct a consensus genome-scale gene regulatory network from complementary inference approaches and use it to elucidate transcriptional regulators of photoprotection. We show that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO2-mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga.
Collapse
Affiliation(s)
- Marius Arend
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Yizhong Yuan
- University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - M Águila Ruiz-Sola
- University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, 41092, Sevilla, Spain
| | - Nooshin Omranian
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
- Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Dimitris Petroutsos
- University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France.
| |
Collapse
|
26
|
Wilson S, Kim E, Ishii A, Ruban AV, Minagawa J. Overexpression of LHCSR and PsbS enhance light tolerance in Chlamydomonas reinhardtii. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 244:112718. [PMID: 37156084 DOI: 10.1016/j.jphotobiol.2023.112718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/17/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
Nonphotochemical quenching (NPQ) is a crucial mechanism for fine-tuning light harvesting and protecting the photosystem II (PSII) reaction centres from excess light energy in plants and algae. This process is regulated by photoprotective proteins LHCSR1, LHCSR3, and PsbS in green algae, such as Chlamydomonas reinhardtii. The det1-2 phot mutant, which overexpresses these photoprotective proteins, resulting in a significantly higher NPQ response, has been recently discovered in C. reinhardtii. Here, we analysed the physiological impact of this response on algal cells and found that det1-2 phot was capable of efficient growth under high light intensities, where wild-type (WT) cells were unable to survive. The mutant exhibited a smaller PSII cross-section in the dark and showed a detachment of the peripheral light-harvesting complex II (LHCII) antenna in the NPQ state, as suggested by a rise in the chlorophyll fluorescence parameter of photochemical quenching in the dark (qPd > 1). Furthermore, fluorescence decay-associated spectra demonstrated a decreased excitation pressure on PSII, with excess energy being directed toward PSI. The amount of LHCSR1, LHCSR3, and PsbS in the mutant correlated with the magnitude of the protective NPQ response. Overall, the study suggests the mechanism by which the overexpression of photoprotective proteins in det1-2 phot brings about an efficient and effective photoprotective response, enabling the mutant to grow and survive under high light intensities that would otherwise be lethal for WT cells.
Collapse
Affiliation(s)
- Sam Wilson
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Eunchul Kim
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Asako Ishii
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Alexander V Ruban
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan.
| |
Collapse
|
27
|
Schmollinger S, Chen S, Merchant SS. Quantitative elemental imaging in eukaryotic algae. Metallomics 2023; 15:mfad025. [PMID: 37186252 PMCID: PMC10209819 DOI: 10.1093/mtomcs/mfad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 05/17/2023]
Abstract
All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.
Collapse
Affiliation(s)
- Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Si Chen
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
28
|
Huang W, Krishnan A, Plett A, Meagher M, Linka N, Wang Y, Ren B, Findinier J, Redekop P, Fakhimi N, Kim RG, Karns DA, Boyle N, Posewitz MC, Grossman AR. Chlamydomonas mutants lacking chloroplast TRIOSE PHOSPHATE TRANSPORTER3 are metabolically compromised and light-sensitive. THE PLANT CELL 2023:koad095. [PMID: 36970811 DOI: 10.1093/plcell/koad095] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/08/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Modulation of photoassimilate export from the chloroplast is essential for controlling the distribution of fixed carbon in the cell and maintaining optimum photosynthetic rates. In this study we identified chloroplast TRIOSE PHOSPHATE/PHOSPHATE TRANSLOCATOR2 (CreTPT2) and CreTPT3 in the green alga Chlamydomonas (Chlamydomonas reinhardtii), which exhibit similar substrate specificities but whose encoding genes are differentially expressed over the diurnal cycle. We focused mostly on CreTPT3 because of its high level of expression and the severe phenotype exhibited by tpt3 relative to tpt2 mutants. Null mutants for CreTPT3 had a pleiotropic phenotype that affected growth, photosynthetic activities, metabolite profiles, carbon partitioning, and organelle-specific accumulation of H2O2. These analyses demonstrated that CreTPT3 is a dominant conduit on the chloroplast envelope for the transport of photoassimilates. In addition, CreTPT3 can serve as a safety valve that moves excess reductant out of the chloroplast and appears to be essential for preventing cells from experiencing oxidative stress and accumulating reactive oxygen species, even under low/moderate light intensities. Finally, our studies indicate subfunctionalization of the CreTPT transporters and suggest that there are differences in managing the export of photoassimilates from the chloroplasts of Chlamydomonas and vascular plants.
Collapse
Affiliation(s)
- Weichao Huang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Anagha Krishnan
- Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Anastasija Plett
- Institute of Plant Biochemistry, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Michelle Meagher
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Nicole Linka
- Institute of Plant Biochemistry, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Yongsheng Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
- School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Bijie Ren
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Justin Findinier
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Petra Redekop
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Neda Fakhimi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Rick G Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Devin A Karns
- Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Nanette Boyle
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Matthew C Posewitz
- Department of Chemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| |
Collapse
|
29
|
Wang X, Wang WX. Cell cycle-dependent Cu uptake explained the heterogenous responses of Chlamydomonas to Cu exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:121013. [PMID: 36608730 DOI: 10.1016/j.envpol.2023.121013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/11/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Growing evidence suggested that microorganisms exhibited heterogeneous sensitivity to toxicants, but their underlying mechanisms remain largely unknown. The asynchronous cell cycle progression in natural population implies the connection between cell cycle and heterogeneity. Here, the heterogenous responses of Chlamydomonas reinhardtii upon Cu stress were confirmed with the aid of a fluorometric probe for imaging Cu(I), implying the connection with cell cycle. Our results further indicated that the increase of labile Cu(I) was related to the cell division, leading to the fluctuation of labile Cu(I) with diurnal cycle and cell cycle, respectively. However, lack of Cu mainly influenced the cell division. We demonstrated that G2/M phase was the critical stage requiring high Cu quota during cell division. Specifically, algae at G2/M phase required 10-fold of Cu quota compared with that at G1 phase, which was related to the mitochondrial replication. Eventually, the heterogeneous Cu uptake ability of algae at different cell phases led to the heterogeneous responses to Cu exposure. Overall, Cu could influence the cell cycle through mediating the cell division, and in turn algae at different cell phases exhibited different Cu sensitivities. This study firstly uncovered the underlying mechanisms of heterogeneous Cu sensitivity for phytoplankton, which could help to evaluate the potential ecological risks of Cu.
Collapse
Affiliation(s)
- Xiangrui Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
| |
Collapse
|
30
|
García-Campa L, Valledor L, Pascual J. The Integration of Data from Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 12:511. [PMID: 36771596 PMCID: PMC9920879 DOI: 10.3390/plants12030511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
The increasing availability of massive omics data requires improving the quality of reference databases and their annotations. The combination of full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics has been successfully used for increasing proteoform characterization, which is a main ongoing goal in biology. However, the potential of including Oxford Nanopore Technologies Direct RNA Sequencing (ONT-DRS) data has not been explored. In this paper, we analyzed the impact of combining Iso-Seq- and ONT-DRS-derived data on the identification of proteoforms in Arabidopsis MS proteomics data. To this end, we selected a proteomics dataset corresponding to senescent leaves and we performed protein searches using three different protein databases: AtRTD2 and AtRTD3, built from the homonymous transcriptomes, regarded as the most complete and up-to-date available for the species; and a custom hybrid database combining AtRTD3 with publicly available ONT-DRS transcriptomics data generated from Arabidopsis leaves. Our results show that the inclusion and combination of long-read sequencing data from Iso-Seq and ONT-DRS into a proteogenomic workflow enhances proteoform characterization and discovery in bottom-up proteomics studies. This represents a great opportunity to further investigate biological systems at an unprecedented scale, although it brings challenges to current protein searching algorithms.
Collapse
Affiliation(s)
- Lara García-Campa
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33003 Oviedo, Spain
- University Institute of Biotechnology of Asturias, University of Oviedo, 33003 Oviedo, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33003 Oviedo, Spain
- University Institute of Biotechnology of Asturias, University of Oviedo, 33003 Oviedo, Spain
| | - Jesús Pascual
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33003 Oviedo, Spain
- University Institute of Biotechnology of Asturias, University of Oviedo, 33003 Oviedo, Spain
| |
Collapse
|
31
|
Salarvan F, Meydan H, Aksoy M. Transcription level and phylogeny analyses of Chlamydomonas reinhardtii arylsulfatases. J Eukaryot Microbiol 2023; 70:e12943. [PMID: 36018447 DOI: 10.1111/jeu.12943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 01/13/2023]
Abstract
Sulfur is a required macroelement for all organisms, and sulfate deficiency causes growth and developmental defects. Arylsulfatases (ARS) hydrolyze sulfate from sulfate esters and make sulfate bioavailable for plant uptake. These enzymes are found in microorganisms and animals; however, plant genomes do not encode any ARS gene. Our database searches found nineteen ARS genes in the genome of Chlamydomonas reinhardtii. Among these, ARS1 and ARS2 were studied in the literature; however, the remaining seventeen gene models were not studied. Our results show that putative polypeptide sequences of the ARS gene models all have the sulfatase domain and sulfatase motifs found in known ARSs. Phylogenetic analyses show that C. reinhardtii proteins are in close branches with Volvox carterii proteins while they were clustered in a separate group from Homo sapiens and bacterial species (Pseudomonas aeruginosa and Rhodopirellula baltica SH1), except human Sulf1, Sulf2, and GNS are clustered with algal ARSs. RT-PCR analyses showed that transcription of ARS6, ARS7, ARS11, ARS12, ARS13, ARS17, and ARS19 increased under sulfate deficiency. However, this increase was not as high as the increase seen in ARS2. Since plant genomes do not encode any ARS gene, our results highlight the importance of microbial ARS genes.
Collapse
Affiliation(s)
- Fatma Salarvan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Hasan Meydan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Münevver Aksoy
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| |
Collapse
|
32
|
Cell Type-Specific Pherophorins of Volvox carteri Reveal Interplay of Both Cell Types in ECM Biosynthesis. Cells 2022; 12:cells12010134. [PMID: 36611928 PMCID: PMC9818292 DOI: 10.3390/cells12010134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
The spheroidal green algae Volvox carteri serves as a model system to investigate the formation of a complex, multifunctional extracellular matrix (ECM) in a relatively simple, multicellular organism with cell differentiation. The V. carteri ECM is mainly composed of hydroxyproline-rich glycoproteins (HRGPs) and there are diverse region-specific, anatomically distinct structures in the ECM. One large protein family with importance for ECM biosynthesis stands out: the pherophorins. The few pherophorins previously extracted from the ECM and characterized, were specifically expressed by somatic cells. However, the localization and function of most pherophorins is unknown. Here, we provide a phylogenetic analysis of 153 pherophorins of V. carteri and its unicellular relative Chlamydomonas reinhardtii. Our analysis of cell type-specific mRNA expression of pherophorins in V. carteri revealed that, contrary to previous assumptions, only about half (52%) of the 102 investigated pherophorin-related genes show stronger expression in somatic cells, whereas about one-third (34%) of the genes show significant higher expression in reproductive cells (gonidia). We fused two pherophorin genes that are expressed by different cell types to yfp, stably expressed them in Volvox and studied the tagged proteins by live-cell imaging. In contrast to earlier biochemical approaches, this genetic approach also allows the in vivo analysis of non-extractable, covalently cross-linked ECM proteins. We demonstrate that the soma-specific pherophorin SSG185 is localized in the outermost ECM structures of the spheroid, the boundary zone and at the flagellar hillocks. SSG185:YFP is detectable as early as 1.5 h after completion of embryogenesis. It is then present for the rest of the life cycle. The gonidia-specific pherophorin PhG is localized in the gonidial cellular zone 1 ("gonidial vesicle") suggesting its involvement in the protection of gonidia and developing embryos until hatching. Even if somatic cells produce the main portion of the ECM of the spheroids, ECM components produced by gonidia are also required to cooperatively assemble the total ECM. Our results provide insights into the evolution of the pherophorin protein family and convey a more detailed picture of Volvox ECM synthesis.
Collapse
|
33
|
Ptushenko VV, Bondarenko GN, Vinogradova EN, Glagoleva ES, Karpova OV, Ptushenko OS, Shibzukhova KA, Solovchenko AE, Lobakova ES. Chilling Upregulates Expression of the PsbS and LhcSR Genes in the Chloroplasts of the Green Microalga Lobosphaera incisa IPPAS C-2047. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1699-1706. [PMID: 36717458 DOI: 10.1134/s0006297922120240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Non-photochemical quenching (NPQ) of excited chlorophyll states is essential for protecting the photosynthetic apparatus (PSA) from the excessive light-induced damage in all groups of oxygenic photosynthetic organisms. The key component of the NPQ mechanism in green algae and some other groups of algae and mosses is the LhcSR protein of the light harvesting complex (LHC) protein superfamily. In vascular plants, LhcSR is replaced by PsbS, another member of the LHC superfamily and a subunit of photosystem II (PSII). PsbS also performs the photoprotective function in mosses. For a long time, PsbS had been believed to be nonfunctional in green algae, although the corresponding gene was discovered in the genome of these organisms. The first evidence of the PsbS accumulation in the model green alga Chlamydomonas reinhardtii in response to the increase in irradiance was obtained only six years ago. However, the observed increase in the PsbS content was short-termed (on an hour-timescale). Here, we report a significant (more than three orders of magnitude) and prolonged (four days) upregulation of PsbS expression in response to the chilling-induced high-light stress followed by a less significant (~ tenfold) increase in the PsbS expression for nine days. This is the first evidence for the long-term upregulation of the PsbS expression in green alga (Chlorophyta) in response to stress. Our data indicate that the role of PsbS in the PSA of Chlorophyta is not limited to the first-line defense against stress, as it was previously assumed, but includes full-scale participation in the photoprotection of PSA from the environmental stress factors.
Collapse
Affiliation(s)
- Vasily V Ptushenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | | | - Elizaveta N Vinogradova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Kurchatov Institute National Research Center, 123182 Moscow Russia
| | - Elena S Glagoleva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga V Karpova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Oxana S Ptushenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Karina A Shibzukhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexei E Solovchenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Pskov State University, Pskov, 128000, Russia
| | - Elena S Lobakova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
34
|
Adler L, Díaz-Ramos A, Mao Y, Pukacz KR, Fei C, McCormick AJ. New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields. PLANT PHYSIOLOGY 2022; 190:1609-1627. [PMID: 35961043 PMCID: PMC9614477 DOI: 10.1093/plphys/kiac373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 05/06/2023]
Abstract
Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.
Collapse
Affiliation(s)
| | | | - Yuwei Mao
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krzysztof Robin Pukacz
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | | |
Collapse
|
35
|
Strenkert D, Yildirim A, Yan J, Yoshinaga Y, Pellegrini M, O'Malley RC, Merchant SS, Umen JG. The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:352-368. [PMID: 35986497 PMCID: PMC9588799 DOI: 10.1111/tpj.15948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/09/2022] [Accepted: 08/14/2022] [Indexed: 05/29/2023]
Abstract
Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. We interrogated the genome-wide distribution pattern of mono- and trimethylated histone H3 lysine 4 (H3K4) using chromatin-immunoprecipitation followed by deep-sequencing (ChIP-seq) during key phases of the Chlamydomonas cell cycle: early G1 phase, Zeitgeber Time 1 (ZT1), when cells initiate biomass accumulation, S/M phase (ZT13) when cells are replicating DNA and undergoing mitosis, and late G0 phase (ZT23) when they are quiescent. Tri-methylated H3K4 was predominantly enriched at transcription start sites of the majority of protein coding genes (85%). The likelihood of a gene being marked by H3K4me3 correlated with it being transcribed at some point during the life cycle but not necessarily by continuous active transcription, as exemplified by early zygotic genes, which may remain transcriptionally dormant for thousands of generations between sexual cycles. The exceptions to this rule were around 120 loci, some of which encode non-poly-adenylated transcripts, such as small nuclear RNAs and replication-dependent histones that had H3K4me3 peaks only when they were being transcribed. Mono-methylated H3K4 was the default state for the vast majority of histones that were bound outside of transcription start sites and terminator regions of genes. A small fraction of the genome that was depleted of any H3 lysine 4 methylation was enriched for DNA cytosine methylation and the genes within these DNA methylation islands were poorly expressed. Besides marking protein coding genes, H3K4me3 ChIP-seq data served also as a annotation tool for validation of hundreds of long non-coding RNA genes.
Collapse
Affiliation(s)
- Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Asli Yildirim
- Institute of Quantitative and Computational Biosciences, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles, CA, 90095, USA
| | - Juying Yan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matteo Pellegrini
- Institute of Quantitative and Computational Biosciences, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ronan C O'Malley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| |
Collapse
|
36
|
Windler M, Stuart R, Deutzmann JS, Mayali X, Navid A, D'haeseleer P, Marcu OE, Lipton M, Nicora C, Spormann AM. Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity. FEMS Microbiol Ecol 2022; 98:6670776. [PMID: 35977399 DOI: 10.1093/femsec/fiac091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/10/2022] [Accepted: 08/12/2022] [Indexed: 11/14/2022] Open
Abstract
Algal-bacterial interactions provide clues to algal physiology, but mutualistic interactions are complicated by dynamic exchange. We characterized the response of Chlamydomonas reinhardtii to the presence of a putative alga-benefitting commensal bacterium (Arthrobacter strain 'P2b'). Co-cultivation promoted chlorophyll content, biomass, average cell size, and number of dividing cells, relative to axenic cultures. Addition of bacterial spent medium (whole, size-fractionated and heat-treated) had similar effects, indicating P2b does not require algal interaction to promote growth. Nutrients and pH were excluded as putative effectors, collectively indicating a commensal interaction mediated by Arthrobacter-released small exometabolite(s). Proteogenomic comparison revealed similar response to co-cultivation and spent media, including differential cell cycle regulation, extensive downregulation of flagellar genes and histones, carbonic anhydrase and RubisCO downregulation, upregulation of some chlorophyll, amino acid and carbohydrate biosynthesis genes, and changes to redox and Fe homeostasis. Further, Arthrobacter protein expression indicated some highly expressed putative secondary metabolites. Together, these results revealed that low molecular weight bacterial metabolites can elicit major physiological changes in algal cell cycle regulation, perhaps through a more productive G1 phase, that lead to substantial increases in photosynthetically-produced biomass. This work illustrates that model commensal interactions can be used to shed light on algal response to stimulating bacteria.
Collapse
Affiliation(s)
- Miriam Windler
- Department of Civil & Environmental Engineering, Stanford University, United States
| | - Rhona Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Joerg S Deutzmann
- Department of Civil & Environmental Engineering, Stanford University, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Ali Navid
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Patrik D'haeseleer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, United States
| | - Oana E Marcu
- SETI Institute, NASA Ames Research Center, United States
| | - Mary Lipton
- Pacific Northwest National Laboratories, United States
| | - Carrie Nicora
- Pacific Northwest National Laboratories, United States
| | - Alfred M Spormann
- Department of Civil & Environmental Engineering, Stanford University, United States.,Department of Chemical Engineering, Stanford University, United States
| |
Collapse
|
37
|
Nef C, Dittami S, Kaas R, Briand E, Noël C, Mairet F, Garnier M. Sharing Vitamin B12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea. Microorganisms 2022; 10:microorganisms10071337. [PMID: 35889056 PMCID: PMC9323062 DOI: 10.3390/microorganisms10071337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Haptophyte microalgae are key contributors to microbial communities in many environments. It has been proposed recently that members of this group would be virtually all dependent on vitamin B12 (cobalamin), an enzymatic cofactor produced only by some bacteria and archaea. Here, we examined the processes of vitamin B12 acquisition by haptophytes. We tested whether co-cultivating the model species Tisochrysis lutea with B12-producing bacteria in vitamin-deprived conditions would allow the microalga to overcome B12 deprivation. While T. lutea can grow by scavenging vitamin B12 from bacterial extracts, co-culture experiments showed that the algae did not receive B12 from its associated bacteria, despite bacteria/algae ratios supposedly being sufficient to allow enough vitamin production. Since other studies reported mutualistic algae–bacteria interactions for cobalamin, these results question the specificity of such associations. Finally, cultivating T. lutea with a complex bacterial consortium in the absence of the vitamin partially rescued its growth, highlighting the importance of microbial interactions and diversity. This work suggests that direct sharing of vitamin B12 is specific to each species pair and that algae in complex natural communities can acquire it indirectly by other mechanisms (e.g., after bacterial lysis).
Collapse
Affiliation(s)
- Charlotte Nef
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
- Correspondence:
| | - Simon Dittami
- Station Biologique de Roscoff, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne University, F-29680 Roscoff, France;
| | - Raymond Kaas
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
| | - Enora Briand
- GENALG, PHYTOX, IFREMER, F-44000 Nantes, France; (E.B.); (M.G.)
| | - Cyril Noël
- SEBIMER, IRSI, IFREMER, F-29280 Brest, France;
| | | | | |
Collapse
|
38
|
Abstract
Economical production of photosynthetic organisms requires the use of natural day/night cycles. These induce strong circadian rhythms that lead to transient changes in the cells, requiring complex modeling to capture. In this study, we coupled times series transcriptomic data from the model green alga Chlamydomonas reinhardtii to a metabolic model of the same organism in order to develop the first transient metabolic model for diurnal growth of algae capable of predicting phenotype from genotype. We first transformed a set of discrete transcriptomic measurements (D. Strenkert, S. Schmollinger, S. D. Gallaher, P. A. Salomé, et al., Proc Natl Acad Sci U S A 116:2374–2383, 2019, https://doi.org/10.1073/pnas.1815238116) into continuous curves, producing a complete database of the cell’s transcriptome that can be interrogated at any time point. We also decoupled the standard biomass formation equation to allow different components of biomass to be synthesized at different times of the day. The resulting model was able to predict qualitative phenotypical outcomes of a starchless mutant. We also extended this approach to simulate all single-knockout mutants and identified potential targets for rational engineering efforts to increase productivity. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition, and intracellular fluxes for diurnal growth. IMPORTANCE We have developed the first transient metabolic model for diurnal growth of algae based on experimental data and capable of predicting phenotype from genotype. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition and intracellular fluxes of the model green alga, Chlamydomonas reinhardtii. The availability of this model will enable faster and more efficient design of cells for production of fuels, chemicals, and pharmaceuticals.
Collapse
|
39
|
Redekop P, Sanz-Luque E, Yuan Y, Villain G, Petroutsos D, Grossman AR. Transcriptional regulation of photoprotection in dark-to-light transition-More than just a matter of excess light energy. SCIENCE ADVANCES 2022; 8:eabn1832. [PMID: 35658034 PMCID: PMC9166400 DOI: 10.1126/sciadv.abn1832] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/18/2022] [Indexed: 05/22/2023]
Abstract
In nature, photosynthetic organisms are exposed to different light spectra and intensities depending on the time of day and atmospheric and environmental conditions. When photosynthetic cells absorb excess light, they induce nonphotochemical quenching to avoid photodamage and trigger expression of "photoprotective" genes. In this work, we used the green alga Chlamydomonas reinhardtii to assess the impact of light intensity, light quality, photosynthetic electron transport, and carbon dioxide on induction of the photoprotective genes (LHCSR1, LHCSR3, and PSBS) during dark-to-light transitions. Induction (mRNA accumulation) occurred at very low light intensity and was independently modulated by blue and ultraviolet B radiation through specific photoreceptors; only LHCSR3 was strongly controlled by carbon dioxide levels through a putative enhancer function of CIA5, a transcription factor that controls genes of the carbon concentrating mechanism. We propose a model that integrates inputs of independent signaling pathways and how they may help the cells anticipate diel conditions and survive in a dynamic light environment.
Collapse
Affiliation(s)
- Petra Redekop
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama St, Stanford, CA 94305, USA
- Corresponding author. (E.S.-L.); (P.R.)
| | - Emanuel Sanz-Luque
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama St, Stanford, CA 94305, USA
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain
- Corresponding author. (E.S.-L.); (P.R.)
| | - Yizhong Yuan
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, France
| | - Gaelle Villain
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, France
| | - Dimitris Petroutsos
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, France
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama St, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
40
|
Carmel Ezra S, Tuller T. Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts. Comput Struct Biotechnol J 2022; 20:2521-2538. [PMID: 35685358 PMCID: PMC9157439 DOI: 10.1016/j.csbj.2022.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/15/2022] [Accepted: 05/15/2022] [Indexed: 11/15/2022] Open
Abstract
The process of translation initiation in prokaryotes is mediated by the hybridization of the 16S rRNA of the small ribosomal subunit with the mRNA in a short region called the ribosomal binding site. However, translation initiation in chloroplasts, which have evolved from an ancestral bacterium, is not well understood. Some studies suggest that in many cases it differs from translation initiation in bacteria and involves various novel interactions of the mRNA structures with intracellular factors; however currently, there is no generic quantitative model related to these aspects in chloroplasts. We developed a novel computational pipeline and models that can be used for understanding and modeling translation regulation in chloroplasts. We demonstrate that local folding and co-folding energy of the rRNA and the mRNA correlates with codon usage estimators of expression levels (r = -0.63) and infer predictive models that connect these energies and codon usage to protein levels (with correlation up to 0.71). In addition, we demonstrate that the ends of the transcripts in chloroplasts are populated with various structural elements that may be functional. Furthermore, we report a database of 166 novel structures in the chloroplast transcripts that are predicted to be functional. We believe that the models reported here improve existing understandings of genomic evolution and the biophysics of translation in chloroplasts; as such, they can aid gene expression engineering in chloroplasts for various biotechnological objectives.
Collapse
Affiliation(s)
- Stav Carmel Ezra
- Department of Biomedical Engineering, Tel Aviv University, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Israel
| |
Collapse
|
41
|
Zhang N, Mattoon EM, McHargue W, Venn B, Zimmer D, Pecani K, Jeong J, Anderson CM, Chen C, Berry JC, Xia M, Tzeng SC, Becker E, Pazouki L, Evans B, Cross F, Cheng J, Czymmek KJ, Schroda M, Mühlhaus T, Zhang R. Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. Commun Biol 2022; 5:460. [PMID: 35562408 PMCID: PMC9106746 DOI: 10.1038/s42003-022-03359-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35°C) and acute (40°C) high temperatures and subsequent recovery at 25°C. We identified previously overlooked unique elements in response to moderate high temperature. Heat at 35°C transiently arrested the cell cycle followed by partial synchronization, up-regulated transcripts/proteins involved in gluconeogenesis/glyoxylate-cycle for carbon uptake and promoted growth. But 40°C disrupted cell division and growth. Both high temperatures induced photoprotection, while 40°C distorted thylakoid/pyrenoid ultrastructure, affected the carbon concentrating mechanism, and decreased photosynthetic efficiency. We demonstrated increased transcript/protein correlation during both heat treatments and hypothesize reduced post-transcriptional regulation during heat may help efficiently coordinate thermotolerance mechanisms. During recovery after both heat treatments, especially 40°C, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops. A systems-wide analysis of the single-cell green alga Chlamydomonas reinhardti reveals shared and unique responses to moderate and acute high temperatures using multiple-level investigation of transcriptomics, proteomics, cell physiology, photosynthetic parameters, and cellular ultrastructure.
Collapse
Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri, 63130, USA
| | - Will McHargue
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri, 63130, USA
| | | | - David Zimmer
- TU Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Kresti Pecani
- The Rockefeller University, New York, New York, 10065, USA
| | - Jooyeon Jeong
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Cheyenne M Anderson
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri, 63130, USA
| | - Chen Chen
- University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Jeffrey C Berry
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Shin-Cheng Tzeng
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Eric Becker
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Leila Pazouki
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Bradley Evans
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Fred Cross
- The Rockefeller University, New York, New York, 10065, USA
| | - Jianlin Cheng
- University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | | | | | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA.
| |
Collapse
|
42
|
King SJ, Jerkovic A, Brown LJ, Petroll K, Willows RD. Synthetic biology for improved hydrogen production in Chlamydomonas reinhardtii. Microb Biotechnol 2022; 15:1946-1965. [PMID: 35338590 PMCID: PMC9249334 DOI: 10.1111/1751-7915.14024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Hydrogen is a clean alternative to fossil fuels. It has applications for electricity generation and transportation and is used for the manufacturing of ammonia and steel. However, today, H2 is almost exclusively produced from coal and natural gas. As such, methods to produce H2 that do not use fossil fuels need to be developed and adopted. The biological manufacturing of H2 may be one promising solution as this process is clean and renewable. Hydrogen is produced biologically via enzymes called hydrogenases. There are three classes of hydrogenases namely [FeFe], [NiFe] and [Fe] hydrogenases. The [FeFe] hydrogenase HydA1 from the model unicellular algae Chlamydomonas reinhardtii has been studied extensively and belongs to the A1 subclass of [FeFe] hydrogenases that have the highest turnover frequencies amongst hydrogenases (21,000 ± 12,000 H2 s−1 for CaHydA from Clostridium acetobutyliticum). Yet to date, limitations in C. reinhardtii H2 production pathways have hampered commercial scale implementation, in part due to O2 sensitivity of hydrogenases and competing metabolic pathways, resulting in low H2 production efficiency. Here, we describe key processes in the biogenesis of HydA1 and H2 production pathways in C. reinhardtii. We also summarize recent advancements of algal H2 production using synthetic biology and describe valuable tools such as high‐throughput screening (HTS) assays to accelerate the process of engineering algae for commercial biological H2 production.
Collapse
Affiliation(s)
- Samuel J King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ante Jerkovic
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Robert D Willows
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
43
|
Zhang N, Pazouki L, Nguyen H, Jacobshagen S, Bigge BM, Xia M, Mattoon EM, Klebanovych A, Sorkin M, Nusinow DA, Avasthi P, Czymmek KJ, Zhang R. Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background). PLANTS (BASEL, SWITZERLAND) 2022; 11:585. [PMID: 35270055 PMCID: PMC8912731 DOI: 10.3390/plants11050585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.
Collapse
Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Leila Pazouki
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Huong Nguyen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Sigrid Jacobshagen
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA;
| | - Brae M. Bigge
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Erin M. Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Anastasiya Klebanovych
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Maria Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Dmitri A. Nusinow
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Prachee Avasthi
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Kirk J. Czymmek
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| |
Collapse
|
44
|
Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nat Ecol Evol 2022; 6:218-229. [DOI: 10.1038/s41559-021-01606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2021] [Indexed: 12/20/2022]
|
45
|
Széles E, Nagy K, Ábrahám Á, Kovács S, Podmaniczki A, Nagy V, Kovács L, Galajda P, Tóth SZ. Microfluidic Platforms Designed for Morphological and Photosynthetic Investigations of Chlamydomonas reinhardtii on a Single-Cell Level. Cells 2022; 11:cells11020285. [PMID: 35053401 PMCID: PMC8774182 DOI: 10.3390/cells11020285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Chlamydomonas reinhardtii is a model organism of increasing biotechnological importance, yet, the evaluation of its life cycle processes and photosynthesis on a single-cell level is largely unresolved. To facilitate the study of the relationship between morphology and photochemistry, we established microfluidics in combination with chlorophyll a fluorescence induction measurements. We developed two types of microfluidic platforms for single-cell investigations: (i) The traps of the “Tulip” device are suitable for capturing and immobilizing single cells, enabling the assessment of their photosynthesis for several hours without binding to a solid support surface. Using this “Tulip” platform, we performed high-quality non-photochemical quenching measurements and confirmed our earlier results on bulk cultures that non-photochemical quenching is higher in ascorbate-deficient mutants (Crvtc2-1) than in the wild-type. (ii) The traps of the “Pot” device were designed for capturing single cells and allowing the growth of the daughter cells within the traps. Using our most performant “Pot” device, we could demonstrate that the FV/FM parameter, an indicator of photosynthetic efficiency, varies considerably during the cell cycle. Our microfluidic devices, therefore, represent versatile platforms for the simultaneous morphological and photosynthetic investigations of C. reinhardtii on a single-cell level.
Collapse
Affiliation(s)
- Eszter Széles
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
- Doctoral School of Biology, University of Szeged, H-6722 Szeged, Hungary
| | - Krisztina Nagy
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (K.N.); (Á.Á.); (P.G.)
| | - Ágnes Ábrahám
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (K.N.); (Á.Á.); (P.G.)
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Sándor Kovács
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
| | - Anna Podmaniczki
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
- Doctoral School of Biology, University of Szeged, H-6722 Szeged, Hungary
| | - Valéria Nagy
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
| | - Péter Galajda
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (K.N.); (Á.Á.); (P.G.)
| | - Szilvia Z. Tóth
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary; (E.S.); (S.K.); (A.P.); (V.N.); (L.K.)
- Correspondence:
| |
Collapse
|
46
|
Hao DC, Li P, Xiao PG, He CN. Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants. PeerJ 2021; 9:e12428. [PMID: 34760397 PMCID: PMC8574218 DOI: 10.7717/peerj.12428] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022] Open
Abstract
Several main families of Ranunculales are rich in alkaloids and other medicinal compounds; many species of these families are used in traditional and folk medicine. Dichocarpum is a representative medicinal genus of Ranunculaceae, but the genetic basis of its metabolic phenotype has not been investigated, which hinders its sustainable conservation and utilization. We use the third-generation high-throughput sequencing and metabolomic techniques to decipher the full-length transcriptomes and metabolomes of five Dichocarpum species endemic in China, and 71,598 non-redundant full-length transcripts were obtained, many of which are involved in defense, stress response and immunity, especially those participating in the biosynthesis of specialized metabolites such as benzylisoquinoline alkaloids (BIAs). Twenty-seven orthologs extracted from trancriptome datasets were concatenated to reconstruct the phylogenetic tree, which was verified by the clustering analysis based on the metabolomic profile and agreed with the Pearson correlation between gene expression patterns of Dichocarpum species. The phylogenomic analysis of phytometabolite biosynthesis genes, e.g., (S)-norcoclaurine synthase, methyltransferases, cytochrome p450 monooxygenases, berberine bridge enzyme and (S)-tetrahydroprotoberberine oxidase, revealed the evolutionary trajectories leading to the chemodiversity, especially that of protoberberine type, aporphine type and bis-BIA abundant in Dichocarpum and related genera. The biosynthesis pathways of these BIAs are proposed based on full-length transcriptomes and metabolomes of Dichocarpum. Within Ranunculales, the gene duplications are common, and a unique whole genome duplication is possible in Dichocarpum. The extensive correlations between metabolite content and gene expression support the co-evolution of various genes essential for the production of different specialized metabolites. Our study provides insights into the transcriptomic and metabolomic landscapes of Dichocarpum, which will assist further studies on genomics and application of Ranunculales plants.
Collapse
Affiliation(s)
| | - Pei Li
- Chinese Academy of Medical Sciences, Beijing, China
| | - Pei-Gen Xiao
- Chinese Academy of Medical Sciences, Beijing, China
| | - Chun-Nian He
- Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
47
|
Chevin LM, Leung C, Le Rouzic A, Uller T. Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map. Genetica 2021; 150:209-221. [PMID: 34617196 DOI: 10.1007/s10709-021-00135-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.
Collapse
Affiliation(s)
- Luis-Miguel Chevin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Christelle Leung
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
48
|
Miyagishima SY, Tanaka K. The Unicellular Red Alga Cyanidioschyzon merolae-The Simplest Model of a Photosynthetic Eukaryote. PLANT & CELL PHYSIOLOGY 2021; 62:926-941. [PMID: 33836072 PMCID: PMC8504449 DOI: 10.1093/pcp/pcab052] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 05/13/2023]
Abstract
Several species of unicellular eukaryotic algae exhibit relatively simple genomic and cellular architecture. Laboratory cultures of these algae grow faster than plants and often provide homogeneous cellular populations exposed to an almost equal environment. These characteristics are ideal for conducting experiments at the cellular and subcellular levels. Many microalgal lineages have recently become genetically tractable, which have started to evoke new streams of studies. Among such algae, the unicellular red alga Cyanidioschyzon merolae is the simplest organism; it possesses the minimum number of membranous organelles, only 4,775 protein-coding genes in the nucleus, and its cell cycle progression can be highly synchronized with the diel cycle. These properties facilitate diverse omics analyses of cellular proliferation and structural analyses of the intracellular relationship among organelles. C. merolae cells lack a rigid cell wall and are thus relatively easily disrupted, facilitating biochemical analyses. Multiple chromosomal loci can be edited by highly efficient homologous recombination. The procedures for the inducible/repressive expression of a transgene or an endogenous gene in the nucleus and for chloroplast genome modification have also been developed. Here, we summarize the features and experimental techniques of C. merolae and provide examples of studies using this alga. From these studies, it is clear that C. merolae-either alone or in comparative and combinatory studies with other photosynthetic organisms-can provide significant insights into the biology of photosynthetic eukaryotes.
Collapse
Affiliation(s)
- Shin-Ya Miyagishima
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
| | - Kan Tanaka
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
| |
Collapse
|
49
|
Geisler K, Scaife MA, Mordaka PM, Holzer A, Tomsett EV, Mehrshahi P, Mendoza Ochoa GI, Smith AG. Exploring the Impact of Terminators on Transgene Expression in Chlamydomonas reinhardtii with a Synthetic Biology Approach. Life (Basel) 2021; 11:life11090964. [PMID: 34575113 PMCID: PMC8471596 DOI: 10.3390/life11090964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/03/2023] Open
Abstract
Chlamydomonas reinhardtii has many attractive features for use as a model organism for both fundamental studies and as a biotechnological platform. Nonetheless, despite the many molecular tools and resources that have been developed, there are challenges for its successful engineering, in particular to obtain reproducible and high levels of transgene expression. Here we describe a synthetic biology approach to screen several hundred independent transformants using standardised parts to explore different parameters that might affect transgene expression. We focused on terminators and, using a standardised workflow and quantitative outputs, tested 9 different elements representing three different size classes of native terminators to determine their ability to support high level expression of a GFP reporter gene. We found that the optimal size reflected the median size of element found in the C. reinhardtii genome. The behaviour of the terminator parts was similar with different promoters, in different host strains and with different transgenes. This approach is applicable to the systematic testing of other genetic elements, facilitating comparison to determine optimal transgene design.
Collapse
Affiliation(s)
- Katrin Geisler
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
| | - Mark A. Scaife
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
- Mara Renewables Corporation, Dartmouth, NS B2Y 4T6, Canada
| | - Paweł M. Mordaka
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
| | - Eleanor V. Tomsett
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
| | - Gonzalo I. Mendoza Ochoa
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; (K.G.); (M.A.S.); (P.M.M.); (A.H.); (E.V.T.); (P.M.); (G.I.M.O.)
- Correspondence: ; Tel.: +44-1223-333952
| |
Collapse
|
50
|
Zhang Y, Wu Z, Feng M, Chen J, Qin M, Wang W, Bao Y, Xu Q, Ye Y, Ma C, Jiang CZ, Gan SS, Zhou H, Cai Y, Hong B, Gao J, Ma N. The circadian-controlled PIF8-BBX28 module regulates petal senescence in rose flowers by governing mitochondrial ROS homeostasis at night. THE PLANT CELL 2021; 33:2716-2735. [PMID: 34043798 PMCID: PMC8408477 DOI: 10.1093/plcell/koab152] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/19/2021] [Indexed: 05/20/2023]
Abstract
Reactive oxygen species (ROS) are unstable reactive molecules that are toxic to cells. Regulation of ROS homeostasis is crucial to protect cells from dysfunction, senescence, and death. In plant leaves, ROS are mainly generated from chloroplasts and are tightly temporally restricted by the circadian clock. However, little is known about how ROS homeostasis is regulated in nonphotosynthetic organs, such as petals. Here, we showed that hydrogen peroxide (H2O2) levels exhibit typical circadian rhythmicity in rose (Rosa hybrida) petals, consistent with the measured respiratory rate. RNA-seq and functional screening identified a B-box gene, RhBBX28, whose expression was associated with H2O2 rhythms. Silencing RhBBX28 accelerated flower senescence and promoted H2O2 accumulation at night in petals, while overexpression of RhBBX28 had the opposite effects. RhBBX28 influenced the expression of various genes related to respiratory metabolism, including the TCA cycle and glycolysis, and directly repressed the expression of SUCCINATE DEHYDROGENASE 1, which plays a central role in mitochondrial ROS (mtROS) homeostasis. We also found that PHYTOCHROME-INTERACTING FACTOR8 (RhPIF8) could activate RhBBX28 expression to control H2O2 levels in petals and thus flower senescence. Our results indicate that the circadian-controlled RhPIF8-RhBBX28 module is a critical player that controls flower senescence by governing mtROS homeostasis in rose.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhicheng Wu
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ming Feng
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jiwei Chen
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Meizhu Qin
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wenran Wang
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ying Bao
- Faculty of Life Science, Tangshan Normal University, Tangshan, 063000, Hebei, China
| | - Qian Xu
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ying Ye
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chao Ma
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Cai-Zhong Jiang
- United States Department of Agriculture, Crop Pathology and Genetic Research Unit, Agricultural Research Service, University of California, Davis, CA, USA
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Su-Sheng Gan
- Plant Biology Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Hougao Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Youming Cai
- Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Bo Hong
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Junping Gao
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Nan Ma
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Author for correspondence:
| |
Collapse
|