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Kfoury B, Rodrigues WFC, Kim SJ, Brandizzi F, Del-Bem LE. Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function. THE NEW PHYTOLOGIST 2024; 242:809-824. [PMID: 38417454 DOI: 10.1111/nph.19595] [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: 05/24/2023] [Accepted: 01/15/2024] [Indexed: 03/01/2024]
Abstract
Plant glycosyl hydrolases (GHs) play a crucial role in selectively breaking down carbohydrates and glycoconjugates during various cellular processes, such as reserve mobilization, pathogen defense, and modification/disassembly of the cell wall. In this study, we examined the distribution of GH genes in the Archaeplastida supergroup, which encompasses red algae, glaucophytes, and green plants. We identified that the GH repertoire expanded from a few tens of genes in early archaeplastidians to over 400 genes in modern angiosperms, spanning 40 GH families in land plants. Our findings reveal that major evolutionary transitions were accompanied by significant changes in the GH repertoire. Specifically, we identified at least 23 GH families acquired by green plants through multiple horizontal gene transfer events, primarily from bacteria and fungi. We found a significant shift in the subcellular localization of GH activity during green plant evolution, with a marked increase in extracellular-targeted GH proteins associated with the diversification of plant cell wall polysaccharides and defense mechanisms against pathogens. In conclusion, our study sheds light on the macroevolutionary processes that have shaped the GH repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and the role of GHs in plant adaptation and defense mechanisms.
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Affiliation(s)
- Beatriz Kfoury
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Wenderson Felipe Costa Rodrigues
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Graduate Program in Plant Biology, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Sang-Jin Kim
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Luiz-Eduardo Del-Bem
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Graduate Program in Plant Biology, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
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2
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Lu KY, Cheng LC, Hung ZC, Chen ZY, Wang CW, Hou HH. The Ethyl Acetate Extract of Caulerpa microphysa Promotes Collagen Homeostasis and Inhibits Inflammation in the Skin. Curr Issues Mol Biol 2024; 46:2701-2712. [PMID: 38534786 DOI: 10.3390/cimb46030170] [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: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Inflammation and collagen-degrading enzymes' overexpression promote collagen decomposition, which affects the structural integrity of the extracellular matrix. The polysaccharide and peptide extracts of the green alga Caulerpa microphysa (C. microphysa) have been proven to have anti-inflammatory, wound healing, and antioxidant effects in vivo and in vitro. However, the biological properties of the non-water-soluble components of C. microphysa are still unknown. In the present study, we demonstrated the higher effective anti-inflammatory functions of C. microphysa ethyl acetate (EA) extract than water extract up to 16-30% in LPS-induced HaCaT cells, including reducing the production of interleukin (IL)-1β, IL-6, IL-8, and tumor necrosis factor-α (TNF-α). Furthermore, the excellent collagen homeostasis effects from C. microphysa were proven by suppressing the matrix metalloproteinase-1 (MMP-1) secretion, enhancing type 1 procollagen and collagen expressions dose-dependently in WS1 cells. Moreover, using UHPLC-QTOF-MS analysis, four terpenoids, siphonaxanthin, caulerpenyne, caulerpal A, and caulerpal B, were identified and may be involved in the superior collagen homeostasis and anti-inflammatory effects of the C. microphysa EA extract.
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Affiliation(s)
- Kuo-Yun Lu
- Department of Nursing, Division of Basic Medical Sciences, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan
| | - Li-Ching Cheng
- Department of Nursing, Division of Basic Medical Sciences, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan
- Department of General Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Zheng-Ci Hung
- Graduate Institute of Oral Biology, School of Dentistry, National Taiwan University, Taipei 100, Taiwan
| | - Ze-Ying Chen
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | - Chuang-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Hsin-Han Hou
- Graduate Institute of Oral Biology, School of Dentistry, National Taiwan University, Taipei 100, Taiwan
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei 100, Taiwan
- Department of Dentistry, National Taiwan University Hospital, Taipei 100, Taiwan
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3
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Kurtović K, Schmidt V, Nehasilová M, Vosolsobě S, Petrášek J. Rediscovering Chara as a model organism for molecular and evo-devo studies. PROTOPLASMA 2024; 261:183-196. [PMID: 37880545 DOI: 10.1007/s00709-023-01900-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023]
Abstract
Chara has been used as a model for decades in the field of plant physiology, enabling the investigation of fundamental physiological processes. In electrophysiological studies, Chara has been utilized thanks to its large internodal cells that can be easily manipulated. Additionally, Chara played a pioneering role in elucidating the presence and function of the cytoskeleton in cytoplasmic streaming, predating similar findings in terrestrial plants. Its representation considerably declined following the establishment and routine application of genetic transformation techniques in Arabidopsis. Nevertheless, the recent surge in evo-devo studies can be attributed to the whole genome sequencing of the Chara braunii, which has shed light on ancestral traits prevalent in land plants. Surprisingly, the Chara braunii genome encompasses numerous genes that were previously regarded as exclusive to land plants, suggesting their acquisition prior to the colonization of terrestrial habitats. This review summarizes the established methods used to study Chara, while incorporating recent molecular data, to showcase its renewed importance as a model organism in advancing plant evolutionary developmental biology.
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Affiliation(s)
- Katarina Kurtović
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Vojtěch Schmidt
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Nehasilová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Stanislav Vosolsobě
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Petrášek
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
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4
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Heise CM, Hagemann M, Schubert H. Photosynthetic response of Chara braunii towards different bicarbonate concentrations. PHYSIOLOGIA PLANTARUM 2024; 176:e14234. [PMID: 38439180 DOI: 10.1111/ppl.14234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
A variety of inorganic carbon acquisition modes have been proposed in Characean algae, however, a broadly applicable inorganic carbon uptake mechanism is unknown for the genus Chara. In the present study, we analyzed if C. braunii can efficiently use HCO3 - as a carbon source for photosynthesis. For this purpose, C. braunii was exposed to different concentrations of NaHCO3 - at different time scales. The photosynthetic electron transport through photosystem I (PSI) and II (PSII), the maximum electron transport rate (ETRmax ), the efficiency of the electron transport rate (α, the initial slope of the ETR), and the light saturation point of photosynthesis (Ek ) were evaluated. Additionally, pigment contents (chlorophyll a, chlorophyll b, and carotenoids) were determined. Bicarbonate addition positively affected ETRmax , after direct HCO3 - application, of both PSII and PSI, but this effect seems to decrease after 1 h and 24 h. Similar trends were seen for Ek , but no significant effect was observed for α. Pigment contents showed no significant changes in relation to different HCO3 - concentrations. To evaluate if cyclic electron flow around PSI was involved in active HCO3 - uptake, the ratio of PSI ETRmax /PSII ETRmax was calculated but did not show a distinctive trend. These results suggest that C. braunii can utilize NaHCO3 - in short-term periods as a carbon source but could rely on other carbon acquisition mechanisms over prolonged time periods. These observations suggest that the minor role of HCO3 - as a carbon source for photosynthesis in this alga might differentiate C. braunii from other examined Chara spp.
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Affiliation(s)
- Carolin Magdalene Heise
- Institute of Biosciences, Department of Aquatic Ecology, University of Rostock, Rostock, Germany
- Institute of Biosciences, Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Martin Hagemann
- Institute of Biosciences, Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Hendrik Schubert
- Institute of Biosciences, Department of Aquatic Ecology, University of Rostock, Rostock, Germany
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Ito K, Sugawara S, Kageyama S, Sawaguchi N, Hyotani T, Miyazawa SI, Makino A, Suzuki Y. Equisetum praealtum and E. hyemale have abundant Rubisco with a high catalytic turnover rate and low CO 2 affinity. JOURNAL OF PLANT RESEARCH 2024; 137:255-264. [PMID: 38112982 DOI: 10.1007/s10265-023-01514-z] [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: 10/02/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
The kinetic properties of Rubisco, a key enzyme for photosynthesis, have been examined in numerous plant species. However, this information on some plant groups, such as ferns, is scarce. This study examined Rubisco carboxylase activity and leaf Rubisco levels in seven ferns, including four Equisetum plants (E. arvense, E. hyemale, E. praealtum, and E. variegatum), considered living fossils. The turnover rates of Rubisco carboxylation (kcatc) in E. praealtum and E. hyemale were comparable to those in the C4 plants maize (Zea mays) and sorghum (Sorghum bicolor), whose kcatc values are high. Rubisco CO2 affinity, estimated from the percentage of Rubisco carboxylase activity under CO2 unsaturated conditions in kcatc in these Equisetum plants, was low and also comparable to that in maize and sorghum. In contrast, kcatc and CO2 affinities of Rubisco in other ferns, including E. arvense and E. variegatum were comparable with those in C3 plants. The N allocation to Rubisco in the ferns examined was comparable to that in the C3 plants. These results indicate that E. praealtum and E. hyemale have abundant Rubisco with high kcatc and low CO2 affinity, whereas the carboxylase activity and abundance of Rubisco in other ferns were similar to those in C3 plants. Herein, the Rubisco properties of E. praealtum and E. hyemale were discussed regarding their evolution and physiological implications.
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Affiliation(s)
- Kana Ito
- Graduate School of Arts and Sciences, Iwate University, Morioka, Japan
| | | | - Sota Kageyama
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Naoki Sawaguchi
- Graduate School of Arts and Sciences, Iwate University, Morioka, Japan
| | - Takuro Hyotani
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | | | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Present address: Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yuji Suzuki
- Faculty of Agriculture, Iwate University, Morioka, Japan.
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Domozych DS, LoRicco JG. The extracellular matrix of green algae. PLANT PHYSIOLOGY 2023; 194:15-32. [PMID: 37399237 PMCID: PMC10762512 DOI: 10.1093/plphys/kiad384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
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Affiliation(s)
- David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY 12866, USA
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7
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Javed T, Gao SJ. WRKY transcription factors in plant defense. Trends Genet 2023; 39:787-801. [PMID: 37633768 DOI: 10.1016/j.tig.2023.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/28/2023]
Abstract
Environmental stressors caused by climate change are fundamental barriers to agricultural sustainability. Enhancing the stress resilience of crops is a key strategy in achieving global food security. Plants perceive adverse environmental conditions and initiate signaling pathways to activate precise responses that contribute to their survival. WRKY transcription factors (TFs) are essential players in several signaling cascades and regulatory networks that have crucial implications for defense responses in plants. This review summarizes advances in research concerning how WRKY TFs mediate various signaling cascades and metabolic adjustments as well as how epigenetic modifications involved in environmental stress responses in plants can modulate WRKYs and/or their downstream genes. Emerging research shows that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing of WRKYs could be used to improve crop resilience.
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Affiliation(s)
- Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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8
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Bellino A, Baldantoni D. Biodiversity, Ecology and Distribution of Mediterranean Charophytes in Southern Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:3434. [PMID: 37836174 PMCID: PMC10574563 DOI: 10.3390/plants12193434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
Charophytes are amongst the most endangered primary producers in freshwater and coastal ecosystems. In spite of the extensive research on the group and its ecological and conservational relevance, scarce information is available on Mediterranean environments, especially rivers and small water reservoirs, where charophytes face challenging summer droughts and changes in hydrological regimes, as well as pervasive anthropogenic pressures. This research aimed, through repeated field observations, detailed analyses of population traits, and extensive characterization of the colonized environments, to foster an understanding of the distribution, biodiversity, and ecology of charophytes in an area of exceptional environmental value and that is still uninvestigated in relation to its charophyte flora, the southern Campania region (Italy). Overall, 17 populations were discovered, belonging to 4 taxa of the Chara genus: C. globularis, C. gymnophylla, C. vulgaris, and C. vulgaris var. papillata, reduced to 12 populations and to the first 3 taxa by the end of the study. The species occupied different ecological niches and colonized environments such as rivers and small ponds, with environment-dependent morphotypes. The occurrence of few taxa with a wide distribution, often forming ephemeral populations, suggests ongoing constraints on charophyte biodiversity in the area, favoring opportunistic species that are able to benefit from temporary refugia.
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9
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Heß D, Holzhausen A, Hess WR. Insight into the nodal cells transcriptome of the streptophyte green alga Chara braunii S276. PHYSIOLOGIA PLANTARUM 2023; 175:e14025. [PMID: 37882314 DOI: 10.1111/ppl.14025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023]
Abstract
Charophyceae are the most complex streptophyte algae, possessing tissue-like structures, rhizoids and a cellulose-pectin-based cell wall akin to embryophytes. Together with the Zygnematophyceae and the Coleochaetophycae, the Charophyceae form a grade in which the Zygnematophyceae share a last common ancestor with land plants. The availability of genomic data, its short life cycle, and the ease of non-sterile cultivation in the laboratory have made the species Chara braunii an emerging model system for streptophyte terrestrialization and early land plant evolution. In this study, tissue containing nodal cells was prepared under the stereomicroscope, and an RNA-seq dataset was generated and compared to transcriptome data from whole plantlets. In both samples, transcript coverage was high for genes encoding ribosomal proteins and a homolog of the putative PAX3- and PAX7-binding protein 1. Gene ontology was used to classify the putative functions of the differently expressed genes. In the nodal cell sample, main upregulated molecular functions were related to protein, nucleic acid, ATP- and DNA binding. Looking at specific genes, several signaling-related genes and genes encoding sugar-metabolizing enzymes were found to be expressed at a higher level in the nodal cell sample, while photosynthesis-and chloroplast-related genes were expressed at a comparatively lower level. We detected the transcription of 21 different genes encoding DUF4360-containing cysteine-rich proteins. The data contribute to the growing understanding of Charophyceae developmental biology by providing a first insight into the transcriptome composition of Chara nodal cells.
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Affiliation(s)
- Daniel Heß
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Anja Holzhausen
- Plant Cell Biology, Department of Biology, Philipps University Marburg, Marburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Pfeifer L, Mueller KK, Utermöhlen J, Erdt F, Zehge JBJ, Schubert H, Classen B. The cell walls of different Chara species are characterized by branched galactans rich in 3-O-methylgalactose and absence of AGPs. PHYSIOLOGIA PLANTARUM 2023; 175:e13989. [PMID: 37616003 DOI: 10.1111/ppl.13989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
Streptophyte algae are the closest relatives to land plants; their latest common ancestor performed the most drastic adaptation in plant evolution around 500 million years ago: the conquest of land. Besides other adaptations, this step required changes in cell wall composition. Current knowledge on the cell walls of streptophyte algae and especially on the presence of arabinogalactan-proteins (AGPs), important signalling molecules in all land plants, is limited. To get deeper insights into the cell walls of streptophyte algae, especially in Charophyceae, we performed sequential cell wall extractions of four Chara species. The three species Chara globularis, Chara subspinosa and Chara tomentosa revealed comparable cell wall compositions, with pectins, xylans and xyloglucans, whereas Chara aspera stood out with higher amounts of uronic acids in the pectic fractions and lack of reactivity with antibodies binding to xylan- and xyloglucan epitopes. Search for AGPs in the four Chara species and in Nitellopsis obtusa revealed the presence of galactans with pyranosidic galactose in 1,3-, 1,6- and 1,3,6-linkage, which are typical galactan motifs in land plant AGPs. A unique feature of these branched galactans was high portions of 3-O-methylgalactose. Only Nitellopsis contained substantial amounts of arabinose A bioinformatic search for prolyl-4-hydroxylases, involved in the biosynthesis of AGPs, revealed one possible functional sequence in the genome of Chara braunii, but no hydroxyproline could be detected in the four Chara species or in Nitellopsis obtusa. We conclude that AGPs that is typical for land plants are absent, at least in these members of the Charophyceae.
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Affiliation(s)
- Lukas Pfeifer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Kim-Kristine Mueller
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jon Utermöhlen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Felicitas Erdt
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jean Bastian Just Zehge
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hendrik Schubert
- Aquatic Ecology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Birgit Classen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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11
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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JM, Dadras A, Zegers JM, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ari JB, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526407. [PMID: 36778228 PMCID: PMC9915684 DOI: 10.1101/2023.01.31.526407] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Jinfang Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Iker Irisarri
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Bo Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Sophie de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Janine M.R. Fürst-Jansen
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jaccoline M.S. Zegers
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tim P. Rieseberg
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Maaike J. Bierenbroodspot
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (UMA-CSIC)
| | - Orestis Nousias
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Tang Li
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W. Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL 60115, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - John M. Archibald
- Dalhousie University, Department of Biochemistry and Molecular Biology, 5850 College Street, Halifax NS B3H 4R2, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Jeffrey P. Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University (EPSAG), Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xiyin Wang
- North China University of Science and Technology
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Cornell University, Plant Biology Section, Ithaca, NY, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE 68588, USA
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jan de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Yanbin Yin
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
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Leterme S, Bastien O, Aiese Cigliano R, Amato A, Michaud M. Phylogenetic and Structural Analyses of VPS13 Proteins in Archaeplastida Reveal Their Complex Evolutionary History in Viridiplantae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231211976. [PMID: 38033810 PMCID: PMC10683392 DOI: 10.1177/25152564231211976] [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: 05/03/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and regulation. Whereas VPS13 organization and function have been extensively studied in yeast and mammals, information in organisms originating from primary endosymbiosis is scarce. In the higher plant Arabidopsis thaliana, four paralogs, AtVPS13S, X, M1, and M2, were identified, AtVPS13S playing a role in the regulation of root growth, cell patterning, and reproduction. In this work, we performed phylogenetic, as well as domain and structural modeling of VPS13 proteins in Archaeplastida in order to understand their general organization and evolutionary history. We confirmed the presence of human VPS13B orthologues in some phyla and described two new VPS13 families presenting a particular domain arrangement: VPS13R in Rhodophytes and VPS13Y in Chlorophytes and Streptophytes. By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. This study reveals the complex evolution of VPS13 family and opens important perspectives for their functional characterization in photosynthetic organisms.
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Affiliation(s)
- Sébastien Leterme
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Olivier Bastien
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | | | - Alberto Amato
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
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Permann C, Gierlinger N, Holzinger A. Zygospores of the green alga Spirogyra: new insights from structural and chemical imaging. FRONTIERS IN PLANT SCIENCE 2022; 13:1080111. [PMID: 36561459 PMCID: PMC9763465 DOI: 10.3389/fpls.2022.1080111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Zygnematophyceae, a class of streptophyte green algae and sister group to land plants (Embryophytes) live in aquatic to semi-terrestrial habitats. The transition from aquatic to terrestrial environments requires adaptations in the physiology of vegetative cells and in the structural properties of their cell walls. Sexual reproduction occurs in Zygnematophyceae by conjugation and results in the formation of zygospores, possessing unique multi-layered cell walls, which might have been crucial in terrestrialization. We investigated the structure and chemical composition of field sampled Spirogyra sp. zygospore cell walls by multiple microscopical and spectral imaging techniques: light microscopy, confocal laser scanning microscopy, transmission electron microscopy following high pressure freeze fixation/freeze substitution, Raman spectroscopy and atomic force microscopy. This comprehensive analysis allowed the detection of the subcellular organization and showed three main layers of the zygospore wall, termed endo-, meso- and exospore. The endo- and exospore are composed of polysaccharides with different ultrastructural appearance, whereas the electron dense middle layer contains aromatic compounds as further characterized by Raman spectroscopy. The possible chemical composition remains elusive, but algaenan or a sporopollenin-like material is suggested. Similar compounds with a non-hydrolysable character can be found in moss spores and pollen of higher plants, suggesting a protective function against desiccation stress and high irradiation. While the tripartite differentiation of the zygospore wall is well established in Zygnematopyhceae, Spirogyra showed cellulose fibrils arranged in a helicoidal pattern in the endo- and exospore. Initial incorporation of lipid bodies during early zygospore wall formation was also observed, suggesting a key role of lipids in zygospore wall synthesis. Multimodal imaging revealed that the cell wall of the sexually formed zygospores possess a highly complex internal structure as well as aromatics, likely acting as protective compounds and leading to impregnation. Both, the newly discovered special three-dimensional arrangement of microfibrils and the integration of highly resistant components in the cell wall are not found in the vegetative state. The variety of methods gave a comprehensive view on the intricate zygospore cell wall and its potential key role in the terrestrial colonization and plant evolution is discussed.
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Affiliation(s)
- Charlotte Permann
- Department of Botany, University of Innsbruck, Functional Plant Biology, Innsbruck, Austria
| | - Notburga Gierlinger
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Andreas Holzinger
- Department of Botany, University of Innsbruck, Functional Plant Biology, Innsbruck, Austria
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