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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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Temperate-zone cultivation of Oedogonium in municipal wastewater effluent to produce cellulose and oxygen. ACTA ACUST UNITED AC 2020; 47:251-262. [DOI: 10.1007/s10295-020-02260-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/09/2020] [Indexed: 01/13/2023]
Abstract
Abstract
Cultivation of the filamentous chlorophyte Oedogonium in municipal wastewater effluent is known to improve water quality and yield lipid- and protein-rich biomass for industrial applications. Chlorophyte celluloses, whose molecular organization and physical traits differ from those of plants, represent yet another valuable extractive, and algal oxygen production is of economic value in wastewater treatment. Consequently, we explored cellulose and oxygen production from Oedogonium biomass batch-cultivated in treated secondary municipal wastewater effluent. We compared biomass, cellulose, and oxygen production outside and within an adjacent greenhouse, under differing dissolved CO2 and pH conditions, and during temperate-zone seasonal change from summer through fall. Overall production did not differ within or outside the greenhouse, but outside production was higher in summer and lower in fall as air temperatures declined. Batch cultivation offered advantages, but high levels of mixing and CO2 were essential to maintain neutral pH for optimal algal growth and oxygen production.
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Gong L, Liu Y, Xiong Y, Li T, Yin C, Zhao J, Yu J, Yin Q, Gupta VK, Jiang Y, Duan X. New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange ( Citrus sinensis). Virulence 2020; 11:748-768. [PMID: 32525727 PMCID: PMC7549954 DOI: 10.1080/21505594.2020.1773038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Blue and green molds, the common phenotypes of post-harvest diseases in fruits, are mainly caused by Penicillium fungal species, including P. italicum, P. digitatum, and P. expansum. We sequenced and assembled the genome of a P. italicum strain, which contains 31,034,623 bp with 361 scaffolds and 627 contigs. The mechanisms underlying the evolution of host specificity among the analyzed Penicillium species were associated with the expansion of protein families, genome restructuring, horizontal gene transfer, and positive selection pressure. A dual-transcriptome analysis following the infection of Valencia orange (Citrus sinensis) by P. italicum resulted in the annotation of 9,307 P. italicum genes and 24,591 Valencia orange genes. The pathogenicity of P. italicum may be due to the activation of effectors, including 51 small secreted cysteine-rich proteins, 110 carbohydrate-active enzymes, and 12 G protein-coupled receptors. Additionally, 211 metabolites related to the interactions between P. italicum and Valencia orange were identified by gas chromatography-time of flight mass spectrography, three of which were further confirmed by ultra-high performance liquid chromatography triple quadrupole mass spectrometry. A metabolomics analysis indicated that P. italicum pathogenicity is associated with the sphingolipid and salicylic acid signaling pathways. Moreover, a correlation analysis between the metabolite contents and gene expression levels suggested that P. italicum induces carbohydrate metabolism in Valencia orange fruits as part of its infection strategy. This study provides useful information regarding the genomic determinants that drive the evolution of host specificity in Penicillium species and clarifies the host-plant specificity during the infection of Valencia orange by P. italicum. IMPORTANCE P. italicum GL_Gan1, a local strain in Guangzhou, China, was sequenced. Comparison of the genome of P. italicum GL_Gan1 with other pathogenic Penicillium species, P. digitatum and P. expansum, revealed that the expansion of protein families, genome restructuring, HGT, and positive selection pressure were related to the host range expansion of the analyzed Penicillium species. Moreover, gene gains or losses might be associated with the speciation of these Penicillium species. In addition, the molecular basis of host-plant specificity during the infection of Valencia orange (Citrus sinensis) by P. italicum was also elucidated by transcriptomic and metabolomics analysis. The data presented herein may be useful for further elucidating the molecular basis of the evolution of host specificity of Penicillium species and for illustrating the host-plant specificity during the infection of Valencia orange by P. italicum.
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Affiliation(s)
- Liang Gong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Yongfeng Liu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Yehui Xiong
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University , Beijing, China
| | - Taotao Li
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Chunxiao Yin
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Juanni Zhao
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Jialin Yu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Qi Yin
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of Technology , Tallinn, Estonia
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Xuewu Duan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
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Mekvipad N, Satjarak A. Evolution of organellar genes of chlorophyte algae: Relevance to phylogenetic inference. PLoS One 2019; 14:e0216608. [PMID: 31059557 PMCID: PMC6502327 DOI: 10.1371/journal.pone.0216608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/24/2019] [Indexed: 11/18/2022] Open
Abstract
Protein-coding genes in organellar genomes have been widely used to resolve relationships of chlorophyte algae. The mode of evolution of these protein-coding genes affects relationship estimations, yet selection effects on genes commonly used as markers in phylogenetic analyses are insufficiently well understood. To gain more understanding about the effects of green algal organelle protein-coding genes on phylogenies, more information is needed about the mode of gene evolution. We used phylogenetic frameworks to examine evolutionary relationships of 58 protein-coding genes present in the organellar genomes of chlorophyte and streptophyte algae at multiple levels: organelle, biological function, and individual gene, and calculated pairwise dN/dS ratios of algal organellar protein-coding genes to investigate mode of evolution. Results indicate that mitochondrial genes have evolved at a higher rate than have chloroplast genes. Low dN/dS ratios indicating relatively high level of conservation indicate that nad2, nad5, atpA, atpE, psbC, and psbD might be particularly good candidates for use as markers in chlorophyte phylogenies. Chlorophycean atp6, nad2, atpF, clpP, rps2, rps3, rps4, and rps7 protein-coding sequences exhibited selective mutations, suggesting that changes in proteins encoded by these genes might have increased fitness in Chlorophyceae.
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Kapust N, Nelson-Sathi S, Schönfeld B, Hazkani-Covo E, Bryant D, Lockhart PJ, Röttger M, Xavier JC, Martin WF. Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication. Genome Biol Evol 2018; 10:1198-1209. [PMID: 29718211 PMCID: PMC5928405 DOI: 10.1093/gbe/evy080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Abstract
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.
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Affiliation(s)
- Nils Kapust
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | | | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Mayo Röttger
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Joana C Xavier
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
- Corresponding author: E-mail:
| | - William F Martin
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
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