1
|
Thanapipatpong P, Vuttipongchaikij S, Chomtong T, Puangtame W, Napaumpaipond P, Gomez LD, Suttangkakul A. Alternative splicing regulates autophagy in response to environmental stresses in cucumber ( Cucumis sativus). All Life 2023. [DOI: 10.1080/26895293.2023.2195987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Affiliation(s)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Thitikorn Chomtong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wilasinee Puangtame
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | | | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
2
|
Taway K, Dachphun I, Vuttipongchaikij S, Suttangkakul A. Evaluation of cucumber UBL5 promoter as a tool for transgene expression and genome editing in plants. Transgenic Res 2023; 32:437-449. [PMID: 37351728 DOI: 10.1007/s11248-023-00359-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Transgene expression and genome editing can help improve cucumber varieties to better respond to climate change. This study aimed to evaluate the applicability of the CsUBL5 promoter in transgene expression and genome editing in cucumber. The CsUBL5 promoter was cloned and analyzed to identify cis-elements that respond to abiotic signals, hormones, signal molecules, and nutrient treatments. 5' deletion constructs of the promoter were tested for their ability to drive GUS reporter expression in cucumber cotyledons, Arabidopsis seedlings, and tobacco leaves, and their response to various treatments including SA, light, drought, IAA, and GA was determined. The results showed that the CsUBL5 promoter effectively drove transgene expression in these plants, and their expressions under treatments were consistent with the predicted cis-elements, with some exceptions. Furthermore, the pCsUBL5-749 deletion construct can improve genome editing efficiency in cucumber when driving Cas9 expression. The editing efficiency of two sgRNAs targeting the ATG6 gene in cucumber was up to 4.6-fold higher using pCsUBL5-749 compared to a rice UBI promoter, although the effects of changing promoter on the editing efficiency is sgRNA specific. These findings highlight the potential utility of the CsUBL5 promoter for improving cucumber varieties through genetic engineering and genome editing. It also demonstrates the importance of modulating Cas9 expression to increase genome editing efficiency in cucumbers.
Collapse
Affiliation(s)
- Kamonchanok Taway
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Issariya Dachphun
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand.
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok, 10900, Thailand.
| |
Collapse
|
3
|
Wannitikul P, Wattana-Amorn P, Sathitnaitham S, Sakulkoo J, Suttangkakul A, Wonnapinij P, Bassel GW, Simister R, Gomez LD, Vuttipongchaikij S. Disruption of a DUF247 Containing Protein Alters Cell Wall Polysaccharides and Reduces Growth in Arabidopsis. Plants (Basel) 2023; 12:1977. [PMID: 37653894 PMCID: PMC10221614 DOI: 10.3390/plants12101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Plant cell wall biosynthesis is a complex process that requires proteins and enzymes from glycan synthesis to wall assembly. We show that disruption of At3g50120 (DUF247-1), a member of the DUF247 multigene family containing 28 genes in Arabidopsis, results in alterations to the structure and composition of cell wall polysaccharides and reduced growth and plant size. An ELISA using cell wall antibodies shows that the mutants also exhibit ~50% reductions in xyloglucan (XyG), glucuronoxylan (GX) and heteromannan (HM) epitopes in the NaOH fraction and ~50% increases in homogalacturonan (HG) epitopes in the CDTA fraction. Furthermore, the polymer sizes of XyGs and GXs are reduced with concomitant increases in short-chain polymers, while those of HGs and mHGs are slightly increased. Complementation using 35S:DUF247-1 partially recovers the XyG and HG content, but not those of GX and HM, suggesting that DUF247-1 is more closely associated with XyGs and HGs. DUF247-1 is expressed throughout Arabidopsis, particularly in vascular and developing tissues, and its disruption affects the expression of other gene members, indicating a regulatory control role within the gene family. Our results demonstrate that DUF247-1 is required for normal cell wall composition and structure and Arabidopsis growth.
Collapse
Affiliation(s)
- Pitchaporn Wannitikul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Pakorn Wattana-Amorn
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand;
| | - Sukhita Sathitnaitham
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK;
| | - Rachael Simister
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Leonardo D. Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| |
Collapse
|
4
|
Promsuk G, Vuttipongchaikij S, Prommarit K, Suttangkakul A, Lazarus CM, Wonnapinij P, Wattana-Amorn P. Anthranilic Acid Accumulation in Saccharomyces cerevisiae Induced by Expression of a Nonribosomal Peptide Synthetase Gene from Paecilomyces cinnamomeus BCC 9616. Chembiochem 2022; 23:e202200573. [PMID: 36250803 DOI: 10.1002/cbic.202200573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/14/2022] [Indexed: 01/25/2023]
Abstract
Heterologous expression of nrps33, a nonribosomal peptide synthetase gene, from Paecilomyces cinnamomeus BCC 9616 in Saccharomyces cerevisiae unexpectedly resulted in the accumulation of anthranilic acid, an intermediate in tryptophan biosynthesis. Based on transcriptomic and real-time quantitative polymerase chain reaction (RT-qPCR) results, expression of nrps33 affected the transcription of tryptophan biosynthesis genes especially TRP1 which is also the selectable auxotrophic marker for the expression vector used in this work. The product of nrps33 could inhibit the activity of Trp4 involved in the conversion of anthranilate to N-(5'-phosphoribosyl)anthranilate and therefore caused the accumulation of anthranilic acid. This accumulation could in turn result in down-regulation of downstream tryptophan biosynthesis genes. Anthranilic acid is typically produced by chemical synthesis and has been used as a substrate for synthesising bioactive compounds including commercial drugs; our results could provide a new biological platform for production of this compound.
Collapse
Affiliation(s)
- Gunlatida Promsuk
- Interdisciplinary Graduate Program in Bioscience Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Kamonchat Prommarit
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Colin M Lazarus
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand
- Omics Centre for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Pakorn Wattana-Amorn
- Interdisciplinary Graduate Program in Bioscience Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Department of Chemistry Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| |
Collapse
|
5
|
Janthabut T, Tristianto C, Sakulkoo J, Sunvittayakul P, Suttangkakul A, Gomez LD, Vuttipongchaikij S, Sakulsingharoj C. Effects of CRISPR/Cas9 generated drooping leaf (dl) alleles on midrib and carpel formations in Oryza sativa Nipponbare. Planta 2022; 256:61. [PMID: 35994211 DOI: 10.1007/s00425-022-03973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
We generated drooping leaf rice mutants by CRISPR/Cas and identified two novel alleles with specific editing that allow underpinning of the function of the DL protein domain towards midrib and carpel formations. The DROOPING LEAF (DL) gene plays an essential role in regulating midrib formation and carpel specification in rice and other grass species, but the specific function of DL protein domains in different developmental processes is unclear. Analysis of different dl mutant alleles will allow dissecting the function of DL. Here, we generated Nipponbare rice dl mutants using CRISPR/Cas gene editing and identified two novel dl alleles with different effects on midrib formation and carpel development. Phenotypic and genotypic analysis of T0 and segregated T1 edited lines showed that while dl-51S allele (a 3 bp deletion and a serine deletion at position 51) reduces midrib sizes and produces normal carpels, the dl-50LS allele (a 6 bp deletion and a leucine-serine deletion at position 50-51) causes the lack of midribs and abnormal stigma. This result indicates that the 51-serine is important for midrib formation and the 50-leucine is essential for midrib and carpel development. These dl mutant alleles contribute to the DL gene functional analysis and to gain insights into possible modifications of leaf architecture of rice and other grass species.
Collapse
Affiliation(s)
- Teerapong Janthabut
- Program in Genetics, Faculty of Science, Maejo University, Chiang Mai, 50290, Thailand
| | - Christian Tristianto
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
| | - Janejira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Pongsakorn Sunvittayakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
| | | |
Collapse
|
6
|
Utthiya S, Wonnapinij P, Napaumpaiporn P, Kittiwongwattana C, Sakulkoo J, Suttangkakul A, Vuttipongchaikij S. Gel purification of gDNA for next-generation sequencing applications. Biotechniques 2022; 73:99-103. [PMID: 35950336 DOI: 10.2144/btn-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We demonstrate that gDNA can be conveniently and efficiently isolated and purified using standard agarose gel electrophoresis, band excision and gel purification. This method yields a substantial amount at microgram levels of gDNA per gel cleanup with high purity. An RNase A treatment step can be omitted. The quality of gDNA is suitable for next-generation sequencing, resulting in >10 Mb reads and high-quality read data (Phred score >28 up to 100 of 150 base reads). Furthermore, the gDNA can be kept intact in a gel slice for several days. This method has been tested for dictyostelids, bacteria and plants.
Collapse
Affiliation(s)
- Supanut Utthiya
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.,Omics Center for Agriculture, Bioresources, Food & Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Pondpan Napaumpaiporn
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Chokchai Kittiwongwattana
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.,Omics Center for Agriculture, Bioresources, Food & Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.,Omics Center for Agriculture, Bioresources, Food & Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| |
Collapse
|
7
|
Suttangkakul A, Li F, Chung T, Vierstra RD. Corrigendum to: The ATG1/ATG13 Protein Kinase Complex Is Both a Regulator and a Target of Autophagic Recycling in Arabidopsis. Plant Cell 2021; 33:3743-3744. [PMID: 34520558 PMCID: PMC9244855 DOI: 10.1093/plcell/koab212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Anongpat Suttangkakul
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research
Programme, Faculty of Biological and Environmental Sciences, University of Helsinki,
Helsinki, Finland
| | - Faqiang Li
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research
Programme, Faculty of Biological and Environmental Sciences, University of Helsinki,
Helsinki, Finland
| | - Taijoon Chung
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research
Programme, Faculty of Biological and Environmental Sciences, University of Helsinki,
Helsinki, Finland
| | - Richard D Vierstra
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research
Programme, Faculty of Biological and Environmental Sciences, University of Helsinki,
Helsinki, Finland
| |
Collapse
|
8
|
Sathitnaitham S, Suttangkakul A, Wonnapinij P, McQueen-Mason SJ, Vuttipongchaikij S. Gel-permeation chromatography-enzyme-linked immunosorbent assay method for systematic mass distribution profiling of plant cell wall matrix polysaccharides. Plant J 2021; 106:1776-1790. [PMID: 33788319 DOI: 10.1111/tpj.15255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Cell walls are dynamic and multi-component materials that play important roles in many areas of plant biology. The composition and interactions of the structural elements give rise to material properties, which are modulated by the activity of wall-related enzymes. Studies of the genes and enzymes that determine wall composition and function have made great progress, but rarely take account of potential compensatory changes in wall polymers that may accompany and accommodate changes in other components, particularly for specific polysaccharides. Here, we present a method that allows the simultaneous examination of the mass distributions and quantities of specific cell wall matrix components, allowing insight into direct and indirect consequences of cell wall manipulations. The method employs gel-permeation chromatography fractionation of cell wall polymers followed by enzyme-linked immunosorbent assay to identify polymer types. We demonstrate the potential of this method using glycan-directed monoclonal antibodies to detect epitopes representing xyloglucans, heteromannans, glucuronoxylans, homogalacturonans (HGs) and methyl-esterified HGs. The method was used to explore compositional diversity in different Arabidopsis organs and to examine the impacts of changing wall composition in a number of previously characterized cell wall mutants. As demonstrated in this article, this methodology allows a much deeper understanding of wall composition, its dynamism and plasticity to be obtained, furthering our knowledge of cell wall biology.
Collapse
Affiliation(s)
- Sukhita Sathitnaitham
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
| | | | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
9
|
Sakulsathaporn A, Wonnapinij P, Suttangkakul A, Apisitwanich S, Vuttipongchaikij S. RNA editing in the chloroplast of Asian Palmyra palm (Borassus flabellifer). Genet Mol Biol 2020; 42:e20180371. [PMID: 31968044 PMCID: PMC7206934 DOI: 10.1590/1678-4685-gmb-2018-0371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 10/02/2019] [Indexed: 11/22/2022] Open
Abstract
We have identified 46 RNA editing sites located in 20 chloroplast (cp) genes of Borassus flabellifer (Asian Palmyra palm), family Arecaceae, and tested these genes for supporting phylogenetic study among the commelinids. Among the 46 sites, 43 sites were found to cause amino acid alterations, which were predicted to increase the hydrophobicity and transmembrane regions of the proteins, and one site was to cause a premature stop codon. Analysis of these editing sites with data obtained from seed plants showed that a number of shared-editing sites depend on the evolutionary relationship between plants. We reconstructed a deep phylogenetic relationship among the commelinids using seven RNA edited genes that are orthologous among monocots. This tree could represent the relationship among subfamilies of Arecaceae family, but was insufficient to represent the relationship among the orders of the commelinid. After adding eight gene sequences with high parsimony-informative characters (PICs), the tree topology was improved and could support the topology for the commelinid orders ((Arecales,Dasypogenaceae) (Zingiberales+Commelinales,Poales)). The result provides support for inherent RNA editing along the evolution of seed plants, and we provide an alternative set of loci for the phylogenetic tree reconstruction of Arecaceae's subfamilies.
Collapse
Affiliation(s)
- Arpakorn Sakulsathaporn
- Center for Agricultural Biotechnology, Kasetsart University,
Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology:
(AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- School of Natural Resource and Environmental Management,
Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai
Campus, Nong Khai 43000, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health,
Kasetsart University (OmiKU), 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900,
Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - Somsak Apisitwanich
- Center for Agricultural Biotechnology, Kasetsart University,
Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology:
(AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health,
Kasetsart University (OmiKU), 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900,
Thailand
| |
Collapse
|
10
|
Suttangkakul A, Sirikhachornkit A, Juntawong P, Puangtame W, Chomtong T, Srifa S, Sathitnaitham S, Dumrongthawatchai W, Jariyachawalid K, Vuttipongchaikij S. Evaluation of strategies for improving the transgene expression in an oleaginous microalga Scenedesmus acutus. BMC Biotechnol 2019; 19:4. [PMID: 30630453 PMCID: PMC6327543 DOI: 10.1186/s12896-018-0497-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/25/2018] [Indexed: 01/04/2023] Open
Abstract
Background Genetic transformation of microalgae has been hampered by inefficient transgene expression, limiting the progress of microalgal biotechnology. Many vector tools and strategies have been developed in recent years to improve transgene expression in the model microalga Chlamydomonas, but these were hardly applied to other microalgae. In this work, naturally-isolated oleaginous microalgae were accessed for genetic transformation, and various expression systems were evaluated in a selected microalga to circumvent inefficient transgene expression. Results Initially, a strain of Scenedesmus acutus was selected from the oleaginous microalgal collection based on its highest transformation rate and transgene stability. This strain, which had very low or no GFP reporter expression, was first tested to improve transgene expression by using intron-containing constructs and the transcript fusion using ble::E2A. The intron-containing constructs yielded 2.5–7.5% of transformants with 2–4-fold fluorescence signals, while the majority of the transformants of the transcript fusion had the fluorescence signals up to 10-fold. Subsequently, three UV-induced S. acutus mutants were isolated with moderate increases in the level and frequency of transgene expression (2–3-fold and 10–12%, respectively). Finally, a transcript fusion system was developed using psy white mutants with an expression vector containing PSY::E2A for complementation and light selection. Transformants with green colonies were selected under light exposure, and the transgene expression was detected at protein levels. Although the improvement using PSY::E2A was only minor (1–2-fold increase and ~ 7% of transformants), this system provides an alternative selectable marker that is compatible with large-scale culture. Conclusions Here, the overall improvement of transgene expression using the Chlamydomonas tools was moderate. The most effective tool so far is the transcript fusion using ble::E2A system. This work demonstrates that, so far, genetic engineering of non-model microalgae is still a challenging task. Further development of tools and strategies for transgene expression in microalgae are critically needed. Electronic supplementary material The online version of this article (10.1186/s12896-018-0497-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anongpat Suttangkakul
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Anchalee Sirikhachornkit
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Piyada Juntawong
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Wilasinee Puangtame
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Thitikorn Chomtong
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Suchada Srifa
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Sukhita Sathitnaitham
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Wasawat Dumrongthawatchai
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand
| | - Kanidtha Jariyachawalid
- PTT Research and Technology Institute, PTT Public Company Limited, Ayuthaya, 13170, Thailand
| | - Supachai Vuttipongchaikij
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand. .,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan road, Chatuchak, Bangkok, 10900, Thailand.
| |
Collapse
|
11
|
Sirikhachornkit A, Suttangkakul A, Vuttipongchaikij S, Juntawong P. De novo transcriptome analysis and gene expression profiling of an oleaginous microalga Scenedesmus acutus TISTR8540 during nitrogen deprivation-induced lipid accumulation. Sci Rep 2018; 8:3668. [PMID: 29487383 PMCID: PMC5829077 DOI: 10.1038/s41598-018-22080-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/16/2018] [Indexed: 11/30/2022] Open
Abstract
Nitrogen deprivation (-N) has been used as a technique to promote lipid accumulation in various microalgae. Scenedesmus acutus is a promising oleaginous green microalga that can be cultivated in organic wastewater for biodiesel production. Nevertheless, the molecular mechanisms controlling S. acutus lipid accumulation in response to -N remain unidentified. Physiological study determined that -N reduced cell growth and photosynthetic pigments. On the other hand, it promoted carbohydrate and neutral lipid accumulation. To find the mechanisms underlying lipid accumulation, we performed de novo transcriptome profiling of the non-model S. acutus in response to -N. The transcriptome analysis revealed that glycolysis and starch degradation were up-regulated; on the contrary, gluconeogenesis, photosynthesis, triacylglycerol (TAG) degradation and starch synthesis were down-regulated by -N. Under -N, the carbon flux was shifted toward fatty acid and TAG synthesis, and the down regulation of TAG lipase genes may contribute to TAG accumulation. A comparative analysis of the -N transcriptomes of oleaginous microalgae identified that the down-regulation of multiple lipase genes was a specific mechanism found only in the -N transcriptome of S. acutus. Our study unraveled the mechanisms controlling -N-induced lipid accumulation in S. acutus, and provided new perspectives for the genetic manipulation of biodiesel-producing microalgae.
Collapse
Affiliation(s)
- Anchalee Sirikhachornkit
- Special Research Unit in Microalgal Molecular Genetics and Functional genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
| | - Anongpat Suttangkakul
- Special Research Unit in Microalgal Molecular Genetics and Functional genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
| | - Supachai Vuttipongchaikij
- Special Research Unit in Microalgal Molecular Genetics and Functional genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
| | - Piyada Juntawong
- Special Research Unit in Microalgal Molecular Genetics and Functional genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand.
| |
Collapse
|
12
|
Keadtidumrongkul P, Suttangkakul A, Pinmanee P, Pattana K, Kittiwongwattana C, Apisitwanich S, Vuttipongchaikij S. Growth modulation effects of CBM2a under the control of AtEXP4 and CaMV35S promoters in Arabidopsis thaliana, Nicotiana tabacum and Eucalyptus camaldulensis. Transgenic Res 2017; 26:447-463. [PMID: 28349287 DOI: 10.1007/s11248-017-0015-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 03/21/2017] [Indexed: 11/29/2022]
Abstract
The expression of cell-wall-targeted Carbohydrate Binding Modules (CBMs) can alter cell wall properties and modulate growth and development in plants such as tobacco and potato. CBM2a identified in xylanase 10A from Cellulomonas fimi is of particular interest for its ability to bind crystalline cellulose. However, its potential for promoting plant growth has not been explored. In this work, we tested the ability of CBM2a to promote growth when expressed using both CaMV35S and a vascular tissue-specific promoter derived from Arabidopsis expansin4 (AtEXP4) in three plant species: Arabidopsis, Nicotiana tabacum and Eucalyptus camaldulensis. In Arabidopsis, the expression of AtEXP4pro:CBM2a showed trends for growth promoting effects including the increase of root and hypocotyl lengths and the enlargements of the vascular xylem area, fiber cells and vessel cells. However, in N. tabacum, the expression of CBM2a under the control of either CaMV35S or AtEXP4 promoter resulted in subtle changes in the plant growth, and the thickness of secondary xylem and vessel and fiber cell sizes were generally reduced in the transgenic lines with AtEXP4pro:CBM2a. In Eucalyptus, while transgenics expressing CaMV35S:CBM2a showed very subtle changes compared to wild type, those transgenics with AtEXP4pro:CBM2a showed increases in plant height, enlargement of xylem areas and xylem fiber and vessel cells. These data provide comparative effects of expressing CBM2a protein in different plant species, and this finding can be applied for plant biomass improvement.
Collapse
Affiliation(s)
- Pornthep Keadtidumrongkul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
| | - Phitsanu Pinmanee
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Kanokwan Pattana
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Chokchai Kittiwongwattana
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok, 10520, Thailand
| | - Somsak Apisitwanich
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, Bangkok, 10900, Thailand.
| |
Collapse
|
13
|
Sirikhachornkit A, Vuttipongchaikij S, Suttangkakul A, Yokthongwattana K, Juntawong P, Pokethitiyook P, Kangvansaichol K, Meetam M. Increasing the Triacylglycerol Content in Dunaliella tertiolecta through Isolation of Starch-Deficient Mutants. J Microbiol Biotechnol 2016; 26:854-66. [DOI: 10.4014/jmb.1510.10022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
14
|
Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL. The plant glycosyltransferase clone collection for functional genomics. Plant J 2014. [PMID: 24905498 DOI: 10.1111/tpj.12577/0960-7412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate-Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell-wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full-length coding sequences without termination codons and are Gateway® compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.
Collapse
Affiliation(s)
- Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL. The plant glycosyltransferase clone collection for functional genomics. Plant J 2014; 79:517-29. [PMID: 24905498 DOI: 10.1111/tpj.12577] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/25/2014] [Accepted: 05/28/2014] [Indexed: 05/18/2023]
Abstract
The glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate-Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell-wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full-length coding sequences without termination codons and are Gateway® compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.
Collapse
Affiliation(s)
- Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Petersen PD, Lau J, Ebert B, Yang F, Verhertbruggen Y, Kim JS, Varanasi P, Suttangkakul A, Auer M, Loqué D, Scheller HV. Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants. Biotechnol Biofuels 2012; 5. [PMID: 23181474 PMCID: PMC3537538 DOI: 10.1186/1754-6834-5-84] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cost-efficient generation of second-generation biofuels requires plant biomass that can easily be degraded into sugars and further fermented into fuels. However, lignocellulosic biomass is inherently recalcitrant toward deconstruction technologies due to the abundant lignin and cross-linked hemicelluloses. Furthermore, lignocellulosic biomass has a high content of pentoses, which are more difficult to ferment into fuels than hexoses. Engineered plants with decreased amounts of xylan in their secondary walls have the potential to render plant biomass a more desirable feedstock for biofuel production. RESULTS Xylan is the major non-cellulosic polysaccharide in secondary cell walls, and the xylan deficient irregular xylem (irx) mutants irx7, irx8 and irx9 exhibit severe dwarf growth phenotypes. The main reason for the growth phenotype appears to be xylem vessel collapse and the resulting impaired transport of water and nutrients. We developed a xylan-engineering approach to reintroduce xylan biosynthesis specifically into the xylem vessels in the Arabidopsis irx7, irx8 and irx9 mutant backgrounds by driving the expression of the respective glycosyltransferases with the vessel-specific promoters of the VND6 and VND7 transcription factor genes. The growth phenotype, stem breaking strength, and irx morphology was recovered to varying degrees. Some of the plants even exhibited increased stem strength compared to the wild type. We obtained Arabidopsis plants with up to 23% reduction in xylose levels and 18% reduction in lignin content compared to wild-type plants, while exhibiting wild-type growth patterns and morphology, as well as normal xylem vessels. These plants showed a 42% increase in saccharification yield after hot water pretreatment. The VND7 promoter yielded a more complete complementation of the irx phenotype than the VND6 promoter. CONCLUSIONS Spatial and temporal deposition of xylan in the secondary cell wall of Arabidopsis can be manipulated by using the promoter regions of vessel-specific genes to express xylan biosynthetic genes. The expression of xylan specifically in the xylem vessels is sufficient to complement the irx phenotype of xylan deficient mutants, while maintaining low overall amounts of xylan and lignin in the cell wall. This engineering approach has the potential to yield bioenergy crop plants that are more easily deconstructed and fermented into biofuels.
Collapse
Affiliation(s)
- Pia Damm Petersen
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Plant Biology and Biotechnology, University of Copenhagen, 40 Thorvaldsensvej, Frederiksberg C, DK-1871, Denmark
| | - Jane Lau
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Berit Ebert
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Fan Yang
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Yves Verhertbruggen
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Jin Sun Kim
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Patanjali Varanasi
- Technology Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Sandia National Laboratories, 7011 East Avenue, Livermore, CA, 94550, USA
| | - Anongpat Suttangkakul
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Manfred Auer
- Technology Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Henrik Vibe Scheller
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
17
|
Suttangkakul A, Li F, Chung T, Vierstra RD. The ATG1/ATG13 protein kinase complex is both a regulator and a target of autophagic recycling in Arabidopsis. Plant Cell 2011; 23:3761-79. [PMID: 21984698 PMCID: PMC3229148 DOI: 10.1105/tpc.111.090993] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 08/29/2011] [Accepted: 09/21/2011] [Indexed: 05/18/2023]
Abstract
Autophagy is an intracellular recycling route in eukaryotes whereby organelles and cytoplasm are sequestered in vesicles, which are subsequently delivered to the vacuole for breakdown. The process is induced by various nutrient-responsive signaling cascades converging on the Autophagy-Related1 (ATG1)/ATG13 kinase complex. Here, we describe the ATG1/13 complex in Arabidopsis thaliana and show that it is both a regulator and a target of autophagy. Plants missing ATG13 are hypersensitive to nutrient limitations and senesce prematurely similar to mutants lacking other components of the ATG system. Synthesis of the ATG12-ATG5 and ATG8-phosphatidylethanolamine adducts, which are essential for autophagy, still occurs in ATG13-deficient plants, but the biogenesis of ATG8-decorated autophagic bodies does not, indicating that the complex regulates downstream events required for autophagosome enclosure and/or vacuolar delivery. Surprisingly, levels of the ATG1a and ATG13a phosphoproteins drop dramatically during nutrient starvation and rise again upon nutrient addition. This turnover is abrogated by inhibition of the ATG system, indicating that the ATG1/13 complex becomes a target of autophagy. Consistent with this mechanism, ATG1a is delivered to the vacuole with ATG8-decorated autophagic bodies. Given its responsiveness to nutrient demands, the turnover of the ATG1/13 kinase likely provides a dynamic mechanism to tightly connect autophagy to a plant's nutritional status.
Collapse
|
18
|
|
19
|
Chung T, Suttangkakul A, Vierstra RD. The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. Plant Physiol 2009; 149:220-34. [PMID: 18790996 PMCID: PMC2613746 DOI: 10.1104/pp.108.126714] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 09/09/2008] [Indexed: 05/18/2023]
Abstract
Plants employ sophisticated mechanisms to recycle intracellular constituents needed for growth, development, and survival under nutrient-limiting conditions. Autophagy is one important route in which cytoplasm and organelles are sequestered in bulk into vesicles and subsequently delivered to the vacuole for breakdown by resident hydrolases. The formation and trafficking of autophagic vesicles are directed in part by associated conjugation cascades that couple the AUTOPHAGY-RELATED8 (ATG8) and ATG12 proteins to their respective targets, phosphatidylethanolamine and the ATG5 protein. To help understand the importance of autophagy to nutrient remobilization in cereals, we describe here the ATG8/12 conjugation cascades in maize (Zea mays) and examine their dynamics during development, leaf senescence, and nitrogen and fixed-carbon starvation. From searches of the maize genomic sequence using Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) counterparts as queries, we identified orthologous loci encoding all components necessary for ATG8/12 conjugation, including a five-member gene family expressing ATG8. Alternative splicing was evident for almost all Atg transcripts, which could have important regulatory consequences. In addition to free ATG8, its membrane-associated, lipidated form was detected in many maize tissues, suggesting that its conjugation cascade is active throughout the plant at most, if not all, developmental stages. Levels of Atg transcripts and/or the ATG8-phosphatidylethanolamine adduct increase during leaf senescence and nitrogen and fixed-carbon limitations, indicating that autophagy plays a key role in nutrient remobilization. The description of the maize ATG system now provides a battery of molecular and biochemical tools to study autophagy in this crop under field conditions.
Collapse
Affiliation(s)
- Taijoon Chung
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706-1574, USA
| | | | | |
Collapse
|
20
|
Thompson AR, Doelling JH, Suttangkakul A, Vierstra RD. Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways. Plant Physiol 2005; 138:2097-110. [PMID: 16040659 PMCID: PMC1183398 DOI: 10.1104/pp.105.060673] [Citation(s) in RCA: 420] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Autophagy is an important mechanism for nonselective intracellular breakdown whereby cytosol and organelles are encapsulated in vesicles, which are then engulfed and digested by lytic vacuoles/lysosomes. In yeast, this encapsulation employs a set of autophagy (ATG) proteins that direct the conjugation of two ubiquitin-like protein tags, ATG8 and ATG12, to phosphatidylethanolamine and the ATG5 protein, respectively. Using an Arabidopsis (Arabidopsis thaliana) atg7 mutant unable to ligate either tag, we previously showed that the ATG8/12 conjugation system is important for survival under nitrogen-limiting growth conditions. By reverse-genetic analyses of the single Arabidopsis gene encoding ATG5, we show here that the subpathway that forms the ATG12-ATG5 conjugate also has an essential role in plant nutrient recycling. Similar to plants missing ATG7, those missing ATG5 display early senescence and are hypersensitive to either nitrogen or carbon starvation, which is accompanied by a more rapid loss of organellar and cytoplasmic proteins. Multiple ATG8 isoforms could be detected immunologically in seedling extracts. Their abundance was substantially elevated in both the atg5 and atg7 mutants, caused in part by an increase in abundance of several ATG8 mRNAs. Using a green fluorescent protein-ATG8a fusion in combination with concanamycin A, we also detected the accumulation of autophagic bodies inside the vacuole. This accumulation was substantially enhanced by starvation but blocked in the atg7 background. The use of this fusion in conjunction with atg mutants now provides an important marker to track autophagic vesicles in planta.
Collapse
Affiliation(s)
- Allison R Thompson
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|