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Tanabe TS, Dahl C. HMSS2: An advanced tool for the analysis of sulphur metabolism, including organosulphur compound transformation, in genome and metagenome assemblies. Mol Ecol Resour 2023; 23:1930-1945. [PMID: 37515475 DOI: 10.1111/1755-0998.13848] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
The global sulphur cycle has implications for human health, climate change, biogeochemistry and bioremediation. The organosulphur compounds that participate in this cycle not only represent a vast reservoir of sulphur but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulphur cycle, it involves the interaction of prokaryotes, eukaryotes and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulphur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulphonated compounds are related to proteins involved in sulphur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulphur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model-based tool for rapid annotation and synteny analysis of organic and inorganic sulphur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS-S-S), HMSS2 includes several new features. HMM-based annotation is now supported by nonhomology criteria and covers the metabolic pathways of important organosulphur compounds, including dimethylsulphoniopropionate, taurine, isethionate, and sulphoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible data sets, and customized sequence FASTA files.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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2
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Devi V, Bhushan B, Gupta M, Sethi M, Kaur C, Singh A, Singh V, Kumar R, Rakshit S, Chaudhary DP. Genetic and molecular understanding for the development of methionine-rich maize: a holistic approach. Front Plant Sci 2023; 14:1249230. [PMID: 37794928 PMCID: PMC10546030 DOI: 10.3389/fpls.2023.1249230] [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] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Maize (Zea mays) is the most important coarse cereal utilized as a major energy source for animal feed and humans. However, maize grains are deficient in methionine, an essential amino acid required for proper growth and development. Synthetic methionine has been used in animal feed, which is costlier and leads to adverse health effects on end-users. Bio-fortification of maize for methionine is, therefore, the most sustainable and environmental friendly approach. The zein proteins are responsible for methionine deposition in the form of δ-zein, which are major seed storage proteins of maize kernel. The present review summarizes various aspects of methionine including its importance and requirement for different subjects, its role in animal growth and performance, regulation of methionine content in maize and its utilization in human food. This review gives insight into improvement strategies including the selection of natural high-methionine mutants, molecular modulation of maize seed storage proteins and target key enzymes for sulphur metabolism and its flux towards the methionine synthesis, expression of synthetic genes, modifying gene codon and promoters employing genetic engineering approaches to enhance its expression. The compiled information on methionine and essential amino acids linked Quantitative Trait Loci in maize and orthologs cereals will give insight into the hotspot-linked genomic regions across the diverse range of maize germplasm through meta-QTL studies. The detailed information about candidate genes will provide the opportunity to target specific regions for gene editing to enhance methionine content in maize. Overall, this review will be helpful for researchers to design appropriate strategies to develop high-methionine maize.
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Affiliation(s)
- Veena Devi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Bharat Bhushan
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Mamta Gupta
- Division of Biotechnology, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Mehak Sethi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Charanjeet Kaur
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Alla Singh
- Division of Biotechnology, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Vishal Singh
- Division of Plant Breeding, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Ramesh Kumar
- Division of Plant Breeding, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Sujay Rakshit
- Division of Plant Breeding, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Dharam P. Chaudhary
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
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Nishikawa M, Noda S, Henmi K, Ogawa K. Sulphate repression of ssuD-dependent alkanesulphonate-sulphur assimilation in Escherichia coli. Microbiology (Reading) 2022; 168. [PMID: 35704379 DOI: 10.1099/mic.0.001190] [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] [Indexed: 11/18/2022]
Abstract
Escherichia coli cells utilize alkanesulphonates including taurine as the sulphur source. We previously reported that when E. coli cells carrying a double deletion in tauD and cysN were inoculated into a taurine-containing minimal medium, they started to grow only after long-term incubation (Nishikawa et al. 2018, Microbiology 164: 1446-1456). We show here that cells that can induce ssuD-dependent alkanesulphonate-sulphur assimilation (SASSA) are essentially rare, but suppressors that can induce SASSA appear during long-term incubation. Mutant cells carrying ΔtauD and ΔcysN, ΔcysC or ΔcysH generated suppressor cells that can induce SASSA at a frequency of about 10-6 in a population. Whereas ΔtauD ΔcysN cells without prior SASSA did not express ssuD even when necessary, the cells with prior SASSA properly expressed ssuD. Whole-genome DNA sequencing of a clone isolated from ΔtauD ΔcysN cells with prior SASSA revealed that the influx of sulphate or thiosulphate may be related to the regulation of SASSA. To clarify whether sulphate or thiosulphate affects the induction of SASSA, the effect of mutations in sbp and cysP, which are responsible for sulphate and thiosulphate uptake with different preferences for substrates, was examined. Only the ΔtauD ΔcysN Δsbp mutant did not show repression of SASSA when no sulphate was added to the medium. When the concentration of the sulphate added was over 10 μM, the Δsbp mutant showed repression of SASSA. Therefore, it was considered that the influx of extracellular sulphate resulted in repression of SASSA.
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Affiliation(s)
- Masanobu Nishikawa
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Okayama, Japan
| | - Soichiro Noda
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Okayama, Japan
| | - Kenji Henmi
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Okayama, Japan
| | - Ken'ichi Ogawa
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Okayama, Japan
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Neequaye M, Steuernagel B, Saha S, Trick M, Troncoso-Rey P, van den Bosch F, Traka MH, Østergaard L, Mithen R. Characterisation of the Introgression of Brassica villosa Genome Into Broccoli to Enhance Methionine-Derived Glucosinolates and Associated Health Benefits. Front Plant Sci 2022; 13:855707. [PMID: 35432397 PMCID: PMC9011106 DOI: 10.3389/fpls.2022.855707] [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] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Broccoli cultivars that have enhanced accumulation of methionine-derived glucosinolates have been developed through the introgression of a novel allele of the MYB28 transcription factor from the wild species Brassica villosa. Through a novel k-mer approach, we characterised the extent of the introgression of unique B. villosa genome sequences into high glucosinolate broccoli genotypes. RNAseq analyses indicated that the introgression of the B. villosa MYB28 C2 allele resulted in the enhanced expression of the MYB28 transcription factor, and modified expression of genes associated with sulphate absorption and reduction, and methionine and glucosinolate biosynthesis when compared to standard broccoli. A adenine-thymine (AT) short tandem repeat (STR) was identified within the 5' untranslated region (UTR) B. villosa MYB28 allele that was absent from two divergent cultivated forms of Brassica oleracea, which may underpin the enhanced expression of B. villosa MYB28.
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Affiliation(s)
- Mikhaela Neequaye
- Quadram Institute Bioscience, Norwich, United Kingdom
- John Innes Centre, Norwich, United Kingdom
| | | | - Shikha Saha
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | | | | | | | | | - Richard Mithen
- Quadram Institute Bioscience, Norwich, United Kingdom
- Liggins Institute, University of Auckland, Auckland, New Zealand
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Drabinska J, Steczkiewicz K, Kujawa M, Kraszewska E. Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22189833. [PMID: 34575996 PMCID: PMC8466066 DOI: 10.3390/ijms22189833] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
For nearly half of the proteome of an important pathogen, Pseudomonas aeruginosa, the function has not yet been recognised. Here, we characterise one such mysterious protein PA2504, originally isolated by us as a sole partner of the RppH RNA hydrolase involved in transcription regulation of multiple genes. This study aims at elucidating details of PA2504 function and discussing its implications for bacterial biology. We show that PA2504 forms homodimers and is evenly distributed in the cytoplasm of bacterial cells. Molecular modelling identified the presence of a Tudor-like domain in PA2504. Transcriptomic analysis of a ΔPA2504 mutant showed that 42 transcripts, mainly coding for proteins involved in sulphur metabolism, were affected by the lack of PA2504. In vivo crosslinking of cellular proteins in the exponential and stationary phase of growth revealed several polypeptides that bound to PA2504 exclusively in the stationary phase. Mass spectrometry analysis identified them as the 30S ribosomal protein S4, the translation elongation factor TufA, and the global response regulator GacA. These results indicate that PA2504 may function as a tether for several important cellular factors.
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Hua L, Stevenson SR, Reyna-Llorens I, Xiong H, Kopriva S, Hibberd JM. The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis. Plant J 2021; 107:268-286. [PMID: 33901336 DOI: 10.1111/tpj.15292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake the rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3 plants, which represents a key target associated with engineering traits such as C4 photosynthesis into Oryza sativa (rice). To better understand the veins, bundle sheath and mesophyll cells of rice, we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis, as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with the presence or absence of specific transcription factors in each cell type, but were instead associated with gradients in expression across the leaf. Comparative analysis with C3 Arabidopsis identified a small gene set preferentially expressed in the bundle sheath cells of both species. This gene set included genes encoding transcription factors from 14 orthogroups and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis were specialized in this manner, and as the species diverged these patterns of gene expression have been maintained.
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Affiliation(s)
- Lei Hua
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Sean R Stevenson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Haiyan Xiong
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Uyy E, Suica VI, Boteanu RM, Safciuc F, Cerveanu-Hogas A, Ivan L, Stavaru C, Simionescu M, Antohe F. Diabetic nephropathy associates with deregulation of enzymes involved in kidney sulphur metabolism. J Cell Mol Med 2020; 24:12131-12140. [PMID: 32935914 PMCID: PMC7579703 DOI: 10.1111/jcmm.15855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/10/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Nephropathy is a major chronic complication of diabetes. A crucial role in renal pathophysiology is played by hydrogen sulphide (H2S) that is produced excessively by the kidney; however, the data regarding H2S bioavailability are inconsistent. We hypothesize that early type 1 diabetes (T1D) increases H2S production by a mechanism involving hyperglycaemia‐induced alterations in sulphur metabolism. Plasma and kidney tissue collected from T1D double transgenic mice were subjected to mass spectrometry‐based proteomic analysis, and the results were validated by immunological and gene expression assays.T1D mice exhibited a high concentration of H2S in the plasma and kidney tissue and histological, showed signs of subtle kidney fibrosis, characteristic for early renal disease. The shotgun proteomic analyses disclosed that the level of enzymes implicated in sulphate activation modulators, H2S‐oxidation and H2S‐production were significantly affected (ie 6 up‐regulated and 4 down‐regulated). Gene expression results corroborated well with the proteomic data. Dysregulation of H2S enzymes underly the changes occurring in H2S production, which in turn could play a key role in the initiation of renal disease. The new findings lead to a novel target in the therapy of diabetic nephropathy. Mass spectrometry data are available via ProteomeXchange with identifier PXD018053.
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Affiliation(s)
- Elena Uyy
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Viorel Iulian Suica
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Raluca Maria Boteanu
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Florentina Safciuc
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Aurel Cerveanu-Hogas
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Luminita Ivan
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Crina Stavaru
- "Cantacuzino" National Institute of Research and Development for Microbiology and Immunology, Bucharest, Romania
| | - Maya Simionescu
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
| | - Felicia Antohe
- Institute of Cellular Biology and Pathology "Nicolae Simionescu", Bucharest, Romania
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Olson KR, Gao Y, DeLeon ER, Markel TA, Drucker N, Boone D, Whiteman M, Steiger AK, Pluth MD, Tessier CR, Stahelin RV. Extended hypoxia-mediated H 2 S production provides for long-term oxygen sensing. Acta Physiol (Oxf) 2020; 228:e13368. [PMID: 31442361 DOI: 10.1111/apha.13368] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/23/2022]
Abstract
AIM Numerous studies have shown that H2 S serves as an acute oxygen sensor in a variety of cells. We hypothesize that H2 S also serves in extended oxygen sensing. METHODS Here, we compare the effects of extended exposure (24-48 hours) to varying O2 tensions on H2 S and polysulphide metabolism in human embryonic kidney (HEK 293), human adenocarcinomic alveolar basal epithelial (A549), human colon cancer (HTC116), bovine pulmonary artery smooth muscle, human umbilical-derived mesenchymal stromal (stem) cells and porcine tracheal epithelium (PTE) using sulphur-specific fluorophores and fluorometry or confocal microscopy. RESULTS All cells continuously produced H2 S in 21% O2 and H2 S production was increased at lower O2 tensions. Decreasing O2 from 21% to 10%, 5% and 1% O2 progressively increased H2 S production in HEK293 cells and this was partially inhibited by a combination of inhibitors of H2 S biosynthesis, aminooxyacetate, propargyl glycine and compound 3. Mitochondria appeared to be the source of much of this increase in HEK 293 cells. H2 S production in all other cells and PTE increased when O2 was lowered from 21% to 5% except for HTC116 cells where 1% O2 was necessary to increase H2 S, presumably reflecting the hypoxic environment in vivo. Polysulphides (H2 Sn , where n = 2-7), the key signalling metabolite of H2 S also appeared to increase in many cells although this was often masked by high endogenous polysulphide concentrations. CONCLUSION These results show that cellular H2 S is increased during extended hypoxia and they suggest this is a continuously active O2 -sensing mechanism in a variety of cells.
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Affiliation(s)
- Kenneth R. Olson
- Indiana University School of Medicine‐South Bend South Bend Indiana
| | - Yan Gao
- Indiana University School of Medicine‐South Bend South Bend Indiana
| | - Eric R. DeLeon
- Indiana University School of Medicine‐South Bend South Bend Indiana
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Troy A. Markel
- Indiana University School of Medicine Riley Hospital for Children at IU Health Indianapolis Indiana
| | - Natalie Drucker
- Indiana University School of Medicine Riley Hospital for Children at IU Health Indianapolis Indiana
| | - David Boone
- Indiana University School of Medicine‐South Bend South Bend Indiana
| | | | - Andrea K. Steiger
- Department of Chemistry and Biochemistry University of Oregon Eugene Oregon
| | - Michael D. Pluth
- Department of Chemistry and Biochemistry University of Oregon Eugene Oregon
| | | | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue University West Lafayette Indiana
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Clemente-Moreno MJ, Omranian N, Sáez P, Figueroa CM, Del-Saz N, Elso M, Poblete L, Orf I, Cuadros-Inostroza A, Cavieres L, Bravo L, Fernie A, Ribas-Carbó M, Flexas J, Nikoloski Z, Brotman Y, Gago J. Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis. New Phytol 2020; 225:754-768. [PMID: 31489634 DOI: 10.1111/nph.16167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 05/28/2023]
Abstract
Understanding the strategies employed by plant species that live in extreme environments offers the possibility to discover stress tolerance mechanisms. We studied the physiological, antioxidant and metabolic responses to three temperature conditions (4, 15, and 23°C) of Colobanthus quitensis (CQ), one of the only two native vascular species in Antarctica. We also employed Dianthus chinensis (DC), to assess the effects of the treatments in a non-Antarctic species from the same family. Using fused LASSO modelling, we associated physiological and biochemical antioxidant responses with primary metabolism. This approach allowed us to highlight the metabolic pathways driving the response specific to CQ. Low temperature imposed dramatic reductions in photosynthesis (up to 88%) but not in respiration (sustaining rates of 3.0-4.2 μmol CO2 m-2 s-1 ) in CQ, and no change in the physiological stress parameters was found. Its notable antioxidant capacity and mitochondrial cytochrome respiratory activity (20 and two times higher than DC, respectively), which ensure ATP production even at low temperature, was significantly associated with sulphur-containing metabolites and polyamines. Our findings potentially open new biotechnological opportunities regarding the role of antioxidant compounds and respiratory mechanisms associated with sulphur metabolism in stress tolerance strategies to low temperature.
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Affiliation(s)
- María José Clemente-Moreno
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
| | - Nooshin Omranian
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Patricia Sáez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, 4030000, Concepción, Chile
| | - Carlos María Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, 3000, Santa Fe, Argentina
| | - Néstor Del-Saz
- Laboratorio de Fisiología Vegetal, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 4030000, Concepción, Chile
| | - Mhartyn Elso
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, 4030000, Concepción, Chile
| | - Leticia Poblete
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, 4030000, Concepción, Chile
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | | | - Lohengrin Cavieres
- ECOBIOSIS, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 4030000, Concepción, Chile
| | - León Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Cs. Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Instituto de Agroindustria, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Alisdair Fernie
- Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Golm, Germany
| | - Miquel Ribas-Carbó
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
| | - Jaume Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), 4000, Plovdiv, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Jorge Gago
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
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Abstract
Systems biology approaches have been applied over the last two decades to study plant sulphur metabolism. These 'sulphur-omics' approaches have been developed in parallel with the advancing field of systems biology, which is characterized by permanent improvements of high-throughput methods to obtain system-wide data. The aim is to obtain a holistic view of sulphur metabolism and to generate models that allow predictions of metabolic and physiological responses. Besides known sulphur-responsive genes derived from previous studies, numerous genes have been identified in transcriptomics studies. This has not only increased our knowledge of sulphur metabolism but has also revealed links between metabolic processes, thus indicating a previously unexpected complex interconnectivity. The identification of response and control networks has been supported through metabolomics and proteomics studies. Due to the complex interlacing nature of biological processes, experimental validation using targeted or systems approaches is ongoing. There is still room for improvement in integrating the findings from studies of metabolomes, proteomes, and metabolic fluxes into a single unifying concept and to generate consistent models. We therefore suggest a joint effort of the sulphur research community to standardize data acquisition. Furthermore, focusing on a few different model plant systems would help overcome the problem of fragmented data, and would allow us to provide a standard data set against which future experiments can be designed and compared.
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Affiliation(s)
- Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Nara Institute of Science and Technology, Ikoma, Japan
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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11
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Villa F, Vasanthakumar A, Mitchell R, Cappitelli F. RNA-based molecular survey of biodiversity of limestone tombstone microbiota in response to atmospheric sulphur pollution. Lett Appl Microbiol 2014; 60:92-102. [DOI: 10.1111/lam.12345] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 10/18/2014] [Accepted: 10/19/2014] [Indexed: 11/30/2022]
Affiliation(s)
- F. Villa
- Dipartimento di Scienze per gli Alimenti; la Nutrizione e l'Ambiente; Università degli Studi di Milano; Milano Italy
| | - A. Vasanthakumar
- Laboratory of Applied Microbiology; School of Engineering and Applied Sciences; Harvard University; Cambridge MA USA
| | - R. Mitchell
- Laboratory of Applied Microbiology; School of Engineering and Applied Sciences; Harvard University; Cambridge MA USA
| | - F. Cappitelli
- Dipartimento di Scienze per gli Alimenti; la Nutrizione e l'Ambiente; Università degli Studi di Milano; Milano Italy
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Liao D, Pajak A, Karcz SR, Chapman BP, Sharpe AG, Austin RS, Datla R, Dhaubhadel S, Marsolais F. Transcripts of sulphur metabolic genes are co-ordinately regulated in developing seeds of common bean lacking phaseolin and major lectins. J Exp Bot 2012; 63:6283-95. [PMID: 23066144 PMCID: PMC3481216 DOI: 10.1093/jxb/ers280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The lack of phaseolin and phytohaemagglutinin in common bean (dry bean, Phaseolus vulgaris) is associated with an increase in total cysteine and methionine concentrations by 70% and 10%, respectively, mainly at the expense of an abundant non-protein amino acid, S-methyl-cysteine. Transcripts were profiled between two genetically related lines differing for this trait at four stages of seed development using a high density microarray designed for common bean. Transcripts of multiple sulphur-rich proteins were elevated, several previously identified by proteomics, including legumin, basic 7S globulin, albumin-2, defensin, albumin-1, the Bowman-Birk type proteinase inhibitor, the double-headed trypsin inhibitor, and the Kunitz trypsin inhibitor. A co-ordinated regulation of transcripts coding for sulphate transporters, sulphate assimilatory enzymes, serine acetyltransferases, cystathionine β-lyase, homocysteine S-methyltransferase and methionine gamma-lyase was associated with changes in cysteine and methionine concentrations. Differential gene expression of sulphur-rich proteins preceded that of sulphur metabolic enzymes, suggesting a regulation by demand from the protein sink. Up-regulation of SERAT1;1 and -1;2 expression revealed an activation of cytosolic O-acetylserine biosynthesis. Down-regulation of SERAT2;1 suggested that cysteine and S-methyl-cysteine biosynthesis may be spatially separated in different subcellular compartments. Analysis of free amino acid profiles indicated that enhanced cysteine biosynthesis was correlated with a depletion of O-acetylserine. These results contribute to our understanding of the regulation of sulphur metabolism in developing seed in response to a change in the composition of endogenous proteins.
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Affiliation(s)
- Dengqun Liao
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Agnieszka Pajak
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Steven R. Karcz
- Agriculture and Agri-Food Canada, Bioproducts and Bioprocesses, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - B. Patrick Chapman
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Andrew G. Sharpe
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ryan S. Austin
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Raju Datla
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
- * To whom correspondence should be addressed. E-mail:
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Falkenberg B, Witt I, Zanor MI, Steinhauser D, Mueller-Roeber B, Hesse H, Hoefgen R. Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism. J Exp Bot 2008; 59:2831-46. [PMID: 18596113 PMCID: PMC2486478 DOI: 10.1093/jxb/ern144] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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: 03/14/2008] [Revised: 04/22/2008] [Accepted: 04/28/2008] [Indexed: 05/18/2023]
Abstract
A systems approach has previously been used to follow the response behaviour of Arabidopsis thaliana plants upon sulphur limitation. A response network was reconstructed from a time series of transcript and metabolite profiles, integrating complex metabolic and transcript data in order to investigate a potential causal relationship. The resulting scale-free network allowed potential transcriptional regulators of sulphur metabolism to be identified. Here, three sulphur-starvation responsive transcription factors, IAA13, IAA28, and ARF-2 (ARF1-Binding Protein), all of which are related to auxin signalling, were selected for further investigation. IAA28 overexpressing and knock-down lines showed no major morphological changes, whereas IAA13- and ARF1-BP-overexpressing plants grew more slowly than the wild type. Steady-state metabolite levels and expression of pathway-relevant genes were monitored under normal and sulphate-depleted conditions. For all lines, changes in transcript and metabolite levels were observed, yet none of these changes could exclusively be linked to sulphur stress. Instead, up- or down-regulation of the transcription factors caused metabolic changes which in turn affected sulphur metabolism. Auxin-relevant transcription factors are thus part of a complex response pattern to nutrient starvation that serve as coordinators of the metabolic shifts driving sulphur homeostasis rather then as direct effectors of the sulphate assimilation pathway. This study provides the first evidence ever presented that correlates auxin-related transcriptional regulators with primary plant metabolism.
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Affiliation(s)
- Bettina Falkenberg
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Isabell Witt
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Maria Inés Zanor
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Dirk Steinhauser
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Bernd Mueller-Roeber
- Universität Potsdam, Institut fuer Biochemie und Biologie, Karl-Liebknecht-Str. 24–25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Holger Hesse
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
- To whom correspondence should be addressed. E-mail:
| | - Rainer Hoefgen
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
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Abstract
Solutions of sodium sulphite have been used to simulate the effect of gaseous sulphur dioxide on the lichen alga Trebouxia sp. The uptake and the metabolism of inorganic and organic [35 S]compounds such as sulphate, sulphite, and cysteine were investigated in cells of Trebouxia under conditions of sulphite preincubation (sulphite-stressed cells: 3 d pretreatment with 50 mmol m-3 and 5 mol m-3 solutions of sodium sulphite). Metabolism was similar, regardless of whether the Trebouxia was provided with [35 S]sulphate or -sulphite. In sulphite-stressed cells, uptake and incorporation into ethanol-soluble compounds, especially cysteine and methionine, was significantly decreased. In Trebouxia exogenous [35 S]cysteine is metabolized only at a very low rate.
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Affiliation(s)
- D Schlee
- University of Halle, Institute of Biochemistry, Division of Plant Biochemistry, D(O)-4050 Halle (Saale), Weinbergweg 16a, Germany
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