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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Falciatore A, Bailleul B, Boulouis A, Bouly JP, Bujaldon S, Cheminant-Navarro S, Choquet Y, de Vitry C, Eberhard S, Jaubert M, Kuras R, Lafontaine I, Landier S, Selles J, Vallon O, Wostrikoff K. Light-driven processes: key players of the functional biodiversity in microalgae. C R Biol 2022; 345:15-38. [PMID: 36847462 DOI: 10.5802/crbiol.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022]
Abstract
Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over the past two decades, breakthroughs in genomics and ecosystem biology, as well as the development of genetic resources in model species, have redrawn the boundaries of our knowledge on the relevance of these microbes in global ecosystems. However, considering their vast biodiversity and complex evolutionary history, our comprehension of algal biology remains limited. As algae rely on light, both as their main source of energy and for information about their environment, we focus here on photosynthesis, photoperception, and chloroplast biogenesis in the green alga Chlamydomonas reinhardtii and marine diatoms. We describe how the studies of light-driven processes are key to assessing functional biodiversity in evolutionary distant microalgae. We also emphasize that integration of laboratory and environmental studies, and dialogues between different scientific communities are both timely and essential to understand the life of phototrophs in complex ecosystems and to properly assess the consequences of environmental changes on aquatic environments globally.
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Dhouioui M, Boulila A, Jemli M, Schiets F, Casabianca H, Zina MS. Fatty Acids Composition and Antibacterial Activity of Aristolochia longa L. and Bryonia dioïca Jacq. Growing Wild in Tunisia. J Oleo Sci 2016; 65:655-61. [PMID: 27430383 DOI: 10.5650/jos.ess16001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The composition of the fatty acids of the roots and aerial parts of Aritolochia longa (Aristolacheae) and Bryonia dioïca (Cucurbutaceae) was analyzed by gas chromatography (GC-FID) and gas chromatography-mass spectrometry (GC-MS). The oils extracted from the aerial parts of both species were rich in polyunsaturated fatty acids with the essential linolenic and linoleic acids being the most prominent compounds. Oleic and linoleic acids were the majors fatty acids in the roots of both species. Whatever the plant part analyzed and the species, the saturated fatty acids were predominantly composed of palmitic and stearic acids. The antibacterial activity, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the lipid extracts were determined against a panel of five bacterial strains. The results showed that the sensitivity to the lipid extracts was different for the test bacterial strains, and the susceptibility of gram positive bacteria was found to be greater than gram negative bacteria. The antibacterial activity of the root lipid extracts was particularly important against Enterococcus feacium (CMI value of 125 µg/mL; CMB values > 250 µg/mL) and Streptococcus agalactiae (CMI value of 125 µg/mL; CMB values 250 µg/mL for A. longa roots). These results indicate that A. longa and B. dioïca could be considered as good sources of essential fatty acids which can act as natural antibacterial agents.
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Affiliation(s)
- Mouna Dhouioui
- Institut National de Recherche et d'Analyse Physico-chimique (INRAP), Laboratoire des Substances Naturelles, Biotechpôle de Sidi Thabet
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Munns DPD. The phytotronist and the phenotype: plant physiology, Big Science, and a Cold War biology of the whole plant. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2015; 50:29-40. [PMID: 25677858 DOI: 10.1016/j.shpsc.2015.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 01/04/2015] [Indexed: 06/04/2023]
Abstract
This paper describes how, from the early twentieth century, and especially in the early Cold War era, the plant physiologists considered their discipline ideally suited among all the plant sciences to study and explain biological functions and processes, and ranked their discipline among the dominant forms of the biological sciences. At their apex in the late-1960s, the plant physiologists laid claim to having discovered nothing less than the "basic laws of physiology." This paper unwraps that claim, showing that it emerged from the construction of monumental big science laboratories known as phytotrons that gave control over the growing environment. Control meant that plant physiologists claimed to be able to produce a standard phenotype valid for experimental biology. Invoking the standards of the physical sciences, the plant physiologists heralded basic biological science from the phytotronic produced phenotype. In the context of the Cold War era, the ability to pursue basic science represented the highest pinnacle of standing within the scientific community. More broadly, I suggest that by recovering the history of an underappreciated discipline, plant physiology, and by establishing the centrality of the story of the plant sciences in the history of biology can historians understand the massive changes wrought to biology by the conceptual emergence of the molecular understanding of life, the dominance of the discipline of molecular biology, and the rise of biotechnology in the 1980s.
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Affiliation(s)
- David P D Munns
- Department of History, John Jay College, The City University of New York, 524 W. 59th St., New York, NY 10019, USA.
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Watching Grass Grow: The Emergence of Brachypodium distachyon as a Model for the Poaceae. ARCHIMEDES 2015. [DOI: 10.1007/978-3-319-12185-7_23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Moroz LL, Kohn AB. On the comparative biology of Nitric Oxide (NO) synthetic pathways: Parallel evolution of NO-mediated signaling. Nitric Oxide 2007. [DOI: 10.1016/s1872-2423(07)01001-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Somerville C, Koornneef M. A fortunate choice: the history of Arabidopsis as a model plant. Nat Rev Genet 2002; 3:883-9. [PMID: 12415318 DOI: 10.1038/nrg927] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past 20 years, the flowering plant Arabidopsis thaliana has been adopted as a model organism by thousands of biologists. This community has developed important tools, resources and experimental approaches that have greatly stimulated plant biological research. Here, we review some of the key events that led to the uptake of Arabidopsis as a model plant and to the growth of the Arabidopsis community.
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Affiliation(s)
- Chris Somerville
- Carnegie Institution, 260 Panama Street, Stanford, California 94305, USA.
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Szabados L, Kovács I, Oberschall A, Abrahám E, Kerekes I, Zsigmond L, Nagy R, Alvarado M, Krasovskaja I, Gál M, Berente A, Rédei GP, Haim AB, Koncz C. Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:233-42. [PMID: 12383088 DOI: 10.1046/j.1365-313x.2002.01417.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Induction of knockout mutations by T-DNA insertion mutagenesis is widely used in studies of plant gene functions. To assess the efficiency of this genetic approach, we have sequenced PCR amplified junctions of 1000 T-DNA insertions and analysed their distribution in the Arabidopsis genome. Map positions of 973 tags could be determined unequivocally, indicating that the majority of T-DNA insertions landed in chromosomal domains of high gene density. Only 4.7% of insertions were found in interspersed, centromeric, telomeric and rDNA repeats, whereas 0.6% of sequenced tags identified chromosomally integrated segments of organellar DNAs. 35.4% of T-DNAs were localized in intervals flanked by ATG and stop codons of predicted genes, showing a distribution of 62.2% in exons and 37.8% in introns. The frequency of T-DNA tags in coding and intergenic regions showed a good correlation with the predicted size distribution of these sequences in the genome. However, the frequency of T-DNA insertions in 3'- and 5'-regulatory regions of genes, corresponding to 300 bp intervals 3' downstream of stop and 5' upstream of ATG codons, was 1.7-2.3-fold higher than in any similar interval elsewhere in the genome. The additive frequency of insertions in 5'-regulatory regions and coding domains provided an estimate for the mutation rate, suggesting that 47.8% of mapped T-DNA tags induced knockout mutations in Arabidopsis.
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Affiliation(s)
- László Szabados
- Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, PO Box 521, Temesvári krt 62, Hungary
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Bressan RA, Zhang C, Zhang H, Hasegawa PM, Bohnert HJ, Zhu JK. Learning from the Arabidopsis experience. The next gene search paradigm. PLANT PHYSIOLOGY 2001; 127:1354-1360. [PMID: 11743073 DOI: 10.1104/pp.010752] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- R A Bressan
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.
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Le J, Vandenbussche F, Van Der Straeten D, Verbelen JP. In the early response of Arabidopsis roots to ethylene, cell elongation is up- and down-regulated and uncoupled from differentiation. PLANT PHYSIOLOGY 2001. [PMID: 11161008 DOI: 10.1104/pp.125.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Affiliation(s)
- J Le
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
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Somerville CR. An early Arabidopsis demonstration. Resolving a few issues concerning photorespiration. PLANT PHYSIOLOGY 2001; 125:20-4. [PMID: 11154287 PMCID: PMC1539316 DOI: 10.1104/pp.125.1.20] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- C R Somerville
- Carnegie Institution of Washington, 260 Panama Street, Stanford, California 94305, USA.
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