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Homa J, Wilms W, Marcinkowska K, Cyplik P, Ławniczak Ł, Woźniak-Karczewska M, Niemczak M, Chrzanowski Ł. Comparative analysis of bacterial populations in sulfonylurea-sensitive and -resistant weeds: insights into community composition and catabolic gene dynamics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:52391-52409. [PMID: 39150664 PMCID: PMC11374828 DOI: 10.1007/s11356-024-34593-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/29/2024] [Indexed: 08/17/2024]
Abstract
This study aimed to compare the impact of iodosulfuron-methyl-sodium and an iodosulfuron-based herbicidal ionic liquid (HIL) on the microbiomes constituting the epiphytes and endophytes of cornflower (Centaurea cyanus L.). The experiment involved biotypes of cornflower susceptible and resistant to acetolactate synthase inhibition, examining potential bacterial involvement in sulfonylurea herbicide detoxification. We focused on microbial communities present on the surface and in the plant tissues of roots and shoots. The research included the synthesis and physicochemical analysis of a novel HIL, evaluation of shifts in bacterial community composition, analysis of the presence of catabolic genes associated with sulfonylurea herbicide degradation and determination of their abundance in all experimental variants. Overall, for the susceptible biotype, the biodiversity of the root microbiome was higher compared to shoot microbiome; however, both decreased notably after herbicide or HIL applications. The herbicide-resistant biotype showed lower degree of biodiversity changes, but shifts in community composition occurred, particularly in case of HIL treatment.
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Affiliation(s)
- Jan Homa
- Department of Chemical Technology, Poznan University of Technology, 60-965, Poznan, Poland.
| | - Wiktoria Wilms
- Department of Chemical Technology, Poznan University of Technology, 60-965, Poznan, Poland
| | - Katarzyna Marcinkowska
- Department of Weed Science, Institute of Plant Protection - National Research Institute, 60-318, Poznan, Poland
| | - Paweł Cyplik
- Department of Food Technology of Plant Origin, Poznan University of Life Sciences, 60-624, Poznan, Poland
| | - Łukasz Ławniczak
- Department of Chemical Technology, Poznan University of Technology, 60-965, Poznan, Poland
| | | | - Michał Niemczak
- Department of Chemical Technology, Poznan University of Technology, 60-965, Poznan, Poland
| | - Łukasz Chrzanowski
- Department of Chemical Technology, Poznan University of Technology, 60-965, Poznan, Poland
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2
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Im G, Choi D. Molecular and physiological characterization of AIP1, encoding the acetolactate synthase regulatory subunit in rice. Biochem Biophys Res Commun 2024; 718:150087. [PMID: 38735139 DOI: 10.1016/j.bbrc.2024.150087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Flooding deprives plants of oxygen and thereby causes severe stress by interfering with energy production, leading to growth retardation. Enzymes and metabolites may help protect plants from waterlogging and hypoxic environmental conditions. Acetolactate synthase (ALS) is a key enzyme in the biosynthesis of branched-chain amino acids (BCAAs), providing the building blocks for proteins and various secondary metabolites. Additionally, under energy-poor conditions, free BCAAs can be used as an alternative energy source by mitochondria through a catabolic enzyme chain reaction. In this study, we characterized ALS-INTERACTING PROTEIN 1 (OsAIP1), which encodes the regulatory subunit of ALS in rice (Oryza sativa). This gene was expressed in all parts of the rice plant, and its expression level was significantly higher in submerged and low-oxygen environments. Rice transformants overexpressing OsAIP1 showed a higher survival rate under hypoxic stress than did non-transgenic control plants under the same conditions. The OsAIP1-overexpressing plants accumulated increased levels of BCAAs, demonstrating that OsAIP1 is an important factor in the hypoxia resistance mechanism. These results suggest that ALS proteins are part of a defense mechanism that improves the tolerance of plants to low-oxygen environments.
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Affiliation(s)
- Geunmuk Im
- Department of Biological Science, Kunsan National University, Gunsan-si, 54150, Republic of Korea
| | - Dongsu Choi
- Department of Biological Science, Kunsan National University, Gunsan-si, 54150, Republic of Korea.
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3
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Gutiérrez-Rey M, Castellar-Visbal L, Acevedo-Vergara K, Vargas-Manotas J, Rivera-Porras D, Londoño-Juliao G, Castillo-Guerrero B, Perdomo-Jiménez MC, Bermúdez V. The Weight of Bariatric Surgery: Wernicke-Korsakoff Syndrome after Vertical Sleeve Gastrectomy-A Case Series. J Pers Med 2024; 14:638. [PMID: 38929859 PMCID: PMC11204981 DOI: 10.3390/jpm14060638] [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: 04/18/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
In this case series, the simultaneous occurrence of Wernicke's encephalopathy (WE) and dry beriberi was reported in three patients who underwent vertical sleeve gastrectomy (VSG) between May 2021 and May 2023. All patients were obese women who underwent vertical sleeve gastrectomy (VSG) without immediate postoperative complications, but two weeks later, hyperemesis and subsequent encephalopathy with ocular movement abnormalities and weakness were observed over the following thirty days. Patients were referred to neurology, where due to the high suspicion of WE, thiamine replacement therapy was initiated; meanwhile, diagnostic neuroimaging and blood tests were conducted. Neurological and psychiatric evaluations and neuroconduction studies were performed to assess the clinical evolution and present sequelae. One year after diagnosis, all patients exhibited affective and behavioral sequelae, anterograde memory impairment, and executive functioning deficits. Two patients met the criteria for Korsakoff syndrome. Additionally, peripheral nervous system sequelae were observed, with all patients presenting with sensorimotor polyneuropathy. In conclusion, Wernicke's encephalopathy requires a high diagnostic suspicion for timely intervention and prevention of irreversible sequelae, which can be devastating. Therefore, raising awareness among medical professionals regarding the significance of this disease is essential.
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Affiliation(s)
- Melissa Gutiérrez-Rey
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
| | - Lily Castellar-Visbal
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
| | | | - José Vargas-Manotas
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
| | - Diego Rivera-Porras
- Universidad Simón Bolívar, Facultad de Ciencias Jurídicas y Sociales, Centro de Investigación en Estudios Fronterizos, Cúcuta 540001, Colombia;
| | - Gloria Londoño-Juliao
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
| | - Brenda Castillo-Guerrero
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
| | - María-Camila Perdomo-Jiménez
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
| | - Valmore Bermúdez
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla 080001, Colombia; (M.G.-R.); (L.C.-V.); (J.V.-M.); (G.L.-J.); (B.C.-G.); (M.-C.P.-J.)
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4
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Wang HL, Sun HP, Zheng PR, Cheng RT, Liu ZW, Yuan H, Gao WY, Li H. Re-investigation of in vitro activity of acetohydroxyacid synthase I holoenzyme from Escherichia coli. Arch Biochem Biophys 2024; 754:109962. [PMID: 38499055 DOI: 10.1016/j.abb.2024.109962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Acetohydroxyacid synthase (AHAS) is one of the key enzymes of the biosynthesis of branched-chain amino acids, it is also an effective target for the screening of herbicides and antibiotics. In this study we present a method for preparing Escherichia coli AHAS I holoenzyme (EcAHAS I) with exceptional stability, which provides a solid ground for us to re-investigate the in vitro catalytic properties of the protein. The results show EcAHAS I synthesized in this way exhibits similar function to Bacillus subtilis acetolactate synthase in its catalysis with pyruvate and 2-ketobutyrate (2-KB) as dual-substrate, producing four 2-hydroxy-3-ketoacids including (S)-2-acetolactate, (S)-2-aceto-2-hydroxybutyrate, (S)-2-propionyllactate, and (S)-2-propionyl-2-hydroxybutyrate. Quantification of the reaction indicates that the two substrates almost totally consume, and compound (S)-2-aceto-2- hydroxybutyrate forms in the highest yield among the four major products. Moreover, the protein also condenses two molecules of 2-KB to furnish (S)-2-propionyl-2-hydroxybutyrate. Further exploration manifests that EcAHAS I ligates pyruvate/2-KB and nitrosobenzene to generate two arylhydroxamic acids N-hydroxy-N-phenylacetamide and N-hydroxy-N-phenyl- propionamide. These findings enhance our comprehension of the catalytic characteristics of EcAHAS I. Furthermore, the application of this enzyme as a catalyst in construction of C-N bonds displays promising potential.
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Affiliation(s)
- Hai-Ling Wang
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Hui-Peng Sun
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Pei-Rong Zheng
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Rui-Tong Cheng
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Zhi-Wen Liu
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Heng Yuan
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Heng Li
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
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Abulfaraj AA, Shami AY, Alotaibi NM, Alomran MM, Aloufi AS, Al-Andal A, AlHamdan NR, Alshehrei FM, Sefrji FO, Alsaadi KH, Abuauf HW, Alshareef SA, Jalal RS. Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum. AMB Express 2024; 14:27. [PMID: 38381255 PMCID: PMC10881953 DOI: 10.1186/s13568-024-01678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/28/2024] [Indexed: 02/22/2024] Open
Abstract
The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes.
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Affiliation(s)
- Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia.
| | - Ashwag Y Shami
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Maryam M Alomran
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Abeer Al-Andal
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Fatimah M Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, Makkah 21955, Saudi Arabia
| | - Fatmah O Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Khloud H Alsaadi
- Department of Biological Science, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Haneen W Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 24381, Saudi Arabia
| | - Sahar A Alshareef
- Department of Biological Science, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21921, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biological Science, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia.
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6
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Haystead J, Gilmour K, Sherry A, Dade-Robertson M, Zhang M. Effect of (in)organic additives on microbially induced calcium carbonate precipitation. J Appl Microbiol 2024; 135:lxad309. [PMID: 38111211 DOI: 10.1093/jambio/lxad309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
AIM This study aimed to understand the morphological effects of (in)organic additives on microbially induced calcium carbonate precipitation (MICP). METHODS AND RESULTS MICP was monitored in real time in the presence of (in)organic additives: bovine serum albumin (BSA), biofilm surface layer protein A (BslA), magnesium chloride (MgCl2), and poly-l-lysine. This monitoring was carried out using confocal microscopy to observe the formation of CaCO3 from the point of nucleation, in comparison to conditions without additives. Complementary methodologies, namely scanning electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction, were employed to assess the visual morphology, elemental composition, and crystalline structures of CaCO3, respectively, following the crystals' formation. The results demonstrated that in the presence of additives, more CaCO3 crystals were produced at 100 min compared to the reaction without additives. The inclusion of BslA resulted in larger crystals than reactions containing other additives, including MgCl2. BSA induced a significant number of crystals from the early stages of the reaction (20 min) but did not have a substantial impact on crystal size compared to conditions without additives. All additives led to a higher content of calcite compared to vaterite after a 24-h reaction, with the exception of MgCl2, which produced a substantial quantity of magnesium calcite. CONCLUSIONS The work demonstrates the effect of several (in)organic additives on MICP and sets the stage for further research to understand additive effects on MICP to achieve controlled CaCO3 precipitation.
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Affiliation(s)
- Jamie Haystead
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Katie Gilmour
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Angela Sherry
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Martyn Dade-Robertson
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, The Quadrangle, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
- Hub for Biotechnology in the Built Environment, Department of Architecture and Built Environment, Northumbria University, NE1 8ST, United Kingdom
| | - Meng Zhang
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
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7
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Yuan P, Xu M, Mao C, Zheng H, Sun D. Dynamically Regulating Glucose Uptake to Reduce Overflow Metabolism with a Quorum-Sensing Circuit for the Efficient Synthesis of d-Pantothenic Acid in Bacillus subtilis. ACS Synth Biol 2023; 12:2983-2995. [PMID: 37664894 DOI: 10.1021/acssynbio.3c00315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
In response to a high concentration of glucose, Bacillus subtilis, a microbial chassis for producing many industrial metabolites, rapidly takes up glucose using the phosphotransferase system (PTS), leading to overflow metabolism, a common phenomenon observed in many bacteria. Although overflow metabolism affects cell growth and reduces the production of many metabolites, effective strategies that reduce overflow metabolism while maintaining normal cell growth remain to be developed. Here, we used a quorum sensing (QS)-mediated circuit to tune the glucose uptake rate and thereby relieve overflow metabolism in an engineered B. subtilis for producing d-pantothenic acid (DPA). A low-efficiency non-PTS system was used for glucose uptake at the early growth stages to avoid a rapid glycolytic flux, while an efficient PTS system, which was activated by a QS circuit, was automatically activated at the late growth stages after surpassing a threshold cell density. This strategy was successfully applied as a modular metabolic engineering process for the high production of DPA. By enhancing the translation levels of key enzymes (3-methyl-2-oxobutanoate hydroxymethytransferase, pantothenate synthetase, aspartate 1-decarboxylase proenzyme, 2-dehydropantoate 2-reductase, dihydroxy-acid dehydratase, and acetolactate synthase) with engineered 5'-untranslated regions (UTRs) of mRNAs, the metabolic flux was promoted in the direction of DPA production, elevating the yield of DPA to 5.11 g/L in shake flasks. Finally, the engineered B. subtilis produced 21.52 g/L of DPA in fed-batch fermentations. Our work not only revealed a new strategy for reducing overflow metabolism by adjusting the glucose uptake rate in combination with promoting the translation of key metabolic enzymes through engineering the 5'-UTR of mRNAs but also showed its power in promoting the bioproduction of DPA in B. subtilis, exhibiting promising application prospects.
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Affiliation(s)
- Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Mengtao Xu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Chengyao Mao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Han Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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8
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Gonzales JN, Treece TR, Mayfield SP, Simkovsky R, Atsumi S. Utilization of lignocellulosic hydrolysates for photomixotrophic chemical production in Synechococcus elongatus PCC 7942. Commun Biol 2023; 6:1022. [PMID: 37813969 PMCID: PMC10562401 DOI: 10.1038/s42003-023-05394-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
To meet the need for environmentally friendly commodity chemicals, feedstocks for biological chemical production must be diversified. Lignocellulosic biomass are an carbon source with the potential for effective use in a large scale and cost-effective production systems. Although the use of lignocellulosic biomass lysates for heterotrophic chemical production has been advancing, there are challenges to overcome. Here we aim to investigate the obligate photoautotroph cyanobacterium Synechococcus elongatus PCC 7942 as a chassis organism for lignocellulosic chemical production. When modified to import monosaccharides, this cyanobacterium is an excellent candidate for lysates-based chemical production as it grows well at high lysate concentrations and can fix CO2 to enhance carbon efficiency. This study is an important step forward in enabling the simultaneous use of two sugars as well as lignocellulosic lysate. Incremental genetic modifications enable catabolism of both sugars concurrently without experiencing carbon catabolite repression. Production of 2,3-butanediol is demonstrated to characterize chemical production from the sugars in lignocellulosic hydrolysates. The engineered strain achieves a titer of 13.5 g L-1 of 2,3-butanediol over 12 days under shake-flask conditions. This study can be used as a foundation for industrial scale production of commodity chemicals from a combination of sunlight, CO2, and lignocellulosic sugars.
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Affiliation(s)
- Jake N Gonzales
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA
| | - Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Stephen P Mayfield
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shota Atsumi
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA.
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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9
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Davison JR, Rajwani R, Zhao G, Bewley CA. The genome of antibiotic-producing colonies of the Pelagophyte alga Chrysophaeum taylorii reveals a diverse and non-canonical capacity for secondary metabolism. Sci Rep 2023; 13:11944. [PMID: 37488207 PMCID: PMC10366177 DOI: 10.1038/s41598-023-38042-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/01/2023] [Indexed: 07/26/2023] Open
Abstract
Chrysophaeum taylorii is a member of an understudied clade of marine algae that can be responsible for harmful coastal blooms and is known to accumulate bioactive natural products including antibiotics of the chrysophaentin class. Whole genome sequencing of laboratory-cultivated samples revealed an extensive and diverse complement of secondary metabolite biosynthetic genes in C. taylorii, alongside a small microbiome with a more limited biosynthetic potential. 16S microbiome analysis of laboratory cultured alongside wild-collected samples revealed several common taxa; however, analysis of biosynthetic genes suggested an algal origin for the chrysophaentins, possibly via one of several non-canonical polyketide synthase genes encoded within the genome.
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Affiliation(s)
- Jack R Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA.
- LifeMine Therapeutics, 30 Acorn Park Dr., Cambridge, MA, 02140, USA.
| | - Rahim Rajwani
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA.
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10
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Chauhan S, Tiwari PN, Payasi DK. Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants. Life (Basel) 2023; 13:1456. [PMID: 37511831 PMCID: PMC10381907 DOI: 10.3390/life13071456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Genome editing aims to revolutionise plant breeding and could assist in safeguarding the global food supply. The inclusion of a 12-40 bp recognition site makes mega nucleases the first tools utilized for genome editing and first generation gene-editing tools. Zinc finger nucleases (ZFNs) are the second gene-editing technique, and because they create double-stranded breaks, they are more dependable and effective. ZFNs were the original designed nuclease-based approach of genome editing. The Cys2-His2 zinc finger domain's discovery made this technique possible. Clustered regularly interspaced short palindromic repeats (CRISPR) are utilized to improve genetics, boost biomass production, increase nutrient usage efficiency, and develop disease resistance. Plant genomes can be effectively modified using genome-editing technologies to enhance characteristics without introducing foreign DNA into the genome. Next-generation plant breeding will soon be defined by these exact breeding methods. There is abroad promise that genome-edited crops will be essential in the years to come for improving the sustainability and climate-change resilience of food systems. This method also has great potential for enhancing crops' resistance to various abiotic stressors. In this review paper, we summarize the most recent findings about the mechanism of abiotic stress response in crop plants and the use of the CRISPR/Cas mediated gene-editing systems to improve tolerance to stresses including drought, salinity, cold, heat, and heavy metals.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Shailja Chauhan
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Prakash Narayan Tiwari
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Zafar K, Khan MZ, Amin I, Mukhtar Z, Zafar M, Mansoor S. Employing template-directed CRISPR-based editing of the OsALS gene to create herbicide tolerance in Basmati rice. AOB PLANTS 2023; 15:plac059. [PMID: 36873055 PMCID: PMC9977225 DOI: 10.1093/aobpla/plac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa) is one of the primary food crops which contributes major portion of daily calorie intake. It is used as model crop for various genome editing studies. Basmati rice was also explored for establishing non-homologous end joining-based genome editing. But it was not clear whether homology-directed repair (HDR)-based genome editing can be done in Basmati rice. The current study was designed to establish HDR-based genome editing in Basmati rice to develop herbicide tolerance. There is severe weed spread when rice is grown via direct planted rice method in various countries to save labour and water resources. Therefore, the use of herbicides is necessary to control weeds. These herbicides can also affect cultivated rice which creates the need to develop herbicide-tolerant rice. In current study, we introduced a point mutation in Acetolactate Synthase gene to convert tryptophan to leucine at position 548. For this purpose, different constructs for HDR were tested with different RNA scaffold and orientation of repair templates. Out of four different architectures, the one having repair template identical to the target DNA strand precisely edited the target site. We successfully established template-directed CRISPR-Cas9 system in Super Basmati rice by detecting desired substitutions at the target site in Acetolactate Synthase locus. Moreover, this editing of Acetolactate Synthase gene resulted in the production of herbicide tolerance in Super Basmati rice. This study suggests that such type of HDR system can be used to precisely edit other genes for crop improvement.
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Affiliation(s)
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Mehak Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
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Zhou S, Zhao LT, Meng FF, Hua XW, Li YH, Liu B, Chen J, Chen AL, Li ZM. Synthesis, herbicidal activity and soil degradation of novel 5-substituted sulfonylureas as AHAS inhibitors. PEST MANAGEMENT SCIENCE 2022; 78:5313-5324. [PMID: 36054636 DOI: 10.1002/ps.7153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 08/03/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Chlorsulfuron, metsulfuron-methyl and ethametsulfuron can damage sensitive crops in rotation pattern as a result of their long persistence in soil. To explore novel sulfonylurea (SU) herbicides with favorable soil degradation rates, four series of SUs were synthesized through a structure-based drug design (SBDD) strategy. RESULTS The target compounds, especially Ia, Id and Ie, exhibited prospective herbicidal activity against dicotyledon oil seed rape (Brassica campestris), amaranth (Amaranthus retroflexus), monocotyledon barnyard grass (Echinochloa crusgalli) and crab grass (Digitaria sanguinalis) at a concentration of 15 a.i. g ha-1 . Additionally, Ia, Id and Ig displayed excellent inhibitory effects against AtAHAS, with Kapp i values of 59.1, 34.5 and 71.8 μm, respectively, which were much lower than that of chlorsulfuron at 149.4 μm. The π-π stack and H-bonds between the Ia conformation and AtAHAS in the molecular docking results confirmed the series of compounds to be conventional AHAS inhibitors. In alkaline soil (pH = 8.46), compounds Ia-Ig revealed various degrees of acceleration in the degradation rate compared with chlorsulfuron. Besides, compound Ia showed considerable wheat and corn safety under postemergence at the concentration of 30, 60 and even 120 a.i. g ha-1 . CONCLUSION Overall, based on the synthetic procedure, herbicidal activity, soil degradation and crop safety, the Ia sulfonylureas series were chosen to be investigated as prospective AHAS inhibitors. The 5-dimethylamino group on SUs accelerated the degradation rate at different levels in alkaline soils which seems to be controllable in conventional cropping systems in their further application. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Sha Zhou
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A&F University State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, China
| | - Lv-Ting Zhao
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A&F University State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Fan-Fei Meng
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, China
| | - Xue-Wen Hua
- College of Agriculture, Liaocheng University, Liaocheng, China
| | - Yong-Hong Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, China
| | - Bin Liu
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, China
| | - Jie Chen
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A&F University State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - An-Liang Chen
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A&F University State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Zheng-Ming Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, China
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Two New Phenylhydrazone Derivatives from the Pearl River Estuary Sediment-Derived Streptomyces sp. SCSIO 40020. Mar Drugs 2022; 20:md20070449. [PMID: 35877742 PMCID: PMC9323291 DOI: 10.3390/md20070449] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Two new phenylhydrazone derivatives and one new alkaloid, penzonemycins A–B (1–2) and demethylmycemycin A (3), together with three known compounds including an alkaloid (4) and two sesquiterpenoids (5–6), were isolated from the Streptomyces sp. SCSIO 40020 obtained from the Pearl River Estuary sediment. Their structures and absolute configurations were assigned by 1D/2D NMR, mass spectroscopy and X-ray crystallography. Compound 1 was evaluated in four human cancer cell lines by the SRB method and displayed weak cytotoxicity in three cancer cell lines, with IC50 values that ranged from 30.44 to 61.92 µM, which were comparable to those of the positive control cisplatin. Bioinformatic analysis of the putative biosynthetic gene cluster indicated a Japp–Klingemann coupling reaction involved in the hydrazone formation of 1 and 2.
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Wu L, Hua XW, Li YH, Wang ZW, Zhou S, Li ZM. Alkaline Soil Degradation and Crop Safety of 5-Substituted Chlorsulfuron Derivatives. Molecules 2022; 27:molecules27103318. [PMID: 35630795 PMCID: PMC9145588 DOI: 10.3390/molecules27103318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Sulfonylurea herbicides can lead to serious weed resistance due to their long degradation times and large-scale applications. This is especially true for chlorsulfuron, a widely used acetolactate synthase inhibitor used around the world. Its persistence in soil often affects the growth of crop seedlings in the following crop rotation, and leads to serious environmental pollution all over the world. Our research goal is to obtain chlorsulfuron-derived herbicides with high herbicidal activities, fast degradation times, as well as good crop safety. On account of the slow natural degradation of chlorsulfuron in alkaline soil, based on the previously reported results in acidic soil, the degradation behaviours of 5-substituted chlorsulfuron analogues (L101–L107) were investigated in a soil with pH 8.39. The experimental data indicated that 5-substituted chlorsulfuron compounds could accelerate degradation rates in alkaline soil, and thus, highlighted the potential for rational controllable degradation in soil. The degradation rates of these chlorsulfuron derivatives were accelerated by 1.84–77.22-fold, compared to chlorsulfuron, and exhibited excellent crop safety in wheat and corn (through pre-emergence treatment). In combination with bioassay activities, acidic and alkaline soil degradation, and crop safety, it was concluded that compounds L104 and L107, with ethyl or methyl groups, are potential green sulfonylurea herbicides for pre-emergence treatment on wheat and corn. This paper provides a reference for the further design of new sulfonylurea herbicides with high herbicidal activity, fast, controllable degradation rates, and high crop safety.
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Affiliation(s)
- Lei Wu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China; (L.W.); (Y.-H.L.); (Z.-W.W.)
| | - Xue-Wen Hua
- College of Agriculture, Liaocheng University, Liaocheng 252059, China;
| | - Yong-Hong Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China; (L.W.); (Y.-H.L.); (Z.-W.W.)
| | - Zhong-Wen Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China; (L.W.); (Y.-H.L.); (Z.-W.W.)
| | - Sha Zhou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China; (L.W.); (Y.-H.L.); (Z.-W.W.)
- Correspondence: (S.Z.); (Z.-M.L.)
| | - Zheng-Ming Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China; (L.W.); (Y.-H.L.); (Z.-W.W.)
- Correspondence: (S.Z.); (Z.-M.L.)
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15
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Genome Editing: A Promising Approach for Achieving Abiotic Stress Tolerance in Plants. Int J Genomics 2022; 2022:5547231. [PMID: 35465040 PMCID: PMC9033345 DOI: 10.1155/2022/5547231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/24/2022] [Indexed: 12/26/2022] Open
Abstract
The susceptibility of crop plants towards abiotic stresses is highly threatening to assure global food security as it results in almost 50% annual yield loss. To address this issue, several strategies like plant breeding and genetic engineering have been used by researchers from time to time. However, these approaches are not sufficient to ensure stress resilience due to the complexity associated with the inheritance of abiotic stress adaptive traits. Thus, researchers were prompted to develop novel techniques with high precision that can address the challenges connected to the previous strategies. Genome editing is the latest approach that is in the limelight for improving the stress tolerance of plants. It has revolutionized crop research due to its versatility and precision. The present review is an update on the different genome editing tools used for crop improvement so far and the various challenges associated with them. It also highlights the emerging potential of genome editing for developing abiotic stress-resilient crops.
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16
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Yu S, Zheng B, Chen Z, Huo YX. Metabolic engineering of Corynebacterium glutamicum for producing branched chain amino acids. Microb Cell Fact 2021; 20:230. [PMID: 34952576 PMCID: PMC8709942 DOI: 10.1186/s12934-021-01721-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background Branched chain amino acids (BCAAs) are widely applied in the food, pharmaceutical, and animal feed industries. Traditional chemical synthetic and enzymatic BCAAs production in vitro has been hampered by expensive raw materials, harsh reaction conditions, and environmental pollution. Microbial metabolic engineering has attracted considerable attention as an alternative method for BCAAs biosynthesis because it is environmentally friendly and delivers high yield. Main text Corynebacterium glutamicum (C. glutamicum) possesses clear genetic background and mature gene manipulation toolbox, and has been utilized as industrial host for producing BCAAs. Acetohydroxy acid synthase (AHAS) is a crucial enzyme in the BCAAs biosynthetic pathway of C. glutamicum, but feedback inhibition is a disadvantage. We therefore reviewed AHAS modifications that relieve feedback inhibition and then investigated the importance of AHAS modifications in regulating production ratios of three BCAAs. We have comprehensively summarized and discussed metabolic engineering strategies to promote BCAAs synthesis in C. glutamicum and offer solutions to the barriers associated with BCAAs biosynthesis. We also considered the future applications of strains that could produce abundant amounts of BCAAs. Conclusions Branched chain amino acids have been synthesized by engineering the metabolism of C. glutamicum. Future investigations should focus on the feedback inhibition and/or transcription attenuation mechanisms of crucial enzymes. Enzymes with substrate specificity should be developed and applied to the production of individual BCAAs. The strategies used to construct strains producing BCAAs provide guidance for the biosynthesis of other high value-added compounds.
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Affiliation(s)
- Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
| | - Bo Zheng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing, 100081, China
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17
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Tussipkan D, Manabayeva SA. Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:747476. [PMID: 34764969 PMCID: PMC8576567 DOI: 10.3389/fpls.2021.747476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/04/2021] [Indexed: 05/07/2023]
Abstract
New breeding technologies have not only revolutionized biological science, but have also been employed to generate transgene-free products. Genome editing is a powerful technology that has been used to modify genomes of several important crops. This review describes the basic mechanisms, advantages and disadvantages of genome editing systems, such as ZFNs, TALENs, and CRISPR/Cas. Secondly, we summarize in detail all studies of the CRISPR/Cas system applied to potato and other tuber crops, such as sweet potato, cassava, yam, and carrot. Genes associated with self-incompatibility, abiotic-biotic resistance, nutrient-antinutrient content, and post-harvest factors targeted utilizing the CRISPR/Cas system are analyzed in this review. We hope that this review provides fundamental information that will be useful for future breeding of tuber crops to develop novel cultivars.
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Affiliation(s)
| | - Shuga A. Manabayeva
- Plant Genetic Engineering Laboratory, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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18
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AIP1, Encoding the Small Subunit of Acetolactate Synthase, Is Partially Responsible for Resistance to Hypoxic Stress in Arabidopsis thaliana. PLANTS 2021; 10:plants10112251. [PMID: 34834615 PMCID: PMC8621687 DOI: 10.3390/plants10112251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Flooding is a significant stress to land plants, depriving them of essential oxygen. Plants have evolved diverse strategies with variable success to survive flooding. Similar strategies have been described in organisms from other kingdoms. Several fungal species can successfully survive a low-oxygen environment by increasing their branched-chain amino acid (BCAA) contents. BCAAs may act as alternative electron acceptors in the respiratory chain under an oxygen-limited environment. The key and first enzyme for BCAA biosynthesis is acetolactate synthase (ALS). We identified two homologous genes encoding the small subunit of ALS in Arabidopsis (Arabidopsis thaliana). We determined that ALS INTERACTING PROTEIN1 (AIP1), which encodes the small subunit of ALS, is strongly expressed in all organs and highly expressed under submergence and low-oxygen stresses. We also showed that the overexpression of AIP1 confers tolerance to low-oxygen stress. These results indicate that ALS may play an essential role under prolonged flooding or oxygen deficiency in Arabidopsis.
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19
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Learning from Yeast about Mitochondrial Carriers. Microorganisms 2021; 9:microorganisms9102044. [PMID: 34683364 PMCID: PMC8539049 DOI: 10.3390/microorganisms9102044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/14/2021] [Accepted: 09/23/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondria are organelles that play an important role in both energetic and synthetic metabolism of eukaryotic cells. The flow of metabolites between the cytosol and mitochondrial matrix is controlled by a set of highly selective carrier proteins localised in the inner mitochondrial membrane. As defects in the transport of these molecules may affect cell metabolism, mutations in genes encoding for mitochondrial carriers are involved in numerous human diseases. Yeast Saccharomyces cerevisiae is a traditional model organism with unprecedented impact on our understanding of many fundamental processes in eukaryotic cells. As such, the yeast is also exceptionally well suited for investigation of mitochondrial carriers. This article reviews the advantages of using yeast to study mitochondrial carriers with the focus on addressing the involvement of these carriers in human diseases.
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20
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Abdel-Wahab SIZ, Aioub AAA, Salem REME, El-Sobki AEA. Electrophoretic banding patterns of protein induced by pinoxaden, tribenuron-methyl, and pyroxsulam herbicides in wheat leaves (Triticum aestivum L.). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:30077-30089. [PMID: 33586103 DOI: 10.1007/s11356-021-12676-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Herbicides are the most effective tool against weed flora in cereal crops that help to maintain and increase crop yields. This investigation was conducted in the winter season of 2018 to study the stress effect of three post-emergence herbicides including pinoxaden, tribenuron-methyl, and pyroxsulam on the biochemical changes at the molecular cell level of wheat. These herbicides were applied either lonely with a rate of 0.45 L.ha-1, 22.5 gm.ha-1, and 0.16 Ib a.i/A, respectively, or in combinations together on three Egyptian varieties of bread wheat known as Misr 1, Giza17 1, and Gemmiza 11. Firstly, the abovementioned herbicides were used at the recommended and half recommended doses with their combinations for these varieties to investigate DNA-protein linkage as a signal effect of herbicides at the molecular cell level.Our data showed that the treatment of wheat varieties with the tested herbicides induced new bands with low and high molecular weights of 37.49, 40.08, 146.55, and 147.23 KDa with relative mobility of 0.1574, 0.1603, 0.2166, and 0.2168, respectively. These bands were not presented in the control treatment, suggesting that it might be used as a biochemical marker for plant defense genes. Meanwhile, the control treatment exhibited only five or six bands in the three varieties. However, the tested varieties showed that the same number of bands, the molecular weights of bands, and their relative mobility were significantly varied between the single and the combinations treatment of herbicides. The best treatment was achieved by the combination between pinoxaden and tribenuron-methyl at a recommended dose which induced a large number of protein bands compared to the control treatment on the wheat variety cv. Misr 1, which gave one band with low molecular weight 71.44 KDa at Rf 0.1854 and other with the highest molecular weight 147.23 KDa at Rf 0.2168, compared to the control treatment.
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Affiliation(s)
- Sarah I Z Abdel-Wahab
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt.
| | - Ali A A Aioub
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Rehab E M E Salem
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ahmed E A El-Sobki
- Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
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21
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 707:108849. [PMID: 33832752 DOI: 10.1016/j.abb.2021.108849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4 kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9 kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, UK; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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Sen MK, Hamouzová K, Mikulka J, Bharati R, Košnarová P, Hamouz P, Roy A, Soukup J. Enhanced metabolism and target gene overexpression confer resistance against acetolactate synthase-inhibiting herbicides in Bromus sterilis. PEST MANAGEMENT SCIENCE 2021; 77:2122-2128. [PMID: 33332713 DOI: 10.1002/ps.6241] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Intensive application of acetolactate synthase (ALS)-inhibiting herbicides has resulted in herbicide-resistance in many weeds, including Bromus sterilis. The present study was conducted to identify the mechanisms conferring resistance to ALS-inhibiting herbicides in a Bromus sterilis biotype. RESULTS Dose-response studies revealed the resistant biotype to be 288 times less sensitive to pyroxsulam than the susceptible biotype. Furthermore, experiment with a single-dose, proved this biotype was also cross-resistant to propoxycarbazone, iodosulfuron plus mesosulfuron and sulfosulfuron. Prior treatment with malathion, a known inhibitor of cytochrome P450s, reduced the level of resistance to pyroxsulam. No mutations were detected from the partial ALS gene sequencing. Flow cytometry and chromosome counting rejected ploidy level variation between the susceptible and resistant biotypes. Relative copy number variation ruled out gene amplification. Quantitative real-time polymerase chain reaction (PCR) detected a significant difference in ALS gene expression between the susceptible and resistant biotypes. CONCLUSIONS Target gene overexpression and enhanced metabolism by cytochrome P450s are likely mechanisms of resistance to pyroxsulam in Bromus sterilis. The current findings highlight the need to monitor additional brome populations for herbicide resistance in Europe and endorse the need for alternate herbicides in integrated weed management to delay the possible evolution of herbicide resistance in these species. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jakub Mikulka
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavlina Košnarová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hamouz
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 701:108807. [PMID: 33587902 DOI: 10.1016/j.abb.2021.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, United Kingdom; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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24
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Kang T, Gao S, Zhao LX, Zhai Y, Ye F, Fu Y. Design, Synthesis, and SAR of Novel 1,3-Disubstituted Imidazolidine or Hexahydropyrimidine Derivatives as Herbicide Safeners. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:45-54. [PMID: 33372787 DOI: 10.1021/acs.jafc.0c04436] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herbicide safeners enhance herbicide detoxification in crops without reducing their herbicidal efficacy against target weeds. To alleviate maize injury caused by the sulfonylurea herbicide nicosulfuron, a series of 1,3-disubstituted imidazolidine or hexahydropyrimidine derivatives were rationally designed via bioisosterism and active subunit combinations. Thirty novel compounds were synthesized using an efficient one-pot method and low-cost raw materials and characterized by IR, 1H NMR, 13C NMR, and high-resolution mass spectrometer (HRMS). Bioactivity and structure-activity relationship (SAR) were evaluated for herbicide safeners tested against nicosulfuron injury. Most of the compounds effectively protected sensitive maize against nicosulfuron damage. The parent skeletons and substituents of the target compounds both substantially influenced their safener activity. Compound I-3 exhibited superior bioactivity compared to the safener isoxadifen-ethyl. Molecular docking simulations disclosed that compound I-3 competed with nicosulfuron for the acetolactate synthase active site and demonstrated that this is the protective mechanism of safeners. The target compound I-3 presented with strong herbicide safener activity in maize and is, therefore, a potential candidate for the development of a novel herbicide safener.
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Affiliation(s)
- Tao Kang
- Department of Applied Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Applied Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xia Zhao
- Department of Applied Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhai
- Department of Applied Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Applied Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Applied Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
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25
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Bhat MA, Bhat MA, Kumar V, Wani IA, Bashir H, Shah AA, Rahman S, Jan AT. The era of editing plant genomes using CRISPR/Cas: A critical appraisal. J Biotechnol 2020; 324:34-60. [DOI: 10.1016/j.jbiotec.2020.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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26
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Zhou S, Meng FF, Hua XW, Li YH, Liu B, Wang BL, Chen J, Chen AL, Li ZM. Controllable Soil Degradation Rate of 5-Substituted Sulfonylurea Herbicides as Novel AHAS Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3017-3025. [PMID: 32059105 DOI: 10.1021/acs.jafc.9b06679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chlorsulfuron has been applied in wheat fields as a recognized herbicide worldwide, yet it was officially banned in China since 2014 for its soil persistence problem. On the basis of our previous research that 5-dimethylamino distinctively accelerated degradation rate in soils, a modified amino moiety (Ia-c) and monosubstituted amino group (Id-e) were introduced onto the fifth position of the benzene ring in sulfonylurea structures, as well as heterocyclic amino substituents (If-g) to seek a suitable soil degradation rate during such an in situ crop rotation system. Referring to the biological data and ScAHAS inhibition and ScAHAS docking results, they turned out to be AHAS inhibitors with high potent herbicidal activities. The various influence on soil degradation rate along with crop safety indicated that different substituents on the fifth position have exerted an apparent impact. Their united study of structure-activity-safety-degradation relationship has great potential to provide valuable information for further development of eco-friendly agrochemicals.
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Affiliation(s)
- Shaa Zhou
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A & F University State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, Zhejiang, China
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Fan-Fei Meng
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xue-Wen Hua
- College of Agriculture, Liaocheng University, Liaocheng 252000, China
| | - Yong-Hong Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bin Liu
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bao-Lei Wang
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jie Chen
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A & F University State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, Zhejiang, China
| | - An-Liang Chen
- Collaborative Innovation Center of Green Pesticide, National Joint Engineering Laboratory of Biopesticide Preparation, Zhejiang A & F University State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, Zhejiang, China
| | - Zheng-Ming Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
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27
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Wang B, Xu X, Gong S, Wang Q, Hu H, Xu D. Synthesis and Herbicidal Activity of O‐(2,6‐Bis(4,6‐dimethoxypyrimidin‐2‐yloxy) benzoyl)oxime 3‐Trifluoromethylacetophenone. ChemistrySelect 2019. [DOI: 10.1002/slct.201902806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin Wang
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Xiangjian Xu
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Shunze Gong
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Qin Wang
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Hang Hu
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Defeng Xu
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
- National & Local Joint Engineering Research Center for High-efficiency Refining and High-quality Utilization of BiomassChangzhou University Changzhou 213164 P. R. China
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28
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Abstract
Tuberculosis (TB) is a major issue in global health and affects millions of people each year. Multidrug-resistant tuberculosis (MDR-TB) annually causes many deaths worldwide. Development of a way to diagnose and treat patients with MDR-TB can potentially reduce the incidence of the disease. The current study reviews the risk factors, pattern of progression, mechanism of resistance, and interaction between bacteria and the host immune system, which disrupts the immune response. It also targets the components of Mycobacterium tuberculosis (Mtb) and diagnosis and treatment options that could be available for clinical use in the near future. Mutations play an important role in development of MDR-TB and the selection of appropriate mutations can help to understand the type of resistance in patients to anti-TB drugs. In this way, they can be initially treated with proper and effective therapeutic choices, which can accelerate the course of treatment and improve patient health. Targeting the components and enzymes of Mtb is necessary for understanding bacterial survival and finding a way to destroy the pathogen and allow patients to recover faster and prevent the spread of disease, especially resistant strains.
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Affiliation(s)
- Majid Faridgohar
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran.,Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
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29
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Que Y, Yue X, Yang N, Xu Z, Tang S, Wang C, Lv W, Xu L, Talbot NJ, Wang Z. Leucine biosynthesis is required for infection-related morphogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae. Curr Genet 2019; 66:155-171. [PMID: 31263943 DOI: 10.1007/s00294-019-01009-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Abstract
The rice blast fungus Magnaporthe oryzae causes one of the most devastating crop diseases world-wide and new control strategies for blast disease are urgently required. We have used insertional mutagenesis in M. oryzae to define biological processes that are critical for blast disease. Here, we report the identification of LEU2A by T-DNA mutagenesis, which putatively encodes 3-isopropylmalate dehydrogenase (3-IPMDH) required for leucine biosynthesis, implicating that synthesis of this amino acid is required for fungal pathogenesis. M. oryzae contains a further predicted 3-IPMDH gene (LEU2B), two 2-isopropylmalate synthase (2-IPMS) genes (LEU4 and LEU9) and an isopropylmalate isomerase (IPMI) gene (LEU1). Targeted gene deletion mutants of LEU1, LEU2A or LEU4 are leucine auxotrophs, and severely defective in pathogenicity. All phenotypes associated with mutants lacking LEU1, LEU2A or LEU4 could be overcome by adding exogenous leucine. The expression levels of LEU1, LEU2A or LEU4 genes were significantly down-regulated by deletion of the transcription factor gene LEU3, an ortholog of Saccharomyces cerevisiae LEU3. We also functionally characterized leucine biosynthesis genes in the wheat pathogen Fusarium graminearum and found that FgLEU1, FgLEU3 and FgLEU4 are essential for wheat head blight disease, suggesting that leucine biosynthesis in filamentous fungal pathogens may be a conserved factor for fungal pathogenicity and, therefore, a potential target for disease control.
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Affiliation(s)
- Yawei Que
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaofeng Yue
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Nan Yang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhe Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shuai Tang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chunyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuyun Lv
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Nicholas J Talbot
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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30
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Sedeek KEM, Mahas A, Mahfouz M. Plant Genome Engineering for Targeted Improvement of Crop Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:114. [PMID: 30809237 PMCID: PMC6379297 DOI: 10.3389/fpls.2019.00114] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/23/2019] [Indexed: 05/18/2023]
Abstract
To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.
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Affiliation(s)
| | | | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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31
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Xie Y, Wen X, Zhao D, Niu C, Zhao Y, Qi H, Xi Z. Interactions between the ACT Domains and Catalytic Subunits of Acetohydroxyacid Synthases (AHASs) from Different Species. Chembiochem 2018; 19:2387-2394. [DOI: 10.1002/cbic.201800367] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Yonghui Xie
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
| | - Dongmei Zhao
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
| | - Congwei Niu
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
| | - Yuefang Zhao
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
| | - Haoman Qi
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry; Department of Chemical Biology; National Pesticide Engineering Research Center (Tianjin); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); College of Chemistry; Nankai University; Tianjin 300071 P.R. China
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32
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Westbrook AW, Ren X, Moo‐Young M, Chou CP. Metabolic engineering ofBacillus subtilisforl‐valine overproduction. Biotechnol Bioeng 2018; 115:2778-2792. [DOI: 10.1002/bit.26789] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Adam W. Westbrook
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
| | - Xiang Ren
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
| | - Murray Moo‐Young
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
| | - C. Perry Chou
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
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33
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Chikhale RV, Barmade MA, Murumkar PR, Yadav MR. Overview of the Development of DprE1 Inhibitors for Combating the Menace of Tuberculosis. J Med Chem 2018; 61:8563-8593. [PMID: 29851474 DOI: 10.1021/acs.jmedchem.8b00281] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1), a vital enzyme for cell wall synthesis, plays a crucial role in the formation of lipoarabinomannan and arabinogalactan. It was first reported as a druggable target on the basis of inhibitors discovered in high throughput screening of a drug library. Since then, inhibitors with different types of chemical scaffolds have been reported for their activity against this enzyme. Formation of a covalent or noncovalent bond by the interacting ligand with the enzyme causes loss of its catalytic activity which ultimately leads to the death of the mycobacterium. This Perspective describes various DprE1 inhibitors as anti-TB agents reported to date.
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Affiliation(s)
- Rupesh V Chikhale
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India.,School of Health Sciences, Division of Pharmacy and Optometry , University of Manchester , Manchester M13 9PL , U.K
| | - Mahesh A Barmade
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
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34
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Su L, Lv M, Kyeremeh K, Deng Z, Deng H, Yu Y. A ThDP-dependent enzymatic carboligation reaction involved in Neocarazostatin A tricyclic carbazole formation. Org Biomol Chem 2018; 14:8679-8684. [PMID: 27714211 DOI: 10.1039/c6ob01651k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although the biosynthetic pathway of Neocarazostatin A (1) has been identified, the detailed enzymatic reactions underlying the assembly of the carbazole ring still remain largely unknown. We demonstrate here that NzsH, a putative thiamine diphosphate dependent enzyme, can catalyze an acyloin coupling reaction between indole-3-pyruvate and pyruvate to generate a β-ketoacid intermediate. Our findings thus shed light on further characterization of the unusual biosynthetic pathway of the bacterial tricyclic carbazole alkaloids.
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Affiliation(s)
- Li Su
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P.R. China.
| | - Meinan Lv
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P.R. China.
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra, Ghana
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P.R. China.
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P.R. China.
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35
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Lonhienne T, Garcia MD, Noble C, Harmer J, Fraser JA, Williams CM, Guddat LW. High Resolution Crystal Structures of the Acetohydroxyacid Synthase‐Pyruvate Complex Provide New Insights into Its Catalytic Mechanism. ChemistrySelect 2017. [DOI: 10.1002/slct.201702128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thierry Lonhienne
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 QLD Australia
| | - Mario D. Garcia
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 QLD Australia
| | - Chris Noble
- Centre for Advanced Imaging The University of Queensland Brisbane 4072 QLD Australia
| | - Jeffrey Harmer
- Centre for Advanced Imaging The University of Queensland Brisbane 4072 QLD Australia
| | - James A. Fraser
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 QLD Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 QLD Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 QLD Australia
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36
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Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. mBio 2017; 8:mBio.01780-17. [PMID: 29138306 PMCID: PMC5686539 DOI: 10.1128/mbio.01780-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection.IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.
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37
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The type II isopentenyl Diphosphate:Dimethylallyl diphosphate isomerase (IDI-2): A model for acid/base chemistry in flavoenzyme catalysis. Arch Biochem Biophys 2017; 632:47-58. [PMID: 28577910 DOI: 10.1016/j.abb.2017.05.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 11/21/2022]
Abstract
The chemical versatility of the flavin coenzyme is nearly unparalleled in enzyme catalysis. An interesting illustration of this versatility can be found in the reaction catalyzed by the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) - an enzyme that interconverts the two essential isoprene units (isopentenyl pyrophosphate and dimethylallyl pyrophosphate) that are needed to initiate the biosynthesis of all isoprenoids. Over the past decade, a variety of biochemical, spectroscopic, structural and mechanistic studies of IDI-2 have provided mounting evidence that the flavin coenzyme of IDI-2 acts in a most unusual manner - as an acid/base catalyst to mediate a 1,3-proton addition/elimination reaction. While not entirely without precedent, IDI-2 is by far the most extensively studied flavoenzyme that employs flavin-mediated acid/base catalysis. Thus, IDI-2 serves as an important mechanistic model for understanding this often overlooked, but potentially widespread reactivity of flavin coenzymes. This review details the most pertinent studies that have contributed to the development of mechanistic proposals for this highly unusual flavoenzyme, and discusses future experiments that may be able to clarify remaining uncertainties in the chemical mechanism of IDI-2.
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Kariuki MN, Nagato EG, Lankadurai BP, Simpson AJ, Simpson MJ. Analysis of Sub-Lethal Toxicity of Perfluorooctane Sulfonate (PFOS) to Daphnia magna Using ¹H Nuclear Magnetic Resonance-Based Metabolomics. Metabolites 2017; 7:metabo7020015. [PMID: 28420092 PMCID: PMC5487986 DOI: 10.3390/metabo7020015] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/05/2017] [Accepted: 04/12/2017] [Indexed: 01/29/2023] Open
Abstract
1H nuclear magnetic resonance (NMR)-based metabolomics was used to characterize the response of Daphnia magna after sub-lethal exposure to perfluorooctane sulfonate (PFOS), a commonly found environmental pollutant in freshwater ecosystems. Principal component analysis (PCA) scores plots showed significant separation in the exposed samples relative to the controls. Partial least squares (PLS) regression analysis revealed a strong linear correlation between the overall metabolic response and PFOS exposure concentration. More detailed analysis showed that the toxic mode of action is metabolite-specific with some metabolites exhibiting a non-monotonic response with higher PFOS exposure concentrations. Our study indicates that PFOS exposure disrupts various energy metabolism pathways and also enhances protein degradation. Overall, we identified several metabolites that are sensitive to PFOS exposure and may be used as bioindicators of D. magna health. In addition, this study also highlights the important utility of environmental metabolomic methods when attempting to elucidate acute and sub-lethal pollutant stressors on keystone organisms such as D. magna.
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Affiliation(s)
- Martha N Kariuki
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4, Canada.
| | - Edward G Nagato
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4, Canada.
| | - Brian P Lankadurai
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4, Canada.
| | - André J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4, Canada.
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4, Canada.
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Dezfulian MH, Foreman C, Jalili E, Pal M, Dhaliwal RK, Roberto DKA, Imre KM, Kohalmi SE, Crosby WL. Acetolactate synthase regulatory subunits play divergent and overlapping roles in branched-chain amino acid synthesis and Arabidopsis development. BMC PLANT BIOLOGY 2017; 17:71. [PMID: 28388946 PMCID: PMC5384131 DOI: 10.1186/s12870-017-1022-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/30/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Branched-chain amino acids (BCAAs) are synthesized by plants, fungi, bacteria, and archaea with plants being the major source of these amino acids in animal diets. Acetolactate synthase (ALS) is the first enzyme in the BCAA synthesis pathway. Although the functional contribution of ALS to BCAA biosynthesis has been extensively characterized, a comprehensive understanding of the regulation of this pathway at the molecular level is still lacking. RESULTS To characterize the regulatory processes governing ALS activity we utilized several complementary approaches. Using the ALS catalytic protein subunit as bait we performed a yeast two-hybrid (Y2H) screen which resulted in the identification of a set of interacting proteins, two of which (denoted as ALS-INTERACTING PROTEIN1 and 3 [AIP1 and AIP3, respectively]) were found to be evolutionarily conserved orthologues of bacterial feedback-regulatory proteins and therefore implicated in the regulation of ALS activity. To investigate the molecular role AIPs might play in BCAA synthesis in Arabidopsis thaliana, we examined the functional contribution of aip1 and aip3 knockout alleles to plant patterning and development and BCAA synthesis under various growth conditions. Loss-of-function genetic backgrounds involving these two genes exhibited differential aberrant growth responses in valine-, isoleucine-, and sodium chloride-supplemented media. While BCAA synthesis is believed to be localized to the chloroplast, both AIP1 and AIP3 were found to localize to the peroxisome in addition to the chloroplast. Analysis of free amino acid pools in the mutant backgrounds revealed that they differ in the absolute amount of individual BCAAs accumulated and exhibit elevated levels of BCAAs in leaf tissues. Despite the phenotypic differences observed in aip1 and aip3 backgrounds, functional redundancy between these loci was suggested by the finding that aip1/aip3 double knockout mutants are severely developmentally compromised. CONCLUSIONS Taken together the data suggests that the two regulatory proteins, in conjunction with ALS, have overlapping but distinct functions in BCAA synthesis, and also play a role in pathways unrelated to BCAA synthesis such as sodium-ion homeostasis, extending to broader aspects of patterning and development.
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Affiliation(s)
- Mohammad H. Dezfulian
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
- Present address: Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Curtis Foreman
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Espanta Jalili
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Mrinal Pal
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Rajdeep K. Dhaliwal
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Don Karl A. Roberto
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Kathleen M. Imre
- Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI USA
| | | | - William L. Crosby
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
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Butt H, Eid A, Ali Z, Atia MAM, Mokhtar MM, Hassan N, Lee CM, Bao G, Mahfouz MM. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule. FRONTIERS IN PLANT SCIENCE 2017; 8:1441. [PMID: 28883826 PMCID: PMC5573723 DOI: 10.3389/fpls.2017.01441] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/03/2017] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Agricultural Research CenterGiza, Egypt
| | - Morad M. Mokhtar
- Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Agricultural Research CenterGiza, Egypt
| | - Norhan Hassan
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Ciaran M. Lee
- Department of Bioengineering, Rice University, HoustonTX, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, HoustonTX, United States
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz,
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Liu Y, Li Y, Wang X. Acetohydroxyacid synthases: evolution, structure, and function. Appl Microbiol Biotechnol 2016; 100:8633-49. [DOI: 10.1007/s00253-016-7809-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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Lloyd Evans D, Joshi SV. Elucidating modes of activation and herbicide resistance by sequence assembly and molecular modelling of the Acetolactate synthase complex in sugarcane. J Theor Biol 2016; 407:184-197. [PMID: 27452529 DOI: 10.1016/j.jtbi.2016.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/14/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
Acetolactate synthase (ALS) catalyzes the first portion of the biosynthetic pathway leading to the generation of branched-chain amino acids. As such it is essential for plant health and is a major target for herbicides. ALS is a very poorly characterized molecule in sugarcane. The enzyme is activated and inhibited by a regulatory subunit (known as VAT1 in plants) whose mode of action is entirely unknown. Using Saccharum halepense as a template we have assembled the ALS gene of sugarcane (Saccharum hybrid) and have modelled the structure of ALS based on an Arabidopsis template (the first ALS model for a monocot). We have also assembled the ALS regulatory proteins (VAT1 and VAT2) from sugarcane and show that VAT2 is specific to true grasses. Employing a bacterial model, we have generated a structural model for VAT1, which explains why the separate domains of the proteins bind to either leucine or valine but not both. Using co-evolution studies we have determined molecular contacts by which we modelled the docking of VAT1 to ALS. In conclusion, we demonstrate how the binding of VAT1 to ALS activates ALS and show how VAT1 can also confer feedback inhibition to ALS. We validate our ALS model against biochemical data and employ this model to explain the function of a novel herbicide binding mutant in sugarcane.
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Affiliation(s)
- Dyfed Lloyd Evans
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban 4300, South Africa; School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban 4000, South Africa.
| | - Shailesh Vinay Joshi
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban 4300, South Africa; School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban 4000, South Africa
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Eram MS, Ma K. Pyruvate decarboxylase activity of the acetohydroxyacid synthase of Thermotoga maritima. Biochem Biophys Rep 2016; 7:394-399. [PMID: 28955930 PMCID: PMC5613635 DOI: 10.1016/j.bbrep.2016.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) catalyzes the production of acetolactate from pyruvate. The enzyme from the hyperthermophilic bacterium Thermotoga maritima has been purified and characterized (kcat ~100 s−1). It was found that the same enzyme also had the ability to catalyze the production of acetaldehyde and CO2 from pyruvate, an activity of pyruvate decarboxylase (PDC) at a rate approximately 10% of its AHAS activity. Compared to the catalytic subunit, reconstitution of the individually expressed and purified catalytic and regulatory subunits of the AHAS stimulated both activities of PDC and AHAS. Both activities had similar pH and temperature profiles with an optimal pH of 7.0 and temperature of 85 °C. The enzyme kinetic parameters were determined, however, it showed a non-Michaelis-Menten kinetics for pyruvate only. This is the first report on the PDC activity of an AHAS and the second bifunctional enzyme that might be involved in the production of ethanol from pyruvate in hyperthermophilic microorganisms. The acetohydroxyacid synthase of T. maritima has pyruvate decarboxylase activity The AHAS and PDC activities share the same temperature and pH optima Reconstitution of the catalytic and regulatory subunits increases both PDC and AHAS activities
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Giovannini PP, Bortolini O, Massi A. Thiamine-Diphosphate-Dependent Enzymes as Catalytic Tools for the Asymmetric Benzoin-Type Reaction. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pier Paolo Giovannini
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
| | - Olga Bortolini
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
| | - Alessandro Massi
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
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Li T, Liu B, Chen CY, Yang B. TALEN-Mediated Homologous Recombination Produces Site-Directed DNA Base Change and Herbicide-Resistant Rice. J Genet Genomics 2016; 43:297-305. [PMID: 27180265 DOI: 10.1016/j.jgg.2016.03.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 12/30/2022]
Abstract
Over the last decades, much endeavor has been made to advance genome editing technology due to its promising role in both basic and synthetic biology. The breakthrough has been made in recent years with the advent of sequence-specific endonucleases, especially zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPRs) guided nucleases (e.g., Cas9). In higher eukaryotic organisms, site-directed mutagenesis usually can be achieved through non-homologous end-joining (NHEJ) repair to the DNA double-strand breaks (DSBs) caused by the exogenously applied nucleases. However, site-specific gene replacement or genuine genome editing through homologous recombination (HR) repair to DSBs remains a challenge. As a proof of concept gene replacement through TALEN-based HR in rice (Oryza sativa), we successfully produced double point mutations in rice acetolactate synthase gene (OsALS) and generated herbicide resistant rice lines by using TALENs and donor DNA carrying the desired mutations. After ballistic delivery into rice calli of TALEN construct and donor DNA, nine HR events with different genotypes of OsALS were obtained in T0 generation at the efficiency of 1.4%-6.3% from three experiments. The HR-mediated gene edits were heritable to the progeny of T1 generation. The edited T1 plants were as morphologically normal as the control plants while displayed strong herbicide resistance. The results demonstrate the feasibility of TALEN-mediated genome editing in rice and provide useful information for further genome editing by other nuclease-based genome editing platforms.
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Affiliation(s)
- Ting Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames 50011, USA
| | - Bo Liu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames 50011, USA
| | - Chih Ying Chen
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames 50011, USA
| | - Bing Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames 50011, USA.
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Tang X, Zan X, Zhao L, Chen H, Chen YQ, Chen W, Song Y, Ratledge C. Proteomics analysis of high lipid-producing strain Mucor circinelloides WJ11: an explanation for the mechanism of lipid accumulation at the proteomic level. Microb Cell Fact 2016; 15:35. [PMID: 26867592 PMCID: PMC4750200 DOI: 10.1186/s12934-016-0428-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/19/2016] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The oleaginous fungus, Mucor circinelloides, is attracting considerable interest as it produces oil rich in γ-linolenic acid. Nitrogen (N) deficiency is a common strategy to trigger the lipid accumulation in oleaginous microorganisms. Although a simple pathway from N depletion in the medium to lipid accumulation has been elucidated at the enzymatic level, global changes at protein levels upon N depletion have not been investigated. In this study, we have systematically analyzed the changes at the levels of protein expression in M. circinelloides WJ11, a high lipid-producing strain (36 %, lipid/cell dry weight), during lipid accumulation. RESULTS Proteomic analysis demonstrated that N depletion increased the expression of glutamine synthetase, involved in ammonia assimilation, for the supply of cellular nitrogen but decreased the metabolism of amino acids. Upon N deficiency, many proteins (e.g., fructose-bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, enolase, pyruvate kinase) involved in glycolytic pathway were up-regulated while proteins involved in the tricarboxylic acid cycle (e.g., isocitrate dehydrogenase, succinyl-CoA ligase, succinate dehydrogenase, fumarate hydratase) were down-regulated, indicating this activity was retarded thereby leading to a greater flux of carbon into fatty acid biosynthesis. Moreover, glucose-6-phosphate dehydrogenase, transaldolase and transketolase, which participate in the pentose phosphate pathway, were up-regulated, leading to the increased production of NADPH, the reducing power for fatty acid biosynthesis. Furthermore, protein and nucleic acid metabolism were down-regulated and some proteins involved in energy metabolism, signal transduction, molecular chaperone and redox homeostasis were up-regulated upon N depletion, which may be the cellular response to the stress produced by the onset of N deficiency. CONCLUSION N limitation increased those expressions of the proteins involved in ammonia assimilation but decreased that involved in the biosynthesis of amino acids. Upon N deprivation, the glycolytic pathway was up-regulated, while the activity of the tricarboxylic acid cycle was retarded, thus, leading more carbon flux to fatty acid biosynthesis. Moreover, the pentose phosphate pathway was up-regulated, then this would increase the production of NADPH. Together, coordinated regulation of central carbon metabolism upon N limitation, provides more carbon flux to acetyl-CoA and NADPH for fatty acid biosynthesis.
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Affiliation(s)
- Xin Tang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
| | - Xinyi Zan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
| | - Lina Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
- Synergistic Innovation Center for Food Safety and Nutrition, Wuxi, People's Republic of China.
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
- Synergistic Innovation Center for Food Safety and Nutrition, Wuxi, People's Republic of China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
- Synergistic Innovation Center for Food Safety and Nutrition, Wuxi, People's Republic of China.
| | - Yuanda Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, People's Republic of China.
| | - Colin Ratledge
- Department of Biological Sciences, University of Hull, Hull, UK.
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Doostmohammadi M, Asadollahi MA, Nahvi I, Biria D, Ghezelbash GR, Kheyrandish M. L-phenylacetylcarbinol production by yeast petite mutants. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-015-1190-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Cheng M, Yoshiyasu H, Okano K, Ohtake H, Honda K. Redirection of the Reaction Specificity of a Thermophilic Acetolactate Synthase toward Acetaldehyde Formation. PLoS One 2016; 11:e0146146. [PMID: 26731734 PMCID: PMC4701669 DOI: 10.1371/journal.pone.0146146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/13/2015] [Indexed: 11/18/2022] Open
Abstract
Acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. Although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. In this study, the reaction specificity of acetolactate synthase from Thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxylase. Error-prone PCR and mutant library screening led to the identification of a quadruple mutant with 3.1-fold higher acetaldehyde-forming activity than the wild-type. Site-directed mutagenesis experiments revealed that the increased activity of the mutant was due to H474R amino acid substitution, which likely generated two new hydrogen bonds near the thiamine pyrophosphate-binding site. These hydrogen bonds might result in the better accessibility of H+ to the substrate-cofactor-enzyme intermediate and a shift in the reaction specificity of the enzyme.
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Affiliation(s)
- Maria Cheng
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Hayato Yoshiyasu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Hisao Ohtake
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102–0076, Japan
- * E-mail:
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Doron L, Segal N, Shapira M. Transgene Expression in Microalgae-From Tools to Applications. FRONTIERS IN PLANT SCIENCE 2016; 7:505. [PMID: 27148328 PMCID: PMC4840263 DOI: 10.3389/fpls.2016.00505] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/29/2016] [Indexed: 05/17/2023]
Abstract
Microalgae comprise a biodiverse group of photosynthetic organisms that reside in water sources and sediments. The green microalgae Chlamydomonas reinhardtii was adopted as a useful model organism for studying various physiological systems. Its ability to grow under both photosynthetic and heterotrophic conditions allows efficient growth of non-photosynthetic mutants, making Chlamydomonas a useful genetic tool to study photosynthesis. In addition, this green alga can grow as haploid or diploid cells, similar to yeast, providing a powerful genetic system. As a result, easy and efficient transformation systems have been developed for Chlamydomonas, targeting both the chloroplast and nuclear genomes. Since microalgae comprise a rich repertoire of species that offer variable advantages for biotech and biomed industries, gene transfer technologies were further developed for many microalgae to allow for the expression of foreign proteins of interest. Expressing foreign genes in the chloroplast enables the targeting of foreign DNA to specific sites by homologous recombination. Chloroplast transformation also allows for the introduction of genes encoding several enzymes from a complex pathway, possibly as an operon. Expressing foreign proteins in the chloroplast can also be achieved by introducing the target gene into the nuclear genome, with the protein product bearing a targeting signal that directs import of the transgene-product into the chloroplast, like other endogenous chloroplast proteins. Integration of foreign genes into the nuclear genome is mostly random, resulting in large variability between different clones, such that extensive screening is required. The use of different selection modalities is also described, with special emphasis on the use of herbicides and metabolic markers which are considered to be friendly to the environment, as compared to drug-resistance genes that are commonly used. Finally, despite the development of a wide range of transformation tools and approaches, expression of foreign genes in microalgae suffers from low efficiency. Thus, novel tools have appeared in recent years to deal with this problem. Finally, while C. reinhardtii was traditionally used as a model organism for the development of transformation systems and their subsequent improvement, similar technologies can be adapted for other microalgae that may have higher biotechnological value.
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Kerfah R, Hamelin O, Boisbouvier J, Marion D. CH3-specific NMR assignment of alanine, isoleucine, leucine and valine methyl groups in high molecular weight proteins using a single sample. JOURNAL OF BIOMOLECULAR NMR 2015; 63:389-402. [PMID: 26566791 DOI: 10.1007/s10858-015-9998-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
A new strategy for the NMR assignment of aliphatic side-chains in large perdeuterated proteins is proposed. It involves an alternative isotopic labeling protocol, the use of an out-and-back (13)C-(13)C TOCSY experiment ((H)C-TOCSY-C-TOCSY-(C)H) and an optimized non-uniform sampling protocol. It has long been known that the non-linearity of an aliphatic spin-system (for example Ile, Val, or Leu) substantially compromises the efficiency of the TOCSY transfers. To permit the use of this efficient pulse scheme, a series of optimized precursors were designed to yield linear (13)C perdeuterated side-chains with a single protonated CH3 group in these three residues. These precursors were added to the culture medium for incorporation into expressed proteins. For Val and Leu residues, the topologically different spin-systems introduced for the pro-R and pro-S methyl groups enable stereospecific assignment. All CH3 can be simultaneously assigned on a single sample using a TOCSY experiment. It only requires the tuning of a mixing delay and is thus more versatile than the relayed COSY experiment. Enhanced resolution and sensi-tivity can be achieved by non-uniform sampling combined with the removal of the large JCC coupling by deconvolution prior to the processing by iterative soft thresholding. This strategy has been used on malate synthase G where a large percentage of the CH3 groups could be correlated directly up to the backbone Ca. It is anticipated that this robust combined strategy can be routinely applied to large proteins.
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Affiliation(s)
- Rime Kerfah
- Université Grenoble Alpes, IBS, 38044, Grenoble, France
- CNRS, IBS, 38044, Grenoble, France
- CEA, IBS, 38044, Grenoble, France
| | - Olivier Hamelin
- Chemistry and Biology of Metals Laboratory, University Grenoble Alpes, 38027, Grenoble, France
| | - Jérôme Boisbouvier
- Université Grenoble Alpes, IBS, 38044, Grenoble, France
- CNRS, IBS, 38044, Grenoble, France
- CEA, IBS, 38044, Grenoble, France
| | - Dominique Marion
- Université Grenoble Alpes, IBS, 38044, Grenoble, France.
- CNRS, IBS, 38044, Grenoble, France.
- CEA, IBS, 38044, Grenoble, France.
- Biomolecular NMR Spectroscopy Group, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044, Grenoble Cedex 9, France.
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