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Aliakbari M, Karkhane AA. In vivo cloning of PCR product via site-specific recombination in Escherichia coli. Appl Microbiol Biotechnol 2024; 108:400. [PMID: 38951186 PMCID: PMC11217044 DOI: 10.1007/s00253-024-13239-7] [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: 03/25/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Over the past years, several methods have been developed for gene cloning. Choosing a cloning strategy depends on various factors, among which simplicity and affordability have always been considered. The aim of this study, on the one hand, is to simplify gene cloning by skipping in vitro assembly reactions and, on the other hand, to reduce costs by eliminating relatively expensive materials. We investigated a cloning system using Escherichia coli harboring two plasmids, pLP-AmpR and pScissors-CmR. The pLP-AmpR contains a landing pad (LP) consisting of two genes (λ int and λ gam) that allow the replacement of the transformed linear DNA using site-specific recombination. After the replacement process, the inducible expressing SpCas9 and specific sgRNA from the pScissors-CmR (CRISPR/Cas9) vector leads to the removal of non-recombinant pLP-AmpR plasmids. The function of LP was explored by directly transforming PCR products. The pScissors-CmR plasmid was evaluated for curing three vectors, including the origins of pBR322, p15A, and pSC101. Replacing LP with a PCR product and fast-eradicating pSC101 origin-containing vectors was successful. Recombinant colonies were confirmed following gene replacement and plasmid curing processes. The results made us optimistic that this strategy may potentially be a simple and inexpensive cloning method. KEY POINTS: •The in vivo cloning was performed by replacing the target gene with the landing pad. •Fast eradication of non-recombinant plasmids was possible by adapting key vectors. •This strategy is not dependent on in vitro assembly reactions and expensive materials.
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Affiliation(s)
- Moein Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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2
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Kaur H, Kalia A, Manchanda P, Singh A. Nano-delivery platforms for bacterial gene transformation: suitability and challenges. Int Microbiol 2024:10.1007/s10123-024-00543-5. [PMID: 38902555 DOI: 10.1007/s10123-024-00543-5] [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: 11/14/2023] [Revised: 05/19/2024] [Accepted: 06/02/2024] [Indexed: 06/22/2024]
Abstract
Nano-scale particles (NPs) have gained increased interest as non-viral vectors for nucleic acid delivery due to their ability to penetrate through unabraded cell membranes. The previous studies performed have evaluated the nanomaterials for their microbial transformation proficiency but have not compared the relative efficacy. The present study aims to identify the most proficient nano-delivery vehicle among the chemically synthesized/functionalized non-metal oxide, metal/metal oxide, and carbon-based (carbon nanotube (CNT), graphene oxide (GO)) nanomaterial(s) (NMs) for the transformation of two gram-negative bacteria, i.e., Escherichia coli and Agrobacterium tumefaciens. The microscopy and spectroscopy studies helped to identify the interaction, adhesion patterns, transformation efficiencies, better delivery, and expression of the target gfp gene by use of NMs. Loading of pgfp on all NMs imparted protection to DNAse I attack except ZnO NPs with maximum by chitosan, layered double hydroxide (LDH), and GO NM-plasmid DNA conjugates. The CNTs and GO significantly enhanced the extra- and intra-cellular protein content, respectively, in both bacteria. However, GO and CNT significantly decreased the cell viability in a time-dependent manner while AuNPs exhibited negligible cell toxicity. Therefore, this study identified the comparative efficiency of metal/metal oxide, non-metal oxide, and carbon nanomaterials with AuNPs as the most biosafe while LDH and chitosan NPs being the most proficient alternative tools for the genetic transformation of gram-negative bacteria by simple incubation method.
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Affiliation(s)
- Harkamal Kaur
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Alla Singh
- ICAR-Indian Institute of Maize Research, PAU Campus, PAU, Ludhiana, Punjab, 141004, India
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3
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Lutz-Wahl S, Mozer H, Kussler A, Schulz A, Seitl I, Fischer L. A new β-galactosidase from Paenibacillus wynnii with potential for industrial applications. J Dairy Sci 2024; 107:3429-3442. [PMID: 38246536 DOI: 10.3168/jds.2023-24122] [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: 08/24/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
Commercial β-galactosidases exhibit undesirable kinetic properties regarding substrate affinity (Michaelis-Menten constant [KM] for lactose) and product inhibition (inhibitor constant [Ki] for galactose). An in silico screening of gene sequences was done and identified a putative β-galactosidase (Paenibacillus wynnii β-galactosidase, BgaPw) from the psychrophilic bacterium Paenibacillus wynnii. The cultivation of the wild-type P. wynnii strain resulted in very low β-galactosidase activities of a maximum of 150 nkat per liter of medium with o-nitrophenyl-β-d-galactopyranoside (oNPGal) as substrate. The recombinant production of BgaPw in Escherichia coli BL21(DE3) increased the yield ∼9,000-fold. Here, a volumetric activity of 1,350.18 ± 11.82 μkatoNPGal/Lculture was achieved in a bioreactor cultivation. The partly purified BgaPw showed a pH optimum at 7.0, a temperature maximum at 40°C, and an excellent stability at 8°C with a half-life of 77 d. Kinetic studies with BgaPw were done in milk or in milk-imitating synthetic buffer (Novo buffer), respectively. Remarkably, the KM value of BgaPw with lactose was as low as 0.63 ± 0.045 mM in milk. It was found that the resulting products of lactose hydrolysis, namely galactose and glucose, did not inhibit the β-galactosidase activity of BgaPw, but instead showed a striking activating effect in both cases (up to 144%). In a comparison study in milk, lactose was completely hydrolyzed by BgaPw in 72 h at 8°C, whereas 2 other known β-galactosidases were less powerful and converted only about 90% of lactose in the same time. Finally, the formation of galactooligosaccharides (GOS) was demonstrated with the new BgaPw, starting with pharma-lactose (400 g/L). A GOS production of about 144 g/L was achieved after 24 h (36.0% yield).
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Affiliation(s)
- Sabine Lutz-Wahl
- Department of Biotechnology and Enzyme Science, Institute for Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Hanna Mozer
- Department of Biotechnology and Enzyme Science, Institute for Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Alena Kussler
- Department of Biotechnology and Enzyme Science, Institute for Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Adriana Schulz
- Department of Biotechnology and Enzyme Science, Institute for Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Ines Seitl
- Department of Biotechnology and Enzyme Science, Institute for Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Lutz Fischer
- Department of Biotechnology and Enzyme Science, Institute for Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany.
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Jacobus AP, Cavassana SD, de Oliveira II, Barreto JA, Rohwedder E, Frazzon J, Basso TP, Basso LC, Gross J. Optimal trade-off between boosted tolerance and growth fitness during adaptive evolution of yeast to ethanol shocks. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:63. [PMID: 38730312 PMCID: PMC11088041 DOI: 10.1186/s13068-024-02503-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND The selection of Saccharomyces cerevisiae strains with higher alcohol tolerance can potentially increase the industrial production of ethanol fuel. However, the design of selection protocols to obtain bioethanol yeasts with higher alcohol tolerance poses the challenge of improving industrial strains that are already robust to high ethanol levels. Furthermore, yeasts subjected to mutagenesis and selection, or laboratory evolution, often present adaptation trade-offs wherein higher stress tolerance is attained at the expense of growth and fermentation performance. Although these undesirable side effects are often associated with acute selection regimes, the utility of using harsh ethanol treatments to obtain robust ethanologenic yeasts still has not been fully investigated. RESULTS We conducted an adaptive laboratory evolution by challenging four populations (P1-P4) of the Brazilian bioethanol yeast, Saccharomyces cerevisiae PE-2_H4, through 68-82 cycles of 2-h ethanol shocks (19-30% v/v) and outgrowths. Colonies isolated from the final evolved populations (P1c-P4c) were subjected to whole-genome sequencing, revealing mutations in genes enriched for the cAMP/PKA and trehalose degradation pathways. Fitness analyses of the isolated clones P1c-P3c and reverse-engineered strains demonstrated that mutations were primarily selected for cell viability under ethanol stress, at the cost of decreased growth rates in cultures with or without ethanol. Under this selection regime for stress survival, the population P4 evolved a protective snowflake phenotype resulting from BUD3 disruption. Despite marked adaptation trade-offs, the combination of reverse-engineered mutations cyr1A1474T/usv1Δ conferred 5.46% higher fitness than the parental PE-2_H4 for propagation in 8% (v/v) ethanol, with only a 1.07% fitness cost in a culture medium without alcohol. The cyr1A1474T/usv1Δ strain and evolved P1c displayed robust fermentations of sugarcane molasses using cell recycling and sulfuric acid treatments, mimicking Brazilian bioethanol production. CONCLUSIONS Our study combined genomic, mutational, and fitness analyses to understand the genetic underpinnings of yeast evolution to ethanol shocks. Although fitness analyses revealed that most evolved mutations impose a cost for cell propagation, combination of key mutations cyr1A1474T/usv1Δ endowed yeasts with higher tolerance for growth in the presence of ethanol. Moreover, alleles selected for acute stress survival comprising the P1c genotype conferred stress tolerance and optimal performance under conditions simulating the Brazilian industrial ethanol production.
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Affiliation(s)
- Ana Paula Jacobus
- Bioenergy Research Institute, São Paulo State University, Rio Claro, Brazil
- SENAI Innovation Institute for Biotechnology, São Paulo, Brazil
| | | | | | | | - Ewerton Rohwedder
- Biological Science Department, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Jeverson Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Thalita Peixoto Basso
- Department of Agri-Food Industry, Food and Nutrition, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Luiz Carlos Basso
- Biological Science Department, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Jeferson Gross
- Bioenergy Research Institute, São Paulo State University, Rio Claro, Brazil.
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Jahn A, Petersen M. Hydroxy(phenyl)pyruvic acid reductase in Actaea racemosa L.: a putative enzyme in cimicifugic and fukinolic acid biosynthesis. PLANTA 2024; 259:102. [PMID: 38549005 PMCID: PMC10978636 DOI: 10.1007/s00425-024-04382-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024]
Abstract
MAIN CONCLUSION Hydroxy(phenyl)pyruvic acid reductase from Actaea racemosa catalyzes dual reactions in reducing 4-hydroxyphenylpyruvic acid as well as β-hydroxypyruvic acid. It thus qualifies to be part of fukinolic and cimicifugic acid biosynthesis and also photorespiration. The accumulation of fukinolic acid and cimicifugic acids is mainly restricted to Actaea racemosa (Ranunculaceae) and other species of the genus Actaea/Cimicifuga. Cimicifugic and fukinolic acids are composed of a hydroxycinnamic acid part esterified with a benzyltartaric acid moiety. The biosynthesis of the latter is unclear. We isolated cDNA encoding a hydroxy(phenyl)pyruvic acid reductase (GenBank OR393286) from suspension-cultured material of A. racemosa (ArH(P)PR) and expressed it in E. coli for protein production. The heterologously synthesized enzyme had a mass of 36.51 kDa and catalyzed the NAD(P)H-dependent reduction of 4-hydroxyphenylpyruvic acid to 4-hydroxyphenyllactic acid or β-hydroxypyruvic acid to glyceric acid, respectively. The optimal temperature was at 38 °C and the pH optimum at pH 7.5. NADPH is the preferred cosubstrate (Km 23 ± 4 µM). Several substrates are accepted by ArH(P)PR with β-hydroxypyruvic acid (Km 0.26 ± 0.12 mM) followed by 4-hydroxyphenylpyruvic acid (Km 1.13 ± 0.12 mM) as the best ones. Thus, ArH(P)PR has properties of β-hydroxypyruvic acid reductase (involved in photorespiration) as well as hydroxyphenylpyruvic acid reductase (possibly involved in benzyltartaric acid formation).
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Affiliation(s)
- Anne Jahn
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Maike Petersen
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany.
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Woodruff AL, Berman J, Anderson M. Strain background of Candida albicans interacts with SIR2 to alter phenotypic switching. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001444. [PMID: 38446018 PMCID: PMC10999749 DOI: 10.1099/mic.0.001444] [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: 09/22/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
The genetic background between strains of a single species and within a single strain lineage can significantly impact the expression of biological traits. This genetic variation may also reshape epigenetic mechanisms of cell identity and environmental responses that are controlled by interconnected transcriptional networks and chromatin-modifying enzymes. Histone deacetylases, including sirtuins, are critical regulators of chromatin state and have been directly implicated in governing the phenotypic transition between the 'sterile' white state and the mating-competent opaque state in Candida albicans, a common fungal commensal and pathogen of humans. Here, we found that a previously ambiguous role for the sirtuin SIR2 in C. albicans phenotypic switching is likely linked to the genetic background of mutant strains produced in the RM lineage of SC5314. SIR2 mutants in a specific lineage of BWP17 displayed increased frequencies of switching to the opaque state compared to the wild-type. Loss of SIR2 in other SC5314-derived backgrounds, including newly constructed BWP17 sir2Δ/Δ mutants, failed to recapitulate the increased white-opaque switching frequencies observed in the original BWP17 sir2Δ/Δ mutant background. Whole-genome sequencing revealed the presence of multiple imbalanced chromosomes and large loss of heterozygosity tracts that likely interact with SIR2 to increase phenotypic switching in this BWP17 sir2Δ/Δ mutant lineage. These genomic changes are not found in other SC5314-derived sir2Δ/Δ mutants that do not display increased opaque cell formation. Thus, complex karyotypes can emerge during strain construction that modify mutant phenotypes and highlight the importance of validating strain background when interpreting phenotypes.
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Affiliation(s)
- Andrew L. Woodruff
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Matthew Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin – Madison, Madison, WI, 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin – Madison, Madison, WI, 53706, USA
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Maloney A, Joseph S. Validating the EMCV IRES Secondary Structure with Structure-Function Analysis. Biochemistry 2024; 63:107-115. [PMID: 38081770 PMCID: PMC10896073 DOI: 10.1021/acs.biochem.3c00579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The encephalomyocarditis virus internal ribosome entry site (EMCV IRES) is a structured RNA sequence found in the 5' UTR of the genomic RNA of the encephalomyocarditis virus. The EMCV IRES structure facilitates efficient translation initiation without needing a 5' m7G cap or the cap-binding protein eIF4E. The secondary structure of IRES has been the subject of several previous studies, and a number of different structural models have been proposed. Though some domains of the IRES are conserved across the different secondary structure models, domain I of the IRES varies greatly across them. A literature comparison led to the identification of three regions of interest that display structural heterogeneity within past secondary structure models. To test the accuracy of the secondary structure models in these regions, we employed mutational analysis and SHAPE probing. Mutational analysis revealed that two helical regions within the identified regions of interest are important for IRES translation. These helical regions are consistent with only one of the structure predictions in the literature and do not form in EMCV IRES structures predicted using modern secondary structure prediction methods. The importance of these regions is further supported by multiple SHAPE protections when probing was performed after in vitro translation, indicating that these regions are involved in the IRES translation complex. This work validates a published structure and demonstrates the importance of domain I during EMCV IRES translation initiation.
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Affiliation(s)
- Adam Maloney
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314, United States
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314, United States
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Guo L, Yang G. Pioneering DNA assembling techniques and their applications in eukaryotic microalgae. Biotechnol Adv 2024; 70:108301. [PMID: 38101551 DOI: 10.1016/j.biotechadv.2023.108301] [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: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.
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Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China; Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; MoE Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China.
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Stierle SA, Harken L, Li SM. P450 in C-C coupling of cyclodipeptides with nucleobases. Methods Enzymol 2023; 693:231-265. [PMID: 37977732 DOI: 10.1016/bs.mie.2023.09.012] [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] [Indexed: 11/19/2023]
Abstract
Bacterial cytochrome P450 enzymes catalyze various and often intriguing tailoring reactions during the biosynthesis of natural products. In contrast to the majority of membrane-bound P450 enzymes from eukaryotes, bacterial P450 enzymes are soluble proteins and therefore represent excellent candidates for in vitro biochemical investigations. In particular, cyclodipeptide synthase-associated cytochrome P450 enzymes have recently gained attention due to the broad spectrum of reactions they catalyze, i.e. hydroxylation, aromatization, intramolecular C-C bond formation, dimerization, and nucleobase addition. The latter reaction has been described during the biosynthesis of guanitrypmycins, guatrypmethines and guatyromycines in various Streptomyces strains, where the nucleobases guanine and hypoxanthine are coupled to cyclodipeptides via C-C, C-N, and C-O bonds. In this chapter, we provide an overview of cytochrome P450 enzymes involved in the C-C coupling of cyclodipeptides with nucleobases and describe the protocols used for the successful characterization of these enzymes in our laboratory. The procedure includes cloning of the respective genes into expression vectors and subsequent overproduction of the corresponding proteins in E. coli as well as heterologous expression in Streptomyces. We describe the purification and in vitro biochemical characterization of the enzymes and protocols to isolate the produced compounds for structure elucidation.
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Affiliation(s)
- Sina A Stierle
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Marburg, Germany
| | - Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Marburg, Germany.
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Jadid N, Rosidah NLA, Ramadani MRN, Prasetyowati I, Sa’adah NN, Widodo AF, Oktafitria D. Plastid DNA Barcoding and RtActin cDNA Fragment Isolation of Reutealis Trisperma: A Promising Bioresource for Biodiesel Production. Bioinform Biol Insights 2023; 17:11779322231182768. [PMID: 37360051 PMCID: PMC10286179 DOI: 10.1177/11779322231182768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Reutealis trisperma belonging to the family Euphorbiaceae is currently used for biodiesel production, and rapid development in plant-based biofuel production has led to its increasing demand. However, massive utilization of bio-industrial plants has led to conservation issues. Moreover, genetic information on R trisperma is still limited, which is crucial for developmental, physiological, and molecular studies. Studying gene expression is essential to explain plant physiological processes. Nonetheless, this technique requires sensitive and precise measurement of messenger RNA (mRNA). In addition, the presence of internal control genes is important to avoid bias. Therefore, collecting and preserving genetic data for R trisperma is indispensable. In this study, we aimed to evaluate the application of plastid loci, rbcL, and matK, to the DNA barcode of R trisperma for use in conservation programs. In addition, we isolated and cloned the RtActin (RtACT) gene fragment for use in gene expression studies. Sequence information was analyzed in silico by comparison with other Euphorbiaceae plants. For actin fragment isolation, reverse-transcription polymerase chain reaction was used. Molecular cloning of RtActin was performed using the pTA2 plasmid before sequencing. We successfully isolated and cloned 592 and 840 bp of RtrbcL and RtmatK fragment genes, respectively. The RtrbcL barcoding marker, rather than the RtmatK plastidial marker, provided discriminative molecular phylogenetic data for R Trisperma. We also isolated 986 bp of RtACT gene fragments. Our phylogenetic analysis demonstrated that R trisperma is closely related to the Vernicia fordii Actin gene (97% identity). Our results suggest that RtrbcL could be further developed and used as a barcoding marker for R trisperma. Moreover, the RtACT gene could be further investigated for use in gene expression studies of plant.
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Affiliation(s)
- Nurul Jadid
- Department of Biology, Institut Teknologi Sepuluh Nopember (ITS), Surabaya, Indonesia
| | | | | | - Indah Prasetyowati
- Department of Biology, Institut Teknologi Sepuluh Nopember (ITS), Surabaya, Indonesia
| | - Noor Nailis Sa’adah
- Department of Biology, Institut Teknologi Sepuluh Nopember (ITS), Surabaya, Indonesia
| | | | - Dwi Oktafitria
- Department of Biology, Universitas PGRI Ronggolawe, Tuban, Indonesia
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11
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Matsuyama A, Hashimoto A, Nishimura S, Yoshida M. A set of vectors and strains for chromosomal integration in fission yeast. Sci Rep 2023; 13:9295. [PMID: 37291244 PMCID: PMC10250367 DOI: 10.1038/s41598-023-36267-1] [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: 02/03/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
The expression of heterologous genes is an important technique in yeast genetics. In fission yeast, the leu1 and ura4 genes have been used mainly as selectable markers for heterologous expression. To expand the repertoire of selection markers available for heterologous expression of genes, here we developed new host-vector systems employing lys1 and arg3. By employing genome editing with the CRISPR/Cas9 system, we isolated several alleles of lys1 and arg3, each having a critical mutation in the ORF region. In parallel, we developed a set of vectors that complement the amino acid auxotrophy of lys1 and arg3 mutants when integrated into each locus. Using these vectors in combination with the previously developed integration vector pDUAL, we successfully observed the localization of three proteins in a cell simultaneously by fusing them with different fluorescent proteins. Thus, these vectors enable combinatorial expression of heterologous genes, which addresses increasingly diverse experimental challenges.
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Affiliation(s)
- Akihisa Matsuyama
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan.
- Laboratory of Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Atsushi Hashimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinichi Nishimura
- Laboratory of Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
- Laboratory of Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
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12
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Gyurkovska V, Murtazina R, Zhao SF, Shikano S, Okamoto Y, Segev N. Dual function of Rab1A in secretion and autophagy: hypervariable domain dependence. Life Sci Alliance 2023; 6:e202201810. [PMID: 36781179 PMCID: PMC9939007 DOI: 10.26508/lsa.202201810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
We currently understand how the different intracellular pathways, secretion, endocytosis, and autophagy are regulated by small GTPases. In contrast, it is unclear how these pathways are coordinated to ensure efficient cellular response to stress. Rab GTPases localize to specific organelles through their hypervariable domain (HVD) to regulate discrete steps of individual pathways. Here, we explored the dual role of Rab1A/B (92% identity) in secretion and autophagy. We show that although either Rab1A or Rab1B is required for secretion, Rab1A, but not Rab1B, localizes to autophagosomes and is required early in stress-induced autophagy. Moreover, replacing the HVD of Rab1B with that of Rab1A enables Rab1B to localize to autophagosomes and regulate autophagy. Therefore, Rab1A-HVD is required for the dual functionality of a single Rab in two different pathways: secretion and autophagy. In addition to this mechanistic insight, these findings are relevant to human health because both the pathways and Rab1A/B were implicated in diseases ranging from cancer to neurodegeneration.
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Affiliation(s)
- Valeriya Gyurkovska
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Rakhilya Murtazina
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sarah F Zhao
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sojin Shikano
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Yukari Okamoto
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
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13
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Zhang ZX, Li ZH, Li SM. Formation of the Fungal Indole Alkaloid Speradine F Implies Multiple Nonenzymatic Oxidation Steps. JOURNAL OF NATURAL PRODUCTS 2023; 86:1053-1060. [PMID: 37043818 DOI: 10.1021/acs.jnatprod.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The highly oxygenated indole alkaloid speradine F (4) with a 6/5/6/5/5/5 hexacyclic skeleton was isolated from a culture of Penicillium palitans, together with its precursors β-cyclopiazonic acid (β-CPA, 5) and cyclopiazonic acid (CPA, 1). Gene deletion and heterologous expression led to the identification of the responsible five-gene spe cluster for the speradine skeleton formation. Precursor supply experiments proved that 1 was enzymatically converted, via 2-oxoCPA (2), to speradine A (3), which subsequently undergoes multistep nonenzymatic hydroxylations to 4.
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Affiliation(s)
- Zheng-Xi Zhang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Zhang-Hai Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
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14
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Alves J, Sousa-Silva M, Soares P, Sauer M, Casal M, Soares-Silva I. Structural characterization of the Aspergillus niger citrate transporter CexA uncovers the role of key residues S75, R192 and Q196. Comput Struct Biotechnol J 2023; 21:2884-2898. [PMID: 37216016 PMCID: PMC10196274 DOI: 10.1016/j.csbj.2023.04.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
The Aspergillus niger CexA transporter belongs to the DHA1 (Drug-H+ antiporter) family. CexA homologs are exclusively found in eukaryotic genomes, and CexA is the sole citrate exporter to have been functionally characterized in this family so far. In the present work, we expressed CexA in Saccharomyces cerevisiae, demonstrating its ability to bind isocitric acid, and import citrate at pH 5.5 with low affinity. Citrate uptake was independent of the proton motive force and compatible with a facilitated diffusion mechanism. To unravel the structural features of this transporter, we then targeted 21 CexA residues for site-directed mutagenesis. Residues were identified by a combination of amino acid residue conservation among the DHA1 family, 3D structure prediction, and substrate molecular docking analysis. S. cerevisiae cells expressing this library of CexA mutant alleles were evaluated for their capacity to grow on carboxylic acid-containing media and transport of radiolabeled citrate. We also determined protein subcellular localization by GFP tagging, with seven amino acid substitutions affecting CexA protein expression at the plasma membrane. The substitutions P200A, Y307A, S315A, and R461A displayed loss-of-function phenotypes. The majority of the substitutions affected citrate binding and translocation. The S75 residue had no impact on citrate export but affected its import, as the substitution for alanine increased the affinity of the transporter for citrate. Conversely, expression of CexA mutant alleles in the Yarrowia lipolytica cex1Δ strain revealed the involvement of R192 and Q196 residues in citrate export. Globally, we uncovered a set of relevant amino acid residues involved in CexA expression, export capacity and import affinity.
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Affiliation(s)
- J. Alves
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M. Sousa-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - P. Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M. Sauer
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - M. Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - I. Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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15
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Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023; 51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
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Affiliation(s)
- Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Karol Kaszuba
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Monika Gaik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Paulina Indyka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | | | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Alexander Hammermeister
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Sebastian Glatt
- To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902;
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16
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Arroyo-Urea S, Watson JF, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. Methods Mol Biol 2023; 2633:33-44. [PMID: 36853454 DOI: 10.1007/978-1-0716-3004-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.
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Affiliation(s)
- Sandra Arroyo-Urea
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain
| | | | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain.
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17
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Nozaki S. Rapid and Accurate Assembly of Large DNA Assisted by In Vitro Packaging of Bacteriophage. ACS Synth Biol 2022; 11:4113-4122. [PMID: 36446634 PMCID: PMC9764419 DOI: 10.1021/acssynbio.2c00419] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Development of DNA assembly methods made it possible to construct large DNA. However, achieving a large DNA assembly easily, accurately, and at a low cost remains a challenge. This study shows that DNA assembled only by annealing of overlapping single-stranded DNA ends, which are generated by exonuclease treatment, without ligation can be packaged in phage particles and can also be transduced into bacterial cells. Based on this, I developed a simple method to construct long DNA of about 40-50 kb from five to ten PCR fragments using the bacteriophage in vitro packaging system. This method, namely, iPac (in vitro Packaging-assisted DNA assembly), allowed accurate and rapid construction of large plasmids and phage genomes. This simple method will accelerate research in molecular and synthetic biology, including the construction of gene circuits or the engineering of metabolic pathways.
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Affiliation(s)
- Shingo Nozaki
- Department
of Life Science, College of Science, Rikkyo
University, Tokyo 171-8501, Japan,Graduate
School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8527, Japan,
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18
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Jacobus AP, Barreto JA, de Bem LS, Menegon YA, Fier Í, Bueno JGR, Dos Santos LV, Gross J. EasyGuide Plasmids Support in Vivo Assembly of gRNAs for CRISPR/Cas9 Applications in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:3886-3891. [PMID: 36257021 DOI: 10.1021/acssynbio.2c00348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Most CRISPR/Cas9 applications in yeast rely on a plasmid-based expression of Cas9 and its guide RNA (gRNA) containing a 20-nucleotides (nts) spacer tailored to each genomic target. The lengthy assembly of this customized gRNA requires at least 3-5 days for its precloning in Escherichia coli, purification, validation, and cotransformation with Cas9 into a yeast strain. Here, we constructed a series of 12 EasyGuide plasmids to simplify CRISPR/Cas9 applications in Saccharomyces cerevisiae. The new vectors provide templates for generating PCR fragments that can assemble up to six functional gRNAs directly into yeasts via homologous recombination between the 20-nts spacers. By dispensing precloning in E. coli, yeast in vivo gRNA assembly significantly reduces the CRISPR/Cas9 experimental workload. A highly efficient yeast genome editing procedure, involving PCR amplification of gRNAs and donors, followed by their transformation into a Cas9-expressing strain, can be easily accomplished through a quick protocol.
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Affiliation(s)
- Ana P Jacobus
- Institute for Bioenergy Research, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
- Ph.D. Program in Bioenergy, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas 13083-970, Brazil
| | - Joneclei A Barreto
- Institute for Bioenergy Research, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
- Ph.D. Program in Bioenergy, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
| | - Lucas S de Bem
- Institute for Bioenergy Research, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas 13083-970, Brazil
| | - Yasmine A Menegon
- Institute for Bioenergy Research, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
- Ph.D. Program in Bioenergy, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
| | - Ícaro Fier
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas 13083-970, Brazil
| | - João G R Bueno
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas 13083-970, Brazil
| | - Leandro V Dos Santos
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas 13083-970, Brazil
- SENAI Innovation Institute for Biotechnology, São Paulo 01130-000, Brazil
| | - Jeferson Gross
- Institute for Bioenergy Research, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
- Ph.D. Program in Bioenergy, Sao Paulo State University, Rio Claro 13500-230, São Paulo, Brazil
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19
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For biotechnological applications: Purification and characterization of recombinant and nanoconjugated xylanase enzyme from thermophilic Bacillus subtilis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Tan SA, Yam HC, Cheong SL, Chow YC, Bok CY, Ho JM, Lee PY, Gunasekaran B. Inhibition of Porphyromonas gingivalis peptidyl arginine deiminase, a virulence factor, by antioxidant-rich Cratoxylum cochinchinense: In vitro and in silico evaluation. Saudi J Biol Sci 2022; 29:2573-2581. [PMID: 35531186 PMCID: PMC9073004 DOI: 10.1016/j.sjbs.2021.12.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 01/03/2023] Open
Abstract
Porphyromonas gingivalis, the cause of periodontitis, is also linked to many systemic disorders due to its citrullination capability from a unique peptidyl arginine deiminase (PPAD). Protein citrullination is able to trigger an autoimmune response, increasing the severity of rheumatoid arthritis. The main objective of this study is to evaluate the inhibitory activity of Cratoxylym cochinchinense leaves extract towards the PPAD in vitro and in silico. Methanolic extract of Cratoxylum cochinchinense (CCM) was tested for total phenolic and flavonoid contents along with antioxidative assays. Inhibition of PPAD activities was conducted thereafter using recombinant PPAD in cell lysate. Phytocompounds postulated present in the CCM such as mangiferin, vismiaquinone A, δ-tocotrienol and α-tocotrienol and canophyllol were used as ligands in a simulated docking study against PPAD. Results obtained indicated high antioxidant potential in CCM while recording abundant phenolic (129.0 ± 2.5495 mg GA/g crude extract) and flavonoid (159.0 ± 2.1529 mg QE/g crude extract) contents. A dose-dependent inhibition of PPAD was observed when CCM was evaluated at various concentrations. CCM at 1 mg/mL exhibited citrulline concentration of 24.37 ± 3.25 mM which was 5 times lower than the negative control (114.23 ± 3.31 mM). Molecular docking simulation revealed that mangiferin and vismiaquinone A engaged in H-bonding and pi-pi interactions with important active site residues (Asp130, Arg152, Arg154 and Trp127) of PPAD and could be the potential phytochemicals that accounted for the inhibitory activities observed in the methanolic leaves extract. As such, CCM could be further explored for its therapeutic properties not only for periodontitis, but also for other systemic diseases like rheumatoid arthritis.
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Key Words
- ABTS, 2,2′-Azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt
- ACPA, Anti-citrullinated peptide antibodies
- Anti-citrullination
- BAEE, Benzoyl-L-arginine ethyl ester
- Cratoxylum cochinchinense
- DNA, Deoxyribonucleic acid
- DPPH, 2,2-diphenyl-1-picrylhydrazyl
- DTT, Dithiothreitol
- EDTA, Ethylenediamine tetraacetic acid
- FRAP, Ferric reducing antioxidant power
- GAE, Gallic acid equivalence
- HPLC, High performance liquid chromatography
- IPTG, Isopropyl β- d-1-thiogalactopyranoside
- Mangiferin
- OPLS, Optimized potentials for liquid simulations
- PAD, Peptidylarginine deiminase
- PCR, Polymerase chain reaction
- PDB, Protein data bank
- PMSF, Phenylmethylsulfonyl fluoride
- PPAD, Porphyromonas gingivalis peptidylarginine deiminase
- Peptidyl arginine deiminase
- Porphyromonas gingivalis
- QE, Quercetin equivalence
- RA, Rheumatoid arthritis
- SD, Standard deviation
- SDS-PAGE, Sodium dodecyl sulphate–polyacrylamide gel electrophoresis
- TFC, Total flavonoid content
- TPC, Total phenolic content
- TPTZ, 2,4,6-Tripyridyl-S-triazine
- Vismiaquinone A
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Affiliation(s)
- Sheri-Ann Tan
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur, Malaysia
| | - Hok Chai Yam
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Siew Lee Cheong
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, 57000 Bukit Jalil, Kuala Lumpur, Malaysia
| | - Yoke Chan Chow
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur, Malaysia
| | - Chui Yin Bok
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur, Malaysia
| | - Jia Min Ho
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur, Malaysia
| | - Pei Yin Lee
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Baskaran Gunasekaran
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia
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21
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Good NM, Lee HD, Hawker ER, Su MZ, Gilad AA, Martinez-Gomez NC. Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy. Front Microbiol 2022; 13:820327. [PMID: 35369483 PMCID: PMC8969499 DOI: 10.3389/fmicb.2022.820327] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Lanthanides (Ln) are a new group of life metals, and many questions remain regarding how they are acquired and used in biology. Methylotrophic bacteria can acquire, transport, biomineralize, and use Ln as part of a cofactor complex with pyrroloquinoline quinone (PQQ) in alcohol dehydrogenases. For most methylotrophic bacteria use is restricted to the light Ln, which range from lanthanum to samarium (atomic numbers 57–62). Understanding how the cell differentiates between light and heavy Ln, and the impacts of these metals on the metabolic network, will advance the field of Ln biochemistry and give insights into enzyme catalysis, stress homeostasis, and metal biomineralization and compartmentalization. We report robust methanol growth with the heavy Ln gadolinium by a genetic variant of the model methylotrophic bacterium Methylorubrum extorquens AM1, named evo-HLn, for “evolved for Heavy Lanthanides.” A non-synonymous single nucleotide polymorphism in a cytosolic hybrid histidine kinase/response regulator allowed for sweeping transcriptional alterations to heavy metal stress response, methanol oxidation, and central metabolism. Increased expression of genes for Ln acquisition and uptake, production of the Ln-chelating lanthanophore, PQQ biosynthesis, and phosphate transport and metabolism resulted in gadolinium hyperaccumulation of 36-fold with a trade-off for light Ln accumulation. Gadolinium was hyperaccumulated in an enlarged acidocalcisome-like compartment. This is the first evidence of a bacterial intracellular Ln-containing compartment that we name the “lanthasome.” Carotenoid and toblerol biosynthesis were also upregulated. Due to its unique capabilities, evo-HLn can be used to further magnetic resonance imaging (MRI) and bioremediation technologies. In this regard, we show that gadolinium hyperaccumulation was sufficient to produce MRI contrast in whole cells, and that evo-HLn was able to readily acquire the metal from the MRI contrast agent gadopentetic acid. Finally, hyperaccumulation of gadolinium, differential uptake of light and heavy Ln, increased PQQ levels, and phosphate transport provide new insights into strategies for Ln recovery.
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Affiliation(s)
- Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Harvey D. Lee
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
| | - Emily R. Hawker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Morgan Z. Su
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Assaf A. Gilad
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - N. Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: N. Cecilia Martinez-Gomez,
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Vo-Nguyen HV, Nguyen TT, Mai QG, Tran TT, Tran TL, Tran-Van H. Recombinase-free cloning (RFC) protocol for gene swapping. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2022; 11:21-27. [PMID: 35463820 PMCID: PMC9012429 DOI: 10.22099/mbrc.2021.41923.1685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recombinant DNA technology has been playing the key role for a long time since its first beginning. DNA ligases have certainly contributed to the development of cloning techniques, as well as molecular study up to now. Despite being a prime cloning tool, DNA ligases still face some shortcomings which lead to their limit of use. Our study provided an improved method that simplified the basic restriction enzyme-based cloning (REC) by eliminating the ligation role, named recombinase-free cloning (RFC). This improved technique was designed with only one PCR reaction, one digestion reaction, and one temperature profile, which takes advantage of endogenous recombinase in E. coli host to create the target recombinant vector inside the cell. All purification steps were eliminated for effectively material- and time-saving. Five different clones were generated by RFC. This method showed relatively low efficiency yet successful at a range of 100% in every conducted trial with fragment sizes from 0.5-1.0 kbp. The RFC method could be completed within a day (about 9 hours), without the need of ligase or recombinase or purification steps, which significantly saved DNA components, materials as well as the time required. In conclusion, we expected to provide a more convenient cloning method, as well as enable faster generation of DNA clones, which would be well applied in the less equipped laboratories.
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Affiliation(s)
- Hai-Vy Vo-Nguyen
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thanh-Tan Nguyen
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Quoc-Gia Mai
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thien-Thien Tran
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thuoc Linh Tran
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hieu Tran-Van
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam,Corresponding Author: Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam, Tel: +8428 62884499; Fax: +8428 38350096. E. mail:
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Wang TN, Hu XG, Chen GX. Uses of knockout, knockdown, and transgenic models in the studies of glucose transporter 4. World J Meta-Anal 2022; 10:1-11. [DOI: 10.13105/wjma.v10.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/10/2021] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Currently, glucose transporter 4 (GLUT4) has been considered as the key player for the insulin-stimulated glucose transport in the muscle and adipose tissues. The development of recombinant DNA techniques allows the creations of genetically knockout, knockdown and transgenic animals and cells for the study of GLUT4’s physiological functions. Here, we have used key words to search the PubMed and summarized the methods used in Slc2a4 gene knockout, GLUT4 knockdown and overexpression in the whole body and tissue specific manner. The whole body GLUT4-null mice have growth retardation, but normal glucose tolerance and basal glucose turnover rates. Compared with whole body Slc2a4 knockout mice, adipose and muscle double knockout mice have impaired insulin tolerance and glucose intolerance. The results of GLUT4 knockdown in 3T3-L1 adipocytes have shown that its expression is needed for lipogenesis after, but not during, differentiation. Transgenic mice with the whole body GLUT4 overexpression have normal body weight and lowered blood glucose level. The adipose tissue specific overexpression of GLUT4 leads to increases in mouse body weight and adipose tissue weight. The insulin-stimulated GLUT4 translocation in the skeletal muscle contributes to the regulation of glucose homeostasis. Data from both transgenic overexpression and tissue specific Slc2a4 knockout indicate that GLUT4 probably plays a role in the glucose uptake in the fasting state. More studies are warranted to use advanced molecular biology tools to decipher the roles of GLUT4 in the control of glucose homeostasis.
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Affiliation(s)
- Tian-Nan Wang
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, United States
| | - Xin-Ge Hu
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, United States
| | - Guo-Xun Chen
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, United States
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Identification, characterization and hydrolase producing performance of thermophilic bacteria: geothermal hot springs in the Eastern and Southeastern Anatolia Regions of Turkey. Antonie van Leeuwenhoek 2022; 115:253-270. [PMID: 35031914 PMCID: PMC8760091 DOI: 10.1007/s10482-021-01678-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/18/2021] [Indexed: 10/28/2022]
Abstract
In the last two decades, researchers have increasingly focused on the rich microorganism-based diversity of natural hot spring sources to explore the benefits of thermophiles in industrial and biotechnological fields. Within the scope of this study, a total of 83 thermophilic Bacilli strains were isolated from 7 different geothermal hot springs (at temperatures ranging between 40 and 85 °C) located in the Eastern and Southeastern Anatolia Regions of Turkey. The physiological, morphological, biochemical and molecular properties of the isolates were determined. As a result of the 16S rRNA gene sequence analysis, 5 different species (Bacillus licheniformis, Bacillus sp., Bacillus subtilis, Geobacillus kaustophilus, and Weizmannia coagulans,) were identified. B. licheniformis and B. subtilis were the most frequently encountered species among those obtained from the researched hot spring sources. Phylogenetic analysis was conducted to evaluate the phylogenetic relationships of the isolated species. The results showed that there was no significant difference between the groups and the bacteria in terms of the locations or optimum temperatures of the isolates. The bacterial isolates were screened for amylase, cellulase, lipase and protease hydrolytic enzyme activities. The hydrolytic enzyme production potentials among the isolates were identified in 68 (82%) isolates for amylase, 34 (41%) for cellulase, 69 (83%) for lipase and 73 (88%) for protease. All isolates were found to have at least one or more extracellular enzyme activities. Additionally, it was determined that 27 of the existing isolates (32.8%) were able to produce all of the aforementioned hydrolytic enzymes.
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Nambu M, Kishikawa A, Yamada T, Ichikawa K, Kira Y, Itabashi Y, Honda A, Yamada K, Murakami H, Yamamoto A. Direct evaluation of cohesin-mediated sister kinetochore associations at meiosis I in fission yeast. J Cell Sci 2022; 135:jcs259102. [PMID: 34851403 DOI: 10.1242/jcs.259102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
Kinetochores drive chromosome segregation by mediating chromosome interactions with the spindle. In higher eukaryotes, sister kinetochores are separately positioned on opposite sides of sister centromeres during mitosis, but associate with each other during meiosis I. Kinetochore association facilitates the attachment of sister chromatids to the same pole, enabling the segregation of homologous chromosomes toward opposite poles. In the fission yeast, Schizosaccharomyces pombe, Rec8-containing meiotic cohesin is suggested to establish kinetochore associations by mediating cohesion of the centromere cores. However, cohesin-mediated kinetochore associations on intact chromosomes have never been demonstrated directly. In the present study, we describe a novel method for the direct evaluation of kinetochore associations on intact chromosomes in live S. pombe cells, and demonstrate that sister kinetochores and the centromere cores are positioned separately on mitotic chromosomes but associate with each other on meiosis I chromosomes. Furthermore, we demonstrate that kinetochore association depends on meiotic cohesin and the cohesin regulators Moa1 and Mrc1, and requires mating-pheromone signaling for its establishment. These results confirm cohesin-mediated kinetochore association and its regulatory mechanisms, along with the usefulness of the developed method for its analysis. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Masashi Nambu
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Atsuki Kishikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Takatomi Yamada
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Kento Ichikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yunosuke Kira
- Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yuta Itabashi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Akira Honda
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kohei Yamada
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hiroshi Murakami
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Ayumu Yamamoto
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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26
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Rapid and Efficient BAC Recombineering: Gain & Loss Screening System. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Rana K, Ding Y, Banga SS, Liao H, Zhao S, Yu Y, Qian W. Sclerotinia sclerotiorum Thioredoxin1 (SsTrx1) is required for pathogenicity and oxidative stress tolerance. MOLECULAR PLANT PATHOLOGY 2021; 22:1413-1426. [PMID: 34459563 PMCID: PMC8518572 DOI: 10.1111/mpp.13127] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/22/2021] [Accepted: 08/04/2021] [Indexed: 05/03/2023]
Abstract
Sclerotinia sclerotiorum infects host plant tissues by inducing necrosis to source nutrients needed for its establishment. Tissue necrosis results from an enhanced generation of reactive oxygen species (ROS) at the site of infection and apoptosis. Pathogens have evolved ROS scavenging mechanisms to withstand host-induced oxidative damage. However, the genes associated with ROS scavenging pathways are yet to be fully investigated in S. sclerotiorum. We selected the S. sclerotiorum Thioredoxin1 gene (SsTrx1) for our investigations as its expression is significantly induced during S. sclerotiorum infection. RNA interference-induced silencing of SsTrx1 in S. sclerotiorum affected the hyphal growth rate, mycelial morphology, and sclerotial development under in vitro conditions. These outcomes confirmed the involvement of SsTrx1 in promoting pathogenicity and oxidative stress tolerance of S. sclerotiorum. We next constructed an SsTrx1-based host-induced gene silencing (HIGS) vector and mobilized it into Arabidopsis thaliana (HIGS-A) and Nicotiana benthamiana (HIGS-N). The disease resistance analysis revealed significantly reduced pathogenicity and disease progression in the transformed genotypes as compared to the nontransformed and empty vector controls. The relative gene expression of SsTrx1 increased under oxidative stress. Taken together, our results show that normal expression of SsTrx1 is crucial for pathogenicity and oxidative stress tolerance of S. sclerotiorum.
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Affiliation(s)
- Kusum Rana
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Yijuan Ding
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Surinder S. Banga
- Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
| | - Hongmei Liao
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Siqi Zhao
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
| | - Yang Yu
- College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Wei Qian
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
- Engineering Research Center of South Upland AgricultureMinistry of EducationChongqingChina
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28
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Li W, Fan J, Liao G, Yin WB, Li SM. Precursor Supply Increases the Accumulation of 4-Hydroxy-6-(4-hydroxyphenyl)-α-pyrone after NRPS-PKS Gene Expression. JOURNAL OF NATURAL PRODUCTS 2021; 84:2380-2384. [PMID: 34286580 DOI: 10.1021/acs.jnatprod.1c00120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Expression of a nonribosomal peptide synthetase-nonreducing polyketide synthase hybrid gene pcr10109 from Penicillium crustosum PRB-2 in Aspergillus nidulans led to the accumulation of 4-hydroxy-6-(4-hydroxyphenyl)-α-pyrone (1). Adding para-hydroxybenzoic acid into the medium in which the overexpressing mutant is growing increased the product yield up to 5-fold. This strategy could be helpful for heterologous gene expression experiments requiring special substrates for product formation.
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Affiliation(s)
- Wen Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Jie Fan
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, People's Republic of China
| | - Ge Liao
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, People's Republic of China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
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29
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Jain K, Wood EA, Romero ZJ, Cox MM. RecA-independent recombination: Dependence on the Escherichia coli RarA protein. Mol Microbiol 2021; 115:1122-1137. [PMID: 33247976 PMCID: PMC8160026 DOI: 10.1111/mmi.14655] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/29/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022]
Abstract
Most, but not all, homologous genetic recombination in bacteria is mediated by the RecA recombinase. The mechanistic origin of RecA-independent recombination has remained enigmatic. Here, we demonstrate that the RarA protein makes a major enzymatic contribution to RecA-independent recombination. In particular, RarA makes substantial contributions to intermolecular recombination and to recombination events involving relatively short (<200 bp) homologous sequences, where RecA-mediated recombination is inefficient. The effects are seen here in plasmid-based recombination assays and in vivo cloning processes. Vestigial levels of recombination remain even when both RecA and RarA are absent. Additional pathways for RecA-independent recombination, possibly mediated by helicases, are suppressed by exonucleases ExoI and RecJ. Translesion DNA polymerases may also contribute. Our results provide additional substance to a previous report of a functional overlap between RecA and RarA.
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Affiliation(s)
- Kanika Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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30
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Ramirez-Chamorro L, Boulanger P, Rossier O. Strategies for Bacteriophage T5 Mutagenesis: Expanding the Toolbox for Phage Genome Engineering. Front Microbiol 2021; 12:667332. [PMID: 33981295 PMCID: PMC8108384 DOI: 10.3389/fmicb.2021.667332] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/19/2021] [Indexed: 12/31/2022] Open
Abstract
Phage genome editing is crucial to uncover the molecular mechanisms of virus infection and to engineer bacteriophages with enhanced antibacterial properties. Phage genetic engineering relies mostly on homologous recombination (HR) assisted by the targeted elimination of wild-type phages by CRISPR-Cas nucleases. These strategies are often less effective in virulent bacteriophages with large genomes. T5 is a virulent phage that infects Escherichia coli. We found that CRISPR-Cas9 system (type II-A) had ununiform efficacies against T5, which impairs a reliable use of CRISPR-Cas-assisted counterselection in the gene editing of T5. Here, we present alternative strategies for the construction of mutants in T5. Bacterial retroelements (retrons) proved to be efficient for T5 gene editing by introducing point mutations in the essential gene A1. We set up a protocol based on dilution-amplification-screening (DAS) of phage pools for mutant enrichment that was used to introduce a conditional mutation in another essential gene (A2), insert a new gene (lacZα), and construct a translational fusion of a late phage gene with a fluorescent protein coding gene (pb10-mCherry). The method should be applicable to other virulent phages that are naturally resistant to CRISPR/Cas nucleases.
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Affiliation(s)
- Luis Ramirez-Chamorro
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pascale Boulanger
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Ombeline Rossier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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31
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Wang JM, Woodruff AL, Dunn MJ, Fillinger RJ, Bennett RJ, Anderson MZ. Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits. mBio 2021; 12:e00586-21. [PMID: 33879584 PMCID: PMC8092256 DOI: 10.1128/mbio.00586-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences and to link these differences to phenotypic traits. C. albicans adapts primarily through clonal evolution, and yet hierarchical clustering of gene expression profiles in this set of isolates did not reproduce their phylogenetic relationship. Strikingly, strain-specific gene expression was prevalent in some strain backgrounds. Association of gene expression with phenotypic data by differential analysis, linear correlation, and assembly of gene networks connected both previously characterized and novel genes with 23 C. albicans traits. Construction of de novo gene modules produced a gene atlas incorporating 67% of C. albicans genes and revealed correlations between expression modules and important phenotypes such as systemic virulence. Furthermore, targeted investigation of two modules that have novel roles in growth and filamentation supported our bioinformatic predictions. Together, these studies reveal widespread transcriptional variation across C. albicans isolates and identify genetic and epigenetic links to phenotypic variation based on coexpression network analysis.IMPORTANCE Infectious fungal species are often treated uniformly despite clear evidence of genotypic and phenotypic heterogeneity being widespread across strains. Identifying the genetic basis for this phenotypic diversity is extremely challenging because of the tens or hundreds of thousands of variants that may distinguish two strains. Here, we use transcriptional profiling to determine differences in gene expression that can be linked to phenotypic variation among a set of 21 Candida albicans isolates. Analysis of this transcriptional data set uncovered clear trends in gene expression characteristics for this species and new genes and pathways that were associated with variation in pathogenic processes. Direct investigation confirmed functional predictions for a number of new regulators associated with growth and filamentation, demonstrating the utility of these approaches in linking genes to important phenotypes.
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Affiliation(s)
- Joshua M Wang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Andrew L Woodruff
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew J Dunn
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Robert J Fillinger
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
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Staerck C, Wasselin V, Budin-Verneuil A, Rincé I, Cacaci M, Weigel M, Giraud C, Hain T, Hartke A, Riboulet-Bisson E. Analysis of glycerol and dihydroxyacetone metabolism in Enterococcus faecium. FEMS Microbiol Lett 2021; 368:6232157. [PMID: 33864460 DOI: 10.1093/femsle/fnab043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
Glycerol (Gly) can be dissimilated by two pathways in bacteria. Either this sugar alcohol is first oxidized to dihydroxyacetone (DHA) and then phosphorylated or it is first phosphorylated to glycerol-3-phosphate (GlyP) followed by oxidation. Oxidation of GlyP can be achieved by NAD-dependent dehydrogenases or by a GlyP oxidase. In both cases, dihydroxyacetone phosphate is the product. Genomic analysis showed that Enterococcus faecium harbors numerous genes annotated to encode activities for the two pathways. However, our physiological analyses of growth on glycerol showed that dissimilation is limited to aerobic conditions and that despite the presence of genes encoding presumed GlyP dehydrogenases, the GlyP oxidase is essential in this process. Although E. faecium contains an operon encoding the phosphotransfer protein DhaM and DHA kinase, which are required for DHA phosphorylation, it is unable to grow on DHA. This operon is highly expressed in stationary phase but its physiological role remains unknown. Finally, data obtained from sequencing of a transposon mutant bank of E. faecium grown on BHI revealed that the GlyP dehydrogenases and a major intrinsic family protein have important but hitherto unknown physiological functions.
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Affiliation(s)
- Cindy Staerck
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Valentin Wasselin
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Aurélie Budin-Verneuil
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Isabelle Rincé
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Margherita Cacaci
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Markus Weigel
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Biomedical Research Facility Seltersberg (BFS), Schubertstrasse 81, D-35392 Giessen, Germany
| | - Caroline Giraud
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Torsten Hain
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Biomedical Research Facility Seltersberg (BFS), Schubertstrasse 81, D-35392 Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, D-35392 Giessen, Germany
| | - Axel Hartke
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
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Busch T, Petersen M. Identification and biochemical characterisation of tyrosine aminotransferase from Anthoceros agrestis unveils the conceivable entry point into rosmarinic acid biosynthesis in hornworts. PLANTA 2021; 253:98. [PMID: 33844079 PMCID: PMC8041713 DOI: 10.1007/s00425-021-03623-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION Tyrosine aminotransferase (AaTAT) from the hornwort Anthoceros agrestis Paton (Anthocerotaceae) was amplified and expressed in E. coli. The active enzyme is able to accept a wide range of substrates with distinct preference for L-tyrosine, therefore, possibly catalysing the initial step in rosmarinic acid biosynthesis. The presence of rosmarinic acid (RA) in the hornwort A. agrestis is well known, and some attempts have been made to clarify the biosynthesis of this caffeic acid ester in lower plants. Parallel to the biosynthesis in vascular plants, the involvement of tyrosine aminotransferase (EC 2.6.1.5; TAT) as the initial step was assumed. The amplification of a nucleotide sequence putatively encoding AaTAT (Genbank MN922307) and expression in E. coli were successful. The enzyme proved to have a high acceptance of L-tyrosine (Km 0.53 mM) whilst slightly preferring 2-oxoglutarate over phenylpyruvate as co-substrate. Applying L-phenylalanine as a potential amino donor or using oxaloacetate or pyruvate as a replacement for 2-oxoglutarate as amino acceptor resulted in significantly lower catalytic efficiencies in each of these cases. To facilitate further substrate search, two methods were introduced, one using ninhydrin after thin-layer chromatography and the other using derivatisation with o-phthalaldehyde followed by HPLC or LC-MS analysis. Both methods proved to be well applicable and helped to confirm the acceptance of further aromatic and aliphatic amino acids. This work presents the first description of a heterologously expressed TAT from a hornwort (A. agrestis) and describes the possible entry into the biosynthesis of RA and other specialised compounds in a so far neglected representative of terrestrial plants and upcoming new model organism.
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Affiliation(s)
- Tobias Busch
- Philipps-Universität Marburg, Institut für Pharmazeutische Biologie und Biotechnologie, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Maike Petersen
- Philipps-Universität Marburg, Institut für Pharmazeutische Biologie und Biotechnologie, Robert-Koch-Str. 4, 35037, Marburg, Germany.
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Chen F, Li YY, Yu YL, Dai J, Huang JL, Lin J. Simplified plasmid cloning with a universal MCS design and bacterial in vivo assembly. BMC Biotechnol 2021; 21:24. [PMID: 33722223 PMCID: PMC7962268 DOI: 10.1186/s12896-021-00679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to clone DNA sequences quickly and precisely into plasmids is essential for molecular biology studies. The recent development of seamless cloning technologies has made significant improvements in plasmid construction, but simple and reliable tools are always desirable for time- and labor-saving purposes. RESULTS We developed and standardized a plasmid cloning protocol based on a universal MCS (Multiple Cloning Site) design and bacterial in vivo assembly. With this method, the vector is linearized first by PCR (Polymerase Chain Reaction) or restriction digestion. Then a small amount (10 ~ 20 ng) of this linear vector can be mixed with a PCR-amplified insert (5× molar ratio against vector) and transformed directly into competent E. coli cells to obtain the desired clones through in vivo assembly. Since we used a 36-bp universal MCS as the homologous linker, any PCR-amplified insert with ~ 15 bp compatible termini can be cloned into the vector with high fidelity and efficiency. Thus, the need for redesigning insert-amplifying primers according to various vector sequences and the following PCR procedures was eliminated. CONCLUSIONS Our protocol significantly reduced hands-on time for preparing transformation reactions, had excellent reliability, and was confirmed to be a rapid and versatile plasmid cloning technique. The protocol contains mostly mixing steps, making it an extremely automation-friendly and promising tool in modern biology studies.
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Affiliation(s)
- Fan Chen
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China.
| | - Yi-Ya Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Yan-Li Yu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jie Dai
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jin-Ling Huang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jie Lin
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
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Discovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus niger. Appl Environ Microbiol 2021; 87:AEM.02701-20. [PMID: 33397706 DOI: 10.1128/aem.02701-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/19/2020] [Indexed: 11/20/2022] Open
Abstract
Salicylic acid plays an important role in the plant immune response, and its degradation is therefore important for plant-pathogenic fungi. However, many nonpathogenic microorganisms can also degrade salicylic acid. In the filamentous fungus Aspergillus niger, two salicylic acid metabolic pathways have been suggested. The first pathway converts salicylic acid to catechol by a salicylate hydroxylase (ShyA). In the second pathway, salicylic acid is 3-hydroxylated to 2,3-dihydroxybenzoic acid, followed by decarboxylation to catechol by 2,3-dihydroxybenzoate decarboxylase (DhbA). A. niger cleaves the aromatic ring of catechol catalyzed by catechol 1,2-dioxygenase (CrcA) to form cis,cis-muconic acid. However, the identification and role of the genes and characterization of the enzymes involved in these pathways are lacking. In this study, we used transcriptome data of A. niger grown on salicylic acid to identify genes (shyA and crcA) involved in salicylic acid metabolism. Heterologous production in Escherichia coli followed by biochemical characterization confirmed the function of ShyA and CrcA. The combination of ShyA and CrcA demonstrated that cis,cis-muconic acid can be produced from salicylic acid. In addition, the in vivo roles of shyA, dhbA, and crcA were studied by creating A. niger deletion mutants which revealed the role of these genes in the fungal metabolism of salicylic acid.IMPORTANCE Nonrenewable petroleum sources are being depleted, and therefore, alternative sources are needed. Plant biomass is one of the most abundant renewable sources on Earth and is efficiently degraded by fungi. In order to utilize plant biomass efficiently, knowledge about the fungal metabolic pathways and the genes and enzymes involved is essential to create efficient strategies for producing valuable compounds such as cis,cis-muconic acid. cis,cis-Muconic acid is an important platform chemical that is used to synthesize nylon, polyethylene terephthalate (PET), polyurethane, resins, and lubricants. Currently, cis,cis-muconic acid is mainly produced through chemical synthesis from petroleum-based chemicals. Here, we show that two enzymes from fungi can be used to produce cis,cis-muconic acid from salicylic acid and contributes in creating alternative methods for the production of platform chemicals.
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Hennell James R, Deme JC, Kjӕr A, Alcock F, Silale A, Lauber F, Johnson S, Berks BC, Lea SM. Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Nat Microbiol 2021; 6:221-233. [PMID: 33432152 PMCID: PMC7116788 DOI: 10.1038/s41564-020-00823-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein secretion system in Bacteroidetes bacteria. Here, we present cryo-electron microscopy structures of the gliding motility/type 9 protein secretion system motors GldLM from Flavobacterium johnsoniae and PorLM from Porphyromonas gingivalis. The motor is an asymmetric inner membrane protein complex in which the single transmembrane helices of two periplasm-spanning GldM/PorM proteins are positioned inside a ring of five GldL/PorL proteins. Mutagenesis and single-molecule tracking identify protonatable amino acid residues in the transmembrane domain of the complex that are important for motor function. Our data provide evidence for a mechanism in which proton flow results in rotation of the periplasm-spanning GldM/PorM dimer inside the intra-membrane GldL/PorL ring to drive processes at the bacterial outer membrane.
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Affiliation(s)
- Rory Hennell James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Andreas Kjӕr
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- CBCB, Newcastle University, Newcastle upon Tyne, UK
| | - Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK
- CBCB, Newcastle University, Newcastle upon Tyne, UK
| | - Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
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Yang Y, Wang T, Yu Q, Liu H, Xun L, Xia Y. The pathway of recombining short homologous ends in Escherichia coli revealed by the genetic study. Mol Microbiol 2021; 115:1309-1322. [PMID: 33372330 DOI: 10.1111/mmi.14677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The recombination of short homologous ends in Escherichia coli has been known for 30 years, and it is often used for both site-directed mutagenesis and in vivo cloning. For cloning, a plasmid and target DNA fragments were converted into linear DNA fragments with short homologous ends, which are joined via recombination inside E. coli after transformation. Here this mechanism of joining homologous ends in E. coli was determined by a linearized plasmid with short homologous ends. Two 3'-5' exonucleases ExoIII and ExoX with nonprocessive activity digested linear dsDNA to generate 5' single-strand overhangs, which annealed with each other. The polymerase activity of DNA polymerase I (Pol I) was exclusively employed to fill in the gaps. The strand displacement activity and the 5'-3' exonuclease activity of Pol I were also required, likely to generate 5' phosphate termini for subsequent ligation. Ligase A (LigA) joined the nicks to finish the process. The model involving 5' single-stranded overhangs is different from established recombination pathways that all generate 3' single-stranded overhangs. This recombination is likely common in bacteria since the involved enzymes are ubiquitous.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,Institute of Marine Science and Technology, Shandong University, Qingdao, People's Republic of China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
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38
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Brands S, Brass HUC, Klein AS, Sikkens JG, Davari MD, Pietruszka J, Ruff AJ, Schwaneberg U. KnowVolution of prodigiosin ligase PigC towards condensation of short-chain prodiginines. Catal Sci Technol 2021. [DOI: 10.1039/d0cy02297g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
One round of KnowVolution enhanced the catalytic activity of prodigiosin ligase PigC with short-chain monopyrroles, opening access to anticancer prodiginines.
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Affiliation(s)
- Stefanie Brands
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Hannah U. C. Brass
- Institute of Bioorganic Chemistry
- Bioeconomy Science Center (BioSC)
- Heinrich Heine University Düsseldorf
- 52426 Jülich
- Germany
| | - Andreas S. Klein
- Institute of Bioorganic Chemistry
- Bioeconomy Science Center (BioSC)
- Heinrich Heine University Düsseldorf
- 52426 Jülich
- Germany
| | - Jarno G. Sikkens
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry
- Bioeconomy Science Center (BioSC)
- Heinrich Heine University Düsseldorf
- 52426 Jülich
- Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- Bioeconomy Science Center (BioSC)
- RWTH Aachen University
- 52074 Aachen
- Germany
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39
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Guleria R, Jain P, Verma M, Mukherjee KJ. Designing next generation recombinant protein expression platforms by modulating the cellular stress response in Escherichia coli. Microb Cell Fact 2020; 19:227. [PMID: 33308214 PMCID: PMC7730785 DOI: 10.1186/s12934-020-01488-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A cellular stress response (CSR) is triggered upon recombinant protein synthesis which acts as a global feedback regulator of protein expression. To remove this key regulatory bottleneck, we had previously proposed that genes that are up-regulated post induction could be part of the signaling pathways which activate the CSR. Knocking out some of these genes which were non-essential and belonged to the bottom of the E. coli regulatory network had provided higher expression of GFP and L-asparaginase. RESULTS We chose the best performing double knockout E. coli BW25113ΔelaAΔcysW and demonstrated its ability to enhance the expression of the toxic Rubella E1 glycoprotein by 2.5-fold by tagging it with sfGFP at the C-terminal end to better quantify expression levels. Transcriptomic analysis of this hyper-expressing mutant showed that a significantly lower proportion of genes got down-regulated post induction, which included genes for transcription, translation, protein folding and sorting, ribosome biogenesis, carbon metabolism, amino acid and ATP synthesis. This down-regulation which is a typical feature of the CSR was clearly blocked in the double knockout strain leading to its enhanced expression capability. Finally, we supplemented the expression of substrate uptake genes glpK and glpD whose down-regulation was not prevented in the double knockout, thus ameliorating almost all the negative effects of the CSR and obtained a further doubling in recombinant protein yields. CONCLUSION The study validated the hypothesis that these up-regulated genes act as signaling messengers which activate the CSR and thus, despite having no casual connection with recombinant protein synthesis, can improve cellular health and protein expression capabilities. Combining gene knockouts with supplementing the expression of key down-regulated genes can counter the harmful effects of CSR and help in the design of a truly superior host platform for recombinant protein expression.
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Affiliation(s)
- Richa Guleria
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Priyanka Jain
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Madhulika Verma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Krishna J Mukherjee
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India. .,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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40
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Tao CC, Yang Y, Li F, Qiao L, Wu Y, Sun XD, Zhang YY, Li CL. Cloning short DNA into plasmids by one-step PCR. Thorac Cancer 2020; 11:3409-3415. [PMID: 33015950 PMCID: PMC7605993 DOI: 10.1111/1759-7714.13660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022] Open
Abstract
Background Plasmid construction of small fragments of interest (such as insertion of small fragment marker genes, expression of shRNA, siRNA, etc) is the basis of many biomolecular experiments. Here, we describe a method to clone short DNA into vectors by polymerase chain reaction (PCR), named one‐step PCR cloning. Our method uses PCR to amplify the entire circular plasmid. The PCR was performed by the primers containing the gene of short DNA with overlapping sequences between 10–15 bp. The PCR products were then transformed into E. coli and cyclized by homologous recombination in vivo. Methods The pEGFP‐N1‐HA plasmid was constructed by one‐step PCR and transformation. Cells were transfected with pEGFP‐N1‐HA and pEGFP‐N1 plasmid using TurboFect transfection reagent. Protein expression was detected by western blotting and the HA‐GFP fusion protein was detected by confocal microscopy. Results The pEGFP‐N1‐HA plasmid was successfully constructed and HA expression in cells. Conclusions Free from the limitations of restriction enzyme sites and omitting the ligation process, our method offers a flexible and economical option of plasmid construction. Key points
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Affiliation(s)
- Cheng-Cheng Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ying Yang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Fang Li
- Department of Medical Oncology, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ling Qiao
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yue Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiao-Dong Sun
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,School of Biological Sciences and Technology, Chengdu Medical College, Chengdu, China
| | - Chang-Long Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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41
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Leelesh RS, Rieske LK. Oral Ingestion of Bacterially Expressed dsRNA Can Silence Genes and Cause Mortality in a Highly Invasive, Tree-Killing Pest, the Emerald Ash Borer. INSECTS 2020; 11:E440. [PMID: 32674291 PMCID: PMC7411747 DOI: 10.3390/insects11070440] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 11/27/2022]
Abstract
RNA interference (RNAi) is a naturally occurring process inhibiting gene expression, and recent advances in our understanding of the mechanism have allowed its development as a tool against insect pests. A major challenge for deployment in the field is the development of convenient and efficient methods for production of double stranded RNA (dsRNA). We assessed the potential for deploying bacterially produced dsRNA as a bio-pesticide against an invasive forest pest, the emerald ash borer (EAB). EAB feeds on the cambial tissue of ash trees (Fraxinus spp.), causing rapid death. EAB has killed millions of trees in North America since its discovery in 2002, prompting the need for innovative management strategies. In our study, bacterial expression and synthesis of dsRNA were performed with E. coli strain HT115 using the L4440 expression vector. EAB-specific dsRNAs (shi and hsp) over-expressed in E. coli were toxic to neonate EAB after oral administration, successfully triggering gene silencing and subsequent mortality; however, a non-specific dsRNA control was not included. Our results suggest that ingestion of transformed E. coli expressing dsRNAs can induce an RNAi response in EAB. To our knowledge, this is the first example of an effective RNAi response induced by feeding dsRNA-expressing bacteria in a forest pest.
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Affiliation(s)
- Ramya Shanivarsanthe Leelesh
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA;
- School of Life Sciences, University of Bedfordshire, Luton LU13JU, UK
| | - Lynne K. Rieske
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA;
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42
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Hay IM, Fearnley GW, Rios P, Köhn M, Sharpe HJ, Deane JE. The receptor PTPRU is a redox sensitive pseudophosphatase. Nat Commun 2020; 11:3219. [PMID: 32591542 PMCID: PMC7320164 DOI: 10.1038/s41467-020-17076-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/05/2020] [Indexed: 01/06/2023] Open
Abstract
The receptor-linked protein tyrosine phosphatases (RPTPs) are key regulators of cell-cell communication through the control of cellular phosphotyrosine levels. Most human RPTPs possess an extracellular receptor domain and tandem intracellular phosphatase domains: comprising an active membrane proximal (D1) domain and an inactive distal (D2) pseudophosphatase domain. Here we demonstrate that PTPRU is unique amongst the RPTPs in possessing two pseudophosphatase domains. The PTPRU-D1 displays no detectable catalytic activity against a range of phosphorylated substrates and we show that this is due to multiple structural rearrangements that destabilise the active site pocket and block the catalytic cysteine. Upon oxidation, this cysteine forms an intramolecular disulphide bond with a vicinal "backdoor" cysteine, a process thought to reversibly inactivate related phosphatases. Importantly, despite the absence of catalytic activity, PTPRU binds substrates of related phosphatases strongly suggesting that this pseudophosphatase functions in tyrosine phosphorylation by competing with active phosphatases for the binding of substrates.
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Affiliation(s)
- Iain M Hay
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
- Signalling Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gareth W Fearnley
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
- Signalling Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Pablo Rios
- Signalling Research Centres BIOSS and CIBSS, and Faculty of Biology, University of Freiburg, Schänzlestr. 18, Freiburg, D-79104, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, and Faculty of Biology, University of Freiburg, Schänzlestr. 18, Freiburg, D-79104, Germany
| | - Hayley J Sharpe
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
- Signalling Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
| | - Janet E Deane
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
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Good NM, Fellner M, Demirer K, Hu J, Hausinger RP, Martinez-Gomez NC. Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function. J Biol Chem 2020; 295:8272-8284. [PMID: 32366463 PMCID: PMC7294098 DOI: 10.1074/jbc.ra120.013227] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Indexed: 01/07/2023] Open
Abstract
The lanthanide elements (Ln3+), those with atomic numbers 57-63 (excluding promethium, Pm3+), form a cofactor complex with pyrroloquinoline quinone (PQQ) in bacterial XoxF methanol dehydrogenases (MDHs) and ExaF ethanol dehydrogenases (EDHs), expanding the range of biological elements and opening novel areas of metabolism and ecology. Other MDHs, known as MxaFIs, are related in sequence and structure to these proteins, yet they instead possess a Ca2+-PQQ cofactor. An important missing piece of the Ln3+ puzzle is defining what features distinguish enzymes that use Ln3+-PQQ cofactors from those that do not. Here, using XoxF1 MDH from the model methylotrophic bacterium Methylorubrum extorquens AM1, we investigated the functional importance of a proposed lanthanide-coordinating aspartate residue. We report two crystal structures of XoxF1, one with and another without PQQ, both with La3+ bound in the active-site region and coordinated by Asp320 Using constructs to produce either recombinant XoxF1 or its D320A variant, we show that Asp320 is needed for in vivo catalytic function, in vitro activity, and La3+ coordination. XoxF1 and XoxF1 D320A, when produced in the absence of La3+, coordinated Ca2+ but exhibited little or no catalytic activity. We also generated the parallel substitution in ExaF to produce ExaF D319S and found that this variant loses the capacity for efficient ethanol oxidation with La3+ These results provide evidence that a Ln3+-coordinating aspartate is essential for the enzymatic functions of XoxF MDHs and ExaF EDHs, supporting the notion that sequences of these enzymes, and the genes that encode them, are markers for Ln3+ metabolism.
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Affiliation(s)
- Nathan M. Good
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthias Fellner
- Department of Biochemistry, Michigan State University, East Lansing, Michigan, USA,Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Kemal Demirer
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA,Okemos High School, Okemos, Michigan, USA
| | - Jian Hu
- Department of Biochemistry, Michigan State University, East Lansing, Michigan, USA,Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA,Department of Biochemistry, Michigan State University, East Lansing, Michigan, USA
| | - N. Cecilia Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, For correspondence: N. Cecilia Martinez-Gomez,
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Kolakowski D, Kaminska J, Zoladek T. The binding of the APT1 domains to phosphoinositides is regulated by metal ions in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183349. [PMID: 32407779 DOI: 10.1016/j.bbamem.2020.183349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/27/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023]
Abstract
Chorein is a protein of the Vps13 family, and defects in this protein cause the rare neurodegenerative disorder chorea-acanthocytosis (ChAc). Chorein is involved in the actin cytoskeleton organization, calcium ion flux, neuronal cell excitability, exocytosis and autophagy. The function of this protein is poorly understood, and obtaining this knowledge is a key to finding a cure for ChAc. Chorein, as well as the Vps13 protein from yeast, contains the APT1 domain. Our previous research has shown that the APT1 domain from yeast Vps13 (yAPT1v) binds phosphatidylinositol 3-phosphate (PI3P) in vitro. In this study, we showed that although the APT1 domain from chorein (hAPT1) binds to PI3P it could not functionally replace yAPT1v. The hAPT1 domain binds, in addition to PI3P, to phosphatidylinositol 5-phosphate (PI5P). The binding of hAPT1 to PI3P, unlike the binding of yAPT1v to PI3P, is regulated by the bivalent ions, calcium and magnesium. Regulation of PI3P binding via calcium is also observed for the APT1 domain of yeast autophagy protein Atg2. The substitution I2771R, found in chorein of patient suffering from ChAc, reduces the binding of the hAPT1 domain to PI3P and PI5P. These results suggest that the ability of APT1 domains to bind phosphoinositides is regulated differently in yeast and human protein and that this regulation is important for chorein function.
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Affiliation(s)
- Damian Kolakowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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Ong TT, Ang Z, Verma R, Koean R, Tam JKC, Ding JL. pHLuc, a Ratiometric Luminescent Reporter for in vivo Monitoring of Tumor Acidosis. Front Bioeng Biotechnol 2020; 8:412. [PMID: 32457886 PMCID: PMC7225611 DOI: 10.3389/fbioe.2020.00412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Even under normoxia, cancer cells exhibit increased glucose uptake and glycolysis, an occurrence known as the Warburg effect. This altered metabolism results in increased lactic acid production, leading to extracellular acidosis and contributing to metastasis and chemoresistance. Current pH imaging methods are invasive, costly, or require long acquisition times, and may not be suitable for high-throughput pre-clinical small animal studies. Here, we present a ratiometric pH-sensitive bioluminescence reporter called pHLuc for in vivo monitoring of tumor acidosis. pHLuc consists of a pH-sensitive GFP (superecliptic pHluorin or SEP), a pH-stable OFP (Antares), and Nanoluc luciferase. The resulting reporter produces a pH-responsive green 510nm emission (from SEP) and a pH-insensitive red-orange 580nm emission (from Antares). The ratiometric readout (R580 / 510) is indicative of changes in extracellular pH (pHe). In vivo proof-of-concept experiments with NSG mice model bearing human synovial sarcoma SW982 xenografts that stably express the pHLuc reporter suggest that the level of acidosis varies across the tumor. Altogether, we demonstrate the diagnostic value of pHLuc as a bioluminescent reporter for pH variations across the tumor microenvironment. The pHLuc reporter plasmids constructed in this work are available from Addgene.
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Affiliation(s)
- Tiffany T Ong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhiwei Ang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Riva Verma
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ricky Koean
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - John Kit Chung Tam
- Division of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jeak Ling Ding
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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46
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Gräwe A, Ranglack J, Weyrich A, Stein V. iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains. Nucleic Acids Res 2020; 48:e24. [PMID: 31925441 PMCID: PMC7039005 DOI: 10.1093/nar/gkz1210] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 02/02/2023] Open
Abstract
Recent years have witnessed increasing efforts to engineer artificial biological functions through recombination of modular-organized toolboxes of protein scaffolds and parts. A critical, yet frequently neglected aspect concerns the identity of peptide linkers or spacers connecting individual domains which remain poorly understood and challenging to assemble. Addressing these limitations, iFlinkC comprises a highly scalable DNA assembly process that facilitates the combinatorial recombination of functional domains with linkers of varying length and flexibility, thereby overcoming challenges with high GC-content and the repeat nature of linker elements. The capacity of iFLinkC is demonstrated in the construction of synthetic protease switches featuring PDZ-FN3-based affinity clamps and single-chain FKBP12-FRB receptors as allosteric inputs. Library screening experiments demonstrate that linker space is highly plastic as the induction of allosterically regulated protease switches can vary from >150-fold switch-ON to >13-fold switch-OFF solely depending on the identity of the connecting linkers and relative orientation of functional domains. In addition, Pro-rich linkers yield the most potent switches contradicting the conventional use of flexible Gly-Ser linkers. Given the ease and efficiency how functional domains can be readily recombined with any type of linker, iFLinkC is anticipated to be widely applicable to the assembly of any type of fusion protein.
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Affiliation(s)
- Alexander Gräwe
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Jan Ranglack
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Anastasia Weyrich
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
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47
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Cloning, expression and purification of the low-complexity region of RanBP9 protein. Protein Expr Purif 2020; 172:105630. [PMID: 32217127 DOI: 10.1016/j.pep.2020.105630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 11/22/2022]
Abstract
Recombinant expression and purification of proteins is key for biochemical and biophysical investigations. Although this has become a routine and standard procedure for many proteins, intrinsically disordered ones and those with low complexity sequences pose difficulties. Proteins containing low complexity regions (LCRs) are increasingly becoming significant for their roles in both normal and pathological processes. Here, we report cloning, expression and purification of N-terminal LCR of RanBP9 protein (Nt-RanBP9). RanBP9 is a scaffolding protein present in both cytoplasm and nucleus that is implicated in many cellular processes. Nt-RanBP9 is a poorly understood region of the protein perhaps due to difficulties posed by the LCR. Indeed, conventional methods presented difficulties in Nt-RanBP9 cloning due to its high GC content resulting in insignificant protein expression. These led us to use a different approach of cloning by expressing the protein as a fusion construct containing mCherry or mEGFP using in vivo DNA recombination methods. Our results indicate that expression of mEGFP-tagged Nt-RanBP9 followed by thrombin cleavage of the tag was the most effective method to obtain the protein with >90% purity and good yields. We report and discuss the challenges in obtaining the N-terminal region of RanBP9, a protein with functional implications in multiple biological processes and neurodegenerative diseases.
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48
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Berepiki A, Kent R, Machado LFM, Dixon N. Development of High-Performance Whole Cell Biosensors Aided by Statistical Modeling. ACS Synth Biol 2020; 9:576-589. [PMID: 32023410 PMCID: PMC7146887 DOI: 10.1021/acssynbio.9b00448] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Whole cell biosensors are genetic systems that link the presence of a chemical, or other stimulus, to a user-defined gene expression output for applications in sensing and control. However, the gene expression level of biosensor regulatory components required for optimal performance is nonintuitive, and classical iterative approaches do not efficiently explore multidimensional experimental space. To overcome these challenges, we used a design of experiments (DoE) methodology to efficiently map gene expression levels and provide biosensors with enhanced performance. This methodology was applied to two biosensors that respond to catabolic breakdown products of lignin biomass, protocatechuic acid and ferulic acid. Utilizing DoE we systematically modified biosensor dose-response behavior by increasing the maximum signal output (up to 30-fold increase), improving dynamic range (>500-fold), expanding the sensing range (∼4-orders of magnitude), increasing sensitivity (by >1500-fold), and modulated the slope of the curve to afford biosensors designs with both digital and analogue dose-response behavior. This DoE method shows promise for the optimization of regulatory systems and metabolic pathways constructed from novel, poorly characterized parts.
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Affiliation(s)
- Adokiye Berepiki
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| | - Ross Kent
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| | - Leopoldo F. M. Machado
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| | - Neil Dixon
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.,E-mail:
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49
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Redox requirements for ubiquitin-like urmylation of Ahp1, a 2-Cys peroxiredoxin from yeast. Redox Biol 2020; 30:101438. [PMID: 32004955 PMCID: PMC7016264 DOI: 10.1016/j.redox.2020.101438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023] Open
Abstract
The yeast peroxiredoxin Ahp1, like related anti-oxidant enzymes in other species, undergoes urmylation, a lysine-directed conjugation to ubiquitin-like modifier Urm1. Ahp1 assembles into a homodimer that detoxifies peroxides via forming intersubunit disulfides between peroxidatic and resolving cysteines that are subsequently reduced by the thioredoxin system. Although urmylation coincides with oxidative stress, it is unclear how this modification happens on a molecular level and whether it affects peroxiredoxin activity. Here, we report that thioredoxin mutants decrease Ahp1 urmylation in yeast and each subunit of the oxidized Ahp1 dimer is modified by Urm1 suggesting coupling of urmylation to dimerization. Consistently, Ahp1 mutants unable to form dimers, fail to be urmylated as do mutants that lack the peroxidatic cysteine. Moreover, Ahp1 urmylation involves at least two lysine residues close to the catalytic cysteines and can be prevented in yeast cells exposed to high organic peroxide concentrations. Our results elucidate redox requirements and molecular determinants critical for Ahp1 urmylation, thus providing insights into a potential link between oxidant defense and Urm1 utilization in cells.
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50
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Xiang P, Ludwig-Radtke L, Yin WB, Li SM. Isocoumarin formation by heterologous gene expression and modification by host enzymes. Org Biomol Chem 2020; 18:4946-4948. [DOI: 10.1039/d0ob00989j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The polyketide synthase product was converted to its methylated and hydroxylated derivatives by host endogenous enzymes.
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Affiliation(s)
- Pan Xiang
- Institut für Pharmazeutische Biologie und Biotechnologie
- Philipps-Universität Marburg
- 35037 Marburg
- Germany
| | - Lena Ludwig-Radtke
- Institut für Pharmazeutische Biologie und Biotechnologie
- Philipps-Universität Marburg
- 35037 Marburg
- Germany
| | - Wen-Bing Yin
- State Key Laboratory of Mycology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing 100101
- China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie
- Philipps-Universität Marburg
- 35037 Marburg
- Germany
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