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Jian J, Wang Z, Chen C, Workman CT, Fang X, Larsen TO, Guo J, Sonnenschein EC. Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity. Microbiol Spectr 2024; 12:e0414823. [PMID: 38940543 PMCID: PMC11302234 DOI: 10.1128/spectrum.04148-23] [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: 12/09/2023] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity. IMPORTANCE The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- BGI Genomics, Shenzhen, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | | | | | - Christopher T. Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Department of Biosciences, Swansea University, Swansea, United Kingdom
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2
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Ibe CN, Bailey SL, Korolev AV, Brett P, Saunders DGO. Isocitrate lyase promotes Puccinia striiformis f. sp. tritici susceptibility in wheat (Triticum aestivum) by suppressing accumulation of glyoxylate cycle intermediates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2033-2044. [PMID: 38949911 DOI: 10.1111/tpj.16908] [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: 01/13/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Plant fungal parasites manipulate host metabolism to support their own survival. Among the many central metabolic pathways altered during infection, the glyoxylate cycle is frequently upregulated in both fungi and their host plants. Here, we examined the response of the glyoxylate cycle in bread wheat (Triticum aestivum) to infection by the obligate biotrophic fungal pathogen Puccinia striiformis f. sp. tritici (Pst). Gene expression analysis revealed that wheat genes encoding the two unique enzymes of the glyoxylate cycle, isocitrate lyase (TaICL) and malate synthase, diverged in their expression between susceptible and resistant Pst interactions. Focusing on TaICL, we determined that the TaICL B homoeolog is specifically upregulated during early stages of a successful Pst infection. Furthermore, disruption of the B homoeolog alone was sufficient to significantly perturb Pst disease progression. Indeed, Pst infection of the TaICL-B disruption mutant (TaICL-BY400*) was inhibited early during initial penetration, with the TaICL-BY400* line also accumulating high levels of malic acid, citric acid, and aconitic acid. Exogenous application of malic acid or aconitic acid also suppressed Pst infection, with trans-aconitic acid treatment having the most pronounced effect by decreasing fungal biomass 15-fold. Thus, enhanced TaICL-B expression during Pst infection may lower accumulation of malic acid and aconitic acid to promote Pst proliferation. As exogenous application of aconitic acid and malic acid has previously been shown to inhibit other critical pests and pathogens, we propose TaICL as a potential target for disruption in resistance breeding that could have wide-reaching protective benefits for wheat and beyond.
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Affiliation(s)
- Carol N Ibe
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah L Bailey
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Paul Brett
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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3
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Sendker FL, Schlotthauer T, Mais CN, Lo YK, Girbig M, Bohn S, Heimerl T, Schindler D, Weinstein A, Metzger BP, Thornton JW, Pillai A, Bange G, Schuller JM, Hochberg GK. Frequent transitions in self-assembly across the evolution of a central metabolic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602260. [PMID: 39005358 PMCID: PMC11245102 DOI: 10.1101/2024.07.05.602260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs. This has led to the proposition that self-assembly may instead vary neutrally within protein families. The extent of such variation has been difficult to ascertain because quaternary structure has until recently been difficult to measure on large scales. Here, we employ mass photometry, phylogenetics, and structural biology to interrogate the evolution of homo-oligomeric assembly across the entire phylogeny of prokaryotic citrate synthases - an enzyme with a highly conserved function. We discover a menagerie of different assembly types that come and go over the course of evolution, including cases of parallel evolution and reversions from complex to simple assemblies. Functional experiments in vitro and in vivo indicate that evolutionary transitions between different assemblies do not strongly influence enzyme catalysis. Our work suggests that enzymes can wander relatively freely through a large space of possible assemblies and demonstrates the power of characterizing structure-function relationships across entire phylogenies.
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Affiliation(s)
- Franziska L. Sendker
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Tabea Schlotthauer
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Mathias Girbig
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Stefan Bohn
- Institute of Structural Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1 Neuherberg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- MaxGENESYS Biofoundry, Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Arielle Weinstein
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Brain P. Metzger
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Joseph W. Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Arvind Pillai
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Gert Bange
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-University Marburg; Hans-Meerwein-Str. 4, 35043 Marburg, Germany
| | - Jan M. Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-University Marburg; Hans-Meerwein-Str. 4, 35043 Marburg, Germany
| | - Georg K.A. Hochberg
- Max-Planck-Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg; Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
- Department of Chemistry, Philipps-University Marburg; Hans-Meerwein-Str. 4, 35043 Marburg, Germany
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4
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Wu C, Wei X, Huang Z, Zheng Z, Zhang W, Chen J, Hong H, Li W. Urinary microbiome dysbiosis is associated with an inflammatory environment and perturbed fatty acids metabolism in the pathogenesis of bladder cancer. J Transl Med 2024; 22:628. [PMID: 38970045 PMCID: PMC11227203 DOI: 10.1186/s12967-024-05446-7] [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: 03/08/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Bladder cancer is a common malignancy with high recurrence rate. Early diagnosis and recurrence surveillance are pivotal to patients' outcomes, which require novel minimal-invasive diagnostic tools. The urinary microbiome is associated with bladder cancer and can be used as biomarkers, but the underlying mechanism is to be fully illustrated and diagnostic performance to be improved. METHODS A total of 23 treatment-naïve bladder cancer patients and 9 non-cancerous subjects were enrolled into the Before group and Control group. After surgery, 10 patients from the Before group were further assigned into After group. Void mid-stream urine samples were collected and sent for 16S rDNA sequencing, targeted metabolomic profiling, and flow cytometry. Next, correlations were analyzed between microbiota, metabolites, and cytokines. Finally, receiver operating characteristic (ROC) curves of the urinary biomarkers were plotted and compared. RESULTS Comparing to the Control group, levels of IL-6 (p < 0.01), IL-8 (p < 0.05), and IL-10 (p < 0.05) were remarkably elevated in the Before group. The α diversity of urine microbiome was also significantly higher, with the feature microbiota positively correlated to the level of IL-6 (r = 0.58, p < 0.01). Significant differences in metabolic composition were also observed between the Before and Control groups, with fatty acids and fatty acylcarnitines enriched in the Before group. After tumor resection, cytokine levels and the overall microbiome structure in the After group remained similar to that of the Before group, but fatty acylcarnitines were significantly reduced (p < 0.05). Pathway enrichment analysis revealed beta-oxidation of fatty acids was significantly involved (p < 0.001). ROC curves showed that the biomarker panel of Actinomycetaceae + arachidonic acid + IL-6 had superior diagnostic performance, with sensitivity of 0.94 and specificity of 1.00. CONCLUSIONS Microbiome dysbiosis, proinflammatory environment and altered fatty acids metabolism are involved in the pathogenesis of bladder cancer, which may throw light on novel noninvasive diagnostic tool development.
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Affiliation(s)
- Cen Wu
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Xiaoyu Wei
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Zhiyang Huang
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Zhixiong Zheng
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Wei Zhang
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Jiajun Chen
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Hongchang Hong
- Department of Urology, Fujian Medical University Affiliated Quanzhou First Hospital, Fujian, 362011, China
| | - Weili Li
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Biotechnology Co., Ltd., 180 Zhangheng Road, Pudong District, Shanghai, 201204, China.
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5
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Jiang Q, Sherlock DN, Elolimy AA, Yoon I, Loor JJ. Feeding a Saccharomyces cerevisiae fermentation product during a gut barrier challenge in lactating Holstein cows impacts the ruminal microbiota and metabolome. J Dairy Sci 2024; 107:4476-4494. [PMID: 38369118 DOI: 10.3168/jds.2023-24147] [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: 08/31/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Through its influence on the gut microbiota, the feeding of Saccharomyces cerevisiae fermentation products (SCFP) has been a successful strategy to enhance the health of dairy cows during periods of physiological stresses. Although production and metabolic outcomes from feeding SCFP are well-known, its combined impacts on the ruminal microbiota and metabolome during gut barrier challenges remain unclear. To address this gap in knowledge, multiparous Holstein cows (97.1 ± 7.6 DIM [SD]; n = 8/group) fed a control diet (CON) or CON plus 19 g/d SCFP for 9 wk were subjected to a feed restriction (FR) challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before FR. The DNA extracted from ruminal fluid was subjected to PacBio full-length 16S rRNA gene sequencing, real-time PCR of 12 major ruminal bacteria, and metabolomics analysis of up to 189 metabolites via GC/MS. High-quality amplicon sequence analyses were performed with the TADA (Targeted Amplicon Diversity Analysis), MicrobiomeAnalyst, PICRUSt2, and STAMP software packages, and metabolomics data were analyzed via MetaboAnalyst 5.0. Ruminal fluid metabolites from the SCFP group exhibited a greater α-diversity Chao 1 (P = 0.03) and Shannon indices (P = 0.05), and the partial least squares discriminant analysis clearly discriminated metabolite profiles between dietary groups. The abundance of CPla_4_termite_group, Candidatus Saccharimonas, Oribacterium, and Pirellula genus in cows fed SCFP was greater. In the SCFP group, concentrations of ethanolamine, 2-amino-4,6-dihydroxypyrimidine, glyoxylic acid, serine, threonine, cytosine, stearic acid, and pyrrole-2-carboxylic acid were greater in ruminal fluid. Both Fretibacterium and Succinivibrio abundances were positively correlated with metabolites across various biological processes: gamma-aminobutyric acid, galactose, butane-2,3-diol, fructose, 5-amino pentanoic acid, β-aminoisobutyric acid, ornithine, malonic acid, 3-hydroxy-3-methylbutyric acid, hexanoic acid, heptanoic acid, cadaverine, glycolic acid, β-alanine, 2-hydroxybutyric acid, methyl alanine, and alanine. In the SCFP group, compared with CON, the mean proportion of 14 predicted pathways based on metabolomics data was greater, whereas 10 predicted pathways were lower. Integrating metabolites and upregulated predicted enzymes (NADP+-dependent glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, serine: glyoxylate aminotransferase, and d-glycerate 3-kinase) indicated that the pentose phosphate pathway and photorespiration pathway were most upregulated by SCFP. Overall, SCFP during FR led to alterations in ruminal microbiota composition and key metabolic pathways. Among those, we identified a shift from the tricarboxylic acid cycle to the glyoxylate cycle, and nitrogenous base production was enhanced.
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Affiliation(s)
- Qianming Jiang
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801
| | | | - Ahmed A Elolimy
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801; Livestock Production and Management, Department of Integrated Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 1551, United Arab Emirates
| | | | - Juan J Loor
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801.
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6
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Cox RM, Papoulas O, Shril S, Lee C, Gardner T, Battenhouse AM, Lee M, Drew K, McWhite CD, Yang D, Leggere JC, Durand D, Hildebrandt F, Wallingford JB, Marcotte EM. Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595818. [PMID: 38853926 PMCID: PMC11160598 DOI: 10.1101/2024.05.26.595818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
All eukaryotes share a common ancestor from roughly 1.5 - 1.8 billion years ago, a single-celled, swimming microbe known as LECA, the Last Eukaryotic Common Ancestor. Nearly half of the genes in modern eukaryotes were present in LECA, and many current genetic diseases and traits stem from these ancient molecular systems. To better understand these systems, we compared genes across modern organisms and identified a core set of 10,092 shared protein-coding gene families likely present in LECA, a quarter of which are uncharacterized. We then integrated >26,000 mass spectrometry proteomics analyses from 31 species to infer how these proteins interact in higher-order complexes. The resulting interactome describes the biochemical organization of LECA, revealing both known and new assemblies. We analyzed these ancient protein interactions to find new human gene-disease relationships for bone density and congenital birth defects, demonstrating the value of ancestral protein interactions for guiding functional genetics today.
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Affiliation(s)
- Rachael M Cox
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tynan Gardner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anna M Battenhouse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - David Yang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Janelle C Leggere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue Pittsburgh, PA 15213, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - John B Wallingford
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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7
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Gerdol M, Nerelli DE, Martelossi N, Ogawa Y, Fujii Y, Pallavicini A, Ozeki Y. Taxonomic Distribution and Molecular Evolution of Mytilectins. Mar Drugs 2023; 21:614. [PMID: 38132935 PMCID: PMC10744619 DOI: 10.3390/md21120614] [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: 11/05/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
R-type lectins are a widespread group of sugar-binding proteins found in nearly all domains of life, characterized by the presence of a carbohydrate-binding domain that adopts a β-trefoil fold. Mytilectins represent a recently described subgroup of β-trefoil lectins, which have been functionally characterized in a few mussel species (Mollusca, Bivalvia) and display attractive properties, which may fuel the development of artificial lectins with different biotechnological applications. The detection of different paralogous genes in mussels, together with the description of orthologous sequences in brachiopods, supports the formal description of mytilectins as a gene family. However, to date, an investigation of the taxonomic distribution of these lectins and their molecular diversification and evolution was still lacking. Here, we provide a comprehensive overview of the evolutionary history of mytilectins, revealing an ancient monophyletic evolutionary origin and a very broad but highly discontinuous taxonomic distribution, ranging from heteroscleromorphan sponges to ophiuroid and crinoid echinoderms. Moreover, the overwhelming majority of mytilectins display a chimera-like architecture, which combines the β-trefoil carbohydrate recognition domain with a C-terminal pore-forming domain, suggesting that the simpler structure of most functionally characterized mytilectins derives from a secondary domain loss.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Daniela Eugenia Nerelli
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Nicola Martelossi
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yukiko Ogawa
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo 859-3298, Japan
| | - Yuki Fujii
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo 859-3298, Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yasuhiro Ozeki
- Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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8
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Wang G, Laranjeiro R, LeValley S, Van Raamsdonk JM, Driscoll M. The glyoxylate shunt protein ICL-1 protects from mitochondrial superoxide stress through activation of the mitochondrial unfolded protein response. Free Radic Biol Med 2023; 208:771-779. [PMID: 37758122 DOI: 10.1016/j.freeradbiomed.2023.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/05/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Disrupting mitochondrial superoxide dismutase (SOD) causes neonatal lethality in mice and death of flies within 24 h after eclosion. Deletion of mitochondrial sod genes in C. elegans impairs fertility as well, but surprisingly is not detrimental to survival of progeny generated. The comparison of metabolic pathways among mouse, flies and nematodes reveals that mice and flies lack the glyoxylate shunt, a shortcut that bypasses part of the tricarboxylic acid (TCA) cycle. Here we show that ICL-1, the sole protein that catalyzes the glyoxylate shunt, is critical for protection against embryonic lethality resulting from elevated levels of mitochondrial superoxide. In exploring the mechanism by which ICL-1 protects against ROS-mediated embryonic lethality, we find that ICL-1 is required for the efficient activation of mitochondrial unfolded protein response (UPRmt) and that ATFS-1, a key UPRmt transcription factor and an activator of icl-1 gene expression, is essential to limit embryonic/neonatal lethality in animals lacking mitochondrial SOD. In sum, we identify a biochemical pathway that highlights a molecular strategy for combating toxic mitochondrial superoxide consequences in cells.
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Affiliation(s)
- Guoqiang Wang
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Ricardo Laranjeiro
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Stephanie LeValley
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Jeremy M Van Raamsdonk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA; Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
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9
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Tao X, Ouyang H, Zhou A, Wang D, Matlock H, Morgan JS, Ren AT, Mu D, Pan C, Zhu X, Han A, Zhou J. Polyethylene Degradation by a Rhodococcous Strain Isolated from Naturally Weathered Plastic Waste Enrichment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13901-13911. [PMID: 37682848 PMCID: PMC10515485 DOI: 10.1021/acs.est.3c03778] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
Polyethylene (PE) is the most widely produced synthetic polymer and the most abundant plastic waste worldwide due to its recalcitrance to biodegradation and low recycle rate. Microbial degradation of PE has been reported, but the underlying mechanisms are poorly understood. Here, we isolated a Rhodococcus strain A34 from 609 day enriched cultures derived from naturally weathered plastic waste and identified the potential key PE degradation enzymes. After 30 days incubation with A34, 1% weight loss was achieved. Decreased PE molecular weight, appearance of C-O and C═O on PE, palmitic acid in the culture supernatant, and pits on the PE surface were observed. Proteomics analysis identified multiple key PE oxidation and depolymerization enzymes including one multicopper oxidase, one lipase, six esterase, and a few lipid transporters. Network analysis of proteomics data demonstrated the close relationships between PE degradation and metabolisms of phenylacetate, amino acids, secondary metabolites, and tricarboxylic acid cycles. The metabolic roadmap generated here provides critical insights for optimization of plastic degradation condition and assembly of artificial microbial communities for efficient plastic degradation.
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Affiliation(s)
- Xuanyu Tao
- Institute
for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Huanrong Ouyang
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Aifen Zhou
- Institute
for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Dongyu Wang
- Department
of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Hagan Matlock
- Institute
for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Josiah S. Morgan
- Institute
for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Abigail T. Ren
- Institute
for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Dashuai Mu
- Marine
College, Shandong University, Weihai 264105, China
| | - Chongle Pan
- Department
of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Xuejun Zhu
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Arum Han
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
| | - Jizhong Zhou
- Institute
for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
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10
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Rabaan AA, Halwani MA, Garout M, Turkistani SA, Alsubki RA, Alawfi A, Alshengeti A, Najim MA, Al Kaabi NA, Alqazih TQ, Aseeri AA, Bahitham AS, Alsubaie MA, Alissa M, Aljeldah M. Identification of natural potent inhibitors against Mycobacterium tuberculosis isocitrate lyase: an in silico study. Mol Divers 2023:10.1007/s11030-023-10711-w. [PMID: 37578620 DOI: 10.1007/s11030-023-10711-w] [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: 03/29/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
Tuberculosis (TB) is a global burden to humanity due to its adverse effects on health and society since time is not clearly defined. The existence of drug-resistant strains and the potential threat posed by latent tuberculosis act as strong impetuses for developing novel anti-tuberculosis drugs. In this study, various flavonoids were tested against the Mycobacterium tuberculosis (Mtb) Isocitrate Lyase (ICL), which has been identified as an authorised therapeutic target for treating Mtb infection. Using in silico drug discovery approach, a library of 241 flavonoid compounds was virtually screened against the binding pocket of the crystalline ligand, the VGX inhibitor, in the Mtb ICL protein. As a result, the top four flavonoids were selected based on binding score and were further considered for redocking and intermolecular contact profiling analysis. The global and local fluctuations in the protein and ligand structure were analysed using their root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values obtained from the GROMACS generated 100 ns molecular dynamics (MD) simulation trajectories. The end-state binding free energy was also calculated using the MMPBSA approach for all the respective docked complexes. All four selected compounds exhibited considerable stability and affinity compared to control ligands, i.e. VGX inhibitor; however, Vaccarin showed the highest stability and affinity against the Mtb ICL protein active site, followed by the Genistin, Glabridin, and Corylin. Therefore, this study recommends selected flavonoids for in vitro and in vivo experimental studies to check their potency and efficacy against Mtb.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha, 4781, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | | | - Roua A Alsubki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11362, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, 41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, 41491, Saudi Arabia
| | - Mustafa A Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah, 41411, Saudi Arabia
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi, 127788, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates
| | - Thikrayat Q Alqazih
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates
| | - Ali A Aseeri
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates
| | - Afnan S Bahitham
- Microbiology Laboratory Department, King Fahad Specialist Hospital, Dammam, 32253, Saudi Arabia
| | - Manal A Alsubaie
- Biochemistry Laboratory Department, King Fahad Specialist Hospital, Dammam, 32253, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, 39831, Saudi Arabia.
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11
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Moggioli G, Panossian B, Sun Y, Thiel D, Martín-Zamora FM, Tran M, Clifford AM, Goffredi SK, Rimskaya-Korsakova N, Jékely G, Tresguerres M, Qian PY, Qiu JW, Rouse GW, Henry LM, Martín-Durán JM. Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms. Nat Commun 2023; 14:2814. [PMID: 37198188 DOI: 10.1038/s41467-023-38521-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies. Genome compaction and extensive gene losses distinguish the heterotrophic symbiosis of the bone-eating worm Osedax frankpressi from the chemoautotrophic symbiosis of deep-sea Vestimentifera. Osedax's endosymbionts complement many of the host's metabolic deficiencies, including the loss of pathways to recycle nitrogen and synthesise some amino acids. Osedax's endosymbionts possess the glyoxylate cycle, which could allow more efficient catabolism of bone-derived nutrients and the production of carbohydrates from fatty acids. Unlike in most Vestimentifera, innate immunity genes are reduced in O. frankpressi, which, however, has an expansion of matrix metalloproteases to digest collagen. Our study supports that distinct nutritional interactions influence host genome evolution differently in highly specialised symbioses.
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Affiliation(s)
- Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Yanan Sun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Daniel Thiel
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Martin Tran
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Alexander M Clifford
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Nadezhda Rimskaya-Korsakova
- Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Zoology and Evolutionary Research, Erbertstr. 1, 07743, Jena, Germany
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Martin Tresguerres
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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12
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Dembech E, Malatesta M, De Rito C, Mori G, Cavazzini D, Secchi A, Morandin F, Percudani R. Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions. Proc Natl Acad Sci U S A 2023; 120:e2218329120. [PMID: 37043529 PMCID: PMC10120013 DOI: 10.1073/pnas.2218329120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/10/2023] [Indexed: 04/13/2023] Open
Abstract
Coevolution at the gene level, as reflected by correlated events of gene loss or gain, can be revealed by phylogenetic profile analysis. The optimal method and metric for comparing phylogenetic profiles, especially in eukaryotic genomes, are not yet established. Here, we describe a procedure suitable for large-scale analysis, which can reveal coevolution based on the assessment of the statistical significance of correlated presence/absence transitions between gene pairs. This metric can identify coevolution in profiles with low overall similarities and is not affected by similarities lacking coevolutionary information. We applied the procedure to a large collection of 60,912 orthologous gene groups (orthogroups) in 1,264 eukaryotic genomes extracted from OrthoDB. We found significant cotransition scores for 7,825 orthogroups associated in 2,401 coevolving modules linking known and unknown genes in protein complexes and biological pathways. To demonstrate the ability of the method to predict hidden gene associations, we validated through experiments the involvement of vertebrate malate synthase-like genes in the conversion of (S)-ureidoglycolate into glyoxylate and urea, the last step of purine catabolism. This identification explains the presence of glyoxylate cycle genes in metazoa and suggests an anaplerotic role of purine degradation in early eukaryotes.
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Affiliation(s)
- Elena Dembech
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Carlo De Rito
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Francesco Morandin
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma43124, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
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13
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Mendoza-Porras O, Broadbent JA, Beale DJ, Escobar-Correas SM, Osborne SA, Simon CJ, Wade NM. Post-prandial response in hepatopancreas and haemolymph of Penaeus monodon fed different diets. Omics insights into glycoconjugate metabolism, energy utilisation, chitin biosynthesis, immune function, and autophagy. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY PART D: GENOMICS AND PROTEOMICS 2023; 46:101073. [PMID: 37018937 DOI: 10.1016/j.cbd.2023.101073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023]
Abstract
Raw materials or bioactive ingredients trigger mechanisms to assimilate nutrients and activate metabolic pathways that promote growth, immune function, or energy storage. Our understanding of these processes at a molecular level remains limited in aquaculture, especially in shrimp. Here, hepatopancreas proteomics and haemolymph metabolomics were used to investigate the post-prandial response of black tiger shrimps (Penaeus monodon) fed a conventional fishmeal diet (FM); a diet supplemented with the microbial biomass Novacq™ (NV); krill meal (KM); or, fasted (FS). Using FM as a control, a 2-fold change in abundance threshold was implemented to determine the significance of proteins and metabolites. NV fed shrimp showed preference for energy derived from carbohydrates indicated by a strong signature of glycoconjugate metabolism and activation of the amino- and nucleotide sugar metabolic pathway. KM activated the glyoxylate and dicarboxylate pathway that denoted shrimp preference for lipidic energy. KM also influenced energy generation by the TCA cycle inferred from higher abundance of the metabolites succinic semialdehyde, citric acid, isocitrate, alpha ketoglutarate and ATP and downregulation of the enzyme isocitrate dehydrogenase that catalyses oxidative decarboxylation of isocitrate. FS shrimp displayed down-regulation of oxidative phosphorylation and resorted to internal lipid reserves for energy homeostasis displaying a strong signature of autophagy. Pyrimidine metabolism was the preferred energy strategy in this group. Our study also provided evidence that during fasting or consumption of specific ingredients, shrimp share common pathways to meet their energy requirements, however, the intensity at which these pathways were impacted was diet dependent.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia.
| | - James A Broadbent
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - David J Beale
- CSIRO Land and Water, Ecosciences Precinct, Dutton Park, QLD, Australia
| | | | - Simone A Osborne
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Cedric J Simon
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Nicholas M Wade
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
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14
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Álvarez-Lugo A, Becerra A. The Fate of Duplicated Enzymes in Prokaryotes: The Case of Isomerases. J Mol Evol 2023; 91:76-92. [PMID: 36580111 DOI: 10.1007/s00239-022-10085-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022]
Abstract
The isomerases are a unique enzymatic class of enzymes that carry out a great diversity of chemical reactions at the intramolecular level. This class comprises about 300 members, most of which are involved in carbohydrate and terpenoid/polyketide metabolism. Along with oxidoreductases and translocases, isomerases are one of the classes with the highest ratio of paralogous enzymes. Due to its relatively small number of members, it is plausible to explore it in greater detail to identify specific cases of gene duplication. Here, we present an analysis at the level of individual isomerases and identify different members that seem to be involved in duplication events in prokaryotes. As was suggested in a previous study, there is no homogeneous distribution of paralogs, but rather they accumulate into a few subcategories, some of which differ between Archaea and Bacteria. As expected, the metabolic processes with more paralogous isomerases have to do with carbohydrate metabolism but also with RNA modification (a particular case involving an rRNA-modifying isomerase is thoroughly discussed and analyzed in detail). Overall, our findings suggest that the most common fate for paralogous enzymes is the retention of the original enzymatic function, either associated with a dosage effect or with differential expression in response to changing environments, followed by subfunctionalization and, to a much lesser degree, neofunctionalization, which is consistent with what has been reported elsewhere.
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Affiliation(s)
- Alejandro Álvarez-Lugo
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, México.,Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, México
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, México.
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15
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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:1613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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Affiliation(s)
| | | | - Pingkalai R. Senthilan
- Neurobiology & Genetics, Theodor-Boveri Institute, Biocenter, Julius-Maximilians-University Würzburg, 97074 Wurzburg, Germany
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16
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Gevi F, Leo P, Cassaro A, Pacelli C, de Vera JPP, Rabbow E, Timperio AM, Onofri S. Metabolomic Profile of the Fungus Cryomyces antarcticus Under Simulated Martian and Space Conditions as Support for Life-Detection Missions on Mars. Front Microbiol 2022; 13:749396. [PMID: 35633719 PMCID: PMC9133366 DOI: 10.3389/fmicb.2022.749396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
The identification of traces of life beyond Earth (e.g., Mars, icy moons) is a challenging task because terrestrial chemical-based molecules may be destroyed by the harsh conditions experienced on extraterrestrial planetary surfaces. For this reason, studying the effects on biomolecules of extremophilic microorganisms through astrobiological ground-based space simulation experiments is significant to support the interpretation of the data that will be gained and collected during the ongoing and future space exploration missions. Here, the stability of the biomolecules of the cryptoendolithic black fungus Cryomyces antarcticus, grown on two Martian regolith analogues and on Antarctic sandstone, were analysed through a metabolomic approach, after its exposure to Science Verification Tests (SVTs) performed in the frame of the European Space Agency (ESA) Biology and Mars Experiment (BIOMEX) project. These tests are building a set of ground-based experiments performed before the space exposure aboard the International Space Station (ISS). The analysis aimed to investigate the effects of different mineral mixtures on fungal colonies and the stability of the biomolecules synthetised by the fungus under simulated Martian and space conditions. The identification of a specific group of molecules showing good stability after the treatments allow the creation of a molecular database that should support the analysis of future data sets that will be collected in the ongoing and next space exploration missions.
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Affiliation(s)
- Federica Gevi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Patrick Leo
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Venice, Italy
| | - Alessia Cassaro
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | | | | | - Elke Rabbow
- German Aerospace Centre, Institute of Aerospace Medicine (DLR), Cologne, Germany
| | - Anna Maria Timperio
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
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17
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Yan L, Sundaram S, Rust BM, Picklo MJ, Bukowski MR. Metabolomes of Lewis lung carcinoma metastases and normal lung tissue from mice fed different diets. J Nutr Biochem 2022; 107:109051. [DOI: 10.1016/j.jnutbio.2022.109051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/02/2022] [Accepted: 04/17/2022] [Indexed: 12/20/2022]
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18
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Glyoxylate protects against cyanide toxicity through metabolic modulation. Sci Rep 2022; 12:4982. [PMID: 35322094 PMCID: PMC8943054 DOI: 10.1038/s41598-022-08803-y] [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: 08/09/2021] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although cyanide's biological effects are pleiotropic, its most obvious effects are as a metabolic poison. Cyanide potently inhibits cytochrome c oxidase and potentially other metabolic enzymes, thereby unleashing a cascade of metabolic perturbations that are believed to cause lethality. From systematic screens of human metabolites using a zebrafish model of cyanide toxicity, we have identified the TCA-derived small molecule glyoxylate as a potential cyanide countermeasure. Following cyanide exposure, treatment with glyoxylate in both mammalian and non-mammalian animal models confers resistance to cyanide toxicity with greater efficacy and faster kinetics than known cyanide scavengers. Glyoxylate-mediated cyanide resistance is accompanied by rapid pyruvate consumption without an accompanying increase in lactate concentration. Lactate dehydrogenase is required for this effect which distinguishes the mechanism of glyoxylate rescue as distinct from countermeasures based solely on chemical cyanide scavenging. Our metabolic data together support the hypothesis that glyoxylate confers survival at least in part by reversing the cyanide-induced redox imbalances in the cytosol and mitochondria. The data presented herein represent the identification of a potential cyanide countermeasure operating through a novel mechanism of metabolic modulation.
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19
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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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20
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Bollati E, Rosenberg Y, Simon-Blecher N, Tamir R, Levy O, Huang D. Untangling the molecular basis of coral response to sedimentation. Mol Ecol 2021; 31:884-901. [PMID: 34738686 DOI: 10.1111/mec.16263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/23/2022]
Abstract
Urbanized coral reefs are often chronically affected by sedimentation and reduced light levels, yet many species of corals appear to be able to thrive under these highly disturbed conditions. Recently, these marginal ecosystems have gained attention as potential climate change refugia due to the shading effect of suspended sediment, as well as potential reservoirs for stress-tolerant species. However, little research exists on the impact of sedimentation on coral physiology, particularly at the molecular level. Here, we investigated the transcriptomic response to sediment stress in corals of the family Merulinidae from a chronically turbid reef (one genet each of Goniastrea pectinata and Mycedium elephantotus from Singapore) and a clear-water reef (multiple genets of G. pectinata from the Gulf of Aqaba/Eilat). In two ex-situ experiments, we exposed corals to either natural sediment or artificial sediment enriched with organic matter and used whole-transcriptome sequencing (RNA sequencing) to quantify gene expression. Analysis revealed a shared basis for the coral transcriptomic response to sediment stress, which involves the expression of genes broadly related to energy metabolism and immune response. In particular, sediment exposure induced upregulation of anaerobic glycolysis and glyoxylate bypass enzymes, as well as genes involved in hydrogen sulphide metabolism and in pathogen pattern recognition. Our results point towards hypoxia as a probable driver of this transcriptomic response, providing a molecular basis to previous work that identified hypoxia as a primary cause of tissue necrosis in sediment-stressed corals. Potential metabolic and immunity trade-offs of corals living under chronic sedimentation should be considered in future studies on the ecology and conservation of turbid reefs.
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Affiliation(s)
- Elena Bollati
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Department of Biology, Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Yaeli Rosenberg
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Simon-Blecher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Raz Tamir
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore.,Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
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21
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Yan L, Sundaram S, Rust BM, Picklo MJ, Bukowski MR. Mammary Tumorigenesis and Metabolome in Male Adipose Specific Monocyte Chemotactic Protein-1 Deficient MMTV-PyMT Mice Fed a High-Fat Diet. Front Oncol 2021; 11:667843. [PMID: 34568008 PMCID: PMC8458874 DOI: 10.3389/fonc.2021.667843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Male breast cancer, while uncommon, is a highly malignant disease. Monocyte chemotactic protein-1 (MCP-1) is an adipokine; its concentration in adipose tissue is elevated in obesity. This study tested the hypothesis that adipose-derived MCP-1 contributes to male breast cancer. In a 2x2 design, male MMTV-PyMT mice with or without adipose-specific Mcp-1 knockout [designated as Mcp-1-/- or wild-type (WT)] were fed the AIN93G standard diet or a high-fat diet (HFD) for 25 weeks. Mcp-1-/- mice had lower adipose Mcp-1 expression than WT mice. Adipose Mcp-1 deficiency reduced plasma concentrations of MCP-1 in mice fed the HFD compared to their WT counterparts. Mcp-1-/- mice had a longer tumor latency (25.2 weeks vs. 18.0 weeks) and lower tumor incidence (19% vs. 56%), tumor progression (2317% vs. 4792%), and tumor weight (0.23 g vs. 0.64 g) than WT mice. Plasma metabolomics analysis identified 56 metabolites that differed among the four dietary groups, including 22 differed between Mcp-1-/- and WT mice. Pathway and network analyses along with discriminant analysis showed that pathways of amino acid and carbohydrate metabolisms are the most disturbed in MMTV-PyMT mice. In conclusion, adipose-derived MCP-1 contributes to mammary tumorigenesis in male MMTV-PyMT. The potential involvement of adipose-derived MCP-1 in metabolomics warrants further investigation on its role in causal relationships between cancer metabolism and mammary tumorigenesis in this male MMTV-PyMT model.
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Affiliation(s)
- Lin Yan
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Sneha Sundaram
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Bret M Rust
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Matthew J Picklo
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
| | - Michael R Bukowski
- U.S. Department of Agriculture, Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND, United States
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22
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Progesterone Promotes Mitochondrial Respiration at the Biochemical and Molecular Level in Germinating Maize Seeds. PLANTS 2021; 10:plants10071326. [PMID: 34209697 PMCID: PMC8309107 DOI: 10.3390/plants10071326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 11/22/2022]
Abstract
This research aimed to investigate the effects of progesterone, a mammalian steroid sex hormone, on the mitochondrial respiration in germinating maize seeds. For this purpose, maize seeds were divided into four different groups (control, 10−6, 10−8, and 10−10 mol·L−1 progesterone) and were grown in a germination cabinet in the dark at 24.5 ± 0.5 °C for 4 d. The changes in gene expression levels of citrate synthase (CS), cytochrome oxidase (COX19), pyruvate dehydrogenase (Pdh1), and ATP synthase (ATP6), which is involved in mitochondrial respiration, were studied in root and cotyledon tissues. Significant increases were recorded in the gene expression levels of all studied enzymes. In addition, progesterone applications stimulated activities of malate synthase (MS), isocitrate lyase (ICL), and alpha-amylase, which are important enzymes of the germination step. The changes in gene expression levels of mas1 and icl1 were found parallel to the rise in these enzymes’ activities. It was determined similar increases in root and coleoptile lengths and total soluble protein and total carbohydrate contents. The most remarkable changes were detected in 10−8 mol·L−1 progesterone-treated seedlings. These results clearly indicate that progesterone stimulates mitochondrial respiration by inducing biochemical and molecular parameters and thus accelerates seed germination thanks to the activation of other pathways related to mitochondrial respiration.
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23
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ATGL activity regulates GLUT1-mediated glucose uptake and lactate production via TXNIP stability in adipocytes. J Biol Chem 2021; 296:100332. [PMID: 33508319 PMCID: PMC7949114 DOI: 10.1016/j.jbc.2021.100332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 01/03/2023] Open
Abstract
Traditionally, lipolysis has been regarded as an enzymatic activity that liberates fatty acids as metabolic fuel. However, recent work has shown that novel substrates, including a variety of lipid compounds such as fatty acids and their derivatives, release lipolysis products that act as signaling molecules and transcriptional modulators. While these studies have expanded the role of lipolysis, the mechanisms underpinning lipolysis signaling are not fully defined. Here, we uncover a new mechanism regulating glucose uptake, whereby activation of lipolysis, in response to elevated cAMP, leads to the stimulation of thioredoxin-interacting protein (TXNIP) degradation. This, in turn, selectively induces glucose transporter 1 surface localization and glucose uptake in 3T3-L1 adipocytes and increases lactate production. Interestingly, cAMP-induced glucose uptake via degradation of TXNIP is largely dependent upon adipose triglyceride lipase (ATGL) and not hormone-sensitive lipase or monoacylglycerol lipase. Pharmacological inhibition or knockdown of ATGL alone prevents cAMP-dependent TXNIP degradation and thus significantly decreases glucose uptake and lactate secretion. Conversely, overexpression of ATGL amplifies the cAMP response, yielding increased glucose uptake and lactate production. Similarly, knockdown of TXNIP elicits enhanced basal glucose uptake and lactate secretion, and increased cAMP further amplifies this phenotype. Overexpression of TXNIP reduces basal and cAMP-stimulated glucose uptake and lactate secretion. As a proof of concept, we replicated these findings in human primary adipocytes and observed TXNIP degradation and increased glucose uptake and lactate secretion upon elevated cAMP signaling. Taken together, our results suggest a crosstalk between ATGL-mediated lipolysis and glucose uptake.
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24
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Gonzalez-Hunt CP, Luz AL, Ryde IT, Turner EA, Ilkayeva OR, Bhatt DP, Hirschey MD, Meyer JN. Multiple metabolic changes mediate the response of Caenorhabditis elegans to the complex I inhibitor rotenone. Toxicology 2021; 447:152630. [PMID: 33188857 PMCID: PMC7750303 DOI: 10.1016/j.tox.2020.152630] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Rotenone, a mitochondrial complex I inhibitor, has been widely used to study the effects of mitochondrial dysfunction on dopaminergic neurons in the context of Parkinson's disease. Although the deleterious effects of rotenone are well documented, we found that young adult Caenorhabditis elegans showed resistance to 24 and 48 h rotenone exposures. To better understand the response to rotenone in C. elegans, we evaluated mitochondrial bioenergetic parameters after 24 and 48 h exposures to 1 μM or 5 μM rotenone. Results suggested upregulation of mitochondrial complexes II and V following rotenone exposure, without major changes in oxygen consumption or steady-state ATP levels after rotenone treatment at the tested concentrations. We found evidence that the glyoxylate pathway (an alternate pathway not present in higher metazoans) was induced by rotenone exposure; gene expression measurements showed increases in mRNA levels for two complex II subunits and for isocitrate lyase, the key glyoxylate pathway enzyme. Targeted metabolomics analyses showed alterations in the levels of organic acids, amino acids, and acylcarnitines, consistent with the metabolic restructuring of cellular bioenergetic pathways including activation of complex II, the glyoxylate pathway, glycolysis, and fatty acid oxidation. This expanded understanding of how C. elegans responds metabolically to complex I inhibition via multiple bioenergetic adaptations, including the glyoxylate pathway, will be useful in interrogating the effects of mitochondrial and bioenergetic stressors and toxicants.
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Affiliation(s)
- Claudia P Gonzalez-Hunt
- Department of Nicholas School of the Environment, Duke University, Durham, NC, 27708, United States
| | - Anthony L Luz
- Department of Nicholas School of the Environment, Duke University, Durham, NC, 27708, United States
| | - Ian T Ryde
- Department of Nicholas School of the Environment, Duke University, Durham, NC, 27708, United States
| | - Elena A Turner
- Department of Nicholas School of the Environment, Duke University, Durham, NC, 27708, United States
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute, Durham, NC, 27710, United States; Sarah W. Stedman Nutrition and Metabolism Center, Durham, NC, 27710, United States
| | - Dhaval P Bhatt
- Duke Molecular Physiology Institute, Durham, NC, 27710, United States
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, Durham, NC, 27710, United States; Sarah W. Stedman Nutrition and Metabolism Center, Durham, NC, 27710, United States; Departments of Medicine and Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, United States
| | - Joel N Meyer
- Department of Nicholas School of the Environment, Duke University, Durham, NC, 27708, United States.
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25
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Tetrick MA, Odle J. What Constitutes a Gluconeogenic Precursor? J Nutr 2020; 150:2239-2241. [PMID: 32652033 DOI: 10.1093/jn/nxaa166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 11/14/2022] Open
Abstract
A gluconeogenic precursor is a biochemical compound acted on by a gluconeogenic pathway enabling the net synthesis of glucose. Recognized gluconeogenic precursors in fasting placental mammals include glycerol, lactate/pyruvate, certain amino acids, and odd-chain length fatty acids. Each of these precursors is capable of contributing net amounts of carbon to glucose synthesis via the tricarboxylic acid cycle (TCA cycle) because they are anaplerotic, that is, they are able to increase the pools of TCA cycle intermediates by the contribution of more carbon than is lost via carbon dioxide. The net synthesis of glucose from even-chain length fatty acids (ECFAs) in fasting placental mammals, via the TCA cycle alone, is not possible because equal amounts of carbon are lost via carbon dioxide as is contributed from fatty acid oxidation via acetyl-CoA. Therefore, ECFAs do not meet the criteria to be recognized as a gluconeogenic precursor via the TCA cycle alone. ECFAs are gluconeogenic precursors in organisms with a functioning glyoxylate cycle, which enables the net contribution of carbon to the intermediates of the TCA cycle from ECFAs and the net synthesis of glucose. The net conversion of ECFAs to glucose in fasting placental mammals via C3 metabolism of acetone may be a competent though inefficient metabolic path by which ECFA could be considered a gluconeogenic precursor. Defining a substrate as a gluconeogenic precursor requires careful articulation of the definition, organism, and physiologic conditions under consideration.
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Affiliation(s)
| | - Jack Odle
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
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26
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Chabanol E, Behrends V, Prévot G, Christophides GK, Gendrin M. Antibiotic Treatment in Anopheles coluzzii Affects Carbon and Nitrogen Metabolism. Pathogens 2020; 9:E679. [PMID: 32825534 PMCID: PMC7558193 DOI: 10.3390/pathogens9090679] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/04/2023] Open
Abstract
The mosquito microbiota reduces the vector competence of Anopheles to Plasmodium and affects host fitness; it is therefore considered as a potential target to reduce malaria transmission. While immune induction, secretion of antimicrobials and metabolic competition are three typical mechanisms of microbiota-mediated protection against invasive pathogens in mammals, the involvement of metabolic competition or mutualism in mosquito-microbiota and microbiota-Plasmodium interactions has not been investigated. Here, we describe a metabolome analysis of the midgut of Anopheles coluzzii provided with a sugar-meal or a non-infectious blood-meal, under conventional or antibiotic-treated conditions. We observed that the antibiotic treatment affects the tricarboxylic acid cycle and nitrogen metabolism, notably resulting in decreased abundance of free amino acids. Linking our results with published data, we identified pathways which may participate in microbiota-Plasmodium interactions via metabolic interactions or immune modulation and thus would be interesting candidates for future functional studies.
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Affiliation(s)
- Estelle Chabanol
- Microbiota of Insect Vectors Group, Institut Pasteur de Guyane, 97306 Cayenne, French Guiana;
- Ecole Doctorale Numéro 587, Diversités, Santé, et Développement en Amazonie, Université de Guyane, 97337 Cayenne, French Guiana
- Tropical Biome and Immunophysiopathology, Université de Guyane, 97300 Cayenne, French Guiana;
| | - Volker Behrends
- Health Sciences Research Centre, University of Roehampton, London SW15 4JD, UK;
| | - Ghislaine Prévot
- Tropical Biome and Immunophysiopathology, Université de Guyane, 97300 Cayenne, French Guiana;
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | | | - Mathilde Gendrin
- Microbiota of Insect Vectors Group, Institut Pasteur de Guyane, 97306 Cayenne, French Guiana;
- Department of Life Sciences, Imperial College London, London SW7 2BU, UK;
- Department of Parasites and Insect Vectors, Institut Pasteur, 75015 Paris, France
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27
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Curran DM, Grote A, Nursimulu N, Geber A, Voronin D, Jones DR, Ghedin E, Parkinson J. Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. eLife 2020; 9:e51850. [PMID: 32779567 PMCID: PMC7419141 DOI: 10.7554/elife.51850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/14/2020] [Indexed: 12/17/2022] Open
Abstract
The filarial nematode Brugia malayi represents a leading cause of disability in the developing world, causing lymphatic filariasis in nearly 40 million people. Currently available drugs are not well-suited to mass drug administration efforts, so new treatments are urgently required. One potential vulnerability is the endosymbiotic bacteria Wolbachia-present in many filariae-which is vital to the worm. Genome scale metabolic networks have been used to study prokaryotes and protists and have proven valuable in identifying therapeutic targets, but have only been applied to multicellular eukaryotic organisms more recently. Here, we present iDC625, the first compartmentalized metabolic model of a parasitic worm. We used this model to show how metabolic pathway usage allows the worm to adapt to different environments, and predict a set of 102 reactions essential to the survival of B. malayi. We validated three of those reactions with drug tests and demonstrated novel antifilarial properties for all three compounds.
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Affiliation(s)
- David M Curran
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
| | - Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Nirvana Nursimulu
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
- Department of Computer Science, University of TorontoTorontoCanada
| | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | | | - Drew R Jones
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
- Department of Epidemiology, School of Global Public Health, New York UniversityNew YorkUnited States
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
- Department of Computer Science, University of TorontoTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
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28
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Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 2020; 369:369/6501/eaba4674. [PMID: 32675347 DOI: 10.1126/science.aba4674] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.
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Affiliation(s)
- Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | | | - Luke A Morris
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Jihanne Shepherd
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Luke Sarre
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Julie Peng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yi Liao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | | | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia.
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.,Program for Mathematical Genomics, Columbia University, New York, NY, USA
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29
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Tandon K, Lu CY, Chiang PW, Wada N, Yang SH, Chan YF, Chen PY, Chang HY, Chiou YJ, Chou MS, Chen WM, Tang SL. Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). THE ISME JOURNAL 2020; 14:1290-1303. [PMID: 32055028 PMCID: PMC7174347 DOI: 10.1038/s41396-020-0610-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 01/24/2023]
Abstract
Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) into dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) draft genomes of strains of the recently added species Endozoicomonas acroporae (Acr-14T, Acr-1, and Acr-5) isolated from the coral Acropora sp. and performed a comparative genomic analysis on the genus Endozoicomonas. We identified DMSP CoA-transferase/lyase-a dddD gene homolog in all sequenced genomes of E. acroporae strains-and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as a carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Ya-Fan Chan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ping-Yun Chen
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Hsiao-Yu Chang
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, 10617, Taiwan
| | - Ming-Shean Chou
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City, 811, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
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30
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Dhiman A, Kumar C, Mishra SK, Sikri K, Datta I, Sharma P, Singh TP, Haldar S, Sharma N, Bansal A, Ahmad Y, Kumar A, Sharma TK, Tyagi JS. Theranostic Application of a Novel G-Quadruplex-Forming DNA Aptamer Targeting Malate Synthase of Mycobacterium tuberculosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:661-672. [PMID: 31704587 PMCID: PMC6849348 DOI: 10.1016/j.omtn.2019.09.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/29/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022]
Abstract
The successful management of tuberculosis (TB) requires efficient diagnosis and treatment. Further, the increasing prevalence of drug-resistant TB highlights the urgent need to develop novel inhibitors against both drug-susceptible and drug-resistant forms of disease. Malate synthase (MS), an enzyme of the glyoxylate pathway, plays a vital role in mycobacterial persistence, and therefore it is considered as an attractive target for novel anti-TB drug development. Recent studies have also ascribed an adhesin function to MS and established it as a potent diagnostic biomarker. In this study, a panel of Mycobacterium tuberculosis (Mtb) MS-specific single-stranded DNA aptamers was identified by Systematic Evolution of Ligands by EXponential enrichment (SELEX). The best-performing G-quadruplex-forming 44-mer aptamer, MS10, was optimized post-SELEX to generate an 11-mer aptamer, MS10-Trunc. This aptamer was characterized by various biochemical, biophysical, and in silico techniques. Its theranostic activity toward Mtb was established using enzyme inhibition, host cell binding, and invasion assays. MS10-Trunc aptamer exhibited high affinity for MS (equilibrium dissociation constant [KD] ∼19 pM) and displayed robust inhibition of MS enzyme activity with IC50 of 251.1 nM and inhibitor constant (Ki) of 230 nM. This aptamer blocked mycobacterial entry into host cells by binding to surface-associated MS. In addition, we have also demonstrated its application in the detection of tuberculous meningitis (TBM) in patients with sensitivity and specificity each of >97%.
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Affiliation(s)
- Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India; Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
| | - Chanchal Kumar
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Kriti Sikri
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ishara Datta
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sagarika Haldar
- Department of Experimental Medicine and Biotechnology, PGIMER, Sector 12, Chandigarh 160012, India; Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Neera Sharma
- Department of Biochemistry, Dr. Ram Manohar Lohia Hospital, New Delhi 110001, India
| | - Anjali Bansal
- Department of Pediatrics, Dr. Ram Manohar Lohia Hospital, New Delhi 110001, India
| | - Yusra Ahmad
- Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India; Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
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31
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Nasir F, Shi S, Tian L, Chang C, Ma L, Li X, Gao Y, Tian C. Strigolactones shape the rhizomicrobiome in rice (Oryza sativa). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:118-133. [PMID: 31300137 DOI: 10.1016/j.plantsci.2019.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/13/2019] [Accepted: 05/18/2019] [Indexed: 05/03/2023]
Abstract
The rhizomicrobiome helps the host plant to better adapt to environmental stresses. In contrast, plant-derived metabolic substances, including phytohormones, play an active role in structuring rhizomicrobiome. Although strigolactones (SLs), a group of phytohormones, serve as potential rhizosphere signaling molecules, their contributions in shaping the rice (Oryza sativa) rhizomicrobiome remain elusive. To address this issue, we compared the rhizomicrobiome of rice mutants defective in either SL biosynthesis or signaling and wild-type (WT) plants. To understand whether SL-regulated metabolic pathways shape the rhizomicrobiome, a correlation network analysis was conducted among the metabolic pathway-related genes and the rhizomicrobiome of rice. Compared to WT, higher bacterial richness (evidenced by the operational taxonomic unit richness) and lower fungal diversity (evidenced by the Shannon index) were observed in both SL deficient dwarf17 (d17) and signaling (d14) mutants. Additionally, remarkable differences were observed in the composition of a large number of bacterial communities than the fungal communities in the d17 and d14 mutants with respect to the WT. The abundance of certain beneficial bacterial taxa, including Nitrosomonadaceae and Rhodanobacter, were significantly decreased in both mutants relative to the WT. Correlation network analysis between SL-regulated metabolic pathway-associated genes and rhizomicrobiome proposed a role for SL-dependent metabolic pathways in shaping rhizomicrobiome composition. Taken together, our study suggests that SL biosynthesis and signaling play a key role in determining the rice rhizomicrobiome, directly or indirectly, through the mediation of distinct metabolic pathways. Based on our findings, the genetic modulation of rice SL biosynthesis and/or signaling pathways may help to recruit/increase the abundance of the desired rhizomicrobiome, which may assist in the stress resilience of rice.
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Affiliation(s)
- Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Yingzhi Gao
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China.
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China.
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Chew SY, Chee WJY, Than LTL. The glyoxylate cycle and alternative carbon metabolism as metabolic adaptation strategies of Candida glabrata: perspectives from Candida albicans and Saccharomyces cerevisiae. J Biomed Sci 2019; 26:52. [PMID: 31301737 PMCID: PMC6626413 DOI: 10.1186/s12929-019-0546-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Carbon utilization and metabolism are fundamental to every living organism for cellular growth. For intracellular human fungal pathogens such as Candida glabrata, an effective metabolic adaptation strategy is often required for survival and pathogenesis. As one of the host defence strategies to combat invading pathogens, phagocytes such as macrophages constantly impose restrictions on pathogens' access to their preferred carbon source, glucose. Surprisingly, it has been reported that engulfed C. glabrata are able to survive in this harsh microenvironment, further suggesting alternative carbon metabolism as a potential strategy for this opportunistic fungal pathogen to persist in the host. MAIN TEXT In this review, we discuss alternative carbon metabolism as a metabolic adaptation strategy for the pathogenesis of C. glabrata. As the glyoxylate cycle is an important pathway in the utilization of alternative carbon sources, we also highlight the key metabolic enzymes in the glyoxylate cycle and its necessity for the pathogenesis of C. glabrata. Finally, we explore the transcriptional regulatory network of the glyoxylate cycle. CONCLUSION Considering evidence from Candida albicans and Saccharomyces cerevisiae, this review summarizes the current knowledge of the glyoxylate cycle as an alternative carbon metabolic pathway of C. glabrata.
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Affiliation(s)
- Shu Yih Chew
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Wallace Jeng Yang Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Zečić A, Dhondt I, Braeckman BP. The nutritional requirements of Caenorhabditis elegans. GENES AND NUTRITION 2019; 14:15. [PMID: 31080524 PMCID: PMC6501307 DOI: 10.1186/s12263-019-0637-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022]
Abstract
Animals require sufficient intake of a variety of nutrients to support their development, somatic maintenance and reproduction. An adequate diet provides cell building blocks, chemical energy to drive cellular processes and essential nutrients that cannot be synthesised by the animal, or at least not in the required amounts. Dietary requirements of nematodes, including Caenorhabditis elegans have been extensively studied with the major aim to develop a chemically defined axenic medium that would support their growth and reproduction. At the same time, these studies helped elucidating important aspects of nutrition-related biochemistry and metabolism as well as the establishment of C. elegans as a powerful model in studying evolutionarily conserved pathways, and the influence of the diet on health.
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Affiliation(s)
- Aleksandra Zečić
- Department of Biology, Laboratory of Aging Physiology and Molecular Evolution, Ghent University, 9000 Ghent, Belgium
| | - Ineke Dhondt
- Department of Biology, Laboratory of Aging Physiology and Molecular Evolution, Ghent University, 9000 Ghent, Belgium
| | - Bart P Braeckman
- Department of Biology, Laboratory of Aging Physiology and Molecular Evolution, Ghent University, 9000 Ghent, Belgium
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Nguyen TV, Alfaro AC, Young T, Green S, Zarate E, Merien F. Itaconic acid inhibits growth of a pathogenic marine Vibrio strain: A metabolomics approach. Sci Rep 2019; 9:5937. [PMID: 30976014 PMCID: PMC6459830 DOI: 10.1038/s41598-019-42315-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/29/2019] [Indexed: 01/28/2023] Open
Abstract
The antimicrobial role of itaconic acid (ITA) has been recently discovered in mammalian cells. In our previous studies, we discovered that marine molluscs biosynthesise substantial quantities of ITA when exposed to marine pathogens, but its antimicrobial function to Vibrio bacteria is currently unknown. Thus, in this study, we used an untargeted gas chromatography-mass spectrometry (GC-MS) platform to identify metabolic changes of Vibrio sp. DO1 (V. corallyliticus/neptunius-like isolate) caused by ITA exposure. Vibrio sp. DO1 was cultured in Luria-Bertani broth supplemented with 3 mM sodium acetate and with different concentrations of ITA (0, 3 and 6 mM) for 24 h. The results showed that ITA completely inhibited Vibrio sp. growth at 6 mM and partially inhibited the bacterial growth at 3 mM. A principal component analysis (PCA) revealed a clear separation between metabolite profiles of Vibrio sp. DO1 in the 3 mM ITA treatment and the control, which were different in 25 metabolites. Among the altered metabolites, the accumulation of glyoxylic acid and other metabolites in glyoxylate cycle (cis-aconitic acid, isocitric acid and fumaric acid) together with the increase of isocitrate lyase (ICL) activity in the 3 mM ITA treatment compared to the control suggest that ITA inhibited Vibrio sp. growth via disruption of central carbon metabolism.
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Affiliation(s)
- Thao Van Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand.
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Saras Green
- Mass Spectrometry Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Erica Zarate
- Mass Spectrometry Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Fabrice Merien
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
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Sun J, Jia H, Wang P, Zhou T, Wu Y, Liu Z. Exogenous gibberellin weakens lipid breakdown by increasing soluble sugars levels in early germination of zanthoxylum seeds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:155-163. [PMID: 30823993 DOI: 10.1016/j.plantsci.2018.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 06/09/2023]
Abstract
Zanthoxylum is a precious medicinal woody plant with a very low seed germination rate in China. The gibberellin (GA) treatment extremely increased the germination rate of zanthoxylum seeds. Our previous transcriptome data showed that exogenous GA played a negative role in the expression levels of genes involved in lipid metabolism during imbibition. Our present data indicated that compared with the GA-treated seeds, the soluble sugars were more quickly consumed and lipid breakdown was prematurely and actively initiated in the water-treated seeds during the early germination. However, the application of sucrose could improve the germination of water-treated seeds and significantly inhibit lipid breakdown. Both the application of sucrose and exogenous GA could significantly reduce the catalytic activities of sugar-dependent 1 (SDP1) and isocitratelyase (ICL), the expressions of SDP1 and ICL genes, and decrease the products of lipid breakdown as well during the early germination. We suggested that exogenous GA might enhance starch hydrolysis by promoting the catalytic activity of ɑ-amylase to supplement metabolically consumed soluble sugars, thus the increased sugars levels would help to inhibit the lipid breakdown to mitigate oxidative damages in the early germination of zanthoxylum seeds. In the end, we summarized the possible molecular mechanism on the exogenous GA weakening lipid breakdown by increasing soluble sugars levels in the early germination of zanthoxylum seeds.
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Affiliation(s)
- Jikang Sun
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, China; Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Hao Jia
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ping Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China.
| | - Tao Zhou
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yan Wu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Zhiming Liu
- Department of Biology, Eastern New Mexico University, Portales, NM, 88130, USA.
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Abstract
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms.
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Larsson S, Voss U. Neuroprotective effects of vitamin D on high fat diet- and palmitic acid-induced enteric neuronal loss in mice. BMC Gastroenterol 2018; 18:175. [PMID: 30463517 PMCID: PMC6249721 DOI: 10.1186/s12876-018-0905-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/08/2018] [Indexed: 01/26/2023] Open
Abstract
Background The role of vitamin D in obesity and diabetes is debated. Obese and/or diabetic patients have elevated levels of free fatty acids, increased susceptibility to gastrointestinal symptoms and are suggested to have altered vitamin D balance. The enteric nervous system is pivotal in regulating gastrointestinal activity and high fat diet (HFD) has been shown to cause loss of enteric neurons in ileum and colon. This study investigates the effect of vitamin D on HFD- and palmitic acid-induced enteric neuronal loss in vivo and in vitro. Methods Mice were fed either a normal diet (ND) or HFD supplemented with varying levels of vitamin D (from 0x to 20x normal vitamin D level) for 19 weeks. Ileum and colon were analyzed for neuronal numbers and remodeling. Primary cultures of myenteric neurons from mouse small intestine were treated with palmitic acid (4x10-4M) and/or 1α,25-hydroxy-vitamin D3 (VD, 10-11- 10-7M) with or without modulators of lipid metabolism and VD pathways. Cultures were analyzed by immunocyto- and histochemical methods. Results Vitamin D supplementation had no effect on enteric neuronal survival in the ND group. HFD caused substantial loss of myenteric neurons in ileum and colon. Vitamin D supplementation between 0-2x normal had no effect on HFD-induced neuronal loss. Supplementation with 20x normal, prevented the HFD-induced neuronal loss. In vitro supplementation of VD prevented the palmitic acid-induced neuronal loss. The VD receptor (VDR) was not identified in enteric neurons. Enteric glia expressed the alternative VD receptor, protein disulphide isomerase family A member 3 (PDIA3), but PDIA3 was not found to mediate the VD response in vitro. Inhibition of peroxisome proliferator-activated receptor gamma (PPARγ) and immune neutralization of isocitrate lyase prevented the VD mediated neuroprotection to palmitic acid exposure. Conclusions Results show that VD protect enteric neurons against HFD and palmitic acid induced neuronal loss. The mechanism behind is suggested to be through activation of PPARγ leading to improved neuronal peroxisome function and metabolism of neuronal lipid intermediates.
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Affiliation(s)
- Sara Larsson
- Unit of Molecular Endocrinology, Department of Experimental Medical Science, Lund University, Sölvegatan 19, BMC C11, 22184, Lund, Sweden
| | - Ulrikke Voss
- Unit of Neurogastroenterology, Department of Experimental Medical Science, Lund University, Sölvegatan 19, BMC B11, 22184, Lund, Sweden.
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Eswarappa SM, Potdar AA, Sahoo S, Sankar S, Fox PL. Metabolic origin of the fused aminoacyl-tRNA synthetase, glutamyl-prolyl-tRNA synthetase. J Biol Chem 2018; 293:19148-19156. [PMID: 30309984 DOI: 10.1074/jbc.ra118.004276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/03/2018] [Indexed: 11/06/2022] Open
Abstract
About 1 billion years ago, in a single-celled holozoan ancestor of all animals, a gene fusion of two tRNA synthetases formed the bifunctional enzyme, glutamyl-prolyl-tRNA synthetase (EPRS). We propose here that a confluence of metabolic, biochemical, and environmental factors contributed to the specific fusion of glutamyl- (ERS) and prolyl- (PRS) tRNA synthetases. To test this idea, we developed a mathematical model that centers on the precursor-product relationship of glutamic acid and proline, as well as metabolic constraints on free glutamic acid availability near the time of the fusion event. Our findings indicate that proline content increased in the proteome during the emergence of animals, thereby increasing demand for free proline. Together, these constraints contributed to a marked cellular depletion of glutamic acid and its products, with potentially catastrophic consequences. In response, an ancient organism invented an elegant solution in which genes encoding ERS and PRS fused to form EPRS, forcing coexpression of the two enzymes and preventing lethal dysregulation. The substantial evolutionary advantage of this coregulatory mechanism is evidenced by the persistence of EPRS in nearly all extant animals.
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Affiliation(s)
- Sandeep M Eswarappa
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India,
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, and
| | - Sarthak Sahoo
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Santhosh Sankar
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
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Krasovec M, Vancaester E, Rombauts S, Bucchini F, Yau S, Hemon C, Lebredonchel H, Grimsley N, Moreau H, Sanchez-Brosseau S, Vandepoele K, Piganeau G. Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage. Genome Biol Evol 2018; 10:2347-2365. [PMID: 30113623 PMCID: PMC6141220 DOI: 10.1093/gbe/evy167] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 01/11/2023] Open
Abstract
While the molecular events involved in cell responses to heat stress have been extensively studied, our understanding of the genetic basis of basal thermotolerance, and particularly its evolution within the green lineage, remains limited. Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Differential gene expression at high and standard temperatures revealed that more of the gene families containing up-regulated genes at high temperature were recently evolved, and less originated at the ancestor of green plants. Inversely, there was an excess of ancient gene families containing transcriptionally repressed genes. Interestingly, there is a striking overlap between the thermotolerance and halotolerance transcriptional rewiring, as more than one-third of the gene families up-regulated at 35 °C were also up-regulated under variable salt concentrations in Picochlorum SE3. Moreover, phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature. Altogether, these results provide new insights about how the genomic basis of adaptation to halo- and thermotolerance evolved in the green lineage.
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Affiliation(s)
- Marc Krasovec
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France.,Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Sheree Yau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Claire Hemon
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hugo Lebredonchel
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hervé Moreau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Belgium
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, Biologie Integrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
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Determination and pharmacokinetic study of Enasidenib in rat plasma by UPLC–MS/MS. J Pharm Biomed Anal 2018; 157:165-170. [DOI: 10.1016/j.jpba.2018.04.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/22/2018] [Accepted: 04/24/2018] [Indexed: 11/21/2022]
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Identification of specific metabolic pathways as druggable targets regulating the sensitivity to cyanide poisoning. PLoS One 2018; 13:e0193889. [PMID: 29879736 PMCID: PMC5991913 DOI: 10.1371/journal.pone.0193889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/20/2018] [Indexed: 11/19/2022] Open
Abstract
Cyanide is a potent toxic agent, and the few available antidotes are not amenable to rapid deployment in mass exposures. As a result, there are ongoing efforts to exploit different animal models to identify novel countermeasures. We have created a pipeline that combines high-throughput screening in zebrafish with subsequent validation in two mammalian small animal models as well as a porcine large animal model. We found that zebrafish embryos in the first 3 days post fertilization (dpf) are highly resistant to cyanide, becoming progressively more sensitive thereafter. Unbiased analysis of gene expression in response to several hours of ultimately lethal doses of cyanide in both 1 and 7 dpf zebrafish revealed modest changes in iron-related proteins associated with the age-dependent cyanide resistance. Metabolomics measurements demonstrated significant age-dependent differences in energy metabolism during cyanide exposure which prompted us to test modulators of the tricarboxylic acid cycle and related metabolic processes as potential antidotes. In cyanide-sensitive 7 dpf larvae, we identified several such compounds that offer significant protection against cyanide toxicity. Modulators of the pyruvate dehydrogenase complex, as well as the small molecule sodium glyoxylate, consistently protected against cyanide toxicity in 7 dpf zebrafish larvae. Together, our results indicate that the resistance of zebrafish embryos to cyanide toxicity during early development is related to an altered regulation of cellular metabolism, which we propose may be exploited as a potential target for the development of novel antidotes against cyanide poisoning.
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Patra T, Ghosh P, Alam N, Murmu N. Supra-physiological concentration of glyoxylate inhibits proliferation of human colon cancer cells through oxidative stress. Life Sci 2018; 207:80-89. [PMID: 29852189 DOI: 10.1016/j.lfs.2018.05.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/03/2018] [Accepted: 05/26/2018] [Indexed: 12/13/2022]
Abstract
AIMS The cytotoxic response of an intermediate metabolite glyoxylate (Glx) on colon carcinoma has been evaluated in vitro. MAIN METHODS The anti-proliferative effect of Glx was assessed on HT-29 and HCT-116 cells by performing MTT assay as well as beta-hexosaminidase assay. Evaluation of apoptotic event of Glx treated cells was measured by flow cytometry using annexin-V/PI staining. The mitochondrial membrane potential and level of ROS were estimated using DiOC6(3)/CCCP and DCFH-DA method, respectively. The assessment of catalase, LDH and IDH were performed. KEY FINDINGS The results of MTT assay indicated that treatment with Glx significantly inhibited the proliferation of HT-29 and HCT-116 cells. Beta-hexosaminidase assay also confirmed the inhibition of cellular viability. The dose-dependent Glx treatment indicated lowering the colony forming ability of HT-29 and HCT-116 cells. Flow cytometric data demonstrated the significant increment of late apoptotic event after Glx treatment. In addition, substantial LDH activity was noticed in both the colon cancer cells whereas the IDH activity was unaltered after extra-cellular addition of Glx. Further, dissipation of mitochondrial membrane potential and subsequently elevated ROS generation was also detected in the Glx treated colon cancer cells. However, gradual elevation of catalase activities indicated that Glx treatment on colon cancer cells exhibit oxidative stress. SIGNIFICANCE This study depicts that supra-physiological concentration of Glx inhibits the proliferation of colon cancer cells due to oxidative stress.
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Affiliation(s)
- Tapas Patra
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute (CNCI), Kolkata 700026, India
| | - Paramita Ghosh
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute (CNCI), Kolkata 700026, India
| | - Neyaz Alam
- Department of Surgical Oncology, Chittaranjan National Cancer Institute (CNCI), Kolkata 700026, India
| | - Nabendu Murmu
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute (CNCI), Kolkata 700026, India.
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Yu Y, Zhang L, Li T, Wu N, Jiang L, Ji X, Huang H. How nitrogen sources influence Mortierella alpina aging: From the lipid droplet proteome to the whole-cell proteome and metabolome. J Proteomics 2018; 179:140-149. [DOI: 10.1016/j.jprot.2018.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/19/2018] [Accepted: 03/16/2018] [Indexed: 01/20/2023]
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Zhao Y, Zhang J, Chen Y, Li Z, Nie H, Peng W, Su S. Altered Serum Metabolite Profiling and Relevant Pathway Analysis in Rats Stimulated by Honeybee Venom: New Insight into Allergy to Honeybee Venom. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:871-880. [PMID: 29322776 DOI: 10.1021/acs.jafc.7b04160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To improve our understanding of the disturbed metabolic pathways and cellular responses triggered by honeybee venom stimulation, we compared the changes in serum metabolites in rats, either stimulated or not by honeybee venom, by performing 1H nuclear magnetic resonance (NMR) spectrometry-based metabonomics to identify potential biomarkers. In this study, 65 metabolites were structurally confirmed and quantified and the following results were obtained. First, by pattern recognition analysis, 14 metabolites were selected as potential biomarkers 3 h after venom stimulation. Second, metabolic pathway analysis showed that methane metabolism, glyoxylate and dicarboxylate metabolism, tricarboxylic acid cycle, glycine, serine, and threonine metabolism, arginine and proline metabolism were affected. Finally, the time-dependent metabolic modifications indicated that rats could recover without medical treatment 24 h after venom stimulation. In summary, this new insight into the changes in serum metabolites in rats after honeybee venom stimulation has enhanced our understanding of the response of an organism to honeybee venom.
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Affiliation(s)
- Yazhou Zhao
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 100093, People's Republic of China
| | - Jianmei Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 100093, People's Republic of China
| | - Yanping Chen
- Bee Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA) , Beltsville, Maryland 20705, United States
| | - Zhiguo Li
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
| | - Hongyi Nie
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
| | - Wenjun Peng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 100093, People's Republic of China
| | - Songkun Su
- College of Bee Sciences/College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou, Fujian 350002, People's Republic of China
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Werling D. WITHDRAWN: Non-infectious stressors and innate immune response. Res Vet Sci 2018:S0034-5288(17)30980-3. [PMID: 29373122 DOI: 10.1016/j.rvsc.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/01/2018] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
This article has been withdrawn at the request of the author(s). The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, United Kingdom.
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46
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Ma Z, Bykova NV, Igamberdiev AU. Cell signaling mechanisms and metabolic regulation of germination and dormancy in barley seeds. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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47
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Chen HH, Jiang JG. Lipid Accumulation Mechanisms in Auto- and Heterotrophic Microalgae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8099-8110. [PMID: 28838232 DOI: 10.1021/acs.jafc.7b03495] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Microalgae lipids have attracted great attention in the world as a result of their potential use for biodiesel productions. Microalgae are cultivated in photoautotrophic conditions in most cases, but several species are able to grow under heterotrophic conditions, in which microalgae are cultivated in the dark where the cell growth and reproduction are supported by organic carbons. This perspective is covering the related studies concerning the difference between hetero- and autotrophic cultivation of microalgae. The auto- and heterotrophic central carbon metabolic pathways in microalgae are described, and the catalyzing reactions of several key metabolic enzymes and their corresponding changes in the protein level are summarized. Under adverse environmental conditions, such as nutrient deprivation, microalgae have the ability to highly store energy by forming triacylglycerol (TAG), the reason for which is analyzed. In addition, the biosynthesis of fatty acids and TAGs and their difference between auto- and heterotrophic conditions are compared at the molecular level. The positive regulatory enzymes, such as glucose transporter protein, fructose-1,6-bisphosphate aldolase, and glycerol-3-phosphate dehydrogenase, and the negative regulation enzymes, such as triose phosphate isomerase, played a crucial role in the lipid accumulation auto- and heterotrophic conditions.
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Affiliation(s)
- Hao-Hong Chen
- College of Food Science and Engineering, South China University of Technology , Guangzhou, Guangdong 510640, People's Republic of China
| | - Jian-Guo Jiang
- College of Food Science and Engineering, South China University of Technology , Guangzhou, Guangdong 510640, People's Republic of China
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48
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Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2017; 114:7617-7622. [PMID: 28679637 DOI: 10.1073/pnas.1706134114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Isocitrate lyase (ICL, types 1 and 2) is the first enzyme of the glyoxylate shunt, an essential pathway for Mycobacterium tuberculosis (Mtb) during the persistent phase of human TB infection. Here, we report 2-vinyl-d-isocitrate (2-VIC) as a mechanism-based inactivator of Mtb ICL1 and ICL2. The enzyme-catalyzed retro-aldol cleavage of 2-VIC unmasks a Michael substrate, 2-vinylglyoxylate, which then forms a slowly reversible, covalent adduct with the thiolate form of active-site Cys191 2-VIC displayed kinetic properties consistent with covalent, mechanism-based inactivation of ICL1 and ICL2 with high efficiency (partition ratio, <1). Analysis of a complex of ICL1:2-VIC by electrospray ionization mass spectrometry and X-ray crystallography confirmed the formation of the predicted covalent S-homopyruvoyl adduct of the active-site Cys191.
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Campilongo R, Fung RKY, Little RH, Grenga L, Trampari E, Pepe S, Chandra G, Stevenson CEM, Roncarati D, Malone JG. One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet 2017; 13:e1006839. [PMID: 28658302 PMCID: PMC5489143 DOI: 10.1371/journal.pgen.1006839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 12/04/2022] Open
Abstract
Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate. Here we show how Pseudomonas controls multiple different primary carbon metabolism pathways by sensing levels of KDPG, an Entner Doudoroff (ED) pathway intermediate. KDPG binds to two highly similar transcription factors; the ED regulator HexR and the previously uncharacterised protein RccR. RccR inversely controls the glyoxylate shunt, gluconeogenesis and pyruvate metabolism, suppressing the first two pathways as pyruvate metabolism genes are expressed, and vice versa. This complex regulation is enabled by two distinct RccR-binding consensus sequences in the RccR regulon promoters. KDPG binding simultaneously increases RccR affinity for the glyoxylate shunt and gluconeogenesis promoters, and releases repression of pyruvate metabolism. This elegant two-regulator circuit allows Pseudomonas to rapidly respond to carbon source availability by sensing a single key intermediate, KDPG.
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Affiliation(s)
- Rosaria Campilongo
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- Istituto Pasteur- Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘C. Darwin”, Sapienza Universita`di Roma, Roma, Italy
| | - Rowena K. Y. Fung
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Richard H. Little
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Lucia Grenga
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Eleftheria Trampari
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Simona Pepe
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Davide Roncarati
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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50
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Cipak Gasparovic A, Zarkovic N, Zarkovic K, Semen K, Kaminskyy D, Yelisyeyeva O, Bottari SP. Biomarkers of oxidative and nitro-oxidative stress: conventional and novel approaches. Br J Pharmacol 2017; 174:1771-1783. [PMID: 27864827 PMCID: PMC5446576 DOI: 10.1111/bph.13673] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 12/14/2022] Open
Abstract
The concept of oxidative stress (OS) that connects altered redox biology with various diseases was introduced 30 years ago and has generated intensive research over the past two decades. Whereas it is now commonly accepted that macromolecule oxidation in response to ROS is associated with a variety of pathologies, the emergence of NO as a key regulator of redox signalling has led to the discovery of the pathophysiological significance of reactive nitrogen species (RNS). RNS can elicit various modifications of macromolecules and lead to nitrative or nitro-OS. In order to investigate oxidative and nitro-OS in human and in live animal models, circulating biomarker assays have been developed. This article provides an overview of key biomarkers used to assess lipid peroxidation and NO/NO2 signalling, thereby stressing the necessity to analyse several OS biomarkers in relation to the overall (aerobic) metabolism and health condition of patients. In addition, the potential interest of heart rate variability as the non-invasive integrative biomarker of OS is discussed. LINKED ARTICLES This article is part of a themed section on Redox Biology and Oxidative Stress in Health and Disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.12/issuetoc.
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Affiliation(s)
| | | | - Kamelija Zarkovic
- Division of Pathology, Clinical Hospital Centre, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Khrystyna Semen
- Department of Propedeutics of Internal Medicine #2, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Danylo Kaminskyy
- Department of Pharmaceutical, Organic, and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Olha Yelisyeyeva
- Department of Histology, Cytology and Embryology, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Serge P Bottari
- Institute for Advanced Biosciences, INSERM U1029, CNRS UMR 5309, Grenoble-Alps University Medical School, Grenoble, France
- Radioanalysis Laboratory, CHU Grenoble-Alpes, Grenoble, France
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