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Patiño-Ruiz MF, Anshari ZR, Gaastra B, Slotboom DJ, Poolman B. Chemiosmotic nutrient transport in synthetic cells powered by electrogenic antiport coupled to decarboxylation. Nat Commun 2024; 15:7976. [PMID: 39266519 PMCID: PMC11392934 DOI: 10.1038/s41467-024-52085-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 08/27/2024] [Indexed: 09/14/2024] Open
Abstract
Cellular homeostasis depends on the supply of metabolic energy in the form of ATP and electrochemical ion gradients. The construction of synthetic cells requires a constant supply of energy to drive membrane transport and metabolism. Here, we provide synthetic cells with long-lasting metabolic energy in the form of an electrochemical proton gradient. Leveraging the L-malate decarboxylation pathway we generate a stable proton gradient and electrical potential in lipid vesicles by electrogenic L-malate/L-lactate exchange coupled to L-malate decarboxylation. By co-reconstitution with the transporters GltP and LacY, the synthetic cells maintain accumulation of L-glutamate and lactose over periods of hours, mimicking nutrient feeding in living cells. We couple the accumulation of lactose to a metabolic network for the generation of intermediates of the glycolytic and pentose phosphate pathways. This study underscores the potential of harnessing a proton motive force via a simple metabolic network, paving the way for the development of more complex synthetic systems.
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Affiliation(s)
- Miyer F Patiño-Ruiz
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Zaid Ramdhan Anshari
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bauke Gaastra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dirk J Slotboom
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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2
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Garrett OS, Druss JJ, Vos EN, Fu YTD, Lucia S, Greenstein PE, Bauer A, Sykut-Cegielska J, Stepien KM, Arbuckle C, Grafakou O, Meyer U, Vanhoutvin N, Pané A, Bosch AM, Rubio-Gozalbo E, Berry GT, Fridovich-Keil JL. Health and well-being of maturing adults with classic galactosemia. J Inherit Metab Dis 2024. [PMID: 39143820 DOI: 10.1002/jimd.12786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
Long-term outcomes in classic galactosemia (CG) have been studied previously, but all prior studies have relied on cohorts of patients that were small in number, or heavily skewed toward children and young adults, or both. Here, we extend what is known about the health and well-being of maturing adults with CG by analyzing the results of anonymous custom surveys completed by 92 affected individuals, ages 30-78, and 38 unaffected sibling controls, ages 30-79. The median age for patients was 38.5 years and for controls was 41 years. These study participants hailed from 12 different countries predominantly representing Europe and North America. Participants reported on their general life experiences and outcomes in seven different domains including: speech/voice/language, cognition, motor function, cataracts, bone health, psychosocial well-being, and gastrointestinal health. We also queried women about ovarian function. Our results indicated a prevalence of long-term complications across all outcome domains that aligned with levels previously reported in younger cohorts. Given the sample size and age range of participants in this study, these findings strongly suggest that the adverse developmental outcomes commonly linked to CG are not progressive with age for most patients. We also tested four candidate modifiers for possible association with each of the outcomes followed, including: days of neonatal milk exposure, rigor of dietary galactose restriction in early childhood, current age, and home continent. We observed no associations that reached even nominal significance, except for the following: cataracts with neonatal milk exposure (p = 2.347e-04), cataracts with age (p = 0.018), and bone health with home continent (p = 0.03).
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Affiliation(s)
- Olivia S Garrett
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jared J Druss
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - E Naomi Vos
- MosaKids Children's Hospital, Department of Pediatrics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Yu-Ting Debbie Fu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Stephanie Lucia
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Patricia E Greenstein
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Anna Bauer
- Department of Inborn Errors of Metabolism and Pediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Pediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Karolina M Stepien
- Adult Inherited Metabolic Disorders Department, Salford Royal Organization, Northern Care Alliance NHS Foundation Trust, Salford, UK
| | - Cameron Arbuckle
- Charles Dent Metabolic Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Olga Grafakou
- Clinical Genetics and Metabolic Disorders Clinic, Department of Pediatrics, Archbishop Makarios III Hospital, State Health Services Organization, Nicosia, Cyprus
| | - Uta Meyer
- Department of Pediatric Kidney, Liver, Metabolic and Neurological Diseases, Hannover Medical School, Hannover, Germany
| | - Nele Vanhoutvin
- Department of Gastroenterology-Hepatology and Metabolic Center, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Adriana Pané
- Endocrinology and Nutrition Department, Hospital Clinic de Barcelona, CIBEROBN, Instituto de Salud Carlos III, Madrid, Spain
| | - Annet M Bosch
- Department of Pediatrics, Division of Metabolic Diseases, Amsterdam Gastroenterology Endocrinology and Metabolism, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Estela Rubio-Gozalbo
- MosaKids Children's Hospital, Department of Pediatrics, Maastricht University Medical Center, Maastricht, Netherlands
- Laboratory of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Gerard T Berry
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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3
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Sun Y, Su X, Zhao L, Sun T, Liu W. Carbon metabolism of a novel isolate from Lacticaseibacillus rhamnosus Probio-M9 derived through space mutant. J Appl Microbiol 2024; 135:lxae205. [PMID: 39152088 DOI: 10.1093/jambio/lxae205] [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: 10/19/2023] [Revised: 07/07/2024] [Accepted: 08/15/2024] [Indexed: 08/19/2024]
Abstract
AIMS Carbon source is a necessary nutrient for bacterial strain growth. In industrial production, the cost of using different carbon sources varies greatly. Moreover, the complex environment in space may cause metabolic a series of changes in the strain, and this method has been successfully applied in some basic research. To date, space mutagenesis is still limited number of studies, particularly in carbon metabolism of probiotics. METHODS AND RESULTS HG-R7970-41 was isolated from bacterium suspension (Probio-M9) after space flight, which can produce capsular polysaccharide after space mutagenesis. Phenotype Microarray (PM) was used to evaluated the metabolism of HG-R7970-41 in 190 single carbon sources. RNA sequencing and total protein identification of two strains revealed their different carbon metabolism mechanisms. PM results demonstrated the metabolism of 10 carbon sources were different between Probio-M9 and HG-R7970-41. Transcriptomic and proteomic analyses revealed that this change in carbon metabolism of HG-R7970-41 mainly related to changes in phosphorylation and the glycolysis pathway. Based on the metabolic mechanism of different carbon sources and related gene cluster analysis, we found that the final metabolic activities of HG-R7970-41 and Probio-M9 were mainly regulated by PTS-specific membrane embedded permease, carbohydrate kinase and two rate-limiting enzymes (phosphofructokinase and pyruvate kinase) in the glycolysis pathway. The expanded culture test also confirmed that HG-R7970-41 had different metabolic characteristics from original strain. CONCLUSIONS These results suggested that space environment could change carbon metabolism of Probio-M9. The new isolate (HG-R7970-41) showed a different carbon metabolism pattern from the original strain mainly by the regulation of two rate-limiting enzymes.
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Affiliation(s)
- Yue Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
- College of Food Science and Technology, Wuhan Business University, Wuhan, Hubei province, 430056, China
| | - Xin Su
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Lixia Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Tiansong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Wenjun Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
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Mikami-Saito Y, Wada Y, Arai-Ichinoi N, Nakajima Y, Suzuki-Ajihara S, Murayama K, Tanaka T, Numakura C, Hamazaki T, Igarashi N, Esaki H, Kagawa R, Kono T, Sawada T, Sawada T, Nyuzuki H, Hirai H, Fumoto S, Matsuda J, Matsunaga A, Maruyama S, Yamaguchi K, Yoshino M, Totsune E, Kikuchi A, Ohura T, Kure S. Phenotypic and genetic spectra of galactose mutarotase deficiency: A nationwide survey conducted in Japan. Genet Med 2024; 26:101165. [PMID: 38762772 DOI: 10.1016/j.gim.2024.101165] [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: 12/10/2023] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
PURPOSE Galactose mutarotase (GALM) deficiency was first reported in 2019 as the fourth type of galactosemia. This study aimed to investigate the clinical and genotypic spectra of GALM deficiency. METHODS This was a questionnaire-based retrospective survey conducted in Japan between February 2022 and March 2023. RESULTS We identified 40 patients with GALM deficiency in Japan (estimated prevalence: 1:181,835). Four of 38 patients (10.5%) developed cataracts, which resolved with lactose restriction in 3 out of 4 patients. Transient transaminitis was the most common symptom (23.1%). All of the patients followed lactose restriction; discontinuation of the restriction after infancy did not cause any complications. Moreover, none of the participants experienced long-term complications. Two variants, GALM NM_138801.3: c.294del and c.424G>A, accounted for 72.5% of the identified pathogenic variants. The patients showed moderately elevated blood galactose levels with lactose intake; however, the elevation was lower than that observed in galactokinase deficiency. CONCLUSION GALM deficiency is characterized by a similar but milder phenotype and lower blood galactose elevation than in galactokinase deficiency. Diagnosis and initiation of lactose restriction in early infancy should be essential for prevention of cataracts, especially in cases of irreversible opacity.
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Affiliation(s)
- Yasuko Mikami-Saito
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Wada
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Natsuko Arai-Ichinoi
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Yoko Nakajima
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Sayaka Suzuki-Ajihara
- Department of Pediatrics and Clinical Genomics, Saitama Medical University, Saitama, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Toju Tanaka
- Department of Pediatrics, National Hospital Organization Hokkaido Medical Center, Sapporo, Japan
| | - Chikahiko Numakura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Takashi Hamazaki
- Department of Pediatrics, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Noboru Igarashi
- Department of Pediatrics, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Hiroyuki Esaki
- Department of Pediatrics, Sasebo City General Hospital, Sasebo, Japan
| | - Reiko Kagawa
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tomotaka Kono
- Division of Endocrinology and Metabolism, Saitama Children's Medical Center, Saitama, Japan
| | - Takaaki Sawada
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomo Sawada
- Department of Pediatrics, Izumi City General Hospital, Osaka, Japan
| | - Hiromi Nyuzuki
- Division of Pediatrics, Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroki Hirai
- Department of Pediatrics, Shikoku Central Hospital of the Mutual Aid Association of Public School Teachers, Shikokuchuo, Japan
| | - Seiko Fumoto
- Department of Pediatrics, Kyorin University School of Medicine, Mitaka, Japan
| | - Junko Matsuda
- Department of Pathophysiology and Metabolism, Kawasaki Medical School, Kurashiki, Japan
| | - Ayako Matsunaga
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Shinsuke Maruyama
- Department of Pediatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kenichiro Yamaguchi
- Department of Pediatrics, National Hospital Organization Kokura Medical Center, Kitakyushu, Japan
| | - Miwa Yoshino
- Department of Pediatrics, Kyushu Hospital, Japan Community Healthcare Organization, Kitakyushu, Japan
| | - Eriko Totsune
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshihiro Ohura
- Division of Clinical Laboratory, Sendai City Hospital, Sendai, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
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5
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Daenzer JMI, Druss JJ, Fridovich-Keil JL. Restoring galactose metabolism without restoring GALT rescues both compromised survival in larvae and an adult climbing deficit in a GALT-null D. Melanogaster model of classic galactosemia. J Inherit Metab Dis 2024. [PMID: 38960603 DOI: 10.1002/jimd.12774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
Classic galactosemia (CG) is an autosomal recessive disorder that results from profound deficiency of galactose-1-phosphate uridylyltransferase (GALT), the middle enzyme in the highly conserved Leloir pathway of galactose metabolism. That galactose metabolism is disrupted in patients with CG, and in GALT-null microbial, cell culture, and animal models of CG, has been known for many years. However, whether the long-term developmental complications of CG result from disrupted galactose metabolism alone, or from loss of some independent moonlighting function of GALT, in addition to disrupted galactose metabolism, has been posed but never resolved. Here, we addressed this question using a GALT-null Drosophila melanogaster model of CG engineered to express uridine diphosphate (UDP)-glucose/galactose pyrophosphorylase (UGGP), a plant enzyme that effectively bypasses GALT in the Leloir pathway by converting substrates uridine triphosphate (UTP) plus galactose-1-phosphate (gal-1P) into products UDP-galactose plus pyrophosphate (PPi). While GALT and UGGP share one substrate (gal-1P) and one product (UDP-galactose), they are structurally and evolutionarily unrelated enzymes. It is therefore extremely unlikely that they would also share a moonlighting function. We found that GALT-null flies expressing UGGP showed not only partial rescue of metabolic abnormalities and acute larval sensitivity to dietary galactose, as expected, but also full rescue of an adult motor deficit otherwise seen in this model. By extension, these results may offer insights to the underlying bases of at least some acute and long-term complications experienced by patients with CG.
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Affiliation(s)
- Jennifer M I Daenzer
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jared J Druss
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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Yun EJ, Lee SH, Kim S, Ryu HS, Kim KH. Catabolism of 2-keto-3-deoxy-galactonate and the production of its enantiomers. Appl Microbiol Biotechnol 2024; 108:403. [PMID: 38954014 PMCID: PMC11219438 DOI: 10.1007/s00253-024-13235-x] [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: 04/11/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
2-Keto-3-deoxy-galactonate (KDGal) serves as a pivotal metabolic intermediate within both the fungal D-galacturonate pathway, which is integral to pectin catabolism, and the bacterial DeLey-Doudoroff pathway for D-galactose catabolism. The presence of KDGal enantiomers, L-KDGal and D-KDGal, varies across these pathways. Fungal pathways generate L-KDGal through the reduction and dehydration of D-galacturonate, whereas bacterial pathways produce D-KDGal through the oxidation and dehydration of D-galactose. Two distinct catabolic routes further metabolize KDGal: a nonphosphorolytic pathway that employs aldolase and a phosphorolytic pathway involving kinase and aldolase. Recent findings have revealed that L-KDGal, identified in the bacterial catabolism of 3,6-anhydro-L-galactose, a major component of red seaweeds, is also catabolized by Escherichia coli, which is traditionally known to be catabolized by specific fungal species, such as Trichoderma reesei. Furthermore, the potential industrial applications of KDGal and its derivatives, such as pyruvate and D- and L-glyceraldehyde, are underscored by their significant biological functions. This review comprehensively outlines the catabolism of L-KDGal and D-KDGal across different biological systems, highlights stereospecific methods for discriminating between enantiomers, and explores industrial application prospects for producing KDGal enantiomers. KEY POINTS: • KDGal is a metabolic intermediate in fungal and bacterial pathways • Stereospecific enzymes can be used to identify the enantiomeric nature of KDGal • KDGal can be used to induce pectin catabolism or produce functional materials.
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Affiliation(s)
- Eun Ju Yun
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Sun-Hee Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Subin Kim
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Hae Seul Ryu
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea.
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Castañeda-Casasola CC, Nieto-Jacobo MF, Soares A, Padilla-Padilla EA, Anducho-Reyes MA, Brown C, Soth S, Esquivel-Naranjo EU, Hampton J, Mendoza-Mendoza A. Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens. Int J Mol Sci 2024; 25:5172. [PMID: 38791210 PMCID: PMC11121469 DOI: 10.3390/ijms25105172] [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: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
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Affiliation(s)
- Cynthia Coccet Castañeda-Casasola
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Centro Nacional de Referencia Fitosanitaria, Tecamac 55740, Mexico
| | | | - Amanda Soares
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Emir Alejandro Padilla-Padilla
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 04510, Mexico
| | - Miguel Angel Anducho-Reyes
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
| | - Chris Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
| | - Sereyboth Soth
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Edgardo Ulises Esquivel-Naranjo
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, Queretaro 76230, Mexico
| | - John Hampton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Artemio Mendoza-Mendoza
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
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8
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Xu Y, Wang X, Zaal EA, Berkers CR, Lorent JH, Heise T, Cox R, Pieters RJ, Breukink E. Specific labeling of newly synthesized lipopolysaccharide via metabolic incorporation of azido-galactose. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159467. [PMID: 38382574 DOI: 10.1016/j.bbalip.2024.159467] [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: 01/02/2024] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
Gram-negative bacteria possess an asymmetric outer membrane (OM) primarily composed of lipopolysaccharides (LPS) on the outer leaflet and phospholipids on the inner leaflet. The outer membrane functions as an effective permeability barrier to compounds such as antibiotics. Studying LPS biosynthesis is therefore helpful to explore novel strategies for new antibiotic development. Metabolic glycan labeling of the bacterial surface has emerged as a powerful method to investigate LPS biosynthesis. However, the previously reported methods of labeling LPS are based on radioactivity or difficult-to-produce analogs of bacterial sugars. In this study, we report on the incorporation of azido galactose into the LPS of the Gram-negative bacteria Escherichia coli and Salmonella typhi via metabolic labeling. As a common sugar analog, azido galactose successfully labeled both O-antigen and core of Salmonella LPS, but not E. coli LPS. This labeling of Salmonella LPS, as shown by SDS-PAGE analysis and fluorescence microscopy, differs from the previously reported labeling of either O-antigen or core of LPS. Our findings are useful for studying LPS biogenesis pathways in Gram-negative bacteria like Salmonella. In addition, our approach is helpful for screening for agents that target LPS biosynthesis as it allows for the detection of newly synthesized LPS that appears in the OM. Furthermore, this approach may also aid in isolating chemically modified LPS for vaccine development or immunotherapy.
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Affiliation(s)
- Yang Xu
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Esther A Zaal
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Celia R Berkers
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Torben Heise
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Ruud Cox
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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9
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Xu J, Zhao Y, Tyler Mertens R, Ding Y, Xiao P. Sweet regulation - The emerging immunoregulatory roles of hexoses. J Adv Res 2024:S2090-1232(24)00157-7. [PMID: 38631430 DOI: 10.1016/j.jare.2024.04.014] [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: 10/04/2023] [Revised: 03/20/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND It is widely acknowledged that dietary habits have profound impacts on human health and diseases. As the most important sweeteners and energy sources in human diets, hexoses take part in a broad range of physiopathological processes. In recent years, emerging evidence has uncovered the crucial roles of hexoses, such as glucose, fructose, mannose, and galactose, in controlling the differentiation or function of immune cells. AIM OF REVIEW Herein, we reviewed the latest research progresses in the hexose-mediated modulation of immune responses, provided in-depth analyses of the underlying mechanisms, and discussed the unresolved issues in this field. KEY SCIENTIFIC CONCEPTS OF REVIEW Owing to their immunoregulatory effects, hexoses affect the onset and progression of various types of immune disorders, including inflammatory diseases, autoimmune diseases, and tumor immune evasion. Thus, targeting hexose metabolism is becoming a promising strategy for reversing immune abnormalities in diseases.
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Affiliation(s)
- Junjie Xu
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuening Zhao
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Yimin Ding
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Xiao
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory for Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou, China.
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10
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Klingler F, Schlossbauer P, Naumann L, Handrick R, Hesse F, Neusüß C, Otte K. Developing microRNAs as engineering tools to modulate monoclonal antibody galactosylation. Biotechnol Bioeng 2024; 121:1355-1365. [PMID: 38079069 DOI: 10.1002/bit.28616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 04/01/2024]
Abstract
N-linked glycosylation is one of the most important post-translational modifications of monoclonal antibodies (mAbs) and is considered to be a critical quality attribute (CQA), as the glycan composition often has immunomodulatory effects. Since terminal galactose residues of mAbs can affect antibody-dependent cellular cytotoxicity (ADCC), complement-dependent cytolysis (CDC) activation, serum half-life, and antiviral activity it has to be monitored, controlled and modulated to ensure therapeutic effects. The ability of small noncoding microRNAs (miRNAs) to modulate glycosylation in Chinese hamster ovary (CHO) production cells was recently reported establishing miRNAs as engineering tools for modulation of protein glycosylation. In this study, we report the characterization and validation of miRNAs as engineering tools for increased (mmu-miR-452-5p, mmu-miR-193b-3p) or decreased (mmu-miR-7646-5p, mmu-miR-7243-3p, mmu-miR-1668, mmu-let-7c-1-3p, mmu-miR-7665-3p, mmu-miR-6403) degree of galactosylation. Furthermore, the biological mode of action regulating gene expression of the galactosylation pathway was characterized as well as their influence on bioprocess-related parameters. Most important, stable plasmid-based overexpression of these miRNAs represents a versatile tool for engineering N-linked galactosylation to achieve favorable phenotypes in cell lines for biopharmaceutical production.
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Affiliation(s)
- Florian Klingler
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Patrick Schlossbauer
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Lukas Naumann
- Department of Chemistry, Aalen University, Aalen, Germany
| | - René Handrick
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Friedemann Hesse
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | | | - Kerstin Otte
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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11
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Benzarti M, Neises L, Oudin A, Krötz C, Viry E, Gargiulo E, Pulido C, Schmoetten M, Pozdeev V, Lorenz NI, Ronellenfitsch MW, Sumpton D, Warmoes M, Jaeger C, Lesur A, Becker B, Moussay E, Paggetti J, Niclou SP, Letellier E, Meiser J. PKM2 diverts glycolytic flux in dependence on mitochondrial one-carbon cycle. Cell Rep 2024; 43:113868. [PMID: 38421868 DOI: 10.1016/j.celrep.2024.113868] [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: 06/08/2023] [Revised: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Modeling tumor metabolism in vitro remains challenging. Here, we used galactose as an in vitro tool compound to mimic glycolytic limitation. In contrast to the established idea that high glycolytic flux reduces pyruvate kinase isozyme M2 (PKM2) activity to support anabolic processes, we have discovered that glycolytic limitation also affects PKM2 activity. Surprisingly, despite limited carbon availability and energetic stress, cells induce a near-complete block of PKM2 to divert carbons toward serine metabolism. Simultaneously, TCA cycle flux is sustained, and oxygen consumption is increased, supported by glutamine. Glutamine not only supports TCA cycle flux but also serine synthesis via distinct mechanisms that are directed through PKM2 inhibition. Finally, deleting mitochondrial one-carbon (1C) cycle reversed the PKM2 block, suggesting a potential formate-dependent crosstalk that coordinates mitochondrial 1C flux and cytosolic glycolysis to support cell survival and proliferation during nutrient-scarce conditions.
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Affiliation(s)
- Mohaned Benzarti
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg; Molecular Disease Mechanisms Group, Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Laura Neises
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anais Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Christina Krötz
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Elodie Viry
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Ernesto Gargiulo
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Coralie Pulido
- Animal Facility, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Maryse Schmoetten
- Molecular Disease Mechanisms Group, Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Vitaly Pozdeev
- Molecular Disease Mechanisms Group, Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Nadia I Lorenz
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany; German Cancer Consortium, Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany; University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Michael W Ronellenfitsch
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany; German Cancer Consortium, Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany; University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - David Sumpton
- Cancer Research U.K. Scotland Institute, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Marc Warmoes
- Metabolomics Platform, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jaeger
- Metabolomics Platform, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Antoine Lesur
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Björn Becker
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Etienne Moussay
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jerome Paggetti
- Tumor Stroma Interactions, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Simone P Niclou
- Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg; NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Elisabeth Letellier
- Molecular Disease Mechanisms Group, Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
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12
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Mori T, Abe I. Lincosamide Antibiotics: Structure, Activity, and Biosynthesis. Chembiochem 2024; 25:e202300840. [PMID: 38165257 DOI: 10.1002/cbic.202300840] [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: 12/12/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/03/2024]
Abstract
Lincosamides are naturally occurring antibiotics isolated from Streptomyces sp. Currently, lincomycin A and its semisynthetic analogue clindamycin are used as clinical drugs. Due to their unique structures and remarkable biological activities, derivatizations of lincosamides via semi-synthesis and biosynthetic studies have been reported. This review summarizes the structures and biological activities of lincosamides, and the recent studies of lincosamide biosynthetic enzymes.
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Grants
- JP20H00490 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP22H05126 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP23H00393 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP23H02641 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JPNP20011 New Energy and Industrial Technology Development Organization
- JP21ak0101164 New Energy and Industrial Technology Development Organization
- JP23ama121027 New Energy and Industrial Technology Development Organization
- JPMJPR20DA Japan Science and Technology Agency
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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13
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Liu W, Huang T, Deng G, Mei X, Zhong S, Shen D, Zhang X, Jiang L, Zhao Q. Genetic and transcriptome analysis of the smb mutant in Bombyx mori. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101167. [PMID: 38113651 DOI: 10.1016/j.cbd.2023.101167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
More than 600 mutations have been discovered in the history of silkworm domestication. It is important to study the formation mechanism of these mutations to further understand the life and development process of silkworms and agricultural pest control. The silkworm mutant smb was isolated from silkworm strain NCV, and transcriptome analysis was performed on the silkworm mutant. 796 differentially expressed genes (DEGs) were detected at 48 h of the second instar stage with 669 genes significantly upregulated and 127 genes significantly downregulated. During the GO enrichment analysis, it was found that the enrichment of biological processes was mainly concentrated in proteolysis, carbohydrate metabolism, aminoglycan metabolism, organic substance metabolism, protein metabolism and so on. Based on the analysis of KEGG pathways, it revealed that the pathways enriched in lysosomes, AMPK signaling, fatty acid metabolism, PPAR signaling, galactose metabolism, and protein digestion and absorption were the most significant. Through these most significantly enriched GO terms and KEGG pathways, DEGs consistent with the phenotypic characteristics of the smb mutant were identified, including small body size, slow development, and successive death after the fourth instar. These results provided experimental evidence for the potential formation mechanism of smb mutants.
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Affiliation(s)
- Weibin Liu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - TianChen Huang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Gang Deng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Xinglin Mei
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Shanshan Zhong
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Dongxu Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; The Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Xuelian Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; The Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Li Jiang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Qiaoling Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; The Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China.
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14
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Sakizli U, Takano T, Yoo SK. GALDAR: A genetically encoded galactose sensor for visualizing sugar metabolism in vivo. PLoS Biol 2024; 22:e3002549. [PMID: 38502638 PMCID: PMC10950222 DOI: 10.1371/journal.pbio.3002549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
Sugar metabolism plays a pivotal role in sustaining life. Its dynamics within organisms is less understood compared to its intracellular metabolism. Galactose, a hexose stereoisomer of glucose, is a monosaccharide transported via the same transporters with glucose. Galactose feeds into glycolysis and regulates protein glycosylation. Defects in galactose metabolism are lethal for animals. Here, by transgenically implementing the yeast galactose sensing system into Drosophila, we developed a genetically encoded sensor, GALDAR, which detects galactose in vivo. Using this heterologous system, we revealed dynamics of galactose metabolism in various tissues. Notably, we discovered that intestinal stem cells do not uptake detectable levels of galactose or glucose. GALDAR elucidates the role for galactokinase in metabolism of galactose and a transition of galactose metabolism during the larval period. This work provides a new system that enables analyses of in vivo sugar metabolism.
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Affiliation(s)
- Uğurcan Sakizli
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
| | - Tomomi Takano
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, Japan
| | - Sa Kan Yoo
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, Japan
- Division of Developmental Biology and Regenerative Medicine, Kobe University, Kobe, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, Japan
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15
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Hernández-Prieto JH, Martini VP, Iulek J. Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie 2024; 218:20-33. [PMID: 37709188 DOI: 10.1016/j.biochi.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The pathogen Paracoccidioides lutzii (Pb01) is found in South America countries Colombia, Ecuador, Venezuela and Brazil, especially in the central, west, and north regions of the latter. It belongs to the Ajellomycetaceae family, Onygenales order, and is typically thermodimorphic, presenting yeast cells when it grows in animal tissues, but mycelia when in the environment, where it produces the infectious propagule. This fungus is one of the etiologic agents of Paracoccidioidomycosis (PCM), the most important endemic fungal infection in Latin America. Investigations on its genome have contributed to a better understanding about its metabolism and revealed the complexity of several metabolic glycolytic pathways. Glyceraldehyde-3-Phosphate Dehydrogenase from Paracoccidioides lutzii (PlGAPDH) is considered a moonlighting protein and participates in several biological processes of this pathogen. The enzyme was expressed and purified, as seen in SDS-PAGE gel, crystallized and had its three dimensional structure (3D) determined in complex with NAD+, a sulphate ion and d-galactonic acid, therefore, a type of 'GAA site'. It is the first GAPDH structure to show this chemical type in this site and how this protein can bind an acid derived from oxidation of a linear hexose.
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Affiliation(s)
| | | | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil.
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16
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Clausen U, Vital ST, Lambertus P, Gehler M, Scheve S, Wöhlbrand L, Rabus R. Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective. Microb Physiol 2024; 34:88-107. [PMID: 38262373 DOI: 10.1159/000536327] [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: 08/28/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology. METHODS P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics. RESULTS The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. CONCLUSIONS The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.
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Affiliation(s)
- Urte Clausen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sören-Tobias Vital
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Pia Lambertus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Martina Gehler
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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17
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Gerrick ER, Zlitni S, West PT, Carter MM, Mechler CM, Olm MR, Caffrey EB, Li JA, Higginbottom SK, Severyn CJ, Kracke F, Spormann AM, Sonnenburg JL, Bhatt AS, Howitt MR. Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell 2024; 187:62-78.e20. [PMID: 38096822 DOI: 10.1016/j.cell.2023.11.018] [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: 08/26/2022] [Revised: 08/01/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.
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Affiliation(s)
- Elias R Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrick T West
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Claire M Mechler
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jessica A Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher J Severyn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Division of Hematology/Oncology/Stem Cell Transplant and Regenerative Medicine Stanford University, Palo Alto, CA 94305, USA
| | - Frauke Kracke
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael R Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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18
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Veenhoven J, Saverwyns S, van Keulen H, van Bommel M, Lynen F. Polysaccharide metabolism in Anacardiaceae (Asian lacquer) cross-linked polymers elucidated using in situ trimethylsilylation pyrolysis-gas chromatography-mass spectrometry. Carbohydr Polym 2024; 323:121373. [PMID: 37940270 DOI: 10.1016/j.carbpol.2023.121373] [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: 07/12/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 11/10/2023]
Abstract
Carbohydrates from polysaccharides in natural thermoset Anacardiaceae polymers of Gluta usitata, Toxicodendron succedaneum and Toxicodendron vernicifluum were identified using pyrolysis-gas chromatography-mass spectrometry with in situ trimethylsilylation. Pyrolysates resulting from the pyrolytic intermolecular chain scission of the polysaccharides were used to elucidate monomeric units. Polysaccharides, dispersed in the phenolic lacasse catalysed cross-linked macromolecules, showed to be metabolised through various catabolic and anabolic routes. Galactose functionalities, abundantly present in the polysaccharides were determined to be enzymatically converted to glucose-6-phosphate, followed by conversion via glycolysis and pentose phosphate pathways. Determination of specific routes of carbohydrate modification via glycolysis and pentose phosphate pathways facilitated differentiating G. usitata, T. succedaneum and T. vernicifluum polymers, based on the carbohydrate content. It was also found that uronic type acids, present as end groups of the branched polysaccharide structure, were biochemically converted to aldonic acids. Following the pentose phosphate and glycolysis routes, carbohydrates in G. usitata and T. vernicifluum polymers showed to be further modified via shikimate and cinnamate pathways to produce phenylpropanoid compounds. Parent molecules and pyrolysis products thereof were verified using analytical standards of high purity. The mass spectra and Kovats retention indices were compiled in an AMDIS library, which can be made available on request.
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Affiliation(s)
- Jonas Veenhoven
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4 Bis, B-9000 Ghent, Belgium; Paintings Lab, Laboratories Department, Royal Institute for Cultural Heritage (KIK-IRPA), Jubelpark 1, B-1000 Brussels, Belgium; Conservation and Restoration of Cultural Heritage, Amsterdam School for Heritage, Memory and Material Culture (AHM), Faculty of Humanities, University of Amsterdam, P.O. Box 94552, 1090 GN Amsterdam, the Netherlands.
| | - Steven Saverwyns
- Paintings Lab, Laboratories Department, Royal Institute for Cultural Heritage (KIK-IRPA), Jubelpark 1, B-1000 Brussels, Belgium.
| | - Henk van Keulen
- Cultural Heritage Laboratory, Cultural Heritage Agency of the Netherlands (RCE), Hobbemastraat 22, 1071 ZC Amsterdam, the Netherlands.
| | - Maarten van Bommel
- Conservation and Restoration of Cultural Heritage, Amsterdam School for Heritage, Memory and Material Culture (AHM), Faculty of Humanities, University of Amsterdam, P.O. Box 94552, 1090 GN Amsterdam, the Netherlands; Analytical Sciences, van 't Hoff Institute for Molecular Sciences, Faculty of Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands.
| | - Frédéric Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4 Bis, B-9000 Ghent, Belgium.
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19
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Hames A, Khan S, Gilliland C, Goldman L, Lo HW, Magda K, Keathley J. Carriers of autosomal recessive conditions: are they really 'unaffected?'. J Med Genet 2023; 61:1-7. [PMID: 37775265 DOI: 10.1136/jmg-2023-109563] [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: 08/04/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023]
Abstract
Mendel's Law of Dominance suggests that recessive disease expression requires the inheritance of two mutated alleles as the dominant, wildtype allele suppresses disease presentation leading to the expression of physiological normal phenotypes. However, there is existing evidence that challenges this school of thought. Here, we summarise existing literature evaluating metabolic and health impacts among carriers of autosomal recessive conditions, focusing on phenylketonuria (PKU), classical homocystinuria, galactosemia and Usher syndrome as examples. Our findings suggest that carriers, often described as 'unaffected', may actually display attenuated symptoms for the recessive disease they are carrying. For instance, PKU is an inborn error of metabolism characterised by the build-up of plasma phenylalanine attributed to the deficiency of the phenylalanine hydroxylase (PAH) enzyme. While less severe, PKU carriers also exhibit this impaired enzymatic activity, leading to elevated plasma phenylalanine levels, especially after phenylalanine consumption. Related to these metabolic alterations in the PAH pathway, there is early evidence to suggest that PKU carriers may have compromised cognitive and mental health outcomes. Overall, research on the health and metabolic impacts of PKU carriers is sparse, with most studies conducted several decades ago. However, early evidence suggests that intermediate phenotypes among carriers of autosomal recessive conditions are plausible. The illustrated possible intermediate phenotypes observed among carriers necessitates future research to determine possible clinical implications among this population.
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Affiliation(s)
- Amber Hames
- Department of Family Relations and Applied Nutrition, University of Guelph, Guelph, Southwestern Ontario, Canada
| | - Sophia Khan
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Southwestern Ontario, Canada
| | - Clara Gilliland
- Department of Food Science, University of Guelph, Guelph, Southwestern Ontario, Canada
| | - Lucy Goldman
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Southwestern Ontario, Canada
| | - Hillary Wh Lo
- Department of Family Relations and Applied Nutrition, University of Guelph, Guelph, Southwestern Ontario, Canada
| | - Kevin Magda
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Southwestern Ontario, Canada
- Department of Biomedical Sciences, University of Guelph, Guelph, Southwestern Ontario, Canada
| | - Justine Keathley
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, Southwestern Ontario, Canada
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20
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Fos-Codoner FS, Bouwman LMS, Keijer J, van Schothorst EM. Dietary Galactose Increases the Expression of Mitochondrial OXPHOS Genes and Modulates the Carbohydrate Oxidation Pathways in Mouse Intestinal Mucosa. J Nutr 2023; 153:3448-3457. [PMID: 37858726 DOI: 10.1016/j.tjnut.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Prolonged lactation provides substantial health benefits, possibly because of galactose as part of milk sugar lactose. Isocaloric replacement of dietary glucose [16 energy%(en%)] with galactose within a normal diet (64en% carbohydrates) during a 3-wk postweaning period provided substantial benefits on short- and long-term physiologic and metabolic parameters at the whole-body level and liver in female mice, which might be attributable to intestinal function. OBJECTIVES This study aimed to investigate if partial dietary replacement of glucose with galactose alters intestinal metabolism underlying hepatic health effects. METHODS Proximal intestinal mucosa gene profiles in female mice were analyzed using RNAseq technology, validated, and correlated with hepatic health parameters. RESULTS Transcriptome analysis revealed that the presence of galactose primarily affected the pathways involved in energy metabolism. A consistently higher expression was observed in the subset of mitochondrial transcripts (78 of 80, all P.adj < 0.1). Oxidative phosphorylation (OXPHOS) represented the most upregulated process (all top 10 pathways) independent of the total mitochondrial mass (P = 0.75). Moreover, galactose consistently upregulated carbohydrate metabolism pathways, specifically glycolysis till acetyl-CoA production and fructose metabolism. Also, the expression of transcripts involved in these pathways was negatively correlated with circulating serum amyloid A3 protein, a marker of hepatic inflammation [R (-0.61, -0.5), P (0.002, 0.01)]. Accordingly, CD163+ cells were decreased in the liver. Additionally, the expression of key fructolytic enzymes in the small intestinal mucosa was negatively correlated with triglyceride accumulation in the liver [R (-0.45, -0.4), P (0.03, 0.05)]. CONCLUSIONS To our knowledge, our results show for the first time the role of galactose as an OXPHOS activator in vivo. Moreover, the concept of intestinal cells acting as the body's metabolic gatekeeper is strongly supported, as they alter substrate availability and thereby contribute to the maintenance of metabolic homeostasis, protecting other organs, as evidenced by their potential ability to shield the liver from the potentially detrimental effects of fructose.
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Affiliation(s)
| | - Lianne M S Bouwman
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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21
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Murthy TPK, Shukla R, Durga Prasad N, Swetha P, Shreyas S, Singh TR, Pattabiraman R, Nair SS, Mathew BB, Kumar KM. Comprehensive analysis of non-synonymous missense SNPs of human galactose mutarotase (GALM) gene: an integrated computational approach. J Biomol Struct Dyn 2023; 41:11178-11192. [PMID: 36591702 DOI: 10.1080/07391102.2022.2160813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/15/2022] [Indexed: 01/03/2023]
Abstract
Missense Non-synonymous single nucleotide polymorphisms (nsSNPs) of Galactose Mutarotase (GALM) are associated with the Novel type of Galactosemia (Galactosemia type 4) together with symptoms such as high blood galactose levels and eye cataracts. The objective of the present study was to identify deleterious nsSNPs of GALM recorded on the dbSNP database through comprehensive insilico analysis. Among the 319 missense nsSNPs reported, various insilco tools predicted R78S, R82G, A163E, P210S, Y281C, E307G and F339C as the most deleterious mutations. Structural analysis, PTM analysis and molecular dynamics simulations (MDS) were carried out to understand the effect of these mutations on the structural and physicochemical properties of the GALM protein. The residues R82G and E307G were found to be part of the binding site that resulted in decreased surface accessibility. Replacing the charged wild-type residue with a neutral mutant type affected its substrate binding. All 7 mutations were found to increase the rigidity of the protein structure, which is unfavorable during ligand binding. The mutation F339E made the protein structure more rigid than all the other mutations. Y281 is a phosphorylated site, and therefore, less significant structural changes were observed when compared to other mutations; however, it may have significant differences in the usual functioning of the protein. In summary, the structural and functional analysis of missense SNPs of GALM is important to reduce the number of potential mutations to be evaluated in vitro to understand the association with some genetic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - N Durga Prasad
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Praveen Swetha
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - S Shreyas
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Ramya Pattabiraman
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Shishira S Nair
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Blessy B Mathew
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, Karnataka, Inida
| | - K M Kumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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22
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Munyayi TA, Mulder DW, Conradie EH, Vorster BC. Feasibility of NAD(P)/NAD(P)H as redox agents in enzymatic plasmonic gold nanostar assays for galactose quantification. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230825. [PMID: 37830025 PMCID: PMC10565372 DOI: 10.1098/rsos.230825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
Plasmonic colorimetric sensors have emerged as powerful analytical tools in biochemistry due to their localized surface plasmon resonance extinction in the visible range. Here, we describe the feasibility of NAD(P)/NAD(P)H as redox agents in enzymatic plasmonic gold nanostar (AuNS) assays for galactose quantification using three model enzymes, GalDH, AR and GalOx, immobilized separately on polyvinylpyrrolidone-capped AuNS scaffolds. These highly specific, sensitive and selective bioassays induce the transformation of AuNS into quasi-spherical nanoparticles during the biorecognition of galactose in water and synthetic blood matrices. As a result, using our inexpensive and simple AuNS plasmon bioassays, the presence of galactose may be detected spectrophotometrically and by the naked eye.
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Affiliation(s)
- Tozivepi Aaron Munyayi
- Centre For Human Metabolomics, Department of Biochemistry, North West University Potchefstroom, 11 Hoffman Street, Potchefstroom 2531, South Africa
| | - Danielle Wingrove Mulder
- Centre For Human Metabolomics, Department of Biochemistry, North West University Potchefstroom, 11 Hoffman Street, Potchefstroom 2531, South Africa
| | - Engela Helena Conradie
- Centre For Human Metabolomics, Department of Biochemistry, North West University Potchefstroom, 11 Hoffman Street, Potchefstroom 2531, South Africa
| | - Barend Christiaan Vorster
- Centre For Human Metabolomics, Department of Biochemistry, North West University Potchefstroom, 11 Hoffman Street, Potchefstroom 2531, South Africa
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23
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Martinez-Garza U, Choi J, Scafidi S, Wolfgang MJ. Proteomics identifies the developmental regulation of HKDC1 in liver of pigs and mice. Am J Physiol Regul Integr Comp Physiol 2023; 325:R389-R400. [PMID: 37545422 PMCID: PMC10639021 DOI: 10.1152/ajpregu.00253.2022] [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: 10/13/2022] [Revised: 06/01/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023]
Abstract
During the perinatal period, unique metabolic adaptations support energetic requirements for rapid growth. To gain insight into perinatal adaptations, quantitative proteomics was performed comparing the livers of Yorkshire pigs at postnatal day 7 and adult. These data revealed differences in the metabolic control of liver function including significant changes in lipid and carbohydrate metabolic pathways. Newborn livers showed an enrichment of proteins in lipid catabolism and gluconeogenesis concomitant with elevated liver carnitine and acylcarnitines levels. Sugar kinases were some of the most dramatically differentially enriched proteins compared with neonatal and adult pigs including galactokinase 1 (Galk1), ketohexokinase (KHK), hexokinase 1 (HK1), and hexokinase 4 (GCK). Interestingly, hexokinase domain containing 1 (HKDC1), a newly identified fifth hexokinase associated with glucose disturbances in pregnant women, was highly enriched in the liver during the prenatal and perinatal periods and continuously declined throughout postnatal development in pigs and mice. These changes were confirmed via Western blot and mRNA expression. These data provide new insights into the developmental and metabolic adaptations in the liver during the transition from the perinatal period to adulthood in multiple mammalian species.
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Affiliation(s)
- Ursula Martinez-Garza
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Joseph Choi
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Susana Scafidi
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Michael J Wolfgang
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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24
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Han X, D'Angelo C, Otamendi A, Cifuente JO, de Astigarraga E, Ochoa-Lizarralde B, Grininger M, Routier FH, Guerin ME, Fuehring J, Etxebeste O, Connell SR. CryoEM analysis of the essential native UDP-glucose pyrophosphorylase from Aspergillus nidulans reveals key conformations for activity regulation and function. mBio 2023; 14:e0041423. [PMID: 37409813 PMCID: PMC10470519 DOI: 10.1128/mbio.00414-23] [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: 02/20/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Invasive aspergillosis is one of the most serious clinical invasive fungal infections, resulting in a high case fatality rate among immunocompromised patients. The disease is caused by saprophytic molds in the genus Aspergillus, including Aspergillus fumigatus, the most significant pathogenic species. The fungal cell wall, an essential structure mainly composed of glucan, chitin, galactomannan, and galactosaminogalactan, represents an important target for the development of antifungal drugs. UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) is a central enzyme in the metabolism of carbohydrates that catalyzes the biosynthesis of UDP-glucose, a key precursor of fungal cell wall polysaccharides. Here, we demonstrate that the function of UGP is vital for Aspergillus nidulans (AnUGP). To understand the molecular basis of AnUGP function, we describe a cryoEM structure (global resolution of 3.5 Å for the locally refined subunit and 4 Å for the octameric complex) of a native AnUGP. The structure reveals an octameric architecture with each subunit comprising an N-terminal α-helical domain, a central catalytic glycosyltransferase A-like (GT-A-like) domain, and a C-terminal (CT) left-handed β-helix oligomerization domain. AnUGP displays unprecedented conformational variability between the CT oligomerization domain and the central GT-A-like catalytic domain. In combination with activity measurements and bioinformatics analysis, we unveil the molecular mechanism of substrate recognition and specificity for AnUGP. Altogether, our study not only contributes to understanding the molecular mechanism of catalysis/regulation of an important class of enzymes but also provides the genetic, biochemical, and structural groundwork for the future exploitation of UGP as a potential antifungal target. IMPORTANCE Fungi cause diverse diseases in humans, ranging from allergic syndromes to life-threatening invasive diseases, together affecting more than a billion people worldwide. Increasing drug resistance in Aspergillus species represents an emerging global health threat, making the design of antifungals with novel mechanisms of action a worldwide priority. The cryoEM structure of UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) from the filamentous fungus Aspergillus nidulans reveals an octameric architecture displaying unprecedented conformational variability between the C-terminal oligomerization domain and the central glycosyltransferase A-like catalytic domain in the individual protomers. While the active site and oligomerization interfaces are more highly conserved, these dynamic interfaces include motifs restricted to specific clades of filamentous fungi. Functional study of these motifs could lead to the definition of new targets for antifungals inhibiting UGP activity and, thus, the architecture of the cell wall of filamentous fungal pathogens.
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Affiliation(s)
- Xu Han
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Cecilia D'Angelo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Ainara Otamendi
- Laboratory of Biology, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, UPV/EHU, San Sebastian, Spain
| | - Javier O. Cifuente
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Elisa de Astigarraga
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Borja Ochoa-Lizarralde
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Marcelo E. Guerin
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jana Fuehring
- Institute for Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Oier Etxebeste
- Laboratory of Biology, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, UPV/EHU, San Sebastian, Spain
| | - Sean R. Connell
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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25
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Shiri TJ, Viau C, Gu X, Xu L, Lu Y, Xia J. The Native Microbiome Member Chryseobacterium sp. CHNTR56 MYb120 Induces Trehalose Production via a Shift in Central Carbon Metabolism during Early Life in C. elegans. Metabolites 2023; 13:953. [PMID: 37623896 PMCID: PMC10456584 DOI: 10.3390/metabo13080953] [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: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Aging is the system-wide loss of homeostasis, eventually leading to death. There is growing evidence that the microbiome not only evolves with its aging host, but also directly affects aging via the modulation of metabolites involved in important cellular functions. The widely used model organism C. elegans exhibits high selectivity towards its native microbiome members which confer a range of differential phenotypes and possess varying functional capacities. The ability of one such native microbiome species, Chryseobacterium sp. CHNTR56 MYb120, to improve the lifespan of C. elegans and to promote the production of Vitamin B6 in the co-colonizing member Comamonas sp. 12022 MYb131 are some of its beneficial effects on the worm host. We hypothesize that studying its metabolic influence on the different life stages of the worm could provide further insights into mutualistic interactions. The present work applied LC-MS untargeted metabolomics and isotope labeling to study the impact of the native microbiome member Chryseobacterium sp. CHNTR56 MYb120 on the metabolism of C. elegans. In addition to the upregulation of biosynthesis and detoxification pathway intermediates, we found that Chryseobacterium sp. CHNTR56 MYb120 upregulates the glyoxylate shunt in mid-adult worms which is linked to the upregulation of trehalose, an important metabolite for desiccation tolerance in older worms.
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Affiliation(s)
- Tanisha Jean Shiri
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Charles Viau
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Xue Gu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Lei Xu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada;
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada;
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26
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Davey LE, Malkus PN, Villa M, Dolat L, Holmes ZC, Letourneau J, Ansaldo E, David LA, Barton GM, Valdivia RH. A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression. Nat Microbiol 2023; 8:1450-1467. [PMID: 37337046 DOI: 10.1038/s41564-023-01407-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
Abstract
Akkermansia muciniphila, a mucophilic member of the gut microbiota, protects its host against metabolic disorders. Because it is genetically intractable, the mechanisms underlying mucin metabolism, gut colonization and its impact on host physiology are not well understood. Here we developed and applied transposon mutagenesis to identify genes important for intestinal colonization and for the use of mucin. An analysis of transposon mutants indicated that de novo biosynthesis of amino acids was required for A. muciniphila growth on mucin medium and that many glycoside hydrolases are redundant. We observed that mucin degradation products accumulate in internal compartments within bacteria in a process that requires genes encoding pili and a periplasmic protein complex, which we term mucin utilization locus (MUL) genes. We determined that MUL genes were required for intestinal colonization in mice but only when competing with other microbes. In germ-free mice, MUL genes were required for A. muciniphila to repress genes important for cholesterol biosynthesis in the colon. Our genetic system for A. muciniphila provides an important tool with which to uncover molecular links between the metabolism of mucins, regulation of lipid homeostasis and potential probiotic activities.
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Affiliation(s)
- Lauren E Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Duke Microbiome Center, Duke University, Durham, NC, USA.
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| | - Per N Malkus
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Max Villa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Lee Dolat
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Jeff Letourneau
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Eduard Ansaldo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Gregory M Barton
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Duke Microbiome Center, Duke University, Durham, NC, USA.
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27
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Protasoni M, Taanman JW. Remodelling of the Mitochondrial Bioenergetic Pathways in Human Cultured Fibroblasts with Carbohydrates. BIOLOGY 2023; 12:1002. [PMID: 37508431 PMCID: PMC10376623 DOI: 10.3390/biology12071002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Mitochondrial oxidative phosphorylation defects underlie many neurological and neuromuscular diseases. Patients' primary dermal fibroblasts are one of the most commonly used in vitro models to study mitochondrial pathologies. However, fibroblasts tend to rely more on glycolysis than oxidative phosphorylation for their energy when cultivated in standard high-glucose medium, rendering it difficult to expose mitochondrial dysfunctions. This study aimed to systematically investigate to which extent the use of galactose- or fructose-based medium switches the fibroblasts' energy metabolism to a more oxidative state. Highly proliferative cells depend more on glycolysis than less proliferative cells. Therefore, we investigated two primary dermal fibroblast cultures from healthy subjects: a highly proliferative neonatal culture and a slower-growing adult culture. Cells were cultured with 25 mM glucose, galactose or fructose, and 4 mM glutamine as carbon sources. Compared to glucose, both galactose and fructose reduce the cellular proliferation rate, but the galactose-induced drop in proliferation is much more profound than the one observed in cells cultivated in fructose. Both galactose and fructose result in a modest increase in mitochondrial content, including mitochondrial DNA, and a disproportionate increase in protein levels, assembly, and activity of the oxidative phosphorylation enzyme complexes. Galactose- and fructose-based media induce a switch of the prevalent biochemical pathway in cultured fibroblasts, enhancing aerobic metabolism when compared to glucose-based medium. While both galactose and fructose stimulate oxidative phosphorylation to a comparable degree, galactose decreases the cellular proliferation rate more than fructose, suggesting that a fructose-based medium is a better choice when studying partial oxidative phosphorylation defects in patients' fibroblasts.
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Affiliation(s)
- Margherita Protasoni
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, Royal Free Campus (M12), Rowland Hill Street, London NW3 2PF, UK
| | - Jan-Willem Taanman
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, Royal Free Campus (M12), Rowland Hill Street, London NW3 2PF, UK
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Mocholi E, Russo L, Gopal K, Ramstead AG, Hochrein SM, Vos HR, Geeven G, Adegoke AO, Hoekstra A, van Es RM, Pittol JR, Vastert S, Rutter J, Radstake T, van Loosdregt J, Berkers C, Mokry M, Anderson CC, O'Connell RM, Vaeth M, Ussher J, Burgering BMT, Coffer PJ. Pyruvate metabolism controls chromatin remodeling during CD4 + T cell activation. Cell Rep 2023; 42:112583. [PMID: 37267106 DOI: 10.1016/j.celrep.2023.112583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/17/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023] Open
Abstract
Upon antigen-specific T cell receptor (TCR) engagement, human CD4+ T cells proliferate and differentiate, a process associated with rapid transcriptional changes and metabolic reprogramming. Here, we show that the generation of extramitochondrial pyruvate is an important step for acetyl-CoA production and subsequent H3K27ac-mediated remodeling of histone acetylation. Histone modification, transcriptomic, and carbon tracing analyses of pyruvate dehydrogenase (PDH)-deficient T cells show PDH-dependent acetyl-CoA generation as a rate-limiting step during T activation. Furthermore, T cell activation results in the nuclear translocation of PDH and its association with both the p300 acetyltransferase and histone H3K27ac. These data support the tight integration of metabolic and histone-modifying enzymes, allowing metabolic reprogramming to fuel CD4+ T cell activation. Targeting this pathway may provide a therapeutic approach to specifically regulate antigen-driven T cell activation.
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Affiliation(s)
- Enric Mocholi
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Laura Russo
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Keshav Gopal
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Andrew G Ramstead
- Huntsman Cancer Institute and Division of Microbiology and Immunology, Department of Pathology, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT, USA
| | - Sophia M Hochrein
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Harmjan R Vos
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Geert Geeven
- Department of Clinical Genetics, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Adeolu O Adegoke
- Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Anna Hoekstra
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Robert M van Es
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jose Ramos Pittol
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sebastian Vastert
- Laboratory for Translational Immunology and Department of Pediatric Rheumatology and Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jared Rutter
- Huntsman Cancer Institute and Division of Microbiology and Immunology, Department of Pathology, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT, USA
| | - Timothy Radstake
- Laboratory for Translational Immunology and Department of Pediatric Rheumatology and Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jorg van Loosdregt
- Laboratory for Translational Immunology and Department of Pediatric Rheumatology and Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Celia Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands; Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Michal Mokry
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands; Cardiovascular Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Colin C Anderson
- Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Ryan M O'Connell
- Huntsman Cancer Institute and Division of Microbiology and Immunology, Department of Pathology, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT, USA
| | - Martin Vaeth
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - John Ussher
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Paul J Coffer
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, the Netherlands.
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29
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Al Naggar Y, Shafiey H, Paxton RJ. Transcriptomic Responses Underlying the High Virulence of Black Queen Cell Virus and Sacbrood Virus following a Change in Their Mode of Transmission in Honey Bees ( Apis mellifera). Viruses 2023; 15:1284. [PMID: 37376584 DOI: 10.3390/v15061284] [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: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Over the last two decades, honey bees (Apis mellifera) have suffered high rates of colony losses that have been attributed to a variety of factors, chief among which are viral pathogens, such as deformed wing virus (DWV), whose virulence has increased because of vector-based transmission by the invasive, ectoparasitic varroa mite (Varroa destructor). A shift in the experimental mode of transmission of the black queen cell virus (BQCV) and sacbrood virus (SBV) from fecal/food-oral (direct horizontal) to vector-mediated (indirect horizontal) transmission also results in high virulence and viral titers in pupal and adult honey bees. Agricultural pesticides represent another factor that acts independently or in interaction with pathogens, and they are also thought to cause colony loss. Understanding the molecular mechanisms underlying the higher virulence following a vector-based mode of transmission provides deeper insight into honey bee colony losses, as does determining whether or not host-pathogen interactions are modulated by exposure to pesticides. METHODS Through an experimental design with controlled laboratory, we investigated the effects of the modes of transmission of BQCV and SBV (feeding vs. vector-mediated via injection) alone or in combination with chronic exposure to sublethal and field-realistic concentrations of flupyradifurone (FPF), a novel agricultural insecticide, on honey bee survival and transcription responses by using high-throughput RNA sequencing (RNA-seq) analysis. RESULTS Co-exposure to viruses via feeding (VF) or injection (VI) and FPF insecticide had no statistically significant interactive effect on their survival compared to, respectively, VF or VI treatments alone. Transcriptomic analysis revealed a distinct difference in the gene expression profiles of bees inoculated with viruses via injection (VI) and exposed to FPF insecticide (VI+FPF). The number of differentially expressed genes (DEGs) at log2 (fold-change) > 2.0 in VI bees (136 genes) or/and VI+FPF insecticide (282 genes) was very high compared to that of VF bees (8 genes) or the VF+FPF insecticide treatment (15 genes). Of these DEGs, the expression in VI and VI+FPF bees of some immune-related genes, such as those for antimicrobial peptides, Ago2, and Dicer, was induced. In short, several genes encoding odorant binding proteins, chemosensory proteins, odor receptors, honey bee venom peptides, and vitellogenin were downregulated in VI and VI+FPF bees. CONCLUSIONS Given the importance of these suppressed genes in honey bees' innate immunity, eicosanoid biosynthesis, and olfactory associative function, their inhibition because of the change in the mode of infection with BQCV and SBV to vector-mediated transmission (injection into haemocoel) could explain the high virulence observed in these viruses when they were experimentally injected into hosts. These changes may help explain why other viruses, such as DWV, represent such a threat to colony survival when transmitted by varroa mites.
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Affiliation(s)
- Yahya Al Naggar
- 1 General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- Zoology Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Hassan Shafiey
- 1 General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Robert J Paxton
- 1 General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
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30
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Lin G, Huang Z, He B, Jiang K, Su T, Zhao F. Evolutionary Adaptation of Genes Involved in Galactose Derivatives Metabolism in Oil-Tea Specialized Andrena Species. Genes (Basel) 2023; 14:genes14051117. [PMID: 37239477 DOI: 10.3390/genes14051117] [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: 05/05/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Oil-tea (Camellia oleifera) is a woody oil crop whose nectar includes galactose derivatives that are toxic to honey bees. Interestingly, some mining bees of the genus Andrena can entirely live on the nectar (and pollen) of oil-tea and are able to metabolize these galactose derivatives. We present the first next-generation genomes for five and one Andrena species that are, respectively, specialized and non-specialized oil-tea pollinators and, combining these with the published genomes of six other Andrena species which did not visit oil-tea, we performed molecular evolution analyses on the genes involved in the metabolizing of galactose derivatives. The six genes (NAGA, NAGA-like, galM, galK, galT, and galE) involved in galactose derivatives metabolism were identified in the five oil-tea specialized species, but only five (with the exception of NAGA-like) were discovered in the other Andrena species. Molecular evolution analyses revealed that NAGA-like, galK, and galT in oil-tea specialized species appeared under positive selection. RNASeq analyses showed that NAGA-like, galK, and galT were significantly up-regulated in the specialized pollinator Andrena camellia compared to the non-specialized pollinator Andrena chekiangensis. Our study demonstrated that the genes NAGA-like, galK, and galT have played an important role in the evolutionary adaptation of the oil-tea specialized Andrena species.
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Affiliation(s)
- Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Bo He
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Kai Jiang
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Tianjuan Su
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
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31
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Li H, Guglielmetti C, Sei YJ, Zilberter M, Le Page LM, Shields L, Yang J, Nguyen K, Tiret B, Gao X, Bennett N, Lo I, Dayton TL, Kampmann M, Huang Y, Rathmell JC, Vander Heiden M, Chaumeil MM, Nakamura K. Neurons require glucose uptake and glycolysis in vivo. Cell Rep 2023; 42:112335. [PMID: 37027294 PMCID: PMC10556202 DOI: 10.1016/j.celrep.2023.112335] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/22/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Neurons require large amounts of energy, but whether they can perform glycolysis or require glycolysis to maintain energy remains unclear. Using metabolomics, we show that human neurons do metabolize glucose through glycolysis and can rely on glycolysis to supply tricarboxylic acid (TCA) cycle metabolites. To investigate the requirement for glycolysis, we generated mice with postnatal deletion of either the dominant neuronal glucose transporter (GLUT3cKO) or the neuronal-enriched pyruvate kinase isoform (PKM1cKO) in CA1 and other hippocampal neurons. GLUT3cKO and PKM1cKO mice show age-dependent learning and memory deficits. Hyperpolarized magnetic resonance spectroscopic (MRS) imaging shows that female PKM1cKO mice have increased pyruvate-to-lactate conversion, whereas female GLUT3cKO mice have decreased conversion, body weight, and brain volume. GLUT3KO neurons also have decreased cytosolic glucose and ATP at nerve terminals, with spatial genomics and metabolomics revealing compensatory changes in mitochondrial bioenergetics and galactose metabolism. Therefore, neurons metabolize glucose through glycolysis in vivo and require glycolysis for normal function.
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Affiliation(s)
- Huihui Li
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Caroline Guglielmetti
- Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94158, USA; Department of Radiology and Biomedical Imaging, San Francisco, CA 94158, USA
| | - Yoshitaka J Sei
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Misha Zilberter
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lydia M Le Page
- Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94158, USA; Department of Radiology and Biomedical Imaging, San Francisco, CA 94158, USA
| | - Lauren Shields
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Joyce Yang
- Graduate Program in Neuroscience, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kevin Nguyen
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Brice Tiret
- Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94158, USA; Department of Radiology and Biomedical Imaging, San Francisco, CA 94158, USA
| | - Xiao Gao
- Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94158, USA; Department of Radiology and Biomedical Imaging, San Francisco, CA 94158, USA; UCSF/UCB Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA 94158, USA
| | - Neal Bennett
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Iris Lo
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Talya L Dayton
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin Kampmann
- Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Graduate Program in Neuroscience, University of California San Francisco, San Francisco, CA 94158, USA; UCSF/UCB Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Graduate Program in Neuroscience, University of California San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey C Rathmell
- Vanderbilt Center for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Myriam M Chaumeil
- Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94158, USA; Department of Radiology and Biomedical Imaging, San Francisco, CA 94158, USA; Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA; UCSF/UCB Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Graduate Program in Neuroscience, University of California San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA.
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32
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Xu HL, Zhou X, Chen S, Xu S, Li Z, Nakanishi H, Gao XD. Rare sugar L-sorbose exerts antitumor activity by impairing glucose metabolism. Commun Biol 2023; 6:259. [PMID: 36906698 PMCID: PMC10008635 DOI: 10.1038/s42003-023-04638-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 02/28/2023] [Indexed: 03/13/2023] Open
Abstract
Rare sugars are monosaccharides with low natural abundance. They are structural isomers of dietary sugars, but hardly be metabolized. Here, we report that rare sugar L-sorbose induces apoptosis in various cancer cells. As a C-3 epimer of D-fructose, L-sorbose is internalized via the transporter GLUT5 and phosphorylated by ketohexokinase (KHK) to produce L-sorbose-1-phosphate (S-1-P). Cellular S-1-P inactivates the glycolytic enzyme hexokinase resulting in attenuated glycolysis. Consequently, mitochondrial function is impaired and reactive oxygen species are produced. Moreover, L-sorbose downregulates the transcription of KHK-A, a splicing variant of KHK. Since KHK-A is a positive inducer of antioxidation genes, the antioxidant defense mechanism in cancer cells can be attenuated by L-sorbose-treatment. Thus, L-sorbose performs multiple anticancer activities to induce cell apoptosis. In mouse xenograft models, L-sorbose enhances the effect of tumor chemotherapy in combination with other anticancer drugs. These results demonstrate L-sorbose as an attractive therapeutic reagent for cancer treatment.
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Affiliation(s)
- Hui-Lin Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoman Zhou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Shuai Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Si Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
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33
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Derks B, Rivera-Cruz G, Hagen-Lillevik S, Vos EN, Demirbas D, Lai K, Treacy EP, Levy HL, Wilkins-Haug LE, Rubio-Gozalbo ME, Berry GT. The hypergonadotropic hypogonadism conundrum of classic galactosemia. Hum Reprod Update 2023; 29:246-258. [PMID: 36512573 PMCID: PMC9976963 DOI: 10.1093/humupd/dmac041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/19/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Hypergonadotropic hypogonadism is a burdensome complication of classic galactosemia (CG), an inborn error of galactose metabolism that invariably affects female patients. Since its recognition in 1979, data have become available regarding the clinical spectrum, and the impact on fertility. Many women have been counseled for infertility and the majority never try to conceive, yet spontaneous pregnancies can occur. Onset and mechanism of damage have not been elucidated, yet new insights at the molecular level are becoming available that might greatly benefit our understanding. Fertility preservation options have expanded, and treatments to mitigate this complication either by directly rescuing the metabolic defect or by influencing the cascade of events are being explored. OBJECTIVE AND RATIONALE The aims are to review: the clinical picture and the need to revisit the counseling paradigm; insights into the onset and mechanism of damage at the molecular level; and current treatments to mitigate ovarian damage. SEARCH METHODS In addition to the work on this topic by the authors, the PubMed database has been used to search for peer-reviewed articles and reviews using the following terms: 'classic galactosemia', 'gonadal damage', 'primary ovarian insufficiency', 'fertility', 'animal models' and 'fertility preservation' in combination with other keywords related to the subject area. All relevant publications until August 2022 have been critically evaluated and reviewed. OUTCOMES A diagnosis of premature ovarian insufficiency (POI) results in a significant psychological burden with a high incidence of depression and anxiety that urges adequate counseling at an early stage, appropriate treatment and timely discussion of fertility preservation options. The cause of POI in CG is unknown, but evidence exists of dysregulation in pathways crucial for folliculogenesis such as phosphatidylinositol 3-kinase/protein kinase B, inositol pathway, mitogen-activated protein kinase, insulin-like growth factor-1 and transforming growth factor-beta signaling. Recent findings from the GalT gene-trapped (GalTKO) mouse model suggest that early molecular changes in 1-month-old ovaries elicit an accelerated growth activation and burnout of primordial follicles, resembling the progressive ovarian failure seen in patients. Although data on safety and efficacy outcomes are still limited, ovarian tissue cryopreservation can be a fertility preservation option. Treatments to overcome the genetic defect, for example nucleic acid therapy such as mRNA or gene therapy, or that influence the cascade of events are being explored at the (pre-)clinical level. WIDER IMPLICATIONS Elucidation of the molecular pathways underlying POI of any origin can greatly advance our insight into the pathogenesis and open new treatment avenues. Alterations in these molecular pathways might serve as markers of disease progression and efficiency of new treatment options.
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Affiliation(s)
- Britt Derks
- Department of Pediatrics and Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,GROW, Maastricht University, Maastricht, The Netherlands.,European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member and United for Metabolic Diseases Member
| | - Greysha Rivera-Cruz
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Synneva Hagen-Lillevik
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Nutrition and Integrative Physiology, University of Utah College of Health, Salt Lake City, UT, USA
| | - E Naomi Vos
- Department of Pediatrics and Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,GROW, Maastricht University, Maastricht, The Netherlands.,European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member and United for Metabolic Diseases Member
| | - Didem Demirbas
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kent Lai
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Nutrition and Integrative Physiology, University of Utah College of Health, Salt Lake City, UT, USA
| | - Eileen P Treacy
- European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member and United for Metabolic Diseases Member.,National Centre for Inherited Metabolic Disorders, Mater Misericordiae University Hospital, Dublin, Ireland.,School of Medicine, Trinity College, Dublin 2, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Harvey L Levy
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Louise E Wilkins-Haug
- Division of Maternal Fetal Medicine, Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Estela Rubio-Gozalbo
- Department of Pediatrics and Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,GROW, Maastricht University, Maastricht, The Netherlands.,European Reference Network for Hereditary Metabolic Disorders (MetabERN) Member and United for Metabolic Diseases Member
| | - Gerard T Berry
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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34
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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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35
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Liu Y, Gan L, Zhao B, Yu K, Wang Y, Männistö S, Weinstein SJ, Huang J, Albanes D. Untargeted metabolomic profiling identifies serum metabolites associated with type 2 diabetes in a cross-sectional study of the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. Am J Physiol Endocrinol Metab 2023; 324:E167-E175. [PMID: 36516224 PMCID: PMC9925157 DOI: 10.1152/ajpendo.00287.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Type 2 diabetes (T2D) is a complex chronic disease with substantial phenotypic heterogeneity affecting millions of individuals. Yet, its relevant metabolites and etiological pathways are not fully understood. The aim of this study is to assess a broad spectrum of metabolites related to T2D in a large population-based cohort. We conducted a metabolomic analysis of 4,281 male participants within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. The serum metabolomic analysis was performed using an LC-MS/GC-MS platform. Associations between 1,413 metabolites and T2D were examined using linear regression, controlling for important baseline risk factors. Standardized β-coefficients and standard errors (SEs) were computed to estimate the difference in metabolite concentrations. We identified 74 metabolites that were significantly associated with T2D based on the Bonferroni-corrected threshold (P < 3.5 × 10-5). The strongest signals associated with T2D were of carbohydrates origin, including glucose, 1,5-anhydroglucitol (1,5-AG), and mannose (β = 0.34, -0.91, and 0.41, respectively; all P < 10-75). We found several chemical class pathways that were significantly associated with T2D, including carbohydrates (P = 1.3 × 10-11), amino acids (P = 2.7 × 10-6), energy (P = 1.5 × 10-4), and xenobiotics (P = 1.2 × 10-3). The strongest subpathway associations were seen for fructose-mannose-galactose metabolism, glycolysis-gluconeogenesis-pyruvate metabolism, fatty acid metabolism (acyl choline), and leucine-isoleucine-valine metabolism (all P < 10-8). Our findings identified various metabolites and candidate chemical class pathways that can be characterized by glycolysis and gluconeogenesis metabolism, fructose-mannose-galactose metabolism, branched-chain amino acids, diacylglycerol, acyl cholines, fatty acid oxidation, and mitochondrial dysfunction.NEW & NOTEWORTHY These metabolomic patterns may provide new additional evidence and potential insights relevant to the molecular basis of insulin resistance and the etiology of T2D.
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Affiliation(s)
- Yuzhao Liu
- Department of Endocrinology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lu Gan
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Bin Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yangang Wang
- Department of Endocrinology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jiaqi Huang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, NIH, Bethesda, Maryland
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36
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Saeui CT, Shah SR, Fernandez-Gil BI, Zhang C, Agatemor C, Dammen-Brower K, Mathew MP, Buettner M, Gowda P, Khare P, Otamendi-Lopez A, Yang S, Zhang H, Le A, Quinoñes-Hinojosa A, Yarema KJ. Anticancer Properties of Hexosamine Analogs Designed to Attenuate Metabolic Flux through the Hexosamine Biosynthetic Pathway. ACS Chem Biol 2023; 18:151-165. [PMID: 36626752 DOI: 10.1021/acschembio.2c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Altered cellular metabolism is a hallmark of cancer pathogenesis and progression; for example, a near-universal feature of cancer is increased metabolic flux through the hexosamine biosynthetic pathway (HBP). This pathway produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), a potent oncometabolite that drives multiple facets of cancer progression. In this study, we synthesized and evaluated peracetylated hexosamine analogs designed to reduce flux through the HBP. By screening a panel of analogs in pancreatic cancer and glioblastoma multiform (GBM) cells, we identified Ac4Glc2Bz─a benzyl-modified GlcNAc mimetic─as an antiproliferative cancer drug candidate that down-regulated oncogenic metabolites and reduced GBM cell motility at concentrations non-toxic to non-neoplastic cells. More specifically, the growth inhibitory effects of Ac4Glc2Bz were linked to reduced levels of UDP-GlcNAc and concomitant decreases in protein O-GlcNAc modification in both pancreatic cancer and GBM cells. Targeted metabolomics analysis in GBM cells showed that Ac4Glc2Bz disturbed glucose metabolism, amino acid pools, and nucleotide precursor biosynthesis, consistent with reduced proliferation and other anti-oncogenic properties of this analog. Furthermore, Ac4Glc2Bz reduced the invasion, migration, and stemness of GBM cells. Importantly, normal metabolic functions mediated by UDP-GlcNAc were not disrupted in non-neoplastic cells, including maintenance of endogenous levels of O-GlcNAcylation with no global disruption of N-glycan production. Finally, a pilot in vivo study showed that a potential therapeutic window exists where animals tolerated 5- to 10-fold higher levels of Ac4Glc2Bz than projected for in vivo efficacy. Together, these results establish GlcNAc analogs targeting the HBP through salvage mechanisms as a new therapeutic approach to safely normalize an important facet of aberrant glucose metabolism associated with cancer.
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Affiliation(s)
- Christopher T Saeui
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Sagar R Shah
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | | | - Cissy Zhang
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States.,Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Christian Agatemor
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Kris Dammen-Brower
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Mohit P Mathew
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Matthew Buettner
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Prateek Gowda
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Pratik Khare
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States.,Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland 21205, United States
| | | | - Shuang Yang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, United States
| | - Anne Le
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States.,Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland 21205, United States
| | | | - Kevin J Yarema
- Department of Biomedical Engineering and The Translational Tissue Engineering Center, The Johns Hopkins University and Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
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37
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Suryatin Alim G, Suzuki T, Honda K. Cell-Free Production and Regeneration of Cofactors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:29-49. [PMID: 37306696 DOI: 10.1007/10_2023_222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cofactors, such as adenosine triphosphate, nicotinamide adenine dinucleotide, and coenzyme A, are involved in nearly 50% of enzymatic reactions and widely used in biocatalytic production of useful chemicals. Although commercial production of cofactors has been mostly dependent on extraction from microbial cells, this approach has a theoretical limitation to achieve a high-titer, high-yield production of cofactors owing to the tight regulation of cofactor biosynthesis in living cells. Besides the cofactor production, their regeneration is also a key challenge to enable continuous use of costly cofactors and improve the feasibility of enzymatic chemical manufacturing. Construction and implementation of enzyme cascades for cofactor biosynthesis and regeneration in a cell-free environment can be a promising approach to these challenges. In this chapter, we present the available tools for cell-free cofactor production and regeneration, the pros and cons, and how they can contribute to promote the industrial application of enzymes.
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Affiliation(s)
- Gladwin Suryatin Alim
- Department of Chemistry, University of Basel, Basel, Switzerland
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Takuma Suzuki
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, Osaka, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
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38
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MoSnf5 Regulates Fungal Virulence, Growth, and Conidiation in Magnaporthe oryzae. J Fungi (Basel) 2022; 9:jof9010018. [PMID: 36675839 PMCID: PMC9861326 DOI: 10.3390/jof9010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Snf5 (sucrose nonfermenting) is a core component of the SWI/SNF complexes and regulates diverse cellular processes in model eukaryotes. In plant pathogenic fungi, its biological function and underlying mechanisms remain unexplored. In this study, we investigated the biological roles of MoSnf5 in plant infection and fungal development in the rice blast pathogen Magnaporthe oryzae. The gene deletion mutants of MoSNF5 exhibited slower vegetative hyphal growth, severe defects in conidiogenesis, and impaired virulence and galactose utilization capacities. Domain dissection assays showed that the Snf5 domain and the N- and C-termini of MoSnf5 were all required for its full functions. Co-immunoprecipitation and yeast two-hybrid assays showed that MoSnf5 physically interacts with four proteins, including a transcription initiation factor MoTaf14. Interestingly, the ∆MoTaf14 mutants showed similar phenotypes as the ∆Mosnf5 mutants on fungal virulence and development. Moreover, assays on GFP-MoAtg8 expression and localization showed that both the ∆Mosnf5 and ∆MoTaf14 mutants were defective in autophagy. Taken together, MoSnf5 regulates fungal virulence, growth, and conidiation, possibly through regulating galactose utilization and autophagy in M. oryzae.
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Katler Q, Stepien KM, Paull N, Patel S, Adams M, Balci MC, Berry GT, Bosch AM, De La O A, Demirbas D, Edman J, Ficicioglu C, Goff M, Hacker S, Knerr I, Lancaster K, Li H, Mendelsohn BA, Nichols B, de Rezende Pinto WBV, Rocha JC, Rubio-Gozalbo ME, Saad-Naguib M, Scholl-Buergi S, Searcy S, de Souza PVS, Wittenauer A, Fridovich-Keil JL. A multinational study of acute and long-term outcomes of Type 1 galactosemia patients who carry the S135L (c.404C > T) variant of GALT. J Inherit Metab Dis 2022; 45:1106-1117. [PMID: 36093991 PMCID: PMC9643640 DOI: 10.1002/jimd.12556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/23/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
Patients with galactosemia who carry the S135L (c.404C > T) variant of galactose-1-P uridylyltransferase (GALT), documented to encode low-level residual GALT activity, have been under-represented in most prior studies of outcomes in Type 1 galactosemia. What is known about the acute and long-term outcomes of these patients, therefore, is based on very limited data. Here, we present a study comparing acute and long-term outcomes of 12 patients homozygous for S135L, 25 patients compound heterozygous for S135L, and 105 patients homozygous for two GALT-null (G) alleles. This is the largest cohort of S135L patients characterized to date. Acute disease following milk exposure in the newborn period was common among patients in all 3 comparison groups in our study, as were long-term complications in the domains of speech, cognition, and motor outcomes. In contrast, while at least 80% of both GALT-null and S135L compound heterozygous girls and women showed evidence of an adverse ovarian outcome, prevalence was only 25% among S135L homozygotes. Further, all young women in this study with even one copy of S135L achieved spontaneous menarche; this is true for only about 33% of women with classic galactosemia. Overall, we observed that while most long-term outcomes trended milder among groups of patients with even one copy of S135L, many individual patients, either homozygous or compound heterozygous for S135L, nonetheless experienced long-term outcomes that were not mild. This was true despite detection by newborn screening and both early and life-long dietary restriction of galactose. This information should empower more evidence-based counseling for galactosemia patients with S135L.
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Affiliation(s)
- Quinton Katler
- Division of Reproductive Endocrinology and Infertility, Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia USA
| | - Karolina M. Stepien
- Adult Inherited Metabolic Diseases Department, Salford Royal Foundation NHS Trust, Salford, Greater Manchester, UK
| | - Nathan Paull
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia USA
| | - Sneh Patel
- Emory College, Emory University, Atlanta, Georgia USA
| | - Michael Adams
- UNC School of Medicine, Division of Pediatric Genetics and Metabolism, Chapel Hill, North Carolina USA
| | - Mehmet Cihan Balci
- Department of Pediatric Metabolic Disease, Istanbul Medical School, Fatihİstanbul, Turkey
| | - Gerard T. Berry
- Division of Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts USA
| | - Annet M. Bosch
- Amsterdam UMC location University of Amsterdam, Emma Children’s Hospital, Department of Pediatrics, Division of Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Didem Demirbas
- Division of Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts USA
| | - Julianna Edman
- Department of Pediatric Genetics, University of Illinois-Chicago, Chicago, Illinois USA
| | - Can Ficicioglu
- The Children’s Hospital of Philadelphia, Division of Human Genetics and Metabolism, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania USA
| | - Melanie Goff
- Division of Genetic and Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio USA
| | - Stephanie Hacker
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida USA
| | - Ina Knerr
- National Centre for Inherited Metabolic Disorders, Temple St. Children’s University Hospital, Dublin, Ireland
| | - Kristen Lancaster
- UNC School of Medicine, Division of Pediatric Genetics and Metabolism, Chapel Hill, North Carolina USA
| | - Hong Li
- Departments of Human Genetics and Pediatrics, Emory University School of Medicine, Atlanta, Georgia USA
| | - Bryce A. Mendelsohn
- Department of Genetics, Oakland Medical Center, Kaiser Permanente, Oakland, California USA
| | - Brandi Nichols
- Department of Clinical Nutrition, Arkansas Children’s Hospital, Little Rock, Arkansas USA
| | | | - Júlio César Rocha
- Nutrition & Metabolism, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa Reference Centre of Inherited Metabolic Diseases, Centro Hospitalar Universitário de Lisboa Central, and Center for Health Technology and Services Research (CINTESIS), NOVA Medical School, Lisboa, Portugal
| | - M Estela Rubio-Gozalbo
- Department of Pediatrics, Department of Clinical Genetics, GROW-School for Oncology and Reproduction, European Reference Network for Hereditary Metabolic Disorders (MetabERN) member and United for Metabolic Diseases member, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Michael Saad-Naguib
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida USA
| | | | - Sarah Searcy
- Division of Genetic and Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio USA
| | | | - Angela Wittenauer
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia USA
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Arzamasov AA, Osterman AL. Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics. Crit Rev Biochem Mol Biol 2022; 57:562-584. [PMID: 36866565 PMCID: PMC10192226 DOI: 10.1080/10409238.2023.2182272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/11/2023] [Accepted: 02/15/2023] [Indexed: 03/04/2023]
Abstract
Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and N-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and N-glycan assimilation abilities vary remarkably within the Bifidobacterium genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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41
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Fridovich-Keil JL, Berry GT. Pathophysiology of long-term complications in classic galactosemia: What we do and do not know. Mol Genet Metab 2022; 137:33-39. [PMID: 35882174 DOI: 10.1016/j.ymgme.2022.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023]
Abstract
Despite many decades of research involving both human subjects and model systems, the underlying pathophysiology of long-term complications in classic galactosemia (CG) remains poorly understood. In this review, intended for those already familiar with galactosemia, we focus on the big questions relating to outcomes, mechanism, and markers, drawing on relevant literature where available, attempting to navigate inconsistencies where they appear, and acknowledging gaps in knowledge where they persist.
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Affiliation(s)
| | - Gerard T Berry
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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42
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Novel Gene-Correction-Based Therapeutic Modalities for Monogenic Liver Disorders. Bioengineering (Basel) 2022; 9:bioengineering9080392. [PMID: 36004917 PMCID: PMC9404740 DOI: 10.3390/bioengineering9080392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The majority of monogenic liver diseases are autosomal recessive disorders, with few being sex-related or co-dominant. Although orthotopic liver transplantation (LT) is currently the sole therapeutic option for end-stage patients, such an invasive surgical approach is severely restricted by the lack of donors and post-transplant complications, mainly associated with life-long immunosuppressive regimens. Therefore, the last decade has witnessed efforts for innovative cellular or gene-based therapeutic strategies. Gene therapy is a promising approach for treatment of many hereditary disorders, such as monogenic inborn errors. The liver is an organ characterized by unique features, making it an attractive target for in vivo and ex vivo gene transfer. The current genetic approaches for hereditary liver diseases are mediated by viral or non-viral vectors, with promising results generated by gene-editing tools, such as CRISPR-Cas9 technology. Despite massive progress in experimental gene-correction technologies, limitations in validated approaches for monogenic liver disorders have encouraged researchers to refine promising gene therapy protocols. Herein, we highlighted the most common monogenetic liver disorders, followed by proposed genetic engineering approaches, offered as promising therapeutic modalities.
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Antioxidative potential of Lactobacillus sp. in ameliorating D-galactose-induced aging. Appl Microbiol Biotechnol 2022; 106:4831-4843. [PMID: 35781838 PMCID: PMC9329405 DOI: 10.1007/s00253-022-12041-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/03/2022]
Abstract
Aging is a progressive, unalterable physiological degradation process of living organisms, which leads to deterioration of biological function and eventually to senescence. The most prevalent factor responsible for aging is the accumulation of damages resulting from oxidative stress and dysbiosis. D-galactose-induced aging has become a hot topic, and extensive research is being conducted in this area. Published literature has reported that the continuous administration of D-galactose leads to the deterioration of motor and cognitive skills, resembling symptoms of aging. Hence, this procedure is employed as a model for accelerated aging. This review aims to emphasize the effect of D-galactose on various bodily organs and underline the role of the Lactobacillus sp. in the aging process, along with its anti-oxidative potential. A critical consideration to the literature describing animal models that have used the Lactobacillus sp. in amending D-galactose-induced aging is also given. KEY POINTS: • D-Galactose induces the aging process via decreasing the respiratory chain enzyme activity as well as ATP synthesis, mitochondrial dysfunction, and increased ROS production. • D-Galactose induced aging primarily affects the brain, heart, lung, liver, kidney, and skin. • The anti-oxidative potential of Lactobacillus sp. in improving D-galactose-induced aging in animal models via direct feeding and feeding of Lactobacillus-fermented food.
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Kim DY, Jung DH, Song EJ, Jang AR, Park JY, Ahn JH, Lee TS, Kim YJ, Lee YJ, Seo IS, Kim HE, Ryu EJ, Sim J, Park JH. D-galactose Intake Alleviates Atopic Dermatitis in Mice by Modulating Intestinal Microbiota. Front Nutr 2022; 9:895837. [PMID: 35799581 PMCID: PMC9254681 DOI: 10.3389/fnut.2022.895837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 01/05/2023] Open
Abstract
Atopic dermatitis (AD) is one of the most prevalent, chronic and persistent inflammatory skin diseases closely associated with intestinal microbiota. To evaluate the effect of D-galactose intake on AD, we orally administered D-galactose to BALB/c mice whose ears and skin were treated with 2,4-dinitrochlorobenzene (DNCB). D-galactose alleviated DNCB-induced AD-like phenotypes such as redness, scaling/dryness and excoriation. Ear thickness was also decreased by D-galactose administration. Histopathological analysis revealed decreased epidermal thickening, infiltration of immune cells, especially mast cells, in the dermis. Total levels of serum IgE representing the immunological response of AD were decreased by D-galactose administration. Microbiota analysis showed that D-galactose administration restored gut microbiota profiles, which were altered in AD mice, characterized by increased abundance of Bacteroidetes and decreased abundance of Firmicutes. The increased abundance of Bacteroides and the decreased abundance of Prevotella and Ruminococcus were reversed by D-galactose treatment, following improvement of AD. Our results suggest the possible use of D-galactose as a prebiotic to alleviate AD by altering gut microbiota.
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Affiliation(s)
- Dong-Yeon Kim
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Do-Hyeon Jung
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Eun-Jung Song
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Ah-Ra Jang
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Ji-Yeon Park
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Jae-Hun Ahn
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Tae-Sung Lee
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Yeong-Jun Kim
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Yun-Ji Lee
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - In-Su Seo
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
| | - Hye-Eun Kim
- Quorum Bio Co., Ltd., School of Dentistry, Seoul National University, Seoul, South Korea
| | - Eun-Ju Ryu
- Quorum Bio Co., Ltd., School of Dentistry, Seoul National University, Seoul, South Korea
| | - Jaehyun Sim
- Quorum Bio Co., Ltd., School of Dentistry, Seoul National University, Seoul, South Korea
| | - Jong-Hwan Park
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, Gwangju, South Korea
- *Correspondence: Jong-Hwan Park
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Yuan Z, Liu S, Song W, Liu Y, Bi G, Xie R, Ren L. Galactose Enhances Chondrogenic Differentiation of ATDC5 and Cartilage Matrix Formation by Chondrocytes. Front Mol Biosci 2022; 9:850778. [PMID: 35615738 PMCID: PMC9124793 DOI: 10.3389/fmolb.2022.850778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022] Open
Abstract
Galactose, an important carbohydrate nutrient, is involved in several types of cellular metabolism, participating in physiological activities such as glycosaminoglycan (GAG) synthesis, glycosylation, and intercellular recognition. The regulatory effects of galactose on osteoarthritis have attracted increased attention. In this study, in vitro cell models of ATDC5 and chondrocytes were prepared and cultured with different concentrations of galactose to evaluate its capacity on chondrogenesis and cartilage matrix formation. The cell proliferation assay demonstrated that galactose was nontoxic to both ATDC5 cells and chondrocytes. RT-PCR and immunofluorescence staining indicated that the gene expressions of cartilage matrix type II collagen and aggrecan were significantly upregulated with increasing galactose concentration and the expression and accumulation of the extracellular matrix (ECM) protein. Overall, these results indicated that a galactose concentration below 8 mM exhibited the best effect on promoting chondrogenesis, which entitles galactose as having considerable potential for cartilage repair and regeneration.
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Affiliation(s)
- Zhongrun Yuan
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, China
| | - Sa Liu
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Sa Liu, ; Renjian Xie, ; Li Ren,
| | - Wenjing Song
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, China
| | - Ying Liu
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, China
| | - Gangyuan Bi
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, China
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, China
| | - Renjian Xie
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
- Jiangxi Key Laboratory of Medical Tissue Engineering Materials and Biofabrication, Gannan Medical University, Ganzhou, China
- *Correspondence: Sa Liu, ; Renjian Xie, ; Li Ren,
| | - Li Ren
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- Guangdong Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Sa Liu, ; Renjian Xie, ; Li Ren,
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46
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Onyeziri MC, Hardy GG, Natarajan R, Xu J, Reynolds IP, Kim J, Merritt PM, Danhorn T, Hibbing ME, Weisberg AJ, Chang JH, Fuqua C. Dual adhesive unipolar polysaccharides synthesized by overlapping biosynthetic pathways in Agrobacterium tumefaciens. Mol Microbiol 2022; 117:1023-1047. [PMID: 35191101 PMCID: PMC9149101 DOI: 10.1111/mmi.14887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
Agrobacterium tumefaciens is a member of the Alphaproteobacteria that pathogenises plants and associates with biotic and abiotic surfaces via a single cellular pole. A. tumefaciens produces the unipolar polysaccharide (UPP) at the site of surface contact. UPP production is normally surface-contact inducible, but elevated levels of the second messenger cyclic diguanylate monophosphate (cdGMP) bypass this requirement. Multiple lines of evidence suggest that the UPP has a central polysaccharide component. Using an A. tumefaciens derivative with elevated cdGMP and mutationally disabled for other dispensable polysaccharides, a series of related genetic screens have identified a large number of genes involved in UPP biosynthesis, most of which are Wzx-Wzy-type polysaccharide biosynthetic components. Extensive analyses of UPP production in these mutants have revealed that the UPP is composed of two genetically, chemically, and spatially discrete forms of polysaccharide, and that each requires a specific Wzy-type polymerase. Other important biosynthetic, processing, and regulatory functions for UPP production are also revealed, some of which are common to both polysaccharides, and a subset of which are specific to each type. Many of the UPP genes identified are conserved among diverse rhizobia, whereas others are more lineage specific.
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Affiliation(s)
| | - Gail G. Hardy
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Ramya Natarajan
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Jing Xu
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Ian P. Reynolds
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Jinwoo Kim
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Peter M. Merritt
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Thomas Danhorn
- Department of Biology, Indiana University, Bloomington, IN 47405
| | | | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN 47405
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47
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Li G, Guo R, Wu S, Cheng S, Li J, Liu Z, Xie W, Sun X, Zhang Q, Li Z, Xu J, Wu J, Wei Z, Hu F. Characterization of Agarolytic Pathway in a Terrestrial Bacterium Cohnella sp. LGH. Front Microbiol 2022; 13:828687. [PMID: 35432256 PMCID: PMC9008576 DOI: 10.3389/fmicb.2022.828687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Previously, we have reported that an endo-type β-agarase AgaW was responsible for the hydrolysis of agarose into the major product neoagarotetraose in a terrestrial agar-degrading bacterium Cohnella sp. LGH. Here, we identify and characterize the following depolymerization pathway in strain LGH through the genomic and enzymatic analysis. In the pathway, neoagarotetraose was depolymerized by a novel α-neoagarooligosaccharide (NAOS) hydrolase CL5012 into 3,6-anhydro-α-L-galactose (L-AHG) and agarotriose; Agarotriose was further depolymerized by a novel agarolytic β-galactosidase CL4994 into D-galactose and neoagarobiose; Neoagarobiose was finally depolymerized by CL5012 into L-AHG and D-galactose. Although α-agarase has not been identified in strain LGH, the combined action of CL5012 and CL4994 unexpectedly plays a critical role in the depolymerization of agarotetraose, one theoretical product of α-agarase hydrolysis of agarose. In this pathway, agarotetraose was depolymerized by CL4994 into D-galactose and neoagarotriose; Neoagarotriose was then depolymerized by CL5012 into L-AHG and agarobiose. Furthermore, another novel endo-type β-agarase CL5055 was identified as an isozyme of AgaW with different pH preference in the hydrolysis of agarose into α-NAOSs. Strain LGH seemed to lack a common exo-type β-agarase responsible for the direct depolymerization of agarose or neoagarooligosaccharide into neoagarobiose. These results highlight the diversity of agarolytic manner in bacteria and provide a novel insight on the diversity of agarolytic pathways.
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Affiliation(s)
- Gen Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Nanjing, China
| | - Rui Guo
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shuqi Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Si Cheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiaqi Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhenzhen Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wangliang Xie
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaolin Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qiuyi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zihan Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - JiaZheng Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Jun Wu,
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Nanjing, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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48
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Pimentel FSA, Machado CM, De-Souza EA, Fernandes CM, De-Queiroz ALFV, Silva GFS, Del Poeta M, Montero-Lomeli M, Masuda CA. Sphingolipid depletion suppresses UPR activation and promotes galactose hypersensitivity in yeast models of classic galactosemia. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166389. [PMID: 35301088 DOI: 10.1016/j.bbadis.2022.166389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022]
Abstract
Classic galactosemia is an inborn error of metabolism caused by deleterious mutations on the GALT gene, which encodes the Leloir pathway enzyme galactose-1-phosphate uridyltransferase. Previous studies have shown that the endoplasmic reticulum unfolded protein response (UPR) is relevant to galactosemia, but the molecular mechanism behind the endoplasmic reticulum stress that triggers this response remains elusive. In the present work, we show that the activation of the UPR in yeast models of galactosemia does not depend on the binding of unfolded proteins to the ER stress sensor protein Ire1p since the protein domain responsible for unfolded protein binding to Ire1p is not necessary for UPR activation. Interestingly, myriocin - an inhibitor of the de novo sphingolipid synthesis pathway - inhibits UPR activation and causes galactose hypersensitivity in these models, indicating that myriocin-mediated sphingolipid depletion impairs yeast adaptation to galactose toxicity. Supporting the interpretation that the effects observed after myriocin treatment were due to a reduction in sphingolipid levels, the addition of phytosphingosine to the culture medium reverses all myriocin effects tested. Surprisingly, constitutively active UPR signaling did not prevent myriocin-induced galactose hypersensitivity suggesting multiple roles for sphingolipids in the adaptation of yeast cells to galactose toxicity. Therefore, we conclude that sphingolipid homeostasis has an important role in UPR activation and cellular adaptation in yeast models of galactosemia, highlighting the possible role of lipid metabolism in the pathophysiology of this disease.
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Affiliation(s)
- Felipe S A Pimentel
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caio M Machado
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evandro A De-Souza
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Ana Luiza F V De-Queiroz
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme F S Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA; Division of Infectious Diseases, Stony Brook, NY, USA; Veteran Administration Medical Center, Northport, New York, USA
| | - Monica Montero-Lomeli
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudio A Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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49
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Chin JHC, Samian MR, Normi YM. Characterization of polyhydroxyalkanoate production capacity, composition and weight synthesized by Burkholderia cepacia JC-1 from various carbon sources. Heliyon 2022; 8:e09174. [PMID: 35368536 PMCID: PMC8971576 DOI: 10.1016/j.heliyon.2022.e09174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 03/17/2022] [Indexed: 12/17/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are microbial polymers that have received widespread attention in recent decades as potential alternatives to some petrochemical-based plastics. However, widespread use of PHA is often impeded by its cost of production. Therefore, the search for and systematic investigation of versatile microbial PHA producers capable of using various carbon sources, even in the form of animal fats, for PHA biosynthesis is desirable. This study highlights the PHA production capacity, monomer composition and molecular weight synthesized by Burkholderia cepacia JC-1, a locally isolated strain from soil, from various carbon sources. In the category of simple sugars and plant oils, the use of glucose and palm oil at C:N ratio of 40 resulted in the highest accumulation of 52 wt% and 36 wt% poly(3-hydroxybutyrate) [P(3HB)] homopolymer and dry cell weight of 2.56 g/L and 3.17 g/L, respectively. Interestingly, B. cepacia JC-1 was able to directly utilize animal-derived lipid in the form of crude and extracted chicken fat, resulting in appreciable dry cell weight and PHA contents of up to 3.19 g/L and 47 wt% respectively, surpassing even that of palm oil in the group of triglycerides as substrates. The presence of antibiotics (streptomycin) in cultivation medium did not significantly affect cell growth and polymer production. The supply of sodium pentanoate as a co-substrate resulted in the incorporation of 3-hydroxyvalerate (3HV) monomer at fractions up to 37 mol%. The molecular weight of polymers produced from glucose, palm oil and chicken fat were in the range of 991–2118 kDa, higher than some reported studies involving native strains. The results from this study form an important basis for possible improvements in using B. cepacia JC-1 and crude chicken fats in solid form for PHA production in the future.
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Affiliation(s)
- Julian Hock-Chye Chin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Mohd Razip Samian
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Bimolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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50
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Meng J, Németh Z, Peng M, Fekete E, Garrigues S, Lipzen A, Ng V, Savage E, Zhang Y, Grigoriev IV, Mäkelä MR, Karaffa L, de Vries RP. GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans. Microb Biotechnol 2022; 15:1839-1851. [PMID: 35213794 PMCID: PMC9151342 DOI: 10.1111/1751-7915.14025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/27/2022] Open
Abstract
Filamentous fungi produce a wide variety of enzymes in order to efficiently degrade plant cell wall polysaccharides. The production of these enzymes is controlled by transcriptional regulators, which also control the catabolic pathways that convert the released monosaccharides. Two transcriptional regulators, GalX and GalR, control d-galactose utilization in the model filamentous fungus Aspergillus nidulans, while the arabinanolytic regulator AraR regulates l-arabinose catabolism. d-Galactose and l-arabinose are commonly found together in polysaccharides, such as arabinogalactan, xylan and rhamnogalacturonan I. Therefore, the catabolic pathways that convert d-galactose and l-arabinose are often also likely to be active simultaneously. In this study, we investigated the interaction between GalX, GalR and AraR in d-galactose and l-arabinose catabolism. For this, we generated single, double and triple mutants of the three regulators, and analysed their growth and enzyme and gene expression profiles. Our results clearly demonstrated that GalX, GalR and AraR co-regulate d-galactose catabolism in A. nidulans. GalX has a prominent role on the regulation of genes of d-galactose oxido-reductive pathway, while AraR can compensate for the absence of GalR and/or GalX.
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Affiliation(s)
- Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Zoltán Németh
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emily Savage
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yu Zhang
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, 00790, Finland
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary.,Institute of Metagenomics, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
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