1
|
Lilay GH, Thiébaut N, du Mee D, Assunção AGL, Schjoerring JK, Husted S, Persson DP. Linking the key physiological functions of essential micronutrients to their deficiency symptoms in plants. New Phytol 2024. [PMID: 38433319 DOI: 10.1111/nph.19645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024]
Abstract
In this review, we untangle the physiological key functions of the essential micronutrients and link them to the deficiency responses in plants. Knowledge of these responses at the mechanistic level, and the resulting deficiency symptoms, have improved over the last decade and it appears timely to review recent insights for each of them. A proper understanding of the links between function and symptom is indispensable for an accurate and timely identification of nutritional disorders, thereby informing the design and development of sustainable fertilization strategies. Similarly, improved knowledge of the molecular and physiological functions of micronutrients will be important for breeding programmes aiming to develop new crop genotypes with improved nutrient-use efficiency and resilience in the face of changing soil and climate conditions.
Collapse
Affiliation(s)
- Grmay Hailu Lilay
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Noémie Thiébaut
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
- Earth and Life Institute, Faculty of Bioscience Engineering, Université Catholique de Louvain, Louvain-la-Neuve, 1348, Belgium
| | - Dorine du Mee
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Ana G L Assunção
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
| | - Jan Kofod Schjoerring
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Søren Husted
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Daniel Pergament Persson
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| |
Collapse
|
2
|
Ngumbau NM, Neary J, Wagner AD, Abuna F, Ochieng B, Dettinger JC, Gómez L, Marwa MM, Watoyi S, Nzove E, Pintye J, Baeten JM, Kinuthia J, John-Stewart G. Cofactors of Partner HIV Self-testing and Oral PrEP Acceptance Among Pregnant Women at High Risk of HIV in Kenya. J Acquir Immune Defic Syndr 2024; 95:238-245. [PMID: 38408215 PMCID: PMC10897494 DOI: 10.1097/qai.0000000000003355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 11/06/2023] [Indexed: 02/28/2024]
Abstract
BACKGROUND Oral pre-exposure prophylaxis (PrEP) and male partner HIV self-testing (HIVST) is being scaled up within antenatal clinics. Few data are available on how co-distribution influences acceptance of both interventions. METHODS We used data from the PrEP Implementation of Mothers in Antenatal Care (NCT03070600) trial in Kenya. Women included in this analysis were determined to be at high risk of HIV and offered oral PrEP and partner HIVST. Characteristics were compared between women who chose: (1) PrEP and HIVST, (2) HIVST-alone, (3) PrEP-alone, or (4) declined both (reference), excluding women who had partners known to be living with HIV. RESULTS Among 911 women, median age was 24 years, 87.3% were married, 43.9% perceived themselves to be at high risk of HIV and 13.0% had history of intimate partner violence (IPV). Overall, 68.9% accepted HIVST and 18.4% accepted PrEP, with 54.7% accepting HIVST-alone, 4.2% PrEP-alone, and 14.3% both HIVST and PrEP. Of women accepting HIVST, partner HIV testing increased from 20% to 82% and awareness of partner HIV status increased from 4.7% to 82.0% between pregnancy and 9 months postpartum (P < 0.001). Compared with women who accepted neither, choosing: (1) HIVST-alone was associated with being married, higher level of education, and residing with partner; (2) PrEP-alone was associated with lower social support, IPV, not residing with partner, longer time living with partner, and suspicion of other partners; and (3) PrEP and HIVST was associated with being married, IPV, and suspicion that partner had other partners. CONCLUSIONS Understanding factors associated with accepting HIVST and PrEP can inform HIV prevention programs for pregnant women. CLINICAL TRIAL NUMBER NCT03070600.
Collapse
Affiliation(s)
- Nancy M Ngumbau
- Research & Programs, Kenyatta National Hospital, Nairobi, Kenya
| | | | | | - Felix Abuna
- Research & Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Ben Ochieng
- Research & Programs, Kenyatta National Hospital, Nairobi, Kenya
| | | | | | - Mary M Marwa
- Research & Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Salphine Watoyi
- Research & Programs, Kenyatta National Hospital, Nairobi, Kenya
| | | | | | | | - John Kinuthia
- Research & Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Grace John-Stewart
- Department of Epidemiology
- Department of Global Health
- Departments of Pediatrics and Medicine, University of Washington, Seattle, WA
| |
Collapse
|
3
|
Laird MG, Adlung N, Koivisto JJ, Scheller S. Thiol-Disulfide Exchange Kinetics and Redox Potential of the Coenzyme M and Coenzyme B Heterodisulfide, an Electron Acceptor Coupled to Energy Conservation in Methanogenic Archaea. Chembiochem 2024; 25:e202300595. [PMID: 37815851 DOI: 10.1002/cbic.202300595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Methanogenic and methanotrophic archaea play important roles in the global carbon cycle by interconverting CO2 and methane. To conserve energy from these metabolic pathways that happen close to the thermodynamic equilibrium, specific electron carriers have evolved to balance the redox potentials between key steps. Reduced ferredoxins required to activate CO2 are provided by energetical coupling to the reduction of the high-potential heterodisulfide (HDS) of coenzyme M (2-mercaptoethanesulfonate) and coenzyme B (7-mercaptoheptanoylthreonine phosphate). While the standard redox potential of this important HDS has been determined previously to be -143 mV (Tietze et al. 2003 DOI: 10.1002/cbic.200390053), we have measured thiol disulfide exchange kinetics and reassessed this value by equilibrating thiol-disulfide mixtures of coenzyme M, coenzyme B, and mercaptoethanol. We determined the redox potential of the HDS of coenzyme M and coenzyme B to be -16.4±1.7 mV relative to the reference thiol mercaptoethanol (E0 '=-264 mV). The resulting E0 ' values are -281 mV for the HDS, -271 mV for the homodisulfide of coenzyme M, and -270 mV for the homodisulfide of coenzyme B. We discuss the importance of these updated values for the physiology of methanogenic and methanotrophic archaea and their implications in terms of energy conservation.
Collapse
Affiliation(s)
- Maxime G Laird
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Norman Adlung
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Jari J Koivisto
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| |
Collapse
|
4
|
Kirjavainen L, Suominen H, Syrjänen K, Waterboer T, Grenman S, Syrjänen S, Louvanto K. Impact of Different Cofactors on Naturally Acquired Human Papillomavirus Antibody Levels Among Unvaccinated Pregnant Women. Viral Immunol 2024; 37:36-43. [PMID: 38315747 DOI: 10.1089/vim.2023.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Human papillomavirus (HPV) infections are common, transmitted by sexual and nonsexual routes. The present case-control setting was designed to examine potential cofactors associated with either persistently low or high HPV-antibody levels. The study subjects were from the Finnish HPV Family cohort of 329 baseline pregnant, non-HPV-vaccinated women, who were sampled for genital and oral HPV-DNA and HPV serology at baseline, and at 12, 24, and 36 months. Antibodies to the L1 major capsid protein of HPV 6, 11, 16, 18, and 45 were analyzed by multiplex HPV serology and HPV genotyping was performed. This study included 59 women, 23 women with persistently low (<200 median fluorescence intensity [MFI]) and 36 women with persistently high and always positive (>200 MFI) levels of these antibodies for all five HPV genotypes. Potential HPV-associated covariates were derived from detailed questionnaires. Only cofactors other than detected HPV genotype significantly impact on the levels of natural HPV antibodies. A higher number of past sexual partners or a history of diagnosed genital warts were significant covariates of high HPV antibody levels (p = 0.023 and p = 0.043, respectively). Of interest, women with a history of allergies presented with low levels of HPV antibodies (p = 0.03), potentially exposing these women to an increased risk of future HPV-related diseases that merit closer surveillance.
Collapse
Affiliation(s)
- Laura Kirjavainen
- Department of Obstetrics and Gynecology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Helmi Suominen
- Department of Obstetrics and Gynecology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Seija Grenman
- Department of Obstetrics and Gynecology, Turku University Hospital, University of Turku, Turku, Finland
| | - Stina Syrjänen
- Department of Oral Pathology, Institute of Dentistry, Faculty of Medicine, University of Turku, Turku, Finland
| | - Karolina Louvanto
- Department of Obstetrics and Gynecology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
| |
Collapse
|
5
|
Twarock R, Towers GJ, Stockley PG. Molecular frustration: a hypothesis for regulation of viral infections. Trends Microbiol 2024; 32:17-26. [PMID: 37507296 DOI: 10.1016/j.tim.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome release. We have proposed a model in which multiple packaging signal (PS) RNA-coat protein (CP) contacts orchestrate different stages of a viral life cycle. Programmed formation and release of specific PS contacts with CP regulates viral particle assembly and genome uncoating during cell entry. We hypothesize that molecular frustration, a concept introduced to understand protein folding, can be used to better rationalize how PSs function in both particle assembly and genome release. More broadly this concept may explain the directionality of viral life cycles, for example, the roles of host cofactors in HIV infection. We propose that this is a universal principle in virology that explains mechanisms of host-virus interaction and suggests diverse therapeutic interventions.
Collapse
Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
6
|
Ting KKY, Jongstra-Bilen J, Cybulsky MI. The multi-faceted role of NADPH in regulating inflammation in activated myeloid cells. Front Immunol 2023; 14:1328484. [PMID: 38106413 PMCID: PMC10722250 DOI: 10.3389/fimmu.2023.1328484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023] Open
Abstract
Recent advances in the immunometabolism field have demonstrated the importance of metabolites in fine-tuning the inflammatory responses in myeloid cells. Cofactors, which are metabolites comprised of inorganic ions and organic molecules, may tightly or loosely bind to distinct sites of enzymes to catalyze a specific reaction. Since many enzymes that mediate inflammatory and anti-inflammatory processes require the same cofactors to function, this raises the possibility that under conditions where the abundance of these cofactors is limited, inflammatory and anti-inflammatory enzymes must compete with each other for the consumption of cofactors. Thus, this competition may reflect a naturally evolved mechanism to efficiently co-regulate inflammatory versus anti-inflammatory pathways, fine-tuning the extent of an inflammatory response. The role of NADPH, the reduced form of nicotinamide adenine dinucleotide phosphate (NADP+), in mediating inflammatory and anti-inflammatory responses in activated myeloid cells has been well-established in the past decades. However, how the dynamic of NADPH consumption mediates the co-regulation between individual inflammatory and anti-inflammatory pathways is only beginning to be appreciated. In this review, we will summarize the established roles of NADPH in supporting inflammatory and anti-inflammatory pathways, as well as highlight how the competition for NADPH consumption by these opposing pathways fine-tunes the inflammatory response in activated myeloid cells.
Collapse
Affiliation(s)
- Kenneth K. Y. Ting
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Jenny Jongstra-Bilen
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Myron I. Cybulsky
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
| |
Collapse
|
7
|
Pałgan K, Tretyn A. Platelet-activating factor as an endogenous cofactor of food anaphylaxis. Biofactors 2023; 49:976-983. [PMID: 37203358 DOI: 10.1002/biof.1956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 03/02/2023] [Indexed: 05/20/2023]
Abstract
Anaphylaxis is a severe, acute, life-threatening generalized or systemic hypersensitivity reaction. The incidence of anaphylaxis is increasing worldwide, with medications and food contributing to most cases. Physical exercise, acute infections, drugs, alcohol, and menstruation are the external cofactors associated with more severe systemic reaction. The aim of this review is to show that platelet-activating factor contributes to the development of severe anaphylactic reaction, and even to anaphylactic shock.
Collapse
Affiliation(s)
- Krzysztof Pałgan
- Department of Allergology, Clinical Immunology and Internal Diseases, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| |
Collapse
|
8
|
Jiang Z, Jiang Y, Wu H, Zhang W, Xin F, Ma J, Jiang M. Cofactor Metabolic Engineering of Escherichia coli for Aerobic L-Malate Production with Lower CO 2 Emissions. Bioengineering (Basel) 2023; 10:881. [PMID: 37627766 PMCID: PMC10451681 DOI: 10.3390/bioengineering10080881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/27/2023] Open
Abstract
Escherichia coli has been engineered for L-malate production via aerobic cultivation. However, the maximum yield obtained through this mode is inferior to that of anaerobic fermentation due to massive amounts of CO2 emissions. Here, we aim to address this issue by reducing CO2 emissions of recombinant E. coli during aerobic L-malate production. Our findings indicated that NADH oxidation and ATP-synthesis-related genes were down-regulated with 2 g/L of YE during aerobic cultivations of E. coli E23, as compared to 5 g/L of YE. Then, E23 was engineered via the knockout of nuoA and the introduction of the nonoxidative glycolysis (NOG) pathway, resulting in a reduction of NAD+ and ATP supplies. The results demonstrate that E23 (ΔnuoA, NOG) exhibited decreased CO2 emissions, and it produced 21.3 g/L of L-malate from glucose aerobically with the improved yield of 0.43 g/g. This study suggests that a restricted NAD+ and ATP supply can prompt E. coli to engage in incomplete oxidization of glucose, leading to the accumulation of metabolites instead of utilizing them in cellular respiration.
Collapse
Affiliation(s)
| | | | | | | | | | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | | |
Collapse
|
9
|
Chaudhury D, Torkelson ER, Meyers KA, Acheson JF, Landucci L, Pu Y, Sun Z, Tonelli M, Bingman CA, Smith RA, Karlen SD, Mansfield SD, Ralph J, Fox BG. Rapid Biocatalytic Synthesis of Aromatic Acid CoA Thioesters by Using Microbial Aromatic Acid CoA Ligases. Chembiochem 2023; 24:e202300001. [PMID: 36821718 PMCID: PMC10467583 DOI: 10.1002/cbic.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
Chemically labile ester linkages can be introduced into lignin by incorporation of monolignol conjugates, which are synthesized in planta by acyltransferases that use a coenzyme A (CoA) thioester donor and a nucleophilic monolignol alcohol acceptor. The presence of these esters facilitates processing and aids in the valorization of renewable biomass feedstocks. However, the effectiveness of this strategy is potentially limited by the low steady-state levels of aromatic acid thioester donors in plants. As part of an effort to overcome this, aromatic acid CoA ligases involved in microbial aromatic degradation were identified and screened against a broad panel of substituted cinnamic and benzoic acids involved in plant lignification. Functional fingerprinting of this ligase library identified four robust, highly active enzymes capable of facile, rapid, and high-yield synthesis of aromatic acid CoA thioesters under mild aqueous reaction conditions mimicking in planta activity.
Collapse
Affiliation(s)
- Debayan Chaudhury
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Ella R Torkelson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Kaya A Meyers
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Leta Landucci
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Yucen Pu
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Zimou Sun
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Rebecca A Smith
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Steven D Karlen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Shawn D Mansfield
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| |
Collapse
|
10
|
Hu Y, Liu Z, Xu S, Zhao Q, Liu G, Song X, Qu Y, Qin Y. The interaction between the histone acetyltransferase complex Hat1-Hat2 and transcription factor AmyR provides a molecular brake to regulate amylase gene expression. Mol Microbiol 2023; 119:471-491. [PMID: 36760021 DOI: 10.1111/mmi.15036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/15/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
The chromatin structure is generally regulated by chromatin remodelers and histone modifiers, which affect DNA replication, repair, and levels of transcription. The first identified histone acetyltransferase was Hat1/KAT1, which belongs to lysine (K) acetyltransferases. The catalytic subunit Hat1 and the regulatory subunit Hat2 make up the core HAT1 complex. In this study, the results of tandem affinity purification and mass spectrometry and bimolecular fluorescence complementation proved that the Penicillium oxalicum PoHat1-Hat2 is the transcriptional cofactor of the sequence-specific transcription factor PoAmyR, a transcription activator essential for the transcription of amylase gene. ChIP-qPCR results demonstrated that the complex PoHat1-Hat2 is recruited by PoAmyR to the promoters of prominent amylase genes Poamy13A and Poamy15A and performs histone H4 lysine12 acetylation. The result of the yeast two-hybrid test indicated that PoHat2 is the subunit that directly interacts with PoAmyR. PoHat1-Hat2 acts as the molecular brake of the PoAmyR-regulating transcription of amylase genes. A putative model for amylase gene regulation by PoAmyR-Hat2-Hat1 was constructed. Our paper is the first report that the Hat1-Hat2 complex acts as a cofactor for sequence-specific TF to regulate gene expression and explains the mechanism of TF AmyR regulating amylase genes expression.
Collapse
Affiliation(s)
- Yueyan Hu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China.,Shandong Lishan Biotechnology Co., Ltd, Jinan, China
| | - Zhongjiao Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shaohua Xu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qinqin Zhao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guodong Liu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Xin Song
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yinbo Qu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China.,NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine, Shandong University, Qingdao, China
| |
Collapse
|
11
|
Chen Q, Wang Y, Luo G. Recycling of Cofactors in Crude Enzyme Hydrogels as Co-immobilized Heterogeneous Biocatalysts for Continuous-Flow Asymmetric Reduction of Ketones. ChemSusChem 2023; 16:e202201654. [PMID: 36269055 DOI: 10.1002/cssc.202201654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Flow biocatalysis involving oxidoreductase is limited by the difficulty in recycling expensive cofactors. In this study, an enzyme-rich hydrogel monolithic microreactor was developed via in situ microfluidic assembly of inexpensive crude enzymes. This porous gel biocatalyst exhibited good tethering functions to nicotinamide cofactors; thus, they were retained by the hydrogel to controllably form a novel heterogeneous biocatalyst with self-sufficient cofactors. The flow asymmetric production of a chiral alcohol in this cofactor-entrapped gel microreactor achieved >99 % enantioselectivity and a high space-time yield of 46.3 g L-1 h-1 at 94.8 % conversion. Moreover, the turnover number of cofactors reached as high as 4800 after continuous operation of 160 reactor volumes, realizing significantly higher utilization of the cofactors compared with many reported strategies. Furthermore, this engineered heterogeneous biocatalyst exhibited improved performance in terms of product tolerance and storage stability, paving the way for a green, cost-effective, and sustainable continuous-flow production of enantiopure alcohols.
Collapse
Affiliation(s)
- Qiang Chen
- The State Key Lab of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yujun Wang
- The State Key Lab of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Guangsheng Luo
- The State Key Lab of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| |
Collapse
|
12
|
Indika NR, Frye RE, Rossignol DA, Owens SC, Senarathne UD, Grabrucker AM, Perera R, Engelen MPKJ, Deutz NEP. The Rationale for Vitamin, Mineral, and Cofactor Treatment in the Precision Medical Care of Autism Spectrum Disorder. J Pers Med 2023; 13. [PMID: 36836486 DOI: 10.3390/jpm13020252] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Children with autism spectrum disorder may exhibit nutritional deficiencies due to reduced intake, genetic variants, autoantibodies interfering with vitamin transport, and the accumulation of toxic compounds that consume vitamins. Importantly, vitamins and metal ions are essential for several metabolic pathways and for neurotransmitter functioning. The therapeutic benefits of supplementing vitamins, minerals (Zinc, Magnesium, Molybdenum, and Selenium), and other cofactors (coenzyme Q10, alpha-lipoic acid, and tetrahydrobiopterin) are mediated through their cofactor as well as non-cofactor functions. Interestingly, some vitamins can be safely administered at levels far above the dose typically used to correct the deficiency and exert effects beyond their functional role as enzyme cofactors. Moreover, the interrelationships between these nutrients can be leveraged to obtain synergistic effects using combinations. The present review discusses the current evidence for using vitamins, minerals, and cofactors in autism spectrum disorder, the rationale behind their use, and the prospects for future use.
Collapse
|
13
|
Marchetti M, Puglisi R, Cellini B, Dindo M, Marchesani F. Editorial: The role of cofactors in protein stability and homeostasis: Focus on human metabolism. Front Mol Biosci 2023; 10:1147451. [PMID: 36762209 PMCID: PMC9907023 DOI: 10.3389/fmolb.2023.1147451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, Parma, Italy,*Correspondence: Marialaura Marchetti,
| | - Rita Puglisi
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Mirco Dindo
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | |
Collapse
|
14
|
Sun Y, Zhang T, Lu B, Li X, Jiang L. Application of cofactors in the regulation of microbial metabolism: A state of the art review. Front Microbiol 2023; 14:1145784. [PMID: 37113222 PMCID: PMC10126289 DOI: 10.3389/fmicb.2023.1145784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Cofactors are crucial chemicals that maintain cellular redox balance and drive the cell to do synthetic and catabolic reactions. They are involved in practically all enzymatic activities that occur in live cells. It has been a hot research topic in recent years to manage their concentrations and forms in microbial cells by using appropriate techniques to obtain more high-quality target products. In this review, we first summarize the physiological functions of common cofactors, and give a brief overview of common cofactors acetyl coenzyme A, NAD(P)H/NAD(P)+, and ATP/ADP; then we provide a detailed introduction of intracellular cofactor regeneration pathways, review the regulation of cofactor forms and concentrations by molecular biological means, and review the existing regulatory strategies of microbial cellular cofactors and their application progress, to maximize and rapidly direct the metabolic flux to target metabolites. Finally, we speculate on the future of cofactor engineering applications in cell factories. Graphical Abstract.
Collapse
Affiliation(s)
- Yang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ting Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Bingqian Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiangfei Li
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, Wuhu, China
- *Correspondence: Xiangfei Li,
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| |
Collapse
|
15
|
Abstract
Cofactors are essential effectors of the transcription control machinery. How this functionally diverse group of factors is used in the genome remains elusive. A recent study by Neumayr, Haberle et al. sheds light on this question, showing that enhancers depend on defined combinations of cofactors for their activation.
Collapse
Affiliation(s)
- Elisa Kreibich
- EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Arnaud R Krebs
- EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| |
Collapse
|
16
|
Diaz-Espinoza R. Catalytically Active Amyloids as Future Bionanomaterials. Nanomaterials (Basel) 2022; 12:3802. [PMID: 36364578 PMCID: PMC9656882 DOI: 10.3390/nano12213802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Peptides and proteins can aggregate into highly ordered and structured conformations called amyloids. These supramolecular structures generally have convergent features, such as the formation of intermolecular beta sheets, that lead to fibrillary architectures. The resulting fibrils have unique mechanical properties that can be exploited to develop novel nanomaterials. In recent years, sequences of small peptides have been rationally designed to self-assemble into amyloids that catalyze several chemical reactions. These amyloids exhibit reactive surfaces that can mimic the active sites of enzymes. In this review, I provide a state-of-the-art summary of the development of catalytically active amyloids. I will focus especially on catalytic activities mediated by hydrolysis, which are the most studied examples to date, as well as novel types of recently reported activities that promise to expand the possible repertoires. The combination of mechanical properties with catalytic activity in an amyloid scaffold has great potential for the development of future bionanomaterials aimed at specific applications.
Collapse
Affiliation(s)
- Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 3363, Chile
| |
Collapse
|
17
|
Ramaswamy K, Rashid M, Ramasamy S, Jayavelu T, Venkataraman S. Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies. Viruses 2022; 14:2200. [PMID: 36298755 DOI: 10.3390/v14102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022] Open
Abstract
RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors.
Collapse
|
18
|
Wasilewski M, Gohil VM, Khalimonchuk O. Editorial: Function and formation of mitochondrial metalloproteome. Front Cell Dev Biol 2022; 10:1020441. [PMID: 36247001 PMCID: PMC9554646 DOI: 10.3389/fcell.2022.1020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/01/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Michał Wasilewski
- International Institute of Molecular Mechanisms and Machines (IMol), Polish Academy of Sciences, Warsaw, Poland,*Correspondence: Michał Wasilewski,
| | - Vishal M. Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE, United States,Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE, United States,Fred & Pamela Buffett Cancer Center, Omaha, NE, United States
| |
Collapse
|
19
|
Molina Ortiz JP, Read MN, McClure DD, Holmes A, Dehghani F, Shanahan ER. High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure. Gut Microbes 2022; 14:2118831. [PMID: 36081364 PMCID: PMC9480837 DOI: 10.1080/19490976.2022.2118831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Human gut microbiome structure and emergent metabolic outputs impact health outcomes. However, what drives such community characteristics remains underexplored. Here, we rely on high throughput genomic reconstruction modeling, to infer the metabolic attributes and nutritional requirements of 816 gut strains, via a framework termed GEMNAST. This has been performed in terms of a group of human vitamins to examine the role vitamin exchanges have at different levels of community organization. We find that only 91 strains can satisfy their vitamin requirements (prototrophs) while the rest show various degrees of auxotrophy/specialization, highlighting their dependence on external sources, such as other members of the microbial community. Further, 79% of the strains in our sample were mapped to 11 distinct vitamin requirement profiles with low phylogenetic consistency. Yet, we find that human gut microbial community enterotype indicators display marked metabolic differences. Prevotella strains display a metabolic profile that can be complemented by strains from other genera often associated with the Prevotella enterotype and agrarian diets, while Bacteroides strains occupy a prototrophic profile. Finally, we identify pre-defined interaction modules (IMs) of gut species from human and mice predicted to be driven by, or highly independent of vitamin exchanges. Our analysis provides mechanistic grounding to gut microbiome stability and to co-abundance-based observations, a fundamental step toward understanding emergent processes that influence health outcomes. Further, our work opens a path to future explorations in the field through applications of GEMNAST to additional nutritional dimensions.
Collapse
Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, the University of Sydney, Sydney, Australia,Centre for Advanced Food Engineering, the University of Sydney, Sydney, Australia,CONTACT Juan P. Molina Ortiz School of Chemical and Biomolecular Engineering, the University of Sydney, Sydney, Australia
| | - Mark Norman Read
- Centre for Advanced Food Engineering, the University of Sydney, Sydney, Australia,School of Computer Science, Faculty of Engineering, the University of Sydney, Sydney, Australia,Charles Perkins Centre, the University of Sydney, Sydney, Australia
| | - Dale David McClure
- School of Chemical and Biomolecular Engineering, the University of Sydney, Sydney, Australia,Centre for Advanced Food Engineering, the University of Sydney, Sydney, Australia,Department of Chemical Engineering, College of Engineering, Design and Physical Sciences, Brunel University, London, UK
| | - Andrew Holmes
- Centre for Advanced Food Engineering, the University of Sydney, Sydney, Australia,Charles Perkins Centre, the University of Sydney, Sydney, Australia,School of Life and Environmental Sciences, Faculty of Science, the University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, the University of Sydney, Sydney, Australia,Centre for Advanced Food Engineering, the University of Sydney, Sydney, Australia
| | - Erin Rose Shanahan
- Charles Perkins Centre, the University of Sydney, Sydney, Australia,School of Life and Environmental Sciences, Faculty of Science, the University of Sydney, Sydney, Australia,Erin Rose Shanahan Charles Perkins Centre, The University of Sydney, Sydney, Australia; School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| |
Collapse
|
20
|
Chatterjee S, Gatreddi S, Gupta S, Nevarez JL, Rankin JA, Turmo A, Hu J, Hausinger RP. Unveiling the mechanisms and biosynthesis of a novel nickel-pincer enzyme. Biochem Soc Trans 2022; 50:1187-1196. [PMID: 35960008 PMCID: PMC9880988 DOI: 10.1042/bst20220490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/31/2023]
Abstract
The nickel-pincer nucleotide (NPN) coenzyme, a substituted pyridinium mononucleotide that tri-coordinates nickel, was first identified covalently attached to a lysine residue in the LarA protein of lactate racemase. Starting from nicotinic acid adenine dinucleotide, LarB carboxylates C5 of the pyridinium ring and hydrolyzes the phosphoanhydride, LarE converts the C3 and C5 carboxylates to thiocarboxylates, and LarC incorporates nickel to form a C-Ni and two S-Ni bonds, during the biosynthesis of this cofactor. LarB uses a novel carboxylation mechanism involving the transient formation of a cysteinyl-pyridinium adduct. Depending on the source of the enzyme, LarEs either catalyze a sacrificial sulfur transfer from a cysteinyl side chain resulting in the formation of dehydroalanine or they utilize a [4Fe-4S] cluster bound by three cysteine residues to accept and transfer a non-core sulfide atom. LarC is a CTP-dependent enzyme that cytidinylylates its substrate, adds nickel, then hydrolyzes the product to release NPN and CMP. Homologs of the four lar genes are widely distributed in microorganisms, with some species containing multiple copies of larA whereas others lack this gene, consistent with the cofactor serving other functions. Several LarA-like proteins were shown to catalyze racemase or epimerase activities using 2-hydroxyacid substrates other than lactic acid. Thus, lactate racemase is the founding member of a large family of NPN-containing enzymes.
Collapse
Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Santhosh Gatreddi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Swati Gupta
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Jorge L. Nevarez
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Joel A. Rankin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
21
|
Abstract
Life and the genetic code are self-referential and so are autocatalytic networks made of simpler, small molecules. Several origins of life theories postulate autocatalytic chemical networks preceding the primordial genetic code, yet demonstration with biochemical systems is lacking. Here, small-molecule reflexively autocatalytic food-generated networks (RAFs) ranging in size from 3 to 619 reactions were found in all of 6683 prokaryotic metabolic networks searched. The average maximum RAF size is 275 reactions for a rich organic medium and 93 for a medium with a single organic cofactor, NAD. In the rich medium, all universally essential metabolites are produced with the exception of glycerol-1-p (archaeal lipid precursor), phenylalanine, histidine and arginine. The 300 most common reactions, present in at least 2732 RAFs, are mostly involved in amino acid biosynthesis and the metabolism of carbon, 2-oxocarboxylic acid and purines. ATP and NAD are central in generating network complexity, and because ATP is also one of the monomers of RNA, autocatalytic networks producing redox and energy currencies are a strong candidate niche of the origin of a primordial information-processing system. The wide distribution of small-molecule autocatalytic networks indicates that molecular reproduction may be much more prevalent in the Universe than hitherto predicted. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
Collapse
Affiliation(s)
- Joana C Xavier
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | |
Collapse
|
22
|
Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Molecules 2022; 27:3494. [PMID: 35684429 PMCID: PMC9182050 DOI: 10.3390/molecules27113494] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial diseases (MDs) may result from mutations affecting nuclear or mitochondrial genes, encoding mitochondrial proteins, or non-protein-coding mitochondrial RNA. Despite the great variability of affected genes, in the most severe cases, a neuromuscular and neurodegenerative phenotype is observed, and no specific therapy exists for a complete recovery from the disease. The most used treatments are symptomatic and based on the administration of antioxidant cocktails combined with antiepileptic/antipsychotic drugs and supportive therapy for multiorgan involvement. Nevertheless, the real utility of antioxidant cocktail treatments for patients affected by MDs still needs to be scientifically demonstrated. Unfortunately, clinical trials for antioxidant therapies using α-tocopherol, ascorbate, glutathione, riboflavin, niacin, acetyl-carnitine and coenzyme Q have met a limited success. Indeed, it would be expected that the employed antioxidants can only be effective if they are able to target the specific mechanism, i.e., involving the central and peripheral nervous system, responsible for the clinical manifestations of the disease. Noteworthily, very often the phenotypes characterizing MD patients are associated with mutations in proteins whose function does not depend on specific cofactors. Conversely, the administration of the antioxidant cocktails might determine the suppression of endogenous oxidants resulting in deleterious effects on cell viability and/or toxicity for patients. In order to avoid toxicity effects and before administering the antioxidant therapy, it might be useful to ascertain the blood serum levels of antioxidants and cofactors to be administered in MD patients. It would be also worthwhile to check the localization of mutations affecting proteins whose function should depend (less or more directly) on the cofactors to be administered, for estimating the real need and predicting the success of the proposed cofactor/antioxidant-based therapy.
Collapse
Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Guido Primiano
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Albina Tummolo
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Lucas Cafferati Beltrame
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Gianluigi La Piana
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Noemi Sgobba
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Giulia Paterno
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Domenico Marzulli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Serenella Servidei
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Giuseppe Petrosillo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Giovanni Lentini
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| |
Collapse
|
23
|
Dello Iacono L, Di Pisa F, Mangani S. Crystal structure of the ternary complex of Leishmania major pteridine reductase 1 with the cofactor NADP +/NADPH and the substrate folic acid. Acta Crystallogr F Struct Biol Commun 2022; 78:170-176. [PMID: 35400669 PMCID: PMC8996148 DOI: 10.1107/s2053230x22002795] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Pteridine reductase 1 (PTR1) is a key enzyme of the folate pathway in protozoan parasites of the genera Leishmania and Trypanosoma and is a valuable drug target for tropical diseases. This enzyme is able to catalyze the NADPH-dependent reduction of both conjugated (folate) and unconjugated (biopterin) pterins to their tetrahydro forms, starting from oxidized- or dihydro-state substrates. The currently available X-ray structures of Leishmania major PTR1 (LmPTR1) show the enzyme in its unbound, unconjugated substrate-bound (with biopterin derivatives) and inhibitor-bound forms. However, no structure has yet been determined of LmPTR1 bound to a conjugated substrate. Here, the high-resolution crystal structure of LmPTR1 in complex with folic acid is presented and the intermolecular forces that drive the binding of the substrate in the catalytic pocket are described. By expanding the collection of LmPTR1 structures in complex with process intermediates, additional insights into the active-site rearrangements that occur during the catalytic process are provided. In contrast to previous structures with biopterin derivatives, a small but significant difference in the orientation of Asp181 and Tyr194 of the catalytic triad is found. This feature is shared by PTR1 from T. brucei (TbPTR1) in complex with the same substrate molecule and may be informative in deciphering the importance of such residues at the beginning of the catalytic process.
Collapse
Affiliation(s)
- Lucia Dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Flavio Di Pisa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| |
Collapse
|
24
|
Hu G, Guo L, Gao C, Song W, Liu L, Chen X. Synergistic Metabolism of Glucose and Formate Increases the Yield of Short-Chain Organic Acids in Escherichia coli. ACS Synth Biol 2022; 11:135-143. [PMID: 34979802 DOI: 10.1021/acssynbio.1c00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial cell factories using a single carbon source (e.g., sugars) have been used to produce a wide variety of chemicals. However, this process is often accompanied by stoichiometric constraints on carbons and redox cofactors. Here, a synthetic pathway was designed and constructed in Escherichia coli to synergistically use glucose and formate as mixed carbon sources. By optimizing this synthetic pathway via enzyme mining, protein engineering, and bioprocess approaches, the yield of pyruvate from glucose was enhanced to 94% of the theoretical glycolysis yield, reaching 1.88 mol/mol. Finally, the optimized synthetic pathway was integrated with a phosphite reductase-based NADH regeneration system in malate-producing E. coli, resulting in the conversion of glucose into l-malate with a high yield of up to 1.65 mol/mol. This synergistic carbon metabolism strategy can be used to establish carbon- and energy-efficient productive processes.
Collapse
Affiliation(s)
- Guipeng Hu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
25
|
Hutchin A, Cordery C, Walsh MA, Webb JS, Tews I. Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. Microbiol Spectr 2021; 9:e0102621. [PMID: 34937179 DOI: 10.1128/spectrum.01026-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.
Collapse
|
26
|
Mengele AK, Weixler D, Amthor S, Eikmanns BJ, Seibold GM, Rau S. Transforming Escherichia coli Proteomembranes into Artificial Chloroplasts Using Molecular Photocatalysis. Angew Chem Int Ed Engl 2021; 61:e202114842. [PMID: 34932847 PMCID: PMC9306768 DOI: 10.1002/anie.202114842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 12/01/2022]
Abstract
During the light‐dependent reaction of photosynthesis, green plants couple photoinduced cascades of redox reactions with transmembrane proton translocations to generate reducing equivalents and chemical energy in the form of NADPH (nicotinamide adenine dinucleotide phosphate) and ATP (adenosine triphosphate), respectively. We mimic these basic processes by combining molecular ruthenium polypyridine‐based photocatalysts and inverted vesicles derived from Escherichia coli. Upon irradiation with visible light, the interplay of photocatalytic nicotinamide reduction and enzymatic membrane‐located respiration leads to the simultaneous formation of two biologically active cofactors, NADH (nicotinamide adenine dinucleotide) and ATP, respectively. This inorganic‐biologic hybrid system thus emulates the cofactor delivering function of an active chloroplast.
Collapse
Affiliation(s)
- Alexander Klaus Mengele
- Ulm University, Institute of Inorganic Chemistry I, Albert-Einstein-Allee 11, 89081, Ulm, GERMANY
| | - Dominik Weixler
- Ulm University, Institute of Microbiology and Biotechnology, Albert-Einstein-Allee 11, 89081, Ulm, GERMANY
| | - Sebastian Amthor
- Ulm University, Institute of Inorganic Chemistry I, Albert-Einstein-Allee 11, 89081, Ulm, GERMANY
| | - Bernhard Johannes Eikmanns
- Ulm University, Institute of Microbiology and Biotechnology, Albert-Einstein-Allee 11, 89081, Ulm, GERMANY
| | - Gerd Michael Seibold
- Technical University of Denmark, Section of Synthetic Biology, Department of Biotechnology and Bioengineering, Søltoftsplads, 2800, Kongens Lyngby, DENMARK
| | - Sven Rau
- University of Ulm, Institute of Inorganic Chemistry I Materials and Catalysis, Albert-Einstein-Allee 11, 89081, Ulm, GERMANY
| |
Collapse
|
27
|
Henriques Pereira DP, Leethaus J, Beyazay T, do Nascimento Vieira A, Kleinermanns K, Tüysüz H, Martin WF, Preiner M. Role of geochemical protoenzymes (geozymes) in primordial metabolism: specific abiotic hydride transfer by metals to the biological redox cofactor NAD . FEBS J 2021; 289:3148-3162. [PMID: 34923745 PMCID: PMC9306933 DOI: 10.1111/febs.16329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
Hydrogen gas, H2, is generated in serpentinizing hydrothermal systems, where it has supplied electrons and energy for microbial communities since there was liquid water on Earth. In modern metabolism, H2 is converted by hydrogenases into organically bound hydrides (H–), for example, the cofactor NADH. It transfers hydrides among molecules, serving as an activated and biologically harnessed form of H2. In serpentinizing systems, minerals can also bind hydrides and could, in principle, have acted as inorganic hydride donors—possibly as a geochemical protoenzyme, a ‘geozyme’— at the origin of metabolism. To test this idea, we investigated the ability of H2 to reduce NAD+ in the presence of iron (Fe), cobalt (Co) and nickel (Ni), metals that occur in serpentinizing systems. In the presence of H2, all three metals specifically reduce NAD+ to the biologically relevant form, 1,4‐NADH, with up to 100% conversion rates within a few hours under alkaline aqueous conditions at 40 °C. Using Henry's law, the partial pressure of H2 in our reactions corresponds to 3.6 mm, a concentration observed in many modern serpentinizing systems. While the reduction of NAD+ by Ni is strictly H2‐dependent, experiments in heavy water (2H2O) indicate that native Fe can reduce NAD+ both with and without H2. The results establish a mechanistic connection between abiotic and biotic hydride donors, indicating that geochemically catalysed, H2‐dependent NAD+ reduction could have preceded the hydrogenase‐dependent reaction in evolution.
Collapse
Affiliation(s)
| | - Jana Leethaus
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Tugce Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Martina Preiner
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Utrecht University, The Netherlands
| |
Collapse
|
28
|
Seigler DS, Friesen JB, Bisson J, Graham JG, Bedran-Russo A, McAlpine JB, Pauli GF. Do Certain Flavonoid IMPS Have a Vital Function? Front Nutr 2021; 8:762753. [PMID: 34926546 PMCID: PMC8672243 DOI: 10.3389/fnut.2021.762753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Flavonoids are a vast group of metabolites that are essential for vascular plant physiology and, thus, occur ubiquitously in plant-based/-derived foods. The solitary designation of thousands of known flavonoids hides the fact that their metabolomes are structurally highly diverse, consist of disparate subgroups, yet undergo a certain degree of metabolic interconversion. Unsurprisingly, flavonoids have been an important theme in nutrition research. Already in the 1930s, it was discovered that the ability of synthetic Vitamin C to treat scurvy was inferior to that of plant extracts containing Vitamin C. Subsequent experimental evidence led to the proposal of Vitamin P (permeability) as an essential phytochemical nutrient. However, attempts to isolate and characterize Vitamin P gave confusing and sometimes irreproducible results, which today can be interpreted as rooted in the unrecognized (residual) complexity of the intervention materials. Over the years, primarily flavonoids (and some coumarins) were known as having Vitamin P-like activity. More recently, in a NAPRALERT meta-analysis, essentially all of these Vitamin P candidates were identified as IMPs (Invalid/Improbable/Interfering Metabolic Panaceas). While the historic inability to define a single compound and specific mode of action led to general skepticism about the Vitamin P proposition for "bioflavonoids," the more logical conclusion is that several abundant and metabolically labile plant constituents fill this essential role in human nutrition at the interface of vitamins, cofactors, and micronutrients. Reviewing 100+ years of the multilingual Vitamin P and C literature provides the rationales for this conclusion and new perspectives for future research.
Collapse
Affiliation(s)
- David S. Seigler
- Department of Plant Biology, University of Illinois at Urbana Champaign, Champaign, IL, United States
| | - J. Brent Friesen
- Center for Natural Products Technologies, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Physical Sciences Department, Dominican University, River Forest, IL, United States
| | - Jonathan Bisson
- Center for Natural Products Technologies, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - James G. Graham
- Center for Natural Products Technologies, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Ana Bedran-Russo
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
| | - James B. McAlpine
- Center for Natural Products Technologies, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Guido F. Pauli
- Center for Natural Products Technologies, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| |
Collapse
|
29
|
Abstract
The iron‐molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E0, reduced states of FeMoco are much less well characterized. The E2 state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E2 state can, however, relax back the E0 state via a H2 side‐reaction, implying a hydride intermediate prior to H2 formation. This E2→E0 pathway is one of the primary mechanisms for H2 formation under low‐electron flux conditions. In this study we present an exploration of the energy surface of the E2 state. Utilizing both cluster‐continuum and QM/MM calculations, we explore various classes of E2 models: including terminal hydrides, bridging hydrides with a closed or open sulfide‐bridge, as well as models without. Importantly, we find the hemilability of a protonated belt‐sulfide to strongly influence the stability of hydrides. Surprisingly, non‐hydride models are found to be almost equally favorable as hydride models. While the cluster‐continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E2 state. These models feature either i) a bridging hydride between Fe2 and Fe6 and an open sulfide‐bridge with terminal SH on Fe6 (E2‐hyd) or ii) a double belt‐sulfide protonated, reduced cofactor without a hydride (E2‐nonhyd). We suggest both models as contenders for the E2 redox state and further calculate a mechanism for H2 evolution. The changes in electronic structure of FeMoco during the proposed redox‐state cycle, E0→E1→E2→E0, are discussed.
Collapse
Affiliation(s)
- Albert Th Thorhallsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| |
Collapse
|
30
|
Hosfelt J, Richards A, Zheng M, Adura C, Nelson B, Yang A, Fay A, Resager W, Ueberheide B, Glickman JF, Lupoli TJ. An allosteric inhibitor of bacterial Hsp70 chaperone potentiates antibiotics and mitigates resistance. Cell Chem Biol 2021; 29:854-869.e9. [PMID: 34818532 DOI: 10.1016/j.chembiol.2021.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
DnaK is the bacterial homolog of Hsp70, an ATP-dependent chaperone that helps cofactor proteins to catalyze nascent protein folding and salvage misfolded proteins. In the pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), DnaK and its cofactors are proposed antimycobacterial targets, yet few small-molecule inhibitors or probes exist for these families of proteins. Here, we describe the repurposing of a drug called telaprevir that is able to allosterically inhibit the ATPase activity of DnaK and to prevent chaperone function by mimicking peptide substrates. In mycobacterial cells, telaprevir disrupts DnaK- and cofactor-mediated cellular proteostasis, resulting in enhanced efficacy of aminoglycoside antibiotics and reduced resistance to the frontline TB drug rifampin. Hence, this work contributes to a small but growing collection of protein chaperone inhibitors, and it demonstrates that these molecules disrupt bacterial mechanisms of survival in the presence of different antibiotic classes.
Collapse
Affiliation(s)
- Jordan Hosfelt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Aweon Richards
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Meng Zheng
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Carolina Adura
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brock Nelson
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Amy Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Insitute, New York, NY 10065, USA
| | - William Resager
- Departments of Biochemistry and Molecular Pharmacology, Neurology and Director Proteomics Lab, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Departments of Biochemistry and Molecular Pharmacology, Neurology and Director Proteomics Lab, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - J Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY 10003, USA.
| |
Collapse
|
31
|
Wang J, Ma W, Fang Y, Zhang H, Liang H, Liu H, Wang T, Chen S, Ji J, Wang X. Engineering the Outer Membrane Could Facilitate Better Bacterial Performance and Effectively Enhance Poly-3-Hydroxybutyrate Accumulation. Appl Environ Microbiol 2021; 87:e0138921. [PMID: 34550763 DOI: 10.1128/AEM.01389-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly-3-hydroxybutyrate (PHB) is an environmentally friendly polymer and can be produced in Escherichia coli cells after overexpression of the heterologous gene cluster phaCAB. The biosynthesis of the outer membrane (OM) consumes many nutrients and influences cell morphology. Here, we engineered the OM by disrupting all gene clusters relevant to the polysaccharide portion of lipopolysaccharide (LPS), colanic acid (CA), flagella, and/or fimbria in E. coli W3110. All these disruptions benefited PHB production. Especially, disrupting all these OM components increased the PHB content to 83.0 wt% (PHB content percentage of dry cell weight), while the wild-type control produced only 1.5 wt% PHB. The increase was mainly due to the LPS truncation to Kdo2 (3-deoxy-d-manno-octulosonic acid)-lipid A, which resulted in 82.0 wt% PHB with a 25-fold larger cell volume, and disrupting CA resulted in 57.8 wt% PHB. In addition, disrupting LPS facilitated advantageous fermentation features, including 69.1% less acetate, a 550% higher percentage of autoaggregated cells among the total culture cells, 69.1% less biofilm, and a higher broken cell ratio. Further detailed mechanism investigations showed that disrupting LPS caused global changes in envelope and cellular metabolism: (i) a sharp decrease in flagella, fimbria, and secretions; (ii) more elastic cells; (iii) much greater carbon flux toward acetyl coenzyme A (acetyl-CoA) and supply of cofactors, including NADP, NAD, and ATP; and (iv) a decrease in by-product acids but increase in γ-aminobutyric acid by activating σE factor. Disrupting CA, flagella, and fimbria also improved the levels of acetyl-CoA and cofactors. The results indicate that engineering the OM is an effective strategy to enhance PHB production and highlight the applicability of OM engineering to increase microbial cell factory performance. IMPORTANCE Understanding the detailed influence of the OM on the cell envelope and cellular metabolism is important for optimizing the E. coli cell factory and many other microorganisms. This study revealed the applicability of remodeling the OM to enhance PHB accumulation as representative inclusion bodies. The results generated in this study give essential information for producing other inclusion bodies or chemicals which need more acetyl-CoA and cofactors but less by-product acids. This study is promising to provide new ideas for the improvement of microbial cell factories.
Collapse
|
32
|
Zhang F, Richers CP, Woods TJ, Rauchfuss TB. Surprising Condensation Reactions of the Azadithiolate Cofactor. Angew Chem Int Ed Engl 2021; 60:20744-20747. [PMID: 34324230 DOI: 10.1002/anie.202108135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/10/2022]
Abstract
Azadithiolate, a cofactor found in all [FeFe]-hydrogenases, is shown to undergo acid-catalyzed rearrangement. Fe2 [(SCH2 )2 NH](CO)6 self-condenses to give Fe6 [(SCH2 )3 N]2 (CO)17 . The reaction, which is driven by loss of NH4 + , illustrates the exchange of the amine group. X-ray crystallography reveals that three Fe2 (SR)2 (CO)x butterfly subunits interconnected by the aminotrithiolate [N(CH2 S)3 ]3- . Mechanistic studies reveal that Fe2 [(SCH2 )2 NR](CO)6 participate in a range of amine exchange reactions, enabling new methodologies for modifying the adt cofactor. Ru2 [(SCH2 )2 NH](CO)6 also rearranges, but proceeds further to give derivatives with Ru-alkyl bonds Ru6 [(SCH2 )3 N][(SCH2 )2 NCH2 ]S(CO)17 and [Ru2 [(SCH2 )2 NCH2 ](CO)5 ]2 S.
Collapse
Affiliation(s)
- Fanjun Zhang
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Casseday P Richers
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Toby J Woods
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S. Goodwin Ave, Urbana, IL, 61801, USA
| |
Collapse
|
33
|
Skypala IJ, Bartra J, Ebo DG, Antje Faber M, Fernández‐Rivas M, Gomez F, Luengo O, Till SJ, Asero R, Barber D, Cecchi L, Diaz Perales A, Hoffmann‐Sommergruber K, Anna Pastorello E, Swoboda I, Konstantinopoulos AP, Ree R, Scala E. The diagnosis and management of allergic reactions in patients sensitized to non-specific lipid transfer proteins. Allergy 2021; 76:2433-2446. [PMID: 33655502 DOI: 10.1111/all.14797] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Sensitization to one or more non-specific lipid transfer proteins (nsLTPs), initially thought to exist mainly in southern Europe, is becoming accepted as a cause of allergic reactions to plant foods across Europe and beyond. The peach nsLTP allergen Pru p 3 is a dominant sensitizing allergen and peaches a common food trigger, although multiple foods can be involved. A frequent feature of reactions is the requirement for a cofactor (exercise, alcohol, non-steroidal anti-inflammatory drugs, Cannabis sativa) to be present for a food to elicit a reaction. The variability in the food and cofactor triggers makes it essential to include an allergy-focused diet and clinical history in the diagnostic workup. Testing on suspected food triggers should also establish whether sensitization to nsLTP is present, using purified or recombinant nsLTP allergens such as Pru p 3. The avoidance of known trigger foods and advice on cofactors is currently the main management for this condition. Studies on immunotherapy are promising, but it is unknown whether such treatments will be useful in populations where Pru p 3 is not the primary sensitizing allergen. Future research should focus on the mechanisms of cofactors, improving diagnostic accuracy and establishing the efficacy of immunotherapy.
Collapse
Affiliation(s)
- Isabel J. Skypala
- Royal Brompton & Harefield NHS Foundation Trust London UK
- Department of Allergy and Clinical Immunology Imperial College London UK
| | - Joan Bartra
- Hospital Clinic Barcelona Spain
- IDIBAPS Universitat de Barcelona ARADyAL, Barcelona Spain
| | - Didier G. Ebo
- Department of Immunology, Allergology, Rheumatology Faculty of Medicine and Health Sciences Infla‐Med Centre of Excellence Antwerp University Hospital University of Antwerp Antwerp Belgium
- Jan Palfijn Ziekenhuis Ghent Ghent Belgium
| | - Margaretha Antje Faber
- Faculty of Medicine and Health Sciences Department of Immunology, Allergology, Rheumatology Infla‐Med Centre of Excellence Antwerp University Hospital University of Antwerp Antwerp Belgium
| | - Montserrat Fernández‐Rivas
- Department of Allergy Hospital Clínico San Carlos Universidad Complutense de Madrid IdISSC ARADyAL Madrid Spain
| | - Francisca Gomez
- Allergy Unit IBIMA—Hospital Regional Universitario de Malaga Malaga Spain
- Spanish Network for Allergy ‐ RETICS de Asma Reaccionesadversas y Alérgicas (ARADyAL Madrid Spain
| | - Olga Luengo
- Allergy Unit Internal Medicine Department Vall d'Hebron University Hospital Universitat Autònoma de Barcelona ARADyAL Barcelona Spain
| | - Stephen J. Till
- Peter Gorer Department of Immunobiology King’s College London London UK
- Department of Allergy Guy’s & St Thomas’ NHS Foundation Trust London UK
| | - Riccardo Asero
- Ambulatorio di Allergologia Clinica San Carlo Paderno Dugnano Italy
| | - Domingo Barber
- IMMA School of Medicine Universidad San Pablo CEU, Universities Madrid Spain
- RETIC ARADYAL RD16/0006/0015 Instituto de Salud Carlos III Madrid Spain
| | - Lorenzo Cecchi
- SOS Allergy and Clinical Immunology USL Toscana Centro Prato Italy
| | - Araceli Diaz Perales
- Centro de Biotecnología y Genómica de Plantas Universidad Politecnica Madrid Spain
| | | | - Elide Anna Pastorello
- Unit of Allergology and Immunology ASST Grande Ospedale Metropolitano Niguarda University of Milan Milan Italy
| | - Ines Swoboda
- Biotechnology Section Campus Vienna Biocenter FH Campus Wien, University of Applied Sciences Vienna Austria
| | | | - Ronald Ree
- Department of Experimental Immunology Amsterdam University Medical Centers, location AMC Amsterdam The Netherlands
- Department of Otorhinolaryngology Amsterdam University Medical Centers, location AMC Amsterdam The Netherlands
| | - Enrico Scala
- Experimental Allergy Unit Istituto Dermopatico dell’Immacolata – IRCCS FLMM Rome Italy
| | | |
Collapse
|
34
|
Olivera A, Laky K, Hogan SP, Frischmeyer-Guerrerio P. Editorial: Innate Cells in the Pathogenesis of Food Allergy. Front Immunol 2021; 12:709991. [PMID: 34177970 PMCID: PMC8222971 DOI: 10.3389/fimmu.2021.709991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ana Olivera
- Mast Cell Biology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Karen Laky
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Simon Patrick Hogan
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Pamela Frischmeyer-Guerrerio
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, United States
| |
Collapse
|
35
|
Ni Z, Wu J, Li Z, Yuan L, Wang Y, Chen X, Yao J. Enhanced bioproduction of fucosylated oligosaccharide 3-fucosyllactose in engineered Escherichia coli with an improved de novo pathway. Biosci Biotechnol Biochem 2021; 85:1772-1781. [PMID: 33904902 DOI: 10.1093/bbb/zbab074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/22/2021] [Indexed: 01/17/2023]
Abstract
3-fucosyllactose (3-FL) and 2'-fucosyllactose (2'-FL), are two important fucosylated oligosaccharides in human milk. Extensive studies on 2'-FL enabled its official approval for use in infant formula. However, development of 3-FL has been somewhat sluggish due to its low content in human milk and poor yield in enlarged production. Here, an α-1,3-fucosyltransferase mutant was introduced into an engineered Escherichia coli (E. coli) capable of producing GDP-L-fucose, leading to a promising 3-FL titer in a 5.0-L bioreactor. To increase the availability of cofactors (NADPH and GTP) for optimized 3-FL production, zwf, pntAB, and gsk genes were successively overexpressed, finally resulting in a higher 3-FL level with a titer of 35.72 g/L and a yield of 0.82 mol 3-FL/mol lactose. Unexpectedly, the deletion of pfkA gene led to a much lower performance of 3-FL production than the control strain. Still, our strategy achieved the highest 3-FL level in E. coli to date.
Collapse
Affiliation(s)
- Zhijian Ni
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China.,Science Island Branch of Graduate School , University of Science & Technology of China, Hefei, P. R. China
| | - Jinyong Wu
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China.,Huainan New Energy Research Center, Institute of Plasma Physics, Chinese Academy of Sciences, Huainan, P. R. China.,Wuhan Zhongke Optics Valley Green Biotechnology Co. Ltd., Wuhan, China
| | - Zhongkui Li
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China.,Science Island Branch of Graduate School , University of Science & Technology of China, Hefei, P. R. China
| | - Lixia Yuan
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China
| | - Yu Wang
- Wuhan Zhongke Optics Valley Green Biotechnology Co. Ltd., Wuhan, China
| | - Xiangsong Chen
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China.,Huainan New Energy Research Center, Institute of Plasma Physics, Chinese Academy of Sciences, Huainan, P. R. China
| | - Jianming Yao
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China.,Science Island Branch of Graduate School , University of Science & Technology of China, Hefei, P. R. China
| |
Collapse
|
36
|
Flensted F, Jensen CH, Daugaard H, Vedel JC, Jørgensen RW. Factors Associated with Increased Risk of Recurrence following Treatment of Trigger Finger with Corticosteroid Injection. J Hand Microsurg 2021; 13:109-13. [PMID: 33867770 DOI: 10.1055/s-0040-1719228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Introduction
The aim of the study was to estimate recurrence rates, time to recurrence, and predisposing factors for recurrence of trigger finger when treated with corticosteroid (CS) injection as primary treatment.
Materials and Methods
In a retrospective chart review, we identified primary trigger fingers treated with CS injection as primary treatment. Affected hand and finger, recurrence, time to recurrence, duration of symptoms, secondary treatment type, and comorbidities were recorded. A total of 539 patients were included with a mean follow-up of 47.6 months
Results
In total, 330/539 (61%) recurrences were registered. Mean time to recurrence was 312 days. Increased risk of recurrence was seen after treatment of the third finger (relative risk [RR]: 1.22; 95% confidence interval [CI]: 1.06–1.39). Several comorbidities were associated with increased risk of recurrence: carpal tunnel syndrome (RR: 1.27; 95% CI: 1.07–1.52), thyroid disease (RR: 1.45; 95% CI: 1.15–1.83), or shoulder diseases (RR: 1.58; 95% CI: 1.36–1.83).
Conclusion
We found a recurrence rate after primary treatment of CS injection for trigger finger of 61%. Most recurrences happened within 2 years and we found treatment of third finger, carpal tunnel syndrome, shoulder, or thyroid disease to be associated with an increased risk of recurrence of symptoms.
Collapse
|
37
|
Buscagan TM, Perez KA, Maggiolo AO, Rees DC, Spatzal T. Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site. Angew Chem Int Ed Engl 2021; 60:5704-5707. [PMID: 33320413 PMCID: PMC7920927 DOI: 10.1002/anie.202015751] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Indexed: 12/31/2022]
Abstract
As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the active-site FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer-Tropsch-type chemistry). The C-C bond forming capabilities of nitrogenase suggest that multiple CO or CO-derived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 Å resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.
Collapse
Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Kathryn A. Perez
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Present address: European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Ailiena O. Maggiolo
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
- Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| | - Thomas Spatzal
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 E. California Blvd.PasadenaCA91125USA
| |
Collapse
|
38
|
Ghosh D, Kumar GR, Subramanian S, Tanaka K. More Than Just a Reagent: The Rise of Renewable Organohydrides for Catalytic Reduction of Carbon Dioxide. ChemSusChem 2021; 14:824-841. [PMID: 33369102 DOI: 10.1002/cssc.202002660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Stoichiometric carbon dioxide reduction to highly reduced C1 molecules, such as formic acid (2e- ), formaldehyde (4e- ), methanol (6e- ) or even most-reduced methane (8e- ), has been successfully achieved by using organosilanes, organoboranes, and frustrated Lewis Pairs (FLPs) in the presence of suitable catalyst. The development of renewable organohydride compounds could be the best alternative in this regard as they have shown promise for the transfer of hydride directly to CO2 . Reduction of CO2 by two electrons and two protons to afford formic acid by using renewable organohydride molecules has recently been investigated by various groups. However, catalytic CO2 reduction to ≥2e- -reduced products by using renewable organohydride-based molecules has rarely been explored. This Minireview summarizes important findings in this regard, encompassing both stoichiometric and catalytic CO2 reduction.
Collapse
Affiliation(s)
- Debashis Ghosh
- Department of Chemistry, St. Joseph's College (Autonomous), Bangalore, 560027, Karnataka, India
| | - George Rajendra Kumar
- Department of Applied Chemistry, Karunya Institute of Technology and Sciences, Coimbatore, 641114, Tamil Nadu, India
| | - Saravanan Subramanian
- Inorganic Materials and Catalysis Division, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, 364002, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Koji Tanaka
- Institute for Integrated Cell-Material Sciences (KUIAS/iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Applied Chemistry, College of Life Science, Ritsumeikan University, 525-8577 Noji-higashi, 1-1-1, Kusatsu, Shiga, Japan
| |
Collapse
|
39
|
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
Collapse
Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
40
|
Poziomkowska-Gęsicka I, Kostrzewska M, Kurek M. Comorbidities and Cofactors of Anaphylaxis in Patients with Moderate to Severe Anaphylaxis. Analysis of Data from the Anaphylaxis Registry for West Pomerania Province, Poland. Int J Environ Res Public Health 2021; 18:ijerph18010333. [PMID: 33466336 PMCID: PMC7794698 DOI: 10.3390/ijerph18010333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/19/2022]
Abstract
Anaphylaxis is a severe, potentially life-threatening systemic hypersensitivity reaction that is still rarely diagnosed. For safety reasons, patients should visit an allergologist to identify potential causes and cofactors of this reaction. This paper presents the analysis of data from the Anaphylaxis Registry gathered over ten years at the Allergy Clinic, Pomeranian Medical University (PMU). A questionnaire-based survey was used for patients visiting the Allergy Clinic to identify potential augmentation factors/comorbidities and/or cofactors of anaphylaxis in patients with a history of moderate to severe anaphylaxis. The registry comprised patients with grade II or higher anaphylaxis. The gathered data concerned chronic comorbidities (cardiovascular diseases, respiratory diseases, and others), recurrence of anaphylaxis, and potential cofactors in anaphylaxis. In the analyzed group, the incidence rate of anaphylaxis was the highest for women aged 19–60 years. Most common comorbidities in patients with moderate to severe anaphylaxis included: cardiovascular diseases, respiratory tract diseases, features of atopy, and thyroid diseases. More than 30% of drug-induced reactions were anaphylactic reactions due to the re-exposure to the same drug, which points to the need for educational initiatives in this area. The incidence rate of anaphylaxis induced by Hymenoptera stings was comparable in patients who had a previous generalized reaction and those who had good tolerance to the previous sting. It is important to take these cofactors into consideration when evaluating patients with anaphylaxis as they may play a role in future anaphylactic reactions.
Collapse
Affiliation(s)
- Iwona Poziomkowska-Gęsicka
- Clinical Allergology Department, Pomeranian Medical University (PMU) in Szczecin, 70-204 Szczecin, Poland;
- Correspondence:
| | - Magdalena Kostrzewska
- Department of Pulmonology, Allergology and Respiratory Oncology, University of Medical Sciences, 60-569 Poznan, Poland;
| | - Michał Kurek
- Clinical Allergology Department, Pomeranian Medical University (PMU) in Szczecin, 70-204 Szczecin, Poland;
| |
Collapse
|
41
|
Abstract
PURPOSE OF REVIEW Primary mitochondrial disease is a highly heterogeneous but collectively common inherited metabolic disorder, affecting at least one in 4300 individuals. Therapeutic management of mitochondrial disease typically involves empiric prescription of enzymatic cofactors, antioxidants, and amino acid and other nutrient supplements, based on biochemical reasoning, historical experience, and consensus expert opinion. As the field continues to rapidly advance, we review here the preclinical and clinical evidence, and specific dosing guidelines, for common mitochondrial medicine therapies to guide practitioners in their prescribing practices. RECENT FINDINGS Since publication of Mitochondrial Medicine Society guidelines for mitochondrial medicine therapies management in 2009, data has emerged to support consideration for using additional therapeutic agents and discontinuation of several previously used agents. Preclinical animal modeling data have indicated a lack of efficacy for vitamin C as an antioxidant for primary mitochondrial disease, but provided strong evidence for vitamin E and N-acetylcysteine. Clinical data have suggested L-carnitine may accelerate atherosclerotic disease. Long-term follow up on L-arginine use as prophylaxis against or acute treatment for metabolic strokes has provided more data supporting its clinical use in individuals with mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome and Leigh syndrome. Further, several precision therapies have been developed for specific molecular causes and/or shared clinical phenotypes of primary mitochondrial disease. SUMMARY We provide a comprehensive update on mitochondrial medicine therapies based on current evidence and our single-center clinical experience to support or refute their use, and provide detailed dosing guidelines, for the clinical management of mitochondrial disease. The overarching goal of empiric mitochondrial medicines is to utilize therapies with favorable benefit-to-risk profiles that may stabilize and enhance residual metabolic function to improve cellular resiliency and slow clinical disease progression and/or prevent acute decompensation.
Collapse
Affiliation(s)
- Isabella Barcelos
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Edward Shadiack
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rebecca D. Ganetzky
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| |
Collapse
|
42
|
Kang W, Rettberg LA, Stiebritz MT, Jasniewski AJ, Tanifuji K, Lee CC, Ribbe MW, Hu Y. X-Ray Crystallographic Analysis of NifB with a Full Complement of Clusters: Structural Insights into the Radical SAM-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew Chem Int Ed Engl 2020; 60:2364-2370. [PMID: 33035363 DOI: 10.1002/anie.202011367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/27/2020] [Indexed: 12/13/2022]
Abstract
NifB is an essential radical SAM enzyme required for the assembly of an 8Fe core of the nitrogenase cofactor. Herein, we report the X-ray crystal structures of Methanobacterium thermoautotrophicum NifB without (apo MtNifB) and with (holo MtNifB) a full complement of three [Fe4 S4 ] clusters. Both apo and holo MtNifB contain a partial TIM barrel core, but unlike apo MtNifB, holo MtNifB is fully assembled and competent in cofactor biosynthesis. The radical SAM (RS)-cluster is coordinated by three Cys, and the adjacent K1- and K2-clusters, representing the precursor to an 8Fe cofactor core, are each coordinated by one His and two Cys. Prediction of substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of SAM between the RS- and K2-clusters and putative paths for entry of SAM and exit of products of SAM cleavage, thereby providing important mechanistic insights into the radical SAM-dependent carbide insertion concomitant with cofactor core formation.
Collapse
Affiliation(s)
- Wonchull Kang
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Lee A Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Martin T Stiebritz
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| |
Collapse
|
43
|
Calvani M, Anania C, Cuomo B, D'Auria E, Decimo F, Indirli GC, Mastrorilli V, Santoro A, Sartorio MUA, Veronelli E. Summation anaphylaxis: A challenging diagnosis. Pediatr Allergy Immunol 2020; 31 Suppl 26:33-35. [PMID: 33236417 DOI: 10.1111/pai.13347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022]
Abstract
Anaphylaxis is the most severe of allergic reactions. The most frequent triggers of anaphylaxis in childhood are food, insect venom, drugs, exercise, etc. In some cases, the presence of more than one trigger is necessary for the allergic reaction, while one trigger alone is tolerated. This rare condition is called summation anaphylaxis (SA). Food-dependent exercise-induced anaphylaxis is the most well-known SA. However, SA may also occur with the association between food and/or exercise plus one or more of the following other cofactors, such as drugs, especially non-steroidal anti-inflammatory (NSAID), alcohol, infections, temperature variation, and menstrual cycle. SA can explain some cases of idiopathic anaphylaxis, as well as cases of an apparent breakdown in a previously acquired tolerance for food, or finally, when faced with a suggestive clinical history of food allergy or exercise anaphylaxis and the provocation test is negative. In these situations, a more careful clinical history looking for other cofactors is necessary.
Collapse
Affiliation(s)
- Mauro Calvani
- UOC di Pediatria, Azienda Ospedaliera S. Camillo Forlanini, Roma, Italy
| | - Caterina Anania
- Dipartimento Materno Infantile e Scienze Urologiche, Policlinico Umberto I, "La Sapienza" Università di Roma, Roma, Italy
| | | | - Enza D'Auria
- Clinica Pediatrica, Ospedale dei Bambini Vittore Buzzi-Università degli Studi di Milano, Milano, Italy
| | - Fabio Decimo
- UO di Pediatria, Università degli Studi della Campania "Luigi Vanvitelli," Napoli, Naples, Italy
| | - Giovanni Cosimo Indirli
- Pediatra e Allergoimmunologo-Coordinatore Regionale della SIAIP per le Regioni Puglia e Basilicata, Copertino, Italy
| | | | - Angelica Santoro
- Clinica Pediatrica, Dipartimento di Medicina e Chirurgia, Azienda Ospedaliero-Universitaria di Parma, Università di Parma, Parma, Italy
| | - Marco U A Sartorio
- Clinica Pediatrica, Ospedale dei Bambini Vittore Buzzi-Università degli Studi di Milano, Milano, Italy
| | | |
Collapse
|
44
|
Diouf D, Diop G, Fall C, Sarr S, Diarra CAT, Ngom AI, Ka S, Lo S, Faye O, Dem A. The Association of Molecular Biomarkers in the Diagnosis of Cervical Pre-Cancer and Cancer and Risk Factors in Senegalese. Asian Pac J Cancer Prev 2020; 21:3221-3227. [PMID: 33247678 PMCID: PMC8033140 DOI: 10.31557/apjcp.2020.21.11.3221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Cervical intraepithelial neoplasia (CIN) grading is subjective and affected by substantial rates of discordance among pathologists. Although recent studies have suggested that p16INK4a may be a useful surrogate biomarker of cervical neoplasia, Ki-67 and human papillomavirus testing have also been shown to be useful in detecting neoplasia. The purpose of this study was to determine the expression of p16INK4a and Ki-67 in cervical neoplasia and its correlations with cofactors. Methods: The study involved 69 patients with and without cervical neoplasia who underwent colposcopic directed biopsy. On each patient, two samples were taken; the first was used for immunohistochemistry and the second for molecular testing, using HPV16and18 genotyping Real-Time PCR Kit. Results: The study revealed the expression level of p16INK4a and Ki-67 in a descending order, from invasive squamous cell carcinoma (SCC), CIN2/3, CIN1 and non-dysplastic lesions. Correlations showed an association between the staining of p16NK4a and Ki-67 with the increase of age (OR: 1.79 (95%IC: 0.49 – 6.55), p = 0.037) and marital status (OR: 0.17 (95%IC: 0.04 – 0.68), p = 0.003). We found that the expressions of p16INK4a and Ki-67 were significantly different between invasive SCC vs non-dysplasia (OR: 44.57 (95%IC: 4.91 – 403.91), p<0.0001). The study showed significant correlation between HPV 16and18 infection with p16 INK4a and Ki-67 expression (OR: 0.13 (95%IC: 0.03 – 0.52), p<0.0001). Strong expression of p16INK4a and Ki-67 were observed in invasive squamous cell carcinoma, moderate staining was found in CIN2/3, weak staining in CIN1 and normal histology. Conclusion: Our findings indicate that p16INK4a and Ki-67 expressions associated strongly with cervical pathology. Therefore, p16/Ki-67 could be considered as a suitable biomarker for cervical cancer screening, particularly in HPV-based screening programs.
Collapse
Affiliation(s)
- Dominique Diouf
- Laboratory of Cytogenetic and Reproductive Biology, Hospital Aristide-Le-Dantec, Pasteur Avenue, Dakar, Senegal.,Laboratory of Anatomy and Pathology, Principal Military Hospital of Dakar, Nelson Mandela Avenue, Dakar, Senegal.,Cancer Studies and Research Group in Senegal (GERCS), FMPO, Cheikh Anta DIOP University, Cheikh Anta Diop Avenue, Dakar, Senegal
| | - Gora Diop
- Cancer Studies and Research Group in Senegal (GERCS), FMPO, Cheikh Anta DIOP University, Cheikh Anta Diop Avenue, Dakar, Senegal.,Cheikh Anta DIOP University, Department of Animal Biology, Faculty of Science and Technology, Postulant Unit of Genetic, Genomic and Bioinformatic of Infectious Diseases and Cancer, Cheikh Anta Diop Avenue, Dakar, Senegal.,Institut Pasteur Dakar, Pole d'immunophysiopathologie des maladies infectieuses (Pole IMI), Pasteur Avenue, Dakar, Senegal
| | - Cheikh Fall
- Institut Pasteur Dakar, Pole de Virologie, PO Box 220. 36, Pasteur Avenue, Dakar, Senegal
| | - Souleymane Sarr
- Laboratory of Anatomy and Pathology, Principal Military Hospital of Dakar, Nelson Mandela Avenue, Dakar, Senegal
| | - Cheikh Ahmadou Tidian Diarra
- Hopital Aristide LeDantec, Service de Cancerologie, Institut-Juliot-Curie, Pasteur Avenue, PO Box 3001, Dakar, Senegal
| | - Aminata Issa Ngom
- Laboratory of Cytogenetic and Reproductive Biology, Hospital Aristide-Le-Dantec, Pasteur Avenue, Dakar, Senegal
| | - Sidy Ka
- Cancer Studies and Research Group in Senegal (GERCS), FMPO, Cheikh Anta DIOP University, Cheikh Anta Diop Avenue, Dakar, Senegal.,Hopital Aristide LeDantec, Service de Cancerologie, Institut-Juliot-Curie, Pasteur Avenue, PO Box 3001, Dakar, Senegal
| | - Seynabou Lo
- Cancer Studies and Research Group in Senegal (GERCS), FMPO, Cheikh Anta DIOP University, Cheikh Anta Diop Avenue, Dakar, Senegal
| | - Oumar Faye
- Laboratory of Cytogenetic and Reproductive Biology, Hospital Aristide-Le-Dantec, Pasteur Avenue, Dakar, Senegal.,Cancer Studies and Research Group in Senegal (GERCS), FMPO, Cheikh Anta DIOP University, Cheikh Anta Diop Avenue, Dakar, Senegal
| | - Ahmadou Dem
- Cancer Studies and Research Group in Senegal (GERCS), FMPO, Cheikh Anta DIOP University, Cheikh Anta Diop Avenue, Dakar, Senegal.,Hopital Aristide LeDantec, Service de Cancerologie, Institut-Juliot-Curie, Pasteur Avenue, PO Box 3001, Dakar, Senegal
| |
Collapse
|
45
|
Liedtke J, Lee CC, Tanifuji K, Jasniewski AJ, Ribbe MW, Hu Y. Characterization of a Mo-Nitrogenase Variant Containing a Citrate-Substituted Cofactor. Chembiochem 2020; 22:151-155. [PMID: 32918851 DOI: 10.1002/cbic.202000598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/04/2020] [Indexed: 11/10/2022]
Abstract
Nitrogenase converts N2 to NH3 , and CO to hydrocarbons, at its cofactor site. Herein, we report a biochemical and spectroscopic characterization of a Mo-nitrogenase variant expressed in an Azotobacter vinelandii strain containing a deletion of nifV, the gene encoding the homocitrate synthase. Designated NifDKCit , the catalytic component of this Mo-nitrogenase variant contains a citrate-substituted cofactor analogue. Activity analysis of NifDKCit reveals a shift of CO reduction from H2 evolution toward hydrocarbon formation and an opposite shift of N2 reduction from NH3 formation toward H2 evolution. Consistent with a shift in the Mo K-edge energy of NifDKCit relative to that of its wild-type counterpart, EPR analysis demonstrates a broadening of the line-shape and a decrease in the intensity of the cofactor-originated S=3/2 signal, suggesting a change in the spin properties of the cofactor upon citrate substitution. These observations point to a crucial role of homocitrate in substrate reduction by nitrogenase and the possibility to tune product profiles of nitrogenase reactions via organic ligand substitution.
Collapse
Affiliation(s)
- Jasper Liedtke
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, 2236 McGaugh Hall, Irvine, CA 92697-3900, USA
| |
Collapse
|
46
|
Li Y, Zhao P, Gong T, Wang H, Jiang X, Cheng H, Liu Y, Wu Y, Bu W. Redox Dyshomeostasis Strategy for Hypoxic Tumor Therapy Based on DNAzyme-Loaded Electrophilic ZIFs. Angew Chem Int Ed Engl 2020; 59:22537-22543. [PMID: 32856362 DOI: 10.1002/anie.202003653] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/27/2020] [Indexed: 12/30/2022]
Abstract
Redox homeostasis is one of the main reasons for reactive oxygen species (ROS) tolerance in hypoxic tumors, limiting ROS-mediated tumor therapy. Proposed herein is a redox dyshomeostasis (RDH) strategy based on a nanoplatform, FeCysPW@ZIF-82@CAT Dz, to disrupt redox homeostasis, and its application to improve ROS-mediated hypoxic tumor therapy. Once endocytosed by tumor cells, the catalase DNAzyme (CAT Dz) loaded zeolitic imidazole framework-82 (ZIF-82@CAT Dz) shell can be degraded into Zn2+ as cofactors for CAT Dz mediated CAT silencing and electrophilic ligands for glutathione (GSH) depletion under hypoxia, both of which lead to intracellular RDH and H2 O2 accumulation. These "disordered" cells show reduced resistance to ROS and are effectively killed by ferrous cysteine-phosphotungstate (FeCysPW) induced chemodynamic therapy (CDT). In vitro and in vivo data demonstrate that the pH/hypoxia/H2 O2 triple stimuli responsive nanocomposite can efficiently kill hypoxic tumors. Overall, the RDH strategy provides a new way of thinking about ROS-mediated treatment of hypoxic tumors.
Collapse
Affiliation(s)
- Yanli Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
| | - Peiran Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
| | - Teng Gong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China.,Center for Interventional Medicine, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, P. R. China
| | - Han Wang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, P. R. China
| | - Xingwu Jiang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Hui Cheng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
| | - Yanyan Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
| | - Yelin Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Wenbo Bu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China.,State Key Laboratory of High-Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, P. R. China
| |
Collapse
|
47
|
Onuh JO, Qiu H. Serum response factor-cofactor interactions and their implications in disease. FEBS J 2020; 288:3120-3134. [PMID: 32885587 PMCID: PMC7925694 DOI: 10.1111/febs.15544] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/21/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022]
Abstract
Serum response factor (SRF), a member of the Mcm1, Agamous, Deficiens, and SRF (MADS) box transcription factor, is widely expressed in all cell types and plays a crucial role in the physiological function and development of diseases. SRF regulates its downstream genes by binding to their CArG DNA box by interacting with various cofactors. However, the underlying mechanisms are not fully understood, therefore attracting increasing research attention due to the importance of this topic. This review's objective is to discuss the new progress in the studies of the molecular mechanisms involved in the activation of SRF and its impacts in physiological and pathological conditions. Notably, we summarized the recent studies on the interaction of SRF with its two main types of cofactors belonging to the myocardin families of transcription factors and the members of the ternary complex factors. The knowledge of these mechanisms will create new opportunities for understanding the dynamics of many traits and disease pathogenesis especially, cardiovascular diseases and cancer that could serve as targets for pharmacological control and treatment of these diseases.
Collapse
Affiliation(s)
- John Oloche Onuh
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA, USA
| | - Hongyu Qiu
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA, USA
| |
Collapse
|
48
|
Chu XY, Zhang HY. Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins. Chembiochem 2020; 21:3161-3168. [PMID: 32515532 DOI: 10.1002/cbic.202000027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Due to their early origin and extreme conservation, cofactors are valuable molecular fossils for tracing the origin and evolution of proteins. First, as the order of protein folds binding with cofactors roughly coincides with protein-fold chronology, cofactors are considered to have facilitated the origin of primitive proteins by selecting them from pools of random amino acid sequences. Second, in the subsequent evolution of proteins, cofactors still played an important role. More interestingly, as metallic cofactors evolved with geochemical variations, some geochemical events left imprints in the chronology of protein architecture; this provides further evidence supporting the coevolution of biochemistry and geochemistry. In this paper, we attempt to review the molecular fossils used in tracing the origin and evolution of proteins, with a special focus on cofactors.
Collapse
Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
49
|
Abstract
Metabolic engineering is crucial in the development of production strains for platform chemicals, pharmaceuticals and biomaterials from renewable resources. The central carbon metabolism (CCM) of heterotrophs plays an essential role in the conversion of biomass to the cellular building blocks required for growth. Yet, engineering the CCM ultimately aims toward a maximization of flux toward products of interest. The most abundant dissimilative carbohydrate pathways amongst prokaryotes (and eukaryotes) are the Embden-Meyerhof-Parnas (EMP) and the Entner-Doudoroff (ED) pathways, which build the basics for heterotrophic metabolic chassis strains. Although the EMP is regarded as the textbook example of a carbohydrate pathway owing to its central role in production strains like Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis, it is either modified, complemented or even replaced by alternative carbohydrate pathways in different organisms. The ED pathway also plays key roles in biotechnological relevant bacteria, like Zymomonas mobilis and Pseudomonas putida, and its importance was recently discovered in photoautotrophs and marine microorganisms. In contrast to the EMP, the ED pathway and its variations are not evolutionary optimized for high ATP production and it differs in key principles such as protein cost, energetics and thermodynamics, which can be exploited in the construction of unique metabolic designs. Single ED pathway enzymes and complete ED pathway modules have been used to rewire carbon metabolisms in production strains and for the construction of cell-free enzymatic pathways. This review focuses on the differences of the ED and EMP pathways including their variations and discusses the use of alternative pathway strategies for in vivo and cell-free metabolic engineering.
Collapse
Affiliation(s)
- Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| |
Collapse
|
50
|
Peng Q, Peng R, Yuan B, Zhao J, Wang M, Wang X, Wang Q, Sun Y, Fan Z, Qi J, Gao GF, Shi Y. Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2. Cell Rep 2020; 31:107774. [PMID: 32531208 PMCID: PMC7260489 DOI: 10.1016/j.celrep.2020.107774] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/23/2020] [Accepted: 05/26/2020] [Indexed: 01/18/2023] Open
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused a huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus (SARS-CoV-2). The viral polymerase is a promising antiviral target. Here, we describe the near-atomic-resolution structure of the SARS-CoV-2 polymerase complex consisting of the nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases and suggests a mechanism of activation by cofactors. Biochemical studies reveal reduced activity of the core polymerase complex and lower thermostability of individual subunits of SARS-CoV-2 compared with SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate adaptation of SARS-CoV-2 toward humans with a relatively lower body temperature than the natural bat hosts. Cryo-EM structure of SARS-CoV-2 nsp12-nsp7-nsp8 core polymerase complex The core complex of SARS-CoV-2 has lower enzymatic activity than SARS-CoV SARS-CoV-2 nsp7-8-12 subunits are less thermostable than the SARS-CoV counterpart
Collapse
Affiliation(s)
- Qi Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yuan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xixi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Sun
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of the Chinese Academy of Sciences, Chongqing 400013, China; College of Basic Medicine, Jilin University, Changchun, Jilin 130021, China.
| |
Collapse
|