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Eckle T, Bertazzo J, Khatua TN, Tabatabaei SRF, Bakhtiari NM, Walker LA, Martino TA. Circadian Influences on Myocardial Ischemia-Reperfusion Injury and Heart Failure. Circ Res 2024; 134:675-694. [PMID: 38484024 PMCID: PMC10947118 DOI: 10.1161/circresaha.123.323522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
The impact of circadian rhythms on cardiovascular function and disease development is well established, with numerous studies in genetically modified animals emphasizing the circadian molecular clock's significance in the pathogenesis and pathophysiology of myocardial ischemia and heart failure progression. However, translational preclinical studies targeting the heart's circadian biology are just now emerging and are leading to the development of a novel field of medicine termed circadian medicine. In this review, we explore circadian molecular mechanisms and novel therapies, including (1) intense light, (2) small molecules modulating the circadian mechanism, and (3) chronotherapies such as cardiovascular drugs and meal timings. These promise significant clinical translation in circadian medicine for cardiovascular disease. (4) Additionally, we address the differential functioning of the circadian mechanism in males versus females, emphasizing the consideration of biological sex, gender, and aging in circadian therapies for cardiovascular disease.
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Affiliation(s)
- Tobias Eckle
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Júlia Bertazzo
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tarak Nath Khatua
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Seyed Reza Fatemi Tabatabaei
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Naghmeh Moori Bakhtiari
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Lori A Walker
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tami A. Martino
- Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
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2
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Sengupta A, Liu D, Pakrasi HB. CRISPR-Cas mediated genome engineering of cyanobacteria. Methods Enzymol 2022; 676:403-432. [DOI: 10.1016/bs.mie.2022.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean. Proc Natl Acad Sci U S A 2021; 118:2112355118. [PMID: 34750267 DOI: 10.1073/pnas.2112355118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton's primary productivity. Trichodesmium has long been portrayed as a diazotrophic genus. By means of genome-resolved metagenomics, here we reveal that nondiazotrophic Trichodesmium species not only exist but also are abundant and widespread in the open ocean, benefiting from a previously overlooked functional lifestyle to expand the biogeography of this prominent marine genus. Near-complete environmental genomes for those closely related candidate species reproducibly shared functional features including a lack of genes related to nitrogen fixation, hydrogen recycling, and hopanoid lipid production concomitant with the enrichment of nitrogen assimilation genes. Our results elucidate fieldwork observations of Trichodesmium cells fixing carbon but not nitrogen. The Black Queen hypothesis and burden of low-oxygen concentration requirements provide a rationale to explain gene loss linked to nitrogen fixation among Trichodesmium species. Disconnecting taxonomic signal for this genus from a microbial community's ability to fix nitrogen will help refine our understanding of the marine nitrogen balance. Finally, we are reminded that established links between taxonomic lineages and functional traits do not always hold true.
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Bartman CM, Eckle T. Circadian-Hypoxia Link and its Potential for Treatment of Cardiovascular Disease. Curr Pharm Des 2020; 25:1075-1090. [PMID: 31096895 DOI: 10.2174/1381612825666190516081612] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/03/2019] [Indexed: 12/29/2022]
Abstract
Throughout the evolutionary time, all organisms and species on Earth evolved with an adaptation to consistent oscillations of sunlight and darkness, now recognized as 'circadian rhythm.' Single-cellular to multisystem organisms use circadian biology to synchronize to the external environment and provide predictive adaptation to changes in cellular homeostasis. Dysregulation of circadian biology has been implicated in numerous prevalent human diseases, and subsequently targeting the circadian machinery may provide innovative preventative or treatment strategies. Discovery of 'peripheral circadian clocks' unleashed widespread investigations into the potential roles of clock biology in cellular, tissue, and organ function in healthy and diseased states. Particularly, oxygen-sensing pathways (e.g. hypoxia inducible factor, HIF1), are critical for adaptation to changes in oxygen availability in diseases such as myocardial ischemia. Recent investigations have identified a connection between the circadian rhythm protein Period 2 (PER2) and HIF1A that may elucidate an evolutionarily conserved cellular network that can be targeted to manipulate metabolic function in stressed conditions like hypoxia or ischemia. Understanding the link between circadian and hypoxia pathways may provide insights and subsequent innovative therapeutic strategies for patients with myocardial ischemia. This review addresses our current understanding of the connection between light-sensing pathways (PER2), and oxygen-sensing pathways (HIF1A), in the context of myocardial ischemia and lays the groundwork for future studies to take advantage of these two evolutionarily conserved pathways in the treatment of myocardial ischemia.
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Affiliation(s)
- Colleen Marie Bartman
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tobias Eckle
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Joshi CJ, Peebles CA, Prasad A. Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Tiruveedula GSS, Wangikar PP. Gene essentiality, conservation index and co-evolution of genes in cyanobacteria. PLoS One 2017; 12:e0178565. [PMID: 28594867 PMCID: PMC5464585 DOI: 10.1371/journal.pone.0178565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/15/2017] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria, a group of photosynthetic prokaryotes, dominate the earth with ~ 1015 g wet biomass. Despite diversity in habitats and an ancient origin, cyanobacterial phylum has retained a significant core genome. Cyanobacteria are being explored for direct conversion of solar energy and carbon dioxide into biofuels. For this, efficient cyanobacterial strains will need to be designed via metabolic engineering. This will require identification of target knockouts to channelize the flow of carbon toward the product of interest while minimizing deletions of essential genes. We propose "Gene Conservation Index" (GCI) as a quick measure to predict gene essentiality in cyanobacteria. GCI is based on phylogenetic profile of a gene constructed with a reduced dataset of cyanobacterial genomes. GCI is the percentage of organism clusters in which the query gene is present in the reduced dataset. Of the 750 genes deemed to be essential in the experimental study on S. elongatus PCC 7942, we found 494 to be conserved across the phylum which largely comprise of the essential metabolic pathways. On the contrary, the conserved but non-essential genes broadly comprise of genes required under stress conditions. Exceptions to this rule include genes such as the glycogen synthesis and degradation enzymes, deoxyribose-phosphate aldolase (DERA), glucose-6-phosphate 1-dehydrogenase (zwf) and fructose-1,6-bisphosphatase class1, which are conserved but non-essential. While the essential genes are to be avoided during gene knockout studies as potentially lethal deletions, the non-essential but conserved set of genes could be interesting targets for metabolic engineering. Further, we identify clusters of co-evolving genes (CCG), which provide insights that may be useful in annotation. Principal component analysis (PCA) plots of the CCGs are demonstrated as data visualization tools that are complementary to the conventional heatmaps. Our dataset consists of phylogenetic profiles for 23,643 non-redundant cyanobacterial genes. We believe that the data and the analysis presented here will be a great resource to the scientific community interested in cyanobacteria.
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Affiliation(s)
- Gopi Siva Sai Tiruveedula
- Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Pramod P. Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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7
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Mueller TJ, Welsh EA, Pakrasi HB, Maranas CD. Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803. ACS Synth Biol 2016; 5:250-8. [PMID: 26692191 DOI: 10.1021/acssynbio.5b00202] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The incorporation of biological nitrogen fixation into a nondiazotrophic photosynthetic organism provides a promising solution to the increasing fixed nitrogen demand, but is accompanied by a number of challenges for accommodating two incompatible processes within the same organism. Here we present regulatory influence networks for two cyanobacteria, Synechocystis PCC 6803 and Cyanothece ATCC 51142, and evaluate them to co-opt native transcription factors that may be used to control the nif gene cluster once it is transferred to Synechocystis. These networks were further examined to identify candidate transcription factors for other metabolic processes necessary for temporal separation of photosynthesis and nitrogen fixation, glycogen catabolism and cyanophycin synthesis. Two transcription factors native to Synechocystis, LexA and Rcp1, were identified as promising candidates for the control of the nif gene cluster and other pertinent metabolic processes, respectively. Lessons learned in the incorporation of nitrogen fixation into a nondiazotrophic prokaryote may be leveraged to further progress the incorporation of nitrogen fixation in plants.
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Affiliation(s)
- Thomas J. Mueller
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16801, United States
| | - Eric A. Welsh
- Cancer
Informatics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Himadri B. Pakrasi
- Department
of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri 63130, United States
- Department
of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Costas D. Maranas
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16801, United States
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Seth JR, Wangikar PP. Challenges and opportunities for microalgae-mediated CO2 capture and biorefinery. Biotechnol Bioeng 2015; 112:1281-96. [PMID: 25899427 DOI: 10.1002/bit.25619] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 03/31/2015] [Accepted: 04/07/2015] [Indexed: 11/10/2022]
Abstract
Aquacultures of microalgae are frontrunners for photosynthetic capture of CO2 from flue gases. Expedient implementation mandates coupling of microalgal CO2 capture with synthesis of fuels and organic products, so as to derive value from biomass. An integrated biorefinery complex houses a biomass growth and harvesting area and a refining zone for conversion to product(s) and separation to desired purity levels. As growth and downstream options require energy and incur loss of carbon, put together, the loop must be energy positive, carbon negative, or add substantial value. Feasibility studies can, thus, aid the choice from among the rapidly evolving technological options, many of which are still in the early phases of development. We summarize basic engineering calculations for the key steps of a biorefining loop where flue gases from a thermal power station are captured using microalgal biomass along with subsequent options for conversion to fuel or value added products. An assimilation of findings from recent laboratory and pilot-scale experiments and life cycle analysis (LCA) studies is presented as carbon and energy yields for growth and harvesting of microalgal biomass and downstream options. Of the biorefining options, conversion to the widely studied biofuel, ethanol, and manufacture of the platform chemical, succinic acid are presented. Both processes yield specific products and do not demand high-energy input but entail 60-70% carbon loss through fermentative respiration. Thermochemical conversions, on the other hand, have smaller carbon and energy losses but yield a mixture of products.
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Affiliation(s)
- Jyoti R Seth
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India. .,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, India. .,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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9
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Coupling of Cellular Processes and Their Coordinated Oscillations under Continuous Light in Cyanothece sp. ATCC 51142, a Diazotrophic Unicellular Cyanobacterium. PLoS One 2015; 10:e0125148. [PMID: 25973856 PMCID: PMC4431719 DOI: 10.1371/journal.pone.0125148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 03/08/2015] [Indexed: 01/12/2023] Open
Abstract
Unicellular diazotrophic cyanobacteria such as Cyanothece sp. ATCC 51142 (henceforth Cyanothece), temporally separate the oxygen sensitive nitrogen fixation from oxygen evolving photosynthesis not only under diurnal cycles (LD) but also in continuous light (LL). However, recent reports demonstrate that the oscillations in LL occur with a shorter cycle time of ~11 h. We find that indeed, majority of the genes oscillate in LL with this cycle time. Genes that are upregulated at a particular time of day under diurnal cycle also get upregulated at an equivalent metabolic phase under LL suggesting tight coupling of various cellular events with each other and with the cell's metabolic status. A number of metabolic processes get upregulated in a coordinated fashion during the respiratory phase under LL including glycogen degradation, glycolysis, oxidative pentose phosphate pathway, and tricarboxylic acid cycle. These precede nitrogen fixation apparently to ensure sufficient energy and anoxic environment needed for the nitrogenase enzyme. Photosynthetic phase sees upregulation of photosystem II, carbonate transport, carbon concentrating mechanism, RuBisCO, glycogen synthesis and light harvesting antenna pigment biosynthesis. In Synechococcus elongates PCC 7942, a non-nitrogen fixing cyanobacteria, expression of a relatively smaller fraction of genes oscillates under LL condition with the major periodicity being 24 h. In contrast, the entire cellular machinery of Cyanothece orchestrates coordinated oscillation in anticipation of the ensuing metabolic phase in both LD and LL. These results may have important implications in understanding the timing of various cellular events and in engineering cyanobacteria for biofuel production.
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10
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Krishnakumar S, Gaudana SB, Digmurti MG, Viswanathan GA, Chetty M, Wangikar PP. Influence of mixotrophic growth on rhythmic oscillations in expression of metabolic pathways in diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. BIORESOURCE TECHNOLOGY 2015; 188:145-152. [PMID: 25736893 DOI: 10.1016/j.biortech.2015.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
This study investigates the influence of mixotrophy on physiology and metabolism by analysis of global gene expression in unicellular diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 (henceforth Cyanothece 51142). It was found that Cyanothece 51142 continues to oscillate between photosynthesis and respiration in continuous light under mixotrophy with cycle time of ∼ 13 h. Mixotrophy is marked by an extended respiratory phase compared with photoautotrophy. It can be argued that glycerol provides supplementary energy for nitrogen fixation, which is derived primarily from the glycogen reserves during photoautotrophy. The genes of NDH complex, cytochrome c oxidase and ATP synthase are significantly overexpressed in mixotrophy during the day compared to autotrophy with synchronous expression of the bidirectional hydrogenase genes possibly to maintain redox balance. However, nitrogenase complex remains exclusive to nighttime metabolism concomitantly with uptake hydrogenase. This study throws light on interrelations between metabolic pathways with implications in design of hydrogen producer strains.
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Affiliation(s)
- S Krishnakumar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sandeep B Gaudana
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Madhuri G Digmurti
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ganesh A Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Madhu Chetty
- School of Information Technology, Federation University Australia, Gippsland Campus, VIC 3841, Australia
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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11
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Sowa SW, Baldea M, Contreras LM. Optimizing metabolite production using periodic oscillations. PLoS Comput Biol 2014; 10:e1003658. [PMID: 24901332 PMCID: PMC4046915 DOI: 10.1371/journal.pcbi.1003658] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 04/17/2014] [Indexed: 12/20/2022] Open
Abstract
Methods for improving microbial strains for metabolite production remain the subject of constant research. Traditionally, metabolic tuning has been mostly limited to knockouts or overexpression of pathway genes and regulators. In this paper, we establish a new method to control metabolism by inducing optimally tuned time-oscillations in the levels of selected clusters of enzymes, as an alternative strategy to increase the production of a desired metabolite. Using an established kinetic model of the central carbon metabolism of Escherichia coli, we formulate this concept as a dynamic optimization problem over an extended, but finite time horizon. Total production of a metabolite of interest (in this case, phosphoenolpyruvate, PEP) is established as the objective function and time-varying concentrations of the cellular enzymes are used as decision variables. We observe that by varying, in an optimal fashion, levels of key enzymes in time, PEP production increases significantly compared to the unoptimized system. We demonstrate that oscillations can improve metabolic output in experimentally feasible synthetic circuits.
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Affiliation(s)
- Steven W. Sowa
- Microbiology Graduate Program, University of Texas at Austin, Austin, Texas, United States of America
| | - Michael Baldea
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (MB); (LMC)
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (MB); (LMC)
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