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Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL. Emerging Priorities for Microbiome Research. Front Microbiol 2020; 11:136. [PMID: 32140140 PMCID: PMC7042322 DOI: 10.3389/fmicb.2020.00136] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [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: 08/13/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.
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Affiliation(s)
- Chad M. Cullen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | | | - Sinem Beyhan
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Clara E. Cho
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT, United States
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
- College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Matteo Convertino
- Nexus Group, Faculty of Information Science and Technology, Gi-CoRE Station for Big Data & Cybersecurity, Hokkaido University, Sapporo, Japan
| | - Sophie J. McCoy
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | | | - Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ananya Sen Gupta
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, United States
| | - Kevin Cheung
- Department of Dermatology, The University of Iowa, Iowa City, IA, United States
| | | | - Zhengqiao Zhao
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail L. Rosen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
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Abstract
The life cycle of Kaposi’s sarcoma-associated herpesvirus (KSHV) consists of two phases, latent and lytic. The virus establishes latency as a strategy for avoiding host immune surveillance and fusing symbiotically with the host for lifetime persistent infection. However, latency can be disrupted and KSHV is reactivated for entry into the lytic replication. Viral lytic replication is crucial for efficient dissemination from its long-term reservoir to the sites of disease and for the spread of the virus to new hosts. The balance of these two phases in the KSHV life cycle is important for both the virus and the host and control of the switch between these two phases is extremely complex. Various environmental factors such as oxidative stress, hypoxia, and certain chemicals have been shown to switch KSHV from latency to lytic reactivation. Immunosuppression, unbalanced inflammatory cytokines, and other viral co-infections also lead to the reactivation of KSHV. This review article summarizes the current understanding of the initiation and regulation of KSHV reactivation and the mechanisms underlying the process of viral lytic replication. In particular, the central role of an immediate-early gene product RTA in KSHV reactivation has been extensively investigated. These studies revealed multiple layers of regulation in activation of RTA as well as the multifunctional roles of RTA in the lytic replication cascade. Epigenetic regulation is known as a critical layer of control for the switch of KSHV between latency and lytic replication. The viral non-coding RNA, PAN, was demonstrated to play a central role in the epigenetic regulation by serving as a guide RNA that brought chromatin remodeling enzymes to the promoters of RTA and other lytic genes. In addition, a novel dimension of regulation by microPeptides emerged and has been shown to regulate RTA expression at the protein level. Overall, extensive investigation of KSHV reactivation and lytic replication has revealed a sophisticated regulation network that controls the important events in KSHV life cycle.
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Affiliation(s)
- Kawalpreet K Aneja
- Department of Microbiology, University of Pennsylvania School of Dental Medicine, PhiladelphiaPA, USA
| | - Yan Yuan
- Department of Microbiology, University of Pennsylvania School of Dental Medicine, PhiladelphiaPA, USA
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Yano T, Rahimian M, Aneja KK, Schechter NM, Rubin H, Scott CP. Mycobacterium tuberculosis type II NADH-menaquinone oxidoreductase catalyzes electron transfer through a two-site ping-pong mechanism and has two quinone-binding sites. Biochemistry 2014; 53:1179-90. [PMID: 24447297 PMCID: PMC3985514 DOI: 10.1021/bi4013897] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Type
II NADH-quinone oxidoreductase (NDH-2) catalyzes the transfer
electrons from NADH to the quinone pool and plays an essential role
in the oxidative phosphorylation system of Mycobacterium tuberculosis (Mtb). The absence of NDH-2 in the mammalian mitochondrial electron
transport chain makes this enzyme an attractive target for antibiotic
development. To fully establish the kinetic properties of this enzyme,
we studied the interaction of Mtb NDH-2 with substrates, NADH, and
various quinone analogues and their products in both membrane and
soluble environments. These studies, and comparative analyses of the
kinetics with thio-NAD+ and quinone electron acceptors,
provided evidence that Mtb NDH-2 catalyzes the transfer electrons
from NADH to quinone substrates by a nonclassical, two-site ping-pong
kinetic mechanism whereby substrate quinones bind to a site that is
distinct from the NADH-binding site. Furthermore, the effects of quinols
on Mtb NDH-2 catalytic activity demonstrate the presence of two binding
sites for quinone ligands, one favoring the reduced form and the other
favoring the oxidized form.
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Affiliation(s)
- Takahiro Yano
- Department of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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Aneja KK, Guha P, Shilpi RY, Chakraborty S, Schramm LM, Haldar D. The presence of distal and proximal promoters for rat mitochondrial glycerol-3-phosphate acyltransferase. Arch Biochem Biophys 2008; 470:35-43. [PMID: 18021946 PMCID: PMC2262852 DOI: 10.1016/j.abb.2007.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 10/05/2007] [Accepted: 10/30/2007] [Indexed: 11/22/2022]
Abstract
Sequence analysis using the Promoser program predicted two promoter-like regions for rat mtGPAT: a distal promoter approximately 30kb upstream and a proximal promoter near the first translational codon. Rat liver cells transfected with pGL3-basic vector containing the distal and proximal promoter resulted in 10.8- and 4.8-fold increase in the luciferase activity, respectively. Results of electromobility shift assay and chromatin immunoprecipitation suggested binding of transcription factors to the distal and proximal promoter regions. 5' RACE PCR showed two transcripts with different transcriptional start sites. When transfected rat liver cells were starved and refed, there was about 2.7-fold increase in the luciferase activity with cells transfected with the distal promoter while the proximal promoter showed no change. Thus, the two promoters could be functionally distinguished. Taken together, the results suggest that there are two promoters for rat mtGPAT gene and that the transcriptional regulation is mediated through the distal promoter.
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Affiliation(s)
- Kawalpreet K Aneja
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
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