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Wang Y, Liu J, Yi Y, Zhu L, Liu M, Zhang Z, Xie Q, Jiang L. Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria. Front Microbiol 2024; 15:1447785. [PMID: 39119139 PMCID: PMC11306087 DOI: 10.3389/fmicb.2024.1447785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights.
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Affiliation(s)
- Yuxian Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yuanyang Yi
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
- College of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, China
| | - Minghui Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Zhidong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
| | - Qiong Xie
- China Astronaut Research and Training Center, Beijing, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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2
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Vauclare P, Wulffelé J, Lacroix F, Servant P, Confalonieri F, Kleman JP, Bourgeois D, Timmins J. Stress-induced nucleoid remodeling in Deinococcus radiodurans is associated with major changes in Heat Unstable (HU) protein dynamics. Nucleic Acids Res 2024; 52:6406-6423. [PMID: 38742631 PMCID: PMC11194088 DOI: 10.1093/nar/gkae379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Bacteria have developed a wide range of strategies to respond to stress, one of which is the rapid large-scale reorganization of their nucleoid. Nucleoid associated proteins (NAPs) are believed to be major actors in nucleoid remodeling, but the details of this process remain poorly understood. Here, using the radiation resistant bacterium D. radiodurans as a model, and advanced fluorescence microscopy, we examined the changes in nucleoid morphology and volume induced by either entry into stationary phase or exposure to UV-C light, and characterized the associated changes in mobility of the major NAP in D. radiodurans, the heat-unstable (HU) protein. While both types of stress induced nucleoid compaction, HU diffusion was reduced in stationary phase cells, but was instead increased following exposure to UV-C, suggesting distinct underlying mechanisms. Furthermore, we show that UV-C-induced nucleoid remodeling involves a rapid nucleoid condensation step associated with increased HU diffusion, followed by a slower decompaction phase to restore normal nucleoid morphology and HU dynamics, before cell division can resume. These findings shed light on the diversity of nucleoid remodeling processes in bacteria and underline the key role of HU in regulating this process through changes in its mode of assembly on DNA.
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Affiliation(s)
- Pierre Vauclare
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Jip Wulffelé
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | | | - Pascale Servant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Fabrice Confalonieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | - Joanna Timmins
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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3
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Kaur J, Kaur J, Nigam A. Extremophiles in Space Exploration. Indian J Microbiol 2024; 64:418-428. [PMID: 39010991 PMCID: PMC11246395 DOI: 10.1007/s12088-024-01297-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/28/2024] [Indexed: 07/17/2024] Open
Abstract
In the era of deep space exploration, extremophile research represents a key area of research w.r.t space survival. This review thus delves into the intriguing realm of 'Space and Astro Microbiology', providing insights into microbial survival, resilience, and behavioral adaptations in space-like environments. This discussion encompasses the modified behavior of extremophilic microorganisms, influencing virulence, stress resistance, and gene expression. It then shifts to recent studies on the International Space Station and simulated microgravity, revealing microbial responses that impact drug susceptibility, antibiotic resistance, and its commercial implications. The review then transitions into Astro microbiology, exploring the possibilities of interplanetary transit, lithopanspermia, and terraforming. Debates on life's origin and recent Martian meteorite discoveries are noted. We also discuss Proactive Inoculation Protocols for selecting adaptable microorganisms as terraforming pioneers. The discussion concludes with a note on microbes' role as bioengineers in bioregenerative life support systems, in recycling organic waste for sustainable space travel; and in promoting optimal plant growth to prepare Martian and lunar basalt. This piece emphasizes the transformative impact of microbes on the future of space exploration.
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Affiliation(s)
- Jasvinder Kaur
- Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110 049 India
| | - Jaspreet Kaur
- Maitreyi College, University of Delhi, New Delhi, 110 021 India
| | - Aeshna Nigam
- Shivaji College, University of Delhi, New Delhi, 110 027 India
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4
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Arias PM, Butler J, Randhawa GS, Soltysiak MPM, Hill KA, Kari L. Environment and taxonomy shape the genomic signature of prokaryotic extremophiles. Sci Rep 2023; 13:16105. [PMID: 37752120 PMCID: PMC10522608 DOI: 10.1038/s41598-023-42518-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as the k-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of [Formula: see text] extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, [Formula: see text]. The supervised learning resulted in high accuracies for taxonomic classifications at [Formula: see text], and medium to medium-high accuracies for environment category classifications of the same datasets at [Formula: see text]. For [Formula: see text], our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.
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Affiliation(s)
- Pablo Millán Arias
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada.
| | - Joseph Butler
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Gurjit S Randhawa
- School of Mathematical and Computational Sciences, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Kathleen A Hill
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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5
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von Kügelgen A, van Dorst S, Yamashita K, Sexton DL, Tocheva EI, Murshudov G, Alva V, Bharat TAM. Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans. Proc Natl Acad Sci U S A 2023; 120:e2215808120. [PMID: 37043530 PMCID: PMC10120038 DOI: 10.1073/pnas.2215808120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/14/2023] [Indexed: 04/13/2023] Open
Abstract
Deinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, due in part to its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite decades of research on this cell envelope, atomic structural details of the S-layer have remained obscure. In this study, we report the electron cryomicroscopy structure of the D. radiodurans S-layer, showing how it is formed by the Hexagonally Packed Intermediate-layer (HPI) protein arranged in a planar hexagonal lattice. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, with each monomer extending into the adjacent hexamer, resulting in a highly interconnected, stable, sheet-like arrangement. Using electron cryotomography and subtomogram averaging from focused ion beam-milled D. radiodurans cells, we have obtained a structure of the cellular S-layer, showing how this HPI S-layer coats native membranes on the surface of cells. Our S-layer structure from the diderm bacterium D. radiodurans shows similarities to immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, highlighting common features in cell surface organization across different domains of life, with connotations on the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Keitaro Yamashita
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Danielle L. Sexton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Garib Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen72076, Germany
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
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6
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The radioresistant and survival mechanisms of Deinococcus radiodurans. RADIATION MEDICINE AND PROTECTION 2023. [DOI: 10.1016/j.radmp.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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7
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Chen Y, Zhang Q, Wang D, Shu YG, Shi H. Memory Effect on the Survival of Deinococcus radiodurans after Exposure in Near Space. Microbiol Spectr 2023; 11:e0347422. [PMID: 36749041 PMCID: PMC10100890 DOI: 10.1128/spectrum.03474-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Near space (20 to 100 km in altitude) is an extreme environment with high radiation and extreme cold, making it difficult for organisms to survive. However, many studies had shown that there were still microbes living in this extremely harsh environment. It was particularly important to study which factors affected the survival of microorganisms living in near space after exposure to irradiation, as this was related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. Survival after radiation was probably influenced by the growth condition before radiation, which is called the memory effect. In this research, we used different growth conditions to affect the growth of Deinococcus radiodurans and lyophilized bacteria in exponential phase to maintain the physiological state at this stage. Then high-altitude scientific balloon exposure experiments were carried out by using the Chinese Academy of Sciences Balloon-Borne Astrobiology Platform (CAS-BAP) at Dachaidan, Qinghai, China (37°44'N, 95°21'E). The aim was to investigate which factors influence survival after near-space exposure. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. If the differences in growth rate were caused by differences in nutrition, the survival rate and growth rate were positively correlated. Moreover, the addition of paraquat and Mn2+ during the growth phase can also increase survival. This finding may help to deepen the understanding of the mechanics of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space. IMPORTANCE Earth's near space is an extreme environment with high radiation and extreme cold. Which factors affect the survival of microbes in near space is related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. We performed several exposure experiments with Deinococcus radiodurans in near space to investigate which factors influence the survival rate after near-space exposure; that is, there was a relationship between survival after radiation and the growth condition before radiation. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. This finding may help to deepen the understanding of the mechanism of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space.
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Affiliation(s)
- Yining Chen
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Deyu Wang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yao-Gen Shu
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Hualin Shi
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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8
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Lewandowski K, Stryjska A. What food will we be eating on our journey to Mars? BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2060135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Krzysztof Lewandowski
- Department of Technical Systems Maintenance and Operation, Faculty of Mechanical Engineering, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Aleksandra Stryjska
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, PR China
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9
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Gao Y, Li N, Zhou Y, Zhang Z, Zhang Y, Fan P, Zhou H, Zhang T, Chang L, Gao H, Li Y, Kang X, Xie Q, Lyu Z, Xu P. iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C 6+ heavy ion irradiation. BMC Microbiol 2022; 22:264. [PMID: 36333788 PMCID: PMC9635210 DOI: 10.1186/s12866-022-02676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Deinococcus radiodurans (D. radiodurans) is best known for its extreme resistance to diverse environmental stress factors, including ionizing radiation (IR), ultraviolet (UV) irradiation, oxidative stress, and high temperatures. Robust DNA repair system and antioxidant system have been demonstrated to contribute to extreme resistance in D. radiodurans. However, practically all studies on the mechanism underlying D. radiodurans’s extraordinary resistance relied on the treated strain during the post-treatment recovery lag phase to identify the key elements involved. The direct gene or protein changes of D. radiodurans after stress have not yet been characterized. Results In this study, we performed a proteomics profiling on D. radiodurans right after the heavy ion irradiation treatment, to discover the altered proteins that were quickly responsive to IR in D. radiodurans. Our study found that D. radiodurans shown exceptional resistance to 12C6+ heavy ion irradiation, in contrast to Escherichia coli (E.coli) strains. By using iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)-based quantitative mass spectrometry analysis, the kinetics of proteome changes induced by various dosages of 12C6+ heavy ion irradiation were mapped. The results revealed that 452 proteins were differentially expressed under heavy ion irradiation, with the majority of proteins being upregulated, indicating the upregulation of functional categories of translation, TCA cycle (Tricarboxylic Acid cycle), and antioxidation regulation under heavy ion irradiation. Conclusions This study shows how D. radiodurans reacts to exposure to 12C6+ heavy ion irradiation in terms of its overall protein expression profile. Most importantly, comparing the proteome profiling of D. radiodurans directly after heavy ion irradiation with research on the post-irradiation recovery phase would potentially provide a better understanding of mechanisms underlying the extreme radioresistance in D. radiodurans. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02676-x.
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Affiliation(s)
- Yuan Gao
- grid.27871.3b0000 0000 9750 7019Central Laboratory of College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Naikang Li
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Yanxia Zhou
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,Beijing Institute of Food Inspection and Research, Beijing Municipal Center for Food Safety Monitoring and Risk Assessment, Beijing, 102206 People’s Republic of China
| | - Zhenpeng Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Yao Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Pengcheng Fan
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Hangfan Zhou
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Tao Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Lei Chang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Huiying Gao
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Yanchang Li
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Xianjiang Kang
- School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Qiong Xie
- grid.418516.f0000 0004 1791 7464China Astronaut Research and Training Center, Beijing, 100094 People’s Republic of China
| | - Zhitang Lyu
- School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Ping Xu
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei, 230032 People’s Republic of China ,grid.443382.a0000 0004 1804 268XMedical School of Guizhou University, Guiyang, 550025 People’s Republic of China ,grid.411866.c0000 0000 8848 7685Second Clinical Medicine Collage, Guangzhou University Chinese Medicine, Guangzhou, 510006 People’s Republic of China
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10
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Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress. Mol Cell Proteomics 2022; 21:100423. [PMID: 36210010 PMCID: PMC9650054 DOI: 10.1016/j.mcpro.2022.100423] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022] Open
Abstract
Organisms have developed different mechanisms to respond to stresses. However, the roles of small ORF-encoded peptides (SEPs) in these regulatory systems remain elusive, which is partially because of the lack of comprehensive knowledge regarding these biomolecules. We chose the extremophile Deinococcus radiodurans R1 as a model species and conducted large-scale profiling of the SEPs related to the stress response. The integrated workflow consisting of multiple omics approaches for SEP identification was streamlined, and an SEPome of D. radiodurans containing 109 novel and high-confidence SEPs was drafted. Forty-four percent of these SEPs were predicted to function as antimicrobial peptides. Quantitative peptidomics analysis indicated that the expression of SEP068184 was upregulated upon oxidative treatment and gamma irradiation of the bacteria. SEP068184 was conserved in Deinococcus and exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Further quantitative and interactive proteomics analyses suggested that SEP068184 might function through metabolic pathways and interact with cytoplasmic proteins. Collectively, our findings demonstrate that SEPs are involved in the regulation of oxidative resistance, and the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms.
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11
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McMackin P, Adam J, Griffin S, Hirsa A. Amyloidogenesis via interfacial shear in a containerless biochemical reactor aboard the International Space Station. NPJ Microgravity 2022; 8:41. [PMID: 36127358 PMCID: PMC9489778 DOI: 10.1038/s41526-022-00227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Fluid interfaces significantly influence the dynamics of protein solutions, effects that can be isolated by performing experiments in microgravity, greatly reducing the amount of solid boundaries present, allowing air-liquid interfaces to become dominant. This investigation examined the effects of protein concentration on interfacial shear-induced fibrillization of insulin in microgravity within a containerless biochemical reactor, the ring-sheared drop (RSD), aboard the international space station (ISS). Human insulin was used as a model amyloidogenic protein for studying protein kinetics with applications to in situ pharmaceutical production, tissue engineering, and diseases such as Alzheimer’s, Parkinson’s, infectious prions, and type 2 diabetes. Experiments investigated three main stages of amyloidogenesis: nucleation studied by seeding native solutions with fibril aggregates, fibrillization quantified using intrinsic fibrillization rate after fitting measured solution intensity to a sigmoidal function, and gelation observed by detection of solidification fronts. Results demonstrated that in surface-dominated amyloidogenic protein solutions: seeding with fibrils induces fibrillization of native protein, intrinsic fibrillization rate is independent of concentration, and that there is a minimum fibril concentration for gelation with gelation rate and rapidity of onset increasing monotonically with increasing protein concentration. These findings matched well with results of previous studies within ground-based analogs.
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Affiliation(s)
- Patrick McMackin
- Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA
| | - Joe Adam
- Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA.,Department of Biological Sciences, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA.,Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA
| | - Shannon Griffin
- Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA.,Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA
| | - Amir Hirsa
- Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA. .,Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, 12180, NY, USA.
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12
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von Kügelgen A, van Dorst S, Alva V, Bharat TAM. A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria. Proc Natl Acad Sci U S A 2022; 119:e2203156119. [PMID: 35943982 PMCID: PMC9388160 DOI: 10.1073/pnas.2203156119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/24/2022] [Indexed: 01/30/2023] Open
Abstract
Deinococcus radiodurans is a phylogenetically deep-branching extremophilic bacterium that is remarkably tolerant to numerous environmental stresses, including large doses of ultraviolet (UV) radiation and extreme temperatures. It can even survive in outer space for several years. This endurance of D. radiodurans has been partly ascribed to its atypical cell envelope comprising an inner membrane, a large periplasmic space with a thick peptidoglycan (PG) layer, and an outer membrane (OM) covered by a surface layer (S-layer). Despite intense research, molecular principles governing envelope organization and OM stabilization are unclear in D. radiodurans and related bacteria. Here, we report a electron cryomicroscopy (cryo-EM) structure of the abundant D. radiodurans OM protein SlpA, showing how its C-terminal segment forms homotrimers of 30-stranded β-barrels in the OM, whereas its N-terminal segment forms long, homotrimeric coiled coils linking the OM to the PG layer via S-layer homology (SLH) domains. Furthermore, using protein structure prediction and sequence-based bioinformatic analysis, we show that SlpA-like putative OM-PG connector proteins are widespread in phylogenetically deep-branching Gram-negative bacteria. Finally, combining our atomic structures with fluorescence and electron microscopy of cell envelopes of wild-type and mutant bacterial strains, we report a model for the cell surface of D. radiodurans. Our results will have important implications for understanding the cell surface organization and hyperstability of D. radiodurans and related bacteria and the evolutionary transition between Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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13
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Protection of the hematopoietic system against radiation-induced damage: drugs, mechanisms, and developments. Arch Pharm Res 2022; 45:558-571. [PMID: 35951164 DOI: 10.1007/s12272-022-01400-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Abstract
Sometimes, people can be exposed to moderate or high doses of radiation accidentally or through the environment. Radiation can cause great harm to several systems within organisms, especially the hematopoietic system. Several types of drugs protect the hematopoietic system against radiation damage in different ways. They can be classified as "synthetic drugs" and "natural compounds." Their cellular mechanisms to protect organisms from radiation damage include free radical-scavenging, anti-oxidation, reducing genotoxicity and apoptosis, and alleviating suppression of the bone marrow. These topics have been reviewed to provide new ideas for the development and research of drugs alleviating radiation-induced damage to the hematopoietic system.
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14
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Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions. Life (Basel) 2021; 12:life12010023. [PMID: 35054415 PMCID: PMC8779699 DOI: 10.3390/life12010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
Rapidly evolving space exploration makes understanding the short- and long- term effects of microgravity on humans, plants, and microorganisms an important task. The ubiquitous presence of the gravitational force has had an influence on the development of all living entities on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the Gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress, and desiccation. Thus increased interest has been placed on this species in the context of space research. The present study aims to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures of D. radiodurans were subjected to microgravity during a single parabola, and metabolic activity was quenched using methanol. Proteins were extracted and subsequently measured using HPLC nESI MS/MS. The results, such as the enrichment of the peptidoglycan biosynthesis pathway with differentially abundant proteins and altered S-layer protein abundance, suggested molecular rearrangements in the cell envelope of D. radiodurans. Altered abundance of proteins involved in energy metabolism and DNA repair could be linked with increased endogenous ROS production that contributes to the stress response. Moreover, changes in protein abundance in response to microgravity show similarities with previously reported stress responses. Thus, the present results could be used to further investigate the complex regulation of the remarkable stress management of this bacterium.
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15
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Yamagishi A, Yokobori SI, Kobayashi K, Mita H, Yabuta H, Tabata M, Higashide M, Yano H. Scientific Targets of Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments at the Japanese Experiment Module Exposed Facility of the International Space Station. ASTROBIOLOGY 2021; 21:1451-1460. [PMID: 34449275 DOI: 10.1089/ast.2020.2426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Tanpopo experiment was the first Japanese astrobiology mission on board the Japanese Experiment Module Exposed Facility on the International Space Station (ISS). The experiments were designed to address two important astrobiological topics, panspermia and the chemical evolution process toward the generation of life. These experiments also tested low-density aerogel and monitored the microdebris environment around low Earth orbit. The following six subthemes were identified to address these goals: (1) Capture of microbes in space: Estimation of the upper limit of microbe density in low Earth orbit; (2) Exposure of microbes in space: Estimation of the survival time course of microbes in the space environment; (3) Capture of cosmic dust on the ISS and analysis of organics: Detection of the possible presence of organic compounds in cosmic dust; (4) Alteration of organic compounds in space environments: Evaluation of decomposition time courses of organic compounds in space; (5) Space verification of the Tanpopo hyper-low-density aerogel: Durability and particle-capturing capability of aerogel; (6) Monitoring of the number of space debris: Time-dependent change in space debris environment. Subthemes 1 and 2 address the panspermia hypothesis, whereas 3 and 4 address the chemical evolution. The last two subthemes contribute to space technology development. Some of the results have been published previously or are included in this issue. This article summarizes the current status of the Tanpopo experiments.
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Affiliation(s)
- Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara, Kanagawa, Japan
| | - Shin-Ichi Yokobori
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kensei Kobayashi
- Department of Chemistry, Yokohama National University, Hodogayaku, Yokohama, Japan
| | - Hajime Mita
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Fukuoka Institute of Technology, Higashiku, Fukuoka, Japan
| | - Hikaru Yabuta
- Department of Earth and Planetary Systems Science, Hiroshima University, Hiroshima, Japan
| | - Makoto Tabata
- Department of Physics, Chiba University, Chiba, Japan
| | - Masumi Higashide
- Research and Development Directorate, Japan Aerospace Exploration Agency, Chofu, Tokyo, Japan
| | - Hajime Yano
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara, Kanagawa, Japan
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16
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McMillan HM, Rogers N, Wadle A, Hsu-Kim H, Wiesner MR, Kuehn MJ, Hendren CO. Microbial vesicle-mediated communication: convergence to understand interactions within and between domains of life. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:664-677. [PMID: 33899070 DOI: 10.1039/d1em00022e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
All cells produce extracellular vesicles (EVs). These biological packages contain complex mixtures of molecular cargo and have a variety of functions, including interkingdom communication. Recent discoveries highlight the roles microbial EVs may play in the environment with respect to interactions with plants as well as nutrient cycling. These studies have also identified molecules present within EVs and associated with EV surfaces that contribute to these functions. In parallel, studies of engineered nanomaterials have developed methods to track and model small particle behavior in complex systems and measure the relative importance of various surface features on transport and function. While studies of EV behavior in complex environmental conditions have not yet employed transdisciplinary approaches, it is increasingly clear that expertise from disparate fields will be critical to understand the role of EVs in these systems. Here, we outline how the convergence of biology, soil geochemistry, and colloid science can both develop and address questions surrounding the basic principles governing EV-mediated interkingdom interactions.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas Rogers
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Austin Wadle
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Meta J Kuehn
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA and Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Christine Ogilvie Hendren
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA and Department of Geological and Environmental Sciences, Appalachian State University, Boone, NC 28608, USA.
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17
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Obulisamy PK, Mehariya S. Polyhydroxyalkanoates from extremophiles: A review. BIORESOURCE TECHNOLOGY 2021; 325:124653. [PMID: 33465644 DOI: 10.1016/j.biortech.2020.124653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.
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Affiliation(s)
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania "Luigi Vanvitelli", Real Casa dell'Annunziata, Italy
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18
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Milojevic T, Kish A, Yamagishi A. Editorial: Astrobiology at the Interface: Interactions Between Biospheres, Geospheres, Hydrospheres and Atmospheres Under Planetary Conditions. Front Microbiol 2021; 12:629961. [PMID: 33643257 PMCID: PMC7906982 DOI: 10.3389/fmicb.2021.629961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tetyana Milojevic
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | | | - Akihiko Yamagishi
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
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19
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Góes-Neto A, Kukharenko O, Orlovska I, Podolich O, Imchen M, Kumavath R, Kato RB, de Carvalho DS, Tiwari S, Brenig B, Azevedo V, Reva O, de Vera JPP, Kozyrovska N, Barh D. Shotgun metagenomic analysis of kombucha mutualistic community exposed to Mars-like environment outside the International Space Station. Environ Microbiol 2021; 23:3727-3742. [PMID: 33476085 DOI: 10.1111/1462-2920.15405] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 12/28/2022]
Abstract
Kombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acid-tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts' health and an efficient source of bacterial nanocellulose. In this study, we compared KMC structure and functions before and after samples were exposed to the space/Mars-like environment outside the International Space Station in order to investigate the changes related to their re-adaptation to Earth-like conditions by shotgun metagenomics, using both diversity and functional analyses of Community Ecology and Complex Networks approach. Our study revealed that the long-term exposure to space/Mars-like conditions on low Earth orbit may disorganize the KMC to such extent that it will not restore the initial community structure; however, KMC core microorganisms of the community were maintained. Nonetheless, there were no significant differences in the community functions, meaning that the KMC communities are ecologically resilient. Therefore, despite the extremely harsh conditions, key KMC species revived and provided the community with the genetic background needed to survive long periods of time under extraterrestrial conditions.
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Affiliation(s)
- Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG, Brazil
| | - Olga Kukharenko
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, Kyiv, 03680, Ukraine
| | - Iryna Orlovska
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, Kyiv, 03680, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, Kyiv, 03680, Ukraine
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakkad P.O., Kasaragod, Kerala, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakkad P.O., Kasaragod, Kerala, 671320, India
| | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG, Brazil
| | - Daniel Santana de Carvalho
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Vasco Azevedo
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakkad P.O., Kasaragod, Kerala, 671320, India
| | - Oleg Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Natalia Kozyrovska
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, Kyiv, 03680, Ukraine
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
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