101
|
Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch DB, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, Decaestecker E, De Schamphelaere KAC, De Meester L. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. Mol Ecol 2017; 27:886-897. [PMID: 28746735 DOI: 10.1111/mec.14261] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023]
Abstract
Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.
Collapse
Affiliation(s)
- Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK
| | - James B Brown
- Environmental Bioinformatics, Centre for Computational Biology, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK.,Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Statistics Department, University of California, Berkeley, CA, USA.,Preminon LLC, Rodeo, CA, USA
| | | | - Dong Li
- School of Computer Science, University of Birmingham Edgbaston, Birmingham, UK
| | - Shan He
- School of Computer Science, University of Birmingham Edgbaston, Birmingham, UK
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA.,Center for Genomics and Bioinformatics, Indiana University and School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Marcus H Stoiber
- Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katina I Spanier
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Donald Gilbert
- Biology Department, Indiana University, Bloomington, IN, USA
| | - Mieke Jansen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Michael E Pfrender
- Department of Biological Sciences, Eck Institute for Global Health & Environmental Change Initiative, Galvin Life Science Center, Notre Dame, IN, USA
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jouni Kvist
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ellen Decaestecker
- Aquatic Biology, Interdisciplinary Research Facility Life Sciences KU Leuven Campus Kortrijk, Kortrijk, Belgium
| | - Karel A C De Schamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab, Ghent University, Ghent, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| |
Collapse
|
102
|
Iglesias-Rodriguez MD, Jones BM, Blanco-Ameijeiras S, Greaves M, Huete-Ortega M, Lebrato M. Physiological responses of coccolithophores to abrupt exposure of naturally low pH deep seawater. PLoS One 2017; 12:e0181713. [PMID: 28750008 PMCID: PMC5531516 DOI: 10.1371/journal.pone.0181713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 07/06/2017] [Indexed: 11/18/2022] Open
Abstract
Upwelling is the process by which deep, cold, relatively high-CO2, nutrient-rich seawater rises to the sunlit surface of the ocean. This seasonal process has fueled geoengineering initiatives to fertilize the surface ocean with deep seawater to enhance productivity and thus promote the drawdown of CO2. Coccolithophores, which inhabit many upwelling regions naturally 'fertilized' by deep seawater, have been investigated in the laboratory in the context of ocean acidification to determine the extent to which nutrients and CO2 impact their physiology, but few data exist in the field except from mesocosms. Here, we used the Porcupine Abyssal Plain (north Atlantic Ocean) Observatory to retrieve seawater from depths with elevated CO2 and nutrients, mimicking geoengineering approaches. We tested the effects of abrupt natural deep seawater fertilization on the physiology and biogeochemistry of two strains of Emiliania huxleyi of known physiology. None of the strains tested underwent cell divisions when incubated in waters obtained from <1,000 m (pH = 7.99-8.08; CO2 = 373-485 p.p.m; 1.5-12 μM nitrate). However, growth was promoted in both strains when cells were incubated in seawater from ~1,000 m (pH = 7.9; CO2 ~560 p.p.m.; 14-17 μM nitrate) and ~4,800 m (pH = 7.9; CO2 ~600 p.p.m.; 21 μM nitrate). Emiliania huxleyi strain CCMP 88E showed no differences in growth rate or in cellular content or production rates of particulate organic (POC) and inorganic (PIC) carbon and cellular particulate organic nitrogen (PON) between treatments using water from 1,000 m and 4,800 m. However, despite the N:P ratio of seawater being comparable in water from ~1,000 and ~4,800 m, the PON production rates were three times lower in one incubation using water from ~1,000 m compared to values observed in water from ~4,800 m. Thus, the POC:PON ratios were threefold higher in cells that were incubated in ~1,000 m seawater. The heavily calcified strain NZEH exhibited lower growth rates and PIC production rates when incubated in water from ~4,800 m compared to ~1,000 m, while cellular PIC, POC and PON were higher in water from 4,800 m. Calcite Sr/Ca ratios increased with depth despite constant seawater Sr/Ca, indicating that upwelling changes coccolith geochemistry. Our study provides the first experimental and field trial of a geoengineering approach to test how deep seawater impacts coccolithophore physiological and biogeochemical properties. Given that coccolithophore growth was only stimulated using waters obtained from >1,000 m, artificial upwelling using shallower waters may not be a suitable approach for promoting carbon sequestration for some locations and assemblages, and should therefore be investigated on a site-by-site basis.
Collapse
Affiliation(s)
- Maria Debora Iglesias-Rodriguez
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, United States of America.,Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton, United Kingdom
| | - Bethan M Jones
- Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton, United Kingdom.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Sonia Blanco-Ameijeiras
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, 66 Boulevard Carl-Vogt, CH, Geneva, Switzerland
| | - Mervyn Greaves
- Department of Earth Sciences, University of Cambridge, Downing St, Cambridge, United Kingdom
| | - Maria Huete-Ortega
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield United Kingdom.,Departamento de Ecología y Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Mario Lebrato
- Department of Geosciences, Christian-Albrechts-University Kiel (CAU), Christian-Albrechts-Platz 4, Kiel, Germany.,Department of Marine Ecology, GEOMAR, Düsternbrooker Weg 20, Kiel, Germany
| |
Collapse
|
103
|
Medvedev KE, Kolchanov NA, Afonnikov DA. Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. J Bioinform Comput Biol 2017; 15:1650036. [DOI: 10.1142/s0219720016500360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The understanding of biological and molecular mechanisms providing survival of cells under extreme temperatures and pressures will help to answer fundamental questions related to the origin of life and to design of biotechnologically important enzymes with new properties. Here, we analyze amino acid sequences of the Nip7 proteins from 35 archaeal species to identify positions containing mutations specific to the hydrostatic pressure and temperature of organism’s habitat. The number of such positions related to pressure change is much lower than related to temperature change. The results suggest that adaptation to temperature changes of the Nip7 protein cause more pronounced modifications in sequence and structure, than to the pressure changes. Structural analysis of residues at these positions demonstrated their involvement in salt-bridge formation, which may reflect the importance of protein structure stabilization by salt-bridges at extreme environmental conditions.
Collapse
Affiliation(s)
- Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern, Medical Center, Dallas, Texas 75390, USA
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl., 1, Moscow 123182, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| |
Collapse
|
104
|
Members of a new subgroup of Streptococcus anginosus harbor virulence related genes previously observed in Streptococcus pyogenes. Int J Med Microbiol 2017; 307:174-181. [DOI: 10.1016/j.ijmm.2017.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/15/2016] [Accepted: 02/24/2017] [Indexed: 11/22/2022] Open
|
105
|
Völler JS, Budisa N. Coupling genetic code expansion and metabolic engineering for synthetic cells. Curr Opin Biotechnol 2017; 48:1-7. [PMID: 28237511 DOI: 10.1016/j.copbio.2017.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/16/2022]
Abstract
Orthogonal protein translation with noncanonical amino acids (ncAAs) has become a standard method in biosciences. Whereas much effort is made to broaden the chemical space of ncAAs, only few attempts on their systematic low-cost in situ production are reported until now. The main aim is to engineer cells with newly designed biosynthetic pathways coupled with orthogonal aminoacyl-tRNA synthetase/tRNA pairs (o-pairs). These should provide cost-effective solutions to industrially relevant bio-production problems, such as peptide/protein production beyond the canonical set of natural molecules and to expand the arsenal of chemistries available for living cells. Therefore, coupling genetic code expansion (GCE) with metabolic engineering is the basic prerequisite to transform orthogonal translation from a standard technique in academic research to industrial biotechnology.
Collapse
Affiliation(s)
- Jan-Stefan Völler
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| |
Collapse
|
106
|
Ha SH, Jin F, Kwak CH, Abekura F, Park JY, Park NG, Chang YC, Lee YC, Chung TW, Ha KT, Son JK, Chang HW, Kim CH. Jellyfish extract induces apoptotic cell death through the p38 pathway and cell cycle arrest in chronic myelogenous leukemia K562 cells. PeerJ 2017; 5:e2895. [PMID: 28133573 PMCID: PMC5251936 DOI: 10.7717/peerj.2895] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/10/2016] [Indexed: 12/21/2022] Open
Abstract
Jellyfish species are widely distributed in the world's oceans, and their population is rapidly increasing. Jellyfish extracts have several biological functions, such as cytotoxic, anti-microbial, and antioxidant activities in cells and organisms. However, the anti-cancer effect of Jellyfish extract has not yet been examined. We used chronic myelogenous leukemia K562 cells to evaluate the mechanisms of anti-cancer activity of hexane extracts from Nomura's jellyfish in vitro. In this study, jellyfish are subjected to hexane extraction, and the extract is shown to have an anticancer effect on chronic myelogenous leukemia K562 cells. Interestingly, the present results show that jellyfish hexane extract (Jellyfish-HE) induces apoptosis in a dose- and time-dependent manner. To identify the mechanism(s) underlying Jellyfish-HE-induced apoptosis in K562 cells, we examined the effects of Jellyfish-HE on activation of caspase and mitogen-activated protein kinases (MAPKs), which are responsible for cell cycle progression. Induction of apoptosis by Jellyfish-HE occurred through the activation of caspases-3,-8 and -9 and phosphorylation of p38. Jellyfish-HE-induced apoptosis was blocked by a caspase inhibitor, Z-VAD. Moreover, during apoptosis in K562 cells, p38 MAPK was inhibited by pretreatment with SB203580, an inhibitor of p38. SB203580 blocked jellyfish-HE-induced apoptosis. Additionally, Jellyfish-HE markedly arrests the cell cycle in the G0/G1 phase. Therefore, taken together, the results imply that the anti-cancer activity of Jellyfish-HE may be mediated apoptosis by induction of caspases and activation of MAPK, especially phosphorylation of p38, and cell cycle arrest at the Go/G1 phase in K562 cells.
Collapse
Affiliation(s)
- Sun-Hyung Ha
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, Sungkyunkwan University, Suwon City, Kyunggi-Do, Republic of Korea
| | - Fansi Jin
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongsang, Republic of Korea
| | - Choong-Hwan Kwak
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, Sungkyunkwan University, Suwon City, Kyunggi-Do, Republic of Korea
| | - Fukushi Abekura
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, Sungkyunkwan University, Suwon City, Kyunggi-Do, Republic of Korea
| | - Jun-Young Park
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, Sungkyunkwan University, Suwon City, Kyunggi-Do, Republic of Korea
| | - Nam Gyu Park
- Department of Biotechnology, College of Fisheries Sciences, Pukyung National University, Busan, Republic of Korea
| | - Young-Chae Chang
- Research Institute of Biomedical Engineering and Department of Medicine, Catholic University of Daegu, Daegu, Republic of Korea
| | - Young-Choon Lee
- Department of Medicinal Biotechnology, College of Health Science, Dong-A University, Busan, Republic of Korea
| | - Tae-Wook Chung
- Division of Applied Medicine, School of Korean Medicine, Pusan National University, Yangsan City, Gyeongsangnam-Do, Republic of Korea
| | - Ki-Tae Ha
- Division of Applied Medicine, School of Korean Medicine, Pusan National University, Yangsan City, Gyeongsangnam-Do, Republic of Korea
| | - Jong-Keun Son
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongsang, Republic of Korea
| | - Hyeun Wook Chang
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongsang, Republic of Korea
| | - Cheorl-Ho Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, Sungkyunkwan University, Suwon City, Kyunggi-Do, Republic of Korea
| |
Collapse
|
107
|
Kaushik A, Ali S, Gupta D. Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways. Sci Rep 2017; 7:40450. [PMID: 28084397 PMCID: PMC5233954 DOI: 10.1038/srep40450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 12/07/2016] [Indexed: 12/13/2022] Open
Abstract
Gene connection rewiring is an essential feature of gene network dynamics. Apart from its normal functional role, it may also lead to dysregulated functional states by disturbing pathway homeostasis. Very few computational tools measure rewiring within gene co-expression and its corresponding regulatory networks in order to identify and prioritize altered pathways which may or may not be differentially regulated. We have developed Altered Pathway Analyzer (APA), a microarray dataset analysis tool for identification and prioritization of altered pathways, including those which are differentially regulated by TFs, by quantifying rewired sub-network topology. Moreover, APA also helps in re-prioritization of APA shortlisted altered pathways enriched with context-specific genes. We performed APA analysis of simulated datasets and p53 status NCI-60 cell line microarray data to demonstrate potential of APA for identification of several case-specific altered pathways. APA analysis reveals several altered pathways not detected by other tools evaluated by us. APA analysis of unrelated prostate cancer datasets identifies sample-specific as well as conserved altered biological processes, mainly associated with lipid metabolism, cellular differentiation and proliferation. APA is designed as a cross platform tool which may be transparently customized to perform pathway analysis in different gene expression datasets. APA is freely available at http://bioinfo.icgeb.res.in/APA.
Collapse
Affiliation(s)
- Abhinav Kaushik
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Shakir Ali
- Department of Biochemistry, Jamia Hamdard, Deemed University, New Delhi 110062, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| |
Collapse
|
108
|
Cairns J, Frickel J, Jalasvuori M, Hiltunen T, Becks L. Genomic evolution of bacterial populations under coselection by antibiotics and phage. Mol Ecol 2017; 26:1848-1859. [DOI: 10.1111/mec.13950] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/06/2016] [Accepted: 11/28/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Johannes Cairns
- Department of Food and Environmental Sciences / Microbiology and Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Jens Frickel
- Department of Evolutionary Ecology / Community Dynamics Group; Max Planck Institute for Evolutionary Biology; August Thienemann Street 2 24306 Plön Germany
| | - Matti Jalasvuori
- Department of Biological and Environmental Science / Centre of Excellence in Biological Interactions; University of Jyväskylä; P.O. Box 35 Jyväskylä 40014 Finland
| | - Teppo Hiltunen
- Department of Food and Environmental Sciences / Microbiology and Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Lutz Becks
- Department of Evolutionary Ecology / Community Dynamics Group; Max Planck Institute for Evolutionary Biology; August Thienemann Street 2 24306 Plön Germany
| |
Collapse
|
109
|
Parreira VR, Russell K, Athanasiadou S, Prescott JF. Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions. BMC Microbiol 2016; 16:186. [PMID: 27520106 PMCID: PMC4983038 DOI: 10.1186/s12866-016-0792-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Necrotic enteritis (NE) caused by netB-positive type A Clostridium perfringens is an important bacterial disease of poultry. Through its complex regulatory system, C. perfringens orchestrates the expression of a collection of toxins and extracellular enzymes that are crucial for the development of the disease; environmental conditions play an important role in their regulation. In this study, and for the first time, global transcriptomic analysis was performed on ligated intestinal loops in chickens colonized with a netB-positive C. perfringens strain, as well as the same strain propagated in vitro under various nutritional and environmental conditions. RESULTS Analysis of the respective pathogen transcriptomes revealed up to 673 genes that were significantly expressed in vivo. Gene expression profiles in vivo were most similar to those of C. perfringens grown in nutritionally-deprived conditions. CONCLUSIONS Taken together, our results suggest a bacterial transcriptome responses to the early stages of adaptation, and colonization of, the chicken intestine. Our work also reveals how netB-positive C. perfringens reacts to different environmental conditions including those in the chicken intestine.
Collapse
Affiliation(s)
| | - Kay Russell
- Disease Systems, Animal and Veterinary Sciences SRUC, Roslin Institute Building, Midlothian, EH25 9RG Scotland
| | - Spiridoula Athanasiadou
- Disease Systems, Animal and Veterinary Sciences SRUC, Roslin Institute Building, Midlothian, EH25 9RG Scotland
| | - John F. Prescott
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1 Canada
| |
Collapse
|
110
|
Abstract
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. Here we analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation in three organisms or cell types each, and show that they follow a version of Hebb's rule which we have termed coherence. More precisely, we find that simultaneously expressed genes with a common target are less likely to act antagonistically at the attractors of the regulatory dynamics. We then investigate the dependence of coherence on structural parameters, such as the mean number of inputs per node and the activatory/repressory interaction ratio, as well as on dynamically determined quantities, such as the basin size and the number of expressed genes.
Collapse
Affiliation(s)
- Neşe Aral
- Department of Physics, Koç University, Rumelifeneri Yolu Sarıyer 34450, Istanbul, Turkey
| | | |
Collapse
|
111
|
Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS. Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BMC SYSTEMS BIOLOGY 2014; 8:122. [PMID: 25394904 PMCID: PMC4236453 DOI: 10.1186/s12918-014-0122-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022]
Abstract
Background Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment. Results We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively. Conclusions This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism. Electronic supplementary material The online version of this article (doi:10.1186/s12918-014-0122-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Fang-Yin Lo
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | | | - Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | - Karlyn D Beer
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA.
| | | | - Marc T Facciotti
- Department of Biomedical Engineering, University of California, Davis, CA, USA. .,Genome Center, University of California, Davis, CA, USA.
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. .,Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Biology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
112
|
Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA. Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species. BMC STRUCTURAL BIOLOGY 2014; 14:23. [PMID: 25315147 PMCID: PMC4209456 DOI: 10.1186/s12900-014-0023-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/03/2014] [Indexed: 11/13/2022]
Abstract
Background The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. Results The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. Conclusions The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.
Collapse
Affiliation(s)
- Kirill E Medvedev
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Nikolay A Alemasov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Prospekt Lavrentyeva 8, Novosibirsk, 630090, Russia.
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,Institute of Solid Chemistry and Mechanochemistry, SB RAS, Novosibirsk, 630090, Russia.
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,NRC Kurchatov Institute, 1, Akademika Kurchatova pl., Moscow, 123182, Russia.
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia.
| |
Collapse
|
113
|
Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A. Macromolecular networks and intelligence in microorganisms. Front Microbiol 2014; 5:379. [PMID: 25101076 PMCID: PMC4106424 DOI: 10.3389/fmicb.2014.00379] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/05/2014] [Indexed: 11/13/2022] Open
Abstract
Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity - particularly activity of the human brain - with a phenomenon we call "intelligence." Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as "human" and "brain" out of the defining features of "intelligence," all forms of life - from microbes to humans - exhibit some or all characteristics consistent with "intelligence." We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.
Collapse
Affiliation(s)
- Hans V. Westerhoff
- Department of Molecular Cell Physiology, Vrije Universiteit AmsterdamAmsterdam, Netherlands
- Manchester Centre for Integrative Systems Biology, The University of ManchesterManchester, UK
- Synthetic Systems Biology, University of AmsterdamAmsterdam, Netherlands
| | - Aaron N. Brooks
- Institute for Systems BiologySeattle, WA, USA
- Molecular and Cellular Biology Program, University of WashingtonSeattle, WA, USA
| | - Evangelos Simeonidis
- Institute for Systems BiologySeattle, WA, USA
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | | | - Fei He
- Department of Automatic Control and Systems Engineering, The University of SheffieldSheffield, UK
| | - Fred C. Boogerd
- Department of Molecular Cell Physiology, Vrije Universiteit AmsterdamAmsterdam, Netherlands
| | | | - Valeri Goncharuk
- Netherlands Institute for NeuroscienceAmsterdam, Netherlands
- Russian Cardiology Research CenterMoscow, Russia
- Department of Medicine, Center for Alzheimer and Neurodegenerative Research, University of AlbertaEdmonton, AB, Canada
| | - Alexey Kolodkin
- Institute for Systems BiologySeattle, WA, USA
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| |
Collapse
|