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Li W, Zhu L, Wu B, Liu Y, Li J, Xu L, Huangfu X, Shi D, Gu L, Chen C. Improving mesophilic anaerobic digestion of food waste by side-stream thermophilic reactor: Activation of methanogenic, key enzymes and metabolism. WATER RESEARCH 2023; 241:120167. [PMID: 37290195 DOI: 10.1016/j.watres.2023.120167] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Anaerobic digestion (AD) is a favorable way to convert organic pollutants, such as food waste (FW), into clean energy through microbial action. This work adopted a side-stream thermophilic anaerobic digestion (STA) strategy to improve a digestive system's efficiency and stability. Results showed that the STA strategy brought higher methane production as well as higher system stability. It quickly adapted to thermal stimulation and increased the specific methane production from 359 mL CH4/g·VS to 439 mL CH4/g·VS, which was also higher than 317 mL CH4/g·VS from single-stage thermophilic anaerobic digestion. Further exploration of the mechanism of STA using metagenomic and metaproteomic analysis revealed enhanced activity of key enzymes. The main metabolic pathway was up-regulated, while the dominant bacteria were concentrated, and the multifunctional Methanosarcina was enriched. These results indicate that STA optimized organic metabolism patterns, comprehensively promoted methane production pathways, and formed various energy conservation mechanisms. Further, the system's limited heating avoided adverse effects from thermal stimulation, and activated enzyme activity and heat shock proteins through circulating slurries, which improved the metabolic process, showing great application potential.
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Affiliation(s)
- Wen Li
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Lirong Zhu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Baocun Wu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Yongli Liu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Jinze Li
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Linji Xu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Xiaoliu Huangfu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Dezhi Shi
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Li Gu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China.
| | - Cong Chen
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
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Ye J, Wang C, Gao C, Fu T, Yang C, Ren G, Lü J, Zhou S, Xiong Y. Solar-driven methanogenesis with ultrahigh selectivity by turning down H 2 production at biotic-abiotic interface. Nat Commun 2022; 13:6612. [PMID: 36329056 PMCID: PMC9633801 DOI: 10.1038/s41467-022-34423-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Integration of methanogens with semiconductors is an effective approach to sustainable solar-driven methanogenesis. However, the H2 production rate by semiconductors largely exceeds that of methanogen metabolism, resulting in abundant H2 as side product. Here, we report that binary metallic active sites (namely, NiCu alloys) are incorporated into the interface between CdS semiconductors and Methanosarcina barkeri. The self-assembled Methanosarcina barkeri-NiCu@CdS exhibits nearly 100% CH4 selectivity with a quantum yield of 12.41 ± 0.16% under light illumination, which not only exceeds the reported biotic-abiotic hybrid systems but also is superior to most photocatalytic systems. Further investigation reveal that the Ni-Cu-Cu hollow sites in NiCu alloys can directly supply hydrogen atoms and electrons through photocatalysis to the Methanosarcina barkeri for methanogenesis via both extracellular and intracellular hydrogen cycles, effectively turning down the H2 production. This work provides important insights into the biotic-abiotic hybrid interface, and offers an avenue for engineering the methanogenesis process.
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Affiliation(s)
- Jie Ye
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chao Wang
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chao Gao
- grid.59053.3a0000000121679639School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026 China
| | - Tao Fu
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chaohui Yang
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Guoping Ren
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jian Lü
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shungui Zhou
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yujie Xiong
- grid.59053.3a0000000121679639School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026 China
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Wang C, Yu J, Ren G, Hu A, Liu X, Chen Y, Ye J, Zhou S, He Z. Self-replicating Biophotoelectrochemistry System for Sustainable CO Methanation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4587-4596. [PMID: 35290037 DOI: 10.1021/acs.est.1c08340] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Efficient conversion of CO-rich gas to methane (CH4) provides an effective energy solution by taking advantage of existing natural gas infrastructures. However, traditional chemical and biological conversions face different challenges. Herein, an innovative biophotoelectrochemistry (BPEC) system using Methanosarcina barkeri-CdS as a biohybrid catalyst was successfully employed for CO methanation. Compared with CO2-fed BPEC, BPEC-CO significantly extended the CH4 producing time by 1.7-fold and exhibited a higher CH4 yield by 9.5-fold under light irradiation. This superior conversion of CO resulted from the fact that CO could serve as an effective quencher of reactive species along with the photoelectron production. In addition, CO was used as a carbon source either directly or indirectly via the produced CO2 for M. barkeri. Such a process improved the redox activities of membrane-bound proteins for BPEC methanogenesis. These results were consistent with the transcriptomic analyses, in which the genes for the putative CO oxidation and CO2 reduction pathways in M. barkeri were highly expressed, while the gene expression for reactive oxygen species detoxification remained relatively stable under light irradiation. This study has provided the first proof-of-concept evidence for sustainable CO methanation under a mild condition in the self-replicating BPEC system.
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Affiliation(s)
- Chao Wang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Yu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoping Ren
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Andong Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiping Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhen He
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Yan Y, Wang W, Wu M, Jetten MSM, Guo J, Ma J, Wang H, Dai X, Wang Y. Transcriptomics Uncovers the Response of Anammox Bacteria to Dissolved Oxygen Inhibition and the Subsequent Recovery Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14674-14685. [PMID: 33147001 DOI: 10.1021/acs.est.0c02842] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding the recovery of anaerobic ammonium-oxidizing (anammox) bacteria after inhibition by dissolved oxygen (DO) is critical for the successful applications of anammox-based processes. Therefore, the effects of oxygen exposure (2 mg L-1 DO for 90 min) and subsequent recovery treatments [N2 purging or nano zero-valent iron (nZVI) addition] on the activity and gene expression in a Kuenenia stuttgartiensis enrichment culture were examined. Combining the self-organizing map clustering and enrichment analysis, we proposed the oxidative stress response of anammox bacteria based on the existing concepts of oxidative stress in microbes: the DO exposure triggered a stringent response in K. stuttgartiensis, which downregulated the transcription levels of genes involved in the central metabolism and diverted energy to a flagellar assembly and metal transport modules; these changes possibly promoted survival during the inhibition of anammox activity. According to the cotranscription with central catabolism genes, putative reactive oxygen species (ROS) scavenger genes (kat and sod) were presumed to detoxify the anammox intermediates rather than ROS. In addition, both activity and mRNA profiles with appropriate amount of nZVI addition (5 and 25 mg L-1) were close to that of control, which proved the effectiveness of nZVI addition in anammox recovery. These results would be relevant to the physio-biochemistry development of anammox bacteria and further enhancement of nitrogen removal in wastewater treatment.
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Affiliation(s)
- Yuan Yan
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Weigang Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Mengxiong Wu
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Mike S M Jetten
- Microbiology, IWWR, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, AJ Nijmegen 6525, The Netherlands
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Jie Ma
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
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Rani S, Sharma A, Goel M. Insights into archaeal chaperone machinery: a network-based approach. Cell Stress Chaperones 2018; 23:1257-1274. [PMID: 30178307 PMCID: PMC6237683 DOI: 10.1007/s12192-018-0933-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Accepted: 08/20/2018] [Indexed: 11/30/2022] Open
Abstract
Molecular chaperones are a diverse group of proteins that ensure proteome integrity by helping the proteins fold correctly and maintain their native state, thus preventing their misfolding and subsequent aggregation. The chaperone machinery of archaeal organisms has been thought to closely resemble that found in humans, at least in terms of constituent players. Very few studies have been ventured into system-level analysis of chaperones and their functioning in archaeal cells. In this study, we attempted such an analysis of chaperone-assisted protein folding in archaeal organisms through network approach using Picrophilus torridus as model system. The study revealed that DnaK protein of Hsp70 system acts as hub in protein-protein interaction network. However, DnaK protein was present only in a subset of archaeal organisms and absent from many archaea, especially members of Crenarchaeota phylum. Therefore, a similar network was created for another archaeal organism, Sulfolobus solfataricus, a member of Crenarchaeota. The chaperone network of S. solfataricus suggested that thermosomes played an integral part of hub proteins in archaeal organisms, where DnaK was absent. We further compared the chaperone network of archaea with that found in eukaryotic systems, by creating a similar network for Homo sapiens. In the human chaperone network, the UBC protein, a part of ubiquitination system, was the most important module, and interestingly, this system is known to be absent in archaeal organisms. Comprehensive comparison of these networks leads to several interesting conclusions regarding similarities and differences within archaeal chaperone machinery in comparison to humans.
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Affiliation(s)
- Shikha Rani
- Department of Biophysics, University of Delhi South Campus, Benito Jurarez Road, New Delhi, 110021, India
| | - Ankush Sharma
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Manisha Goel
- Department of Biophysics, University of Delhi South Campus, Benito Jurarez Road, New Delhi, 110021, India.
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Walter A, Probst M, Hinterberger S, Müller H, Insam H. Biotic and abiotic dynamics of a high solid-state anaerobic digestion box-type container system. WASTE MANAGEMENT (NEW YORK, N.Y.) 2016; 49:26-35. [PMID: 26860425 DOI: 10.1016/j.wasman.2016.01.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
A solid-state anaerobic digestion box-type container system for biomethane production was observed in 12 three-week batch fermentations. Reactor performance was monitored using physico-chemical analysis and the methanogenic community was identified using ANAEROCHIP-microarrays and quantitative PCR. A resilient community was found in all batches, despite variations in inoculum to substrate ratio, feedstock quality, and fluctuating reactor conditions. The consortia were dominated by mixotrophic Methanosarcina that were accompanied by hydrogenotrophic Methanobacterium, Methanoculleus, and Methanocorpusculum. The relationship between biotic and abiotic variables was investigated using bivariate correlation analysis and univariate analysis of variance. High amounts of biogas were produced in batches with high copy numbers of Methanosarcina. High copy numbers of Methanocorpusculum and extensive percolation, however, were found to negatively correlate with biogas production. Supporting these findings, a negative correlation was detected between Methanocorpusculum and Methanosarcina. Based on these results, this study suggests Methanosarcina as an indicator for well-functioning reactor performance.
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Affiliation(s)
- Andreas Walter
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria; Hochschule Hamm-Lippstadt, Biotechnologie, Marker Allee 76-78, 59063 Hamm, Germany.
| | - Maraike Probst
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria.
| | | | - Horst Müller
- Müller Abfallprojekte GmbH, Hauptstraße 34, 4675 Weibern, Austria.
| | - Heribert Insam
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria.
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Morozova D, Moeller R, Rettberg P, Wagner D. Enhanced Radiation Resistance of Methanosarcina soligelidi SMA-21, a New Methanogenic Archaeon Isolated from a Siberian Permafrost-Affected Soil in Direct Comparison to Methanosarcina barkeri. ASTROBIOLOGY 2015; 15:951-960. [PMID: 26544020 DOI: 10.1089/ast.2015.1319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED Permafrost-affected soils are characterized by a high abundance and diversity of methanogenic communities, which are considered suitable model organisms for potential life on Mars. Methanogens from Siberian permafrost have been proven to be highly resistant against divers stress conditions such as subzero temperatures, desiccation, and simulated thermophysical martian conditions. Here, we studied the radiation resistance of the currently described new species Methanosarcina soligelidi SMA-21, which was isolated from a Siberian permafrost-affected soil, in comparison to Methanosarcina barkeri, which is used as a reference organism from a nonpermafrost soil environment. Both strains were exposed to solar UV and ionizing radiation to assess their limits of survival. Methanosarcina soligelidi exhibit an increase in radiation resistance to UV (2.5- to 13.8-fold) and ionizing radiation (46.6-fold) compared to M. barkeri. The F10 (UVC) and D10 (X-rays) values of M. soligelidi are comparable to values for the well-known, highly radioresistant species Deinococcus radiodurans. In contrast, the radiation response of M. barkeri was highly sensitive to UV and ionizing radiation comparably to Escherichia coli and other radiosensitive microorganisms. This study showed that species of the same genus respond differently to UV and ionizing radiation, which might reflect the adaptation of Methanosarcina soligelidi SMA-21 to the harsh environmental conditions of the permafrost habitat. KEY WORDS Methanogenic archaea-Environmental UV-Ionizing radiation-Permafrost-Radiation resistance-Mars.
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Affiliation(s)
- Daria Morozova
- 1 GFZ German Research Centre for Geosciences , Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
| | - Ralf Moeller
- 2 German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Köln, Germany
| | - Petra Rettberg
- 2 German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Köln, Germany
| | - Dirk Wagner
- 1 GFZ German Research Centre for Geosciences , Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
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Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina. BMC Evol Biol 2015; 15:102. [PMID: 26044078 PMCID: PMC4455057 DOI: 10.1186/s12862-015-0393-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/29/2015] [Indexed: 12/29/2022] Open
Abstract
Background Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae. Results About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons. Conclusions While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0393-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.
| | - Marat D Kazanov
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia. .,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia.
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Huang S, Chen L, Te R, Qiao J, Wang J, Zhang W. Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation in Synechocystis sp. PCC 6803. MOLECULAR BIOSYSTEMS 2014; 9:2565-74. [PMID: 23942477 DOI: 10.1039/c3mb70188c] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequential adaptation to environmental stress needs complex regulation at different cellular levels in cyanobacteria. To uncover the regulatory mechanism in response to nitrogen starvation, we investigated the genome-wide correlation between protein abundance and gene expression in a model cyanobacterium Synechocystis sp. PCC 6803 using complementary quantitative iTRAQ proteomics and RNA-seq transcriptomics. Consistent with the cell growth inhibition, proteomic analysis indicated phase-dependent down-regulation of proteins related to nitrogen metabolism, ribosome complexes, glycolysis pathway and tricarboxylic acid (TCA) cycles by nitrogen starvation. Transcriptomic analysis also showed that genes related to "Photosynthesis", "Protein synthesis" and "Energy metabolism" were significantly down-regulated by nitrogen starvation. Interestingly, the concordance between protein abundances and their corresponding mRNAs exhibited a functional categories-dependent pattern, with some categories, such as "Protein synthesis" and "Energy metabolism", having a relatively high correlation, while others even with numerous discordant changes in protein-mRNA pairs, indicated divergent regulation of transcriptional and post-transcriptional processes. In particular, an increased abundance of proteins related to "Photosynthesis" upon nitrogen starvation was found to be reversely correlated with the down-regulation of their corresponding mRNAs. In addition, two metabolic modules highly correlated with nitrogen starvation were identified by a co-expression network analysis, and were found to contain mostly photosynthetic proteins and hypothetical proteins, respectively. We further confirmed the involvement of the photosynthetic genes in nitrogen starvation tolerance by constructing and analyzing the psbV gene deletion mutant.
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Affiliation(s)
- Siqiang Huang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China.
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Alexandre A, Laranjo M, Oliveira S. Global transcriptional response to heat shock of the legume symbiont Mesorhizobium loti MAFF303099 comprises extensive gene downregulation. DNA Res 2013; 21:195-206. [PMID: 24277738 PMCID: PMC3989490 DOI: 10.1093/dnares/dst050] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Rhizobia, the bacterial legume symbionts able to fix atmospheric nitrogen inside root nodules, have to survive in varied environmental conditions. The aim of this study was to analyse the transcriptional response to heat shock of Mesorhizobium loti MAFF303099, a rhizobium with a large multipartite genome of 7.6 Mb that nodulates the model legume Lotus japonicus. Using microarray analysis, extensive transcriptomic changes were detected in response to heat shock: 30% of the protein-coding genes were differentially expressed (2067 genes in the chromosome, 62 in pMLa and 57 in pMLb). The highest-induced genes are in the same operon and code for two sHSP. Only one of the five groEL genes in MAFF303099 genome was induced by heat shock. Unlike other prokaryotes, the transcriptional response of this Mesorhizobium included the underexpression of an unusually large number of genes (72% of the differentially expressed genes). This extensive downregulation of gene expression may be an important part of the heat shock response, as a way of reducing energetic costs under stress. To our knowledge, this study reports the heat shock response of the largest prokaryote genome analysed so far, representing an important contribution to understand the response of plant-interacting bacteria to challenging environmental conditions.
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Affiliation(s)
- Ana Alexandre
- 1ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas (Laboratório de Microbiologia do Solo), Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554 Évora, Portugal
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11
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A functional approach to uncover the low-temperature adaptation strategies of the archaeon Methanosarcina barkeri. Appl Environ Microbiol 2013; 79:4210-9. [PMID: 23645201 DOI: 10.1128/aem.03787-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Low-temperature anaerobic digestion (LTAD) technology is underpinned by a diverse microbial community. The methanogenic archaea represent a key functional group in these consortia, undertaking CO2 reduction as well as acetate and methylated C1 metabolism with subsequent biogas (40 to 60% CH4 and 30 to 50% CO2) formation. However, the cold adaptation strategies, which allow methanogens to function efficiently in LTAD, remain unclear. Here, a pure-culture proteomic approach was employed to study the functional characteristics of Methanosarcina barkeri (optimum growth temperature, 37°C), which has been detected in LTAD bioreactors. Two experimental approaches were undertaken. The first approach aimed to characterize a low-temperature shock response (LTSR) of M. barkeri DSMZ 800(T) grown at 37°C with a temperature drop to 15°C, while the second experimental approach aimed to examine the low-temperature adaptation strategies (LTAS) of the same strain when it was grown at 15°C. The latter experiment employed cell viability and growth measurements (optical density at 600 nm [OD600]), which directly compared M. barkeri cells grown at 15°C with those grown at 37°C. During the LTSR experiment, a total of 127 proteins were detected in 37°C and 15°C samples, with 20 proteins differentially expressed with respect to temperature, while in the LTAS experiment 39% of proteins identified were differentially expressed between phases of growth. Functional categories included methanogenesis, cellular information processing, and chaperones. By applying a polyphasic approach (proteomics and growth studies), insights into the low-temperature adaptation capacity of this mesophilically characterized methanogen were obtained which suggest that the metabolically diverse Methanosarcinaceae could be functionally relevant for LTAD systems.
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Contribution of transcriptomics to systems-level understanding of methanogenic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:586369. [PMID: 23533330 PMCID: PMC3600222 DOI: 10.1155/2013/586369] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/24/2012] [Accepted: 01/23/2013] [Indexed: 01/25/2023]
Abstract
Methane-producing Archaea are of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic constraints of methanogenesis alone or in syntrophic metabolism, methanogens must carefully regulate their catabolic pathways including the regulation of RNA transcripts. The transcriptome is a dynamic and important control point in microbial systems. This paper assesses the impact of mRNA (transcriptome) studies on the understanding of methanogenesis with special consideration given to how methanogenesis is regulated to cope with nutrient limitation, environmental variability, and interactions with syntrophic partners. In comparison with traditional microarray-based transcriptome analyses, next-generation high-throughput RNA sequencing is greatly advantageous in assessing transcription start sites, the extent of 5′ untranslated regions, operonic structure, and the presence of small RNAs. We are still in the early stages of understanding RNA regulation but it is already clear that determinants beyond transcript abundance are highly relevant to the lifestyles of methanogens, requiring further study.
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De Vrieze J, Hennebel T, Boon N, Verstraete W. Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. BIORESOURCE TECHNOLOGY 2012; 112:1-9. [PMID: 22418081 DOI: 10.1016/j.biortech.2012.02.079] [Citation(s) in RCA: 435] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 05/07/2023]
Abstract
Anaerobic digestion is an important technology in the framework of renewable energy production. The anaerobic digestion system is susceptible to perturbations due to the sensitivity of the methanogens towards environmental factors. Currently, technology is evolving from conventional waste treatment, i.e. the removal of pollutants, to very intensive biogas production from concentrated wastes, in the framework of bio-energy production. In the latter configuration Methanosarcina species appear to be of crucial importance. Methanosarcina sp. are, compared to other methanogens, quite robust towards different impairments. They are reported to be tolerant to total ammonium concentrations up to 7000 mg L(-1), salt concentrations up to 18,000 mg Na(+)L(-1), a pH shock of 0.8-1.0 units and acetate concentrations up to 15,000 mg CODL(-1). The possibilities of Methanosarcina sp. as key organisms in specific types of anaerobic digestion systems are demonstrated in this review.
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Affiliation(s)
- Jo De Vrieze
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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14
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Yin H, Tang M, Zhou Z, Fu X, Shen L, Liang Y, Li Q, Liu H, Liu X. Distinctive heat-shock response of bioleaching microorganism Acidithiobacillus ferrooxidans observed using genome-wide microarray. Can J Microbiol 2012; 58:628-36. [PMID: 22524627 DOI: 10.1139/w2012-023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Temperature plays an important role in the heap bioleaching. The maldistribution of ventilation in the heap leads to local hyperthermia, which does exert a tremendous stress on bioleaching microbes. In this study, the genome-wide expression profiles of Acidithiobacillus ferrooxidans at 40 °C were detected using the microarray. The results showed that some classic proteases like Lon and small heat-shock proteins were not induced, and heat-inducible membrane proteins were suggested to be under the control of σ(E). Moreover, expression changes of energy metabolism are noteworthy, which is different from that in heterotrophic bacteria upon heat stress. The induced enzymes catalyzed the central carbon metabolism pathway that might mainly provide precursors of amino acids for protein synthesis. These results will deepen the understanding of the mechanisms of heat-shock response on autotrophic bacteria.
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Affiliation(s)
- Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 Hunan, China
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15
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Desiccation as a long-term survival mechanism for the archaeon Methanosarcina barkeri. Appl Environ Microbiol 2011; 78:1473-9. [PMID: 22194299 DOI: 10.1128/aem.06964-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viable methanogens have been detected in dry, aerobic environments such as dry reservoir sediment, dry rice paddies and aerobic desert soils, which suggests that methanogens have mechanisms for long-term survival in a desiccated state. In this study, we quantified the survival rates of the methanogenic archaeon Methanosarcina barkeri after desiccation under conditions equivalent to the driest environments on Earth and subsequent exposure to different stress factors. There was no significant loss of viability after desiccation for 28 days for cells grown with either hydrogen or the methylotrophic substrates, but recovery was affected by growth phase, with cells desiccated during the stationary phase of growth having a higher rate of recovery after desiccation. Synthesis of methanosarcinal extracellular polysaccharide (EPS) significantly increased the viability of desiccated cells under both anaerobic and aerobic conditions compared with that of non-EPS-synthesizing cells. Desiccated M. barkeri exposed to air at room temperature did not lose significant viability after 28 days, and exposure of M. barkeri to air after desiccation appeared to improve the recovery of viable cells compared with that of desiccated cells that were never exposed to air. Desiccated M. barkeri was more resistant to higher temperatures, and although resistance to oxidative conditions such as ozone and ionizing radiation was not as robust as in other desiccation-resistant microorganisms, the protection mechanisms are likely adequate to maintain cell viability during periodic exposure events. The results of this study demonstrate that after desiccation M. barkeri has the innate capability to survive extended periods of exposure to air and lethal temperatures.
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Angel R, Matthies D, Conrad R. Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS One 2011; 6:e20453. [PMID: 21655270 PMCID: PMC3105065 DOI: 10.1371/journal.pone.0020453] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 04/26/2011] [Indexed: 11/20/2022] Open
Abstract
Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ(13)C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H(2)/CO(2) under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-Methanosarcina and Methanocella; their abundance and activity in transcribing the mcrA gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle.
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Affiliation(s)
- Roey Angel
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Diethart Matthies
- Plant Ecology, Department of Ecology, University of Marburg, Marburg, Germany
| | - Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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Park SH, Lee HW, Cao W. Screening of nitrosative stress resistance genes in Coxiella burnetii: Involvement of nucleotide excision repair. Microb Pathog 2010; 49:323-9. [PMID: 20705129 DOI: 10.1016/j.micpath.2010.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/28/2010] [Accepted: 08/02/2010] [Indexed: 11/18/2022]
Abstract
Coxiella burnetii, an obligate intracellular Gram-negative bacterium, is the etiological agent of Q fever. This work takes advantage of a hypersensitive Escherichia coli genetic system to identify genes involved in resistance to nitrosative stress imposed by reactive nitrogen intermediates. Among the ten candidate genes identified, the transposase, UvrB and DNA topoisomerase IV are involved in DNA transaction; the sigma-32 factor and the putative DNA-binding protein may be involved in transcriptional regulation; IF-2 is involved in protein translation; malate dehydrogenase and carbamoyl-phosphate synthase are metabolic enzymes; and the ABC transporter is a membrane-bound protein. In addition, a hypothetical protein was identified. The role of the DNA repair gene uvrB in resistance to RNI was further confirmed by investigating the sensitivity of uvrB deletion mutant and complementation by C. burnetii uvrB. Deletion of two other components of the UvrABC nuclease, uvrA and uvrC also renders the cell sensitive to RNI. The relationship between UvrABC and nitrosative stress is discussed.
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Affiliation(s)
- Sung-Hyun Park
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, Room 219 Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA
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Plugge CM, Scholten JCM, Culley DE, Nie L, Brockman FJ, Zhang W. Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism. MICROBIOLOGY-SGM 2010; 156:2746-2756. [PMID: 20576691 DOI: 10.1099/mic.0.038539-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Desulfovibrio vulgaris is a metabolically flexible micro-organism. It can use sulfate as an electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with a hydrogen-scavenging partner to relieve inhibition by hydrogen. These alternative metabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntrophic in a lactate-oxidizing dual-culture with Methanosarcina barkeri to a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 h after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Upregulation was observed for genes encoding ATPase and the membrane-integrated energy-conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipoproteins and membrane-bound proteins was downregulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologues found only in another syntrophic bacterium, Syntrophobacter fumaroxidans, and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome-encoding genes, which may be involved in the sulfidogenic metabolism.
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Affiliation(s)
- Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Johannes C M Scholten
- Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA
| | - David E Culley
- Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA
| | - Lei Nie
- Department of Biostatistics, Biomathematics, and Bioinformatics, Georgetown University, Washington DC, USA
| | - Fred J Brockman
- Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA
| | - Weiwen Zhang
- Center for Ecogenomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.,Microbiology Group, Pacific Northwest National Laboratory, PO Box 999, Mail Stop J4-18, Richland, WA 99352, USA
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19
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Hot Transcriptomics. ARCHAEA 2010; 2010:897585. [PMID: 21350598 PMCID: PMC3038420 DOI: 10.1155/2010/897585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/19/2010] [Accepted: 12/20/2010] [Indexed: 12/14/2022]
Abstract
DNA microarray technology allows for a quick and easy comparison of complete transcriptomes, resulting in improved molecular insight in fluctuations of gene expression. After emergence of the microarray technology about a decade ago, the technique has now matured and has become routine in many molecular biology laboratories. Numerous studies have been performed that have provided global transcription patterns of many organisms under a wide range of conditions. Initially, implementation of this high-throughput technology has lead to high expectations for ground breaking discoveries. Here an evaluation is performed of the insight that transcriptome analysis has brought about in the field of hyperthermophilic archaea. The examples that will be discussed have been selected on the basis of their impact, in terms of either biological insight or technological progress.
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20
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Kanai T, Takedomi S, Fujiwara S, Atomi H, Imanaka T. Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis. J Biochem 2009; 147:361-70. [PMID: 19887527 DOI: 10.1093/jb/mvp177] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The hyperthermophilic archaeon Thermococcus kodakaraensis harbors a putative transcriptional regulator (Tk-Phr) that is orthologous to the Pyrococcus furiosus Phr (Pf-Phr). Pf-Phr, a transcriptional regulator, represses genes encoding the small heat shock protein (sHSP), AAA(+) ATPase and Pf-Phr itself under normal growth temperatures. Here we constructed a gene disruption strain of Tk-Phr (strain KHR1). KHR1 cells showed similar specific growth rates with those of the wild-type strain under various temperatures. A whole genome microarray analysis was performed between KHR1 and wild-type cells grown at 80 degrees C. Transcript levels of more than 20 genes were significantly higher in KHR1 cells. Most genes contained a sequence motif virtually identical to that of Pf-Phr in their 5'-flanking regions. The Tk-Phr regulon included genes encoding sHSP, AAA(+) ATPase, prefoldin, RecA superfamily ATPase and Tip49. On the other hand, more than half of the members in the regulon encoded conserved/hypothetical proteins, raising the possibility that these proteins participate in unidentified processes of the heat shock response. In contrast, Tk-Phr deletion did not lead to dramatic increase in transcript and protein levels of a chaperonin (CpkB) previously shown to respond to heat shock, suggesting the presence of a second, Phr-independent heat shock response mechanism in T. kodakaraensis.
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Affiliation(s)
- Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
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Qing DJ, Lu HF, Li N, Dong HT, Dong DF, Li YZ. Comparative profiles of gene expression in leaves and roots of maize seedlings under conditions of salt stress and the removal of salt stress. PLANT & CELL PHYSIOLOGY 2009; 50:889-903. [PMID: 19264788 DOI: 10.1093/pcp/pcp038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We studied the transcriptional profiles of leaves and roots of three-leaf stage seedlings of the maize inbred line YQ7-96 under conditions of salt stress (100 mM NaCl) and removal of salt stress (RSS). A total of 296 genes were regulated specifically by the stress, of which 206 were specific to leaves and 90 were specific to roots. Stress-regulated genes were classified into eight and seven expression patterns for leaves and roots, respectively. There were 60 genes which were regulated specifically by RSS, 27 of which were specific to leaves and 33 specific to roots. No genes were found to be co-regulated in tissues and to be regulated commonly by the stress and RSS. It can be concluded that (i) at the early stage of the stress, transcriptional responses are directed at water deficit in maize leaves but at both water deficit and Na+ accumulation in roots; (ii) at the later stage, the responses in leaves and roots result from dual effects of both water deficit and Na+ accumulation; (iii) the polyamine metabolic pathway is an important linker for the co-ordination between leaves and roots to accomplish the tolerance of the whole maize plant to the stress; (iv) the stress can lead to genomic restructuring and nuclear transport in maize; (v) maize leaves are distinct from roots in terms of molecular mechanisms for responses to and growth recovery from the stress; and (vi) mechanisms for the maize responses to the stress differ from those for their growth recovery during RSS.
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Affiliation(s)
- Dong-Jin Qing
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi 530005, PR China
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22
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Abstract
A survey of archaeal genomes for the presence of homologues of bacterial and eukaryotic chaperones reveals several interesting features. All archaea contain chaperonins, also known as Hsp60s (where Hsp is heat-shock protein). These are more similar to the type II chaperonins found in the eukaryotic cytosol than to the type I chaperonins found in bacteria, mitochondria and chloroplasts, although some archaea also contain type I chaperonin homologues, presumably acquired by horizontal gene transfer. Most archaea contain several genes for these proteins. Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea also possess genes for prefoldin proteins and for small heat-shock proteins, but they generally lack genes for Hsp90 and Hsp100 homologues. Genes for Hsp70 (DnaK) and Hsp40 (DnaJ) homologues are only found in a subset of archaea. Thus chaperone-assisted protein folding in archaea is likely to display some unique features when compared with that in eukaryotes and bacteria, and there may be important differences in the process between euryarchaea and crenarchaea.
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Yang S, Tschaplinski TJ, Engle NL, Carroll SL, Martin SL, Davison BH, Palumbo AV, Rodriguez M, Brown SD. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics 2009; 10:34. [PMID: 19154596 PMCID: PMC2651186 DOI: 10.1186/1471-2164-10-34] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 01/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zymomonas mobilis ZM4 (ZM4) produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. Z. mobilis performs best under anaerobic conditions, but is an aerotolerant organism. However, the genetic and physiological basis of ZM4's response to various stresses is understood poorly. RESULTS In this study, transcriptomic and metabolomic profiles for ZM4 aerobic and anaerobic fermentations were elucidated by microarray analysis and by high-performance liquid chromatography (HPLC), gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) analyses. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Greater amounts of other end-products such as acetate, lactate, and acetoin were detected under aerobic conditions and at 26 h there was only 1.7% of the amount of ethanol present aerobically as there was anaerobically. In the early exponential growth phase, significant differences in gene expression were not observed between aerobic and anaerobic conditions via microarray analysis. HPLC and GC analyses revealed minor differences in extracellular metabolite profiles at the corresponding early exponential phase time point. Differences in extracellular metabolite profiles between conditions became greater as the fermentations progressed. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 contained lower levels of amino acids such as alanine, valine and lysine, and other metabolites like lactate, ribitol, and 4-hydroxybutanoate under anaerobic conditions relative to aerobic conditions. Stationary phase microarray analysis revealed that 166 genes were significantly differentially expressed by more than two-fold. Transcripts for Entner-Doudoroff (ED) pathway genes (glk, zwf, pgl, pgk, and eno) and gene pdc, encoding a key enzyme leading to ethanol production, were at least 30-fold more abundant under anaerobic conditions in the stationary phase based on quantitative-PCR results. We also identified differentially expressed ZM4 genes predicted by The Institute for Genomic Research (TIGR) that were not predicted in the primary annotation. CONCLUSION High oxygen concentrations present during Z. mobilis fermentations negatively influence fermentation performance. The maximum specific growth rates were not dramatically different between aerobic and anaerobic conditions, yet oxygen did affect the physiology of the cells leading to the buildup of metabolic byproducts that ultimately led to greater differences in transcriptomic profiles in stationary phase.
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Affiliation(s)
- Shihui Yang
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Kato S, Kosaka T, Watanabe K. Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli. Environ Microbiol 2007; 10:893-905. [PMID: 18036179 DOI: 10.1111/j.1462-2920.2007.01508.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Methanothermobacter thermautotrophicus strain DeltaH is a model hydrogenotrophic methanogen, for which the complete genome sequence and extensive biochemical information are available. Little is known, however, about how this organism regulates its cellular functions in response to environmental stimuli. In this study, whole-genome oligonucleotide microarrays were constructed for M. thermautotrophicus and used to gain insights into how this organism responds to different environmental stimuli, including hydrogen depletion, shifts in pH and temperature and the occurrence of toxics (hydrogen peroxide and ammonia). Our analysis confirmed that methanogenesis genes (including mtd, mer, frh and mcr) were upregulated under hydrogen-limited conditions, while some of them were affected by other environmental stimuli. Concerning stress responses of this organism, several unique features were revealed. First, there was no universal stress response in this organism. Second, genes for alternative redox enzymes, such as rubrerythrin, were upregulated under the oxidative stress, but those for typical antioxidant enzymes were not. Third, genes relevant to the modification of cell surface structures were differentially expressed under stress conditions. Finally, energy-requiring CO(2) assimilation systems were downregulated under stress conditions. These findings suggest that M. thermautotrophicus has complex transcriptional regulation mechanisms that facilitate it to survive in unstable ecosystems such as an anaerobic digester.
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Affiliation(s)
- Souichiro Kato
- Laboratory of Applied Microbiology, Marine Biotechnology Institute, Kamaishi, Iwate 026-0001, Japan
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25
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Scholten JCM, Culley DE, Nie L, Munn KJ, Chow L, Brockman FJ, Zhang W. Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress. Biochem Biophys Res Commun 2007; 358:571-7. [PMID: 17498652 DOI: 10.1016/j.bbrc.2007.04.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 04/26/2007] [Indexed: 11/20/2022]
Abstract
The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.
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Affiliation(s)
- Johannes C M Scholten
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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Morozova D, Wagner D. Stress response of methanogenic archaea from Siberian permafrost compared with methanogens from nonpermafrost habitats. FEMS Microbiol Ecol 2007; 61:16-25. [PMID: 17428303 DOI: 10.1111/j.1574-6941.2007.00316.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We examined the survival potential of methanogenic archaea exposed to different environmental stress conditions such as low temperature (down to -78.5 degrees C), high salinity (up to 6 M NaCl), starvation (up to 3 months), long-term freezing (up to 2 years), desiccation (up to 25 days) and oxygen exposure (up to 72 h). The experiments were conducted with methanogenic archaea from Siberian permafrost and were complemented by experiments on well-studied methanogens from nonpermafrost habitats. Our results indicate a high survival potential of a methanogenic archaeon from Siberian permafrost when exposed to the extreme conditions tested. In contrast, these stress conditions were lethal for methanogenic archaea isolated from nonpermafrost habitats. A better adaptation to stress was observed at a low temperature (4 degrees C) compared with a higher one (28 degrees C). Given the unique metabolism of methanogenic archaea in general and the long-term survival and high tolerance to extreme conditions of the methanogens investigated in this study, methanogenic archaea from permafrost should be considered as primary candidates for possible subsurface Martian life.
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Affiliation(s)
- Daria Morozova
- Alfred Wegener Institute for Polar and Marine Research, Potsdam, Germany.
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